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The Mutability and Repair of DNA
B.Sc (Hons) Microbiology (CBCS Structure) C-7: Molecular Biology Unit 2: Replication of DNA The Mutability and Repair of DNA Dr. Rakesh Kumar Gupta Department of Microbiology Ram Lal Anand College New Delhi - 110021 Reference – Molecular Biology of the Gene (6th Edition) by Watson et. al. Pearson education, Inc Principles of Genetics (8th Edition) by D. Peter Snustad, D. Snustad, Eldon Gardner, and Michael J. Simmons, Wiley publications Replication errors and their repair The Nature of Mutations: • Transitions: A kind of the simplest mutation which is pyrimidine-to-pyrimidine and purine-to- purine substitutions such as T to C and A to G • Transversions: The other kind of mutation which are pyrimidine-to-purine and purine-to- pyrimidine substitutions such as T to A or G and ATransitions to C or T. Transversions 8 types 4 types Synonymous substitution Non synonymous substitution • Point mutations: Mutations that alter a single nucleotide Other kinds of mutations (which cause more drastic changes in DNA): • Insertions • Deletions • Gross rearrangements of Thesechromosome mutations might be caused by insertion by transposon or by aberrant action of cellular recombination processes. Mutation • Substitution, deletion, or insertion of a base pair. • Chromosomal deletion, insertion, or rearrangement. Somatic mutations occur in somatic cells and only affect the individual in which the mutation arises. Germ-line mutations alter gametes and passed to the next generation. Mutations are quantified in two ways: 1. Mutation rate = probability of a particular type of mutation per unit time (or generation). 2. Mutation frequency = number of times a particular mutation occurs in a population of cells or individuals. -
Mutation by Dr. Ty C.M. Hoffman
Mutation by Dr. Ty C.M. Hoffman Slide 1 Transcription features a one-to-one correspondence between DNA nucleotides in the gene and RNA nucleotides in the RNA transcript. However, the four nucleotide types used in RNA are insufficient to individually specify all twenty biological amino acids during translation. Instead, a sequence of three mRNA nucleotides (collectively called a codon) specifies a single amino acid. Since there are three nucleotide positions within a codon, and each position can be occupied by any of four types of nucleotide, there are sixty-four possible codons. This is more than enough to specify the twenty biological amino acids. Slide 2 The genetic code is universal in that all organisms (with very few exceptions) use the same code for specifying amino acids with mRNA codons. The genetic code is redundant in that more than one codon can specify the same amino acid. This is because there are more types of codons than there are types of amino acids used by organisms. The genetic code is not ambiguous, however, because each codon always specifies the same amino acid. Four of the codons serve special functions. One operates as a start codon (signaling initiation of translation), and three codons operate as stop codons (signaling the termination of translation). Slide 3 Mutation is a random change in the DNA sequence of nucleotides. Mutation can be purely accidental (by a mistake made during DNA replication), or mutation can result from exposure of DNA to a mutagen (something that causes mutation). Mutations can be classified into two major types: • Base-pair substitutions do not change the number of nucleotides in the DNA, because one base pair is substituted for another. -
Bio 102 Practice Problems Genetic Code and Mutation
Bio 102 Practice Problems Genetic Code and Mutation Multiple choice: Unless otherwise directed, circle the one best answer: 1. Choose the one best answer: Beadle and Tatum mutagenized Neurospora to find strains that required arginine to live. Based on the classification of their mutants, they concluded that: A. one gene corresponds to one protein. B. DNA is the genetic material. C. "inborn errors of metabolism" were responsible for many diseases. D. DNA replication is semi-conservative. E. protein cannot be the genetic material. 2. Choose the one best answer. Which one of the following is NOT part of the definition of a gene? A. A physical unit of heredity B. Encodes a protein C. Segement of a chromosome D. Responsible for an inherited characteristic E. May be linked to other genes 3. A mutation converts an AGA codon to a TGA codon (in DNA). This mutation is a: A. Termination mutation B. Missense mutation C. Frameshift mutation D. Nonsense mutation E. Non-coding mutation 4. Beadle and Tatum performed a series of complex experiments that led to the idea that one gene encodes one enzyme. Which one of the following statements does not describe their experiments? A. They deduced the metabolic pathway for the synthesis of an amino acid. B. Many different auxotrophic mutants of Neurospora were isolated. C. Cells unable to make arginine cannot survive on minimal media. D. Some mutant cells could survive on minimal media if they were provided with citrulline or ornithine. E. Homogentisic acid accumulates and is excreted in the urine of diseased individuals. 5. -
Therapy for Speech Sound Disorders.Pdf
2018 Fall Conference Salem, Oregon Friday, October 12, 2018 Therapy for Speech Sound Disorders: What Works and Why NSOME Don't Work Presented by: Gregory L. Lof, PhD, CCC-SLP, FASHA Educational Consultant Professor Emeritus MGH Institute of Health Professions, Boston, MA Theory and Evidence Against the Use of Nonspeech Oral Motor Exercises (NSOME) to Change Speech Sound Productions in Children Gregory L. Lof, PhD, CCC-SLP, FASHA October, 2018 Nonspeech Oral Motor Movements Defined • NSOMs are motor acts performed by various parts of the speech musculature to accomplish specific movement or postural goals that are not sufficient in themselves to have phonetic identity (Kent, 2015). Nonspeech Oral Motor Exercises (NSOME) Defined • Any technique that does not require the child to produce a speech sound but is used to influence the development of speaking abilities (Lof & Watson, 2008). • A collection of nonspeech methods and procedures that claim to influence tongue, lip, and jaw resting postures, increase strength, improve muscle tone, facilitate range of motion, and develop muscle control (Ruscello, 2008). • Oral-motor exercises (OMEs) are nonspeech activities that involve sensory stimulation to or actions of the lips, jaw, tongue, soft palate, larynx, and respiratory muscles which are intended to influence the physiologic underpinnings of the oropharyngeal mechanism and thus improve its functions. They include active muscle exercise, muscle stretching, passive exercise, and sensory stimulation (McCauley, Strand, Lof, et al., 2009). Do SLPs use NSOME? What Kind? • 85% of SLPs in the USA use NSOME to change speech sound productions (Lof & Watson, 2008); 85% of Canadian SLPs use NSOME (Hodge et al., 2005); 79% in Kentucky (Cima et al., 2009); 81% in South Carolina (Lemmon et al., 2010); 46% in Minnesota (Louma & Collins, 2012); 91% in India (Thomas & Kaipa, 2015); 49% in Australia (Rumbach, Rose, & Cheah, 2018). -
Clinical and Genetic Characteristics and Prenatal Diagnosis of Patients
Lin et al. Orphanet J Rare Dis (2020) 15:317 https://doi.org/10.1186/s13023-020-01599-y RESEARCH Open Access Clinical and genetic characteristics and prenatal diagnosis of patients presented GDD/ID with rare monogenic causes Liling Lin1, Ying Zhang1, Hong Pan1, Jingmin Wang2, Yu Qi1 and Yinan Ma1* Abstract Background: Global developmental delay/intellectual disability (GDD/ID), used to be named as mental retardation (MR), is one of the most common phenotypes in neurogenetic diseases. In this study, we described the diagnostic courses, clinical and genetic characteristics and prenatal diagnosis of a cohort with patients presented GDD/ID with monogenic causes, from the perspective of a tertiary genetic counseling and prenatal diagnostic center. Method: We retrospectively analyzed the diagnostic courses, clinical characteristics, and genetic spectrum of patients presented GDD/ID with rare monogenic causes. We also conducted a follow-up study on prenatal diagnosis in these families. Pathogenicity of variants was interpreted by molecular geneticists and clinicians according to the guidelines of the American College of Medical Genetics and Genomics (ACMG). Results: Among 81 patients with GDD/ID caused by rare monogenic variants it often took 0.5–4.5 years and 2–8 referrals to obtain genetic diagnoses. Devlopmental delay typically occurred before 3 years of age, and patients usu- ally presented severe to profound GDD/ID. The most common co-existing conditions were epilepsy (58%), micro- cephaly (21%) and facial anomalies (17%). In total, 111 pathogenic variants were found in 62 diferent genes among the 81 pedigrees, and 56 variants were novel. The most common inheritance patterns in this outbred Chinese popula- tion were autosomal dominant (AD; 47%), following autosomal recessive (AR; 37%), and X-linked (XL; 16%). -
Code Description
Code Description 0061 Chronic intestinal amebiasis without mention of abscess 0062 Amebic nondysenteric colitis 0063 Amebic liver abscess 0064 Amebic lung abscess 00642 West Nile fever with other neurologic manifestation 00649 West Nile fever with other complications 0065 Amebic brain abscess 0066 Amebic skin ulceration 0068 Amebic infection of other sites 0069 Amebiasis, unspecified 0070 Other protozoal intestinal diseases, balantidiasis (Infection by Balantidium coli) 0071 Other protozoal intestinal diseases, giardiasis 0072 Other protozoal intestinal diseases, coccidiosis 0073 Other protozoal intestinal diseases, trichomoniasis 0074 Other protozoal intestinal diseases, cryptosporidiosis 0075 Other protozoal intestional disease cyclosporiasis 0078 Other specified protozoal intestinal diseases 0079 Unspecified protozoal intestinal disease 01000 Primary tuberculous infection, unspecified 01001 Primary tuberculous infection bacteriological or histological examination not done 01002 Primary tuberculous infection, bacteriological or histological examination results unknown 01003 Primary tuberculous infection, tubercle bacilli found by microscopy 01004 Primary tuberculous infection, tubercle bacilli found by bacterial culture 01005 Primary tuberculous infection, tubercle bacilli confirmed histolgically 01006 Primary tuberculous infection, tubercle bacilli found by other methods 01010 Tuberculous pleurisy in primary progressive tuberculosis unspecified 01011 Tuberculous pleurisy bacteriological or histological examination not done 01012 Tuberculous -
Speech-Language Pathology: Student Clinical Handbook
DEPARTMENT OF COMMUNICATION DISORDERS SPEECH-LANGUAGE PATHOLOGY: STUDENT CLINICAL HANDBOOK 1 Table of Contents Page Overview of LSUHSC Graduate Program A. Departmental Mission 4 B. Sources of Information 5 1. LSUHSC Catalogue/Bulletin 5 2. LSUHSC Department of Communication Disorders 5 3. ASHA Certification Handbook 5 4. Speech-Language Pathology Handbook 5 General In-House Clinic Policies A. Timeliness 6 B. Illness 6 C. Dress Code 6 D. Attendance 7 E. Clinical Resources 8 F. Infection Control Procedures 9 G. Clinic Cleanup 10 H. Emergency Procedures 11 1. Medical Emergencies or Accidents 11 2. Fire Procedures 11 I. Confidentiality 12 J. Medical Records 13 Clinic Practicum A. Observations 15 B. Clinic: Treatment 16 1. Client Preparation 16 2. Telephone Contact 16 3. Treatment Room Sign-Up 16 4. First Week of Treatment Session 17 5. Program Planning 17 6. Treatment Documentation: Routing 17 7. Types of Treatment Documentation 18 8. Conferencing 19 9. End of Semester Duties 19 C. Clinic: Diagnostics/Evaluations 20 1. Assignments 20 2. Confirmation Phone Call 20 3. Illness 21 4. Greeting Client 21 5. Client Conference/Counseling 21 6. Concluding the Evaluation 22 7. Filing of Test Forms 22 8. Diagnostic/Evaluation Documentation: Routing 22 9. Diagnostic Protocols 23 10. Case Staffing 23 2 D. Patient Satisfaction Surveys 23 E. Grading Policy for Students in Clinic 24 1. Observations 24 2. Clinical Practicum 24 F. Procedures for Student Experiencing Clinic Difficulty 24 G. Evaluation of Clinical Supervisor 25 H. Recording Clinical Hours 25 Complaints, Comments and Concerns 27 Appendices A. Confirmation Phone Scripts 29 B. -
Inside This Issue
Winter 2014 No. 77 Inside this issue Group News | Fundraising | Members’ Letters | One Family Living with Two Different Chromosome Disorders | Bristol Conference 2014 | Unique Leaflets | Christmas Card Order Form Sophie, Unique’s Chair of Trustees Dear Members, In the past month a few things have reminded me of why it is so important to make connections through Unique but also to draw support from other parents around us. I’ve just returned from Unique’s most recent family conference in Bristol where 150 of us parents and carers had a lovely time in workshops, meals and activities, chatting and watching our children milling around together like one big family since – although we had never met before – we have shared so many experiences in common. However in contrast I have also just met a new mum who has just moved to my area from far away with two toddlers, one with a rare joys of the internet, it is becoming easier to meet others with similar, chromosome disorder, who is starting from scratch with no even very rare, chromosome disorders around the world and to find professional, medical or social support. She reminds me of how yourself talking to them in the middle of the night about some lonely I felt when Max was newly diagnosed, when I knew no one interesting things our children share in common (obsession with with a disabled child let alone anyone with a rare chromosome catalogues, anyone?) And of course we also have an enormous disorder. Elsewhere our latest Unique Facebook group, Unique amount in common with so many parents of children with other Russia, is also just starting up – so far it includes just a small special needs or disabilities around us in our own communities who number of members sharing very different experiences to mine here will often be walking the same path as us. -
Computational Genomics and Genetics of Developmental Disorders
Computational genomics and genetics of developmental disorders Hongjian Qi Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2018 © 2018 Hongjian Qi All Rights Reserved ABSTRACT Computational genomics and genetics of developmental disorders Hongjian Qi Computational genomics is at the intersection of computational applied physics, math, statistics, computer science and biology. With the advances in sequencing technology, large amounts of comprehensive genomic data are generated every year. However, the nature of genomic data is messy, complex and unstructured; it becomes extremely challenging to explore, analyze and understand the data based on traditional methods. The needs to develop new quantitative methods to analyze large-scale genomics datasets are urgent. By collecting, processing and organizing clean genomics datasets and using these datasets to extract insights and relevant information, we are able to develop novel methods and strategies to address specific genetics questions using the tools of applied mathematics, statistics, and human genetics. This thesis describes genetic and bioinformatics studies focused on utilizing and developing state-of-the-art computational methods and strategies in order to identify and interpret de novo mutations that are likely causing developmental disorders. We performed whole exome sequencing as well as whole genome sequencing on congenital diaphragmatic hernia parents-child trios and identified a new candidate risk gene MYRF. Additionally, we found male and female patients carry a different burden of likely-gene-disrupting mutations, and isolated and complex patients carry different gene expression levels in early development of diaphragm tissues for likely-gene-disrupting mutations. -
©Ferrata Storti Foundation
Haematologica 2000; 85:1207-1210 Acute Leukemias case of the month Cytogenetic characterization of acute myeloid leukemia in Shwachman's syndrome. A case report FRANCESCA R. SPIRITO, BARBARA CRESCENZI, CATERINA MATTEUCCI, MASSIMO F. MARTELLI, CRISTINA MECUCCI Hematology and Bone Marrow Transplantation Unit, University of Perugia, Italy ABSTRACT We report on a case of acute myeloid leukemia in a tion. A recent analysis of 21 patients with SDS 17-year old boy affected by Shwachman Diamond showed that the incidence of myelodysplasia syndrome (SDS). Conventional cytogenetics at diag- and transformation to acute myeloid leukemia nosis revealed an abnormal clone with complex 4 karyotypic changes including typical myeloid aber- is 33% and 24%, respectively. A few cases of rations, such as monosomy 5, tetrasomy of chro- acute lymphoblastic leukemia have also been 5-7 mosome 8, trisomy 9, and deletion of the short arm described as well as one case of a juvenile form of chromosome 12. The boy was treated with con- of chronic myeloid leukemia.8 When leukemia ventional chemotherapy and reached complete develops, due to the preceding bone marrow remission of leukemia, confirmed by cytogenetics failure, serious complications may be induced and fluorescence in situ hybridization. Nevertheless by chemotherapy and, because of the underly- he failed to regenerate normal marrow cellularity ing organ dysfunctions, these patients should and blood cell count. Cytogenetic information on be managed with extreme caution when treat- hematologic malignancies in SDS patients are dis- cussed. ed with allogeneic bone marrow transplanta- 9-13 ©2000; Ferrata Storti Foundation tion. We describe here the cytogenetic char- acterization and clinical course of an acute Key words: Shwachman’s syndrome, leukemia, cytogenetics myeloid leukemia occurring in a young patient affected by Shwachman's syndrome. -
The Cytogenetics of Hematologic Neoplasms 1 5
The Cytogenetics of Hematologic Neoplasms 1 5 Aurelia Meloni-Ehrig that errors during cell division were the basis for neoplastic Introduction growth was most likely the determining factor that inspired early researchers to take a better look at the genetics of the The knowledge that cancer is a malignant form of uncon- cell itself. Thus, the need to have cell preparations good trolled growth has existed for over a century. Several biologi- enough to be able to understand the mechanism of cell cal, chemical, and physical agents have been implicated in division became of critical importance. cancer causation. However, the mechanisms responsible for About 50 years after Boveri’s chromosome theory, the this uninhibited proliferation, following the initial insult(s), fi rst manuscripts on the chromosome makeup in normal are still object of intense investigation. human cells and in genetic disorders started to appear, fol- The fi rst documented studies of cancer were performed lowed by those describing chromosome changes in neoplas- over a century ago on domestic animals. At that time, the tic cells. A milestone of this investigation occurred in 1960 lack of both theoretical and technological knowledge with the publication of the fi rst article by Nowell and impaired the formulations of conclusions about cancer, other Hungerford on the association of chronic myelogenous leu- than the visible presence of new growth, thus the term neo- kemia with a small size chromosome, known today as the plasm (from the Greek neo = new and plasma = growth). In Philadelphia (Ph) chromosome, to honor the city where it the early 1900s, the fundamental role of chromosomes in was discovered (see also Chap. -
Bone Marrow Karyotypes of Children with Nonlymphocytic Leukemia
Pediat. Res. 13: 1247-1254 (1979) Chromosome abnormalities nonlymphotic leukemia leukemia, childhood Bone Marrow Karyotypes of Children with Nonlymphocytic Leukemia A. HAGEMEIJER, G. E. VAN ZANEN, E. M. E. SMIT, AND K. HAHLEN Department of Cell Biology and Genetics (A. H.. E. M.E. S.) and Department of Pediatric Oncology (G. E. K Z.. K H.) Sophia Children's Hospital, Erasmus University, Rotterdam, The Netherlands Summary studies with modern banding techniques. The Ph' chromosome may be found in some cases if childhbod CML, and its presence Bone marrow (BM) karyotypes from 16 consecutive children can differentiate the adult type of CML with its more protracted presenting with nonlymphocytic leukemia were established with course, from the juvenile variant. Nonrandom acquired abnor- the use of banding techniques, before therapy. The two patients malities have also been reported in a small number of children with chronic myeloid leukemia (CML) showed the Philadelphia with ANLL: monosomy 7 was reported three times in AML, (Phl) translocation (9q+;22q-). Five of the 14 patients with an AMMoL, and EL (7, 10, 17) deletion 7q22 was found twice in acute nonlymphocytic leukemia (ANLL) presented no acquired AML (9), and monosomy 9 was described once in AML (8). An cytogenetic abnormalities, but one of these five showed a high extensive report of cytogenetic abnormalities in childhood leuke- level of hypodiploidy. One patient with AML evidenced a variant mia has been published by Zuelzer et al. in 1976 (3 l), but it deals of the Phl chromosome originated as a translocation (12p+;22q-). mainly with acute lymphocytic leukemia; furthermore, this study Nonrandom abnormalities (-7; 7q-; +8; t(8;21); -21) were found started before the use of banding techniques, making the karyo- in six patients, isolated or in association with other aberrations.