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Polymorphisms of the BARX1 and ADAMTS17 Locus Genes in Individuals with Gastroesophageal Reflux Disease
J Neurogastroenterol Motil, Vol. 25 No. 3 July, 2019 pISSN: 2093-0879 eISSN: 2093-0887 https://doi.org/10.5056/jnm18183 JNM Journal of Neurogastroenterology and Motility Original Article Polymorphisms of the BARX1 and ADAMTS17 Locus Genes in Individuals With Gastroesophageal Reflux Disease Alexandra Argyrou,1 Evangelia Legaki,1 Christos Koutserimpas,2 Maria Gazouli,1* Ioannis Papaconstantinou,3 George Gkiokas,3 and George Karamanolis4 1Department of Basic Medical Sciences, Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece; 22nd Department of General Surgery, “Sismanoglio General Hospital of Athens, Athens, Greece; 32nd Department of Surgery, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece; and 4Gastroenterology Unit, 2nd Department of Surgery, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece Background/Aims Gastroesophageal reflux disease (GERD) represents a common condition having a substantial impact on the patients’ quality of life, as well as the health system. According to many studies, the BARX1 and ADAMTS17 genes have been suggested as genetic risk loci for the development of GERD and its complications. The purpose of this study is to investigate the potential association between GERD and BARX1 and ADAMTS17 polymorphisms. Methods The present is a prospective cohort study of 160 GERD patients and 180 healthy control subjects of Greek origin, examined for BARX1 and ADAMTS17 polymorphisms (rs11789015 and rs4965272) and a potential correlation to GERD. Results The rs11789015 AG and GG genotypes were found to be significantly associated with GERD (P = 0.032; OR, 1.65; 95% CI, 1.06- 2.57 and P = 0.033; OR, 3.00; 95% CI, 1.15-7.82, respectively), as well as the G allele (P = 0.007; OR, 1.60; 95% CI, 1.14- 2.24). -
Dog Coat Colour Genetics: a Review Date Published Online: 31/08/2020; 1,2 1 1 3 Rashid Saif *, Ali Iftekhar , Fatima Asif , Mohammad Suliman Alghanem
www.als-journal.com/ ISSN 2310-5380/ August 2020 Review Article Advancements in Life Sciences – International Quarterly Journal of Biological Sciences ARTICLE INFO Open Access Date Received: 02/05/2020; Date Revised: 20/08/2020; Dog Coat Colour Genetics: A Review Date Published Online: 31/08/2020; 1,2 1 1 3 Rashid Saif *, Ali Iftekhar , Fatima Asif , Mohammad Suliman Alghanem Authors’ Affiliation: 1. Institute of Abstract Biotechnology, Gulab Devi Educational anis lupus familiaris is one of the most beloved pet species with hundreds of world-wide recognized Complex, Lahore - Pakistan breeds, which can be differentiated from each other by specific morphological, behavioral and adoptive 2. Decode Genomics, traits. Morphological characteristics of dog breeds get more attention which can be defined mostly by 323-D, Town II, coat color and its texture, and considered to be incredibly lucrative traits in this valued species. Although Punjab University C Employees Housing the genetic foundation of coat color has been well stated in the literature, but still very little is known about the Scheme, Lahore - growth pattern, hair length and curly coat trait genes. Skin pigmentation is determined by eumelanin and Pakistan 3. Department of pheomelanin switching phenomenon which is under the control of Melanocortin 1 Receptor and Agouti Signaling Biology, Tabuk Protein genes. Genetic variations in the genes involved in pigmentation pathway provide basic understanding of University - Kingdom melanocortin physiology and evolutionary adaptation of this trait. So in this review, we highlighted, gathered and of Saudi Arabia comprehend the genetic mutations, associated and likely to be associated variants in the genes involved in the coat color and texture trait along with their phenotypes. -
Expression and Function of FERMT Genes in Colon Carcinoma Cells
ANTICANCER RESEARCH 33: 167-174 (2013) Expression and Function of FERMT Genes in Colon Carcinoma Cells KENJI KIRIYAMA1,2,3, YOSHIHIKO HIROHASHI1, TOSHIHIKO TORIGOE1, TERUFUMI KUBO1, YASUAKI TAMURA1, TAKAYUKI KANASEKI1, AKARI TAKAHASHI1, EMIRI NAKAZAWA1, ERI SAKA1, CHARLOTTE RAGNARSSON1, MUNEHIDE NAKATSUGAWA1, SATOKO INODA1,2, HIROKO ASANUMA4, HIDEO TAKASU5, TADASHI HASEGAWA4, TAKAHIRO YASOSHIMA3, KOICHI HIRATA2 and NORIYUKI SATO1 Department of 1Pathology, 2Surgery Ist and 4Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan; 3Department of Surgery, Shinsapporo Keiaikai Hospital, Sapporo, Japan; 5Dainippon Sumitomo Pharma Co., Ltd., Osaka, Japan Abstract. Invasion into the matrix is one of hallmarks of Colon carcinoma is a major malignancy, with a high malignant diseases and is the first step for tumor metastasis. mortality rate. In the process of tumorigenesis, tumor cells Thus, analysis of the molecular mechanisms of invasion is undergo multiple steps of genetic events (1), and multiple essential to overcome tumor cell invasion. In the present study, steps are also required for the cells to obtain several different we screened for colon carcinoma-specific genes using a cDNA phenotypes. Tissue invasion and metastasis are hallmarks microarray database of colon carcinoma tissues and normal that distinguish malignant from benign diseases (2). Several colon tissues, and we found that fermitin family member-1 classes of proteins are involved in the process of tissue (FERMT1) is overexpressed in colon carcinoma cells. FRRMT1, invasion; however, the exact molecular mechanisms of FERMT2 and FERMT3 expression was investigated in colon invasion remain unclear. carcinoma cells. Reverse transcription polymerase chain Fermitin family member (FERMT) genes include FERMT1, reaction (RT-PCR) analysis revealed that only FERMT1 had FERMT2 and FERMT3, and these genes have been reported cancer cell-specific expression. -
Seq2pathway Vignette
seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway. -
Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491 -
Dog Breeds of the World
Dog Breeds of the World Get your own copy of this book Visit: www.plexidors.com Call: 800-283-8045 Written by: Maria Sadowski PlexiDor Performance Pet Doors 4523 30th St West #E502 Bradenton, FL 34207 http://www.plexidors.com Dog Breeds of the World is written by Maria Sadowski Copyright @2015 by PlexiDor Performance Pet Doors Published in the United States of America August 2015 All rights reserved. No portion of this book may be reproduced or transmitted in any form or by any electronic or mechanical means, including photocopying, recording, or by any information retrieval and storage system without permission from PlexiDor Performance Pet Doors. Stock images from canstockphoto.com, istockphoto.com, and dreamstime.com Dog Breeds of the World It isn’t possible to put an exact number on the Does breed matter? dog breeds of the world, because many varieties can be recognized by one breed registration The breed matters to a certain extent. Many group but not by another. The World Canine people believe that dog breeds mostly have an Organization is the largest internationally impact on the outside of the dog, but through the accepted registry of dog breeds, and they have ages breeds have been created based on wanted more than 340 breeds. behaviors such as hunting and herding. Dog breeds aren’t scientifical classifications; they’re It is important to pick a dog that fits the family’s groupings based on similar characteristics of lifestyle. If you want a dog with a special look but appearance and behavior. Some breeds have the breed characterics seem difficult to handle you existed for thousands of years, and others are fairly might want to look for a mixed breed dog. -
Sequence Analysis of Familial Neurodevelopmental Disorders
SEQUENCE ANALYSIS OF FAMILIAL NEURODEVELOPMENTAL DISORDERS by Joseph Mark Tilghman A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland December 2020 © 2020 Joseph Tilghman All Rights Reserved Abstract: In the practice of human genetics, there is a gulf between the study of Mendelian and complex inheritance. When diagnosis of families affected by presumed monogenic syndromes is undertaken by genomic sequencing, these families are typically considered to have been solved only when a single gene or variant showing apparently Mendelian inheritance is discovered. However, about half of such families remain unexplained through this approach. On the other hand, common regulatory variants conferring low risk of disease still predominate our understanding of individual disease risk in complex disorders, despite rapidly increasing access to rare variant genotypes through sequencing. This dissertation utilizes primarily exome sequencing across several developmental disorders (having different levels of genetic complexity) to investigate how to best use an individual’s combination of rare and common variants to explain genetic risk, phenotypic heterogeneity, and the molecular bases of disorders ranging from those presumed to be monogenic to those known to be highly complex. The study described in Chapter 2 addresses putatively monogenic syndromes, where we used exome sequencing of four probands having syndromic neurodevelopmental disorders from an Israeli-Arab founder population to diagnose recessive and dominant disorders, highlighting the need to consider diverse modes of inheritance and phenotypic heterogeneity. In the study described in Chapter 3, we address the case of a relatively tractable multifactorial disorder, Hirschsprung disease. -
Gpnmb in Inflammatory and Metabolic Diseases
Functional characterization of Gpnmb in inflammatory and metabolic diseases Dissertation zur Erlangung des akademischen Grades D octor rerum naturalium (Dr. rer. nat.) eingereicht an der Lebenswissenschaftlichen Fakultät der Humboldt-Universität zu Berlin von M.Sc., Bernadette Nickl Präsidentin der Humboldt-Universität zu Berlin Prof. Dr.-Ing. Dr. Sabine Kunst Dekan der Lebenswissenschaftlichen Fakultät Prof. Dr. Bernhard Grimm Gutachter: Prof. Dr. Michael Bader Prof. Dr. Karl Stangl Prof. Dr. Thomas Sommer Tag der mündlichen Prüfung: 28. Februar 2020 For Sayeeda Summary Summary In 2018, the World Health Organization reported for the first time that “Overweight and obesity are linked to more deaths worldwide than underweight”A. Obesity increases the risk for the development of diabetes, atherosclerosis and cardiovascular diseases. Those metabolic diseases are associated with inflammation and the expression of glycoprotein nonmetastatic melanoma protein b (Gpnmb), a transmembrane protein that is expressed by macrophages and dendritic cells. We studied the role of Gpnmb in genetically- and diet-induced atherosclerosis as well as diet-induced obesity in Gpnmb-knockout and respective wildtype control mice. To this purpose, a mouse deficient in Gpnmb was created using Crispr-Cas9 technology. Body weight and blood lipid parameters remained unaltered in both diseases. Gpnmb was strongly expressed in atherosclerotic lesion-associated macrophages. Nevertheless, the absence of Gpnmb did not affect the development of aortic lesion size. However, macrophage and inflammation markers in epididymal fat tissue were increased in Gpnmb-deficient mice. In comparison to atherosclerosis, the absence of Gpnmb elicited stronger effects in obesity. For the first time, we observed a positive influence of Gpnmb on insulin and glucose plasma levels. -
Supplementary Materials
Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine -
Dog Breeds in Groups
Dog Facts: Dog Breeds & Groups Terrier Group Hound Group A breed is a relatively homogeneous group of animals People familiar with this Most hounds share within a species, developed and maintained by man. All Group invariably comment the common ancestral dogs, impure as well as pure-bred, and several wild cousins on the distinctive terrier trait of being used for such as wolves and foxes, are one family. Each breed was personality. These are feisty, en- hunting. Some use created by man, using selective breeding to get desired ergetic dogs whose sizes range acute scenting powers to follow qualities. The result is an almost unbelievable diversity of from fairly small, as in the Nor- a trail. Others demonstrate a phe- purebred dogs which will, when bred to others of their breed folk, Cairn or West Highland nomenal gift of stamina as they produce their own kind. Through the ages, man designed White Terrier, to the grand Aire- relentlessly run down quarry. dogs that could hunt, guard, or herd according to his needs. dale Terrier. Terriers typically Beyond this, however, generali- The following is the listing of the 7 American Kennel have little tolerance for other zations about hounds are hard Club Groups in which similar breeds are organized. There animals, including other dogs. to come by, since the Group en- are other dog registries, such as the United Kennel Club Their ancestors were bred to compasses quite a diverse lot. (known as the UKC) that lists these and many other breeds hunt and kill vermin. Many con- There are Pharaoh Hounds, Nor- of dogs not recognized by the AKC at present. -
Greater Swissswiss Mountainmountain Dogdog
AKCAKC JudgesJudges BREEDBREED STUDYSTUDY TheThe GreaterGreater SwissSwiss MountainMountain DogDog Presented by The Greater Swiss Mountain Dog Club of America Judges Education Committee HISTORY: FORM & FUNCTION Of the four Sennenhund breeds developed in Switzerland, the GREATER SWISS is both the LARGEST and the OLDEST. Developed in the remote and isolated areas of Switzerland, the GSMD was adapted to general farm use as a LIVESTOCK DROVER, GUARD DOG, and UTILITARIAN DRAFT DOG. Thus, when judging the GSMD, keep in mind, first and foremost that the dog should have the SUBSTANCE, STRUCTURE and TEMPERAMENT suited to the many duties for which it was bred. Clockwise from upper left: • Historical pair of GSMD with wagon • Bitch droving sheep • Working Weight Pull dog • Working Pack Dog (bitch) GENERAL APPEARANCE The GSMD is a striking, tri-colored, large, powerful, confident dog of sturdy appearanCe. It is a heavy boned and well muscled dog…. HistoriCal Photos TYPICAL DOG TYPICAL BITCH Current Photos …which, in spite of its size and weight, is agile enough to perform the all-purpose farm duties of the mountainous regions of its origin. SIZE, PROPORTION and SUBSTANCE Height at the highest point of the shoulder is ideally: •DOGS: 25.5 to 28.5 inches “Body LENGTH to HEIGHT is approximately a 10 to 9 PROPORTION, thus appearing slightly longer than tall”. It is a HEAVY BONED and WELL MUSCLED dog of STURDY appearance. •BITCHES: 23.5 to 27 inches A B As implied by its name, the GREATER Swiss Mountain Dog should be a LARGE, powerful dog. The adult GSMD males pictured above meet the breed Standard for height. -
Genetic Characterization of Congenital Defects in Dogs: Caudal Dysplasia, Ectodermal Dysplasia and Mucopolysaccharidosis Vii
Department of Veterinary Biosciences Biochemistry and Developmental Biology, Institute of Biomedicine Research Programs Unit, Molecular Neurology University of Helsinki and Department of Molecular Genetics The Folkhälsan Institute of Genetics GENETIC CHARACTERIZATION OF CONGENITAL DEFECTS IN DOGS: CAUDAL DYSPLASIA, ECTODERMAL DYSPLASIA AND MUCOPOLYSACCHARIDOSIS VII Marjo Hytönen ACADEMIC DISSERTATION To be presented, with the permission of the Faculty of Veterinary Medicine of the University of Helsinki, for public examination in Auditorium XIV, University Main Building, on 6th September 2013, at 12 noon. Helsinki 2013 Supervisors: Professor Hannes Lohi University of Helsinki, Finland Docent Kirsi Sainio University of Helsinki, Finland Reviewers: Professor Seppo Vainio University of Oulu, Finland Docent Janna Waltimo-Sirén University of Helsinki, Finland Opponent: Professor Frode Lingaas Norwegian School of Veterinary Science, Norway ISBN 978-952-10-9170-4 (pbk.) ISBN 978-952-10-9171-1 (PDF) Unigrafia Oy Helsinki 2013 Abstract Since the sequencing of the Canis lupus familiaris genome the dog has become a powerful tool for scientists. Selective breeding has created more than 400 different breeds each representing genetic isolates with breed-specific morphological and behavioral characteristics. Unique population history, available genealogical records, veterinary diagnostics and novel genomic tools greatly facilitate gene mapping studies in dogs. Given that over 600 genetic disorders have been described in dogs and that most of them are