Dissertation
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Table SI. Genes Upregulated ≥ 2-Fold by MIH 2.4Bl Treatment Affymetrix ID
Table SI. Genes upregulated 2-fold by MIH 2.4Bl treatment Fold UniGene ID Description Affymetrix ID Entrez Gene Change 1558048_x_at 28.84 Hs.551290 231597_x_at 17.02 Hs.720692 238825_at 10.19 93953 Hs.135167 acidic repeat containing (ACRC) 203821_at 9.82 1839 Hs.799 heparin binding EGF like growth factor (HBEGF) 1559509_at 9.41 Hs.656636 202957_at 9.06 3059 Hs.14601 hematopoietic cell-specific Lyn substrate 1 (HCLS1) 202388_at 8.11 5997 Hs.78944 regulator of G-protein signaling 2 (RGS2) 213649_at 7.9 6432 Hs.309090 serine and arginine rich splicing factor 7 (SRSF7) 228262_at 7.83 256714 Hs.127951 MAP7 domain containing 2 (MAP7D2) 38037_at 7.75 1839 Hs.799 heparin binding EGF like growth factor (HBEGF) 224549_x_at 7.6 202672_s_at 7.53 467 Hs.460 activating transcription factor 3 (ATF3) 243581_at 6.94 Hs.659284 239203_at 6.9 286006 Hs.396189 leucine rich single-pass membrane protein 1 (LSMEM1) 210800_at 6.7 1678 translocase of inner mitochondrial membrane 8 homolog A (yeast) (TIMM8A) 238956_at 6.48 1943 Hs.741510 ephrin A2 (EFNA2) 242918_at 6.22 4678 Hs.319334 nuclear autoantigenic sperm protein (NASP) 224254_x_at 6.06 243509_at 6 236832_at 5.89 221442 Hs.374076 adenylate cyclase 10, soluble pseudogene 1 (ADCY10P1) 234562_x_at 5.89 Hs.675414 214093_s_at 5.88 8880 Hs.567380; far upstream element binding protein 1 (FUBP1) Hs.707742 223774_at 5.59 677825 Hs.632377 small nucleolar RNA, H/ACA box 44 (SNORA44) 234723_x_at 5.48 Hs.677287 226419_s_at 5.41 6426 Hs.710026; serine and arginine rich splicing factor 1 (SRSF1) Hs.744140 228967_at 5.37 -
Supplemental Information
Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig. -
Virulent Diuraphis Noxia Aphids Over-Express Calcium Signaling Proteins to Overcome Defenses of Aphid-Resistant Wheat Plants
RESEARCH ARTICLE Virulent Diuraphis noxia Aphids Over-Express Calcium Signaling Proteins to Overcome Defenses of Aphid-Resistant Wheat Plants Deepak K. Sinha1,2, Predeesh Chandran2, Alicia E. Timm2, Lina Aguirre-Rojas2,C. Michael Smith2* 1 International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India, 2 Department of Entomology, Kansas State University, Manhattan, Kansas 66506–4004, United States of America * [email protected] Abstract The Russian wheat aphid, Diuraphis noxia, an invasive phytotoxic pest of wheat, Triticum aestivum, and barley, Hordeum vulgare, causes huge economic losses in Africa, South America, and North America. Most acceptable and ecologically beneficial aphid manage- OPEN ACCESS ment strategies include selection and breeding of D. noxia-resistant varieties, and numer- Citation: Sinha DK, Chandran P, Timm AE, Aguirre- ous D. noxia resistance genes have been identified in T. aestivum and H. vulgare. North Rojas L, Smith CM (2016) Virulent Diuraphis noxia American D. noxia biotype 1 is avirulent to T. aestivum varieties possessing Dn4 or Dn7 Aphids Over-Express Calcium Signaling Proteins to genes, while biotype 2 is virulent to Dn4 and avirulent to Dn7. The current investigation uti- Overcome Defenses of Aphid-Resistant Wheat Plants. PLoS ONE 11(1): e0146809. doi:10.1371/ lized next-generation RNAseq technology to reveal that biotype 2 over expresses proteins journal.pone.0146809 involved in calcium signaling, which activates phosphoinositide (PI) metabolism. Calcium Editor: Guangxiao Yang, Huazhong University of signaling proteins comprised 36% of all transcripts identified in the two D. noxia biotypes. Science & Technology(HUST), CHINA Depending on plant resistance gene-aphid biotype interaction, additional transcript groups Received: September 3, 2015 included those involved in tissue growth; defense and stress response; zinc ion and related cofactor binding; and apoptosis. -
(12) United States Patent (10) Patent No.: US 8.440,393 B2 Birrer Et Al
USOO8440393B2 (12) United States Patent (10) Patent No.: US 8.440,393 B2 Birrer et al. (45) Date of Patent: May 14, 2013 (54) PRO-ANGIOGENIC GENES IN OVARIAN OTHER PUBLICATIONS TUMORENDOTHELIAL CELL, SOLATES Boyd (The Basic Science of Oncology, 1992, McGraw-Hill, Inc., p. (75) Inventors: Michael J. Birrer, Mt. Airy, MD (US); 379). Tomas A. Bonome, Washington, DC Tockman et al. (Cancer Res., 1992, 52:2711s-2718s).* (US); Anil Sood, Pearland, TX (US); Pritzker (Clinical Chemistry, 2002, 48: 1147-1150).* Chunhua Lu, Missouri City, TX (US) Benedict et al. (J. Exp. Medicine, 2001, 193(1) 89-99).* Jiang et al. (J. Biol. Chem., 2003, 278(7) 4763-4769).* (73) Assignees: The United States of America as Matsushita et al. (FEBS Letters, 1999, vol. 443, pp. 348-352).* Represented by the Secretary of the Singh et al. (Glycobiology, 2001, vol. 11, pp. 587-592).* Department of Health and Human Abbosh et al. (Cancer Res. Jun. 1, 2006 66:5582-55.91 and Supple Services, Washington, DC (US); The mental Figs. S1-S7).* University of MD Anderson Cancer Zhai et al. (Chinese General Practice Aug. 2008, 11(8A): 1366 Center, Houston, TX (US) 1367).* Lu et al. (Cancer Res. Feb. 15, 2007, 64(4): 1757-1768).* (*) Notice: Subject to any disclaimer, the term of this Bagnato et al., “Activation of Mitogenic Signaling by Endothelin 1 in patent is extended or adjusted under 35 Ovarian Carcinoma Cells', Cancer Research, vol. 57, pp. 1306-1311, U.S.C. 154(b) by 194 days. 1997. Bouras et al., “Stanniocalcin 2 is an Estrogen-responsive Gene (21) Appl. -
Supplemental Table 3 Site ID Intron Poly(A) Site Type NM/KG Inum
Supplemental Table 3 Site ID Intron Poly(A) site Type NM/KG Inum Region Gene ID Gene Symbol Gene Annotation Hs.120277.1.10 chr3:170997234:170996860 170996950 b NM_153353 7 CDS 151827 LRRC34 leucine rich repeat containing 34 Hs.134470.1.27 chr17:53059664:53084458 53065543 b NM_138962 10 CDS 124540 MSI2 musashi homolog 2 (Drosophila) Hs.162889.1.18 chr14:80367239:80329208 80366262 b NM_152446 12 CDS 145508 C14orf145 chromosome 14 open reading frame 145 Hs.187898.1.27 chr22:28403623:28415294 28404458 b NM_181832 16 3UTR 4771 NF2 neurofibromin 2 (bilateral acoustic neuroma) Hs.228320.1.6 chr10:115527009:115530350 115527470 b BC036365 5 CDS 79949 C10orf81 chromosome 10 open reading frame 81 Hs.266308.1.2 chr11:117279579:117278191 117278967 b NM_032046 12 CDS 84000 TMPRSS13 transmembrane protease, serine 13 Hs.266308.1.4 chr11:117284536:117281662 117283722 b NM_032046 9 CDS 84000 TMPRSS13 transmembrane protease, serine 13 Hs.2689.1.4 chr10:53492398:53563605 53492622 b NM_006258 7 CDS 5592 PRKG1 protein kinase, cGMP-dependent, type I Hs.280781.1.6 chr18:64715646:64829150 64715837 b NM_024781 4 CDS 79839 C18orf14 chromosome 18 open reading frame 14 Hs.305985.2.25 chr12:8983686:8984438 8983942 b BX640639 17 3UTR NA NA NA Hs.312098.1.36 chr1:151843991:151844258 151844232 b NM_003815 15 CDS 8751 ADAM15 a disintegrin and metalloproteinase domain 15 (metargidin) Hs.314338.1.11 chr21:39490293:39481214 39487623 b NM_018963 41 CDS 54014 BRWD1 bromodomain and WD repeat domain containing 1 Hs.33368.1.3 chr15:92685158:92689361 92688314 b NM_018349 6 CDS 55784 MCTP2 multiple C2-domains with two transmembrane regions 2 Hs.346736.1.21 chr2:99270738:99281614 99272414 b AK126402 10 3UTR 51263 MRPL30 mitochondrial ribosomal protein L30 Hs.445061.1.19 chr16:69322898:69290216 69322712 b NM_018052 14 CDS 55697 VAC14 Vac14 homolog (S. -
Identification of Bleomycin and Radiation-Induced Pulmonary Fibrosis Susceptibility Genes in Mice Anne-Marie Lemay Department Of
Identification of bleomycin and radiation-induced pulmonary fibrosis susceptibility genes in mice Anne-Marie Lemay Department of Human Genetics McGill University, Montréal February 4th, 2010 A thesis submitted to McGill University in partial fulfilment of the requirements of the degree of Doctor of Philosophy © Anne-Marie Lemay 2010 Comme il est profond, ce mystère de l’Invisible ! Nous ne pouvons le sonder avec nos sens misérables, avec nos yeux qui ne savent apercevoir ni le trop petit, ni le trop grand, ni le trop près, ni le trop loin, ni les habitants d’une étoile, ni les habitants d’une goutte d’eau… Guy de Maupassant Le Horla ii Table of contents Table of contents ................................................................................................... iii Abstract...................................................................................................................vi Résumé ................................................................................................................ viii Acknowledgments................................................................................................... x Abbreviations........................................................................................................ xii Original contributions to knowledge...................................................................xiv Author contribution to research...........................................................................xv List of figures ........................................................................................................ -
Supplemental Figure 1 Characterization of Lung Tumors In
Supplemental Figure 1 Characterization of lung tumors in KC mice. (A) Scatter plots of visible spontaneous tumors counted on the lung surfaces at necropsy. Each dot represents a value from a single mouse, and the bars and whiskers show the mean SD for each cohort from a single experiment. P value, two-tailed Student’s t-test. (B) Histologic analysis of spontaneous lung tumors in (A). Results indicate the numbers of lung lesions per histologic subtype per genotype. N, cohort sample sizes. P values, Fisher's exact test. Supplemental Figure 2 Surfactant protein C (SPC) expression in p21-deficient (KC) and –replete (K) tumor cell lines. Immunofluorescence staining with anti-surfactant protein C antibody (green) or normal IgG as a negative control. DAPI, blue. SPC/DAPI and IgG/DAPI are merged images. Scale bar, 20 µm. Supplemental Figure 3 Somatic recombination of latent KrasG12D allele and detection of p21 protein in p21-deficient (KC) and –replete (K) tumor cell lines. (A) PCR analysis of the K-rasLA1 and K-rasWT alleles in genomic DNA. Somatic recombination of the K-rasLA1 allele leads to loss of the PCR product (upper band, arrow). Wild-type K-ras allele detected (250 bp). Tail DNAs from KrasLA1 mice (KrasLA1/+) and wild-type mice (Kras+/+) were used as positive and negative controls, respectively, for the presence of the germline K-rasLA1 allele. (B) Immunoblot analysis of p21 expression. Actin was used as a loading control. Supplemental Figure 4 Growth and metastasis of p21-deficient (KC) tumor cell lines in Cdkn1a-null or –wild-type mice. -
(12) Patent Application Publication (10) Pub. No.: US 2013/0274315 A1 Birrer Et Al
US 201302743 15A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2013/0274315 A1 Birrer et al. (43) Pub. Date: Oct. 17, 2013 (54) PRO-ANGIOGENC GENES IN OVARAN (60) Provisional application No. 60/901,455, filed on Feb. TUMORENDOTHELIAL CELL, SOLATES 14, 2007. (71) Applicants: The University of Texas MD Anderson Publication Classification Cancer Center, Houston, TX (US); The Government of the U.S.A as (51) Int. Cl. represented by the Secretary of the CI2O I/68 (2006.01) Department of He, Rockville, MD (US) (52) U.S. Cl. CPC .................................... CI2O I/6886 (2013.01) (72) Inventors: Michael J. Birrer, Mt. Airy, MD (US); USPC ............... 514/44A: 435/6.12: 506/9: 435/7.1 Tomas A. Bonome, Washington, DC (US); Anil Sood, Pearland, TX (US); (57) ABSTRACT Chunhua Lu, Missouri City, TX (US) A gene profiling signature for ovarian tumor endothelial cells is disclosed herein. The gene signature can be used to diag nosis or prognosis an ovarian tumor, identify agents to treat an (21) Appl. No.: 13/863,219 ovariantumor, to predict the metastatic potential of an ovarian tumor and to determine the effectiveness of ovarian tumor (22) Filed: Apr. 15, 2013 treatments. Thus, methods are provided for identifying agents that can be used to treat ovarian cancer, for determining the effectiveness of an ovarian tumor treatment, or to diagnose or Related U.S. Application Data prognose an ovarian tumor. Methods of treatment are also (60) Division of application No. 12/541,729, filed on Aug. disclosed which include administering a composition that 14, 2009, now Pat. -
Agricultural University of Athens
ΓΕΩΠΟΝΙΚΟ ΠΑΝΕΠΙΣΤΗΜΙΟ ΑΘΗΝΩΝ ΣΧΟΛΗ ΕΠΙΣΤΗΜΩΝ ΤΩΝ ΖΩΩΝ ΤΜΗΜΑ ΕΠΙΣΤΗΜΗΣ ΖΩΙΚΗΣ ΠΑΡΑΓΩΓΗΣ ΕΡΓΑΣΤΗΡΙΟ ΓΕΝΙΚΗΣ ΚΑΙ ΕΙΔΙΚΗΣ ΖΩΟΤΕΧΝΙΑΣ ΔΙΔΑΚΤΟΡΙΚΗ ΔΙΑΤΡΙΒΗ Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων ΕΙΡΗΝΗ Κ. ΤΑΡΣΑΝΗ ΕΠΙΒΛΕΠΩΝ ΚΑΘΗΓΗΤΗΣ: ΑΝΤΩΝΙΟΣ ΚΟΜΙΝΑΚΗΣ ΑΘΗΝΑ 2020 ΔΙΔΑΚΤΟΡΙΚΗ ΔΙΑΤΡΙΒΗ Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων Genome-wide association analysis and gene network analysis for (re)production traits in commercial broilers ΕΙΡΗΝΗ Κ. ΤΑΡΣΑΝΗ ΕΠΙΒΛΕΠΩΝ ΚΑΘΗΓΗΤΗΣ: ΑΝΤΩΝΙΟΣ ΚΟΜΙΝΑΚΗΣ Τριμελής Επιτροπή: Aντώνιος Κομινάκης (Αν. Καθ. ΓΠΑ) Ανδρέας Κράνης (Eρευν. B, Παν. Εδιμβούργου) Αριάδνη Χάγερ (Επ. Καθ. ΓΠΑ) Επταμελής εξεταστική επιτροπή: Aντώνιος Κομινάκης (Αν. Καθ. ΓΠΑ) Ανδρέας Κράνης (Eρευν. B, Παν. Εδιμβούργου) Αριάδνη Χάγερ (Επ. Καθ. ΓΠΑ) Πηνελόπη Μπεμπέλη (Καθ. ΓΠΑ) Δημήτριος Βλαχάκης (Επ. Καθ. ΓΠΑ) Ευάγγελος Ζωίδης (Επ.Καθ. ΓΠΑ) Γεώργιος Θεοδώρου (Επ.Καθ. ΓΠΑ) 2 Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων Περίληψη Σκοπός της παρούσας διδακτορικής διατριβής ήταν ο εντοπισμός γενετικών δεικτών και υποψηφίων γονιδίων που εμπλέκονται στο γενετικό έλεγχο δύο τυπικών πολυγονιδιακών ιδιοτήτων σε κρεοπαραγωγικά ορνίθια. Μία ιδιότητα σχετίζεται με την ανάπτυξη (σωματικό βάρος στις 35 ημέρες, ΣΒ) και η άλλη με την αναπαραγωγική -
Small Noncoding RNA Signatures for Determining the Developmental Potential of an Embryo at the Morula Stage
International Journal of Molecular Sciences Article Small Noncoding RNA Signatures for Determining the Developmental Potential of an Embryo at the Morula Stage Angelika Timofeeva * , Yulia Drapkina, Ivan Fedorov, Vitaliy Chagovets, Nataliya Makarova, Maria Shamina, Elena Kalinina and Gennady Sukhikh Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Ministry of Health of Russia, Ac. Oparina 4, 117997 Moscow, Russia; [email protected] (Y.D.); [email protected] (I.F.); [email protected] (V.C.); [email protected] (N.M.); [email protected] (M.S.); [email protected] (E.K.); [email protected] (G.S.) * Correspondence: [email protected]; Tel.: +7-495-531-4444 Received: 7 November 2020; Accepted: 8 December 2020; Published: 10 December 2020 Abstract: As part of the optimization of assisted reproductive technology programs, the aim of the study was to identify key small noncoding RNA (sncRNA) molecules that participate in maternal-to-zygotic transition and determine development potential and competence to form a healthy fetus. Small RNA deep sequencing followed by quantitative real-time RT-PCR was used to profile sncRNAs in 50 samples of spent culture medium from morula with different development potentials (no potential (degradation/developmental arrest), low potential (poor-quality blastocyst), and high potential (good/excellent quality blastocyst capable of implanting and leading to live birth)) obtained from 27 subfertile couples who underwent in vitro fertilization. We have shown that the quality of embryos at the morula stage is determined by secretion/uptake rates of certain sets of piRNAs and miRNAs, namely hsa_piR_011291, hsa_piR_019122, hsa_piR_001311, hsa_piR_015026, hsa_piR_015462, hsa_piR_016735, hsa_piR_019675, hsa_piR_020381, hsa_piR_020485, hsa_piR_004880, hsa_piR_000807, hsa-let-7b-5p, and hsa-let-7i-5p. -
Detection of Tissue-Specific Genes and Computational Analysis of Testis
Detection of tissue-specific genes and Title computational analysis of testis-specific gene expression regulatory regions Author(s) 山下, 明史 Citation Issue Date Text Version ETD URL http://hdl.handle.net/11094/2599 DOI rights Note Osaka University Knowledge Archive : OUKA https://ir.library.osaka-u.ac.jp/ Osaka University Detection of tissue-specific genes and computational analysis of testis-specific gene expression regulatory regions (組織特異的遺伝子の検出と精巣特異的遺伝子の 発現制御領域のコンピュータを使った解析) by Akifumi Yamashita Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan February, 2009 1/97 Contents LIST of ABBREVIATIONS 5 ABSTRACT 6 1 INTRODUCTION 7 2 METHODS 10 2.1 Detection of tissue-specific genes 10 2.2 Annotation of tissue-specific genes 10 2.3 Extracting the 5′-regulatory regions 11 2.4 Selection of over-represented 8-mers 11 2.5 Comparison of the 8-mer frequency within regulatory regions of 13 testis-specific genes with those of non-testis-specific genes. 3 RESULTS 14 3.1 Detection of tissue-specific genes 14 3.2 Selection of testis-specific genes which can be used for the 14 following analysis 3.3 Classification of the over-represented 8-mers 15 3.4 Conservations of the flanking region of highlighted 8-mers 16 2/97 4 DISCUSSION 18 ACKNOWLEDGEMENTS 23 REFERENCES 24 TABLES 27 Table 1 - Number of tissue-specific genes 27 Table 2 - Classification of 117 representative 8-mers on the basis of their 28 testis association level Table 3 - 8-mers which appeared near by the other 8-mers 31 FIGURES 32 Fig. -
(12) Patent Application Publication (10) Pub. No.: US 2006/01992.04 A1 Dix Et Al
US 2006O1992.04A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2006/01992.04 A1 Dix et al. (43) Pub. Date: Sep. 7, 2006 (54) GENETIC TESTING FOR MALE FACTOR (60) Provisional application No. 60/327.525, filed on Oct. INFERTILITY 5, 2001. (75) Inventors: David Jacob Dix, Raleigh, NC (US); Publication Classification Stephen A. Krawetz, Detroit, MI (US); David Miller, Belmont Grove (GB) (51) Int. Cl. CI2O I/68 (2006.01) Correspondence Address: (52) U.S. Cl. .................................................................. 435/6 BROWDY AND NEIMARK, P.L.L.C. 624 NINTH STREET, NW SUTE 3OO WASHINGTON, DC 20001-5303 (US) (57) ABSTRACT (73) Assignees: G EPA, Washington, DC (US); Wayne RNA in sperm can be used as a diagnostic to distinguish ate University, Detroit, MI (US); Uni- - versity of Leeds, Belmont Grove (GB) betweendiagnostic normal transcripts and affectedis provided individuals. which is A compared list of specific with (21) Appl. No.: 11/357,423 transcripts obtained from the sperm of a subject. Correlation between the two transcripts is used to identify normal sperm (22) Filed: Feb. 21, 2006 or affected sperm. Addition, genetic testing for male infer tility or damage to spermatozoa is accomplished by provid Related U.S. Application Data ing a microarray of DNA probes with a sample of sperma tozoa to determine the mRNA fingerprints of the sample, and (63) Continuation-in-part of application No. 10/264,321, comparing the mRNA fingerprints of the sample with the filed on Oct. 4, 2002, now abandoned. mRNA fingerprints of normal fertile male spermatozoa. Patent Application Publication Sep.