Chapter # EVOLUTION AND ORIGIN OF NEUROFIBROMIN, THE PRODUCT OF THE NEUROFIBROMATOSIS TYPE 1 (NF1) TUMOR-SUPRESSOR GENE
|
|
- Linda Scott
- 6 years ago
- Views:
Transcription
1 142 Part 5 Chapter # EVOLUTION AND ORIGIN OF NEUROFIBROMIN, THE PRODUCT OF THE NEUROFIBROMATOSIS TYPE 1 (NF1) TUMOR-SUPRESSOR GENE Golovnina K. *1, Blinov A. 1, Chang L.-S. 2 1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia; 2 Center for Childhood Cancer, Children s Research Institute, Children s Hospital and Department of Pediatrics, The Ohio State University, USA * Corresponding author: ksu@bionet.nsc.ru Key words: neurofibromin, the Neurofibromatosis type 1 (NF1) gene, RasGAP protein family, GTPase-activator proteins for Ras-like GTPase, phylogeny, BLAST SUMMARY Motivation: Neurofibromatosis type 1 (NF1) is a common genetic disorder, which predisposes affected individuals to a variety of clinical features including tumors of the central and peripheral nervous systems. The product of the NF1 gene, neurofibromin, is a tumor suppressor which most likely acts through the interaction of its GTPase activating protein (GAP) related domain (GRD) with RAS to regulate cellular growth. While clinical features of NF1 as well as functional activity of human neurofibromin are intensively studied now little is understood about its evolution, diversity, and overall distribution among different taxa. Results: By combining bioinformatic and phylogenetic approaches, we demonstrated that NF1 homologs are present across a wide range of eukaryotic lineages. We observed 26 similar to NF1 amino-acid sequences from Chordata, Echinodermata, Arthropoda, Platyhelmintes and Fungi taxons. Taking into account a presence of NF1 gene in fungi, we can suggest the derivation of this gene before the Metazoan origin. In this case, an absence of NF1 in Nematoda and Mollusca should be a result of this gene elimination. INTRODUCTION Clinical features of NF1. Neurofibromatosis type I (NF1) or von Recklinghausen neurofibromatosis is the most common cancer predisposition syndrome affecting the nervous system with the incidence of 1 in 3000 worldwide (Gutmann, 2001). Typical manifestations include café au lait spots (hyperpigmented macules), cutaneous and subcutaneous neurofibromas (benign tumors), and malignancies of the central and peripheral nervous systems. The less common abnormalities observed in NF1 patients include learning disabilities (although frank mental retardation is rare) and skeletal abnormalities such as scoliosisand pseudoarthrosis (Skuse, Cappione, 1997). In addition to these features, children with NF1 can present within the first 6 years of life with lowgrade glial tumors involving the optic parthway. Two intriguing features of NF1 are the wide range of potentially affected tissues and the great variation in expressivity of disease traits across those affected. To date, the underlying source of this variation remains somewhat unclear, but evidence suggests that aberrations in normal NF1 RNA processing may be involved (Skuse, Cappione, 1997).
2 Comparative and evolutionary genomics and proteomics 143 Genetic features of NF1. Early insights into the patogenesis of NF1-associated tumors began with the identification of the NF1 gene in 1990 (Wallace et al., 1990). The NF1 gene itself, located at 17q11.2, encompasses >300 kb of human chromosome 17 (Li et al., 1995). The 60 exons which constitute the human NF1 gene give rise to several alternatively spliced transcripts. Within the central portion of the NF1 encoded protein, neurofibromin, lies a region with homology with the mammalian GTPase activating proteins (GAP) and the yeast inhibitor of RAS proteins 1 and 2 termed the GAP related domain (GRD). Neurofibromatoses. Discussions about neurofibromatoses include two the most common forms of this disorder: neurofibromatosis 1(NF1) and neurofibromatosis 2 (NF2). Individuals with two inherited cancer syndromes, NF1 and NF2 develop both benign and malignant tumors. The corresponding genes mutated in these two disorders encode tumor suppressor proteins, termed neurofibromin (NF1) and merlin (NF2), which have a similar function to regulate cell growth and differentiation. While both genes are not related and located on the different chromosomes in human, nothing is known about their relationships, distribution and function in other organism as well as about their origin. In the previous study we investigated evolution of merlin and postulated its origin in early metazoan (Golovnina et al., 2005). Here we represent the initial phylogenetic research of NF1 protein and its homologs based on bioinformatics approaches. METHODS AND ALGORITHMS BLAST search. Initial sequences of genes and proteins of interest from various organisms were identified by performing multiple TBLASTN and BLASTP (Altschul et al., 1997) searches against GenBank ( Ensembl ( ) and wormbase ( databases. In each case putative H.sapiens NF1 protein were used as the query sequence. Only NF1-like representatives of insects were located by D. melanogaster NF1 protein homology. To obtain more information we then searched the desirable sequences across genomic databases of completely or partially sequenced genomes available at The Sanger Institute ( and The Institute for Genomic Research (TIGR) ( Doe Joint Genome Institute (JGI) ( The Broad Institute ( The predicted nucleotide and aminoacid sequences of many species were assembled manually using available contigs and assemblies of genomes by homology to query sequence. Alignments and phylogeny. The Clustal X program (Thompson et al., 1997) was used to align the characterized or predicted protein sequences from different species. All alignments were corrected for obvious alignment ambiguity The resultant alignment contained 3888 aligned positions and was used to construct phylogenetic tree. Phylogenetic analysis was carried out using the Neighbor-Joining method in MEGA 3.1 program (Kumar et al., 2004). RESULTS AND DISCUSSION In total, 22 NF1-like sequences, that have overall homology, from Deuterostomia, Arthropoda, Platyhelmintes have been located in the present investigation. The main criterion for identification these sequences was their evident homology to known NF1 proteins. Moreover, we have found four Fungi proteins that show not so strongly similarity to NF1-like sequences. Five of 22 NF1-like proteins are experimentally annotated, namely H. sapiens NF1, M. musculus NF1, R. norvegicus NF1, T. rubripes NF1, and D. melanogaster NF1. Eight homologs were bioinformatics predicted previously and were located by initial BLASTP search across NCBI database
3 144 Part 5 (P. troglodytes, C. familiaris, G. gallus, A. gambiae), as well as NF1-related protein of N. crassa and three other RasGAPs of fungi. The rest sequences were assembled manually by parts using available paired scaffolds, contigs, and assemblies of the sequenced genomes together with protein and EST databases. Based on the obtained NF1 sequences and the close related proteins the phylogenetic tree was constructed (Fig. 1). RasGap family members from another groups were included in our analysis as an outgroup to show a homology of all obtained NF1- like sequences. We conducted phylogenetic analysis including only RasGap domain and corresponding sequences of newly identified proteins in view of possible different origin of some other domains except RasGap (Fig. 2) Both trees are similar in topology with small alterations in Fungi group. Figure 1. Phylogenetic analysis of NF1 homologs and its close related proteins from RasGAP group. NF1 clade is shown by solid line on the right. The dashed line denotes observed fungi proteins that are similar to NF1. UniProt accession numbers for full length sequences are represented in bold letters, GenBank in regular.
4 Comparative and evolutionary genomics and proteomics 145 Figure 2. Phylogenetic analysis of NF1 homologs and its close related proteins from RasGAP group based on RasGap domain sequences. Fungi proteins that have similarity with NF1-like sequences are marked with dark round. Phylogenetic analysis demonstrate a distribution of NF1 homologs across all investigated and available to date the major metazoan (chordata, urochordata, echinodermata, insects, and platyhelmintes) and fungi lineages. Among all species investigated, no NF1 sequences have been found in round worms (C. elegans, C. briggsae, C. remanie, B. malayi) and mollusk (B. glabrata). There are two possible explanations: (i) the derivation of NF1 gene occured after a separation of both Nematoda and mollusca or (ii) it was lost specifically in these groups. In C. elegans genome were previously annotated RasGAP family members (GAP1 and GAP2) that have homologs in C. briggsae genome. They are clasterized together with synras group of proteins that means their evolutionary relatedness. The presence of NF1-related sequences in fungi is disputable. NF1-like proteins have been found in four species of fungi kingdom, belonging to both Ascomycota and Basidiomycota. These amino-acid sequences have overall similarity to other NF1-like proteins but not so strong besides sequences corresponding to RasGap domain are more similar to other fungi RasGap proteins (Fig. 2). One of them (N. crassa) was previously annotated as NF1-related protein. On the other hands, no NF1-like sequences were detected in the rest fungi species examined.
5 146 Part 5 Therefore, the root of neurofibromin origin is unclear now and with the great progress in genome sequencing projects it promised to be more definite. Previously, no merlin homologs (another tumor suppressor) in fungi were observed. ACKNOWLEDGEMENTS This study was supported by grants from the US Department of Defense Neurofibromatosis Research Program. REFERENCES Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res., 25, Golovnina K., Blinov A., Akhmametyeva E.M., Omelyanchuk L.V., Chang L.-S. (2005) Evolution and origin of merlin, the product of the neurofibromatosis type 2 (NF2) tumor-suppressor gene. BMC Evolutionary Biology, 5, 69. Gutmann D.H. (2001) The neurofibromatosis: when less is more. Hum. Mol. Genet., 10, Kumar S., Tamura K., Nei M. (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics, 5, Li Y., O Connell P., Breidenbach H.H., Cawthon R., Stevens J., Xu G., Neil S., Robertson M., White R., Viskochil D. (1995) Genomic organization of the neurofibromatosis 1 gene (NF1). Genomics, 25, Skuse G.R., Cappione A.J. (1997) RNA processing and clinical variability in neurofibromatosis type I (NF1). Hum. Mol. Genet., 6, Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res., 15, Wallace M.R., Marchuk D.A., Andersen L.B., Letcher R., Odeh H.M., Saulino A.M., Fountain J.W., Brereton A., Nicholson J., Mitchell A.L. et al. (1990) Type 1 neurofibromatosis gene: identification of a large transcript disrupted in three NF1 patients. Science, 249,
Sequence Alignment Techniques and Their Uses
Sequence Alignment Techniques and Their Uses Sarah Fiorentino Since rapid sequencing technology and whole genomes sequencing, the amount of sequence information has grown exponentially. With all of this
More informationSmall RNA in rice genome
Vol. 45 No. 5 SCIENCE IN CHINA (Series C) October 2002 Small RNA in rice genome WANG Kai ( 1, ZHU Xiaopeng ( 2, ZHONG Lan ( 1,3 & CHEN Runsheng ( 1,2 1. Beijing Genomics Institute/Center of Genomics and
More informationEnsembl focuses on metazoan (animal) genomes. The genomes currently available at the Ensembl site are:
Comparative genomics and proteomics Species available Ensembl focuses on metazoan (animal) genomes. The genomes currently available at the Ensembl site are: Vertebrates: human, chimpanzee, mouse, rat,
More information08/21/2017 BLAST. Multiple Sequence Alignments: Clustal Omega
BLAST Multiple Sequence Alignments: Clustal Omega What does basic BLAST do (e.g. what is input sequence and how does BLAST look for matches?) Susan Parrish McDaniel College Multiple Sequence Alignments
More informationHands-On Nine The PAX6 Gene and Protein
Hands-On Nine The PAX6 Gene and Protein Main Purpose of Hands-On Activity: Using bioinformatics tools to examine the sequences, homology, and disease relevance of the Pax6: a master gene of eye formation.
More informationGiri Narasimhan. CAP 5510: Introduction to Bioinformatics CGS 5166: Bioinformatics Tools. Evaluation. Course Homepage.
CAP 5510: Introduction to Bioinformatics CGS 5166: Bioinformatics Tools Giri Narasimhan ECS 389; Phone: x3748 giri@cis.fiu.edu www.cis.fiu.edu/~giri/teach/bioinfs06.html 1/12/06 CAP5510/CGS5166 1 Evaluation
More informationBIOINFORMATICS LAB AP BIOLOGY
BIOINFORMATICS LAB AP BIOLOGY Bioinformatics is the science of collecting and analyzing complex biological data. Bioinformatics combines computer science, statistics and biology to allow scientists to
More informationBioinformatics. Dept. of Computational Biology & Bioinformatics
Bioinformatics Dept. of Computational Biology & Bioinformatics 3 Bioinformatics - play with sequences & structures Dept. of Computational Biology & Bioinformatics 4 ORGANIZATION OF LIFE ROLE OF BIOINFORMATICS
More informationGenomes and Their Evolution
Chapter 21 Genomes and Their Evolution PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
More informationComputational Biology: Basics & Interesting Problems
Computational Biology: Basics & Interesting Problems Summary Sources of information Biological concepts: structure & terminology Sequencing Gene finding Protein structure prediction Sources of information
More informationExample of Function Prediction
Find similar genes Example of Function Prediction Suggesting functions of newly identified genes It was known that mutations of NF1 are associated with inherited disease neurofibromatosis 1; but little
More informationBLAST. Varieties of BLAST
BLAST Basic Local Alignment Search Tool (1990) Altschul, Gish, Miller, Myers, & Lipman Uses short-cuts or heuristics to improve search speed Like speed-reading, does not examine every nucleotide of database
More informationTaxonomy. Content. How to determine & classify a species. Phylogeny and evolution
Taxonomy Content Why Taxonomy? How to determine & classify a species Domains versus Kingdoms Phylogeny and evolution Why Taxonomy? Classification Arrangement in groups or taxa (taxon = group) Nomenclature
More informationSupplemental Data. Perea-Resa et al. Plant Cell. (2012) /tpc
Supplemental Data. Perea-Resa et al. Plant Cell. (22)..5/tpc.2.3697 Sm Sm2 Supplemental Figure. Sequence alignment of Arabidopsis LSM proteins. Alignment of the eleven Arabidopsis LSM proteins. Sm and
More informationVisit to BPRC. Data is crucial! Case study: Evolution of AIRE protein 6/7/13
Visit to BPRC Adres: Lange Kleiweg 161, 2288 GJ Rijswijk Utrecht CS à Den Haag CS 9:44 Spoor 9a, arrival 10:22 Den Haag CS à Delft 10:28 Spoor 1, arrival 10:44 10:48 Delft Voorzijde à Bushalte TNO/Lange
More informationSUPPLEMENTARY INFORMATION
Supplementary information S1 (box). Supplementary Methods description. Prokaryotic Genome Database Archaeal and bacterial genome sequences were downloaded from the NCBI FTP site (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)
More informationAmira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut
Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic analysis Phylogenetic Basics: Biological
More informationUSING BLAST TO IDENTIFY PROTEINS THAT ARE EVOLUTIONARILY RELATED ACROSS SPECIES
USING BLAST TO IDENTIFY PROTEINS THAT ARE EVOLUTIONARILY RELATED ACROSS SPECIES HOW CAN BIOINFORMATICS BE USED AS A TOOL TO DETERMINE EVOLUTIONARY RELATIONSHPS AND TO BETTER UNDERSTAND PROTEIN HERITAGE?
More informationTHEORY. Based on sequence Length According to the length of sequence being compared it is of following two types
Exp 11- THEORY Sequence Alignment is a process of aligning two sequences to achieve maximum levels of identity between them. This help to derive functional, structural and evolutionary relationships between
More informationInDel 3-5. InDel 8-9. InDel 3-5. InDel 8-9. InDel InDel 8-9
Lecture 5 Alignment I. Introduction. For sequence data, the process of generating an alignment establishes positional homologies; that is, alignment provides the identification of homologous phylogenetic
More informationDr. Amira A. AL-Hosary
Phylogenetic analysis Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic Basics: Biological
More informationIntroduction to Bioinformatics. Shifra Ben-Dor Irit Orr
Introduction to Bioinformatics Shifra Ben-Dor Irit Orr Lecture Outline: Technical Course Items Introduction to Bioinformatics Introduction to Databases This week and next week What is bioinformatics? A
More informationProcedure to Create NCBI KOGS
Procedure to Create NCBI KOGS full details in: Tatusov et al (2003) BMC Bioinformatics 4:41. 1. Detect and mask typical repetitive domains Reason: masking prevents spurious lumping of non-orthologs based
More informationBioinformatics Chapter 1. Introduction
Bioinformatics Chapter 1. Introduction Outline! Biological Data in Digital Symbol Sequences! Genomes Diversity, Size, and Structure! Proteins and Proteomes! On the Information Content of Biological Sequences!
More informationBioinformatics Exercises
Bioinformatics Exercises AP Biology Teachers Workshop Susan Cates, Ph.D. Evolution of Species Phylogenetic Trees show the relatedness of organisms Common Ancestor (Root of the tree) 1 Rooted vs. Unrooted
More informationComparing Genomes! Homologies and Families! Sequence Alignments!
Comparing Genomes! Homologies and Families! Sequence Alignments! Allows us to achieve a greater understanding of vertebrate evolution! Tells us what is common and what is unique between different species
More informationAlgorithms in Computational Biology (236522) spring 2008 Lecture #1
Algorithms in Computational Biology (236522) spring 2008 Lecture #1 Lecturer: Shlomo Moran, Taub 639, tel 4363 Office hours: 15:30-16:30/by appointment TA: Ilan Gronau, Taub 700, tel 4894 Office hours:??
More informationIntroduction to Bioinformatics
Introduction to Bioinformatics Jianlin Cheng, PhD Department of Computer Science Informatics Institute 2011 Topics Introduction Biological Sequence Alignment and Database Search Analysis of gene expression
More informationBLAST Database Searching. BME 110: CompBio Tools Todd Lowe April 8, 2010
BLAST Database Searching BME 110: CompBio Tools Todd Lowe April 8, 2010 Admin Reading: Read chapter 7, and the NCBI Blast Guide and tutorial http://www.ncbi.nlm.nih.gov/blast/why.shtml Read Chapter 8 for
More informationHomology Modeling. Roberto Lins EPFL - summer semester 2005
Homology Modeling Roberto Lins EPFL - summer semester 2005 Disclaimer: course material is mainly taken from: P.E. Bourne & H Weissig, Structural Bioinformatics; C.A. Orengo, D.T. Jones & J.M. Thornton,
More informationBSC 4934: QʼBIC Capstone Workshop" Giri Narasimhan. ECS 254A; Phone: x3748
BSC 4934: QʼBIC Capstone Workshop" Giri Narasimhan ECS 254A; Phone: x3748 giri@cs.fiu.edu http://www.cs.fiu.edu/~giri/teach/bsc4934_su10.html July 2010 7/12/10 Q'BIC Bioinformatics 1 Overview of Course"
More informationMultiple Sequence Alignment. Sequences
Multiple Sequence Alignment Sequences > YOR020c mstllksaksivplmdrvlvqrikaqaktasglylpe knveklnqaevvavgpgftdangnkvvpqvkvgdqvl ipqfggstiklgnddevilfrdaeilakiakd > crassa mattvrsvksliplldrvlvqrvkaeaktasgiflpe
More informationBioinformatics (GLOBEX, Summer 2015) Pairwise sequence alignment
Bioinformatics (GLOBEX, Summer 2015) Pairwise sequence alignment Substitution score matrices, PAM, BLOSUM Needleman-Wunsch algorithm (Global) Smith-Waterman algorithm (Local) BLAST (local, heuristic) E-value
More informationBasic Local Alignment Search Tool
Basic Local Alignment Search Tool Alignments used to uncover homologies between sequences combined with phylogenetic studies o can determine orthologous and paralogous relationships Local Alignment uses
More informationSUPPLEMENTARY INFORMATION
Supplementary information S3 (box) Methods Methods Genome weighting The currently available collection of archaeal and bacterial genomes has a highly biased distribution of isolates across taxa. For example,
More informationCladistics and Bioinformatics Questions 2013
AP Biology Name Cladistics and Bioinformatics Questions 2013 1. The following table shows the percentage similarity in sequences of nucleotides from a homologous gene derived from five different species
More informationProcesses of Evolution
15 Processes of Evolution Forces of Evolution Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Natural selection can act on quantitative traits in three ways: Stabilizing selection
More informationSequences, Structures, and Gene Regulatory Networks
Sequences, Structures, and Gene Regulatory Networks Learning Outcomes After this class, you will Understand gene expression and protein structure in more detail Appreciate why biologists like to align
More informationA profile-based protein sequence alignment algorithm for a domain clustering database
A profile-based protein sequence alignment algorithm for a domain clustering database Lin Xu,2 Fa Zhang and Zhiyong Liu 3, Key Laboratory of Computer System and architecture, the Institute of Computing
More informationPhylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?
Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Phylogeny: the evolutionary history of a species
More informationName: Class: Date: ID: A
Class: _ Date: _ Ch 17 Practice test 1. A segment of DNA that stores genetic information is called a(n) a. amino acid. b. gene. c. protein. d. intron. 2. In which of the following processes does change
More informationCGS 5991 (2 Credits) Bioinformatics Tools
CAP 5991 (3 Credits) Introduction to Bioinformatics CGS 5991 (2 Credits) Bioinformatics Tools Giri Narasimhan 8/26/03 CAP/CGS 5991: Lecture 1 1 Course Schedules CAP 5991 (3 credit) will meet every Tue
More informationBIOINFORMATICS: An Introduction
BIOINFORMATICS: An Introduction What is Bioinformatics? The term was first coined in 1988 by Dr. Hwa Lim The original definition was : a collective term for data compilation, organisation, analysis and
More information- conserved in Eukaryotes. - proteins in the cluster have identifiable conserved domains. - human gene should be included in the cluster.
NCBI BLAST Services DELTA-BLAST BLAST (http://blast.ncbi.nlm.nih.gov/), Basic Local Alignment Search tool, is a suite of programs for finding similarities between biological sequences. DELTA-BLAST is a
More informationPhylogenetics in the Age of Genomics: Prospects and Challenges
Phylogenetics in the Age of Genomics: Prospects and Challenges Antonis Rokas Department of Biological Sciences, Vanderbilt University http://as.vanderbilt.edu/rokaslab http://pubmed2wordle.appspot.com/
More informationStatistical Machine Learning Methods for Biomedical Informatics II. Hidden Markov Model for Biological Sequences
Statistical Machine Learning Methods for Biomedical Informatics II. Hidden Markov Model for Biological Sequences Jianlin Cheng, PhD William and Nancy Thompson Missouri Distinguished Professor Department
More informationSupplementary text for the section Interactions conserved across species: can one select the conserved interactions?
1 Supporting Information: What Evidence is There for the Homology of Protein-Protein Interactions? Anna C. F. Lewis, Nick S. Jones, Mason A. Porter, Charlotte M. Deane Supplementary text for the section
More informationMap of AP-Aligned Bio-Rad Kits with Learning Objectives
Map of AP-Aligned Bio-Rad Kits with Learning Objectives Cover more than one AP Biology Big Idea with these AP-aligned Bio-Rad kits. Big Idea 1 Big Idea 2 Big Idea 3 Big Idea 4 ThINQ! pglo Transformation
More informationIntroduction to protein alignments
Introduction to protein alignments Comparative Analysis of Proteins Experimental evidence from one or more proteins can be used to infer function of related protein(s). Gene A Gene X Protein A compare
More informationHomology and Information Gathering and Domain Annotation for Proteins
Homology and Information Gathering and Domain Annotation for Proteins Outline Homology Information Gathering for Proteins Domain Annotation for Proteins Examples and exercises The concept of homology The
More informationGenome Annotation. Bioinformatics and Computational Biology. Genome sequencing Assembly. Gene prediction. Protein targeting.
Genome Annotation Bioinformatics and Computational Biology Genome Annotation Frank Oliver Glöckner 1 Genome Analysis Roadmap Genome sequencing Assembly Gene prediction Protein targeting trna prediction
More informationMiGA: The Microbial Genome Atlas
December 12 th 2017 MiGA: The Microbial Genome Atlas Jim Cole Center for Microbial Ecology Dept. of Plant, Soil & Microbial Sciences Michigan State University East Lansing, Michigan U.S.A. Where I m From
More informationPrinciples of Genetics
Principles of Genetics Snustad, D ISBN-13: 9780470903599 Table of Contents C H A P T E R 1 The Science of Genetics 1 An Invitation 2 Three Great Milestones in Genetics 2 DNA as the Genetic Material 6 Genetics
More informationAn Efficient Algorithm for Protein-Protein Interaction Network Analysis to Discover Overlapping Functional Modules
An Efficient Algorithm for Protein-Protein Interaction Network Analysis to Discover Overlapping Functional Modules Ying Liu 1 Department of Computer Science, Mathematics and Science, College of Professional
More informationChapter 5. Proteomics and the analysis of protein sequence Ⅱ
Proteomics Chapter 5. Proteomics and the analysis of protein sequence Ⅱ 1 Pairwise similarity searching (1) Figure 5.5: manual alignment One of the amino acids in the top sequence has no equivalent and
More informationBiology Scope and Sequence Student Outcomes (Objectives Skills/Verbs)
C-4 N.12.A 1-6 N.12.B.1-4 Scientific Literacy/ Nature of (embedded throughout course) Scientific Inquiry is the process by which humans systematically examine the natural world. Scientific inquiry is a
More informationMETHODS FOR DETERMINING PHYLOGENY. In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task.
Chapter 12 (Strikberger) Molecular Phylogenies and Evolution METHODS FOR DETERMINING PHYLOGENY In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task. Modern
More informationIn-Depth Assessment of Local Sequence Alignment
2012 International Conference on Environment Science and Engieering IPCBEE vol.3 2(2012) (2012)IACSIT Press, Singapoore In-Depth Assessment of Local Sequence Alignment Atoosa Ghahremani and Mahmood A.
More informationTiffany Samaroo MB&B 452a December 8, Take Home Final. Topic 1
Tiffany Samaroo MB&B 452a December 8, 2003 Take Home Final Topic 1 Prior to 1970, protein and DNA sequence alignment was limited to visual comparison. This was a very tedious process; even proteins with
More informationHereditary Hemochromatosis
Hereditary Hemochromatosis The HFE gene Becky Reese What is hereditary hemochromatosis? Recessively inherited Iron overload disorder Inability to regulate iron absorption No cure http://www.consultant360.com/article/genetics-gastroenterology-what-you-need-know-part-1
More informationCSCE555 Bioinformatics. Protein Function Annotation
CSCE555 Bioinformatics Protein Function Annotation Why we need to do function annotation? Fig from: Network-based prediction of protein function. Molecular Systems Biology 3:88. 2007 What s function? The
More informationA A A A B B1
LEARNING OBJECTIVES FOR EACH BIG IDEA WITH ASSOCIATED SCIENCE PRACTICES AND ESSENTIAL KNOWLEDGE Learning Objectives will be the target for AP Biology exam questions Learning Objectives Sci Prac Es Knowl
More informationInvestigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST
Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST Introduction Bioinformatics is a powerful tool which can be used to determine evolutionary relationships and
More informationI. Molecules and Cells: Cells are the structural and functional units of life; cellular processes are based on physical and chemical changes.
I. Molecules and Cells: Cells are the structural and functional units of life; cellular processes are based on physical and chemical changes. A. Chemistry of Life B. Cells 1. Water How do the unique chemical
More informationGrundlagen der Bioinformatik Summer semester Lecturer: Prof. Daniel Huson
Grundlagen der Bioinformatik, SS 10, D. Huson, April 12, 2010 1 1 Introduction Grundlagen der Bioinformatik Summer semester 2010 Lecturer: Prof. Daniel Huson Office hours: Thursdays 17-18h (Sand 14, C310a)
More information"Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky
MOLECULAR PHYLOGENY "Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky EVOLUTION - theory that groups of organisms change over time so that descendeants differ structurally
More informationI. Molecules & Cells. A. Unit One: The Nature of Science. B. Unit Two: The Chemistry of Life. C. Unit Three: The Biology of the Cell.
I. Molecules & Cells A. Unit One: The Nature of Science a. How is the scientific method used to solve problems? b. What is the importance of controls? c. How does Darwin s theory of evolution illustrate
More informationMULTIPLE SEQUENCE ALIGNMENT FOR CONSTRUCTION OF PHYLOGENETIC TREE
MULTIPLE SEQUENCE ALIGNMENT FOR CONSTRUCTION OF PHYLOGENETIC TREE Manmeet Kaur 1, Navneet Kaur Bawa 2 1 M-tech research scholar (CSE Dept) ACET, Manawala,Asr 2 Associate Professor (CSE Dept) ACET, Manawala,Asr
More informationAlgorithms in Bioinformatics FOUR Pairwise Sequence Alignment. Pairwise Sequence Alignment. Convention: DNA Sequences 5. Sequence Alignment
Algorithms in Bioinformatics FOUR Sami Khuri Department of Computer Science San José State University Pairwise Sequence Alignment Homology Similarity Global string alignment Local string alignment Dot
More informationTools and Algorithms in Bioinformatics
Tools and Algorithms in Bioinformatics GCBA815, Fall 2015 Week-4 BLAST Algorithm Continued Multiple Sequence Alignment Babu Guda, Ph.D. Department of Genetics, Cell Biology & Anatomy Bioinformatics and
More informationAP Biology Essential Knowledge Cards BIG IDEA 1
AP Biology Essential Knowledge Cards BIG IDEA 1 Essential knowledge 1.A.1: Natural selection is a major mechanism of evolution. Essential knowledge 1.A.4: Biological evolution is supported by scientific
More informationChapter 16: Reconstructing and Using Phylogenies
Chapter Review 1. Use the phylogenetic tree shown at the right to complete the following. a. Explain how many clades are indicated: Three: (1) chimpanzee/human, (2) chimpanzee/ human/gorilla, and (3)chimpanzee/human/
More informationGroup activities: Making animal model of human behaviors e.g. Wine preference model in mice
Lecture schedule 3/30 Natural selection of genes and behaviors 4/01 Mouse genetic approaches to behavior 4/06 Gene-knockout and Transgenic technology 4/08 Experimental methods for measuring behaviors 4/13
More informationNIH Public Access Author Manuscript Immunogenetics. Author manuscript; available in PMC 2006 May 31.
NIH Public Access Author Manuscript Published in final edited form as: Immunogenetics. 2005 April ; 57(1-2): 151 157. Origin and evolution of the Ig-like domains present in mammalian leukocyte receptors:
More informationCourse Descriptions Biology
Course Descriptions Biology BIOL 1010 (F/S) Human Anatomy and Physiology I. An introductory study of the structure and function of the human organ systems including the nervous, sensory, muscular, skeletal,
More informationBig Idea 3: Living systems store, retrieve, transmit, and respond to information essential to life processes.
Big Idea 3: Living systems store, retrieve, transmit, and respond to information essential to life processes. Enduring understanding 3.A: Heritable information provides for continuity of life. Essential
More informationTandem repeat 16,225 20,284. 0kb 5kb 10kb 15kb 20kb 25kb 30kb 35kb
Overview Fosmid XAAA112 consists of 34,783 nucleotides. Blat results indicate that this fosmid has significant identity to the 2R chromosome of D.melanogaster. Evidence suggests that fosmid XAAA112 contains
More informationPhylogeny 9/8/2014. Evolutionary Relationships. Data Supporting Phylogeny. Chapter 26
Phylogeny Chapter 26 Taxonomy Taxonomy: ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences Carolus Linnaeus developed binomial nomenclature,
More informationComputational approaches for functional genomics
Computational approaches for functional genomics Kalin Vetsigian October 31, 2001 The rapidly increasing number of completely sequenced genomes have stimulated the development of new methods for finding
More informationEarly History up to Schedule. Proteins DNA & RNA Schwann and Schleiden Cell Theory Charles Darwin publishes Origin of Species
Schedule Bioinformatics and Computational Biology: History and Biological Background (JH) 0.0 he Parsimony criterion GKN.0 Stochastic Models of Sequence Evolution GKN 7.0 he Likelihood criterion GKN 0.0
More informationBIOLOGY Grades Summer Units: 10 high school credits UC Requirement Category: d. General Description:
Summer 2015 Units: 10 high school credits UC Requirement Category: d General Description: BIOLOGY Grades 9-12 Summer session biology will be an intense, fast paced course. Students will gain an understanding
More informationC3020 Molecular Evolution. Exercises #3: Phylogenetics
C3020 Molecular Evolution Exercises #3: Phylogenetics Consider the following sequences for five taxa 1-5 and the known outgroup O, which has the ancestral states (note that sequence 3 has changed from
More informationThe nonsynonymous/synonymous substitution rate ratio versus the radical/conservative replacement rate ratio in the evolution of mammalian genes
MBE Advance Access published July, 00 1 1 1 1 1 1 1 1 The nonsynonymous/synonymous substitution rate ratio versus the radical/conservative replacement rate ratio in the evolution of mammalian genes Kousuke
More information86 Part 4 SUMMARY INTRODUCTION
86 Part 4 Chapter # AN INTEGRATION OF THE DESCRIPTIONS OF GENE NETWORKS AND THEIR MODELS PRESENTED IN SIGMOID (CELLERATOR) AND GENENET Podkolodny N.L. *1, 2, Podkolodnaya N.N. 1, Miginsky D.S. 1, Poplavsky
More informationComparative Bioinformatics Midterm II Fall 2004
Comparative Bioinformatics Midterm II Fall 2004 Objective Answer, part I: For each of the following, select the single best answer or completion of the phrase. (3 points each) 1. Deinococcus radiodurans
More informationStatistical Machine Learning Methods for Bioinformatics II. Hidden Markov Model for Biological Sequences
Statistical Machine Learning Methods for Bioinformatics II. Hidden Markov Model for Biological Sequences Jianlin Cheng, PhD Department of Computer Science University of Missouri 2008 Free for Academic
More informationRELATIONSHIPS BETWEEN GENES/PROTEINS HOMOLOGUES
Molecular Biology-2018 1 Definitions: RELATIONSHIPS BETWEEN GENES/PROTEINS HOMOLOGUES Heterologues: Genes or proteins that possess different sequences and activities. Homologues: Genes or proteins that
More informationGENETICS - CLUTCH CH.1 INTRODUCTION TO GENETICS.
!! www.clutchprep.com CONCEPT: HISTORY OF GENETICS The earliest use of genetics was through of plants and animals (8000-1000 B.C.) Selective breeding (artificial selection) is the process of breeding organisms
More informationSCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION. Using Anatomy, Embryology, Biochemistry, and Paleontology
SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION Using Anatomy, Embryology, Biochemistry, and Paleontology Scientific Fields Different fields of science have contributed evidence for the theory of
More informationComparison and Analysis of Heat Shock Proteins in Organisms of the Kingdom Viridiplantae. Emily Germain, Rensselaer Polytechnic Institute
Comparison and Analysis of Heat Shock Proteins in Organisms of the Kingdom Viridiplantae Emily Germain, Rensselaer Polytechnic Institute Mentor: Dr. Hugh Nicholas, Biomedical Initiative, Pittsburgh Supercomputing
More informationAnalytical Study of Hexapod mirnas using Phylogenetic Methods
Analytical Study of Hexapod mirnas using Phylogenetic Methods A.K. Mishra and H.Chandrasekharan Unit of Simulation & Informatics, Indian Agricultural Research Institute, New Delhi, India akmishra@iari.res.in,
More information8/23/2014. Phylogeny and the Tree of Life
Phylogeny and the Tree of Life Chapter 26 Objectives Explain the following characteristics of the Linnaean system of classification: a. binomial nomenclature b. hierarchical classification List the major
More informationName Block Date Final Exam Study Guide
Name Block Date Final Exam Study Guide Unit 7: DNA & Protein Synthesis List the 3 building blocks of DNA (sugar, phosphate, base) Use base-pairing rules to replicate a strand of DNA (A-T, C-G). Transcribe
More informationAP Curriculum Framework with Learning Objectives
Big Ideas Big Idea 1: The process of evolution drives the diversity and unity of life. AP Curriculum Framework with Learning Objectives Understanding 1.A: Change in the genetic makeup of a population over
More informationSequence alignment methods. Pairwise alignment. The universe of biological sequence analysis
he universe of biological sequence analysis Word/pattern recognition- Identification of restriction enzyme cleavage sites Sequence alignment methods PstI he universe of biological sequence analysis - prediction
More informationBioinformatics tools for phylogeny and visualization. Yanbin Yin
Bioinformatics tools for phylogeny and visualization Yanbin Yin 1 Homework assignment 5 1. Take the MAFFT alignment http://cys.bios.niu.edu/yyin/teach/pbb/purdue.cellwall.list.lignin.f a.aln as input and
More informationHonors Biology Reading Guide Chapter 11
Honors Biology Reading Guide Chapter 11 v Promoter a specific nucleotide sequence in DNA located near the start of a gene that is the binding site for RNA polymerase and the place where transcription begins
More informationEffects of Gap Open and Gap Extension Penalties
Brigham Young University BYU ScholarsArchive All Faculty Publications 200-10-01 Effects of Gap Open and Gap Extension Penalties Hyrum Carroll hyrumcarroll@gmail.com Mark J. Clement clement@cs.byu.edu See
More informationHow to read and make phylogenetic trees Zuzana Starostová
How to read and make phylogenetic trees Zuzana Starostová How to make phylogenetic trees? Workflow: obtain DNA sequence quality check sequence alignment calculating genetic distances phylogeny estimation
More informationIntroduction to Bioinformatics Integrated Science, 11/9/05
1 Introduction to Bioinformatics Integrated Science, 11/9/05 Morris Levy Biological Sciences Research: Evolutionary Ecology, Plant- Fungal Pathogen Interactions Coordinator: BIOL 495S/CS490B/STAT490B Introduction
More information