Teachers Notes(.Pdf, 116.2
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
To Find Information About Arabidopsis Genes Leonore Reiser1, Shabari
UNIT 1.11 Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes Leonore Reiser1, Shabari Subramaniam1, Donghui Li1, and Eva Huala1 1Phoenix Bioinformatics, Redwood City, CA USA ABSTRACT The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource of Arabidopsis biology for plant scientists. TAIR curates and integrates information about genes, proteins, gene function, orthologs gene expression, mutant phenotypes, biological materials such as clones and seed stocks, genetic markers, genetic and physical maps, genome organization, images of mutant plants, protein sub-cellular localizations, publications, and the research community. The various data types are extensively interconnected and can be accessed through a variety of Web-based search and display tools. This unit primarily focuses on some basic methods for searching, browsing, visualizing, and analyzing information about Arabidopsis genes and genome, Additionally we describe how members of the community can share data using TAIR’s Online Annotation Submission Tool (TOAST), in order to make their published research more accessible and visible. Keywords: Arabidopsis ● databases ● bioinformatics ● data mining ● genomics INTRODUCTION The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource for the biology of Arabidopsis thaliana (Huala et al., 2001; Garcia-Hernandez et al., 2002; Rhee et al., 2003; Weems et al., 2004; Swarbreck et al., 2008, Lamesch, et al., 2010, Berardini et al., 2016). The TAIR database contains information about genes, proteins, gene expression, mutant phenotypes, germplasms, clones, genetic markers, genetic and physical maps, genome organization, publications, and the research community. In addition, seed and DNA stocks from the Arabidopsis Biological Resource Center (ABRC; Scholl et al., 2003) are integrated with genomic data, and can be ordered through TAIR. -
Spontaneous Puberty in 46,XX Subjects with Congenital Lipoid Adrenal Hyperplasia
Spontaneous puberty in 46,XX subjects with congenital lipoid adrenal hyperplasia. Ovarian steroidogenesis is spared to some extent despite inactivating mutations in the steroidogenic acute regulatory protein (StAR) gene. K Fujieda, … , T Sugawara, J F Strauss 3rd J Clin Invest. 1997;99(6):1265-1271. https://doi.org/10.1172/JCI119284. Research Article Congenital lipoid adrenal hyperplasia (lipoid CAH) is the most severe form of CAH in which the synthesis of all gonadal and adrenal cortical steroids is markedly impaired. We report here the clinical, endocrinological, and molecular analyses of two unrelated Japanese kindreds of 46,XX subjects affected with lipoid CAH who manifested spontaneous puberty. Phenotypic female infants with 46,XX karyotypes were diagnosed with lipoid CAH as newborns based on a clinical history of failure to thrive, hyperpigmentation, hyponatremia, hyperkalemia, and low basal values of serum cortisol and urinary 17-hydroxycorticosteroid and 17-ketosteroid. These patients responded to treatment with glucocorticoid and 9alpha- fludrocortisone. Spontaneous thelarche occurred in association with increased serum estradiol levels at the age of 10 and 11 yr, respectively. Pubic hair developed at the age of 12 yr 11 mo in one subject and menarche was at the age of 12 yr in both cases. Both subjects reported periodic menstrual bleeding and subsequently developed polycystic ovaries. To investigate the molecular basis of the steroidogenic lesion in these patients, the StAR gene was characterized by PCR and direct DNA sequence -
Homology & Alignment
Protein Bioinformatics Johns Hopkins Bloomberg School of Public Health 260.655 Thursday, April 1, 2010 Jonathan Pevsner Outline for today 1. Homology and pairwise alignment 2. BLAST 3. Multiple sequence alignment 4. Phylogeny and evolution Learning objectives: homology & alignment 1. You should know the definitions of homologs, orthologs, and paralogs 2. You should know how to determine whether two genes (or proteins) are homologous 3. You should know what a scoring matrix is 4. You should know how alignments are performed 5. You should know how to align two sequences using the BLAST tool at NCBI 1 Pairwise sequence alignment is the most fundamental operation of bioinformatics • It is used to decide if two proteins (or genes) are related structurally or functionally • It is used to identify domains or motifs that are shared between proteins • It is the basis of BLAST searching (next topic) • It is used in the analysis of genomes myoglobin Beta globin (NP_005359) (NP_000509) 2MM1 2HHB Page 49 Pairwise alignment: protein sequences can be more informative than DNA • protein is more informative (20 vs 4 characters); many amino acids share related biophysical properties • codons are degenerate: changes in the third position often do not alter the amino acid that is specified • protein sequences offer a longer “look-back” time • DNA sequences can be translated into protein, and then used in pairwise alignments 2 Find BLAST from the home page of NCBI and select protein BLAST… Page 52 Choose align two or more sequences… Page 52 Enter the two sequences (as accession numbers or in the fasta format) and click BLAST. -
Assembly Exercise
Assembly Exercise Turning reads into genomes Where we are • 13:30-14:00 – Primer Design to Amplify Microbial Genomes for Sequencing • 14:00-14:15 – Primer Design Exercise • 14:15-14:45 – Molecular Barcoding to Allow Multiplexed NGS • 14:45-15:15 – Processing NGS Data – de novo and mapping assembly • 15:15-15:30 – Break • 15:30-15:45 – Assembly Exercise • 15:45-16:15 – Annotation • 16:15-16:30 – Annotation Exercise • 16:30-17:00 – Submitting Data to GenBank Log onto ILRI cluster • Log in to HPC using ILRI instructions • NOTE: All the commands here are also in the file - assembly_hands_on_steps.txt • If you are like me, it may be easier to cut and paste Linux commands from this file instead of typing them in from the slides Start an interactive session on larger servers • The interactive command will start a session on a server better equipped to do genome assembly $ interactive • Switch to csh (I use some csh features) $ csh • Set up Newbler software that will be used $ module load 454 A norovirus sample sequenced on both 454 and Illumina • The vendors use different file formats unknown_norovirus_454.GACT.sff unknown_norovirus_illumina.fastq • I have converted these files to additional formats for use with the assembly tools unknown_norovirus_454_convert.fasta unknown_norovirus_454_convert.fastq unknown_norovirus_illumina_convert.fasta Set up and run the Newbler de novo assembler • Create a new de novo assembly project $ newAssembly de_novo_assembly • Add read data to the project $ addRun de_novo_assembly unknown_norovirus_454.GACT.sff -
Nonclassic Congenital Lipoid Adrenal Hyperplasia Diagnosed at 17 Months in a Korean Boy with Normal Male Genitalia: Emphasis on Pigmentation As a Diagnostic Clue
Case report https://doi.org/10.6065/apem.2020.25.1.46 Ann Pediatr Endocrinol Metab 2020;25:4651 Nonclassic congenital lipoid adrenal hyperplasia diagnosed at 17 months in a Korean boy with normal male genitalia: emphasis on pigmentation as a diagnostic clue Hosun Bae, MD1, Congenital lipoid adrenal hyperplasia (CLAH) is one of the most fatal conditions Min-Sun Kim, MD1, caused by an abnormality of adrenal and gonadal steroidogenesis. CLAH results Hyojung Park, MD1, from loss-of-function mutations of the steroidogenic acute regulatory (STAR) Ja-Hyun Jang, MD, PhD2, gene; the disease manifests with electrolyte imbalances and hyperpigmentation Jong-Moon Choi, MD, PhD2, in neonates or young infants due to adrenocortical hormone deficiencies, and 46, Sae-Mi Lee, MD, PhD2, XY genetic male CLAH patients can be phenotypically female. Meanwhile, some Sung Yoon Cho, MD, PhD1, patients with STAR mutations develop hyperpigmentation and mild signs of adrenal insufficiency, such as hypoglycemia, after infancy. These patients are classified as Dong-Kyu Jin, MD, PhD1 having nonclassic CLAH (NCCLAH) caused by STAR mutations that retain partial 1Department of Pediatrics, Samsung activity of STAR. We present the case of a Korean boy with normal genitalia who Medical Center, Sungkyunkwan Univer was diagnosed with NCCLAH. He presented with whole-body hyperpigmentation sity School of Medicine, Seoul, Korea and electrolyte abnormalities, which were noted at the age of 17 months after 2GC Genome, Yongin, Korea an episode of sepsis with peritonitis. The compound heterozygous mutations p.Gly221Ser and c.653C>T in STAR were identified by targeted gene-panel sequencing. Skin hyperpigmentation should be considered an important clue for diagnosing NCCLAH. -
Epigenomics Profiling Services
EPIGENOMICS PROFILING SERVICES • Chromatin analysis • DNA methylation analysis • RNA-seq analysis Diagenode helps you uncover the mysteries of epigenetics PAGE 3 Integrative epigenomics analysis DNA methylation analysis • Reduced representation bisulfite sequencing (RRBS) • Whole genome bisulfite sequencing analysis (WGBS) • Genome-wide DNA methylation • Differentially methylated region analysis DNA Chromatin RNA ChIP-seq/ChIP-qPCR analysis RNA-seq analysis • Histone modification ChIP-seq analysis • Small RNA-sequencing • Promoter analysis • mRNA analysis • Enhancer analysis • Whole transcriptome analysis • Transcription factor ChIP-seq analysis • Gene expression profiling • Customized NGS service • Chromatin accessibility (ATAC-seq) www.diagenode.com | PAGE 4 DIAGENODE EPIGENOMICS PROFILING SERVICES Expertise that you can trust Our Epigenomics Profiling Services assure the sample preparation expertise and quality data that you seek. We provide epigenome-wide analyses for understanding epigenetic mechanisms, epigenetics-related drug discovery, epigenetic biomarker identification, and functional epigenomics. Why Diagenode? • Expertise and trust: Recognized epigenetics leader, official partner of BLUEPRINT, IHEC and FAANG • Innovative technology: Utilization of the signature Bioruptor® sonication device for optimal chromatin and DNA shearing and the IP-Star® Automation device give reproducible and reliable optimization and results • Quality: Multiple QC steps in all workflows and validated antibodies plus reagents deliver superior data Human -
Long-Term Follow-Up in a Chinese Child with Congenital Lipoid Adrenal
Zhao et al. BMC Endocrine Disorders (2018) 18:78 https://doi.org/10.1186/s12902-018-0307-6 CASEREPORT Open Access Long-term follow-up in a Chinese child with congenital lipoid adrenal hyperplasia due to a StAR gene mutation Xiu Zhao1,ZheSu1* , Xia Liu1,JianmingSong2,YungenGan3, Pengqiang Wen4,ShoulinLi5,LiWang1 and Lili Pan1 Abstract Background: Congenital lipoid adrenal hyperplasia (CLAH) is an extremely rare and the most severe form of congenital adrenal hyperplasia. Typical features include disorder of sex development, early-onset adrenal crisis and enlarged adrenal glands with fatty accumulation. Case presentation: We report a case of CLAH caused by mutations in the steroidogenic acute regulatory protein (StAR) gene. The patient had typical early-onset adrenal crisis at 2 months of age. She had normal-appearing female genitalia and a karyotype of 46, XY. The serum cortisol and adrenal steroids levels were always nearly undetectable, but the adrenocorticotropic hormone levels were extremely high. Genetic analysis revealed compound heterozygous mutations at c. 229C > T (p.Q77X) in exon 3 and c. 722C > T (p.Q258X) in exon 7 of the StAR gene. The former mutation was previously detected in only two other Chinese CLAH patients. Both mutations cause truncation of the StAR protein.Thecasereportedhereappearstobeaclassicexample of CLAH with very small adrenal glands and is the second reported CLAH case with small adrenal glands thus far. In a 15-year follow-up, the patient’sheight wasapproximatelyaverageforfemalesbeforeage4andfellto− 1 SDS at 10 years of age. Her bone age was similar to her chronological age from age 4 to age 15 years. Conclusions: In conclusion, this is a classic case of CLAH with exceptionally small adrenal glands. -
The Uniprot Knowledgebase BLAST
Introduction to bioinformatics The UniProt Knowledgebase BLAST UniProtKB Basic Local Alignment Search Tool A CRITICAL GUIDE 1 Version: 1 August 2018 A Critical Guide to BLAST BLAST Overview This Critical Guide provides an overview of the BLAST similarity search tool, Briefly examining the underlying algorithm and its rise to popularity. Several WeB-based and stand-alone implementations are reviewed, and key features of typical search results are discussed. Teaching Goals & Learning Outcomes This Guide introduces concepts and theories emBodied in the sequence database search tool, BLAST, and examines features of search outputs important for understanding and interpreting BLAST results. On reading this Guide, you will Be aBle to: • search a variety of Web-based sequence databases with different query sequences, and alter search parameters; • explain a range of typical search parameters, and the likely impacts on search outputs of changing them; • analyse the information conveyed in search outputs and infer the significance of reported matches; • examine and investigate the annotations of reported matches, and their provenance; and • compare the outputs of different BLAST implementations and evaluate the implications of any differences. finding short words – k-tuples – common to the sequences Being 1 Introduction compared, and using heuristics to join those closest to each other, including the short mis-matched regions Between them. BLAST4 was the second major example of this type of algorithm, From the advent of the first molecular sequence repositories in and rapidly exceeded the popularity of FastA, owing to its efficiency the 1980s, tools for searching dataBases Became essential. DataBase searching is essentially a ‘pairwise alignment’ proBlem, in which the and Built-in statistics. -
"The Genecards Suite: from Gene Data Mining to Disease Genome Sequence Analyses". In: Current Protocols in Bioinformat
The GeneCards Suite: From Gene Data UNIT 1.30 Mining to Disease Genome Sequence Analyses Gil Stelzer,1,5 Naomi Rosen,1,5 Inbar Plaschkes,1,2 Shahar Zimmerman,1 Michal Twik,1 Simon Fishilevich,1 Tsippi Iny Stein,1 Ron Nudel,1 Iris Lieder,2 Yaron Mazor,2 Sergey Kaplan,2 Dvir Dahary,2,4 David Warshawsky,3 Yaron Guan-Golan,3 Asher Kohn,3 Noa Rappaport,1 Marilyn Safran,1 and Doron Lancet1,6 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 2LifeMap Sciences Ltd., Tel Aviv, Israel 3LifeMap Sciences Inc., Marshfield, Massachusetts 4Toldot Genetics Ltd., Hod Hasharon, Israel 5These authors contributed equally to the paper 6Corresponding author GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It au- tomatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. Var- Elect’s capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. -
Multiple Alignments, Blast and Clustalw
Multiple alignments, blast and clustalW 1. Blast idea: a. Filter out low complexity regions (tandem repeats… that sort of thing) [optional] b. Compile list of high-scoring strings (words, in BLAST jargon) of fixed length in query (threshold T) c. Extend alignments (highs scoring pairs) d. Report High Scoring pairs: score at least S (or an E value lower than some threshold) 2. Multiple Sequence Alignments: a. Attempts to extend dynamic programming techniques to multiple sequences run into problems after only a few proteins (8 average proteins were a problem early in 2000s) b. Heuristic approach c. Idea (Progressive Approach): i. homologous sequences are evolutionarily related ii. Build multiple alignment by series of pairwise alignments based off some phylogenetic tree (the initial tree or the guide tree ) iii. Add in more distantly related sequences d. Progressive Sequence alignment example: 1. NYLS & NKYLS: N YLS N(K|-)YLS NKYLS 2. NFS & NFLS: N YLS NF S NF(L|-)S NKYLS NFLS 3. N(K|-)YLS & NF(L|-)S N YLS N(K|-)(Y|F)(L|-)S NKYLS N YLS N F S N FLS e. Assessment: i. Works great for fairly similar sequences ii. Not so well for highly divergent ones f. Two Problems: i. local minimum problem: Algorithm greedily adds sequences based off of tree— might miss global solution ii. Alignment parameters: Mistakes (misaligned regions) early in procedure can’t be corrected later. g. ClustalW does multiple alignments and attempts to solve alignment parameter problem i. gap costs are dynamically varied based on position and amino acid ii. weight matrices are changed as the level of divergence between sequence increases (say going from PAM30 -> PAM60) iii. -
BLAST Practice
Using BLAST BLAST (Basic Local Alignment Search Tool) is an online search tool provided by NCBI (National Center for Biotechnology Information). It allows you to “find regions of similarity between biological sequences” (nucleotide or protein). The NCBI maintains a huge database of biological sequences, which it compares the query sequences to in order to find the most similar ones. Using BLAST, you can input a gene sequence of interest and search entire genomic libraries for identical or similar sequences in a matter of seconds. The amount of information on the BLAST website is a bit overwhelming — even for the scientists who use it on a frequent basis! You are not expected to know every detail of the BLAST program. BLAST results have the following fields: E value: The E value (expected value) is a number that describes how many times you would expect a match by chance in a database of that size. The lower the E value is, the more significant the match. Percent Identity: The percent identity is a number that describes how similar the query sequence is to the target sequence (how many characters in each sequence are identical). The higher the percent identity is, the more significant the match. Query Cover: The query cover is a number that describes how much of the query sequence is covered by the target sequence. If the target sequence in the database spans the whole query sequence, then the query cover is 100%. This tells us how long the sequences are, relative to each other. FASTA format FASTA format is used to represent either nucleotide or peptide sequences. -
Long-Term Clinical Data and Molecular Defects in the STAR Gene in Five
European Journal of Endocrinology (2013) 168 351–359 ISSN 0804-4643 CLINICAL STUDY Long-term clinical data and molecular defects in the STAR gene in five Greek patients Amalia Sertedaki, Maria Dracopoulou, Antonis Voutetakis, Kalliopi Stefanaki1, Dimitra Rontogianni2, Alexandra-Maria Magiakou, Christina Kanaka-Gantenbein, George Chrousos and Catherine Dacou-Voutetakis Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, ‘Agia Sophia’ Children’s Hospital, Athens University School of Medicine, Athens, Greece, 1Department of Pathology, ‘Agia Sophia’ Children’s Hospital, Athens, Greece and 2Department of Pathology, Evangelismos Hospital, Athens, Greece (Correspondence should be addressed to C Dacou-Voutetakis; Email: [email protected]) Abstract Context: Steroidogenic acute regulatory (STAR) gene mutations lead to adrenal and gonadal failure. Interesting, though as yet unexplained, features are the formation of ovarian cysts and the potential presence of CNS findings. Objective: To report biochemical, genetic, and long-term clinical data in five Greek patients from four different families with STAR gene defects (three 46,XX and two 46,XY). Methods and results: All patients presented in early infancy with adrenal insufficiency. The STAR gene mutation c.834del11bp, detected in three of our patients, completely alters the carboxyl end of the STAR protein and has not thus far been described in other population groups. These three patients belong to three separate families, possibly genetically related, as they live in different villages located in a small region of a Greek island. However, their interrelationship has not been proven. A second mutation, p.W250X, detected in our fourth family, was previously described only in two Serbian patients.