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PubMed2005

Why disease persists: an evolutionary nosology.

Although natural selection might be expected to reduce the incidence and severity of disease, disease persists. Natural selection leads to increases in the mean fitness of populations and so will reduce the frequency of disease-associated alleles, but other evolutionary processes, such as mutation and gene flow, may introduce or increase the frequency of these deleterious alleles. The pleiotropic actions of genes and the epistatic interactions between them complicate the relationship between genotype and phenotype, and may result in the preservation of disease-associated alleles. Deleterious alleles may also be maintained because of linkage to beneficial alleles. The inability of natural selection to eliminate diseases of aging is a reminder that fitness -- success in producing progeny, or in contributing genes to the population gene pool -- is not equivalent to the absence of disease. Nutritional or psychosocial cues may lead to life history strategies that maximize survival to reproductive maturity at the expense of disease later in life. Natural selection acts on genes, cells, and groups, as well as on organisms; the outcome of evolution reflects selection at different levels of biological organization. Finally, the human environment is constantly changing, largely because of the evolution of our parasites and because of changes in cultural beliefs and practices; genetic evolution is comparatively slow and lags behind environmental change. An evolutionary nosology complements traditional medical nosologies and enhances our understanding of the persistence of disease and the meaning of human variation.

Environment↗

PubMed1987

Genetic relatedness of Colorado tick fever virus isolates by RNA-RNA blot hybridization.

The sequence relatedness of ten isolates of the Colorado tick fever (CTF) serogroup of orbiviruses was examined by RNA-RNA blot hybridization. The 12 dsRNA genome segments of each of the isolates were electrophoresed in a 10% polyacrylamide gel, the segments were transferred electrophoretically to membranes and hybridized to radiolabelled genomic RNA from CTF Florio mouse-adapted strain (CTF FMA) or CTF SS-18. All genome segments of the ten CTF viruses exhibited cross-hybridization signals with either CTF FMA or CTF SS-18, under conditions in which greater than or equal to 74% sequence homology was required to form stable hybrids. Although the dsRNA polyacrylamide gel profiles were unique for each isolate examined, the CTF genes did not exhibit sequence divergence as has been seen among other Orbivirus serogroups. These hybridization analyses suggest that the CTF gene pool is relatively homogeneous which may be a reflection of the lack of multiple serotypes of CTF strains in neutralization tests. Nevertheless, the hybridization signals of segments 4 and 6 were lighter than those of the other genes, indicating that these two genes exhibited the highest degree of sequence variability among these isolates. These data are compared with hybridization data on other Orbivirus serogroups.

Colorado tick fever virus↗

PubMed1995

The ontogeny of Gaia: the role of microorganisms in planetary information network.

The Gaia theory states that the whole surface layer of the globe, including organisms, atmosphere, hydrosphere and lithosphere, can be viewed as a self-evolving homeostatic system. Bacteria play a principal role in this formative process. This line of thinking should answer several questions: Is the biosphere simply a set of essentially selfish individuals, each testing its fitness? Is memory in the biosphere confined to genes? Is the composition of ecosystems and their behavior only kind of dynamic equilibrium? Or is there a huge amount of epigenetic information that enables organisms to interpret properly their situation and behave accordingly? It is suggested here that it is the information flow, rather than pure thermodynamics and natural selection, that enables living beings not only to "read" their environment, interpret their situation and behave accordingly to this understanding, but also to establish geophysiology, to become part of Gaia. This flow comprises genes as well as signals, diffusible as well as permanent. From an analogy with the situation in the multicellular organism, three types of information mediators inside the body of Gaia are suggested: ultrastructure, diffusible signals and gene flux. With a shared gene pool, intricate ultrastructure and quickly diffusible signals, it is legitimate to consider Gaia a superorganism with an ontogeny.

Animals↗

PubMed1993

High-sequence conservation among the United States bluetongue viruses cognate M2 genes which encode the nonstructural NS1 tubule protein.

Full-length cDNA copies of the M2 gene of BTV-2, -11, and -13 serotypes obtained by a modified polymerase chain reaction (Clamp-R) were cloned into pUC19 plasmid. The entire nucleotide sequences of each M2 gene were determined and compared with BTV-10 and BTV-17, thus completing the sequencing of these cognate M2 gene segments from all five U.S. BTV serotypes. Each M2 segment contained 1769 nucleotides, a single open reading frame (ORF) with an initiation codon at nucleotides 35-37, and a termination codon at nucleotides 1691-1693. This ORF can encode the 552-amino-acid NS1 protein (64 KDa) which has an isoelectric point of 7. Analyses of the nucleotide and deduced amino acid sequences of the five U.S. BTV serotypes indicated that the most recently isolated BTV-2 serotype was more distantly related than BTV-10, -11, -13, or -17. Analyses of the evolutionary relatedness of the cognate M2 genes by codon positions indicate that the rate of mismatch accumulations in the first and second base codon positions are less than 4%. However, the mismatch accumulations in the third base codon position are quite evident (23%) when BTV-2 serotype was compared with the other U.S. BTV serotypes. This suggests that BTV-2 has separated from the other four U.S. serotypes long before they themselves diverged. These data also indicate that the five U.S. BTV serotypes were apparently derived from two distinct gene pools that reflected geographic distribution in North America.

Base Sequence↗

PubMed2006

A role for the tet(O) plasmid in maintaining Campylobacter plasticity.

Genomic sequencing projects are beginning to reveal regions of extensive DNA homology between bacterial genera. Public fears of the spread of genetically modified organisms into the food chain and the increasing prevalence of multi-drug resistant disease in humans highlight the implications of horizontal gene transfer. The striking DNA sequence similarity between the two uniquely identified tetracycline resistant (Tc(R)) Campylobacter plasmids, pCC31 and pTet, suggests their conserved acquisition and maintenance within Campylobacter [Batchelor, R.A., Pearson, B.M., Friis, L.M., Guerry, P., Wells, J.M. 2004. Nucleotide sequences and comparison of two large conjugative plasmids from different Campylobacter species. Microbiology 150, 3507-3517]. It is thus likely that these and other conjugative plasmids are highly prevalent and broadly distributed across several continents. Microarray technology is now enabling fast and extensive genomic comparisons to be made and allows us to investigate intra- and inter-genetic conservation and variability. This study details the development of a microarray specific for genes from Campylobacter plasmids pCC31, pTet and pVir and its application to the analysis of Campylobacter plasmid gene presence and preservation throughout environmental and clinical isolates. Application of the iterative algorithm GENCOM (freely available at ) is used as a rapid and effective way of comparing the content and conservation of plasmids in bacteria and provides details of the Campylobacter flexible gene pool and its contribution to genomic plasticity.

Algorithms↗

PubMed1988

Intra- and inter-serogroup genetic relatedness of orbiviruses. I. Blot hybridization of viruses of Australian serogroups.

Viruses in the Eubenangee, Wallal and Warrego serogroups of orbiviruses have been isolated primarily in Australia. Several isolates in these three serogroups were examined by gel electrophoresis and blot hybridization of genomic RNA. Conserved and variant genes were identified by the degree of hybridization between cognate genes. The dsRNA profiles of isolates within a serogroup exhibited heterogeneity in polyacrylamide gels, but they were indistinguishable in agarose gels. Isolates within a serogroup generally showed a high level of cross-hybridization in eight segments with cognate segments 2 and 6 exhibiting hybridization signal variants. Although Pata virus has been classified in the Eubenangee serogroup, it was not closely related to other Eubenangee isolates by hybridization. Similarly, Mitchell River virus was not closely related to other members of the Warrego serogroup. The taxonomic status of Pata and Mitchell River viruses should be reviewed, and in the interim they should be placed in the ungrouped set of orbiviruses. Inter-serogroup relatedness was also examined by blot hybridization. Representatives from the Eubenangee, Wallal, Warrego, bluetongue, epizootic haemorrhagic disease and Corriparta serogroups were examined. Several of the serogroups were distantly related, and the low level of relatedness was suggestive of a common ancestry. While many of these serogroups may co-circulate in nature, these data suggest that each serogroup represents a distinct gene pool. The taxonomic significance of these data is discussed.

Animals↗

PubMed1999

Evidence for gene flow between wild and cultivated Medicago sativa (Leguminosae)based on allozyme markers andquantitative traits.

Genetic differentiation between co-occurring crops and their wild relatives will be greatly modified by crop-to-weed gene flow and variation between human and natural selective pressures. The maintenance of original morphological features in most natural populations of Medicago sativa in Spain questions the relative extent of these antagonistic forces. In this paper, we measured and compared the pattern of population differentiation within and among the wild and cultivated gene pool with respect to both allozymes and quantitative traits. Patterns of diversity defined three kinds of natural populations. First, some populations were intermediate with respect to both allozymes and quantitative traits. This suggests that crop-to-weed gene flow may have created hybrid populations in some locations. Second, some populations were different from all the cultivated landraces with respect to both allozymes and quantitative traits. This probably results from variable gene flow in space and in time, due to demographic stochasticity in either natural or cultivated populations. Third, differentiation from cultivated landraces was only achieved for the quantitative traits but not for allozymes in two populations. This suggests that natural selection in some locations may oppose gene flow to establish cultivated traits into the natural introgressed populations.

Journal Article↗

PubMed2003

Mitochondrial DNA polymorphisms in nine aboriginal groups of Taiwan: implications for the population history of aboriginal Taiwanese.

Mitochondrial DNA (mtDNA) polymorphisms in the D-loop region and the intergenic COII/tRNA(Lys) 9-bp deletion were examined in 180 individuals from all nine aboriginal Taiwanese groups: Atayal, Saisiat, Bunun, Tsou, Rukai, Paiwan, Ami, Puyuma, and Yami. A comparison of 563-bp sequences showed that there were 61 different sequence types, of which 42 types were specific to respective aboriginal groups. D-loop sequence variation and phylogenetic analysis enabled the 180 aboriginal lineages to be classified into eight monophyletic clusters (designated C1-C8). Phylogeographic analysis revealed that two (C2 and C4) of the eight clusters were new characteristic clusters of aboriginal Taiwanese and accounted for 8.3% and 13.9% of the aboriginal lineages, respectively. From the estimated coalescent times for the two unique clusters, the mtDNA lineages leading to such clusters were inferred to have been introduced into Taiwan approximately 11,000-26,000 years ago, suggesting ancient immigrations of the two mtDNA lineages. Genetic distances, based on net nucleotide diversities between populations, revealed three distinct clusters that were comprised of northern mountain (Atayal and Saisiat), southern mountain (Rukai and Paiwan), and middle mountain/east coast (Bunun, Tsou, Ami, Puyuma, and Yami) groups, respectively. Furthermore, phylogenetic analysis of 16 human populations (including six other Asian populations and one African population) confirmed that the three clusters for aboriginal Taiwanese had remained largely intact. Each of the clusters (north, south, and middle-east coast) was characterized by a high frequency of a particular lineage (C4, C2, and 9-bp deletion, respectively). This may result from random genetic drift among the aboriginal groups after a single introduction of all the mtDNA lineages into Taiwan, but another plausible explanation is that at least three genetically distinct ancestral populations have contributed to the maternal gene pool of aboriginal Taiwanese.

Base Sequence↗

PubMed2001

Genetic and genomic relationships in Leymus Hochst.

Genetic and genomic relationships among three taxonomically related species of Leymus, northern European L. arenarius (octoploid, 2n = 56), northern American/Pacific L. mollis (tetraploid, 2n = 28) and central Eurasian L. racemosus (tetraploid, 2n = 28), were examined using molecular and cytogenetic methods. The amplified fragment length polymorphism (AFLP) analysis clearly differentiated Icelandic populations of L. arenarius from Alaskan populations of L. mollis. The former group is more genetically homogeneous than the latter. Leymus arenarius in Iceland has a common gene pool and a relatively recent origin. The Alaskan L. mollis, on the other hand, is probably a glacial survival that has accumulated high level of genetic variation and has differentiated into subspecies. Analysis of the 18S-26S ribosomal genes, by restriction fragment length polymorphism (RFLP) and fluorescence in situ hybridization (FISH), revealed a very close relationship between the octoploid northern European L. arenarius and the tetraploid Eurasian L. racemosus, such that the former could have originated from the latter, probably via interspecific hybridization. Leymus-specific DNA sequences were isolated and used for analyzing genetic relatedness among five Leymus species and four Psathyrostachys species. The RFLP analysis of retrotransposon sequence pLm44 and ribosomal clone pTa71 clearly revealed a close relationship between these two genera, i.e. higher variation was found within genera than between them. The results support the previous notion that Leymus is autopolyploid having all genomes being designated Ns as in Psathyrostachys, but a major taxonomic revision of this group would require analysis of more species.

Blotting, Southern↗

PubMed1991

Gene targeting and gene trap screens using embryonic stem cells: new approaches to mammalian development.

Mouse embryonic stem cell lines offer an attractive route for introducing rare genetic alternations into the gene pool since the cells can be pre-screened in culture and the mutations then transmitted into the germline through chimera production. Two applications of this technique that seem ideally suited for a genetic analysis of development are enhancer and gene trap screens for loci expressed during gastrulation and production of targeted mutations using homologous recombination. These approaches should greatly increase the number of mouse developmental mutants available and help to elucidate the genetic hierarchy controlling embryogenesis.

Animals↗

PubMedDate not supplied

[Evolution as resistance to entropy. II. A conservative role of the sexual reproduction].

It is claimed that biological meaning of the sex and meiotic genetic recombination is a creation of a barrier for evolution. The transition to sexuality is not merely a change in reproduction mode but a leap to a new known as cohesion. In a sexual population, the lineages of different individuals become tangled into multidimensional net, resulting in a creation of gene pool and new superindividual entity--biological species. A sexual individual can not reproduce its particular genocopy and its fitness is sacrificed to some extent for the fitness of the species. The competition between individuals is replaced with the competition between gene alleles given that the competitors have after all the common offspring. The genotype of the "outstanding" individuals with a highest fitness are not transmitted to next generation, being scattered and shuffled in new combination after unavoidable crossing with the "ordinary" partners. So, the sexual reproduction can evolve only as a whole. Genetic recombination in meiosis changes a character of mutations distribution among gametes enhancing the classes with mutation load both lower and higher than average. By this, an efficiency of the truncated selection (elimination of the individuals with multiple mutations) is enhanced and an ability to restore the initial genotype appears. Evolution within the species becomes reversible, which is equivalent to its virtual cessation. The species acquires an evolution resistance that can be overcome by rare concurrence of circumstances.

Animals↗

PubMed1983

Gene duplication in bovine brain myelin proteolipid and homology with related proteins.

Analysis of the amino acid sequence of bovine brain myelin proteolipid reveals not only extensive internal homology, but also homology with portions of the myelin basic protein, the peripheral nerve myelin protein, Po, and with the small proteolipid subunit of mitochondrial ATP synthase. These results suggest that the myelin proteolipid gene has been constructed from a small number of genetic elements, and that these elements are also found in non-myelin proteins. Furthermore, the proteolipid appears to have evolved by acquisition of elements from a 'gene pool' over a period of time, rather than by a simple duplication mechanism.

Amino Acid Sequence↗

PubMed2006

Race: a risk factor for dengue hemorrhagic fever.

Cuban DHF/DSS outbreaks have provided evidence of a reduced risk of people of Negroid race for DHF/DSS compared to those of Caucasoid race. These observations from Cuban dengue outbreaks have significant epidemiological interest, as the differences in susceptibility to DHF/DSS among racial groups in Cuba coincide with that reported in African and Black Caribbean populations. In this article, we review the literature on race as a risk factor for DHF/DSS and discuss recent results from ongoing studies. Taking into consideration the origins of contemporary Cuban inhabitants, we propose that the Cuban, Caribbean Black and African populations share a common gene pool that could explain, at least partially, the low incidence of dengue hemorrhagic fever in Cuba and Caribbean and African countries. The central role played by immunological mechanisms in the pathogenesis of DHF/DSS has led us to consider that the polymorphic genes associated with the immune response must be carefully considered among those human genes regulating dengue disease severity that might be distributed unequally in Blacks and Whites.

Black People↗

PubMed2006

High incidence of single nucleotide polymorphisms in the prion protein gene of native Brazilian Caracu cattle.

Different alleles of the human and ovine prion protein gene correlate with a varying susceptibility to transmissible spongiform encephalopathies. However, the pathogenic implications of specific polymorphisms in the bovine prion protein gene (PRNP) are only poorly understood. Previous studies on the bovine PRNP gene investigated common European and North American cattle breeds. As a consequence of decades of intensive breeding for specific traits, these modern breeds represent only a small fraction of the bovine gene pool. In this study, we analysed PRNP polymorphisms in the native Brazilian Caracu breed, which developed in geographical isolation since the 16th century. A total of 10 single nucleotide polymorphisms (SNPs) were discovered in the coding region of the Caracu PRNP gene. Eight of the SNPs occurred at high frequencies in Caracu cattle (variant allele frequencies = 0.10-0.76), but were absent or only rarely observed in European and North American breeds. One of the Caracu SNPs was associated with an amino acid exchange from serine to asparagine (f = 0.17). This SNP was not detected in Holstein-Friesian, Simmental and German Gelbvieh and was only rarely detected in beef cattle (f = 0.01). We found 17 haplotypes for PRNP in the Caracu breed.

Animals↗

PubMed1989

Identification of the cystic fibrosis gene: genetic analysis.

Approximately 70 percent of the mutations in cystic fibrosis patients correspond to a specific deletion of three base pairs, which results in the loss of a phenylalanine residue at amino acid position 508 of the putative product of the cystic fibrosis gene. Extended haplotype data based on DNA markers closely linked to the putative disease gene locus suggest that the remainder of the cystic fibrosis mutant gene pool consists of multiple, different mutations. A small set of these latter mutant alleles (about 8 percent) may confer residual pancreatic exocrine function in a subgroup of patients who are pancreatic sufficient. The ability to detect mutations in the cystic fibrosis gene at the DNA level has important implications for genetic diagnosis.

Alleles↗

PubMed2000

Deletion pattern in the dystrophin gene in Turks and a comparison with Europeans and Indians.

Patterns of dystrophin gene deletions in DMD/BMD patients were compared in four populations: Turks (n = 146 deletions), Europeans (n = 838), North Indians (n = 89), and Indians from all over India (n = 103). Statistical tests revealed that there are differences in the proportions of small deletions. In contrast, the distribution of deletion breakpoints and the frequencies of specific deletions commonly observed in the four populations are not significantly different. The variations strongly suggest that sequence differences exist in the introns, and the differences are in agreement with genetic distances among populations. The similarities suggest that some intronic sequences have been conserved and that those will trigger recurrent deletions, since it is unlikely that gene flow would disperse the deleted chromosomes, which vanish from the gene pool in a few generations.

DNA Mutational Analysis↗

PubMed1999

Frequency and stability of chromosomal integration of adenovirus vectors.

One of the limitations of adenovirus vectors is the lack of machinery necessary for their integration into host chromosomes, resulting in short-term gene expression in dividing cells. We analyzed frequencies of integration and persistence of gene expression from integrated adenovirus vectors. Both E1-substituted and helper-dependent adenovirus vectors achieved similar integration efficiencies of approximately 10(-3) to 10(-5) per cell, with the helper-dependent vector showing slightly higher efficiencies. In stable cell pools, gene expression of the integrated vector persisted for at least 50 cell divisions without selection. However, some stable cell clones showed changes in gene expression, which were accompanied by structural changes in the integrated vector DNA.

3T3 Cells↗

PubMed1985

Influence of genetic composition of test-animal populations on chronic toxicity studies used for risk estimation.

A lifespan exposure of mice to benzidine dihydrochloride was conducted for 33 m using both sexes of two populations of mice with the same gene pool. One population was the genetically homogeneous F1 hybrid produced by crossing BALB/cStCrlC3Hf/Nctr males with C57BL/6jfC3Hf/Nctr females. The second population consisted of genetically heterogenous monohybrid cross (MC) offspring produced by mating the F1 hybrids inter se. Data comparisons were made to determine if gene distribution among members of a population affects the response to a toxic insult. Endpoints tested consisted of mortality, liver tumor incidence and time of tumor onset, mortality from reticulum-cell sarcoma, and body weights. In most instances it was noted that among animals not dosed (controls), the F1 population had lower background incidence of lesions and lived longer than the MC population. However, among the dosed animals, the F1 mice were generally more susceptible to the toxic agent and developed higher incidences of the chemically induced lesions than did the MC population. The F1 hybrid population gave a more conservative estimate of risk than did the MC population. The calculation of the liver tumor risk for these two populations showed that lifespan exposure to benzidine would be predicted to result in a larger number (higher risk) when using the F1 data. A 4.5-fold difference in the toxic response was observed between the F1 females and the MC males. This emphasizes the importance of gene distribution in risk estimation studies.

Animals↗