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  1. Article ; Online: Cohesin loading and sliding.

    Ocampo-Hafalla, Maria T / Uhlmann, Frank

    Journal of cell science

    2011  Volume 124, Issue Pt 5, Page(s) 685–691

    Abstract: Cohesin is best known as a crucial component of chromosomal stability. Composed of several essential subunits in budding yeast, cohesin forms a ring-like complex that is thought to embrace sister chromatids, thereby physically linking them until their ... ...

    Abstract Cohesin is best known as a crucial component of chromosomal stability. Composed of several essential subunits in budding yeast, cohesin forms a ring-like complex that is thought to embrace sister chromatids, thereby physically linking them until their timely segregation during cell division. The ability of cohesin to bind chromosomes depends on the Scc2-Scc4 complex, which is viewed as a loading factor for cohesin onto DNA. Notably, in addition to its canonical function in sister chromatid cohesion, cohesin has also been implicated in gene regulation and development in organisms ranging from yeast to human. Despite its importance, both as a mediator of sister chromatid cohesion and as a modulator of gene expression, the nature of the association of cohesin with chromosomes that enables it to fulfil both of these roles remains incompletely understood. The mechanism by which cohesin is loaded onto chromosomes, and how cohesin and the related condensin and Smc5-Smc6 complexes promote DNA interactions require further elucidation. In this Commentary, we critically review the evidence for cohesin loading and its subsequent apparent sliding along chromosomes, and discuss the implications gained from cohesin localisation studies for its important functions in chromosome biology.
    MeSH term(s) Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Cell Cycle Proteins/chemistry ; Cell Cycle Proteins/metabolism ; Chromatids/metabolism ; Chromosomal Proteins, Non-Histone/chemistry ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosomes/metabolism ; DNA/metabolism ; DNA-Binding Proteins/metabolism ; Humans ; Multiprotein Complexes/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Cohesins
    Chemical Substances Cell Cycle Proteins ; Chromosomal Proteins, Non-Histone ; DNA-Binding Proteins ; Multiprotein Complexes ; SCC2 protein, S cerevisiae ; SCC4 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; condensin complexes ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; Adenosine Triphosphatases (EC 3.6.1.-)
    Language English
    Publishing date 2011-02-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2993-2
    ISSN 1477-9137 ; 0021-9533
    ISSN (online) 1477-9137
    ISSN 0021-9533
    DOI 10.1242/jcs.073866
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Cohesin loading and sliding

    Ocampo-Hafalla, Maria T / Uhlmann, Frank

    Journal of cell science. 2011 Mar. 1, v. 124, no. 5

    2011  

    Abstract: Cohesin is best known as a crucial component of chromosomal stability. Composed of several essential subunits in budding yeast, cohesin forms a ring-like complex that is thought to embrace sister chromatids, thereby physically linking them until their ... ...

    Abstract Cohesin is best known as a crucial component of chromosomal stability. Composed of several essential subunits in budding yeast, cohesin forms a ring-like complex that is thought to embrace sister chromatids, thereby physically linking them until their timely segregation during cell division. The ability of cohesin to bind chromosomes depends on the Scc2-Scc4 complex, which is viewed as a loading factor for cohesin onto DNA. Notably, in addition to its canonical function in sister chromatid cohesion, cohesin has also been implicated in gene regulation and development in organisms ranging from yeast to human. Despite its importance, both as a mediator of sister chromatid cohesion and as a modulator of gene expression, the nature of the association of cohesin with chromosomes that enables it to fulfil both of these roles remains incompletely understood. The mechanism by which cohesin is loaded onto chromosomes, and how cohesin and the related condensin and Smc5-Smc6 complexes promote DNA interactions require further elucidation. In this Commentary, we critically review the evidence for cohesin loading and its subsequent apparent sliding along chromosomes, and discuss the implications gained from cohesin localisation studies for its important functions in chromosome biology.
    Language English
    Dates of publication 2011-0301
    Size p. 685-691.
    Publishing place The Company of Biologists Limited
    Document type Article
    ZDB-ID 2993-2
    ISSN 1477-9137 ; 0021-9533
    ISSN (online) 1477-9137
    ISSN 0021-9533
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: Displacement and re-accumulation of centromeric cohesin during transient pre-anaphase centromere splitting.

    Ocampo-Hafalla, Maria T / Katou, Yuki / Shirahige, Katsuhiko / Uhlmann, Frank

    Chromosoma

    2007  Volume 116, Issue 6, Page(s) 531–544

    Abstract: The ring-shaped cohesin complex links sister chromatids until their timely segregation during mitosis. Cohesin is enriched at centromeres where it provides the cohesive counterforce to bipolar tension produced by the mitotic spindle. As a consequence of ... ...

    Abstract The ring-shaped cohesin complex links sister chromatids until their timely segregation during mitosis. Cohesin is enriched at centromeres where it provides the cohesive counterforce to bipolar tension produced by the mitotic spindle. As a consequence of spindle tension, centromeric sequences transiently split in pre-anaphase cells, in some organisms up to several micrometers. This 'centromere breathing' presents a paradox, how sister sequences separate where cohesin is most enriched. We now show that in the budding yeast Saccharomyces cerevisiae, cohesin binding diminishes over centromeric sequences that split during breathing. We see no evidence for cohesin translocation to surrounding sequences, suggesting that cohesin is removed from centromeres during breathing. Two pools of cohesin can be distinguished. Cohesin loaded before DNA replication, which has established sister chromatid cohesion, disappears during breathing. In contrast, cohesin loaded after DNA replication is partly retained. As sister centromeres re-associate after transient separation, cohesin is reloaded in a manner independent of the canonical cohesin loader Scc2/Scc4. Efficient centromere re-association requires the cohesion establishment factor Eco1, suggesting that re-establishment of sister chromatid cohesion contributes to the dynamic behaviour of centromeres in mitosis. These findings provide new insights into cohesin behaviour at centromeres.
    MeSH term(s) Anaphase/genetics ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Centromere/genetics ; Centromere/metabolism ; Chromosomal Proteins, Non-Histone/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Cohesins
    Chemical Substances Cell Cycle Proteins ; Chromosomal Proteins, Non-Histone ; Nuclear Proteins ; Saccharomyces cerevisiae Proteins
    Language English
    Publishing date 2007-09-01
    Publishing country Austria
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 203083-4
    ISSN 1432-0886 ; 0009-5915
    ISSN (online) 1432-0886
    ISSN 0009-5915
    DOI 10.1007/s00412-007-0118-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Displacement and re-accumulation of centromeric cohesin during transient pre-anaphase centromere splitting

    Ocampo-Hafalla, Maria T / Katou, Yuki / Shirahige, Katsuhiko / Uhlmann, Frank

    Chromosoma. 2007 Dec., v. 116, no. 6

    2007  

    Abstract: The ring-shaped cohesin complex links sister chromatids until their timely segregation during mitosis. Cohesin is enriched at centromeres where it provides the cohesive counterforce to bipolar tension produced by the mitotic spindle. As a consequence of ... ...

    Abstract The ring-shaped cohesin complex links sister chromatids until their timely segregation during mitosis. Cohesin is enriched at centromeres where it provides the cohesive counterforce to bipolar tension produced by the mitotic spindle. As a consequence of spindle tension, centromeric sequences transiently split in pre-anaphase cells, in some organisms up to several micrometers. This 'centromere breathing' presents a paradox, how sister sequences separate where cohesin is most enriched. We now show that in the budding yeast Saccharomyces cerevisiae, cohesin binding diminishes over centromeric sequences that split during breathing. We see no evidence for cohesin translocation to surrounding sequences, suggesting that cohesin is removed from centromeres during breathing. Two pools of cohesin can be distinguished. Cohesin loaded before DNA replication, which has established sister chromatid cohesion, disappears during breathing. In contrast, cohesin loaded after DNA replication is partly retained. As sister centromeres re-associate after transient separation, cohesin is reloaded in a manner independent of the canonical cohesin loader Scc2/Scc4. Efficient centromere re-association requires the cohesion establishment factor Eco1, suggesting that re-establishment of sister chromatid cohesion contributes to the dynamic behaviour of centromeres in mitosis. These findings provide new insights into cohesin behaviour at centromeres.
    Keywords DNA replication ; Saccharomyces cerevisiae ; breathing ; centromeres ; chromatids ; chromosome translocation ; cohesion ; mitosis ; mitotic spindle apparatus ; yeasts
    Language English
    Dates of publication 2007-12
    Size p. 531-544.
    Publisher Springer-Verlag
    Publishing place Berlin/Heidelberg
    Document type Article
    ZDB-ID 203083-4
    ISSN 1432-0886 ; 0009-5915
    ISSN (online) 1432-0886
    ISSN 0009-5915
    DOI 10.1007/s00412-007-0118-4
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Rapid movement and transcriptional re-localization of human cohesin on DNA.

    Davidson, Iain F / Goetz, Daniela / Zaczek, Maciej P / Molodtsov, Maxim I / Huis In 't Veld, Pim J / Weissmann, Florian / Litos, Gabriele / Cisneros, David A / Ocampo-Hafalla, Maria / Ladurner, Rene / Uhlmann, Frank / Vaziri, Alipasha / Peters, Jan-Michael

    The EMBO journal

    2016  Volume 35, Issue 24, Page(s) 2671–2685

    Abstract: The spatial organization, correct expression, repair, and segregation of eukaryotic genomes depend on cohesin, ring-shaped protein complexes that are thought to function by entrapping DNA It has been proposed that cohesin is recruited to specific genomic ...

    Abstract The spatial organization, correct expression, repair, and segregation of eukaryotic genomes depend on cohesin, ring-shaped protein complexes that are thought to function by entrapping DNA It has been proposed that cohesin is recruited to specific genomic locations from distal loading sites by an unknown mechanism, which depends on transcription, and it has been speculated that cohesin movements along DNA could create three-dimensional genomic organization by loop extrusion. However, whether cohesin can translocate along DNA is unknown. Here, we used single-molecule imaging to show that cohesin can diffuse rapidly on DNA in a manner consistent with topological entrapment and can pass over some DNA-bound proteins and nucleosomes but is constrained in its movement by transcription and DNA-bound CCCTC-binding factor (CTCF). These results indicate that cohesin can be positioned in the genome by moving along DNA, that transcription can provide directionality to these movements, that CTCF functions as a boundary element for moving cohesin, and they are consistent with the hypothesis that cohesin spatially organizes the genome via loop extrusion.
    MeSH term(s) CCCTC-Binding Factor ; Cell Cycle Proteins/metabolism ; Chromosomal Proteins, Non-Histone/metabolism ; DNA/metabolism ; Humans ; Repressor Proteins/metabolism ; Single Molecule Imaging ; Time Factors ; Transcription, Genetic ; Cohesins
    Chemical Substances CCCTC-Binding Factor ; CTCF protein, human ; Cell Cycle Proteins ; Chromosomal Proteins, Non-Histone ; Repressor Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2016-10-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 586044-1
    ISSN 1460-2075 ; 0261-4189
    ISSN (online) 1460-2075
    ISSN 0261-4189
    DOI 10.15252/embj.201695402
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics.

    Selth, Luke A / Lorch, Yahli / Ocampo-Hafalla, Maria T / Mitter, Richard / Shales, Michael / Krogan, Nevan J / Kornberg, Roger D / Svejstrup, Jesper Q

    Molecular and cellular biology

    2009  Volume 29, Issue 15, Page(s) 4220–4234

    Abstract: The histone chaperone Vps75 forms a complex with, and stimulates the activity of, the histone acetyltransferase Rtt109. However, Vps75 can also be isolated on its own and might therefore possess Rtt109-independent functions. Analysis of epistatic ... ...

    Abstract The histone chaperone Vps75 forms a complex with, and stimulates the activity of, the histone acetyltransferase Rtt109. However, Vps75 can also be isolated on its own and might therefore possess Rtt109-independent functions. Analysis of epistatic miniarray profiles showed that VPS75 genetically interacts with factors involved in transcription regulation whereas RTT109 clusters with genes linked to DNA replication/repair. Additional genetic and biochemical experiments revealed a close relationship between Vps75 and RNA polymerase II. Furthermore, Vps75 is recruited to activated genes in an Rtt109-independent manner, and its genome-wide association with genes correlates with transcription rate. Expression microarray analysis identified a number of genes whose normal expression depends on VPS75. Interestingly, histone H2B dynamics at some of these genes are consistent with a role for Vps75 in histone H2A/H2B eviction/deposition during transcription. Indeed, reconstitution of nucleosome disassembly using the ATP-dependent chromatin remodeler Rsc and Vps75 revealed that these proteins can cooperate to remove H2A/H2B dimers from nucleosomes. These results indicate a role for Vps75 in nucleosome dynamics during transcription, and importantly, this function appears to be largely independent of Rtt109.
    MeSH term(s) Acetylation ; Binding Sites/genetics ; Chromatin Immunoprecipitation ; Cluster Analysis ; Gene Expression Profiling ; Genome, Fungal/genetics ; Histone Acetyltransferases/genetics ; Histone Acetyltransferases/metabolism ; Histones/genetics ; Histones/metabolism ; Lysine/genetics ; Lysine/metabolism ; Molecular Chaperones/genetics ; Molecular Chaperones/metabolism ; Mutation ; Nucleosomes/metabolism ; Oligonucleotide Array Sequence Analysis ; Protein Binding ; RNA Polymerase II/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription, Genetic
    Chemical Substances Histones ; Molecular Chaperones ; Nucleosomes ; Saccharomyces cerevisiae Proteins ; Vps75 protein, S cerevisiae ; Histone Acetyltransferases (EC 2.3.1.48) ; Rtt109 protein, S cerevisiae (EC 2.3.1.48) ; RNA Polymerase II (EC 2.7.7.-) ; RPB1 protein, S cerevisiae (EC 2.7.7.-) ; Lysine (K3Z4F929H6)
    Language English
    Publishing date 2009-05-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 779397-2
    ISSN 1098-5549 ; 0270-7306
    ISSN (online) 1098-5549
    ISSN 0270-7306
    DOI 10.1128/MCB.01882-08
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Targeted deletion of the genes encoding NTH1 and NEIL1 DNA N-glycosylases reveals the existence of novel carcinogenic oxidative damage to DNA.

    Chan, Michael K / Ocampo-Hafalla, Maria T / Vartanian, Vladimir / Jaruga, Pawel / Kirkali, Güldal / Koenig, Karen L / Brown, Stuart / Lloyd, R Stephen / Dizdaroglu, Miral / Teebor, George W

    DNA repair

    2009  Volume 8, Issue 7, Page(s) 786–794

    Abstract: We have generated a strain of mice lacking two DNA N-glycosylases of base excision repair (BER), NTH1 and NEIL1, homologs of bacterial Nth (endonuclease three) and Nei (endonuclease eight). Although these enzymes remove several oxidized bases from DNA, ... ...

    Abstract We have generated a strain of mice lacking two DNA N-glycosylases of base excision repair (BER), NTH1 and NEIL1, homologs of bacterial Nth (endonuclease three) and Nei (endonuclease eight). Although these enzymes remove several oxidized bases from DNA, they do not remove the well-known carcinogenic oxidation product of guanine: 7,8-dihydro-8-oxoguanine (8-OH-Gua), which is removed by another DNA N-glycosylase, OGG1. The Nth1-/-Neil1-/- mice developed pulmonary and hepatocellular tumors in much higher incidence than either of the single knockouts, Nth1-/- and Neil1-/-. The pulmonary tumors contained, exclusively, activating GGT-->GAT transitions in codon 12 of K-ras of their DNA. Such transitions contrast sharply with the activating GGT-->GTT transversions in codon 12 of K-ras of the pathologically similar pulmonary tumors, which arose in mice lacking OGG1 and a second DNA N-glycosylase, MUTY. To characterize the biochemical phenotype of the knockout mice, the content of oxidative DNA base damage was analyzed from three tissues isolated from control, single and double knockout mice. The content of 8-OH-Gua was indistinguishable among all genotypes. In contrast, the content of 4,6-diamino-5-formamidopyrimidine (FapyAde) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua) derived from adenine and guanine, respectively, were increased in some but not all tissues of Neil1-/- and Neil1-/-Nth1-/- mice. The high incidence of tumors in our Nth1-/-Neil1-/- mice together with the nature of the activating mutation in the K-ras gene of their pulmonary tumors, reveal for the first time, the existence of mutagenic and carcinogenic oxidative damage to DNA which is not 8-OH-Gua.
    MeSH term(s) Animals ; Base Sequence ; Brain/metabolism ; Brain/pathology ; DNA Damage ; DNA Glycosylases/genetics ; DNA Glycosylases/metabolism ; DNA Mutational Analysis ; Deoxyribonuclease (Pyrimidine Dimer)/genetics ; Deoxyribonuclease (Pyrimidine Dimer)/metabolism ; Female ; Gas Chromatography-Mass Spectrometry ; Gene Deletion ; Genes, ras/genetics ; Guanine/analogs & derivatives ; Guanine/metabolism ; Kidney/metabolism ; Kidney/pathology ; Liver/metabolism ; Liver/pathology ; Liver Neoplasms/genetics ; Liver Neoplasms/metabolism ; Liver Neoplasms/pathology ; Lung Neoplasms/genetics ; Lung Neoplasms/metabolism ; Lung Neoplasms/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred Strains ; Mice, Knockout ; Mutation ; Oxidation-Reduction ; Pyrimidines/metabolism
    Chemical Substances 7,8-dihydro-8-oxoguanine ; Pyrimidines ; 2,6-diamino-4-hydroxy-5-formamidopyrimidine (133310-38-0) ; 4,6-diamino-5-N-formamidopyrimidine (5122-36-1) ; Guanine (5Z93L87A1R) ; Deoxyribonuclease (Pyrimidine Dimer) (EC 3.1.25.1) ; Nthl1 protein, mouse (EC 3.1.25.1) ; DNA Glycosylases (EC 3.2.2.-) ; Neil1 protein, mouse (EC 3.2.2.-)
    Language English
    Publishing date 2009-04-05
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2009.03.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Repair of thymine glycol by hNth1 and hNeil1 is modulated by base pairing and cis-trans epimerization.

    Ocampo-Hafalla, Maria T / Altamirano, Alvin / Basu, Ashis K / Chan, Michael K / Ocampo, Jose Eliseo A / Cummings, Archie / Boorstein, Robert J / Cunningham, Richard P / Teebor, George W

    DNA repair

    2006  Volume 5, Issue 4, Page(s) 444–454

    Abstract: Oxidation of thymine yields 5,6-dihydroxy-5,6-dihydrothymine (thymine glycol. Tg) which, as cis 5S,6R and 5R,6S 2'-deoxyribonucleoside diastereoisomers (dTg1, dTg2), are in equilibrium with their trans 5S,6S and 5R,6R epimers. The stereoselective ... ...

    Abstract Oxidation of thymine yields 5,6-dihydroxy-5,6-dihydrothymine (thymine glycol. Tg) which, as cis 5S,6R and 5R,6S 2'-deoxyribonucleoside diastereoisomers (dTg1, dTg2), are in equilibrium with their trans 5S,6S and 5R,6R epimers. The stereoselective excision of Tg from DNA by the mammalian orthologs of E. coli DNA N-glycosylase/AP lyases Nth and Nei was reported using substrates in which Tg opposed adenine. Since we showed that Tg is the major product of oxidation of 5-methylcytosine, we asked if the opposing purine influenced stereospecific enzymatic excision. The human ortholog hNth1 released Tg2 much more rapidly than Tg1 regardless of the opposing purine. In contrast, hNeil1 released Tg non-stereoselectively, but the rate of excision was much greater when Tg opposed guanine. Remarkably, the kinetics of excision of Tg by hNth1 and hNeil1 were biphasic, describing a double exponential curve which yielded two rate constants. We suggest that the greater rate constant describes the rate of enzymatic excision of Tg. The smaller rate constant represents the equilibrium constant for the cis and trans epimerization of dTg1 and dTg2 in high molecular weight DNA. Thus, only one of the epimers of dTg1 and dTg2 are enzymatically processed but it is not yet known whether it is cis or trans. Thus, base excision repair of Tg in mammals is mediated by at least two DNA N-glycosylase/AP lyases which are affected by the nature of the diastereoisomer of dTg, the rate of cis-trans epimerization of each diastereoisomer, and the nature of the opposing purine.
    MeSH term(s) Base Pairing ; Catalysis ; DNA Damage ; DNA Glycosylases/metabolism ; DNA Repair ; Deoxyribonuclease (Pyrimidine Dimer)/metabolism ; Deoxyribose/chemical synthesis ; Escherichia coli Proteins/metabolism ; Humans ; Isomerism ; Kinetics ; Oligonucleotides/chemical synthesis ; Purines/metabolism ; Substrate Specificity ; Thymine/analogs & derivatives ; Thymine/chemistry ; Thymine/metabolism
    Chemical Substances Escherichia coli Proteins ; Oligonucleotides ; Purines ; thymine glycol (2943-56-8) ; Deoxyribose (533-67-5) ; Deoxyribonuclease (Pyrimidine Dimer) (EC 3.1.25.1) ; NTH protein, E coli (EC 3.1.25.1) ; NTHL1 protein, human (EC 3.1.25.1) ; DNA Glycosylases (EC 3.2.2.-) ; NEIL1 protein, human (EC 3.2.2.-) ; Thymine (QR26YLT7LT)
    Language English
    Publishing date 2006-04-08
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2005.12.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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