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Bedoya-Reina OC, Ratan A, Burhans R, Kim HL, Giardine B, Riemer C, Li Q, Olson TL, Loughran TP, Vonholdt BM, Perry GH, Schuster SC, Miller W. Galaxy tools to study genome diversity. Gigascience 2013; 2:17. [PMID: 24377391 PMCID: PMC3877877 DOI: 10.1186/2047-217x-2-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 12/12/2013] [Indexed: 12/02/2022] Open
Abstract
Background Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for small labs to obtain full-genome variation data from their species of interest. However, those labs may not have easy access to, and familiarity with, computational tools to analyze those data. Results We have created a suite of tools for the Galaxy web server aimed at handling nucleotide and amino-acid polymorphisms discovered by full-genome sequencing of several individuals of the same species, or using a SNP genotyping microarray. In addition to providing user-friendly tools, a main goal is to make published analyses reproducible. While most of the examples discussed in this paper deal with nuclear-genome diversity in non-human vertebrates, we also illustrate the application of the tools to fungal genomes, human biomedical data, and mitochondrial sequences. Conclusions This project illustrates that a small group can design, implement, test, document, and distribute a Galaxy tool collection to meet the needs of a particular community of biologists.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Webb Miller
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.
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Giardine B, Borg J, Viennas E, Pavlidis C, Moradkhani K, Joly P, Bartsakoulia M, Riemer C, Miller W, Tzimas G, Wajcman H, Hardison RC, Patrinos GP. Updates of the HbVar database of human hemoglobin variants and thalassemia mutations. Nucleic Acids Res 2013; 42:D1063-9. [PMID: 24137000 PMCID: PMC3964999 DOI: 10.1093/nar/gkt911] [Citation(s) in RCA: 318] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology and ethnic occurrence, accompanied by mutation frequencies and references. Here, we report updates to >600 HbVar entries, inclusion of population-specific data for 28 populations and 27 ethnic groups for α-, and β-thalassemias and additional querying options in the HbVar query page. HbVar content was also inter-connected with two other established genetic databases, namely FINDbase (http://www.findbase.org) and Leiden Open-Access Variation database (http://www.lovd.nl), which allows comparative data querying and analysis. HbVar data content has contributed to the realization of two collaborative projects to identify genomic variants that lie on different globin paralogs. Most importantly, HbVar data content has contributed to demonstrate the microattribution concept in practice. These updates significantly enriched the database content and querying potential, enhanced the database profile and data quality and broadened the inter-relation of HbVar with other databases, which should increase the already high impact of this resource to the globin and genetic database community.
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Affiliation(s)
- Belinda Giardine
- The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, PA, USA, Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta, MGC-Department of Cell Biology and Genetics, Erasmus MC, Faculty of Medicine and Health Sciences, Rotterdam, The Netherlands, Department of Computer Engineering and Informatics, University of Patras, Faculty of Engineering, Patras, Greece, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece, Department of Medical Genetics, Laboratory of Cytogenetics, Institute of Biology, Nantes, France, Hôpital Edouard Herriot, Unité de Pathologie Moléculaire du Globule Rouge, Lyon, France, Department of Computer and Informatics Engineering, Technological Educational Institute of Western Greece, Patras, Greece, INSERM U955, CHU Henri Mondor, Creteil, France and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
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Lugeder A, Jäger C, Fecht E, Riemer C, Sattler M, Kalbe P, Zeichen J. [Salter-Harris type IV epipyseal fracture of the lateral malleolus. A rare injury in childhood]. Unfallchirurg 2013; 117:169-73. [PMID: 23703619 DOI: 10.1007/s00113-013-2362-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This is a case presentation of a 9-year-old boy who sustained a rare Salter-Harris type IV distal fibular fracture including an avulsion fracture of the anterior inferior tibiofibular ligament at the fibular attachment. Treatment consisted of open reduction and internal fixation by Kirschner wire and cerclage. Possible posttraumatic growth disturbances and the major implications are highlighted.
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Affiliation(s)
- A Lugeder
- Abteilung der Berufsgenossenschaftlichen Unfallklinik Duisburg, Klinik für Unfallchirurgie und Orthopädie, Johannes Wesling Klinikum Minden, Hans-Nolte-Straße 1, 32429, Minden, Deutschland,
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Giardine BM, Riemer C, Burhans R, Ratan A, Miller W. Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome. Curr Protoc Bioinformatics 2012; Chapter 15:15.2.1-15.2.27. [PMID: 22948727 PMCID: PMC3548453 DOI: 10.1002/0471250953.bi1502s39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This unit focuses on some of the tools available on the public Galaxy server that are useful for exploring possible associations between human genetic variants and phenotypes. We trace step-by-step through an example illustrating several methods for examining a single full-coverage genome to look for single-nucleotide polymorphisms (SNPs) that are either known to be associated with disease or suspected to have impact for other reasons. It makes use of public genomic data, tools designed specifically for working with variants, and also some general tools for text manipulation and operations on genomic coordinates.
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Song G, Riemer C, Dickins B, Kim HL, Zhang L, Zhang Y, Hsu CH, Hardison RC, Nisc Comparative Sequencing Program, Green ED, Miller W. Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. Genome Biol Evol 2012; 4:586-601. [PMID: 22454131 PMCID: PMC3342878 DOI: 10.1093/gbe/evs032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2012] [Indexed: 12/13/2022] Open
Abstract
Many software tools for comparative analysis of genomic sequence data have been released in recent decades. Despite this, it remains challenging to determine evolutionary relationships in gene clusters due to their complex histories involving duplications, deletions, inversions, and conversions. One concept describing these relationships is orthology. Orthologs derive from a common ancestor by speciation, in contrast to paralogs, which derive from duplication. Discriminating orthologs from paralogs is a necessary step in most multispecies sequence analyses, but doing so accurately is impeded by the occurrence of gene conversion events. We propose a refined method of orthology assignment based on two paradigms for interpreting its definition: by genomic context or by sequence content. X-orthology (based on context) traces orthology resulting from speciation and duplication only, while N-orthology (based on content) includes the influence of conversion events. We developed a computational method for automatically mapping both types of orthology on a per-nucleotide basis in gene cluster regions studied by comparative sequencing, and we make this mapping accessible by visualizing the output. All of these steps are incorporated into our newly extended CHAP 2 package. We evaluate our method using both simulated data and real gene clusters (including the well-characterized α-globin and β-globin clusters). We also illustrate use of CHAP 2 by analyzing four more loci: CCL (chemokine ligand), IFN (interferon), CYP2abf (part of cytochrome P450 family 2), and KIR (killer cell immunoglobulin-like receptors). These new methods facilitate and extend our understanding of evolution at these and other loci by adding automated accurate evolutionary inference to the biologist's toolkit. The CHAP 2 package is freely available from http://www.bx.psu.edu/miller_lab.
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Affiliation(s)
- Giltae Song
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, PA, USA.
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Song G, Hsu CH, Riemer C, Zhang Y, Kim HL, Hoffmann F, Zhang L, Hardison RC, Green ED, Miller W. Conversion events in gene clusters. BMC Evol Biol 2011; 11:226. [PMID: 21798034 PMCID: PMC3161012 DOI: 10.1186/1471-2148-11-226] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 07/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are difficult to analyze due to their structural complexity and their complicated evolutionary histories, reflecting a variety of large-scale mutational events. In particular, conversion events can mislead inferences about the relationships among these regions, as traced by traditional methods such as construction of phylogenetic trees or multi-species alignments. RESULTS To correct the distorted information generated by such methods, we have developed an automated pipeline called CHAP (Cluster History Analysis Package) for detecting conversion events. We used this pipeline to analyze the conversion events that affected two well-studied gene clusters (α-globin and β-globin) and three gene clusters for which comparative sequence data were generated from seven primate species: CCL (chemokine ligand), IFN (interferon), and CYP2abf (part of cytochrome P450 family 2). CHAP is freely available at http://www.bx.psu.edu/miller_lab. CONCLUSIONS These studies reveal the value of characterizing conversion events in the context of studying gene clusters in complex genomes.
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Affiliation(s)
- Giltae Song
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802 USA.
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Abstract
BACKGROUND Gene clusters are genetically important, but their analysis poses significant computational challenges. One of the major reasons for these difficulties is gene conversion among the duplicated regions of the cluster, which can obscure their true relationships. Many computational methods for detecting gene conversion events have been released, but their performance has not been assessed for wide deployment in evolutionary history studies due to a lack of accurate evaluation methods. RESULTS We designed a new method that simulates gene cluster evolution, including large-scale events of duplication, deletion, and conversion as well as small mutations. We used this simulation data to evaluate several different programs for detecting gene conversion events. CONCLUSIONS Our evaluation identifies strengths and weaknesses of several methods for detecting gene conversion, which can contribute to more accurate analysis of gene cluster evolution.
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Affiliation(s)
- Giltae Song
- Center for Comparative Genomics and Bioinformatics, 506 Wartik Lab, Pennsylvania State University, University Park, PA 16802, USA
| | - Chih-Hao Hsu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Cathy Riemer
- Center for Comparative Genomics and Bioinformatics, 506 Wartik Lab, Pennsylvania State University, University Park, PA 16802, USA
| | - Webb Miller
- Center for Comparative Genomics and Bioinformatics, 506 Wartik Lab, Pennsylvania State University, University Park, PA 16802, USA
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Elnitski L, Burhans R, Riemer C, Hardison R, Miller W. MultiPipMaker: a comparative alignment server for multiple DNA sequences. ACTA ACUST UNITED AC 2010; Chapter 10:10.4.1-10.4.14. [PMID: 20521245 DOI: 10.1002/0471250953.bi1004s30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The MultiPipMaker World Wide Web server (http://www.bx.psu.edu) provides a tool for aligning multiple DNA sequences and visualizing regions of conservation among them. This unit describes its use and gives an explanation of the resulting output files and supporting tools. Features provided by the server include alignment of up to 20 very long genomic sequences, output choices of a true, nucleotide-level multiple alignment and/or stacked, pairwise percent identity plots, and support for user-specified annotations of genomic features and arbitrary regions, with clickable links to additional information. Input sequences other than the reference can be fragmented, unordered, and unoriented.
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Affiliation(s)
- Laura Elnitski
- The Pennsylvania State University, University Park, Pennsylvania, USA
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Abstract
PipMaker is a World-Wide Web site used to compare two long genomic sequences and identify conserved segments between them. This unit describes the use of the PipMaker server and explains the resulting output files. PipMaker provides an efficient method of aligning genomic sequences and returns a compact, but easy-to-interpret form of output, the percent identity plot (pip). For each aligning segment between two sequences the pip shows both the position relative to the first sequence and the degree of similarity. Optional annotations on the pip provide additional information to assist in the interpretation of the alignment. The default parameters of the underlying blastz alignment program are tuned for human-mouse alignments.
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Affiliation(s)
- Laura Elnitski
- The Pennsylvania State University, University Park, Pennsylvania, USA
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10
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Elnitski L, Riemer C, Burhans R, Hardison R, Miller W. MultiPipMaker: comparative alignment server for multiple DNA sequences. ACTA ACUST UNITED AC 2008; Chapter 10:Unit10.4. [PMID: 18428743 DOI: 10.1002/0471250953.bi1004s9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The MultiPipMaker World Wide Web server (http://www.bx.psu.edu) provides a useful tool for aligning multiple sequences and visualizing regions of conservation between them. This unit describes the use of the MultiPipMaker server and gives an explanation of the resulting output files and supporting tools. Features provided by the server include alignment of up to 20 very long genomic sequences, output choices of a true, nucleotide-level multiple alignment or stacked, pairwise percent identity plots, and user-specified annotations for genomic features and elements of choice, with clickable links to additional information. Alignments can include unordered, unoriented secondary sequences.
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Affiliation(s)
- Laura Elnitski
- The Pennsylvania State University, University Park, Pennsylvania, USA
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Schulze J, Riemer C, Dressler M, Zielen S. Vergleich zweier Kurzprotokolle der bronchialen Methacholin Provokation, PC20FEV1 versus PD20FEV1. Pneumologie 2008. [DOI: 10.1055/s-2008-1074282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Michael D, Okuducu AF, Holtkamp N, Bamme T, Jehn CF, Riemer C, Baier M. Sarcomas predominate in mice deficient for PrPc and p53. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.21039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
21039 Background: For cellular prion protein (PrPc) putative roles in many cellular processes including signalling, survival, adhesion, proliferation and differentation have been proposed. The hallmarks of cancer include some of these traits and in human tumors both increased and decreased levels of PrPc have been observed. However PrPc deficient mice show no increased rate of tumor formation. To characterize the possible role of PrPc in tumorigenesis we generated PrPc-/-/p53-/- mice. Methods: Organ and tumor samples were surgically removed post mortem and processed for histological analysis. Time to death was defined as the latency between birth and spontaneous death or a terminal disease state as indicated by tumor burden and other symptoms of severe disease. Results: As reported previously lymphomas are the most frequent tumors in p53-/- mice [5 out of 7 (71 %)]. In contrast, sarcomas predominate in PrPc-/-/p53-/- mice [9 out of 21 (43 %)]. This was accompanied by a decrease in the incidence of lymphomas in PrPc-/-/p53-/- mice [7 out of 21 (33 %)]. Conclusions: These results indicate for PrPc, in the context of p53 deficiency, a role in sarcoma tumorigenesis and the PrPc-/-/p53-/- mice might provide a clinical relevant model for the study of sarcomas. No significant financial relationships to disclose.
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Affiliation(s)
- D. Michael
- University Hospital Charite, Berlin, Germany; Robert Koch Institute, Berlin, Germany
| | - A. F. Okuducu
- University Hospital Charite, Berlin, Germany; Robert Koch Institute, Berlin, Germany
| | - N. Holtkamp
- University Hospital Charite, Berlin, Germany; Robert Koch Institute, Berlin, Germany
| | - T. Bamme
- University Hospital Charite, Berlin, Germany; Robert Koch Institute, Berlin, Germany
| | - C. F. Jehn
- University Hospital Charite, Berlin, Germany; Robert Koch Institute, Berlin, Germany
| | - C. Riemer
- University Hospital Charite, Berlin, Germany; Robert Koch Institute, Berlin, Germany
| | - M. Baier
- University Hospital Charite, Berlin, Germany; Robert Koch Institute, Berlin, Germany
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Albert US, Duda V, Kalder M, Zwiork L, Baumann K, Engenhart-Cabillic R, Klose KJ, Moll R, Neubauer A, Hoffmann M, Assmann V, Dreyer P, Scharf LG, Trolp L, Riemer C, Wagner U. Brustzentrum und DMP: Bilanz einer regionalen Qualitätsentwicklung. Geburtshilfe Frauenheilkd 2007. [DOI: 10.1055/s-2007-984638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Hardison R, Giardine B, Riemer C, Miller W, Chui D, Wajcman H, Patrinos G. HbVar database for human hemoglobin variants and thalassemia mutations. Blood Cells Mol Dis 2007. [DOI: 10.1016/j.bcmd.2006.10.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Giardine B, van Baal S, Kaimakis P, Riemer C, Miller W, Samara M, Kollia P, Anagnou NP, Chui DHK, Wajcman H, Hardison RC, Patrinos GP. HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update. Hum Mutat 2007; 28:206. [PMID: 17221864 DOI: 10.1002/humu.9479] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
HbVar (http://globin.bx.psu.edu/hbvar) is a locus-specific database (LSDB) developed in 2001 by a multi-center academic effort to provide timely information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology, and ethnic occurrence, accompanied by mutation frequencies and references. In addition to the regular updates to entries, we report significant advances and updates, which can be useful not only for HbVar users but also for other LSDB development and curation in general. The query page provides more functionality but in a simpler, more user-friendly format and known single nucleotide polymorphisms in the human alpha- and beta-globin loci are provided automatically. Population-specific beta-thalassemia mutation frequencies for 31 population groups have been added and/or modified and the previously reported delta- and alpha-thalassemia mutation frequency data from 10 population groups have also been incorporated. In addition, an independent flat-file database, named XPRbase (http://www.goldenhelix.org/xprbase), has been developed and linked to the main HbVar web page to provide a succinct listing of 51 experimental protocols available for globin gene mutation screening. These updates significantly augment the database profile and quality of information provided, which should increase the already high impact of the HbVar database, while its combination with the UCSC powerful genome browser and the ITHANET web portal paves the way for drawing connections of clinical importance, that is from genome to function to phenotype.
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Affiliation(s)
- Belinda Giardine
- The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania, USA
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Riemer C, Hoersten S, Li Y, Moerike C, Haverich A, Simon A. 66: Significance of endothelial CD26 in acute rejection after orthotopic single lung transplantation in the rat. J Heart Lung Transplant 2007. [DOI: 10.1016/j.healun.2006.11.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Giardine B, Riemer C, Hefferon T, Thomas D, Hsu F, Zielenski J, Sang Y, Elnitski L, Cutting G, Trumbower H, Kern A, Kuhn R, Patrinos GP, Hughes J, Higgs D, Chui D, Scriver C, Phommarinh M, Patnaik SK, Blumenfeld O, Gottlieb B, Vihinen M, Väliaho J, Kent J, Miller W, Hardison RC. PhenCode: connecting ENCODE data with mutations and phenotype. Hum Mutat 2007; 28:554-62. [PMID: 17326095 DOI: 10.1002/humu.20484] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
PhenCode (Phenotypes for ENCODE; http://www.bx.psu.edu/phencode) is a collaborative, exploratory project to help understand phenotypes of human mutations in the context of sequence and functional data from genome projects. Currently, it connects human phenotype and clinical data in various locus-specific databases (LSDBs) with data on genome sequences, evolutionary history, and function from the ENCODE project and other resources in the UCSC Genome Browser. Initially, we focused on a few selected LSDBs covering genes encoding alpha- and beta-globins (HBA, HBB), phenylalanine hydroxylase (PAH), blood group antigens (various genes), androgen receptor (AR), cystic fibrosis transmembrane conductance regulator (CFTR), and Bruton's tyrosine kinase (BTK), but we plan to include additional loci of clinical importance, ultimately genomewide. We have also imported variant data and associated OMIM links from Swiss-Prot. Users can find interesting mutations in the UCSC Genome Browser (in a new Locus Variants track) and follow links back to the LSDBs for more detailed information. Alternatively, they can start with queries on mutations or phenotypes at an LSDB and then display the results at the Genome Browser to view complementary information such as functional data (e.g., chromatin modifications and protein binding from the ENCODE consortium), evolutionary constraint, regulatory potential, and/or any other tracks they choose. We present several examples illustrating the power of these connections for exploring phenotypes associated with functional elements, and for identifying genomic data that could help to explain clinical phenotypes.
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Affiliation(s)
- Belinda Giardine
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Chiou LC, Liao YY, Fan PC, Kuo PH, Wang CH, Riemer C, Prinssen EP. Nociceptin/orphanin FQ peptide receptors: pharmacology and clinical implications. Curr Drug Targets 2007; 8:117-35. [PMID: 17266536 DOI: 10.2174/138945007779315605] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The advance of functional genomics revealed the superfamily of G-protein coupled receptors (GPCRs). Hundreds of GPCRs have been cloned but many of them are orphan GPCRs with unidentified ligands. The first identified orphan GPCR is the opioid receptor like orphan receptor, ORL1. It was cloned in 1994 during the identification of opioid receptor subtypes and was de-orphanized in 1995 by the discovery of its endogenous ligand, nociceptin or orphanin FQ (N/OFQ). This receptor was renamed as N/OFQ peptide (NOP) receptor. Several selective ligands acting at NOP receptors or other anti-N/OFQ agents have been reported. These include N/OFQ-derived peptides acting as agonists (cyclo[Cys(10),Cys(14)]N/OFQ, [Arg(14), Lys(15)]N/OFQ, [pX]Phe(4)N/OFQ(1-13)-NH(2), UFP-102, [(pF)Phe(4),Aib(7), Aib(11),Arg(14),Lys(15)]N/OFQ-NH(2)) or antagonists (Phe(1)psi(CH(2)-NH)Gly(2)]N/OFQ(1-13)-NH(2), [Nphe(1)]N/OFQ(1-13)-NH(2), UFP-101, [Nphe(1), (pF)Phe(4),Aib(7),Aib(11),Arg(14),Lys(15)]N/OFQ-NH(2)), hexapeptides, other peptide derivatives (peptide III-BTD, ZP-120, OS-461, OS-462, OS-500), non-peptide agonists (NNC 63-0532, Ro 64-6198, (+)-5a compound, W-212393, 3-(4-piperidinyl)indoles, 3-(4-piperidinyl) pyrrolo[2,3-b]pyridines) and antagonists (TRK-820, J-113397, JTC-801, octahydrobenzimidazol-2-ones, 2-(1,2,4-oxadiazol-5-yl)-1 H-indole, N-benzyl-D-prolines, SB-612111), biostable RNA Spiegelmers specific against N/OFQ, and a functional antagonist, nocistatin. Buprenorphine and naloxone benzoylhydrazone are two opioid receptor ligands showing high affinity for NOP receptors. NOP receptor agonists might be beneficial in the treatment of pain, anxiety, stress-induced anorexia, cough, neurogenic bladder, edema, drug dependence, and, less promising, in cerebral ischemia and epilepsy, while antagonists might be of help in the management of pain, depression, dementia and Parkinsonism. N/OFQ is also involved in cardiovascular, gastrointestinal and immune regulation. Altered plasma levels of N/OFQ have been reported in patients with various pain states, depression and liver diseases. This review summarizes the pharmacological characteristics of, and studies with, the available NOP receptor ligands and their possible clinical implications.
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Affiliation(s)
- L-C Chiou
- Department of Pharmacology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Rd., Section 1, Taipei 100, Taiwan.
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Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005; 15:1451-5. [PMID: 16169926 PMCID: PMC1240089 DOI: 10.1101/gr.4086505] [Citation(s) in RCA: 1395] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.
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Affiliation(s)
- Belinda Giardine
- Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA
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20
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Elnitski L, Giardine B, Shah P, Zhang Y, Riemer C, Weirauch M, Burhans R, Miller W, Hardison RC. Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. Nucleic Acids Res 2005; 33:D466-70. [PMID: 15608239 PMCID: PMC539999 DOI: 10.1093/nar/gki045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2004] [Revised: 09/28/2004] [Accepted: 09/28/2004] [Indexed: 12/02/2022] Open
Abstract
We describe improvements to two databases that give access to information on genomic sequence similarities, functional elements in DNA and experimental results that demonstrate those functions. GALA, the database of Genome ALignments and Annotations, is now a set of interlinked relational databases for five vertebrate species, human, chimpanzee, mouse, rat and chicken. For each species, GALA records pairwise and multiple sequence alignments, scores derived from those alignments that reflect the likelihood of being under purifying selection or being a regulatory element, and extensive annotations such as genes, gene expression patterns and transcription factor binding sites. The user interface supports simple and complex queries, including operations such as subtraction and intersections as well as clustering and finding elements in proximity to features. dbERGE II, the database of Experimental Results on Gene Expression, contains experimental data from a variety of functional assays. Both databases are now run on the DB2 database management system. Improved hardware and tuning has reduced response times and increased querying capacity, while simplified query interfaces will help direct new users through the querying process. Links are available at http://www.bx.psu.edu/.
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Affiliation(s)
- Laura Elnitski
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
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21
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Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004; 14:708-15. [PMID: 15060014 PMCID: PMC383317 DOI: 10.1101/gr.1933104] [Citation(s) in RCA: 1037] [Impact Index Per Article: 51.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We define a "threaded blockset," which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for "threaded blockset aligner") builds a threaded blockset under the assumption that all matching segments occur in the same order and orientation in the given sequences; inversions and duplications are not addressed. TBA is designed to be appropriate for aligning many, but by no means all, megabase-sized regions of multiple mammalian genomes. The output of TBA can be projected onto any genome chosen as a reference, thus guaranteeing that different projections present consistent predictions of which genomic positions are orthologous. This capability is illustrated using a new visualization tool to view TBA-generated alignments of vertebrate Hox clusters from both the mammalian and fish perspectives. Experimental evaluation of alignment quality, using a program that simulates evolutionary change in genomic sequences, indicates that TBA is more accurate than earlier programs. To perform the dynamic-programming alignment step, TBA runs a stand-alone program called MULTIZ, which can be used to align highly rearranged or incompletely sequenced genomes. We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser.
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Affiliation(s)
- Mathieu Blanchette
- Howard Hughes Medical Institute, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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22
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Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004; 428:493-521. [PMID: 15057822 DOI: 10.1038/nature02426] [Citation(s) in RCA: 1512] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Accepted: 02/20/2004] [Indexed: 01/16/2023]
Abstract
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
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Affiliation(s)
- Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu
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23
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Riemer C, Bayer T, Schmitt H, Kessler H. 3-Azido-aspartic acid derivatives - orthogonally protected precursors for the stereoselective incorporation of 2,3-diaminosuccinic acid into peptide structures. J Pept Res 2004; 63:196-9. [PMID: 15049830 DOI: 10.1111/j.1399-3011.2003.00117.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The stereoselective synthesis of orthogonally protected 3-azido aspartic acid derivatives is described. The convenience of their application as 2,3-diaminosuccinic acid in peptide chemistry was demonstrated by the incorporation of the nonproteinogenic diamino diacid as a cystine-substitute into the core structure of somatostatin.
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Affiliation(s)
- C Riemer
- Institut für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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24
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Patrinos GP, Giardine B, Riemer C, Miller W, Chui DHK, Anagnou NP, Wajcman H, Hardison RC. Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies. Nucleic Acids Res 2004; 32:D537-41. [PMID: 14681476 PMCID: PMC308741 DOI: 10.1093/nar/gkh006] [Citation(s) in RCA: 250] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
HbVar (http://globin.cse.psu.edu/globin/hbvar/) is a relational database developed by a multi-center academic effort to provide up-to-date and high quality information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Extensive information is recorded for each variant and mutation, including sequence alterations, biochemical and hematological effects, associated pathology, ethnic occurrence and references. In addition to the regular updates to entries, we report two significant advances: (i) The frequencies for a large number of mutations causing beta-thalassemia in at-risk populations have been extracted from the published literature and made available for the user to query upon. (ii) HbVar has been linked with the GALA (Genome Alignment and Annotation database, available at http://globin.cse.psu.edu/gala/) so that users can combine information on hemoglobin variants and thalassemia mutations with a wide spectrum of genomic data. It also expands the capacity to view and analyze the data, using tools within GALA and the University of California at Santa Cruz (UCSC) Genome Browser.
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Affiliation(s)
- George P Patrinos
- MGC-Department of Cell Biology and Genetics, Erasmus MC, Faculty of Medicine and Health Sciences, PO Box 1738, 3000 DR, Rotterdam, The Netherlands.
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25
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Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, Smit A, Green ED, Hardison RC, Miller W. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res 2003; 31:3518-24. [PMID: 12824357 PMCID: PMC168985 DOI: 10.1093/nar/gkg579] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Analysis of multiple sequence alignments can generate important, testable hypotheses about the phylogenetic history and cellular function of genomic sequences. We describe the MultiPipMaker server, which aligns multiple, long genomic DNA sequences quickly and with good sensitivity (available at http://bio.cse.psu.edu/ since May 2001). Alignments are computed between a contiguous reference sequence and one or more secondary sequences, which can be finished or draft sequence. The outputs include a stacked set of percent identity plots, called a MultiPip, comparing the reference sequence with subsequent sequences, and a nucleotide-level multiple alignment. New tools are provided to search MultiPipMaker output for conserved matches to a user-specified pattern and for conserved matches to position weight matrices that describe transcription factor binding sites (singly and in clusters). We illustrate the use of MultiPipMaker to identify candidate regulatory regions in WNT2 and then demonstrate by transfection assays that they are functional. Analysis of the alignments also confirms the phylogenetic inference that horses are more closely related to cats than to cows.
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Affiliation(s)
- Scott Schwartz
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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26
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Abstract
We describe EnteriX, a suite of three web-based visualization tools for graphically portraying alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome (http://bio.cse.psu.edu/). The first visualization, Enteric, displays stacked pairwise alignments between a reference genome and each of the related bacteria, represented schematically as PIPs (Percent Identity Plots). Encoded in the views are large-scale genomic rearrangement events and functional landmarks. The second visualization, Menteric, computes and displays 1 Kb views of nucleotide-level multiple alignments of the sequences, together with annotations of genes, regulatory sites and conserved regions. The third, a Java-based tool named Maj, displays alignment information in two formats, corresponding roughly to the Enteric and Menteric views, and adds zoom-in capabilities. The uses of such tools are diverse, from examining the multiple sequence alignment to infer conserved sites with potential regulatory roles, to scrutinizing the commonalities and differences between the genomes for pathogenicity or phylogenetic studies. The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments.
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Affiliation(s)
- Liliana Florea
- Informatics Research, Celera/Applied Biosystems, 45 W. Gude Drive, Rockville, MD 20850, USA.
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27
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Giardine B, Elnitski L, Riemer C, Makalowska I, Schwartz S, Miller W, Hardison RC. GALA, a database for genomic sequence alignments and annotations. Genome Res 2003; 13:732-41. [PMID: 12671007 PMCID: PMC430176 DOI: 10.1101/gr.603103] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2002] [Accepted: 01/24/2003] [Indexed: 01/26/2023]
Abstract
We have developed a relational database to contain whole genome sequence alignments between human and mouse with extensive annotations of the human sequence. Complex queries are supported on recorded features, both directly and on proximity among them. Searches can reveal a wide variety of relationships, such as finding all genes expressed in a designated tissue that have a highly conserved noncoding sequence 5' to the start site. Other examples are finding single nucleotide polymorphisms that occur in conserved noncoding regions upstream of genes and identifying CpG islands that overlap the 5' ends of divergently transcribed genes. The database is available online at http://globin.cse.psu.edu/ and http://bio.cse.psu.edu/.
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Affiliation(s)
- Belinda Giardine
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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28
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Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C, Schwartz S, Haussler D, Roskin KM, Weber RJ, Diekhans M, Kent WJ, Weiss MJ, Welch J, Miller W. Global predictions and tests of erythroid regulatory regions. Cold Spring Harb Symp Quant Biol 2003; 68:335-44. [PMID: 15338635 DOI: 10.1101/sqb.2003.68.335] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- R C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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29
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Riemer C, Simon D, Neidhold S, Schultz J, Schwarz A, Baier M. BSE, scrapie, and vCJD: infectious neurodegenerative diseases. Ernst Schering Res Found Workshop 2002:85-103. [PMID: 12066418 DOI: 10.1007/978-3-662-05073-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- C Riemer
- Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
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30
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Elnitski L, Riemer C, Petrykowska H, Florea L, Schwartz S, Miller W, Hardison R. PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics 2002; 80:681-90. [PMID: 12504859 DOI: 10.1006/geno.2002.7018] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sequence conservation between species is useful both for locating coding regions of genes and for identifying functional noncoding segments. Hence interspecies alignment of genomic sequences is an important computational technique. However, its utility is limited without extensive annotation. We describe a suite of software tools, PipTools, and related programs that facilitate the annotation of genes and putative regulatory elements in pairwise alignments. The alignment server PipMaker uses the output of these tools to display detailed information needed to interpret alignments. These programs are provided in a portable format for use on common desktop computers and both the toolkit and the PipMaker server can be found at our Web site (http://bio.cse.psu.edu/). We illustrate the utility of the toolkit using annotation of a pairwise comparison of the mouse MHC class II and class III regions with orthologous human sequences and subsequently identify conserved, noncoding sequences that are DNase I hypersensitive sites in chromatin of mouse cells.
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Affiliation(s)
- Laura Elnitski
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
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31
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Dittrich B, Koritsánszky T, Grosche M, Scherer W, Flaig R, Wagner A, Krane HG, Kessler H, Riemer C, Schreurs AMM, Luger P. Reproducability and transferability of topological properties; experimental charge density of the hexapeptide cyclo-(D,L-Pro)2-(L-Ala)4 monohydrate. Acta Crystallogr B 2002; 58:721-7. [PMID: 12149563 DOI: 10.1107/s0108768102005839] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2002] [Accepted: 04/02/2002] [Indexed: 11/10/2022]
Abstract
The charge density of a hexapeptide was determined from high-resolution CCD area-detector experiments at 100 K. Two datasets, one from a rotating anode and a second one from synchrotron radiation, were measured and the results are compared. The data are interpreted in terms of the 'rigid pseudoatom' model. The topology of the experimental density is analyzed and compared with the topology of the constituting amino acids, and shows good agreement. All critical points of the electron density at the covalent and hydrogen bonds, as well as those of the Laplacian, were located. With respect to the transferability of electronic and bond topological properties the six peptide bonds were compared with values given in the literature.
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Affiliation(s)
- B Dittrich
- Institut für Chemie/Kristallographie der Freien Universität Berlin, D-14195 Berlin, Germany
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32
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Nicolaou KC, Zuccarello G, Riemer C, Estevez VA, Dai WM. Design, synthesis, and study of simple monocyclic conjugated enediynes. The 10-membered ring enediyne moiety of the enediyne anticancer antibiotics. J Am Chem Soc 2002. [DOI: 10.1021/ja00045a005] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Hardison RC, Chui DHK, Giardine B, Riemer C, Patrinos GP, Anagnou N, Miller W, Wajcman H. HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server. Hum Mutat 2002; 19:225-33. [PMID: 11857738 DOI: 10.1002/humu.10044] [Citation(s) in RCA: 282] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have constructed a relational database of hemoglobin variants and thalassemia mutations, called HbVar, which can be accessed on the web at http://globin.cse.psu.edu. Extensive information is recorded for each variant and mutation, including a description of the variant and associated pathology, hematology, electrophoretic mobility, methods of isolation, stability information, ethnic occurrence, structure studies, functional studies, and references. The initial information was derived from books by Dr. Titus Huisman and colleagues [Huisman et al., 1996, 1997, 1998]. The current database is updated regularly with the addition of new data and corrections to previous data. Queries can be formulated based on fields in the database. Tables of common categories of variants, such as all those involving the alpha1-globin gene (HBA1) or all those that result in high oxygen affinity, are maintained by automated queries on the database. Users can formulate more precise queries, such as identifying "all beta-globin variants associated with instability and found in Scottish populations." This new database should be useful for clinical diagnosis as well as in fundamental studies of hemoglobin biochemistry, globin gene regulation, and human sequence variation at these loci.
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Affiliation(s)
- Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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34
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Magdolen V, Bürgle M, de Prada NA, Schmiedeberg N, Riemer C, Schroeck F, Kellermann J, Degitz K, Wilhelm OG, Schmitt M, Kessler H. Cyclo19,31[D-Cys19]-uPA19-31 is a potent competitive antagonist of the interaction of urokinase-type plasminogen activator with its receptor (CD87). Biol Chem 2001; 382:1197-205. [PMID: 11592401 DOI: 10.1515/bc.2001.150] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Urokinase-type plasminogen activator (uPA) represents a central molecule in pericellular proteolysis and is implicated in a variety of physiological and pathophysiological processes such as tissue remodelling, wound healing, tumor invasion, and metastasis. uPA binds with high affinity to a specific cell surface receptor, uPAR (CD87), via a well defined sequence within the N-terminal region of uPA (uPA19-31). This interaction directs the proteolytic activity of uPA to the cell surface which represents an important step in tumor cell proliferation, invasion, and metastasis. Due to its fundamental role in these processes, the uPA/uPAR-system has emerged as a novel target for tumor therapy. Previously, we have identified a synthetic, cyclic, uPA-derived peptide, cyclo19,31uPA19-31, as a lead structure for the development of low molecular weight uPA-analogues, capable of blocking uPA/uPAR-interaction [Burgle et al., Biol. Chem. 378 (1997), 231-237]. We now searched for peptide variants of cyclo19,31uPA19-31 with elevated affinities for uPAR binding. Among other tasks, we performed a systematic D-amino acid scan of uPA19-31, in which each of the 13 L-amino acids was individually substituted by the corresponding D-amino acid. This led to the identification of cyclo19,31[D-Cys19]-uPA19-31 as a potent inhibitor of uPA/uPAR-interaction, displaying only a 20 to 40-fold lower binding capacity as compared to the naturally occurring uPAR-ligands uPA and its amino-terminal fragment. Cyclo19,31[D-Cys19]-uPA19-31 not only blocks binding of uPA to uPAR but is also capable of efficiently displacing uPAR-bound uPA from the cell surface and to inhibit uPA-mediated, tumor cell-associated plasminogen activation and fibrin degradation. Thus, cyclo19,31[D-Cys19]-uPA19-31 represents a promising therapeutic agent to significantly affect the tumor-associated uPA/uPAR-system.
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Affiliation(s)
- V Magdolen
- Frauenklinik der Technischen Universität München, Germany
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35
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Abstract
A new synthesis of orthogonally protected diaminoglutaric acid containing peptides using the Ugi four component condensation is presented. To demonstrate that this method is useful to replace cystine by diaminoglutaric acid in biologically interesting peptides, we built up two cyclic somatostatin analogues deriving from Sandostatin and from TT-232. A photolytically cleavable amine derivative of the nitroveratryl type is used for the Ugi four component condensation. Because of a racemic build up of the new stereocentre of the diaminoglutaric acid, and racemization of the isonitrile component, four diastereomeric peptides resulted that were separated by HPLC. The stereochemistry of the cyclopeptides could be easily and unambiguously assigned by chiral gas chromatography and a reference sample of enantiomerically pure (2S,4S)-diaminoglutaric acid.
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Affiliation(s)
- T Bayer
- Institut für Organische Chemie und Biochemie, Technische Universität München, Garching, Germany
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36
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Hardison RC, Chui DH, Riemer C, Giardine B, Lehväslaiho H, Wajcman H, Miller W. Databases of human hemoglobin variants and other resources at the globin gene server. Hemoglobin 2001; 25:183-93. [PMID: 11480780 DOI: 10.1081/hem-100104027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Building on the pioneering efforts of Professor Huisman, several different databases of hemoglobin variants have been developed, each with progressively increased capacity for sophisticated queries and prompt updating. These resources are reviewed in the context of a larger plan for providing related resources on hemoglobins, benign and pathological variation in these proteins and the genes that encode them, and the regulation of the globin genes.
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Affiliation(s)
- R C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802, USA.
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37
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Wilson MD, Riemer C, Martindale DW, Schnupf P, Boright AP, Cheung TL, Hardy DM, Schwartz S, Scherer SW, Tsui LC, Miller W, Koop BF. Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5. Nucleic Acids Res 2001; 29:1352-65. [PMID: 11239002 PMCID: PMC29746 DOI: 10.1093/nar/29.6.1352] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene-dense, GC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes. A 296 kb segment from the physical map, spanning ACHE: to Tfr2, was compared with 267 kb of human sequence. We identified a conserved linkage of 12 genes including an open reading frame flanked by ACHE: and Asr2, a novel cation-chloride cotransporter interacting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from our comparative sequence analysis. Adjacent unfinished sequence data from the mouse contains an orthologous block of 10 additional genes including three novel cDNA sequences that we subsequently mapped to human 7q22. Methods for displaying comparative genomic information, including unfinished sequence data, are becoming increasingly important. We supplement our printed comparative analysis with a new, Web-based program called Laj (local alignments with java). Laj provides interactive access to archived pairwise sequence alignments via the WWW. It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse-human comparison can be viewed at http://web.uvic.ca/~bioweb/laj.html. Laj is available at http://bio.cse.psu.edu/, along with online documentation and additional examples of annotated genomic regions.
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Affiliation(s)
- M D Wilson
- Department of Biology, Centre for Environmental Health, PO Box 3020, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
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38
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Bös M, Sleight AJ, Godel T, Martin JR, Riemer C, Stadler H. 5-HT(6) receptor antagonists: lead optimisation and biological evaluation of N-aryl and N-heteroaryl 4-amino-benzene sulfonamides. Eur J Med Chem 2001; 36:165-78. [PMID: 11311747 DOI: 10.1016/s0223-5234(00)01209-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
RO-04-6790 (6a) has been identified in a random screen for 5-HT(6) receptor antagonists. In a medicinal chemistry optimisation program a series of analogs comprising N-heteroaryl- and N-arylbenzenesulfonamides have been synthesised and investigated for their binding affinity. Compounds with a logD profile indicative of brain penetration have been subjected to in vivo testing for reversal of a scopolamine-induced retention deficit in a passive avoidance paradigm.
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Affiliation(s)
- M Bös
- Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, H7S 2G5, Québec, Canada.
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39
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Abstract
The pathogenesis of scrapie, and of neurodegenerative diseases in general, is still insufficiently understood and is therefore being intensely researched. There is abundant evidence that the activation of glial cells precedes neurodegeneration and may thus play an important role in disease development and progression. The identification of genes with altered expression patterns in the diseased brain may provide insight on the molecular level into the process which ultimately leads to neuronal loss. Differentially expressed genes in scrapie-infected brain tissue were enriched by the suppression subtractive hybridization technique, molecularly cloned, and further characterized. Northern blotting and nucleotide sequencing confirmed the identities of 19 upregulated genes, 11 of which were unknown to be affected by scrapie. A considerable number of these 19 genes, namely those encoding interferon-inducible protein 10 (IP-10), 2',5'-oligo(A) synthetase, Mx protein, IIGP protein, major histocompatibility complex classes I and II, complement, and beta(2)-microglobulin, were inducible by interferons (IFNs), suggesting that an IFN response is a possible mechanism of gene activation in scrapie. Among the newly found genes, that coding for 2',5'-oligo(A) synthetase is of special interest because it could contribute to the apoptotic loss of neuronal cells via RNase L activation. In addition, upregulation of the chemokine IP-10 and B-lymphocyte chemoattractant mRNAs was seen at relatively early stages of the disease and was sustained throughout disease development.
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Affiliation(s)
- C Riemer
- Robert-Koch-Institut, 13353 Berlin, Germany
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40
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Florea L, Riemer C, Schwartz S, Zhang Z, Stojanovic N, Miller W, McClelland M. Web-based visualization tools for bacterial genome alignments. Nucleic Acids Res 2000; 28:3486-96. [PMID: 10982867 PMCID: PMC110741 DOI: 10.1093/nar/28.18.3486] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With the increase in the flow of sequence data, both in contigs and whole genomes, visual aids for comparison and analysis studies are becoming imperative. We describe three web-based tools for visualizing alignments of bacterial genomes. The first, called Enteric, produces a graphical, hypertext view of pairwise alignments between a reference genome and sequences from each of several related organisms, covering 20 kb around a user-specified position. Insertions, deletions and rearrangements relative to the reference genome are color-coded, which reveals many intriguing differences among genomes. The second, Menteric, computes and displays nucleotide-level multiple alignments of the same sequences, together with annotations of ORFs and regulatory sites, in a 1 kb region surrounding a given address. The third, a Java-based viewer called Maj, combines some features of the previous tools, and adds a zoom-in mechanism. We compare the Escherichia coli K-12 genome with the partially sequenced genomes of Klebsiella pneumoniae, Yersinia pestis, Vibrio cholerae, and the Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A. Examination of the pairwise and multiple alignments in a region allows one to draw inferences about regulatory patterns and functional assignments. For example, these tools revealed that rffH, a gene involved in enterobacterial common antigen (ECA) biosynthesis, is partly deleted in one of the genomes. We used PCR to show that this deletion occurs sporadically in some strains of some serovars of S.enterica subspecies I but not in any strains tested from six other subspecies. The resulting cell surface diversity may be associated with selection by the host immune response.
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Affiliation(s)
- L Florea
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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41
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Florea L, Li M, Riemer C, Giardine B, Miller W, Hardison R. Validating Computer Programs for Functional Genomics in Gene Regulatory Regions. Curr Genomics 2000. [DOI: 10.2174/1389202003351733] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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42
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Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W. PipMaker--a web server for aligning two genomic DNA sequences. Genome Res 2000; 10:577-86. [PMID: 10779500 PMCID: PMC310868 DOI: 10.1101/gr.10.4.577] [Citation(s) in RCA: 840] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/1999] [Accepted: 02/01/2000] [Indexed: 11/25/2022]
Abstract
PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree of similarity for each aligning segment between the two sequences in a compact and easily understandable form. Positions along the horizontal axis can be labeled with features such as exons of genes and repetitive elements, and colors can be used to clarify and enhance the display. The web site also provides a plot of the locations of those segments in both species (similar to a dot plot). PipMaker is appropriate for comparing genomic sequences from any two related species, although the types of information that can be inferred (e.g., protein-coding regions and cis-regulatory elements) depend on the level of conservation and the time and divergence rate since the separation of the species. Gene regulatory elements are often detectable as similar, noncoding sequences in species that diverged as much as 100-300 million years ago, such as humans and mice, Caenorhabditis elegans and C. briggsae, or Escherichia coli and Salmonella spp. PipMaker supports analysis of unfinished or "working draft" sequences by permitting one of the two sequences to be in unoriented and unordered contigs.
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Affiliation(s)
- S Schwartz
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park 16802, USA
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43
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Stojanovic N, Florea L, Riemer C, Gumucio D, Slightom J, Goodman M, Miller W, Hardison R. Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Res 1999; 27:3899-910. [PMID: 10481030 PMCID: PMC148654 DOI: 10.1093/nar/27.19.3899] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Conserved segments in DNA or protein sequences are strong candidates for functional elements and thus appropriate methods for computing them need to be developed and compared. We describe five methods and computer programs for finding highly conserved blocks within previously computed multiple alignments, primarily for DNA sequences. Two of the methods are already in common use; these are based on good column agreement and high information content. Three additional methods find blocks with minimal evolutionary change, blocks that differ in at most k positions per row from a known center sequence and blocks that differ in at most k positions per row from a center sequence that is unknown a priori. The center sequence in the latter two methods is a way to model potential binding sites for known or unknown proteins in DNA sequences. The efficacy of each method was evaluated by analysis of three extensively analyzed regulatory regions in mammalian beta-globin gene clusters and the control region of bacterial arabinose operons. Although all five methods have quite different theoretical underpinnings, they produce rather similar results on these data sets when their parameters are adjusted to best approximate the experimental data. The optimal parameters for the method based on information content varied little for different regulatory regions of the beta-globin gene cluster and hence may be extrapolated to many other regulatory regions. The programs based on maximum allowed mismatches per row have simple parameters whose values can be chosen a priori and thus they may be more useful than the other methods when calibration against known functional sites is not available.
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Affiliation(s)
- N Stojanovic
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park 16802, USA
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44
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Abstract
Information on gene expression and regulation is expanding rapidly, and the complexity of the experimental design and data makes unique demands on databases to store the results. We describe a prototype database containing experimental results on the expression of mammalian beta-like globin genes, along with several query methods for accessing the information. The database has tables for DNA transfer experiments, protein-DNA binding results, and positions of DNase hypersensitive sites, which make extensive use of nested data structures. Comparison of data from various mammals is accomplished by providing a common coordinate system via a simultaneous alignment of matching DNA sequences. Interactive access to the database is available at a site called the Globin Gene Server on the World Wide Web (http://globin.cse. psu.edu). This software should be useful for any genetic system in which DNA sequence data are available.
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Affiliation(s)
- C Riemer
- The Center for Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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45
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Boess FG, Riemer C, Bös M, Bentley J, Bourson A, Sleight AJ. The 5-hydroxytryptamine6 receptor-selective radioligand [3H]Ro 63-0563 labels 5-hydroxytryptamine receptor binding sites in rat and porcine striatum. Mol Pharmacol 1998; 54:577-83. [PMID: 9730917 DOI: 10.1124/mol.54.3.577] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ro 63-0563 [4-amino-N-(2,6 bis-methylamino-pyridin-4-yl)-benzene sulfonamide] is a high affinity 5-hydroxytryptamine6 (HT6) receptor antagonist with more than 100-fold selectivity for the 5-HT6 receptor compared with 69 other receptors and binding sites. The present study describes the properties of [3H]Ro 63-0563, the first selective 5-HT6 receptor radioligand. Specific binding of [3H]Ro 63-0563 (nonspecific binding defined in the presence of 10 microM methiothepin) to recombinant rat and human 5-HT6 receptors was saturable, rapid, and reversible with equilibrium dissociation constants (Kd) of 6.8 nM and 4.96 nM, respectively. The pharmacological profile of the rat 5-HT6 receptor labeled with [3H]Ro 63-0563 (methiothepin > D-lysergic acid diethylamide > clozapine approximately Ro 63-0563 > lisuride > ergotamine approximately Ro 04-6790 > 5-HT > amitriptyline approximately metergoline approximately mianserin approximately ritanserin > methysergide > mesulergine) was similar to that obtained by using either [3H]D-lysergic acide diethylamide or [3H]5-HT as radioligand. In equilibrium binding studies with rat striatal membranes, [3H]Ro 63-0563 labeled a single binding site with Kd and Bmax values of 11. 7 nM and 175 fmol/mg protein, respectively. In porcine striatal membranes, [3H]Ro 63-0563 also labeled a single binding site with Kd and Bmax values of 8.0 nM and 130 fmol/mg protein, respectively. The affinities of 14 5-HT6 receptor ligands at this binding site were similar to those found for the recombinant rat and human 5-HT6 receptor, which suggested the presence of 5-HT6 receptors in porcine striatum.
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Affiliation(s)
- F G Boess
- Pharma Division, Preclinical Research, F. Hoffmann-La Roche, Ltd., 4070 Basel, Switzerland
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46
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Sleight AJ, Boess FG, Bös M, Levet-Trafit B, Riemer C, Bourson A. Characterization of Ro 04-6790 and Ro 63-0563: potent and selective antagonists at human and rat 5-HT6 receptors. Br J Pharmacol 1998; 124:556-62. [PMID: 9647481 PMCID: PMC1565407 DOI: 10.1038/sj.bjp.0701851] [Citation(s) in RCA: 149] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
1. This study describes the in vitro characterization of two potent and selective 5-HT6 receptor antagonists at the rat and human recombinant 5-HT6 receptor. 2. In binding assays with [3H]-LSD, 4-amino-N-(2,6 bis-methylamino-pyrimidin-4-yl)-benzene sulphonamide (Ro 04-6790) and 4-amino-N-(2,6 bis-methylamino-pyridin-4-yl)-benzene sulphonamide (Ro 63-0563) had mean pKi values +/-s.e.mean at the rat 5-HT6 receptor of 7.35+/-0.04 and 7.83+/-0.01, respectively and pKi values at the human 5-HT6 receptor of 7.26+/-0.06 and 7.91+/-0.02, respectively. 3 .Both compounds were found to be over 100 fold selective for the 5-HT6 receptor compared to 23 (Ro 04-6790) and 69 (Ro 63-0563) other receptor binding sites. 4. In functional studies, neither compound had any significant effect on basal levels of cyclicAMP accumulation in Hela cells stably expressing the human 5-HT6 receptor, suggesting that the compounds are neither agonists nor inverse agonists at the 5-HT6 receptor. However, both Ro 04-6790 and Ro 63-0563 behaved as competitive antagonists with mean +/-s.e.mean pA2 values of 6.75+/-0.07 and 7.10+/-0.09, respectively. 5. In rats habituated to observation cages, Ro 04-6790 produced a behavioural syndrome similar to that seen following treatment with antisense oligonucleotides designed to reduce the expression of 5-HT6 receptors. This behavioural syndrome consisted of stretching, yawning and chewing. 6. Ro 04-6790 and Ro 63-0563 represent valuable pharmacological tools for the identification of 5-HT6 receptors in natural tissues and the study of their physiological function.
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Affiliation(s)
- A J Sleight
- Pharma Division, Preclinical Research, F. Hoffmann-La Roche Ltd, Basel, Switzerland
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47
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Chui DH, Hardison R, Riemer C, Miller W, Carver MF, Molchanova TP, Efremov GD, Huisman TH. An electronic database of human hemoglobin variants on the World Wide Web. Blood 1998; 91:2643-4. [PMID: 9531571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- D H Chui
- Provincial Hemoglobinopathy DNA Diagnostic Laboratory and Department of Pathology, McMaster University, Hamilton, Ontario, Canada
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48
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Hardison R, Riemer C, Chui DH, Huisman TH, Miller W. Electronic access to sequence alignments, experimental results, and human mutations as an aid to studying globin gene regulation. Genomics 1998; 47:429-37. [PMID: 9480762 DOI: 10.1006/geno.1997.5147] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- R Hardison
- Department of Biochemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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49
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Luther T, Magdolen V, Albrecht S, Kasper M, Riemer C, Kessler H, Graeff H, Müller M, Schmitt M. Epitope-mapped monoclonal antibodies as tools for functional and morphological analyses of the human urokinase receptor in tumor tissue. Am J Pathol 1997; 150:1231-44. [PMID: 9094980 PMCID: PMC1858180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
uPAR (CD87), the receptor for the urokinase-type plasminogen activator (uPA) facilitates tumor cell invasion and metastasis by focusing uPA proteolytic activity to the cell surface. As uPAR exists in various molecular forms, it is desirable to use well defined antibodies for analyses of uPAR antigen expression in human malignant tumors by immunological methods. Therefore, twelve monoclonal antibodies (MAbs) directed against uPAR were generated by using nonglycosylated, recombinant human uPAR (spanning amino acids 1 to 284), expressed in Escherichia coli, as the immunogen. The reaction pattern of these MAbs with the immunogen and a series of carboxyl-terminally truncated versions of uPAR demonstrated that at least six different epitopes of uPAR are recognized. All MAbs reacted under reducing conditions in immunoblot analyses with E. coli-expressed uPA and also with highly glycosylated, functionally intact, recombinant human uPAR expressed in Chinese hamster ovary (CHO) cells. Seven of the MAbs recognized CHO uPAR under nonreducing conditions as well. By flow cytofluorometric analyses, three of these MAbs were shown to bind to native human uPAR present on the cell surface of monocytoid U937 cells with MAb IIIF10 being the best. Saturation of uPAR with uPA on U937 cells completely blocked interaction of MAb IIIF10 with uPAR (mapped epitope, amino acids 52 to 60 of domain I of uPAR). In turn, preincubation of U937 cells with MAb IIIF10 efficiently reduced binding of uPA to uPAR, indicating that the epitope detected by MAb IIIF10 is located within or closely to the uPA-binding site of uPAR, and thus, this site may be a target to influence uPA/uPAR-mediated proteolysis in tumors. Binding of MAbs IID7 or IIIB11 (mapped epitope, amino acids 125 to 132 of domain II of uPAR) to uPAR is not affected when uPAR is occupied by uPA. As these MAbs reacted strongly with cellular uPAR antigen in formalin-fixed paraffin-embedded tumor sections, the domain-II-specific antibodies IID7 and IIIB11 may be useful for immunohistochemical studies of uPAR expression in tissue remodeling processes in tumor invasion. In conclusion, we have devised well defined and epitope-mapped MAbs to uPAR that are highly specific tools for detection and targeting of uPAR in tumor tissue.
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MESH Headings
- Animals
- Antibodies, Monoclonal/biosynthesis
- Antibodies, Monoclonal/chemistry
- Antibodies, Neoplasm/chemistry
- Breast Neoplasms/chemistry
- Breast Neoplasms/immunology
- CHO Cells
- Carcinoma/chemistry
- Carcinoma/immunology
- Cricetinae
- Epitope Mapping
- Female
- Flow Cytometry
- Humans
- Leukemia, Promyelocytic, Acute
- Mice
- Mice, Inbred BALB C
- Receptors, Cell Surface/immunology
- Receptors, Cell Surface/physiology
- Receptors, Urokinase Plasminogen Activator
- Tumor Cells, Cultured
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Affiliation(s)
- T Luther
- Institut für Pathologie, Technische Universität Dresden, Germany
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50
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Bürgle M, Koppitz M, Riemer C, Kessler H, König B, Weidle UH, Kellermann J, Lottspeich F, Graeff H, Schmitt M, Goretzki L, Reuning U, Wilhelm O, Magdolen V. Inhibition of the interaction of urokinase-type plasminogen activator (uPA) with its receptor (uPAR) by synthetic peptides. Biol Chem 1997; 378:231-7. [PMID: 9165076 DOI: 10.1515/bchm.1997.378.3-4.231] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Focusing of the serine protease urokinase-type plasminogen activator (uPA) to the cell surface via interaction with its specific receptor (uPAR, CD87) is an important step for tumor cell invasion and metastasis. The ability of a synthetic peptide derived from the uPAR-binding region of uPA (comprising amino acids 16-32 of uPA; uPA(16-32)) to inhibit binding of fluorescently labeled uPA to uPAR on human promyeloid U937 cells was assessed by quantitative flow cytofluorometric analysis (FACS) and compared to the inhibitory capacities of other synthetic peptides known to interfere with uPA/uPAR-interaction. An about 3000-fold molar excess of uPA(16-32) resulted in 50% inhibition of pro-uPA binding to cell surface-associated uPAR. Using a solid-phase uPA-ligand binding assay employing recombinant soluble uPAR coated to microtiter plates, the minimal binding region of wild-type uPA was determined. The linear peptide uPA(19-31) and its more stable disulfide-bridged cyclic form (cyclo(19,31)uPA(19-31)) displayed uPAR-binding activity whereas other peptides such as uPA(18-30), uPA(20-32) or uPA(20-30) did not react with uPAR. Cyclic peptide derivatives of cyclo(19,31)uPA(19-31) in which certain amino acids were deleted and/or replaced by other amino acids as well as uPAR-derived wild-type peptides did also not inhibit uPA/uPAR-interaction. Therefore, the present investigations identified cyclo(19,31)uPA(19-31) as a potential lead structure for the development of uPA-peptide analogues to block uPA/uPAR-interaction.
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Affiliation(s)
- M Bürgle
- Institut für Organische Chemie und Biochemie der Technischen Universität Munchen, Garching, Germany
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