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PubMed1992

Infectious in vitro transcripts from amplified cDNAs of the Y and Kin strains of cucumber mosaic virus.

Using a method based on the polymerase chain reaction (PCR) with primers that include the phi 10 promoter of bacteriophage T7, we obtained cDNA clones of the three RNA genomes of two different strains of cucumber mosaic virus (CMV; Kin and Y strains) from which infectious in vitro transcripts were generated, and demonstrated that the same primers could be used for amplification of at least two other strains of CMV (O and Py). This method is rapid and requires only limited nucleotide (nt) sequence data (16-18 nt) from the termini of the RNA species. Either viral RNA or unpurified RNA samples from infected plants can be used as template for first-strand cDNA synthesis. For cDNAs of RNA1 and RNA2 of the Y strain, the transcription efficiency was substantially lower than with the Kin strain, unless the primer sequence included transcribed G residues on the 5' side of the viral cDNA, so that the promoter for T7 RNA polymerase resembled more closely the canonical sequence from the bacteriophage T7 phi 10 promoter. The lower specific infectivity of transcripts of the modified cDNAs was more than compensated for by increased transcription efficiency. The possibility that the PCR process may introduce deleterious mutations into the viral cDNA was investigated by re-amplification of a functional cloned cDNA of RNA2: all six cDNA clones of the re-amplified cDNA produced transcripts as infectious as those from the progenitor cDNA.

Base Sequence↗

PubMed1990

Three parallel linkage groups of human acidic keratin genes.

Two regions of human genomic DNA, each containing several keratin genes, were isolated and partially sequenced. The keratin genes are inactive, having suffered deleterious mutations. Both regions contain at least four keratin genes arranged in a head-to-tail orientation including a pseudogene for keratin K#16. Within each segment there are two keratin genes in close linkage with only 1.5 kb of DNA between them. Sequence comparison of the two regions showed 98.9% identity in both the coding and the intronic segments of the pseudogenes. The pseudogenes show 94% identity to their functional counterparts. Southern hybridization analysis showed that the segments are paralogous, not allelic. The regions are products of two independent, recent duplication events. The first occurred approximately 24 million years ago, after the separation of primates from the rhesus/baboon line. The second is specific for the human lineage, having occurred approximately 3.8 million years ago. Analysis of the genomic DNAs of primates showed the presence of only one of the regions in the DNAs of gibbon and gorilla, while rhesus monkey and baboon were missing both copies. We conclude that the human keratin genes are still actively evolving, with new duplications having occurred as recently as after the separation of human and gorilla ancestors.

Amino Acid Sequence↗

PubMedDate not supplied

Glucocerebrosidase recombinant allele: molecular evolution of the glucocerebrosidase gene and pseudogene in primates.

Glucocerebrosidase is a lysosomal enzyme that hydrolyses the beta-glycosidic linkage of glucocerebroside, a ubiquitous sphingolipid present in the plasma membrane of mammalian cells. Deleterious mutations in the glucocerebrosidase gene result in Gaucher disease, the most prevalent lysosomal storage disease. Humans have one glucocerebrosidase functional gene and pseudogene that were located 16 kb apart on chromosome 1q21 and share 96% overall sequence similarity. Recombination between the two genes creates a 'complex allele' that renders glucocerebrosidase non-functional and accounts for >20% of the total Gaucher disease mutations in some population. The glucocerebrosidase pseudogene is absent in all other mammalian species surveyed so far. In order to learn more about the molecular evolution of the glucocerebrosidase functional gene and pseudogene, we have sequenced approximately 1.1 kb of the C-terminal region of these genes that encodes the enzyme catalytic site, from PCR-amplified genomic DNA of gorilla, chimpanzee, orangutan (the great apes), and squirrel monkey (a new-world monkey). In gorilla, chimpanzee, and orangutan, there are two copies of the glucocerebrosidase gene while the squirrel monkey possesses only a single copy. Similar to human, the second copy of glucocerebrosidase gene in gorilla and chimpanzee is non-functional because of a 55-bp deletion in exon 9, while that in orangutan appears to be unaffected and may still be functional. These data suggest that the glucocerebrosidase gene duplication event occurred after squirrel monkey divergence from the great apes, and that the exon 9 deletion that rendered the second copy of the glucocerebrosidase gene non-functional occurred prior to the divergence of gorilla and chimpanzee but after the divergence of orangutan from their common ancestor to human. The two genes in each species are least similar in gorilla and chimpanzee (97.8%) and most similar in orangutan (99.5%). None of the nucleotide variations in the GBA gene among the primates correspond to known mutations in Gaucher disease. Phylogenetic tree analysis using DNAstar and PAUP4.0 software indicates that gene conversion caused the evolution of glucocerebrosidase functional gene and pseudogene to be concerted.

Alleles↗

PubMed2006

Autosomal recessive hypercholesterolaemia: discrimination of ARH protein and LDLR function in the homozygous FH phenotype.

BACKGROUND: Phenocopies of homozygous familial hypercholesterolemia (hoFH) having autosomal recessive inheritance, were recently found to arise from defects in the LDL receptor (LDLR) adapter protein, called ARH, which facilitates the clearance of circulating LDL. Discrimination between the two causes of the phenotype at a clinical level may not be possible when parents display moderate hypercholesterolaemia. An effective strategy is thus required to identify the appropriate mechanism for the disorder. METHODS: Fibroblast LDL uptake studies were coupled with Western blotting for ARH protein in cell extracts, to identify the defective gene before DNA studies were initiated. Two subjects with the hoFH phenotype, but with indeterminate dyslipidaemia in their parents, were fully worked up. RESULTS: Defective LDL metabolism was established in both patients by functional and protein studies and further confirmed by detecting deleterious mutations, in the LDLR and ARH genes. The ARH patient is the first subject of Negroid identity to be described and records a specific mutation in this racial grouping. CONCLUSION: This study highlights the occasional complexity and uncertainty of a clinical diagnosis of hoFH and presents Western blotting of leucocyte extracts for ARH protein, as a rapid strategy for the detection of ARH before sequencing the gene for mutation(s). This strategy may be particularly useful in populations where founder mutations for ARH and LDLR defects are rare or co-exist.

Adaptor Proteins, Signal Transducing↗

PubMed2026

Escape and survival: transposon adaptations in the face of insect host silencing.

Transposable elements (TEs) are mobile genetic sequences that have long resided within host genomes. Over this shared history, a continuous process of co-evolution has forged a diverse array of dynamic TE-host interactions. In an evolutionary arms race, hosts must silence TEs to protect genome integrity from deleterious mutations by TE insertions, while TEs must evade this silencing to survive. TE adaptations to host genomes have recently gained prominence, following many discoveries in eukaryotic genomes. Here, I discuss TE strategies to evade host silencing and ensure their long-term persistence within host genomes, focusing on insects as the primary model system. Furthermore, by describing host silencing, I postulate potential evasive mechanisms that may drive TE adaptation within host genomes.

Journal Article↗

PubMed2006

Evolutionary fate of duplicate genes encoding aspartic proteinases. Nothepsin case study.

Gene duplication is considered an important evolutionary mechanism leading to new gene functions. According to the classical model, one gene copy arising from gene duplication retains the ancestral function, whilst the other becomes subject to directional selection for some novel functions. Hence, according to this model, long-term persistence of two paralogous genes is possible only with the acquisition of functional innovation. In the absence of neofunctionalization, one of the duplicate genes may be lost following accumulation of deleterious mutations, ultimately leading to the loss of function. Recently, new mechanisms have been proposed according to which both paralogs are maintained without apparent neofunctionalization. In this paper we describe the molecular evolution of the aspartic proteinase gene family, with particular regard for the nothepsin gene, a sex- and tissue-specific form of aspartic proteinase active in fish. The finding of nothepsin in a reptile is indicative of the presence of this gene in organisms other than fish. However, the failure to find any nothepsin-like gene in avian, murine and human genome suggests that the gene has been lost in certain lineages during evolution. At variance with piscine nothepsin expressed exclusively in female liver under the estrogens action, the reptilian counterpart lacks both tissue and sex specificity, as it is constitutively expressed in different tissues of male and female specimens. The expression of the nothepsin gene in fish and lizard is accompanied by the expression of a paralogous gene encoding for cathepsin D. Functional divergence analysis indicates that cathepsin D accumulated amino acid substitutions, whereas nothepsin retained most of the ancestral functions. Phylogenetic analysis shows a preponderance of replacement substitutions compared to silent substitutions in the branch leading to the cathepsin D clade, whilst nothepsin evolves under negative selection. To explain the loss of the nothepsin gene in certain lineages, we propose a model that takes into account the complementary degenerative mutations occurring in regulatory elements of the promoter regions of the two genes. According to this model, gene loss occurs whenever the two genes acquire the same expression pattern. The coexistence of cathepsin D and nothepsin is explained in terms of metabolic cooperation of the two enzymes.

Amino Acid Sequence↗

PubMed2005

Clinicopathologic features and long-term outcome of patients with medullary breast carcinoma managed with breast-conserving therapy (BCT).

PURPOSE: The purpose of this study is to compare the clinical characteristics and outcome of medullary carcinoma to infiltrating ductal carcinoma of the breast in a large cohort of conservatively managed patients with long-term follow-up. METHODS AND MATERIALS: Chart records of patients with invasive breast cancer managed with breast-conserving therapy (BCT) at the therapeutic radiology facilities of Yale University School of Medicine before 2001 were reviewed. Forty-six cases (1971-2001) were identified with medullary histology; 1,444 patients with infiltrating ductal carcinoma served as a control group. RESULTS: The medullary cohort presented at a younger age with a higher percentage of patients in the 35 years or younger age group (26.1% vs. 6.6%, p < 0.00001). Twelve patients with medullary histology underwent genetic screening, and 6 patients were identified with deleterious mutations. This group showed greater association with BRCA1/2 mutations compared with screened patients in the control group (50.0% vs. 15.8%, p = 0.0035). The medullary cohort was also significantly associated with greater T stage and tumor size (37.0% vs. 17.2% T2, mean size 3.2 vs. 2.5 cm, p = 0.00097) as well as negative ER (84.9% vs. 37.6%, p < 0.00001) and PR (87.5% vs. 48.1%, p = 0.00001) status. As of February 2003, median follow-up times for the medullary and control groups were 13.9 and 14.0 years, respectively. Although breast relapse-free rates were not significantly different (76.7% vs. 85.2%), 10-year distant relapse-free survival in the medullary cohort was significantly better than in the control group (94.9% vs. 77.5%, p = 0.028). CONCLUSIONS: Despite poor clinicopathologic features, patients with medullary histology demonstrate favorable long-term distant relapse-free survival. Local control rates of patients with medullary and infiltrating ductal carcinoma are comparable. These findings suggest that patients diagnosed with medullary carcinoma are appropriate candidates for BCT and are associated with favorable long-term prognosis.

Adult↗

PubMed2004

Molecular basis of fitness loss and fitness recovery in vesicular stomatitis virus.

Viral populations subjected to repeated genetic bottleneck accumulate deleterious mutations in a process known as Muller's ratchet. Asexual viruses, such as vesicular stomatitis virus (VSV) can recover from Muller's ratchet by replication with large effective population sizes. However, mutants with a history of bottleneck transmissions often show decreased adaptability when compared to non-bottlenecked populations. We have generated a collection of bottlenecked mutants and allowed them to recover by large population passages. We have characterized fitness changes and the complete genomes of these strains. Mutations accumulated during the operation of Muller's ratchet led to the identification of two potential mutational hot spots in the VSV genome. As in other viral systems, transitions were more common than transversions. Both back mutation and compensatory mutations contributed to recovery, although a significant level of fitness increase was observed in nine of the 13 bottlenecked strains with no obvious changes in the consensus sequence. Additional replication of three strains resulted in the fixation of single point mutations. Only two mutations previously found in non-bottlenecked, high-fitness populations that had been adapting to the same environment were identified in the recovered strains.

Animals↗

PubMed2006

Kinetic computational alanine scanning: application to p53 oligomerization.

We have developed a novel computational alanine scanning approach that involves analysis of ensemble unfolding kinetics at high temperature to identify residues that are critical for the stability of a given protein. This approach has been applied to dimerization of the oligomerization domain (residues 326-355) of tumor suppressor p53. As validated by experimental results, our approach has reasonable success in identifying deleterious mutations, including mutations that have been linked to cancer. We discuss a method for determining the effect of mutations on the location of the dimerization transition state.

Alanine↗

PubMed2005

Background selection and population differentiation.

A general analytical formula is derived, which predicts the effects of background selection on population differentiation at a neutral locus as a result of its linkage with selected loci of deleterious mutations. The theory is based on the assumptions of random mating, multiplicative fitness, and weak selection in hermaphrodite plants in the island model of population structure. The analytical results show that Fst at the neutral locus increases as a result of the effects of background selection, regardless of the dependence or independence among linked background selective loci. The increment in Fst is closely related to the magnitude of linkage disequilibria between the neutral locus and selected loci, and can be estimated by the ratio of Fst with background selection to Fst without background selection minus one. The steady-state linkage disequilibrium between a neutral locus and a selected locus in subpopulations, primarily attained by gene flow, decreases with the recombination rate, and can be enhanced when there are dependence among linked selected loci. Monte Carlo computer simulations with two- and three-locus models show that the analytical formulae perform well under general conditions. Application of the present theory may aid in analyzing the genome-wide mapping of the effect of background selection in terms of Fst.

Computer Simulation↗

PubMed2005

Single nucleotide polymorphisms in the apoptosis receptor gene TNFRSF6.

The homotrimeric Fas receptor, an inducer of lymphocyte apoptosis, plays a critical role in cellular pathways of immune homeostasis and immunologic tolerance. Inherited and acquired defects in the Fas gene, TNFRSF6 (tumor necrosis factor receptor superfamily member 6) have been associated with human autoimmune lymphoproliferative syndrome (ALPS) and a spectrum of other complex autoimmune diseases and malignancies. In addition to over 60 deleterious mutations associated with dominant inhibitory defects or null mutations of TNFRSF6, several sequence variants have been noted. To facilitate interpretation of genotypes of this important locus, we sequenced DNA from unrelated, healthy Caucasians and African Americans. Two new and 12 previously recorded SNPs were confirmed, and their allele frequencies were determined. We also investigated haplotype frequencies and linkage disequilibrium (LD) coefficients for these SNPs in Caucasians. Four TNFRSF6 SNP pairs were found to be in strong LD. The TNRFSF6 SNPs are useful for linkage and loss of heterozygosity studies probing the role of Fas-mediated apoptosis in autoimmune diseases and malignancies.

Black or African American↗

PubMed2006

[Identification and management of hereditary breast-ovarian cancers (2004 update)].

BACKGROUND: Since the last recommendations, up to 2500 new references had been published on that topic. METHODOLOGY: On the behalf of the health Minister, the Ad Hoc Committee consisted of 13 experts carried out a first version revisited by five additional experts who critically analyzed the first version of the report. MAIN UPDATING: Breast and ovarian cancer seem to be associated with fewer deleterious mutations of BRCA1 and BRCA2 than previously thought. The screening of ovarian cancer is still not an attractive option while in contrast MRI may be soon for these young women with dense breast, the recommended option for breast cancer screening. The effectiveness of prophylactic surgeries is now well established. French position is to favor such surgeries with regard to a quality of life in line with the expected benefit, and providing precise and standardized process described in the recommendation. CONCLUSIONS: Due to methodological flaws, the low power and a short follow-up of the surveys, this statement cannot however aspire to a high stability.

Breast Neoplasms↗

PubMed2004

GroEL and the maintenance of bacterial endosymbiosis.

Many eukaryotic organisms have symbiotic associations with obligate intracellular bacteria. The clonal transmission of endosymbionts between host generations should lead to the irreversible fixation of slightly deleterious mutations in their non-recombinant genome by genetic drift. However, the stability of endosymbiosis indicates that some mechanism is involved in the amelioration of the effects of these mutations. We propose that the chaperone GroEL was involved in the acquisition of an endosymbiotic lifestyle not only by means of its over-production, as proposed by Moran, but also by its adaptive evolution mediated by positive selection to improve the interaction with the unstable endosymbiont proteome.

Bacterial Physiological Phenomena↗

PubMed2004

Genic capture and resolving the lek paradox.

The genic capture hypothesis offers a resolution to the question of how genetic variation in male sexually selected traits is maintained in the face of strong female preferences. The hypothesis is that male display traits are costly to produce and hence depend upon overall condition, which itself is dependent upon genes at many loci. Few attempts have been made to test the assumptions and predictions of the genic capture hypothesis rigorously and, in particular, little attention has been paid to determining the genetic basis of condition. Such tests are crucial to our understanding of the maintenance of genetic variation and in the evaluation of recent models that propose a role for sexual selection in the maintenance of sex. Here, we review approaches to testing the link between genetically determined condition and levels of sexual trait expression and consider the probable importance of deleterious mutations.

Journal Article↗

PubMed2004

Control of human host immunity to mycobacteria.

Infection with Mycobacterium tuberculosis results in disease in 5-10% of exposed individuals, whereas the remainder controls infection effectively. Similar inter-individual differences in disease susceptibility are characteristic features of leprosy, typhoid fever, leishmaniasis and other chronic infectious diseases, including viral infections. Although the outcome of infection is influenced by many factors, it is clear that genetic host factors play an important role in controlling disease susceptibility to intracellular pathogens. Knowledge of the genes involved and their downstream cellular pathways will provide new insights for the design of improved and rationalized strategies to enhance host-resistance, e.g. by vaccination. In addition, this knowledge will aid in identifying better biomarkers of protection and disease, which are essential tools for the monitoring of vaccination and other intervention trials. The recent identification of patients with deleterious mutations in genes that encode major proteins in the type-1 cytokine (IL-12/IL23-IFN-gamma) axis, that suffered from severe infections due to otherwise poorly pathogenic mycobacteria (non-tuberculous mycobacteria (NTM) or M. bovis Bacille Calmette-Guerin (BCG)) or Salmonella species has revealed the major role of this system in innate and adaptive immunity to mycobacteria and salmonellae. Clinical tuberculosis has now been described in a number of patients with IL-12/IL23-IFN-gamma system defects. Moreover, unusual mycobacterial infections were reported in several patients with genetic defects in NEMO, a key regulatory molecule in the NFkappaB pathway. These new findings will be discussed since they provide further insights into the role of type-1 cytokines in immunity to mycobacteria, including M. tuberculosis.

Adjuvants, Immunologic↗

PubMed2004

The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand.

Dengue represents a major public health problem in Thailand, with all four viral serotypes co-circulating. Dengue virus serotype 4 (DENV-4) is the least frequently sampled serotype, although one that is often associated with hemorrhagic fever during secondary infection. To determine the evolutionary forces shaping the genetic diversity of DENV-4, and particularly whether its changing prevalence could be attributed to instances of adaptive evolution in the viral genome, we undertook a large-scale molecular epidemiological analysis of DENV-4 in Bangkok, Thailand, using both E gene and complete coding region sequences. This analysis revealed extensive genetic diversity within a single locality at a single time, including the discovery of a new and divergent genotype of DENV-4, as well as a pattern of continual lineage turnover. We also recorded the highest average rate of evolutionary change for this serotype, at 1.072 x 10(-3) nucleotide substitutions per site, per year. However, despite this abundant genetic variation, there was no evidence for adaptive evolution in any gene, codon, or lineage of DENV-4, with the highest rate of nonsynonymous substitution observed in NS2A. Consequently, the rapid turnover of DENV-4 lineages through time is most likely the consequence of a high rate of deleterious mutation in the viral genome coupled to seasonal fluctuations in the size of the vector population.

Adolescent↗

PubMed2002

A high frequency of mtDNA polymorphisms in HeLa cell sublines.

The complete mtDNA sequences from the uncloned "founder" HeLa cells and from five sublines have been determined. These sequences all carry a common "core" of 38 single basepair alterations relative to the revised Cambridge Reference Sequence (CRS). The HeLa mitochondrial genome is of African descent and it is a member of the African L3 haplogroup. The sequence of the HeLa mtDNA resolves the uncertainty surrounding the mosaic composition of the original CRS for human mtDNA. Most importantly, we detected a total of eight polymorphisms that have arisen in the mtDNA coding region of different HeLa sublines. These observations suggest that HeLa mtDNA has a high rate of sequence divergence, relative to the phylogenetically-derived divergence rate for mtDNAs in the human population, which results from a relaxation of negative selection against the fixation of deleterious mutations. Furthermore, this high frequency of polymorphisms in HeLa mtDNA may reflect a process similar to the accumulation of somatic mtDNA mutations in human cancers. Preliminary analysis of single-cell derived subclone lines revealed the occurrence of another polymorphism and provided evidence for a large number of mtDNA segregation units.

Base Sequence↗

PubMed1998

The conflict theory of genomic imprinting: how much can be explained?

In some mammalian genes, paternally and maternally derived alleles are expressed differently: this phenomenon is called genomic imprinting. Several-explanations have been proposed for the observed patterns of genomic imprinting, but the most successful explanation is the genetic conflict hypothesis--natural selection operating on the gene expression produces the parental origin-dependent gene expression--because the paternally derived allele tends to be less related to the siblings of the same mother than the maternal allele and hence the paternal allele should evolve to be more aggressive in obtaining maternal resources. The successes and failures of this argument have been examined in explaining the observed patterns of genomic imprinting in mammals. After a brief summary of the observations with some examples, a quantitative genetic model describing the evolution of the cis-regulating element of a gene affecting the maternal resource acquisition was presented. The model supports the verbal argument that the growth enhancer should evolve to show imprinting with the paternal allele expressed and the maternal allele inactive, whereas a growth suppressor gene tends to have an inactive paternal allele and an active maternal allele. There are four major problems of the genetic conflict hypothesis. (1) Some genes affect embryonic growth but are not imprinted (e.g., Igf1), which can be explained by considering recessive, deleterious mutations on the coding regions, (2) A gene exists that shows the pattern that is a perfect reversal (Mash2), which is needed for placental growth, and yet has an active maternal allele and an inactive paternal allele. This can be explained if the overproduction of this gene causes dose-sensitive abortion to occur in early gestation. (3) Paternal disomies are sometimes smaller than normal embryos. This is a likely outcome of evolution if imprinted genes control the allocation between placenta and embryo by modifying the cell developmental fate. (4) Genes on X chromosomes do not follow the predictions of the genetic conflict hypothesis. For genes on X chromosomes, two additional forces of natural selection (sex differentiation and dosage compensation) cause genomic imprinting, possibly in the opposite direction. Available evidence suggests that these processes are stronger than the natural selection caused by female multiple mating. Finally, the same formalism of evolution can handle an alternative nonconflict hypothesis: genomic imprinting might have evolved because it reduces the risk of the spontaneous development of parthenogenetic embryo, causing a serious threat to the life of the mother (ovarian time bomb hypothesis). This hypothesis can also explain major patterns of genomic imprinting. In conclusion, the genetic conflict hypothesis is very successful in explaining the observed patterns of imprinting for autosomal genes and probably is the most likely evolutionary explanation for them. However, for genes on X chromosomes, other processes of natural selection are more important. Considering that a nonconflict hypothesis can also explain the patterns in principle, we need a quantitative estimate of various parameters, such as the rate of dose-dependent abortion, the degree of female promiscuity, and the rate of spontaneous development of the parthenogenetic embryo, in order to make judgments on the relative importance of different forces of natural selection to form genomic imprinting.

Abortion, Veterinary↗