8 results on '"Frederick Lopez"'
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2. The DNA sequence and comparative analysis of human chromosome 5
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Nancy Hammon, Arthur Kobayashi, Stacey Black, Uffe Hellsten, Daniel S. Rokhsar, Lauren Haydu, Frederick Lopez, Nina Thayer, Diego Martinez, Mirian Denys, Paul Predki, Laurie Gordon, Eva Bajorek, Eidelyn Gonzales, Catherine Medina, Richard D. Nandkeshwar, Sanjay Israni, Richard M. Myers, Hope Tice, Jean F. Challacombe, Anne O. Olsen, Chenier Caoile, State Lowry, Alex Rodriguez, Paul G. Richardson, Kevin Wu, D. Scott, Xinwei She, Matthew Groza, James P. Noonan, Anna Ustaszewska, María Laura Ríos Gómez, Jane Grimwood, Jeremy Wheeler, Len A. Pennacchio, Martin O. Pollard, Tijana Glavina, Dea Fotopulos, Joel Martin, Heather Kimbal, Kristen Kadner, Dave Flowers, Joan Yang, Astrid Terry, Lucía Ramírez, Ming Tsai, Yee Man Chan, Michael R. Altherr, Susan Lucas, Jan Fang Cheng, Sam Pitluck, Sam Rash, Igor V. Grigoriev, Wayne Huang, Yunian Lou, Chris Detter, Shyam Prabhakar, James Priest, Angelica Salazar, Gary Xie, Nu Vo, Elbert Branscomb, Jamie Jett, Stephanie Rogers, David Goodstenin, Olivier Couronne, Julio Escobar, James Retterer, Mary Bao Tran-Gyamfi, Trevor Hawkins, Jeremy Schmutz, Evan E. Eichler, Andrea Aerts, Mark Dickson, Jenna Morgan, Edward M. Rubin, and Asaf Salamov
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Pan troglodytes ,Molecular Sequence Data ,Biology ,Synteny ,Muscular Atrophy, Spinal ,Complete sequence ,Chromosome 15 ,Gene Duplication ,Chromosome 19 ,Animals ,Humans ,Conserved Sequence ,Chromosome 12 ,Genetics ,Chromosome 7 (human) ,Base Composition ,Multidisciplinary ,Interleukins ,Genetic Diseases, Inborn ,Genomics ,Sequence Analysis, DNA ,Cadherins ,Physical Chromosome Mapping ,Chromosome 17 (human) ,Genes ,Vertebrates ,Chromosomes, Human, Pair 5 ,Chromosome 21 ,Pseudogenes - Abstract
Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.
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- 2004
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3. The sequence and analysis of duplication-rich human chromosome 16
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Kimberly L. Mcmurray, James Retterer, Nancy C. Brown, Dea Fotopulos, Michael R. Altherr, Judith G. Tesmer, Jane Grimwood, Joel Martin, Jonathan L. Longmire, Elizabeth Saunders, P. Scott White, Malinda Stalvey, Elbert Branscomb, Norman A. Doggett, Nina Thayer, C.E. Hildebrand, Mary Bao Tran-Gyamfi, Yunian Lou, Trevor Hawkins, Lucía Ramírez, Shyam Prabhakar, Ming Tsai, D. Scott, Hope Tice, Linda Meincke, Jean F. Challacombe, Gary Xie, Maria Gomez, Eidelyn Gonzales, Jeremy Schmutz, Kevin Wu, Marie-Claude Krawczyk, Heather Kimball, Graham A. Mark, David C. Torney, John C. Detter, Laurie Gordon, Albert L. Williams, Susan Lucas, Len A. Pennacchio, Linda S. Thompson, Robert K. Moyzis, Kristen Kadner, Arthur Kobayashi, Larry L. Deaven, Richard D. Nandkeshwar, E.W. Campbell, Patricia L. Wills, Andrea Aerts, Joan Yang, Darryl O. Ricke, Mark Dickson, Astrid Terry, Steve Lowry, Paul Gilna, Paul G. Richardson, Thom Ludeman, Olivier Couronne, Timothy Shough, Chitra Manohar, David Bruce, Jamie Jett, Evan E. Eichler, Pieter J. deJong, Mark Mundt, Judith M. Buckingham, Robert D. Sutherland, Roxanne Tapia, Heather Blumer, Wayne Huang, Leslie Chasteen, A. Christine Munk, Sanjay Israni, Deborah L. Grady, Igor V. Grigoriev, Stacey Black, Judith D. Cohn, David F. Callen, Han C. Chi, William J. Bruno, Cliff Han, Mirian Denys, Mira Dimitrijevic-Bussod, Martin Pollard, Connie S. Campbell, Richard M. Myers, Yee Man Chan, Sam Pitluck, Sam Rash, Joseph J. Fawcett, Mari Christensen, Lauren Haydu, Frederick Lopez, Lynn M. Clark, Julio Escobar, B. Parson-Quintana, Raymond L. Stallings, Tina Leyba, Dave Flowers, Eva Bajorek, Jenna Morgan, Mary L. Campbell, Anna Ustaszewska, Donna L. Robinson, Nu Vo, Edward M. Rubin, Lynne Goodwin, Paul Predki, Uffe Hellsten, Daniel S. Rokhsar, Phillip B. Jewett, Matthew Groza, Tijana Glavina, Chenier Caoile, Alex Rodriguez, Xinwei She, David Goodstein, Jung-Rung Wu, Levy E. Ulanovsky, Asaf Salamov, Nancy Hammon, and Olga Chertkov
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Genetics ,Multidisciplinary ,Autosome ,Polymorphism, Genetic ,Sequence analysis ,Pseudogene ,Molecular Sequence Data ,Genomics ,Sequence Analysis, DNA ,Biology ,Physical Chromosome Mapping ,Synteny ,Chromosome 16 ,Genes ,Gene Duplication ,Heterochromatin ,Gene duplication ,Gene family ,Animals ,Humans ,Gene ,Chromosomes, Human, Pair 16 ,Segmental duplication - Abstract
Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.
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- 2004
4. The DNA sequence and biology of human chromosome 19
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Mary Bao Tran-Gyamfi, Ivan Ovcharenko, Trevor Hawkins, Maria Gomez, Mirian Denys, Victor V. Solovyev, Terrence S. Furey, Jamie Jett, Jeremy Schmutz, Dea Fotopulos, David Gordon, Tom Slezak, Kevin Wu, Heather Kimball, Pieter J. deJong, Catherine Medina, Vladimer Larionov, Paula McCready, Stephanine Rogers, James Retterer, John C. Detter, Diego Martinez, Richard M. Myers, Paul Predki, Stacey Black, Eva Bajorek, Chenier Caoile, Alex Rodriguez, Isaac Ho, Arthur Kobayashi, Jane Lamerdin, Xinwei She, Yunian Lou, Jane Grimwood, Kristen Kadner, Alex Copeland, Wayne Huang, Sanjay Israni, Carmen Rosa Albacete García, Gary Xie, Doug Smith, Anthony V. Carrano, Matthew Groza, Catherine A. Cleland, Matt Nolan, Paul G. Richardson, Eidelyn Gonzales, Nina Thayer, Anna Ustaszewska, Eileen Dalin, Olivier Couronne, Evan E. Eichler, Tijana Glavina, Astrid Terry, Sun-Hee Leem, Steve Lowry, Anne S. Olsen, Lucía Ramírez, Ming Tsai, Stephanie Malfatti, Hope Tice, Uffe Hellsten, David Goodstein, Martin Pollard, Daniel S. Rokhsar, Nancy Hammon, Angelica Salazar, Jenna Morgan, Yee Man Chan, Michael R. Altherr, Paramvir S. Dehal, Nu Vo, Linda K. Ashworth, Elbert Branscomb, Laurie Gordon, Julio Escobar, Anthony P. Popkie, Dave Flowers, Anca M. Georgescu, Len A. Pennacchio, Sam Pitluck, Sam Rash, Edward M. Rubin, Sean Caenepeel, Glenda Quan, Asaf Salamov, Inna Dubchak, Lisa Stubbs, Andrea Aerts, Mark Dickson, Kathryn Nelson, Mari Christensen, Lauren Haydu, Frederick Lopez, Mark C. Wagner, Jeremy Wheeler, Joan Yang, and Susan Lucas
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Genetics, Medical ,Molecular Sequence Data ,Biology ,Evolution, Molecular ,Chromosome 15 ,Mice ,Chromosome 16 ,Chromosome 19 ,Gene Duplication ,Animals ,Humans ,Conserved Sequence ,Genetics ,Base Composition ,Multidisciplinary ,Sequence Analysis, DNA ,Physical Chromosome Mapping ,Chromosome 17 (human) ,Alternative Splicing ,Chromosome 4 ,Chromosome 3 ,Genes ,Multigene Family ,CpG Islands ,Chromosome 21 ,Chromosome 22 ,Chromosomes, Human, Pair 19 ,Pseudogenes - Abstract
Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.
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- 2003
5. Quality assessment of the human genome sequence
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Lucía Ramírez, Ming Tsai, Mirian Denys, Jane Grimwood, Angelica Salazar, Yee Man Chan, Chenier Caoile, Alex Rodriguez, Richard M. Myers, Mark Dickson, Eidelyn Gonzales, Dave Flowers, Jeremy Schmutz, Lauren Haydu, Frederick Lopez, M. Gómez, Joan Yang, Stacey Black, Dea Fotopulos, Jeremy Wheeler, Stephanie Rogers, Eva Bajorek, Julio Escobar, James Retterer, and Carmen Rosa Albacete García
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Genetics ,Quality Control ,Multidisciplinary ,Quality assessment ,Genome, Human ,Nucleic acid sequence ,Computational Biology ,Computational biology ,Sequence Analysis, DNA ,Biology ,Genome ,Sensitivity and Specificity ,DNA sequencing ,Research Design ,Human Genome Project ,Humans ,Human genome ,Computational analysis ,Base Pairing ,Reference genome ,Sequence (medicine) - Abstract
As the final sequencing of the human genome has now been completed, we present the results of the largest examination of the quality of the finished DNA sequence. The completed study covers the major contributing sequencing centres and is based on a rigorous combination of laboratory experiments and computational analysis.
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- 2003
6. A high-resolution radiation hybrid map of the human genome draft sequence
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Amy J. Perou, Kelly Sheppard, Eva Bajorek, Nu T. Vo, Michael Olivier, Amita Aggarwal, Tonya J. Jeffrey, Joseph P. Marquis, Wei-Lin Sun, Xia Liu, Tisha R. Chung, Saskia C. Lewis, Valerie I. Bustos, Nguyet M. Tran, Ellen M. Beasley, Ravi Sachidanandam, Barbara J. Trask, Angela Chu, Robert W. Freudenberg, Robert A. Martinez, Nedda S. Misherghi, Mirian Denys, Margaret K. Matsuura, Frederick Lopez, David Hadley, Tim Reif, Michelle R. Levy, Shaying Zhao, Brent Louie, Fawn Qin, Richard M. Myers, Vida Shokoohi, Tejeda, Annalisa A. Almendras, Jannette M. Bushard, Elizabeth A. Stewart, J. Fernando, Nicole Y. Fang, Libby R. Hamilton, Deborah L. Zierten, Tonatiuh Trejo, Laura C. Lazzeroni, Christopher Piercy, Adam B. Olshen, Shanti M. Perkins, Mark Piercy, Shannon D. Brady, David R. Cox, Geoff A. Smick, Brian D. Foster, Rakly Dominguez, Jolanna A. Norton, Simon C. M. Yan, Jennifer Allen, Libusha Kelly, and Anniek de Witte
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Chromosomes, Artificial, Bacterial ,Databases, Factual ,Sequence analysis ,Biology ,Genome ,Polymerase Chain Reaction ,Contig Mapping ,Sequence-tagged site ,Human Genome Project ,Humans ,In Situ Hybridization, Fluorescence ,Genomic organization ,Sequence (medicine) ,Sequence Tagged Sites ,Whole genome sequencing ,Genetics ,Radiation Hybrid Mapping ,Multidisciplinary ,Genome, Human ,Computational Biology ,Sequence Analysis, DNA ,Physical Chromosome Mapping ,Human genome ,Algorithms ,Software - Abstract
We have constructed a physical map of the human genome by using a panel of 90 whole-genome radiation hybrids (the TNG panel) in conjunction with 40,322 sequence-tagged sites (STSs) derived from random genomic sequences as well as expressed sequences. Of 36,678 STSs on the TNG radiation hybrid map, only 3604 (9.8%) were absent from the unassembled draft sequence of the human genome. Of 20,030 STSs ordered on the TNG map as well as the assembled human genome draft sequence and the Celera assembled human genome sequence, 36% of the STSs had a discrepant order between the working draft sequence and the Celera sequence. The TNG map order was identical to one of the two sequence orders in 60% of these discrepant cases.
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- 2001
7. Monoclonal antibody to transferrin receptor blocks transferrin binding and inhibits human tumor cell growth in vitro
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Frederick Lopez and Ian S. Trowbridge
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medicine.drug_class ,T-Lymphocytes ,Dose-Response Relationship, Immunologic ,Receptors, Cell Surface ,Transferrin receptor ,Monoclonal antibody ,Ferric Compounds ,Cell Line ,chemistry.chemical_compound ,Receptors, Transferrin ,medicine ,Humans ,Ferrous Compounds ,Interphase ,chemistry.chemical_classification ,Leukemia ,Multidisciplinary ,biology ,Cell growth ,Transferrin ,Antibodies, Monoclonal ,Molecular biology ,Hep G2 ,chemistry ,Biochemistry ,Cell culture ,biology.protein ,Growth inhibition ,Antibody ,Cell Division ,Research Article - Abstract
A murine hybridoma has been obtained that produces a monoclonal antibody against the human transferrin receptor. In contrast to previously characterized monoclonal antibodies that recognize the transferrin receptor, this antibody, designated 42/6, blocks the binding of transferrin to its receptor and inhibits the growth of the human T leukemic cell line, CCRF-CEM, in vitro. Inhibition of cell growth was dose dependent, and as little as 2.5 micrograms of purified antibody per ml had a detectable effect, even though transferrin was present in the tissue culture medium in large molar excess. Cells grown in the presence of antibody for 7 days accumulated in S phase of the cell cycle. The addition of iron to antibody-treated cultures in the form of ferric complexes or ferrous sulfate did not overcome the growth inhibitory effects of the anti-transferrin-receptor antibodies. This result suggests that either transferrin is the only means by which CCRF-CEM leukemic cells can be provided with sufficient iron in vitro or that other factors in addition to iron starvation are involved in the antibody-mediated growth inhibition. The inhibition of cell growth by 42/6 monoclonal antibody suggests that monoclonal antibodies against proliferation-associated cell surface antigens, such as the transferrin receptor, may be useful pharmacological reagents to modify cell growth in vitro.
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- 1982
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8. 3H-N-n-propylnorapomorphine: a novel agonist ligand for central dopamine receptors
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Frederick Lopez, Ian Creese, Linda Padgett, and Enrico Fazzini
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Pharmacology ,Agonist ,Apomorphine ,medicine.drug_class ,Stereochemistry ,Chemistry ,D1-like receptor ,Stereoisomerism ,In Vitro Techniques ,Ligands ,Partial agonist ,Binding, Competitive ,Receptors, Dopamine ,D2-like receptor ,Dopamine receptor D3 ,Dopamine receptor ,medicine ,Inverse agonist ,Animals ,Cattle ,Caudate Nucleus ,Endogenous agonist - Published
- 1979
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