51
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LUKAS D, VIGILANT L. Reply: facts, faeces and setting standards for the study of MHC genes using noninvasive samples. Mol Ecol 2005. [DOI: 10.1111/j.1365-294x.2005.02459.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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52
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Lukas D, Bradley BJ, Nsubuga AM, Doran-Sheehy D, Robbins MM, Vigilant L. Major histocompatibility complex and microsatellite variation in two populations of wild gorillas. Mol Ecol 2005; 13:3389-402. [PMID: 15487998 DOI: 10.1111/j.1365-294x.2004.02353.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In comparison to their close relatives the chimpanzees and humans, very little is known concerning the amount and structure of genetic variation in gorillas. Two species of gorillas are recognized and while the western gorillas number in the tens of thousands, only several hundred representatives of the mountain gorilla subspecies of eastern gorillas survive. To analyse the possible effects of these different population sizes, this study compares the variation observed at microsatellite and major histocompatibility complex (MHC) loci in samples of wild western and mountain gorillas, collected using a sampling scheme that targeted multiple social groups within defined geographical areas. Noninvasive samples proved a viable source of DNA for sequence analysis of the second exon of the DRB loci of the MHC. Observed levels of variation at the MHC locus were similar between the two gorilla species and were comparable to those in other primates. Comparison of results from analysis of variation at multiple microsatellite loci found only a slight reduction in heterozygosity for the mountain gorillas despite the relatively smaller population size.
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Affiliation(s)
- D Lukas
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
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53
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Miller HC, Lambert DM. Genetic drift outweighs balancing selection in shaping post-bottleneck major histocompatibility complex variation in New Zealand robins (Petroicidae). Mol Ecol 2005; 13:3709-21. [PMID: 15548285 DOI: 10.1111/j.1365-294x.2004.02368.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Chatham Island black robin, Petroica traversi, is a highly inbred, endangered passerine with extremely low levels of variation at hypervariable neutral DNA markers. In this study we investigated variation in major histocompatibility complex (MHC) class II genes in both the black robin and its nonendangered relative, the South Island robin Petroica australis australis. Previous studies have shown that Petroica have at least four expressed class II B MHC genes. In this study, the sequences of introns flanking exon 2 of these loci were characterized to design primers for peptide-binding region (PBR) sequence analysis. Intron sequences were comprised of varying numbers of repeated units, with highly conserved regions immediately flanking exon 2. Polymerase chain reaction primers designed to this region amplified three or four sequences per black robin individual, and eight to 14 sequences per South Island robin individual. MHC genes are fitness-related genes thought to be under balancing selection, so they may be more likely to retain variation in bottlenecked populations. To test this, we compared MHC variation in the black robin with artificially bottlenecked populations of South Island robin, and with their respective source populations, using restriction fragment length polymorphism analyses and DNA sequencing of the PBR. Our results indicate that the black robin is monomorphic at class II B MHC loci, while both source and bottlenecked populations of South Island robin have retained moderate levels of variation. Comparison of MHC variation with minisatellite DNA variation indicates that genetic drift outweighs balancing selection in determining MHC diversity in the bottlenecked populations. However, balancing selection appears to influence MHC diversity over evolutionary timescales, and the effects of gene conversion are evident.
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Affiliation(s)
- Hilary C Miller
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Private Bag 102904, Auckland, New Zealand
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54
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Jarvi SI, Tarr CL, McIntosh CE, Atkinson CT, Fleischer RC. Natural selection of the major histocompatibility complex (Mhc) in Hawaiian honeycreepers (Drepanidinae). Mol Ecol 2004; 13:2157-68. [PMID: 15245391 DOI: 10.1111/j.1365-294x.2004.02228.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The native Hawaiian honeycreepers represent a classic example of adaptive radiation and speciation, but currently face one the highest extinction rates in the world. Although multiple factors have likely influenced the fate of Hawaiian birds, the relatively recent introduction of avian malaria is thought to be a major factor limiting honeycreeper distribution and abundance. We have initiated genetic analyses of class II beta chain Mhc genes in four species of honeycreepers using methods that eliminate the possibility of sequencing mosaic variants formed by cloning heteroduplexed polymerase chain reaction products. Phylogenetic analyses group the honeycreeper Mhc sequences into two distinct clusters. Variation within one cluster is high, with dN > dS and levels of diversity similar to other studies of Mhc (B system) genes in birds. The second cluster is nearly invariant and includes sequences from honeycreepers (Fringillidae), a sparrow (Emberizidae) and a blackbird (Emberizidae). This highly conserved cluster appears reminiscent of the independently segregating Rfp-Y system of genes defined in chickens. The notion that balancing selection operates at the Mhc in the honeycreepers is supported by transpecies polymorphism and strikingly high dN/dS ratios at codons putatively involved in peptide interaction. Mitochondrial DNA control region sequences were invariant in the i'iwi, but were highly variable in the 'amakihi. By contrast, levels of variability of class II beta chain Mhc sequence codons that are hypothesized to be directly involved in peptide interactions appear comparable between i'iwi and 'amakihi. In the i'iwi, natural selection may have maintained variation within the Mhc, even in the face of what appears to a genetic bottleneck.
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Affiliation(s)
- Susan I Jarvi
- Molecular Genetics Laboratory, National Zoological Park, Smithsonian Institution, Washington, USA.
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55
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Chow C, Gauci CG, Cowman AF, Lightowlers MW. Echinococcus granulosus: oncosphere-specific transcription of genes encoding a host-protective antigen. Exp Parasitol 2004; 106:183-6. [PMID: 15172227 DOI: 10.1016/j.exppara.2004.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2003] [Revised: 02/20/2004] [Accepted: 03/19/2004] [Indexed: 11/20/2022]
Abstract
A recombinant antigen vaccine has been developed which is effective in preventing the hydatid parasite, Echinococcus granulosus from infecting its animal intermediate hosts. The vaccine antigen, designated EG95, is expressed by a cDNA cloned from E. granulosus oncosphere mRNA. The gene encoding EG95 belongs to a small gene family where six of the members are transcribed in the oncosphere. Conditions were established which allowed specific RT-PCR amplification of mRNA for each gene family member and these conditions were applied to determine transcription patterns for each gene family member in gravid adult worms, oncospheres, and protoscoleces. The four eg95 gene family members which encode an identical EG95 protein, were transcribed only in the oncosphere. In contrast, two gene family members that encode variant EG95 proteins did not have transcription patterns confined to the oncosphere. These findings suggest a common biological role for four genes in the gene family and a separate role for the other, more variant gene family members.
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Affiliation(s)
- Conan Chow
- University of Melbourne, Veterinary Clinical Centre, Princes Highway, Werribee, Vic. 3030, Australia
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56
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Steele EJ, Franklin A, Blanden RV. Genesis of the strand‐biased signature in somatic hypermutation of rearranged immunoglobulin variable genes. Immunol Cell Biol 2004; 82:209-18. [PMID: 15061776 DOI: 10.1046/j.0818-9641.2004.01224.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The history and current development of the reverse transcriptase model of somatic hypermutation (RT-model) is reviewed with particular reference to the genesis of strand-biased mutation signatures in rearranged immunoglobulin variable genes (V(D)J). The recent disagreement in the field as to whether strand bias really exists or not has been critically analysed and the confusion traced to the putative presence, in some mutated V(D)J sequence collections, of polymerase chain reaction (PCR)-recombinant artefacts. Recent analysis of somatic hypermutation in xeroderma pigmentosum variant patients, by the group of PJ Gearhart and others, has established that the Y-family translesion DNA repair enzyme, DNA polymerase eta (eta), is responsible for the striking A-T targeted strand-bias mutation signature seen in all mouse and human collections of somatically mutated V(D)J sequences. This evidence, together with our own recent demonstration that human DNA polymerase eta is a reverse transcriptase, leads to the conclusion that the strand-biased A-T mutation signature is caused either by: (i) error-prone DNA-dependent DNA repair synthesis by pol-eta of single-strand nicks preferentially in the non-transcribed strand; and/or (ii) by error-prone cDNA synthesis of the transcribed strand by pol-eta using the pre-mRNA as the copying template, primed by the nicked transcribed DNA strand, followed by replacement of the original transcribed strand by cDNA. Analysis of the total mutation pattern also suggests that the major transitions observed in SHM (A-->G, C-->T and G-->A) can be explained by known RNA editing mechanisms active on pre-mRNA which are then written into cDNA during synthesis of the transcribed strand by error-prone cellular reverse transcriptases such as pol-eta.
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Affiliation(s)
- Edward J Steele
- Division of Immunology and Genetics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia.
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57
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Thalmann O, Hebler J, Poinar HN, Pääbo S, Vigilant L. Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol Ecol 2004; 13:321-35. [PMID: 14717890 DOI: 10.1046/j.1365-294x.2003.02070.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Analysis of mitochondrial DNA sequence variation has been used extensively to study the evolutionary relationships of individuals and populations, both within and across species. So ubiquitous and easily acquired are mtDNA data that it has been suggested that such data could serve as a taxonomic 'barcode' for an objective species classification scheme. However, there are technical pitfalls associated with the acquisition of mtDNA data. One problem is the presence of translocated pieces of mtDNA in the nuclear genome of many taxa that may be mistaken for authentic organellar mtDNA. We assessed the extent to which such 'numt' sequences may pose an overlooked problem in analyses of mtDNA from humans and apes. Using long-range polymerase chain reaction (PCR), we generated necessarily authentic mtDNA sequences for comparison with sequences obtained using typical methods for a segment of the mtDNA control region in humans, chimpanzees, bonobos, gorillas and orangutans. Results revealed that gorillas are notable for having such a variety of numt sequences bearing high similarity to authentic mtDNA that any analysis of mtDNA using standard approaches is rendered impossible. Studies on humans, chimpanzees, bonobos or orangutans are apparently less problematic. One implication is that explicit measures need to be taken to authenticate mtDNA sequences in newly studied taxa or when any irregularities arise. Furthermore, some taxa may not be amenable to analysis of mtDNA variation at all.
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Affiliation(s)
- O Thalmann
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
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58
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Tomimura K, Gibbs AJ, Jenner CE, Walsh JA, Ohshima K. The phylogeny of Turnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent 'emergence' in east Asia. Mol Ecol 2003; 12:2099-111. [PMID: 12859632 DOI: 10.1046/j.1365-294x.2003.01881.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genomes of a representative world-wide collection of 32 Turnip mosaic virus (TuMV) isolates were sequenced and these, together with six previously reported sequences, were analysed. At least one-fifth of the sequences were recombinant. In phylogenetic analyses, using genomic sequences of Japanese yam mosaic virus as an outgroup, the TuMV sequences that did not show clear recombination formed a monophyletic group with four well-supported lineages. These groupings correlated with differences in pathogenicity and provenance; the sister group to all others was of Eurasian B-strain isolates from nonbrassicas, and probably represents the ancestral TuMV population, and the most recently 'emerged' branch of the population was probably that of the BR-strain isolates found only in east Asia. Eight isolates, all from east Asia, were clear recombinants, probably the progeny of recent recombination events, whereas a similar number, from other parts of the world, were seemingly older recombinants. This difference indicates that the presence of clear recombinants in a subpopulation may be a molecular signature of a recent 'emergence'.
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Affiliation(s)
- K Tomimura
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
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59
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Zylstra P, Franklin A, Hassan KA, Powell KL, Steele EJ, Blanden RV. Molecular evolution of V(H)9 germline genes isolated from DBA, BALB, 129 and C57BL mouse strains and sublines. Immunogenetics 2003; 55:182-188. [PMID: 12733005 DOI: 10.1007/s00251-003-0565-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2002] [Revised: 02/13/2003] [Indexed: 10/26/2022]
Abstract
We have used the polymerase chain reaction (PCR) in an attempt to clone and sequence the exons and hitherto unavailable contiguous flanks of all members of the small V(H) 9 germline gene family from inbred mouse strains and sublines that have had a common ancestry within the last century, and to analyze the molecular evolution of these sequences. Fifteen genuine germline genes were isolated (designated V(H) 9.1 through V(H) 9.15) from strains and sublines of DBA, BALB, 129 and C57BL inbred mice. Of the 15 genuine isolates, nine are novel: seven sequences from DBA strains and sublines ( V(H) 9.3 to V(H) 9.9) and two sequences from C57BL strains ( V(H) 9.13 and V(H) 9.14). We have identified sequencing errors and PCR recombinant artefacts in previously published sequences. We detected no sequence divergence of individual genes shared by the strains and sublines studied. However, we isolated two genes from DBA strains and sublines, V(H) 9.1 and V(H) 9.3, that differ only by five nucleotides encoding three amino acid changes that are concentrated within a 33 nucleotide (11 codon) region. Of these 11 codons, eight encode a putative antigen binding site. There were no differences in the remaining 733 nucleotides sequenced (including both 5' and 3' flanking regions). Potential explanations for the generation of V(H) 9.1 and V(H) 9.3 are discussed.
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Affiliation(s)
- Paula Zylstra
- Department of Biological Sciences, The University of Wollongong, Northfields Avenue, NSW 2522, Wollongong, Australia
- Division of Immunology and Genetics, The John Curtin School of Medical Research, Australian National University, PO Box 334, ACT 2601, Canberra, Australia
| | - Andrew Franklin
- Division of Immunology and Genetics, The John Curtin School of Medical Research, Australian National University, PO Box 334, ACT 2601, Canberra, Australia
| | - Karl A Hassan
- Department of Biological Sciences, The University of Wollongong, Northfields Avenue, NSW 2522, Wollongong, Australia
| | - Kim L Powell
- Division of Immunology and Genetics, The John Curtin School of Medical Research, Australian National University, PO Box 334, ACT 2601, Canberra, Australia
| | - Edward J Steele
- Department of Biological Sciences, The University of Wollongong, Northfields Avenue, NSW 2522, Wollongong, Australia
- Division of Immunology and Genetics, The John Curtin School of Medical Research, Australian National University, PO Box 334, ACT 2601, Canberra, Australia
| | - Robert V Blanden
- Division of Immunology and Genetics, The John Curtin School of Medical Research, Australian National University, PO Box 334, ACT 2601, Canberra, Australia.
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60
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Jiggins FM. Male-killing Wolbachia and mitochondrial DNA: selective sweeps, hybrid introgression and parasite population dynamics. Genetics 2003; 164:5-12. [PMID: 12750316 PMCID: PMC1462540 DOI: 10.1093/genetics/164.1.5] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) sequences are widely used as neutral genetic markers in insects. However, patterns of mtDNA variability are confounded by the spread of maternally transmitted parasites, which are genetically linked to the mitochondria. We have investigated these effects in the butterflies Acraea encedon (which is host to two strains of male-killing Wolbachia bacteria) and A. encedana (which is host to one strain). Within a population, the mitochondria are in linkage disequilibrium with the different male-killers. Furthermore, there has been a recent selective sweep of the mtDNA, which has led to the loss of mitochondrial variation within populations and erased any geographical structure. We also found that one of the male-killers, together with the associated mtDNA, has introgressed from A. encedana into A. encedon within the last 16,000 years. Interestingly, because butterflies are female heterogametic, this will presumably have also led to the introgression of genes on the W sex chromosome. Finally, in A. encedon the mitochondria in uninfected females are unaltered by the spread of the male-killer and have diverse, geographically structured mtDNA. This means we can reject the hypothesis that the male-killer is at a stable equilibrium maintained by imperfect transmission of the bacterium. Instead, some other form of balancing selection may be maintaining uninfected females in the population and preventing the species from going extinct due to a shortage of males.
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Affiliation(s)
- Francis M Jiggins
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom.
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61
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Whinnett A, Mundy NI. Isolation of novel olfactory receptor genes in marmosets (Callithrix): insights into pseudogene formation and evidence for functional degeneracy in non-human primates. Gene 2003; 304:87-96. [PMID: 12568718 DOI: 10.1016/s0378-1119(02)01182-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Nineteen olfactory receptor (OR) genes were isolated from three OR subfamilies in two species of marmoset (Callithrix). Olfactory receptor 912-93 has high sequence similarity among marmosets and between marmosets and humans, suggesting strong conservation of function. All of the remaining seventeen OR genes identified from subfamilies 3A and 1E were pseudogenes. Following pseudogene formation, marmoset OR genes in both 1E and 3A subfamilies underwent duplications, indel events and a high rate of nucleotide substitution. These results provide a contrast to previous studies, and show that in spite of the keen olfactory sense of marmosets, they harbour many OR pseudogenes. A high rate of in vitro recombination using Pfu polymerase but not Taq polymerase was confirmed. The rapid molecular evolution of OR pseudogenes suggests that they do not provide a useful source of sequence variation for conversion to intact OR genes over evolutionary timescales. The overall pattern of OR evolution in marmosets is comparable to the 'birth-and-death' model of gene family evolution. An unbiased view on the evolutionary timing of the reduction of the functional olfactory repertoire in humans must await more data.
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Affiliation(s)
- Alaine Whinnett
- Department of Biological Anthropology, University of Oxford, Oxford, UK
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62
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Longeri M, Zanotti M, Damiani G. Recombinant DRB sequences produced by mismatch repair of heteroduplexes during cloning in Escherichia coli. EUROPEAN JOURNAL OF IMMUNOGENETICS : OFFICIAL JOURNAL OF THE BRITISH SOCIETY FOR HISTOCOMPATIBILITY AND IMMUNOGENETICS 2002; 29:517-23. [PMID: 12437611 DOI: 10.1046/j.1365-2370.2002.00356.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recombinant chimeric sequences originating from a mixture of the sequences of two different alleles are frequently found after amplification and cloning in Escherichia coli of exon 2 of the major histocompatibility complex (MHC) DRB genes. Several authors have suggested that the recombinant molecules result from in vitro recombination during PCR; nevertheless, a clear experimental demonstration of this hypothesis is lacking. In order to understand the mechanism producing the chimeric sequences, we set up a simple experiment based on the different restriction patterns of parental and recombinant sequences. Our data demonstrate that in the analysed case most of the recombinant variants were not produced by in vitro recombination during PCR, but were the result of the mismatch repair of heteroduplex molecules during cloning in E. coli. The high mutation rate in the alpha-helix region of DRB expressed genes, both after cloning in E. coli and after the germ-line differentiation process in vertebrates, suggests that the observed mutations are the result of similar gene conversion processes, probably favoured by chi-dependent microrecombination events.
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Affiliation(s)
- M Longeri
- Istituto di Zootecnica, Faculty of Veterinary Medicine, University of Milan, Italy.
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63
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Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, Tan Z, Sano T, Azuhata F, Walsh JA, Fletcher J, Chen J, Gera A, Gibbs A. Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 2002; 83:1511-1521. [PMID: 12029167 DOI: 10.1099/0022-1317-83-6-1511] [Citation(s) in RCA: 187] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Turnip mosaic virus (TuMV), a species of the genus Potyvirus, occurs worldwide. Seventy-six isolates of TuMV were collected from around the world, mostly from Brassica and Raphanus crops, but also from several non-brassica species. Host tests grouped the isolates into one or other of two pathotypes; Brassica (B) and Brassica-Raphanus (BR). The nucleotide sequences of the first protein (P1) and coat protein (CP) genes of the isolates were determined. One-tenth of the isolates were found to have anomalous and variable phylogenetic relationships as a result of recombination. The 5'-terminal 300 nt of the P1 gene of many isolates was also variable and phylogenetically anomalous, whereas the 380 nt 3' terminus of the CP gene was mostly conserved. Trees calculated from the remaining informative parts of the two genes of the non-recombinant sequences by neighbour-joining, maximum-likelihood and maximum-parsimony methods were closely similar, and so these parts of the sequences were concatenated and trees calculated from the resulting 1150 nt. The isolates fell into four consistent groups; only the relationships of these groups with one another and with the outgroup differed. The "basal-B" cluster of eight B-pathotype isolates was most variable, was not monophyletic, and came from both brassicas and non-brassicas from southwest and central Eurasia. Closest to it, and forming a monophyletic subgroup of it in most trees, and similarly variable, was the "basal-BR" group of eight BR pathotype Eurasian isolates. The third and least variable group, the "Asian-BR" group, was of 22 BR-pathotype isolates, all from brassicas, mostly Raphanus, and all from east Asia mostly Japan. The fourth group of 36 isolates, the "world-B" group, was from all continents, most were isolated from brassicas and most were of the B-pathotype. The simplest of several possible interpretations of the trees is that TuMV originated, like its brassica hosts, in Europe and spread to the other parts of the world, and that the BR pathotype has recently evolved in east Asia.
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Affiliation(s)
- Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1
| | - Yuka Yamaguchi
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1
| | - Ryo Hirota
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1
| | - Tamaki Hamamoto
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1
| | - Kenta Tomimura
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1
| | - Zhongyang Tan
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1
| | - Teruo Sano
- Laboratory of Plant Pathology, Faculty of Agriculture & Life Sciences, Hirosaki University, Hirosaki 036-8561, Japan2
| | | | - John A Walsh
- Plant Pathology & Microbiology Department, Horticulture Research International, Wellesbourne, Warwick CV35 9EF, UK4
| | - John Fletcher
- Crop & Food Research, Private Bag 4704, Christchurch, New Zealand5
| | - Jishuang Chen
- Faculty of Life Science, Zhenjiang University, Hangzhou 310029, PR China6
| | - Abed Gera
- Department of Virology, Agriculture Research Organization, The Volcani Centre, Bet Dagan 50250, Israel7
| | - Adrian Gibbs
- Faculty of Science, Australian National University, Canberra, ACT 2601, Australia8
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64
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Abstract
DNA-based sex tests now exist for many avian species. However, none of these tests are widely applicable to ratites. We present DNA sequence data for a locus that is W chromosome-linked in the kiwi, ostrich, cassowary, rhea, and emu. At the amino acid level, this sequence has significant homology to X-linked genes in platyfish and Caenorhabditis elegans. Polymerase chain reaction (PCR) primers designed to this locus allow the assignment of sex in all species of living ratites.
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Affiliation(s)
- Leon Huynen
- Institute of Molecular BioSciences and Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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65
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Goossens T, Bräuninger A, Klein U, Küppers R, Rajewsky K. Receptor revision plays no major role in shaping the receptor repertoire of human memory B cells after the onset of somatic hypermutation. Eur J Immunol 2001; 31:3638-48. [PMID: 11745384 DOI: 10.1002/1521-4141(200112)31:12<3638::aid-immu3638>3.0.co;2-g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In order to determine whether V gene replacement accompanies somatic hypermutation in the germinal center (GC) reaction in the human, we analyzed V(kappa)J(kappa) and V(lambda)J(lambda) joints and the kappa-deleting element in single lambda(+) naive and post GC B cells for rearrangements at the kappa and lambda loci. Among 265 lambda(+) post GC B cells, not a single unequivocal and only two potential examples of a cell that switched to lambda light chain expression after accumulation of (unfavorable) mutations in its productive V(kappa) rearrangement were observed. Taking the PCR efficiency into account, the frequency of such cells is likely below 3 %. In addition, heavy and light chain gene rearrangements were amplified and sequenced from the oligoclonal population of IgD-only peripheral blood post GC B cells which display extensive intraclonal sequence diversity. Among 61 IgD-only B cells belonging to 15 clones with intraclonal diversity, no combination of V gene rearrangements indicating receptor revision during clonal expansion was observed. Moreover, among 124 and 49 V(H) genes amplified from IgD-only and class-switched B cells, respectively, not a single example of V(H) revision through V(H) hybrid generation was detected. These results suggest that in the human GC reaction V gene replacement either does not usually accompany somatic hypermutation or is mostly counterselected.
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Affiliation(s)
- T Goossens
- Institute for Genetics, University of Cologne, Cologne, Germany
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66
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Zhou H, Hickford JG. Novel fimbrial subunit genes of Dichelobacter nodosus: recombination in vivo or in vitro? Vet Microbiol 2000; 76:163-74. [PMID: 10946146 DOI: 10.1016/s0378-1135(00)00233-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Polymerase chain reaction (PCR) was used to amplify the variable region of the fimbrial subunit encoding gene (fimA) of Dichelobacter nodosus from sheep and goats infected with footrot. Two amplimers (designated X and Y) generated single-strand conformation polymorphism (SSCP) patterns different to those of previously identified serogroups and serotypes. DNA sequencing revealed that these two fragments were novel. The upstream of X (nt 1-183) was identical to serotype M1 while its downstream (nt 223-414) was identical to serotype F1; the upstream of Y (nt 1-116) was identical to serotype E1, whereas its downstream (nt 148-423) was identical to serotype F1. A 14-mer sequence consisting of two partially overlapping Chi-like sequences, 5'-GCTGGTGCTGGTGA-3', was also found in these fragments. Two primer sets with the downstream primer specific for serotype F1 and the upstream primer specific for serotype M or E1, generated PCR products of the expected sizes from the footrot samples from which fragments X and Y were isolated, respectively. These primer sets did not appear to amplify artificially mixed genomic DNA from serotypes M and F1 or E1 and F1. However, when the reactions were re-amplified, PCR recombination artifacts were observed, suggesting that PCR recombination does occur, but at a low frequency. It, therefore, seems more likely that fragments X and Y reflect genuine fimA genes of D. nodosus which have resulted from in vivo DNA recombination rather than from a PCR recombination artifact.
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Affiliation(s)
- H Zhou
- Animal & Food Sciences Division, P.O. Box 84, Lincoln University, Canterbury, Lincoln, New Zealand
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McClure P, Curran R, Boneham S, Ball JK. A polymerase chain reaction method for the amplification of full-length envelope genes of HIV-1 from DNA samples containing single molecules of HIV-1 provirus. J Virol Methods 2000; 88:73-80. [PMID: 10921844 DOI: 10.1016/s0166-0934(00)00179-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Polymerase chain reaction (PCR) amplification of full-length envelope genes from the human immunodeficiency virus type 1 (HIV-1) directly from uncultured clinical samples is difficult. This paper describes a comparative assessment of the performance of three thermostable polymerases in an HIV-1 full-length envelope gene PCR. The PCR method utilising Expand HiFi polymerase was successful when using DNA samples extracted from a variety of sources including blood, semen and various tissues. This method generated high and specific yields of product from samples containing as little as one copy of HIV-1 proviral DNA. The resulting PCR products were suitable for a variety of downstream analytical methods including DNA sequence analysis.
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Affiliation(s)
- P McClure
- Division of Microbiology and Infectious Diseases, University of Nottingham, Queen's Medical Centre, UK
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Mihara M, Tan I, Chuzhin Y, Reddy B, Budhai L, Holzer A, Gu Y, Davidson A. CTLA4Ig inhibits T cell-dependent B-cell maturation in murine systemic lupus erythematosus. J Clin Invest 2000; 106:91-101. [PMID: 10880052 PMCID: PMC314360 DOI: 10.1172/jci9244] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Long-term administration of CTLA4Ig prevents the onset of disease in systemic lupus erythematosus-prone (SLE-prone) NZB/NZW F1 mice. To determine the mechanism of this effect, we engineered an adenovirus that expresses murine CTLA4Ig. Administration of a single high dose of this virus results in long-term expression of CTLA4Ig in the serum and absence of an immune response to the adenoviral vector. We administered Ad-CTLA4Ig to 19- to 22-week-old NZB/NZW F1 mice and evaluated the effect on anti-DNA antibody-producing B cells. We show that CTLA4Ig has a beneficial effect on murine SLE for as long as it is present in the serum. This effect is associated with decreased expansion of both the IgM and IgG autoreactive B-cell population, inhibition of immunoglobulin class switching, decreased frequency and altered pattern of somatic mutation, and a marked decrease in the numbers of activated CD4-positive T cells. In contrast, intrinsic B-cell hyperreactivity and the survival of plasma cells in the bone marrow, both of which are less dependent on T-cell help, appear to be unaffected by CTLA4Ig. High-dose CTLA4Ig did not induce permanent tolerance in this autoimmune disease model. Furthermore, although the mice survived in a conventional housing facility, treatment with Ad-CTLA4Ig was immunosuppressive.
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Affiliation(s)
- M Mihara
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
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