Sequencing and analysis of the gastrula transcriptome of the brittle star Ophiocoma wendtii

Background The gastrula stage represents the point in development at which the three primary germ layers diverge. At this point the gene regulatory networks that specify the germ layers are established and the genes that define the differentiated states of the tissues have begun to be activated. These networks have been well-characterized in sea urchins, but not in other echinoderms. Embryos of the brittle star Ophiocoma wendtii share a number of developmental features with sea urchin embryos, including the ingression of mesenchyme cells that give rise to an embryonic skeleton. Notable differences are that no micromeres are formed during cleavage divisions and no pigment cells are formed during development to the pluteus larval stage. More subtle changes in timing of developmental events also occur. To explore the molecular basis for the similarities and differences between these two echinoderms, we have sequenced and characterized the gastrula transcriptome of O. wendtii. Methods Development of Ophiocoma wendtii embryos was characterized and RNA was isolated from the gastrula stage. A transcriptome data base was generated from this RNA and was analyzed using a variety of methods to identify transcripts expressed and to compare those transcripts to those expressed at the gastrula stage in other organisms. Results Using existing databases, we identified brittle star transcripts that correspond to 3,385 genes, including 1,863 genes shared with the sea urchin Strongylocentrotus purpuratus gastrula transcriptome. We characterized the functional classes of genes present in the transcriptome and compared them to those found in this sea urchin. We then examined those members of the germ-layer specific gene regulatory networks (GRNs) of S. purpuratus that are expressed in the O. wendtii gastrula. Our results indicate that there is a shared ‘genetic toolkit’ central to the echinoderm gastrula, a key stage in embryonic development, though there are also differences that reflect changes in developmental processes. Conclusions The brittle star expresses genes representing all functional classes at the gastrula stage. Brittle stars and sea urchins have comparable numbers of each class of genes and share many of the genes expressed at gastrulation. Examination of the brittle star genes in which sea urchin orthologs are utilized in germ layer specification reveals a relatively higher level of conservation of key regulatory components compared to the overall transcriptome. We also identify genes that were either lost or whose temporal expression has diverged from that of sea urchins

G4 Resolvase 1 tightly binds and unwinds unimolecular G4-DNA

It has been previously shown that the DHX36 gene product, G4R1/RHAU, tightly binds tetramolecular G4-DNA with high affinity and resolves these structures into single strands. Here, we test the ability of G4R1/RHAU to bind and unwind unimolecular G4-DNA. Gel mobility shift assays were used to measure the binding affinity of G4R1/RHAU for unimolecular G4-DNA-formed sequences from the Zic1 gene and the c-Myc promoter. Extremely tight binding produced apparent Kd's of 6, 3 and 4 pM for two Zic1 G4-DNAs and a c-Myc G4-DNA, respectively. The low enzyme concentrations required for measuring these Kd's limit the precision of their determination to upper boundary estimates. Similar tight binding was not observed in control non-G4 forming DNA sequences or in single-stranded DNA having guanine-rich runs capable of forming tetramolecular G4-DNA. Using a peptide nucleic acid (PNA) trap assay, we show that G4R1/RHAU catalyzes unwinding of unimolecular Zic1 G4-DNA into an unstructured state capable of hybridizing to a complementary PNA. Binding was independent of adenosine triphosphate (ATP), but the PNA trap assay showed that unwinding of G4-DNA was ATP dependent. Competition studies indicated that unimolecular Zic1 and c-Myc G4-DNA structures inhibit G4R1/RHAU-catalyzed resolution of tetramolecular G4-DNA. This report provides evidence that G4R1/RHAU tightly binds and unwinds unimolecular G4-DNA structure

The Importance Of Being Earnest Playbill

Providence College Department of Theatre, Dance & Film Blackfriars Theatre The Importance of Being Earnest by Oscar Wilde October 21-23 & 28-30, 1983, 8PM Director, Mary G. Farrell Scenery and Lighting, Jim Eddy Stage Manager, Alicia Roy Theatre Program Director, John Garrity Cast: John Worthing, J.P. of the Manor House, Woolton, Hertfordshire - Mark Enright; Algernon Moncrieff, his friend - Paul Morin; Rev. Canon Chasuble, D.D., Rector of Woolton - Ted Deasy; Merriman, butler to Mr. Worthing - Joseph M. Mecca; Lane, Mr. Moncrieff\u27s man-servant - Jim Maher; Lady Bracknell - Lisa Gould; Hon. Gwendoline Fairfax, her daughter - Mary Vining; Cecily Cardew, John Worthing\u27s ward - Mary Donovan; Miss Prism - Julie Marrinuccihttps://digitalcommons.providence.edu/earnest_pubs/1008/thumbnail.jp

Pippin Playbill

Providence College Department of Theatre, Dance & Film Blackfriars Theatre Pippin, A musical comedy by Robert O. Hirson. Music and Lyrics by Stephan Schwartz February 3-5 & 10-12, 1984 Director, John Garrity Choreography, Patricia Sharkey Musical Director, James Ascoli Scenery and Lighting, James Eddy Costumes, Mary Farrell Cast: Leading Player - Julie Marrinucci; Pippin - Joseph Henderson; Charles - Ted Deasy; Lewis - William Lovely; Fastrada - Lorie Savoca; Berthe - Mary Donovan; Catherine - Patty Carver; Theo - Aaron Burr; A Band of Players - Lisa Gould, John Healy, Anne Marie LaRoche, Anthony Longobardi, Traci Oravec, Catherine Sullivan, Jennifer Wiegand, Carol Yewcichttps://digitalcommons.providence.edu/pippin_1984_pubs/1008/thumbnail.jp

The Diary Of Anne Frank Playbill

Providence College Department of Theatre, Dance & Film Blackfriars Theatre The Diary of Anne Frank, dramatized by Frances Goodrich & Albert Hackett March 30 - April 1 & April 6 - 8, 1984, 8PM Director, Richard Warner Scenic & Lighting Design, Jim Eddy Costume Design, Mary G. Farrell Research Consultant, Rev. Matthew Powell, O.P. Theatre Program Director, John Garrity Cast: Mrs. Van Daan - Lisa Gould; Mr. Van Daan - Mark Enright; Peter Van Daan - John Brewer; Mr. Frank - James H. Maher; Miep - Mary Donovan; Mrs. Frank - Patricia Carver; Margot Frank - Mary Vining; Franz Kraler - Joseph Henderson; Anne Frank - Julie Marrinucci; Mr. Dussel - Fr. John Corbett, O.P.https://digitalcommons.providence.edu/annefrank_pubs/1004/thumbnail.jp

Relative Efficacy of AS03-Adjuvanted Pandemic Influenza A(H1N1) Vaccine in Children: Results of a Controlled, Randomized Efficacy Trial

Background. the vaccine efficacy (VE) of 1 or 2 doses of AS03-adjuvanted influenza A(H1N1) vaccine relative to that of 2 doses of nonadjuvanted influenza A(H1N1) vaccine in children 6 months to <10 years of age in a multinational study conducted during 2010-2011.Methods. A total of 6145 children were randomly assigned at a ratio of 1: 1: 1 to receive 2 injections 21 days apart of A/California/7/2009(H1N1)-AS03 vaccine at dose 1 and saline placebo at dose 2, 2 doses 21 days apart of A/California/7/2009(H1N1)-AS03 vaccine (the Ad2 group), or 2 doses 21 days apart of nonadjuvanted A/California/7/2009(H1N1) vaccine (the NAd2 group). Active surveillance for influenza-like illnesses continued from days 14 to 385. Nose and throat samples obtained during influenza-like illnesses were tested for A/California/7/2009 (H1N1), using reverse-transcriptase polymerase chain reaction. Immunogenicity, reactogenicity, and safety were assessed.Results. There were 23 cases of confirmed 2009 pandemic influenza A(H1N1) (A[H1N1]pdm09) infection for the primary relative VE analysis. the VE in the Ad2 group relative to that in the NAd2 group was 76.8% (95% confidence interval, 18.5%-93.4%). the benefit of the AS03 adjuvant was demonstrated in terms of the greater immunogenicity observed in the Ad2 group, compared with the NAd2 group.Conclusion. the 4-8-fold antigen-sparing adjuvanted pandemic influenza vaccine demonstrated superior and clinically important prevention of A(H1N1)pdm09 infection, compared with nonadjuvanted vaccine, with no observed increase in medically attended or serious adverse events. These data support the use of adjuvanted influenza vaccines during influenza pandemics.GlaxoSmithKline BiologicalsUniv Melbourne, Murdoch Childrens Res Inst, Carlton, Vic 3010, AustraliaUniv Melbourne, Melbourne Sch Populat & Global Hlth, Carlton, Vic 3010, AustraliaGlaxoSmithKline Vaccines, King of Prussia, PA USANovavax, Rockville, MD USAMary Chiles Gen Hosp, Dept Pediat, Manila, PhilippinesDe La Salle Hlth Sci Inst, Dept Pediat, Dasmarinas City, PhilippinesRes Inst Trop Med, Dept Hlth, Muntinlupa, PhilippinesUniversidade Federal de São Paulo, Dept Pediat, São Paulo, BrazilFac Ciencias Med Santa Casa São Paulo, Dept Pediat, São Paulo, BrazilAssoc Fundo Incent Pesquisa, São Paulo, BrazilInst Costarricense Invest Clin, San Jose, Costa RicaNatl Inst Publ Hlth Mexico, Cuernavaca, Morelos, MexicoUniv Autonoma Nuevo Leon, Serv Med, Monterrey, MexicoInst Nacl Pediat Mexico, Mexico City, DF, MexicoHosp Gen Durango, Durango, MexicoPhramongkutklao Hosp, Infect Dis Unit, Dept Pediat, Bangkok, ThailandKhon Kaen Univ, Dept Pediat, Fac Med, Khon Kaen, ThailandNatl Healthcare Grp Polyclin, Singapore, SingaporeCtr Estudios Infect Pediat, Cali, ColombiaGlaxoSmithKline Vaccines, Wavre, BelgiumGlaxoSmithKline Vaccines, Rixensart, BelgiumUniversidade Federal de São Paulo, Dept Pediat, São Paulo, BrazilWeb of Scienc

Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach:A multi-institutional research study

Contains fulltext : 195300.pdf (publisher's version ) (Open Access

Phylogenomic approaches to DNA barcoding of herbal medicines: developing clade-specific diagnostic characters for Berberis

DNA barcoding of herbal medicines has been mainly concerned with authentication of products in trade and has raised awareness of species substitution and adulteration. More recently DNA barcodes have been included in pharmacopoeias, providing tools for regulatory purposes. The commonly used DNA barcoding regions in plants often fail to resolve identification to species level. This can be especially challenging in evolutionarily complex groups where incipient or reticulate speciation is ongoing. In this study, we take a phylogenomic approach, analyzing whole plastid sequences from the evolutionarily complex genus Berberis in order to develop DNA barcodes for the medicinally important species B. aristata. The phylogeny reconstructed from an alignment of ~160k bp of chloroplast DNA for 57 species reveals that the pharmacopoeial species in question is polyphyletic, complicating development of a species-specific DNA barcode. Instead we propose a DNA barcode that is clade specific, using our phylogeny to define Operational Phylogenetic Units (OPUs). The plastid alignment is then reduced to small, informative DNA regions including nucleotides diagnostic for these OPUs. These DNA barcodes were tested on commercial samples, and shown to discriminate plants in trade and therefore to meet the requirement of a pharmacopoeial standard. The proposed method provides an innovative approach for inferring DNA barcodes for evolutionarily complex groups for regulatory purposes and quality control

Determination of quantitative trait loci (QTL) for early maturation in rainbow trout (Oncorhynchus mykiss)

To identify quantitative trait loci (QTL) influencing early maturation (EM) in rainbow trout (Oncorhynchus mykiss), a genome scan was performed using 100 microsatellite loci across 29 linkage groups. Six inter-strain paternal half-sib families using three inter-strain F(1) brothers (approximately 50 progeny in each family) derived from two strains that differ in the propensity for EM were used in the study. Alleles derived from both parental sources were observed to contribute to the expression of EM in the progeny of the brothers. Four genome-wide significant QTL regions (i.e., RT-8, -17, -24, and -30) were observed. EM QTL detected on RT-8 and -24 demonstrated significant and suggestive QTL effects in both male and female progeny. Furthermore, within both male and female full-sib groupings, QTL on RT-8 and -24 were detected in two or more of the five parents used. Significant genome-wide and several strong chromosome-wide QTL for EM localized to different regions in males and females, suggesting some sex-specific control. Namely, QTL detected on RT-13, -15, -21, and -30 were associated with EM only in females, and those on RT-3, -17, and -19 were associated with EM only in males. Within the QTL regions identified, a comparison of syntenic EST markers from the rainbow trout linkage map with the zebrafish (Danio rerio) genome identified several putative candidate genes that may influence EM. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10126-008-9098-5) contains supplementary material, which is available to authorized users