ALBERT — All Library Books, journals and Electronic Records Telegrafenberg

1

Electronic Resource

Isolation of Mhc Class II DMA and DMB cDNA Sequences in a Marsupial: The Gray Short-Tailed Opossum (Monodelphis domestica) (1998)

O'hUigin, Colm ; Sültmann, Holger ; Tichy, Herbert ; [et al.]

Springer

Journal of molecular evolution 47 (1998), S. 578-585

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ISSN: 1432-1432

Keywords: Key words:Mhc class II —DM— Marsupials — Opossum

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract. We report the cDNA sequences for the DMA and DMB family of Mhc genes of the gray short-tailed opossum. Until now DM sequences were available only in eutherian mammals. The marsupial sequences indicate that both members of the family are old and probably diverged from other classical class II families about the time of the radiation of jawed vertebrates some 450 million years ago. We examine the evolutionary rates of equivalent sets of classical and nonclassical genes to check for rate heterogeneity. We find the α-1 domain of the DR genes to be untypically conservative in its evolutionary mode. The DM genes appear to evolve at rates typical of other class II genes, indicating that their placement at the root of class II gene evolutionary trees may be justified.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/PL00006414

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2

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Class I Mhc genes of cichlid fishes: identification, expression, and polymorphism (1997)

Sato, Akie ; Klein, Dagmar ; Sültmann, Holger ; [et al.]

Springer

Immunogenetics 46 (1997), S. 63-72

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ISSN: 1432-1211

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Notes: Abstract Cichlid fishes of the East African Rift Valley lakes constitute an important model of adaptive radiation. Explosive speciation in the Great Lakes, in some cases as recently as 12 400 years ago, generated large species flocks that have been the focus of evolutionary studies for some time. The studies have, however, been hampered by the paucity of biochemical markers for phylogenetic reconstruction. Here, we describe a set of markers which should help to alleviate this problem. They are the class I genes of the major histocompatibility complex. We provide evidence for the existence of at least 17 class I loci in cichlid fishes, and for extensive polymorphism of three of these loci. Since the polymorphism has a trans-species character, it will be possible to use it in investigating the founding events of the individual species. The sequences of the cichlid class I fishes support the monophyly of actinopterygian fish on the one hand, and of tetrapods on the other.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002510050243

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3

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Mhc class I gene of African lungfish (2000)

Sato, A. ; Sültmann, Holger ; Mayer, Werner E. ; [et al.]

Springer

Immunogenetics 51 (2000), S. 491-495

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ISSN: 1432-1211

Keywords: Key words Major histocompatibility complex ; Protopterus aethiopicus ; Fish Mhc ; Tetrapod ancestry

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002510050649

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4

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Mhc class II B gene evolution in East African cichlid fishes (2000)

Figueroa, F. ; Mayer, Werner E. ; Sültmann, Holger ; [et al.]

Springer

Immunogenetics 51 (2000), S. 556-575

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ISSN: 1432-1211

Keywords: Key words Major histocompatibility complex ; Haplochromines ; Convergent evolution ; Gene conversion ; Oreochromis

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Notes: Abstract A distinctive feature of essential major histocompatibility complex (Mhc) loci is their polymorphism characterized by large genetic distances between alleles and long persistence times of allelic lineages. Since the lineages often span several successive speciations, we investigated the behavior of the Mhc alleles during or close to the speciation phase. We sequenced exon 2 of the class II B locus 4 from 232 East African cichlid fishes representing 32 related species. The divergence times of the (sub)species ranged from 6000 to 8.4 million years. Two types of evolutionary analysis were used to elucidate the pattern of exon 2 sequence divergence. First, phylogenetic methods were applied to reconstruct the most likely evolutionary pathways leading from the last common ancestor of the set to the extant sequences, and to assess the probable mechanisms involved in allelic diversification. Second, pairwise comparisons of sequences were carried out to detect differences seemingly incompatible with origin by nonparallel point mutations. The analysis revealed point mutations to be the most important mechanism behind allelic divergences, with recombination playing only an auxiliary part. Comparison of sequences from related species revealed evidence of random allelic (lineage) losses apparently associated with speciation. Sharing of identical alleles could be demonstrated between species that diverged 2 million years ago. The phylogeny of the exon was incongruent with that of the flanking introns, indicating either a high degree of convergent evolution at the peptide-binding region-encoding sites, or intron homogenization.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002510000181

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5

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Major histocompatibility complex class II A genes in cichlid fishes: identification, expression, linkage relationships, and haplotype variation (2000)

Murray, Brent W. ; Shintani, Seikou ; Sültmann, Holger ; [et al.]

Springer

Immunogenetics 51 (2000), S. 576-586

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ISSN: 1432-1211

Keywords: Key words Mhc ; Oreochromis ; Tilapia ; Haplochromis ; Cichlidae

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Notes: Abstract Two cichlid species, the haplochromine Aulonocara hansbaenschi and the tilapiine Oreochromis niloticus, were used to study the major histocompatibility complex (Mhc) class II A variation within this group. Multiple class II A sequences were recovered from A. hansbaenschi and O. niloticus cDNA libraries and three sequence families, DAA, DBA, and DCA, were identified. Sets of O. niloticus haploid embryo families were used to determine the linkage relationships of these genes. Two independently assorting linkage groups were detected, DAA and DBA/DCA, neither of which is linked to the previously described Mhc class I gene cluster. Three DCA genes and up to four DBA genes were found to segregate in different haplotypes, whereas DAA occurred as a single locus. Four DBA haplotypes, DBA*H1-H4, were identified and shown to co-segregate with the previously described class II B haplotypes. Four DCA haplotypes, DCA*H1-H4, were found at a distance of 37 cM from the DBA/class II B cluster; in one DCA haplotype, DCA*H5, the genes were tightly linked to the DBA/class II B clusters. Transcripts of DAA and DBA genes were found in O. niloticus hepatopancreas and spleen; transcripts of DCA genes were detected in the A. hansbaenschi cDNA library, but not in O. niloticus. These findings provide a basis for using class II haplotypes as markers in the study of adaptive radiation in the cichlid species flocks of the East African Great Lakes.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002510000177

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6

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Zebrafish Mhc class II α chain-encoding genes: polymorphism, expression, and function (1993)

Sültmann, Holger ; Mayer, Werner E. ; Figueroa, Felipe ; [et al.]

Springer

Immunogenetics 38 (1993), S. 408-420

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ISSN: 1432-1211

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Notes: Abstract Its small size and short generation time renders the zebrafish (Brachydanio rerio) an ideal vertebrate for immunological research involving large populations. A prerequisite for this is the identification of the molecules critical for an immune response in this species. In earlier studies, we cloned the zebrafish genes coding for the β chains of the class I and class II major histocompatibility complex (MHc) molecules. Here. we describe the cloning of the zebrafish α chain-encoding class II gene, which represents the first identification of a class II A gene in teleost fishes. The gene, which is less than 3 kilobases (kb) distant from one of the β chain-encoding genes, is approximately 1.2 kb long and consist of four exons interrupted by very short (〈200 base pairs) introns. Its organization is similar to that of the mammalian class II A genes, but its sequence differs greatly from the sequence of the latter (36% sequence similarity). Among the most conserved parts is the promoter region, which contains X, Y, and TATA boxes with high sequence similarity to the corresponding mammalian boxes. The observed striking conservation of the promoter region suggests that the regulatory system of the class II genes was established more than 400 million years ago and has, principally, remained the same ever since. Like the DMA, but unlike all other mammalian class II A genes, the zebrafish gene codes for two cysteine residues which might potentially be involved in the formation of a disulfide bond in the α1 domain. The primary transcript of the gene is 1196 nucleotides long and contains 708 bucleotides of coding sequence. The gene is expressed in tissues with a high content of lymphoid/myeloid cells (spleen, pronephros, hepatopancreas, and intestine). The analyzed genomic and cDNA sequences are probably derived from different loci (their overall sequence similarity in the coding region is 73% and their 3′ untranslated regions are highly divergent form each other). The genes are apparently functional. Comparison of genes from different zebrafish populations reveals high exon 2 variability concentrated in positions coding for the putative peptide-binding region. Phylogenetic analysis suggests that the zebrafish class II A genes stem form a different ancestor than the mammalian class II A genes and the recently cloned shark class II gene.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00184521

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7

Electronic Resource

New family of Mhc class II A genes identified from cDNA sequences in the cichlid fish Aulonocara hansbaenschi (1999)

Murray, Brent W. ; Sültmann, Holger ; Klein, J.

Springer

Immunogenetics 49 (1999), S. 544-548

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ISSN: 1432-1211

Keywords: Key words Mhc ; Class II A ; Cichlid ; Fish ; Evolution

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002510050533

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8

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Parameter estimation for the calibration and variance stabilization of microarray data (2003)

Huber, Wolfgang ; von Heydebreck, Anja ; Sueltmann, Holger ; [et al.]

Berkeley, Calif. : Berkeley Electronic Press (now: De Gruyter)

Statistical applications in genetics and molecular biology 2.2003, 1, art3

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ISSN: 1544-6115

Source: Berkeley Electronic Press Academic Journals

Topics: Biology

Notes: We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances of the transformed intensities become approximately independent of their expected values. The transformation is similar to the logarithm in the high intensity range, but has a smaller slope for intensities close to zero. Applications have shown better sensitivity and specificity for the detection of differentially expressed genes. In this paper, we describe the theoretical aspects of the method. We incorporate calibration and variance-mean dependence into a statistical model and use a robust variant of the maximum-likelihood method to estimate the transformation parameters. Using simulations, we investigate the size of the estimation error and its dependence on sample size and the presence of outliers. We find that the error decreases with the square root of the number of probes per array and that the estimation is robust against the presence of differentially expressed genes. Software is publicly available as an R package through the Bioconductor project (http://www.bioconductor.org).

Type of Medium: Electronic Resource

URL: http://www.bepress.com/sagmb/vol2/iss1/art3

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9

Electronic Resource

Linkage Relationships and Haplotype Variation of the Major Histocompatibility Complex Class I A Genes in the Cichlid Fish Oreochromis niloticus (2000)

Murray, Brent W. ; Nilsson, Philomeen ; Zaleska-Rutczynska, Zofia ; [et al.]

Springer

Marine biotechnology 2 (2000), S. 437-448

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ISSN: 1436-2236

Keywords: Key words: major histocompatibility complex, class I haplotypes, tilapia, cichlid, Oreochromis.

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology

Notes: Abstract: The haplochromine cichlid species flocks of the East African Great Lakes are one of the best examples of adaptive radiation. Analysis of genetic variation among these species provides valuable information on species relationships and timing of speciation events. Although the haplochromine cichlids generally display little genetic variation, the major histocompatibility complex (Mhc) genes have been found to be highly variable. A study of the linkage relationships of the Mhc class I A genes in the cichlid fish Oreochromis niloticus was therefore undertaken. Class I loci were identified, and their segregation in seven mothers and their haploid embryos was determined. In total, 56 class I A sequences were found among the seven families. A strong concordance of segregation was observed in five haplotypes among the embryos, indicating a close linkage of all loci. The number of loci per haplotype varied from 11 to 17, while the total number of distinct loci found among all families was 22. These findings show that all class I A loci are linked in a single genetic cluster in O. niloticus.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s101260000000

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