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  • 1
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    Isolation and characterization of a novel calmodulin-binding protein from potato (2002)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: Tuberization in potato is controlled by hormonal and environmental signals. Ca(2+), an important intracellular messenger, and calmodulin (CaM), one of the primary Ca(2+) sensors, have been implicated in controlling diverse cellular processes in plants including tuberization. The regulation of cellular processes by CaM involves its interaction with other proteins. To understand the role of Ca(2+)/CaM in tuberization, we have screened an expression library prepared from developing tubers with biotinylated CaM. This screening resulted in isolation of a cDNA encoding a novel CaM-binding protein (potato calmodulin-binding protein (PCBP)). Ca(2+)-dependent binding of the cDNA-encoded protein to CaM is confirmed by (35)S-labeled CaM. The full-length cDNA is 5 kb long and encodes a protein of 1309 amino acids. The deduced amino acid sequence showed significant similarity with a hypothetical protein from another plant, Arabidopsis. However, no homologs of PCBP are found in nonplant systems, suggesting that it is likely to be specific to plants. Using truncated versions of the protein and a synthetic peptide in CaM binding assays we mapped the CaM-binding region to a 20-amino acid stretch (residues 1216-1237). The bacterially expressed protein containing the CaM-binding domain interacted with three CaM isoforms (CaM2, CaM4, and CaM6). PCBP is encoded by a single gene and is expressed differentially in the tissues tested. The expression of CaM, PCBP, and another CaM-binding protein is similar in different tissues and organs. The predicted protein contained seven putative nuclear localization signals and several strong PEST motifs. Fusion of the N-terminal region of the protein containing six of the seven nuclear localization signals to the reporter gene beta-glucuronidase targeted the reporter gene to the nucleus, suggesting a nuclear role for PCBP.
    Keywords: Life Sciences (General)
    Type: The Journal of biological chemistry (ISSN 0021-9258); Volume 277; 6; 4206-14
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  • 2
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    Genes encoding calmodulin-binding proteins in the Arabidopsis genome (2002)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.
    Keywords: Life Sciences (General)
    Type: The Journal of biological chemistry (ISSN 0021-9258); Volume 277; 12; 9840-52
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  • 3
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    A pollen-specific novel calmodulin-binding protein with tetratricopeptide repeats (2000)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: Calcium is essential for pollen germination and pollen tube growth. A large body of information has established a link between elevation of cytosolic Ca(2+) at the pollen tube tip and its growth. Since the action of Ca(2+) is primarily mediated by Ca(2+)-binding proteins such as calmodulin (CaM), identification of CaM-binding proteins in pollen should provide insights into the mechanisms by which Ca(2+) regulates pollen germination and tube growth. In this study, a CaM-binding protein from maize pollen (maize pollen calmodulin-binding protein, MPCBP) was isolated in a protein-protein interaction-based screening using (35)S-labeled CaM as a probe. MPCBP has a molecular mass of about 72 kDa and contains three tetratricopeptide repeats (TPR) suggesting that it is a member of the TPR family of proteins. MPCBP protein shares a high sequence identity with two hypothetical TPR-containing proteins from Arabidopsis. Using gel overlay assays and CaM-Sepharose binding, we show that the bacterially expressed MPCBP binds to bovine CaM and three CaM isoforms from Arabidopsis in a Ca(2+)-dependent manner. To map the CaM-binding domain several truncated versions of the MPCBP were expressed in bacteria and tested for their ability to bind CaM. Based on these studies, the CaM-binding domain was mapped to an 18-amino acid stretch between the first and second TPR regions. Gel and fluorescence shift assays performed with CaM and a CaM-binding synthetic peptide further confirmed MPCBP binding to CaM. Western, Northern, and reverse transcriptase-polymerase chain reaction analysis have shown that MPCBP expression is specific to pollen. MPCBP was detected in both soluble and microsomal proteins. Immunoblots showed the presence of MPCBP in mature and germinating pollen. Pollen-specific expression of MPCBP, its CaM-binding properties, and the presence of TPR motifs suggest a role for this protein in Ca(2+)-regulated events during pollen germination and growth.
    Keywords: Life Sciences (General)
    Type: The Journal of biological chemistry (ISSN 0021-9258); Volume 275; 45; 35457-70
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  • 4
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    A calmodulin binding protein from Arabidopsis is induced by ethylene and contains a DNA-binding motif (2000)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: Calmodulin (CaM), a key calcium sensor in all eukaryotes, regulates diverse cellular processes by interacting with other proteins. To isolate CaM binding proteins involved in ethylene signal transduction, we screened an expression library prepared from ethylene-treated Arabidopsis seedlings with 35S-labeled CaM. A cDNA clone, EICBP (Ethylene-Induced CaM Binding Protein), encoding a protein that interacts with activated CaM was isolated in this screening. The CaM binding domain in EICBP was mapped to the C-terminus of the protein. These results indicate that calcium, through CaM, could regulate the activity of EICBP. The EICBP is expressed in different tissues and its expression in seedlings is induced by ethylene. The EICBP contains, in addition to a CaM binding domain, several features that are typical of transcription factors. These include a DNA-binding domain at the N terminus, an acidic region at the C terminus, and nuclear localization signals. In database searches a partial cDNA (CG-1) encoding a DNA-binding motif from parsley and an ethylene up-regulated partial cDNA from tomato (ER66) showed significant similarity to EICBP. In addition, five hypothetical proteins in the Arabidopsis genome also showed a very high sequence similarity with EICBP, indicating that there are several EICBP-related proteins in Arabidopsis. The structural features of EICBP are conserved in all EICBP-related proteins in Arabidopsis, suggesting that they may constitute a new family of DNA binding proteins and are likely to be involved in modulating gene expression in the presence of ethylene.
    Keywords: Life Sciences (General)
    Type: Biochemical and biophysical research communications (ISSN 0006-291X); Volume 279; 3; 762-9
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  • 5
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    Design and engineering of an O(2) transport protein (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-03-20
    Description: The principles of natural protein engineering are obscured by overlapping functions and complexity accumulated through natural selection and evolution. Completely artificial proteins offer a clean slate on which to define and test these protein engineering principles, while recreating and extending natural functions. Here we introduce this method with the design of an oxygen transport protein, akin to human neuroglobin. Beginning with a simple and unnatural helix-forming sequence with just three different amino acids, we assembled a four-helix bundle, positioned histidines to bis-histidine ligate haems, and exploited helical rotation and glutamate burial on haem binding to introduce distal histidine strain and facilitate O(2) binding. For stable oxygen binding without haem oxidation, water is excluded by simple packing of the protein interior and loops that reduce helical-interface mobility. O(2) affinities and exchange timescales match natural globins with distal histidines, with the remarkable exception that O(2) binds tighter than CO.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539743/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539743/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koder, Ronald L -- Anderson, J L Ross -- Solomon, Lee A -- Reddy, Konda S -- Moser, Christopher C -- Dutton, P Leslie -- R01 GM041048/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Mar 19;458(7236):305-9. doi: 10.1038/nature07841.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295603" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Transport ; Carbon Monoxide/metabolism ; Carrier Proteins/*chemical synthesis/chemistry/*metabolism ; Drug Design ; Globins/chemistry ; Glutamic Acid/metabolism ; Heme/metabolism ; Histidine/metabolism ; Humans ; Kinetics ; Ligands ; Nerve Tissue Proteins/chemistry ; Oxidation-Reduction ; Oxygen/*metabolism ; *Protein Engineering ; Protein Structure, Secondary ; Rotation ; Spectroscopy, Fourier Transform Infrared ; Substrate Specificity ; Water/analysis/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Integrating common and rare genetic variation in diverse human populations (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-09-03
    Description: Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of 〈or=5%, and demonstrated the feasibility of imputing newly discovered CNPs and SNPs. This expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173859/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173859/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉International HapMap 3 Consortium -- Altshuler, David M -- Gibbs, Richard A -- Peltonen, Leena -- Dermitzakis, Emmanouil -- Schaffner, Stephen F -- Yu, Fuli -- Bonnen, Penelope E -- de Bakker, Paul I W -- Deloukas, Panos -- Gabriel, Stacey B -- Gwilliam, Rhian -- Hunt, Sarah -- Inouye, Michael -- Jia, Xiaoming -- Palotie, Aarno -- Parkin, Melissa -- Whittaker, Pamela -- Chang, Kyle -- Hawes, Alicia -- Lewis, Lora R -- Ren, Yanru -- Wheeler, David -- Muzny, Donna Marie -- Barnes, Chris -- Darvishi, Katayoon -- Hurles, Matthew -- Korn, Joshua M -- Kristiansson, Kati -- Lee, Charles -- McCarrol, Steven A -- Nemesh, James -- Keinan, Alon -- Montgomery, Stephen B -- Pollack, Samuela -- Price, Alkes L -- Soranzo, Nicole -- Gonzaga-Jauregui, Claudia -- Anttila, Verneri -- Brodeur, Wendy -- Daly, Mark J -- Leslie, Stephen -- McVean, Gil -- Moutsianas, Loukas -- Nguyen, Huy -- Zhang, Qingrun -- Ghori, Mohammed J R -- McGinnis, Ralph -- McLaren, William -- Takeuchi, Fumihiko -- Grossman, Sharon R -- Shlyakhter, Ilya -- Hostetter, Elizabeth B -- Sabeti, Pardis C -- Adebamowo, Clement A -- Foster, Morris W -- Gordon, Deborah R -- Licinio, Julio -- Manca, Maria Cristina -- Marshall, Patricia A -- Matsuda, Ichiro -- Ngare, Duncan -- Wang, Vivian Ota -- Reddy, Deepa -- Rotimi, Charles N -- Royal, Charmaine D -- Sharp, Richard R -- Zeng, Changqing -- Brooks, Lisa D -- McEwen, Jean E -- 068545/Wellcome Trust/United Kingdom -- 068545/Z/02/Wellcome Trust/United Kingdom -- 076113/Wellcome Trust/United Kingdom -- 077011/Wellcome Trust/United Kingdom -- 077014/Wellcome Trust/United Kingdom -- 082371/Wellcome Trust/United Kingdom -- 089061/Wellcome Trust/United Kingdom -- 089062/Wellcome Trust/United Kingdom -- 091746/Wellcome Trust/United Kingdom -- G0000934/Medical Research Council/United Kingdom -- P30 DK043351/DK/NIDDK NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Sep 2;467(7311):52-8. doi: 10.1038/nature09298.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA. altshuler@molbio.mgh.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20811451" target="_blank"〉PubMed〈/a〉
    Keywords: *DNA Copy Number Variations ; *Genome, Human ; Human Genome Project ; Humans ; *Polymorphism, Single Nucleotide ; Population Groups/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    elk, tissue-specific ets-related genes on chromosomes X and 14 near translocation breakpoints (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-04-07
    Description: The myb-ets-containing acute leukemia virus, E26, transforms myeloblasts and erythroblasts in culture and causes a mixed erythroid and myeloid leukemia in chicks. Genes (ets-1, ets-2, and erg) with variable relatedness to the v-ets oncogene of the E26 virus have been identified, cloned, and characterized in several species. Two new members (elk-1 and elk-2) of the ets oncogene superfamily have now been identified. Nucleotide sequence analysis of the elk-1 cDNA clone revealed that this gene encodes a 428-residue protein whose predicted amino acid sequence showed 82% similarity to the 3' region of v-ets. The elk or related sequences appear to be transcriptionally active in testis and lung. The elk cDNA probe detects two loci in the human genome, elk-1 and elk-2, which map to chromosome regions Xp11.2 and 14q32.3, respectively. These loci are near the translocation breakpoint seen in the t(X;18) (p11.2;q11.2), which is characteristic of synovial sarcoma, and the chromosome 14q32 breakpoints seen in ataxia telangiectasia and other T cell malignancies. This suggests the possibility that rearrangements of elk loci may be involved in pathogenesis of certain tumors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rao, V N -- Huebner, K -- Isobe, M -- ar-Rushdi, A -- Croce, C M -- Reddy, E S -- CA-21124/CA/NCI NIH HHS/ -- CA-25875/CA/NCI NIH HHS/ -- CA-39860/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1989 Apr 7;244(4900):66-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wistar Institute of Anatomy and Biology, Philadelphia, PA 19104.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2539641" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Avian Leukosis Virus/*genetics ; Base Sequence ; Chick Embryo ; Chickens ; Chromosome Mapping ; Cloning, Molecular ; DNA Probes ; *DNA-Binding Proteins ; Humans ; Mice ; Molecular Sequence Data ; *Oncogenes ; *Proto-Oncogene Proteins ; Rats ; Retroviridae Proteins/*genetics/isolation & purification ; *Transcription Factors ; *Translocation, Genetic ; *X Chromosome ; ets-Domain Protein Elk-1
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Amplification and molecular cloning of HTLV-I sequences from DNA of multiple sclerosis patients (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-01-27
    Description: Techniques of gene amplification, molecular cloning, and sequence analysis were used to test for the presence of sequences related to human T-lymphotropic virus type I (HTLV-I) in peripheral blood mononuclear cells of six patients with multiple sclerosis (MS) and 20 normal individuals. HTLV-I sequences were detected in all six MS patients and in one individual from the control group by DNA blot analysis and molecular cloning of amplified DNAs. The viral sequence in MS patients were associated with adherent cell populations consisting predominantly of monocytes and macrophages. Molecular cloning and nucleotide sequence analysis indicated that these amplified viral sequences were related to the HTLV-I proviral genome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reddy, E P -- Sandberg-Wollheim, M -- Mettus, R V -- Ray, P E -- DeFreitas, E -- Koprowski, H -- CA-10815/CA/NCI NIH HHS/ -- NS-11036/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1989 Jan 27;243(4890):529-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wistar Institute of Anatomy and Biology, Philadelphia, PA 19104.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2536193" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Base Sequence ; Child ; *Cloning, Molecular ; DNA Restriction Enzymes ; DNA, Viral/*genetics ; Female ; *Gene Amplification ; Human T-lymphotropic virus 1/*genetics ; Humans ; Leukocytes, Mononuclear/analysis/microbiology ; Macrophages/analysis/microbiology ; Male ; Molecular Sequence Data ; Multiple Sclerosis/*microbiology ; Nucleic Acid Hybridization ; Oligonucleotide Probes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Amplification and Molecular Cloning of HTLV-I Sequences from DNA of Multiple Sclerosis Patients. Correction (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-10-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reddy, E P -- New York, N.Y. -- Science. 1989 Oct 6;246(4926):10-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2781296" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA, Single-Stranded/genetics ; Gene Amplification ; Human T-lymphotropic virus 1/*genetics ; Humans ; Multiple Sclerosis/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Virus sharing, genetic sequencing, and global health security (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-09-13
    Description: This Perspective focuses on the future of the Pandemic Influenza Preparedness (PIP) Framework, which was initially established to promote the fair sharing of public health-related pandemic influenza samples between countries. We examine the changes that need to be made to address the growing likelihood that genetic sequence data might be shared instead of physical virus samples, as well as the need to expand the PIP framework's scope and to improve its fairness.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gostin, Lawrence O -- Phelan, Alexandra -- Stoto, Michael A -- Kraemer, John D -- Reddy, K Srinath -- New York, N.Y. -- Science. 2014 Sep 12;345(6202):1295-6. doi: 10.1126/science.1257622.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC 20001, USA. ; Department of Health Systems Administration, Georgetown University, Washington, DC 20057, USA. ; O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC 20001, USA. Department of Health Systems Administration, Georgetown University, Washington, DC 20057, USA. ; President, Public Health Foundation of India, New Delhi 110070, India.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25214618" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Disaster Planning ; *Global Health ; Health Services Accessibility ; Humans ; Influenza A Virus, H1N1 Subtype/*genetics ; Influenza A Virus, H5N1 Subtype/*genetics ; *Influenza Vaccines ; Influenza in Birds/epidemiology/prevention & control ; Influenza, Human/epidemiology/*prevention & control/virology ; Intellectual Property ; Orthomyxoviridae Infections/prevention & control/virology ; Pandemics/*prevention & control/veterinary ; Poultry ; Sequence Analysis, DNA ; Swine
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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