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PubMedDate not supplied

Restriction analysis of the MD infectious bursal disease virus strain.

The variant MD strain of infectious bursal disease virus (IBDV) was examined using restriction fragment length polymorphism (RFLP) and the molecular variation was compared with published sequences of both variant and classic IBDV strains. Viral RNA was transcribed into cDNA using reverse transcriptase and then amplified by the polymerase chain reaction (PCR). Three separate but overlapping fragments of 1603 bp, 1496 bp, and 1066 bp containing the entire coding region for VP2, VP4, and VP3, respectively, were amplified. These amplified products were initially cloned using the TA Cloning kit and further subcloned into the pGEM-3Zf and pUC19. Eight restriction enzymes, PstI, BamHI, AvaI, EcoRI, HindII, XmaI, SmaI, and XbaI, were tested for their ability to digest the MD PCR products. The resulting RFLP was analyzed and compared with the published genome segment A sequences of the classic IBDV strain STC and the variant IBDV strain GLS. Differences in restriction fragment profiles were observed after digestion with BamHI, EcoRI, XmaI, and SmaI, with the absence of the EcoRI site in both variant strains, GLS and MD. The MD PCR products lacked both XmaI and SmaI sites, which were present in both STC and GLS. The MD PCR products contained a BamHI site within the hypervariable region of VP2, which is present in STC but not in the variant GLS. An additional BamHI site was identified in the VP4 gene of MD and GLS but not in STC.

Animals↗
PubMed2006

Detailed analysis of the E2-IgM complex in hepatitis C-related type II mixed cryoglobulinaemia.

Hepatitis C virus (HCV) plays a major role in the induction of type II mixed cryoglobulinaemia (MCII). The role of HCV proteins and virus-host interaction in the pathogenesis of MC remains to be defined. To address this issue, we have characterized, in detail, the monoclonal IgM and the viral component of circulating immune complexes in eight patients with HCV-associated MCII. The proportion of HCV-RNA compartmentalized in the cryoprecipitate (CP) varied greatly (10-80% of total HCV-RNA). The complementary determining region (CDR)3 sequences of monoclonal immunoglobulin M (IgM) VH and VK genes were highly homologous to rheumatoid factor and to antibodies against HCV-E2. Furthermore, the CDR3 sequences in some of our MCII patients were highly similar to those described in HCV-positive patients with non-Hodgkin's lymphoma (NHL). From these results, it appears that, as in the case of NHL, the IgM-rheumatoid factor (RF) production in MCII patients is antigen driven, namely by E2. However, the limited number of mutations in VH and VK genes with respect to the germline and their distribution showed that the B-cell response in these cases was prevented from undergoing affinity maturation. Furthermore, in patients with monoclonal IgM and definite compartmentalization of HCV in either CP or supernatant, a highly homogeneous E2-hypervariable region (HVR)1 sequence distribution was found (90-100% identical clones), a feature of the quasispecies frequently associated with an impaired humoral immune response to HCV. These findings suggest that in patients with HCV-associated MCII, maturation of monoclonal B lymphocytes may be blocked in a primitive stage preventing serious damaging effects because of the auto-reactivity of their secreted immunoglobulins.

Aged↗
PubMed2006

Sarcomas and myelocytomas induced by a retrovirus related to myeloblastosis-associated virus type 1 in White Leghorn egg layer chickens.

An outbreak of subcutaneous sarcomas in commercial White Leghorn egg layers was observed in the northeastern United States during late 2004. Subcutaneous tumors were confined to three flocks distributed in two locations and belonging to the same company. The tumors were first observed grossly by farm personnel at approximately 7 wk of age and persisted throughout the economic life of the flocks. Most of the tumors observed during the growing period were present on the facial region or around the head, wings, and legs. There was no gross evidence of bursal or visceral involvement. Microscopically, most tumors were undifferentiated sarcomas and myxomas. There was no microscopic evidence of Marek's disease or lymphoid leukosis. Reticuloendotheliosis virus proviral DNA was not detected by polymerase chain reaction either in tumors or in cell cultures. Egg production and mortality rates were within normal limits in the affected flocks and many of the chickens exhibiting tumors seemed healthy otherwise, albeit approximately one-half of the daily mortality exhibited tumors. Avian myeloblastosis-associated virus type 1 (MAV-1) was isolated from tumors, plasma, and serum. Upon initial virus neutralization, the viruses isolated seemed at least partially related antigenically to avian leukosis virus (ALV) subgroups A and B but not to subgroup J (ALV-J). Sequencing of the variable and hypervariable regions of gp85 in the envelope gene revealed that the viruses involved are closely related to MAV-1. Attempts to reproduce subcutaneous sarcomas with MAV-1 isolated from White Leghorn chickens in the case herein reported produced exclusively myelocytomas indistinguishable histologically from those induced by ALV-J in meat type chickens.

Animals↗
PubMed1985

Complete primary structure of the human alpha 2 type V procollagen COOH-terminal propeptide.

Recently we presented the partial covalent structure of a type V collagen chain. Analysis of amino acids 796-1020 in the human alpha 2(V) Gly-X-Y region showed strong conservation of charged positions with the interstitial collagens but also revealed substitutions unique to type V. To gain more information about this procollagen and primarily to resolve the ambiguous nature of the 3' noncollagenous propeptide, we sequenced several cDNA clones coding for amino acids adjacent to the carboxyl end of the alpha chain. Here we report the complete primary structure of the alpha 2(V) COOH-terminal propeptide. In general, the latter sequence (270 residues) bears a greater degree of similarity to those of the interstitial rather than the basement membrane procollagens. Compared to the interstitial procollagens, however, more divergence has occurred in alpha 2(V) surrounding the conserved N-asparaginyl-linked carbohydrate attachment site at residues 171-173, and alpha 2(V) possesses an additional potential glycosylation site (Asn-Lys-Thr) located in a hypervariable region near the NH2 terminus. Although certainly premature to form any rigid hypothesis, a pattern emerges that may be characteristic of alpha 2 versus alpha 1 chains. Both the alpha 2(I) and alpha 2(V) telopeptides are devoid of a lysine, which in alpha 1 chains forms an interchain cross-link with residue 87 of the collagenous region. Also in contrast to the interstitial alpha 1 carboxyl propeptides is the absence in alpha 2(I) and alpha 2(V) of a cysteine that probably participates in an interchain disulfide bond. Therefore, one can speculate that those alpha 2 chains, represented only once in procollagen trimers, may not be under the same selective pressure as alpha 1 chains to maintain certain residues responsible for stabilizing the triple helical molecules.

Amino Acid Sequence↗
PubMed1999

Dynamic analysis of hepatitis C virus replication and quasispecies selection in long-term cultures of adult human hepatocytes infected in vitro.

Primary human hepatocytes were used to develop a culture model for in vitro propagation of hepatitis C virus (HCV). Production of positive- strand full-length viral RNA in cells and culture supernatants was monitored by PCR methods targeting three regions of the viral genome: the 5' NCR, the 3' X-tail and the envelope glycoprotein E2. De novo synthesis of negative-strand RNA was also demonstrated. Evidence for a gradual increase in viral components over a 3 month period was obtained by two quantitative assays: one for evaluation of genomic titre (quantitative PCR) and one for detection of the core antigen. Production of infectious viral particles was indicated by passage of infection to naive hepatocyte cultures. Reproducibility of the experiments was assessed using cultures from three liver donors and eleven sera. Neither the genotype, nor the genomic titre, nor the anti-HCV antibody content, were reliable predictive factors of serum infectivity, while the liver donor appeared to play a role in the establishment of HCV replication. Quasispecies present in hepatocyte cultures established from three different liver donors were analysed by sequencing hypervariable region 1 of the E2 protein. In all three cases, the complexity of viral quasispecies decreased after in vitro infection, but the major sequences recovered were different. These data strongly suggest that human primary hepatocytes are a valuable model for study of persistent and complete HCV replication in vitro and for identification of the factors (viral and/or cellular) associated with successful infection.

Adult↗
PubMed1989

Variable region primary structures of a high affinity anti-fluorescein immunoglobulin M cryoglobulin exhibiting oxazolone cross-reactivity.

Previous studies of murine IgM hybridoma protein 18-2-3, derived from an (NZB/NZW)F1 mouse following hyperimmunization with fluorescein (Fl)-conjugated keyhole limpet hemocyanin, demonstrated a high affinity for Fl (Ka = 2.9 x 10(10) M-1) and cryoprecipitation that was abrogated upon Fl binding to the antibody-combining site. V region sequences of 18-2-3 were determined by Edman degradation and nucleotide sequence analysis. The VH region of 18-2-3 was encoded by a gene VHI(B) of the Q52 VH family with 96% homology to anti-oxazolone antibody NQ7.5.3 but utilized a larger D region (DQ52 plus N region). The V kappa region of 18-2-3 was encoded by a gene V kappa IV with an amino acid sequence 97% homologous to that of anti-oxazolone antibody NQ11.1.18. Although monoclonal anti-Fl antibodies 18-2-3 and 4-4-20 possessed similar binding affinities and quenched bound fluorescein to the same extent (Qmax greater than 96%), they utilized different VH, D, V kappa, and J kappa genes, but the same JH gene segment (JH4). Solid-phase analyses showed that 18-2-3 was not idiotypically related to 4-4-20 and 9-40, prototypic anti-Fl antibodies. Fine specificity binding patterns of Fl analogues by 18-2-3 IgM and IgMs were distinct from other anti-Fl antibodies. Monoclonal antibody 18-2-3 bound phenyloxazolone bovine serum albumin with a lower affinity than for Fl-bovine serum albumin. The first hypervariable region of the 18-2-3 light chain showed homology to human cryoglobulins. This is the first variable region sequence of a murine IgM which self-aggregates at low temperature.

Amino Acid Sequence↗
PubMed1990

Sequence analysis of HLA-DR4B1 subtypes: additional first domain variability is detected by oligonucleotide hybridization and nucleotide sequencing.

The stimulating capacity of HLA-DR4 variants in mixed leukocyte culture correlates with variation in the polymorphic regions of the first domains of their DR beta 1 chains. Variability between amino acids 67 and 86 appears largely to determine HLA-DR4,Dw type. We have used a combination of a DR4B1-specific primer set in the polymerase chain reaction and specific oligonucleotide probes to examine DR4,Dw-associated nucleotide polymorphisms. Phenotype and gene frequencies are reported among 44 normal DR4 Caucasoids. Oligonucleotide probes were selected which enabled definition of Dw4-, w14-, w10-, w13-, and w15-associated sequences. Unexpectedly, several subjects were positive for Dw15 sequences which are usually characteristic of Oriental populations. Dw15 assignment was confirmed by nucleotide sequencing of DR4B1 polymerase chain reaction products. A pair of oligonucleotides informative for the glycine or valine dimorphism at position 86 was used to identify two novel DR4B1 alleles, designated 13.2 and 14.2. Nucleotide sequencing shows that these represent recombinants between third hypervariable regions associated with Dw13 and Dw14 and a codon for glycine at position 86 which is usually found associated with Dw4 and Dw15 sequences.

Alleles↗
PubMed1990

[Genetic origins of anti-DNA autoantibodies].

A detailed analysis of variable region sequences, derived from monoclonal lupus anti-DNA autoantibodies has led to several conclusions with respect to the etiology and pathogenesis of systemic lupus erythematosus (SLE). It was found that the gene elements which are expressed in anti-DNA heavy and light chains are present in the germ lines of normal and diseased animals. However, several VH gene segments are not normally expressed in antibodies to external antigens and may, therefore, be excluded by the regulatory mechanism of self-tolerance. The presence of somatic point mutations, which may serve to change antigenic specificity as well as to increase affinity, indicates that an antigen (DNA)-driven mechanism rather than a polyclonal activation is responsible for the autoimmune response in SLE. An additional unique motif of anti-DNA heavy chains was found to consist of an arginine-rich basic peptide in the third complementarity-determining (hypervariable) region. These data have enabled us to build a computer model of the anti-DNA binding site and to design specific inhibitors of the autoimmune reaction.

Animals↗
PubMed1990

HLA-D region genes associated with autoantibody responses to histidyl-transfer RNA synthetase (Jo-1) and other translation-related factors in myositis.

Myositis has been associated with HLA-B8 and DR3, especially in white patients with polymyositis and serum anti-Jo-1 antibodies. Twenty-eight patients with myositis and serum translation-related autoantibodies anti-Jo-1, anti-PL-7, anti-PL-12, anti-KJ, and anti-SRP were studied for HLA class II specificities by Southern blotting with HLA-DR beta, DQ beta, and DQ alpha probes. The association of HLA-DR3 (DRw17) with anti-Jo-1 antibodies in white myositis patients was confirmed (P = 0.003, relative risk 8.9). However, HLA-DRw52 haplotypes, regardless of subtype, were present in all of the white and black patients with serum anti-Jo-1 and other translation-related autoantibodies. Moreover, one anti-Jo-1 positive patient had HLA-DRw8, an HLA-DRw52 haplotype on which the DR beta 3 gene has been partially deleted. No HLA-DQ specificity or allele was common to all patients. The HLA-DR3, DR5, DRw6, and DRw8 haplotypes, which bear the HLA-DRw52 specificity, share the most homology in the DR beta 1 first hypervariable region at amino acid positions 9-13. Thus, this DR beta 1 region appears to be the most likely candidate "epitope" for translation-related autoimmune responses in inflammatory myositis.

Alleles↗
PubMed1996

Primate DRB6 gene expression and evolution: a study in Macaca mulatta and Cercopithecus aethiops.

DRB6 has been found to be transcribed in human and apes. Promoter region and exon 1 come from a 5' LTR from a mammary tumour retrovirus. However, the putative protein structure would be very different to other DR molecules and it is doubtful that it may function as an antigen presenting molecule. Primate DRB6 alleles previously published together with the two new macaque sequences reported here support the existence of a strong selective pressure working on exon 2 to generate stop codons at the end of the exon (between codons 74 and 94) during at least 23 million years. The topology of dendrograms constructed with different primate DRB6 alleles supports the "trans-species" evolution proposed for MHC class I, class II and possibly C4 genes. Finally, DRB6, which is one of the oldest DRB genes, has been lost in the HLA-DRB3 (or DR52) group of haplotypes (DR3, DR5, DR6 and DR8) and a small DRB6 sequence is present at the exon 2 first hypervariable region of DRB4 (or DR53) gene, which is present in DR4, DR7 and DR9 haplotypes.

Animals↗
PubMedDate not supplied

Direct production of Fv-fragments from a family of monoclonal IgGs papain digestion.

Fv fragments of four monoclonal antibodies specific for morphine binding have been produced from their divalent IgG forms by papain digestion using the classic procedure for Fab formation. The binding characteristics of one of the Fv fragments have been determined relative to the intact antibody by equilibrium dialysis. Its dissociation constant is a factor of five lower than the IgG. Previous work had resulted in the sequences of each the chains for the four Fv fragments. The light chains are all from the highly homologous lambda subclass while the gamma heavy chains are closely related except for their CDR regions. In this work optical molar extinction coefficients are predicted from amino acid sequences for each of the fragments. It is found that they differ significantly from each other and from the commonly used value for intact IgG. Detailed comparisons between our results and those reported previously on the molecular masses of Fv-derived light and heavy chains and hapten-Fv dissociation constants are given based on analytical gel electrophoresis and electroblotting experiments using dye and immunovisualization techniques. Isoelectric focusing experiments have been performed and the pIs obtained are compared to those predicted theoretically from the chain sequences. Gel filtration column chromatography, acrylamide gel electrophoresis and equilibrium dialysis experiments are consistent with significant aggregation of the Fv fragments in neutral solution with accompanying inactivation of the binding site. Comparison of sequences for the Fv light and heavy chains are made with those which have been proposed to be important for chain dimer association and for canonical hypervariable regions. This methods of Fv production is not regarded as a general one. However, it may be an approach which is general to lambda chain containing antibodies.

Animals↗
PubMed1997

Two ways of legumin-precursor processing in conifers. Characterization and evolutionary relationships of Metasequoia cDNAs representing two divergent legumin gene subfamilies.

Subunit monomers and oligomers of crystalloid-type legumins are major components of SDS-soluble fractions from Metasequoia glyptostroboides (Dawn redwood, Taxodiaceae) seed proteins. The subunits are made up of disulfide linked alpha-polypeptides and beta-polypeptides with molecular masses of 33 kDa and 23-25 kDa, respectively. Unusually for legumins, those from Metasequoia are glycosylated and the carbohydrate moieties are residing in the C-terminal region of the respective beta-polypeptides. A Metasequoia endosperm cDNA library has been constructed and legumin-encoding transcripts representing two divergent gene subfamilies have been characterized. Intersubfamily comparisons reveal 75% identity at the amino acid level and the values range from 53-35% when the legumin precursors deduced were compared with those from angiosperms. The predicted sequences together with data from amino acid sequencing prove that post-translational processing of Metasequoia prolegumins is directed to two different processing sites, each of them specific for one of the legumin subfamilies. The sites involved differ in their relative position and in the junction to be cleaved: Metasequoia legumin precursors MgLeg18 and MgLeg26 contain the conventional post-translational Asn-Gly processing site, which is generally regarded as highly conserved. In contrast, the MgLeg4 precursor is lacking this site and post-translational cleavage is directed to an unusual Asn-Thr processing site located in its hypervariable region, causing N-terminal extension of the beta-polypeptide relative to those hitherto known. Evidence is given that the unusual variant of processing also occurs in other conifers. Phylogenetic analysis reveals the precursors concerned as representatives of a distinct legumin subfamily, originating from duplication of an ancestral gene prior to or at the beginning of Taxodiaceae diversification.

Amino Acid Sequence↗
PubMed2003

Autoreactive responses to an environmental factor: 1. phthalate induces antibodies exhibiting anti-DNA specificity.

Environmental factors have been implicated in the induction of autoimmune disorders. We report here that a common chemical, phthalate, used widely in synthetic polymers and cosmetics induces serum anti-self DNA antibodies in BALB/c, NZB and autoimmune-prone NZB/W F1 mice. The latter group experiences a high mortality, and significantly higher anti-DNA antibody levels along with nephritis and other histopathologic changes in kidney. Comparison of amino acid sequences of an anti-phthalate BALB/c B-cell hybrid, 2C3 with the known database at the National Center for Biotechnology Information reveals a striking homology between the variable regions of 2C3-Ig (gamma1, kappa) and an anti-DNA antibody, BV04-01 (gamma2b,kappa) isolated from the lupus-prone NZB/W F1 mice. The homology is 98% for kappa light chain and 70% for gamma heavy chain. Like 2C3-Ig, BV04-01 also has specificity for d(pT)4. Furthermore, the light chains of both 2C3-Ig and BV04-01 are products of Vkappa1 gene. To understand the nature of anti-phthalate responses in general, hybridomas generated from phthalate-keyhole limpet haemocyanin-primed BALB/c splenocytes were characterized. The study identifies cross-reactive populations that strongly bind phthalate, DNA, or both. Of the 14 hybridomas evaluated, six express the same Vkappa1 gene-derived light chain as 2C3, and bind both phthalate and ds and ss-DNA. They specifically recognize the oligonucleotides, d(pT)4, and d(pT)10. Additionally, when antisera raised against idiopeptides corresponding to 2C3-Ig hypervariable regions are allowed to react with 2C3-Ig, their binding is blocked specifically by both d(pT)4 and phthalate. This study clearly demonstrates that phthalate exposure leads to activation of a significant number of autoreactive B-cells, with the consequence of a significant pathogenic progression in susceptible NZB/W F1 mice but not in non-autoimmune-prone BALB/c.

Amino Acid Sequence↗
PubMed1999

Analysis of the genetic diversity of Helicobacter pylori: the tale of two genomes.

Infection with Helicobacter pylori has been linked to numerous severe gastroduodenal diseases including peptic ulcer and gastric cancer. Several techniques have been used to measure the genetic heterogeneity of H. pylori at several different levels and to determine whether there is any correlation with severity of disease. The availability of two completed genome sequences from unrelated strains (J99 and 26,695) has allowed an analysis of the level of diversity from a large-scale yet detailed perspective. Although the two chromosomes are organized differently in a limited number of discrete regions, the genome size and gene order of these two "high-virulence" (cagA+ and vacA+) H. pylori isolates was found to be highly similar. The regions of organizational difference are associated with insertion sequences, DNA restriction/modification genes, repeat sequences, or a combination of the above. A significant level of variation at the nucleotide level is seen across the genome, providing an explanation for why the nucleotide-based typing techniques have such high discriminatory power among independent H. pylori isolates. This nucleotide variation together with the organizational rearrangements appears to have provided an over-estimation of the gene order diversity of H. pylori as assessed by pulse-field gel electrophoresis. Functional assignments are assigned to approximately only 60% of the gene products in each strain, with one-half of the remaining gene products of unknown function having homologues in other bacteria, while the remainder appear to be H. pylori-specific. Between 6% and 7% of the coding capacity of each strain are genes that are absent from the other strain, with almost one-half of these strain-specific genes located in a single hypervariable region called the plasticity zone. The majority of the strain-specific genes in each strain are also H. pylori-specific, with no homologues being identified in the public databases. Significantly, over one-half of the functionally assigned strain-specific genes in both H. pylori J99 and 26695 encode DNA restriction/modification enzymes. Analysis of the level of conservation between orthologues from the two strains indicates that the H. pylori specific genes have a lower level of conservation than those orthologues to which a putative function can be assigned. The plasticity zone represents one of several regions across each genome that is comprised of lower (G+C)% content DNA, some of which has been detected in self-replicating plasmids, suggesting that both horizontal transfer from other species and plasmid integration are responsible for the strain-specific diversity at this locus. These analyses have yielded results with important implications for understanding the genetic diversity of H. pylori and its associated diseases, and imply a need to reassess the respective roles of bacterial and host factors in H. pylori associated diseases.

Genes, Bacterial↗
PubMed1994

Immunogenetics of chronic liver diseases.

The genetic background of autoimmune diseases becomes more and more evident. Immunogenetics comprises the analysis of genes and their products located at the region 6p21 on the short arm of chromosome 6, which is also known as the major histocompatibility complex (MHC). MHC class I and II genes are highly polymorphic. The complement genes C2, C4A, C4B, and BF, which are also polymorphic, became known as MHC class III genes. In autoimmune hepatitis type 1, there is a dual association for white persons with either HLA-A1-B8-DR3 or HLA-DR4. In patients from Japan, autoimmune hepatitis type 1 is predominantly associated with HLA-DR4. This dual association is confirmed at the DNA level. Whereas only limited data are available for autoimmune hepatitis type 2, the association of primary biliary cirrhosis with HLA-DR8 is based on several studies. Primary sclerosing cholangitis is associated with HLA-B8-DR3 and -DR52a. This association was confirmed at the DNA level because of a significant increase of the DRB3*0101 allele. For DRB3*0101-negative individuals, a second association with DRB5*0101 (= DR2) was described. Further analysis of the hypervariable region of the HLA class II molecule indicates that lysine at position 71 is crucial for autoimmune hepatitis type 1 in white persons, whereas position 13 is important for people from Japan. In contrast, leucine at position 35 is important for patients with primary biliary cirrhosis, whereas leucine at position 38 is an important risk factor for primary sclerosing cholangitis. The MHC class III allele C4A-QO is significantly increased in autoimmune hepatitis type 1 and 2 and in primary biliary cirrhosis. Advances in immunogenetics will certainly increase our knowledge of the etiology and pathogenesis of immune-mediated liver diseases, which hopefully will lead to more specific therapeutic interventions.

Chronic Disease↗
PubMed1992

Assembly of IgH CDR3: mechanism, regulation, and influence on antibody diversity.

The most variable portion of immunoglobulin molecules is the third complementarity determining region (CDR3) of the heavy chain. This is simply because CDR3 encompasses the region of the rearranged gene where the three gene segments (VH-DH-JH) are joined. Since imprecisions exist in the recombinase reaction, significant differences can be generated at the sites of recombination. This results in the generation of antigen receptor molecules which can differ in their antigen specificity even though they derive from the same germline information. In sum, the significance of the inaccuracy in recombination is that antibodies which are reactive to different antigens can be derived from identical genetic information. This explains how the immune system (using only a limited amount of genetic information) can generate antibodies to virtually any antigen. Though the basic phenomenon of VH-DH-JH assembly has been appreciated for years, two recent findings demonstrate that the generation of CDR3 is more complex than originally believed. First, junctional modification is not a stochastic process as was initially presumed, but is in part developmentally regulated. Second, it has now been well documented that more complex recombinations (for example VH-DH-DH-JH, VH-DH-invDH-JH, etc.) are involved in generating the third hypervariable region of the heavy chain. Not only do these unusual rearrangements--which break the so-called "12/23" recombination rule--occur, but interestingly, certain predicted rearrangements (even some which do follow the "12/23" recombination rule) cannot be demonstrated and apparently do not occur. To date, there is no adequate explanation for the lack of these predicted recombinations. These results have important implications for both the generation of antibody diversity and the recombinase reaction itself.

Animals↗
PubMed2005

Microevolution in prehistoric Andean populations: chronologic mtDNA variation in the desert valleys of northern Chile.

Archeological evidence suggests that the iconographic and technological developments that took place in the highlands around Lake Titicaca in the Central Andean region had an influence on the cultural elaborations of the human groups in the valleys and the Pacific coast of northern Chile. In a previous communication, we were able to show, by means of a distance analysis, that a craniofacial differentiation accompanied the process of cultural evolution in the valleys (Rothhammer and Santoro [2001] Lat. Am. Antiq. 12:59-66). Recently, numerous South Amerindian mtDNA studies were published, and more accurate molecular techniques to study ancient mtDNA are available. In view of these recent developments, we decided 1) to study chronological changes of ancient mtDNA haplogroup frequencies in the nearby Lluta, Azapa, and Camarones Valleys, 2) to identify microevolutionary forces responsible for such changes, and 3) to compare ancient mtDNA haplogroup frequencies with previous data in order to validate craniometrical results and to reconstruct the biological history of the prehistoric valley groups in the context of their interaction with culturally more developed highland populations. From a total of 97 samples from 83 individuals, 68 samples (61 individuals) yielded amplifications for the fragments that harbor classical mtDNA markers. The haplogroup distribution among the total sample was as follows: 26.2%, haplogroup A; 34.4%, haplogroup B; 14.8%, haplogroup C; 3.3%, haplogroup D; and 21.3%, other haplogroups. Haplogroup B tended to increase, and haplogroup A to decrease during a 3,900-year time interval. The sequence data are congruent with the haplogroup analysis. In fact, the sequencing of hypervariable region I of 30 prehistoric individuals revealed 43 polymorphic sites. Sequence alignment and subsequent phylogenetic tree construction showed two major clusters associated with the most common restriction haplogroups. Individuals belonging to haplogroups C and D tended to cluster together with nonclassical lineages.

Base Sequence↗
PubMedDate not supplied

Emergence of subtype strains of the Arkansas serotype of infectious bronchitis virus in Delmarva broiler chickens.

Infectious bronchitis virus (IBV) field isolates of the Arkansas (Ark) serotype were identified by reverse transcription-polymerase chain reaction (RT-PCR) as the most common serotype isolated from 1993 to 1997. These isolates were recovered from broiler flocks with respiratory disease raised on the Delmarva peninsula in spite of Ark vaccination in the region. For the purposes of investigating this apparently paradoxical finding, five RT-PCR Ark-positive field isolates recovered in 1995 and 1996 were selected for further characterization. The isolates were compared with Ark reference strains by reciprocal virus neutralization (VN) in embryonated eggs, S-1 gene sequence analysis, and challenge of immunity studies in specific-pathogen-free (SPF) chickens. Antigenic (VN) comparisons and S-1 gene analysis confirmed that the five RT-PCR Ark-positive field isolates were of the Ark serotype but also revealed that the viruses could be readily distinguished from Ark reference strains. Four of the isolates (Ark/213/96, Ark/15C/96, Ark/1529/95, Ark/1534/95) were found to have higher antigenic relatedness percentages to each other (95%-100%) than to Ark reference strains DPI (52%-72%) and Georgia variant (Georgia var) (53%-68%) by VN. Another isolate, Ark/1535/95, was found to differ antigenically from the other four RT-PCR Ark-positive field isolates (34%-61%), Ark DPI (44%), and Georgia var (43%) strains. The trends in the S-1 gene sequencing results were similar to those observed for the VN findings. Isolates Ark/213/96, Ark/15C/96, Ark/1529/95, and Ark/1534/95 demonstrated a higher degree of predicted S-1 amino acid similarity to each other (96.5%-98.7%) than to Ark DPI (92.4%-93.7%), Ark 99 (93.2%-94.7%), and Georgia var (89.3%-90.8%). Ark/1535/95 S-1 amino acid similarity values were lower compared with those of the other four RT-PCR Ark-positive field isolates (93.4%-94.8%), Ark DPI (91.9%), Ark 99 (93.0%), and Georgia var (88.7%). Furthermore, the isolates could be distinguished from the Ark reference strains by a characteristic sequence polymorphism, a six-nucleotide deletion encoding amino acids 57 (Asp) and 58 (Asp) in hypervariable region 1 of S-1. On the basis of the VN and sequencing findings, isolates Ark/213/96, Ark/15C/96, Ark/1529/95, and Ark/1534/95 were considered to be a single subtype of the Ark serotype. The fifth isolate, Ark/1535/95, may constitute another subtype of the Ark serotype. Vaccination of SPF chickens with a high-titering commercially available live vaccine containing the Ark DPI strain provided solid protection (>90%) against challenge with the RT-PCR Ark-positive field isolates. Immunization of SPF chickens with Ark/213/96 produced 100% protection against challenge with the homologous strain, as well as isolates Ark/1535/95 and Ark 99 but lower levels of protection against Ark DPI (58%) and Georgia var (55%). Primers for RT-PCR were designed to distinguish between the Ark subtypes and the Ark reference strains on the basis of the characteristic six-nucleotide deletion identified in the S-1 gene of the Ark subtypes. Retrospective analysis of RT-PCR Ark-positive isolates found that the Ark subtypes existed as early as 1992 in Delmarva broilers and became prevalent by 1995. With RT-PCR, restriction fragment length polymorphism analysis, and DNA sequencing techniques, the presence of Ark subtype viruses was demonstrated in two commercial Ark DPI strain vaccines and in our Ark DPI laboratory stocks that were the original source of the virus used for vaccine development. The demonstration of the Ark subtype and reference strains in the Ark DPI strain is evidence of the existence of IBV quasispecies. Factors possibly influencing the emergence of the Ark subtype in commercial broilers are discussed.

Animals↗