And Y-Linked Ampliconic Genes in Human Populations
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Prenatal Diagnosis of Sex Chromosome Mosaicism with Two Marker Chromosomes in Three Cell Lines and a Review of the Literature
MOLECULAR MEDICINE REPORTS 19: 1791-1796, 2019 Prenatal diagnosis of sex chromosome mosaicism with two marker chromosomes in three cell lines and a review of the literature JIANLI ZHENG1, XIAOYU YANG2, HAIYAN LU1, YONGJUAN GUAN1, FANGFANG YANG1, MENGJUN XU1, MIN LI1, XIUQING JI3, YAN WANG3, PING HU3 and YUN ZHOU1 1Department of Prenatal Diagnosis, Laboratory of Clinical Genetics, Maternity and Child Health Care Hospital, Yancheng, Jiangsu 224001; 2Department of Clinical Reproductive Medicine, State Key Laboratory of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029; 3Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210004, P.R. China Received March 31, 2018; Accepted November 21, 2018 DOI: 10.3892/mmr.2018.9798 Abstract. The present study described the diagnosis of a fetus identifying the karyotype, identifying the origin of the marker with sex chromosome mosaicism in three cell lines and two chromosome and preparing effective genetic counseling. marker chromosomes. A 24-year-old woman underwent amniocentesis at 21 weeks and 4 days of gestation due to Introduction noninvasive prenatal testing identifying that the fetus had sex chromosome abnormalities. Amniotic cell culture revealed a Abnormalities involving sex chromosomes account for karyotype of 45,X[13]/46,X,+mar1[6]/46,X,+mar2[9], and approximately 0.5% of live births. Individuals with mosaic prenatal ultrasound was unremarkable. The woman underwent structural aberrations of the X and Y chromosomes exhibit repeat amniocentesis at 23 weeks and 4 days of gestation for complicated and variable phenotypes. The phenotypes of molecular detection. -
Tyrosine Kinase Oncogenes in Normal Hematopoiesis and Hematological Disease
Oncogene (2002) 21, 3314 ± 3333 ã 2002 Nature Publishing Group All rights reserved 0950 ± 9232/02 $25.00 www.nature.com/onc Tyrosine kinase oncogenes in normal hematopoiesis and hematological disease Blanca Scheijen1,2 and James D Grin*,1,2 1Department of Adult Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts, MA 02115, USA; 2Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA Tyrosine kinase oncogenes are formed as a result of Adaptors do not contain intrinsic catalytic activity but mutations that induce constitutive kinase activity. Many consist of independent functioning interaction modules of these tyrosine kinase oncogenes that are derived from like SH2-domain (mediates binding to phosphotyrosine genes, such as c-Abl, c-Fes, Flt3, c-Fms, c-Kit and residues), SH3-domain (interacts with polyproline-rich PDGFRb, that are normally involved in the regulation of PXXP stretch) or pleckstrin homology (PH) domain hematopoiesis or hematopoietic cell function. Despite (binds to inositol lipids). dierences in structure, normal function, and subcellular The ®rst tyrosine kinase oncogene associated with location, many of the tyrosine kinase oncogenes signal human hematologic disease, Bcr ± Abl, was identi®ed through the same pathways, and typically enhance almost twenty years ago, and there is now evidence for proliferation and prolong viability. They represent involvement of multiple tyrosine kinase oncogenes in excellent potential drug targets, and it is likely that acute and chronic leukemias, lymphomas, and myelo- additional mutations will be identi®ed in other kinases, mas. In each case, the tyrosine kinase activity of the their immediate downstream targets, or in proteins oncogene is constitutively activated by mutations that regulating their function. -
Anti-GRAP Antibody (ARG63124)
Product datasheet [email protected] ARG63124 Package: 100 μg anti-GRAP antibody Store at: -20°C Summary Product Description Goat Polyclonal antibody recognizes GRAP Tested Reactivity Hu Predict Reactivity Ms, Rat, Cow Tested Application WB Host Goat Clonality Polyclonal Isotype IgG Target Name GRAP Antigen Species Human Immunogen C-GFFPRSYVQPVHL Conjugation Un-conjugated Alternate Names GRB2-related adapter protein Application Instructions Application table Application Dilution WB 0.3 - 1 µg/ml Application Note WB: Recommend incubate at RT for 1h. * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Calculated Mw 25 kDa Properties Form Liquid Purification Purified from goat serum by ammonium sulphate precipitation followed by antigen affinity chromatography using the immunizing peptide. Buffer Tris saline (pH 7.3), 0.02% Sodium azide and 0.5% BSA Preservative 0.02% Sodium azide Stabilizer 0.5% BSA Concentration 0.5 mg/ml Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C or below. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. www.arigobio.com 1/2 Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Database links GeneID: 10750 Human Swiss-port # Q13588 Human Background This gene encodes a member of the GRB2/Sem5/Drk family and functions as a cytoplasmic signaling protein which contains an SH2 domain flanked by two SH3 domains. -
Biological Databases What Is a Database ?
BIOLOGICAL DATABASES WHAT IS A DATABASE ? A structured collection of data held in computer storage; esp. one that incorporates software to make it accessible in a variety of ways; any large collection of information. A collection of data structured searchable (index) -> table of contents updated periodically (release) -> new edition cross-referenced (hyperlinks ) -> links with other db Includes also associated tools (software) necessary for access, updating, information insertion, information deletion…. A database consists of basic units called records or entries. Each record consists of fields, which hold pre-defined data related to the record. For example, a protein database would have protein sequences as records and protein properties as fields (e.g., name of protein, length, amino-acid sequence, …) 2 DATABASES ON THE INTERNET Biological databases often have web interfaces, which allow users to send queries to the databases. Some databases can be accessed by different web servers, each offering a different interface. request query web page result User Web server Database server 3 WHY BIOLOGICAL DATABASES ? Exponential growth in biological data. Data (genomic sequences, 3D structures, 2D gel analysis, MS analysis, Microarrays….) are no longer published in a conventional manner, but directly submitted to databases. Essential tools for biological research. The only way to publish massive amounts of data without using all the paper in the world. 4 NUCLEOTIDES 5 COMPLETE GENOMES Until 2018: Eukaryotes 5262 Prokaryotes 131446 Viruses 14027 6 SOME STATISTICS More than 1000 different ‘biological’ databases Variable size: <100Kb to >20Gb DNA: > 20 Gb Protein: 1 Gb 3D structure: 5 Gb Other: smaller Update frequency: daily to annually to seldom to forget about it . -
Region Based Gene Expression Via Reanalysis of Publicly Available Microarray Data Sets
University of Louisville ThinkIR: The University of Louisville's Institutional Repository Electronic Theses and Dissertations 5-2018 Region based gene expression via reanalysis of publicly available microarray data sets. Ernur Saka University of Louisville Follow this and additional works at: https://ir.library.louisville.edu/etd Part of the Bioinformatics Commons, Computational Biology Commons, and the Other Computer Sciences Commons Recommended Citation Saka, Ernur, "Region based gene expression via reanalysis of publicly available microarray data sets." (2018). Electronic Theses and Dissertations. Paper 2902. https://doi.org/10.18297/etd/2902 This Doctoral Dissertation is brought to you for free and open access by ThinkIR: The University of Louisville's Institutional Repository. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of ThinkIR: The University of Louisville's Institutional Repository. This title appears here courtesy of the author, who has retained all other copyrights. For more information, please contact [email protected]. REGION BASED GENE EXPRESSION VIA REANALYSIS OF PUBLICLY AVAILABLE MICROARRAY DATA SETS By Ernur Saka B.S. (CEng), University of Dokuz Eylul, Turkey, 2008 M.S., University of Louisville, USA, 2011 A Dissertation Submitted To the J. B. Speed School of Engineering in Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Computer Science and Engineering Department of Computer Engineering and Computer Science University of Louisville Louisville, Kentucky May 2018 Copyright 2018 by Ernur Saka All rights reserved REGION BASED GENE EXPRESSION VIA REANALYSIS OF PUBLICLY AVAILABLE MICROARRAY DATA SETS By Ernur Saka B.S. (CEng), University of Dokuz Eylul, Turkey, 2008 M.S., University of Louisville, USA, 2011 A Dissertation Approved On April 20, 2018 by the following Committee __________________________________ Dissertation Director Dr. -
Genetics of Azoospermia
International Journal of Molecular Sciences Review Genetics of Azoospermia Francesca Cioppi , Viktoria Rosta and Csilla Krausz * Department of Biochemical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, 50139 Florence, Italy; francesca.cioppi@unifi.it (F.C.); viktoria.rosta@unifi.it (V.R.) * Correspondence: csilla.krausz@unifi.it Abstract: Azoospermia affects 1% of men, and it can be due to: (i) hypothalamic-pituitary dysfunction, (ii) primary quantitative spermatogenic disturbances, (iii) urogenital duct obstruction. Known genetic factors contribute to all these categories, and genetic testing is part of the routine diagnostic workup of azoospermic men. The diagnostic yield of genetic tests in azoospermia is different in the different etiological categories, with the highest in Congenital Bilateral Absence of Vas Deferens (90%) and the lowest in Non-Obstructive Azoospermia (NOA) due to primary testicular failure (~30%). Whole- Exome Sequencing allowed the discovery of an increasing number of monogenic defects of NOA with a current list of 38 candidate genes. These genes are of potential clinical relevance for future gene panel-based screening. We classified these genes according to the associated-testicular histology underlying the NOA phenotype. The validation and the discovery of novel NOA genes will radically improve patient management. Interestingly, approximately 37% of candidate genes are shared in human male and female gonadal failure, implying that genetic counselling should be extended also to female family members of NOA patients. Keywords: azoospermia; infertility; genetics; exome; NGS; NOA; Klinefelter syndrome; Y chromosome microdeletions; CBAVD; congenital hypogonadotropic hypogonadism Citation: Cioppi, F.; Rosta, V.; Krausz, C. Genetics of Azoospermia. 1. Introduction Int. J. Mol. Sci. -
Product Description SALSA MLPA Probemix P360-B2 Y-Chromosome
MRC-Holland ® Product Description version B2-01; Issued 20 March 2019 MLPA Product Description SALSA ® MLPA ® Probemix P360-B2 Y-Chromosome Microdeletions To be used with the MLPA General Protocol. Version B2. As compared to version B1, one probe length has been adjusted . For complete product history see page 14. Catalogue numbers: • P360-025R: SALSA MLPA Probemix P360 Y-Chromosome Microdeletions, 25 reactions. • P360-050R: SALSA MLPA Probemix P360 Y-Chromosome Microdeletions, 50 reactions. • P360-100R: SALSA MLPA Probemix P360 Y-Chromosome Microdeletions, 100 reactions. To be used in combination with a SALSA MLPA reagent kit, available for various number of reactions. MLPA reagent kits are either provided with FAM or Cy5.0 dye-labelled PCR primer, suitable for Applied Biosystems and Beckman capillary sequencers, respectively (see www.mlpa.com ). This SALSA MLPA probemix is for basic research and intended for experienced MLPA users only! This probemix is intended to quantify genes or chromosomal regions in which the occurrence of copy number changes is not yet well-established and the relationship between genotype and phenotype is not yet clear. Interpretation of results can be complicated. MRC-Holland recommends thoroughly screening any available literature. Certificate of Analysis: Information regarding storage conditions, quality tests, and a sample electropherogram from the current sales lot is available at www.mlpa.com . Precautions and warnings: For professional use only. Always consult the most recent product description AND the MLPA General Protocol before use: www.mlpa.com . It is the responsibility of the user to be aware of the latest scientific knowledge of the application before drawing any conclusions from findings generated with this product. -
Molecular Pathogenesis of a Malformation Syndrome Associated with a Pericentric Chromosome 2 Inversion
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA ANIMAL Molecular pathogenesis of a malformation syndrome associated with a pericentric chromosome 2 inversion Manuela Pinto Cardoso Mestrado em Biologia Humana e do Ambiente Dissertação orientada por: Doutor Dezsö David Doutora Deodália Dias 2017 ACKNOWLEDGEMENTS I would like to say “thank you!” to all the people that contributed in some way to this thesis. First and foremost, I would like to express my deepest gratitude to my supervisor, Dr. Dezsö David, for giving me the opportunity to work in his research group and for everything he taught me. Without his mentorship I would have never learned so much. I am grateful for Prof. Deodália Dias’s encouragement and support in all these years that I have been under her wings. I would like to extent my thanks to everyone at the National Health Institute Dr. Ricardo Jorge, for their continuous help in all stages of this thesis. To the team at Harvard Medical School, thank you for the technical assistance, and in special Dr. Cynthia Morton and Dr. Michael Talkowski. I am also grateful to Dr. Rui Gonçalves and Dr. João Freixo, who accompanied this case study and shared their medical knowledge. Of course, I am grateful for the family members for their involvement in this study. To my lab mates, a shout-out to them all! I really hold them dear for their help and the many laughs we shared every day. Thank you Mariana for being there literally since day one and for playing the role of a more mature counterpart. -
Male Infertility G.R
Guidelines on Male Infertility G.R. Dohle, A. Jungwirth, G. Colpi, A. Giwercman, T. Diemer, T.B. Hargreave © European Association of Urology 2008 TABLE OF CONTENTS PAGE 1. INTRODUCTION 6 1.1 Definition 1.2 Epidemiology and aetiology 6 1.3 Prognostic factors 6 1.4 Recommendations 7 1.5 References 7 2. INVESTIGATIONS 7 2.1 Semen analysis 7 2.1.1 Frequency of semen analysis 7 2.2 Recommendations 8 2.3 References 8 3. PRIMARY SPERMATOGENIC FAILURE 8 3.1 Definition 8 3.2 Aetiology 8 3.3 History and physical examination 8 3.4 Investigations 9 3.4.1 Semen analysis 9 3.4.2 Hormonal determinations 9 3.4.3 Testicular biopsy 9 3.5 Treatment 9 3.6 Conclusions 10 3.7 Recommendations 10 3.8 References 10 4. GENETIC DISORDERS IN INFERTILITY 14 4.1 Introduction 14 4.2 Chromosomal abnormalities 14 4.2.1 Sperm chromosomal abnormalities 14 4.2.2 Sex chromosome abnormalities (Klinefelter’s syndrome and variants [mosaicism] 14 4.2.3 Autosomal abnormalities 14 4.2.4 Translocations 15 4.3 Genetic defects 15 4.3.1 X-linked genetic disorders and male fertility 15 4.3.2 Kallmann’s syndrome 15 4.3.3 Androgen insensitivity: Reifenstein’s syndrome 15 4.3.4 Other X-disorders 15 4.3.5 X-linked disorders not associated with male infertility 15 4.4. Y genes and male infertility 15 4.4.1 Introduction 15 4.4.2 Clinical implications of Y microdeletions 16 4.4.2.1 Testing for Y microdeletions 16 4.4.2.2 Recommendations 16 4.4.3 Autosomal defects with severe phenotypic abnormalities as well as infertility 16 4.5 Cystic fibrosis mutations and male infertility 17 4.6 Unilateral or bilateral absence/abnormality of the vas and renal anomalies 17 4.7 Other single gene disorders 18 4.8 Unknown genetic disorders 18 4.9 Genetic and DNA abnormalities in sperm 18 4.10 Genetic counselling and ICSI 18 4.11 Conclusions 19 4.12 Recommendations 19 4.13 References 19 2 UPDATE MARCH 2007 5. -
Chromosomal Instability and Copy Number Alterations in Barrett's Esophagus and Esophageal Adenocarcinoma Thomas G
Human Cancer Biology Chromosomal Instability and Copy Number Alterations in Barrett's Esophagus and Esophageal Adenocarcinoma Thomas G. Paulson,1,2 Carlo C. Maley,4,5 Xiaohong Li,2 Hongzhe Li,6 Carissa A. Sanchez,1,2 Dennis L. Chao,3 Robert D. Odze,7 Thomas L. Vaughan,2,8 Patricia L. Blount,1,2,10 and Brian J. Reid1,2,9,10 Abstract Purpose: Chromosomal instability, as assessed by many techniques, including DNA content aneuploidy, loss of heterozygosity, and comparative genomic hybridization, has consistently been reported to be common in cancer and rare in normal tissues. Recently, a panel of chromosome instability biomarkers, including loss of heterozygos- ity and DNA content, has been reported to identify patients at high and low risk of pro- gression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA), but required multiple platforms for implementation. Although chromosomal instability in- volving amplifications and deletions of chromosome regions have been observed in nearly all cancers, copy number alterations (CNA) in premalignant tissues have not been well characterized or evaluated in cohort studies as biomarkers of cancer risk. Experimental Design: We examined CNAs in 98 patients having either BE or EA using Bacterial Artificial Chromosome (BAC) array comparative genomic hybridization to char- acterize CNAs at different stages of progression ranging from early BE to advanced EA. Results: CNAs were rare in early stages (less than high-grade dysplasia) but were pro- gressively more frequent and larger in later stages (high-grade dysplasia and EA), in- cluding high-level amplifications. The number of CNAs correlated highly with DNA content aneuploidy. -
NLRP3 and ASC Differentially Affect the Lung Transcriptome During Pneumococcal Pneumonia
UvA-DARE (Digital Academic Repository) Cell-specific pattern recognition receptor signaling in antibacterial defense van Lieshout, M.H.P. Publication date 2015 Document Version Final published version Link to publication Citation for published version (APA): van Lieshout, M. H. P. (2015). Cell-specific pattern recognition receptor signaling in antibacterial defense. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:30 Sep 2021 Chapter 7 NLRP3 and ASC differentially affect the lung transcriptome during pneumococcal pneumonia American Journal of Respiratory Cell and Molecular Biology 2014 Apr;50(4):699-712 DOI: 10.1165/rcmb.2013-0015OC Miriam H.P. van Lieshout 1,2 Brendon P. Scicluna 1,2 Sandrine Florquin 3 Tom van der Poll 1,2,4 Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands: 1Center of Infection and Immunity Amsterdam 2Center of Experimental and Molecular Medicine 3Department of Pathology 4Division of Infectious Diseases Chapter 7 Abstract Streptococcus (S.) pneumoniae is the most frequently isolated causative pathogen of community-acquired pneumonia, a leading cause of mortality worldwide. -
GRAP (NM 006613) Human Tagged ORF Clone Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RG208908 GRAP (NM_006613) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: GRAP (NM_006613) Human Tagged ORF Clone Tag: TurboGFP Symbol: GRAP Synonyms: DFNB114 Vector: pCMV6-AC-GFP (PS100010) E. coli Selection: Ampicillin (100 ug/mL) Cell Selection: Neomycin ORF Nucleotide >RG208908 representing NM_006613 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGGAGTCCGTGGCCCTGTACAGCTTTCAGGCTACAGAGAGCGACGAGCTGGCCTTCAACAAGGGAGACA CACTCAAGATCCTGAACATGGAGGATGACCAGAACTGGTACAAGGCCGAGCTCCGGGGTGTCGAGGGATT TATTCCCAAGAACTACATCCGCGTCAAGCCCCATCCGTGGTACTCGGGCAGGATTTCCCGGCAGCTGGCC GAAGAGATTCTGATGAAGCGGAACCATCTGGGAGCCTTCCTGATCCGGGAGAGTGAGAGCTCCCCAGGGG AGTTCTCTGTGTCTGTGAACTATGGAGACCAGGTGCAGCACTTCAAGGTGCTGCGTGAGGCCTCGGGGAA GTACTTCCTGTGGGAGGAGAAGTTCAACTCCCTCAACGAGCTGGTCGACTTCTACCGCACCACCACCATC GCCAAGAAGCGGCAGATCTTCCTGCGCGACGAGGAGCCCTTGCTCAAGTCACCTGGGGCCTGCTTTGCCC AGGCCCAGTTTGACTTCTCAGCCCAGGACCCCTCGCAGCTCAGCTTCCGCCGTGGCGACATCATTGAGGT CCTGGAGCGCCCAGACCCCCACTGGTGGCGGGGCCGGTCCTGCGGGCGCGTTGGCTTCTTCCCACGGAGT TACGTGCAGCCCGTGCACCTG ACGCGTACGCGGCCGCTCGAG - GFP Tag - GTTTAA Protein Sequence: >RG208908 representing NM_006613 Red=Cloning site Green=Tags(s) MESVALYSFQATESDELAFNKGDTLKILNMEDDQNWYKAELRGVEGFIPKNYIRVKPHPWYSGRISRQLA EEILMKRNHLGAFLIRESESSPGEFSVSVNYGDQVQHFKVLREASGKYFLWEEKFNSLNELVDFYRTTTI