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Monoclonal antibody 6B6.6 defines a cross-reactive kappa light chain idiotope on human monoclonal and polyclonal rheumatoid factors.

Mouse monoclonal antibody (MAb) 6B6.6 was raised against a cross-reactive idiotope (CRI) present on the light chains of 2 human IgM paraproteins with rheumatoid factor (RF) activity. The MAb inhibited the IgG-binding activity of these proteins, and thus appears to react with an epitope located at or near the RF-binding site. Enzyme-linked immunosorbent assay (ELISA) and Western immunoblotting studies indicate that the 6B6.6 CRI is associated with kappa IIIa sub-subgroup light chains, is not related to the Wa, Po, and Bla RF cross-idiotypic specificities, and is clearly distinct from the kappa IIIb-associated CRI detected by MAb 17.109. Using an ELISA, we detected 6B6.6 CRI in 59% of 107 sera and 48% of 50 synovial fluids from patients with seropositive rheumatoid arthritis (RA). However, the quantities of CRI-positive RF were small, and the amount of CRI-positive RF did not correlate with the amount of IgM-RF. The 6B6.6 CRI was shown to occur primarily in the IgM fraction of RA sera by both chromatographic studies and isotype-specific ELISA, although small quantities appeared to be associated with IgA and IgG in some sera. The presence of 6B6.6 CRI on both monoclonal and polyclonal RF is consistent with the view that both are derived, at least in part, from a common gene pool. However, its occurrence in relatively low levels suggests that the number of germline genes encoding for RF is large or that extensive mutation occurs in the course of RF expression in RA.

Antibodies, Monoclonal↗

Applications of high efficiency lithium acetate transformation of intact yeast cells using single-stranded nucleic acids as carrier.

The highly efficient yeast lithium acetate transformation protocol of Schiestl and Gietz (1989) was tested for its applicability to some of the most important needs of current yeast molecular biology. The method allows efficient cloning of genes by direct transformation of gene libraries into yeast. When a random gene pool ligation reaction was transformed into yeast, the LEU2, HIS3, URA3, TRP1 and ARG4 genes were found among the primary transformants at a frequency of approximately 0.1%. The RAD4 gene, which is toxic to Escherichia coli, was also identified among the primary transformants of a ligation library at a frequency of 0.18%. Non-selective transformation using this transformation protocol was shown to increase the frequency of gene disruption three-fold. Co-transformation showed that 30-40% of the transformation-competent cells take up more than one DNA molecule which can be used to enrich for integration and deletion events 30- to 60-fold. Co-transformation was used in the construction of simultaneous double gene disruptions as well as disrupting both copies of one gene in a diploid which occurred at 2-5% the frequency of the single event.

Cloning, Molecular↗

Cloning of hexokinase isoenzyme PI from Saccharomyces cerevisiae: PI transformants confirm the unique role of hexokinase isoenzyme PII for glucose repression in yeasts.

Hexokinase isoenzyme PI was cloned using a gene pool obtained from a yeast strain having only one functional hexokinase, isoenzyme PI. The gene was characterized using 20 restriction enzymes and located within a region of 2.0 kbp. The PI plasmid strongly hybridized with the PII plasmids isolated previously (Fröhlich et al. 1984). Hence there was a close relationship between the two genes, one of which must have been derived from the other by gene duplication. In contrast, glucose repression was restored only in hexokinase PII transformants; PI transformants remained non-repressible. This observation provided additional evidence for the hypothesis of Entian (1980) that only hexokinase PII is necessary for glucose repression. Furthermore, glucose phosphorylating activity in PI transformants exceeded that of wild-type cells, giving clear evidence that the phosphorylating capacity is not important for glucose repression.

Cloning, Molecular↗

Genetic effects on susceptibility, clinical expression, and treatment outcome of type 1 autoimmune hepatitis.

Currently, three genetic factors have been short-listed as possible modulators of susceptibility and severity in type 1 AIH. They are female sex, HLA DRB alleles encoding lysine at position DR beta 71, and the CTLA4*G allele. The fourth association (i.e., TNFRSF6) remains to be confirmed. There are many other candidates to investigate. Current hypotheses suggest that the autoimmune genotype will include multiple (some linked, others discrete) loci which make a permissive background. Not all "at risk" individuals will develop clinical disease, and selection will depend on the interaction of this "permissive gene pool" (i.e., the host) with the environment. The resulting autoimmune phenotype will depend on gene dose and gene interaction. The human genome project has presented medical science with the challenge to identify the genes that determine common human diseases, including autoimmunity [1]. Although type 1 AIH is considerably less common than diabetes or RA, it may serve as a useful model for other autoimmune diseases. Diagnosis depends on histologic findings, and liver biopsy examinations are part of the usual assessment strategy in type 1 AIH. The availability of these tissue specimens provides a clear basis for monitoring disease progression and may permit investigators to study the impact of genetic polymorphism on disease activity. The emergence of high throughput technologies will significantly enhance our ability to study the interactions between constellations of polymorphic genes and both disease expression and behavior. An abundance of polymorphism is found in the genome. In many diseases, functional studies and genome scanning have helped revise and reduce the list of candidates. Affected families are rare in type 1 AIH, and patients are at risk if corticosteroid treatment is withheld. Under these circumstances, genetic studies may be the most practical, low risk means to investigate the pathogenesis of type 1 AIH and many other autoimmune diseases.

Genetic Predisposition to Disease↗

Metagenomics, gene discovery and the ideal biocatalyst.

With the rapid development of powerful protein evolution and enzyme-screening technologies, there is a growing belief that optimum conditions for biotransformation processes can be established without the constraints of the properties of the biocatalyst. These technologies can then be applied to find the "ideal biocatalyst" for the process. In identifying the ideal biocatalyst, the processes of gene discovery and enzyme evolution play major roles. However, in order to expand the pool genes for in vitro evolution, new technologies, which circumvent the limitations of microbial culturability, must be applied. These technologies, which currently include metagenomic library screening, gene-specific amplification methods and even full metagenomic sequencing, provide access to a volume of "sequence space" that is not addressed by traditional screening.

Bacterial Proteins↗

Genetic organization of the psbAD region in phages infecting marine Synechococcus strains.

The discovery of the genes psbA and psbD, encoding the D1 and D2 core components of the photosynthetic reaction center PSII (photosystem II), in the genome of the bacteriophage S-PM2 (a cyanomyovirus) that infects marine cyanobacteria begs the question as to how these genes were acquired. In an attempt to answer this question, it was established that the occurrence of the genes is widespread among marine cyanomyovirus isolates and may even extend to podoviruses. The phage psbA genes fall into a clade that includes the psbA genes from their potential Synechococcus and Prochlorococcus hosts, and thus, this phylogenetic analysis provides evidence to support the idea of the acquisition of these genes by horizontal gene transfer from their cyanobacterial hosts. However, the phage psbA genes form distinct subclades within this lineage, which suggests that their acquisition was not very recent. The psbA genes of two phages contain identical 212-bp insertions that exhibit all of the canonical structural features of a group I self-splicing intron. The different patterns of genetic organization of the psbAD region are consistent with the idea that the psbA and psbD genes were acquired more than once by cyanomyoviruses and that their horizontal transfer between phages via a common phage gene pool, as part of mobile genetic modules, may be a continuing process. In addition, genes were discovered encoding a high-light inducible protein and a putative key enzyme of dark metabolism, transaldolase, extending the areas of host-cell metabolism that may be affected by phage infection.

Bacterial Proteins↗

The molecular evolution of terminal ear1, a regulatory gene in the genus Zea.

Nucleotide diversity in the terminal ear1 (te1) gene, a regulatory locus hypothesized to be involved in the morphological evolution of maize (Zea mays ssp. mays), was investigated for evidence of past selection. Nucleotide polymorphism in a 1.4-kb region of te1 was analyzed for a sample of 26 sequences isolated from 12 maize lines, five populations of the maize progenitor, Z. mays ssp. parviglumis, six other Zea populations, and two Tripsacum species. Although nucleotide diversity in te1 in maize is reduced relative to ssp. parviglumis, phylogenetic and statistical analyses of the pattern of polymorphism among these sequences provided no evidence of past selection, indicating that the region of the gene studied was probably not involved in maize evolution. The level of reduction in genetic diversity in te1 in maize relative to its progenitor is comparable to that found in previous reports for isozymes and other neutrally evolving maize genes and is consistent with a genome-wide reduction of genetic diversity resulting from a domestication bottleneck. An estimate of the age (1.2-1.4 million yr) of the maize gene pool based on te1 is roughly consistent with previous estimates based on other neutral genes, but may be biased by the apparently slow synonymous substitution rate at te1.

Base Sequence↗

Phenotypic differences in Schistosoma mattheei ova from populations sympatric and allopatric to S. haematobium.

Schistosoma mattheei ova were collected from cattle in different localities in South Africa and after hatching, miracidia were used to infest Bulinus (Physopsis) globosus. Cercariae harvested from these snails were used to infest the definitive host Praomys (Mastomys) coucha and eggs from the resulting female S. mattheei were collected. These ova were compared with a Schistosoma haematobium X S. mattheei hybrid similarly collected from an infested P. (M.) coucha. The results indicate that S. mattheei populations which are sympatric to S. haematobium possess S. haematobium characteristics. It is suggested that the gene pools of populations of the parasite in these areas are infiltrated with S. haematobium genes via the S. mattheei X S. haematobium hybrid originating from human hosts.

Animals↗

Immunoglobulin allotypes and estimation of genetic admixture among populations of Kinnaur District, Himachal Pradesh, India.

Four regional populations of the Kanet (Puh, Kalpa, Sangla, and Nachar) and an endogamous group of Koli from Kinnaur District, Himachal Pradesh, India, were studied to determine the extent of genetic variation of immunoglobulin allotypes (GM, KM, and AM) and the genetic contribution from ancestral populations of Tibet and northwest India. Haplotype GM*A G showed a higher frequency in the Kanet (40-60%)-a frequency that is more comparable to Asian populations-whereas in the Koli a lower frequency was observed, which is nearer the values for populations from northwest India. The IG haplotype data suggest that the Kanet population of Kinnaur District and the northeastern population of Nepal have different European origins than the more central population of India, represented by a sample from Delhi. The present results suggest that the populations of Kinnaur District are of admixed origin with contributions of Tibetan genes of 87.3%, 51.3%, 49.9%, 40.0%, and 9.5% in the Puh, Kalpa, Sangla, and Nachar Kanet and the Koli, respectively. The genetic distance obtained from 19 loci (9 blood groups, 8 biochemical markers, GM, and KM) showed an inverse relationship between the distance of the hybrid population from the parental gene pool. The Puh Kanet, nearest the Tibetan border, had the highest proportion of Tibetan genes but showed the lowest genetic distance with Tibetans. As the geographic distance of the other regional populations of the Kanet increases from the border of Tibet, genetic distance compared with the parental Tibetan population increases and the proportion of Tibetan admixture decreases. In the Kinnaur District admixture seems to contribute largely to the present-day observed high level of genetic differentiation.

Ethnicity↗

Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species.

BACKGROUND: Mature saturated brine (crystallizers) communities are largely dominated (> 80% of cells) by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and the sequencing of its genome allows comparison with the metagenome of this taxonomically simplified environment. Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present. RESULTS: The metagenome of the microbial community of a crystallizer pond has been analyzed by end sequencing a 2000 clone fosmid library and comparing the sequences obtained with the genome sequence of "Haloquadratum walsbyi". The genome of the sequenced strain was retrieved nearly complete within this environmental DNA library. However, many ORF's that could be ascribed to the "Haloquadratum" metapopulation by common genome characteristics or scaffolding to the strain genome were not present in the specific sequenced isolate. Particularly, three regions of the sequenced genome were associated with multiple rearrangements and the presence of different genes from the metapopulation. Many transposition and phage related genes were found within this pool which, together with the associated atypical GC content in these areas, supports lateral gene transfer mediated by these elements as the most probable genetic cause of this variability. Additionally, these sequences were highly enriched in putative regulatory and signal transduction functions. CONCLUSION: These results point to a large pan-genome (total gene repertoire of the genus/species) even in this highly specialized extremophile and at a single geographic location. The extensive gene repertoire is what might be expected of a population that exploits a diverse nutrient pool, resulting from the degradation of biomass produced at lower salinities.

Base Composition↗

Genetic relationships among South-East Turkey wild barley populations and sampling strategies of Hordeum spontaneum.

To assess the genetic diversity and the genetic structure of Turkish wild barley (Hordeum spontaneum Tell.) populations, 76 genotypes from ten ecologically and geographically different locations were analyzed by means of amplified fragment length polymorphism (AFLP) markers. Five primer combinations produced 187 scorable bands, of which 117 (62.6%) were polymorphic. Several population-specific and genotype-specific bands were identified, which differentiate populations or genotypes. Genetic distance, determined by Nei's distance coefficient, varied from 0.07 to 0.21 with an average of 0.13. In the UPGMA dendrogram based on Nei genetic distances, the Hordeum spontaneum populations were separated into two major clusters. Genetic diversity was larger among (68%) than within (32%) populations. Eight AFLP bands were strongly correlated to the altitude of the collecting site, while no clear trend was detected between geographical origin and genetic diversity. Our results strongly suggest the need for a change in Hordeum spontaneum sampling strategy: more populations, rather then more individuals within population, should be sampled to appraise and safeguard genetic diversity in the wild barley gene pool.

Genes, Plant↗

The allele (A)(-110) in the promoter region of the HSP70-1 gene is unfavorable to longevity in women.

Heat shock proteins (HSPs) are crucial for maintenance of cell homeostasis and survival both during and after various stresses. The capability to cope with stress is believed to affect the chance of health and survival at organismal level. We have investigated whether the gene pool relevant to the (A/C)(-110) polymorphism in the promoter region of the HSP70-1 gene changes as the population ages and survival selection occurs. A total of 591 southern Italian subjects were enrolled in the study (263 males and 328 females; age range 18-109 years), free of clinically manifest diseases and with normal haemato-chemical parameters. A significant age-related decrease of the frequency of allele (A)(-110) was observed in females. The probability ratio of 0.403 (95% confidence interval [0.163, 0.910]) computed by considering female centenarians as cases and young women (18-49 years old) as controls showed that the (A)(-110) allele is unfavorable to longevity in females.

Adolescent↗

Inbreeding and the incidence of childhood genetic disorders in Karnataka, South India.

Consanguineous marriages are strongly favoured among the populations of South India. In a study conducted on 407 infants and children, a total of 35 genetic diseases was diagnosed in 63 persons: 44 with single gene defects, 12 with polygenic disorders, and seven with Down's syndrome. The coefficient of inbreeding of the total study group, F = 0.0414, was significantly higher than that previously calculated for the general population, F = 0.0271, and autosomal recessive disorders formed the largest single disease category diagnosed. The results suggest that long term inbreeding may not have resulted in appreciable elimination of recessive lethals and sub-lethals from the gene pool.

Genes, Dominant↗

[The distribution of surnames in the Saguenay and Charlevoix regions as indicators of population structure in the nineteenth and twentieth centuries].

"This paper presents a statistical analysis of surnames, revealing a striking similarity between the Saguenay and Charlevoix regions in the province of Quebec, since the 19th century. Indeed, a migration study also shows that the former region was created in the 1840's by immigrants coming mostly from the latter. An analysis by decade also shows that the Saguenay population structure has remained relatively stable since the middle of the 19th century. It is suggested that this kind of surnames analysis may be a useful indicator not only of the dynamics of a population, but also of the evolution of the whole gene pool. It seems however to reflect very poorly the movement or diffusion of any deleterious gene in particular." (SUMMARY IN ENG AND SPA)

Americas↗

[Biochemical gene markers in Komy populations].

Gene pool of two Komy groups and Komy-Permiakh group has been characterized for biochemical gene markers Hp, Tf, Gc, C'3, PGM1, EsD, AcP, GLO1. Genetical characteristics of the groups investigated, other Finnish-Ugorh peoples and those neighbouring Komy peoples of no Finnish-Ugorh origin are compared. Genetical position of Komy peoples in the system of peoples of the Euro-Asia has been defined.

Ethnicity↗

Ethics and genetic selection in purebred dogs.

There is an ongoing revolution in medicine that is changing the way that veterinarians will be counselling clients regarding inherited disorders. Clinical applications will emerge rapidly in veterinary medicine as we obtain new information from canine and comparative genome projects (Meyers-Wallen 2001: Relevance of the canine genome project to veterinary medical practice. International Veterinary Information Service, New York). The canine genome project is described by three events: mapping markers on canine chromosomes, mapping gene locations on canine chromosomes (Breen et al. 2001: Genome Res. 11, 1784-1795), and obtaining the nucleotide sequence of the entire canine genome. Information from such research has provided a few DNA tests for single gene mutations [Aguirre 2000: DNA testing for inherited canine diseases. In: Bonagura, J (ed), Current Veterinary Therapy XIII. Philadelphia WB Saunders Co, 909-913]. Eventually it will lead to testing of thousands of genes at a time and production of DNA profiles on individual animals. The DNA profile of each dog could be screened for all known genetic disease and will be useful in counselling breeders. As part of the pre-breeding examination, DNA profiles of prospective parents could be compared, and the probability of offspring being affected with genetic disorders or inheriting desirable traits could be calculated. Once we can examine thousands of genes of individuals easily, we have powerful tools to reduce the frequency of, or eliminate, deleterious genes from a population. When we understand polygenic inheritance, we can potentially eliminate whole groups of deleterious genes from populations. The effect of such selection on a widespread basis within a breed could rapidly improve health within a few generations. However, until we have enough information on gene interaction, we will not know whether some of these genes have other functions that we wish to retain. And, other population effects should not be ignored. At least initially it may be best to use this new genetic information to avoid mating combinations that we know will produce affected animals, rather than to eliminate whole groups of genes from a population. This is particularly important for breeds with small gene pools, where it is difficult to maintain genetic diversity. Finally, we will eventually have enough information about canine gene function to select for specific genes encoding desirable traits and increase their frequencies in a population. This is similar to breeding practices that have been applied to animals for hundreds of years. The difference is that we will have a large pool of objective data that we can use rapidly on many individuals at a time. This has great potential to improve the health of the dog population as a whole. However, if we or our breeder clients make an error, we can inadvertently cause harm through massive, rapid selection. Therefore, we should probably not be advising clients on polygenic traits or recommend large scale changes in gene frequencies in populations until much more knowledge of gene interaction is obtained. By then it is likely that computer modelling will be available to predict the effect of changing one or several gene frequencies in a dog population over time. And as new mutations are likely to arise in the future, these tools will be needed indefinitely to detect, treat and eliminate genetic disorders from dog populations. Information available from genetic research will only be useful in improving canine health if veterinarians have the knowledge and skills to use it ethically and responsibly. There is not only a great potential to improve overall canine health through genetic selection, but also the potential to do harm if we fail to maintain genetic diversity. Our profession must be in a position to correctly advise clients on the application of this information to individual dogs as well as to populations of dogs, and particularly purebred dogs.

Animals↗

Accessory DNA in the genomes of representatives of the Escherichia coli reference collection.

Different strains of the Escherichia coli reference collection (ECOR) differ widely in chromosomal size. To analyze the nature of the differential gene pool carried by different strains, we have followed an approach in which random amplified polymorphic DNA (RAPD) was used to generate several PCR fragments. Those present in some but not all the strains were screened by hybridization to assess their distribution throughout the ECOR collection. Thirteen fragments with various degrees of occurrence were sequenced. Three of them corresponded to RAPD markers of widespread distribution. Of these, two were housekeeping genes shown by hybridization to be present in all the E. coli strains and in Salmonella enterica LT2; the third fragment contained a paralogous copy of dnaK with widespread, but not global, distribution. The other 10 RAPD markers were found in only a few strains. However, hybridization results demonstrated that four of them were actually present in a large selection of the ECOR collection (between 42 and 97% of the strains); three of these fragments contained open reading frames associated with phages or plasmids known in E. coli K-12. The remaining six fragments were present in only between one and four strains; of these, four fragments showed no similarity to any sequence in the databases, and the other two had low but significant similarity to a protein involved in the Klebsiella capsule synthesis and to RNA helicases of archaeal genomes, respectively. Their percent GC, dinucleotide content, and codon adaptation index suggested an exogenous origin by horizontal transfer. These results can be interpreted as reflecting the presence of a large pool of strain-specific genes, whose origin could be outside the species boundaries.

Bacteriology↗

Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays.

Whole genome DNA microarrays were constructed and used to investigate genomic diversity in 18 Campylobacter jejuni strains from diverse sources. New algorithms were developed that dynamically determine the boundary between the conserved and variable genes. Seven hypervariable plasticity regions (PR) were identified in the genome (PR1 to PR7) containing 136 genes (50%) of the variable gene pool. When comparisons were made with the sequenced strain NCTC11168, the number of absent or divergent genes ranged from 2.6% (40 genes) to 10.2% (163) and in total 16.3% (269) of the genes were variable. PR1 contains genes important in the utilisation of alternative electron acceptors for respiration and may confer a selective advantage to strains in restricted oxygen environments. PR2, 3 and 7 contain many outer membrane and periplasmic proteins and hypothetical proteins of unknown function that might be linked to phenotypic variation and adaptation to different ecological niches. PR4, 5 and 6 contain genes involved in the production and modification of antigenic surface structures.

Algorithms↗