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Antigenic and genetic variation in human respiratory syncytial virus.

BACKGROUND: Human respiratory syncytial virus (HRSV) is a leading cause of serious pediatric respiratory disease worldwide. Natural infection provides only partial protection as repeat infections occur throughout life. A brief review of the extent of antigenic and genetic variation observed in HRSV clinical isolates is presented. METHODS AND RESULTS: Recent experimental research is reviewed, describing key factors that may explain the ability of HRSV to cause multiple infections in the same individual even in the presence of an existing immune response. It is well-appreciated that variability of the G protein, both between and within antigenic subgroups A and B, is partially responsible for repeat HRSV infections. A high level of nucleotide change resulting in amino acid change provides strong evidence for selective pressure for change in G sequences, thus new HRSV variants. Although little variation in gene-coding sequences is observed in the F protein (the second major protective antigen), new evidence of genetic variation has identified alteration of gene expression levels by selection of changes in the gene end termination signal that precedes the gene encoding the F protein. Due to obligatory sequential transcription, these changes affect downstream gene expression levels. These data suggest that modulation of F protein levels may provide a selective advantage in the presence of a preexisting immune response. CONCLUSIONS: Experimental data in HRSV demonstrate that variation exists not only in gene-coding sequences but also in the signals that control gene expression. Thus alteration in the expression of key proteins provides a second type of antigenic "variation." A better understanding of these differences is critical to the development of an effective vaccine.

Adolescent↗

The stress-responsive gene GADD45G is a functional tumor suppressor, with its response to environmental stresses frequently disrupted epigenetically in multiple tumors.

The CpG island of GADD45G was identified as a target sequence during the identification of hypermethylated genes using methylation-sensitive representational difference analysis combined with 5-aza-2'-deoxycytidine demethylation. Located at the commonly deleted region 9q22, GADD45G is a member of the DNA damage-inducible gene family. In response to stress shock, GADD45G inhibits cell growth and induces apoptosis. Same as other GADD45 members, GADD45G is ubiquitously expressed in all normal adult and fetal tissues. However, its transcriptional silencing or down-regulation and promoter hypermethylation were frequently detected in tumor cell lines, including 11 of 13 (85%) non-Hodgkin's lymphoma, 3 of 6 (50%) Hodgkin's lymphoma, 8 of 11 (73%) nasopharyngeal carcinoma, 2 of 4 (50%) cervical carcinoma, 5 of 17 (29%) esophageal carcinoma, and 2 of 5 (40%) lung carcinoma and other cell lines but not in any immortalized normal epithelial cell line, normal tissue, or peripheral blood mononuclear cells. The silencing of GADD45G could be reversed by 5-aza-2'-deoxycytidine or genetic double knockout of DNMT1 and DNMT3B, indicating a direct epigenetic mechanism. Aberrant methylation was further frequently detected in primary lymphomas although less frequently in primary carcinomas. Only one single sequence change in the coding region was detected in 1 of 25 cell lines examined, indicating that genetic inactivation of GADD45G is very rare. GADD45G could be induced by heat shock or UV irradiation in unmethylated cell lines; however, this stress response was abolished when its promoter becomes hypermethylated. Ectopic expression of GADD45G strongly suppressed tumor cell growth and colony formation in silenced cell lines. These results show that GADD45G can act as a functional new-age tumor suppressor but being frequently inactivated epigenetically in multiple tumors.

Antigens, Differentiation↗

Red queen dynamics of protein translation.

We explore adaptive theories for the diversity of translational binding based on the genetic code viewed as a primitive mechanism of resistance. Modifying the set of codons bound by tRNA anticodon molecules or changing the specificity of binding, reduces the replication rate of translational parasites such as viruses. Increased translational efficiency of the parasite requires a high degree of specificity of host tRNAs for the parasite codons. This suggests that the genetic code might serve as the first line of defense against infection. We construct a red queen theory for translational diversity: a theory in which host-translational strategies- as defined by the degree of redundancy (a single anticodon binding many codons for a single amino acid) or degeneracy (many anticodons binding many codons for a single amino acid)-are constantly shifting through time to evade parasitism but where neither parasite nor host gain a systematic advantage.

Animals↗

Narcolepsy and disorders of excessive somnolence.

Recent studies provide valid criteria that help differentiate idiopathic narcolepsy from other disorders of excessive daytime somnolence [3]. Research to date suggests that idiopathic narcolepsy might properly be considered a disorder of excessive sleepiness with dysfunctional REM-sleep mechanisms, clinically evidenced as cataplexy and electrophysiologically recognized as SOREMPs. Given these criteria, a diagnosis can generally be made using a combination of history, PSG, and MSLT. Traditionally, the medical treatment of idiopathic narcolepsy has centered on a two-drug regimen (stimulants for sleepiness and TCAs for cataplexy and auxiliary symptoms). Some newer medications are proving efficacious for sleepiness with minimal adverse effects, whereas others may provide a single-drug regimen that simultaneously addresses sleepiness and cataplexy [18]. New research has allowed some experts to hypothesize that idiopathic narcolepsy may be the result of a genetic predisposition to autoimmune disease [176]. It is possible that aberrant genetic coding of elements in the hypocretin/orexin systems allows a sensitivity to inducible and possibly virally mediated changes, which leave cells in the lateral hypothalamus susceptible to autoimmune attack [96]. As such, genetic screening of high-risk individuals might eventually rationalize the prophylactic use of immunosuppressants in some instances. In the future, for atypical cases(poorly responsive to therapy), genetic, CSF, and brain imaging studies, and possibly even neuronal transplantation may prove beneficial in the assessment and treatment of idiopathic narcolepsy.

Cataplexy↗

Chemical xenogenization of experimental tumors.

Chemical xenogenization occurs when experimental tumors, treated in vivo or in vitro with selected chemicals, become immunogenic, i.e., able to induce a strong rejection response, immunological in nature, in the histocompatible hosts. Unlike modifications induced by haptens, changes in tumor cell immunogenicity associated with chemical xenogenization are heritable as a result of drug interference with the genetic code. Drugs endowed with potent mutagenic activity are known to be powerful xenogenizing agents, and their mechanism of action is traditionally regarded as involving changes in DNA nucleotide sequence. Triazene and nitrosoguanidine derivatives are among the best known examples of this type of compound, and a large body of information has been accumulated over the years regarding the immunogenic properties of the tumor variants obtained following treatment with those xenogenizing agents. The present paper reviews this information, and also discusses the therapeutic implications of xenogenization in experimental systems of tumor immunotherapy. Xenogenization of murine tumors has also been obtained by means of chemicals devoid of mutagenic activity but capable of affecting gene transcriptional activity. The characteristics of this 'new' type of xenogenization are also reviewed and compared to those of triazene xenogenization.

Animals↗

Regularities in mutational variability in selected protein families and the Markovian model of amino acid replacement.

Three families of proteinase inhibitors and the trypsin family were the subjects of the analysis of amino acid replacements at aligned positions. This approach concerned some specific types of replacement and the mechanisms that can be involved in their control. The usefulness of the Markovian model for interpretation of mutational replacement within homologous proteins was examined. The same sequences were also analyzed with the use of the non-Markovian algorithm of genetic semihomology. This study leads to the conclusion that the Markovian model is not suitable for the interpretation of protein mutational variability since: (1) The information about the history of a variable unit is included in its genetic code. (2) This information plays an important role in the probability of further possible changes of the unit.

Algorithms↗

LTR and tat variability of HIV-1 isolates from patients with divergent rates of disease progression.

The genetic heterogeneity and transcription activity of the human immunodeficiency virus type 1 (HIV-1) LTR region and tat gene have been examined. Comparison involved the relevant genomic regions of viruses isolated from twenty long-term survivors and from ten typical progressors. No significant differences were observed in mutation frequencies among the two groups, although there was a significant higher proportion of synonymous substitutions in the tat gene of viruses from typical progressors. Four LTR sequences showed an insertion of 20-31 residues at the junction between the LTR Nef-coding and the LTR noncoding region. Neither these insertions nor other genetic changes found in these sequences affected the LTR transcription function, as measured in transient expression assays using transfection of both established cell lines and peripheral blood lymphocytes with plasmid DNA. The results did not allow the association of structural or functional alterations in LTR or tat with a degree of disease progression. The results reinforce the concepts of complexity of HIV-1 evolution in infected individuals, and the multifactorial nature of progression to AIDS.

Adult↗

Eukaryotes versus prokaryotes: an estimate of evolutionary distance.

The divergence of nucleated organisms and bacteria was 2.6 times more remote in evolution than the divergences of the nucleated organisms into sparate kingdoms, as evidenced by genetic changes in cytochrome c and transfer RNA. The development of the genetic code through the differentiation of transfer RNA's for different amino acids was still more remote in evolution. The overall states of transfer RNA evolution in bacteria and nucleated organisms were comparable.

Bacteria↗

A blueprint for a Human Epigenome Project: the AACR Human Epigenome Workshop.

Epigenetic processes control the packaging and function of the human genome and contribute to normal and pathologic states, including cancer. The time is ripe to undertake an international effort to identify all the chemical changes and relationships between chromatin constituents that provide function to the genetic code. A timely workshop of leading experts, convened by the American Association for Cancer Research (AACR), confirmed that the technology is at hand to begin defining human epigenomes at high resolution.

DNA Methylation↗

Future applications of biotechnology in poultry.

The major biotechnological advances that can be applied in the poultry industry will include molecular genetics, molecular immunology, and solid-state reactions. The elucidation of the genetic code and the development of techniques to manipulate genes offer new opportunities for changing pathogenic agents and changing chickens to reduce the effect of disease and improve productivity. The monoclonal antibody technique and the discovery that cells of the immune response communicate with one another through peptide factors will permit improved diagnostic techniques and enhanced immune responses to vaccines. Immunologic and biochemical reactions that occur on a solid substrate can be used to simplify and accelerate diagnostic tests and to purify antigens and antibodies. These advances will lead to improvements in diagnosis, disease resistance, and productivity of poultry.

Animals↗

Mutation and evolutionary analyses identify NR2E1-candidate-regulatory mutations in humans with severe cortical malformations.

Nuclear receptor 2E1 (NR2E1) is expressed in human fetal and adult brains; however, its role in human brain-behavior development is unknown. Previously, we have corrected the cortical hypoplasia and behavioral abnormalities in Nr2e1(-/-) mice using a genomic clone spanning human NR2E1, which bolsters the hypothesis that NR2E1 may similarly play a role in human cortical and behavioral development. To test the hypothesis that humans with abnormal brain-behavior development may have null or hypomorphic NR2E1 mutations, we undertook the first candidate mutation screen of NR2E1 by sequencing its entire coding region, untranslated, splice site, proximal promoter and evolutionarily conserved non-coding regions in 56 unrelated patients with cortical disorders, namely microcephaly. We then genotyped the candidate mutations in 325 unrelated control subjects and 15 relatives. We did not detect any coding region changes in NR2E1; however, we identified seven novel candidate regulatory mutations that were absent from control subjects. We used in silico tools to predict the effects of these candidate mutations on neural transcription factor binding sites (TFBS). Four candidate mutations were predicted to alter TFBS. To facilitate the present and future studies of NR2E1, we also elucidated its molecular evolution, genetic diversity, haplotype structure and linkage disequilibrium by sequencing an additional 94 unaffected humans representing Africa, the Americas, Asia, Europe, the Middle East and Oceania, as well as great apes and monkeys. We detected strong purifying selection, low genetic diversity, 21 novel polymorphisms and five common haplotypes at NR2E1. We conclude that protein-coding changes in NR2E1 do not contribute to cortical and behavioral abnormalities in the patients examined here, but that regulatory mutations may play a role.

Animals↗

Hypermutability of homonucleotide runs in mismatch repair and DNA polymerase proofreading yeast mutants.

Homonucleotide runs in coding sequences are hot spots for frameshift mutations and potential sources of genetic changes leading to cancer in humans having a mismatch repair defect. We examined frameshift mutations in homonucleotide runs of deoxyadenosines ranging from 4 to 14 bases at the same position in the LYS2 gene of the yeast Saccharomyces cerevisiae. In the msh2 mismatch repair mutant, runs of 9 to 14 deoxyadenosines are 1,700-fold to 51,000-fold, respectively, more mutable for single-nucleotide deletions than are runs of 4 deoxyadenosines. These frameshift mutations can account for up to 99% of all forward mutations inactivating the 4-kb LYS2 gene. Based on results with single and double mutations of the POL2 and MSH2 genes, both DNA polymerase epsilon proofreading and mismatch repair are efficient for short runs while only the mismatch repair system prevents frameshift mutations in runs of > or = 8 nucleotides. Therefore, coding sequences containing long homonucleotide runs are likely to be at risk for mutational inactivation in cells lacking mismatch repair capability.

Base Sequence↗

On codon reassignment.

Schultz and Yarus (J. Mol. Biol. 235:1377-1380, 1994) have proposed that reassignment of codons in the genetic code passes through a stage in which the codons are ambiguously translated. In contrast we state that such ambiguity would be deleterious, and that, to be reassigned, a codon, together with the tRNA that translates the codon, must first disappear from coding sequences, after which a tRNA appears with a mutated anticodon, and this enables the codon to reappear with a changed meaning. In the case of a stop codon, the relevant release factor must change so as to recognize it.

Codon↗

[Gilbert's syndrome: a clinicogenetic trial].

AIM: To improve diagnosis of Gilbert's syndrome (GS) basing on functional and genetic methods of examination. MATERIAL AND METHODS: GS was diagnosed in 88 patients aged 15-72 years using clinical and genetic tests. RESULTS: Genotyping has detected changes in promotor part of the gene coding uridindiphosphateglucuroniltransferase. In homozygous carriers GS was characterized by a higher baseline level of bilirubin, distinct response to functional tests, frequent combination with essential tremor. In heterozygous patients GS often ran latently. CONCLUSION: Four variants of GS course were established: dispepsic, asthenovegetative, jaundice, latent. Low-caloric diet followed by fenobarbital raised sensitivity and specificity of the test. A clinical classification of GS is proposed. The detected disorders of antipirin pharmacokinetics allow prognosis of the risk of unwanted reactions to the drugs metabolized by monooxigenases of the liver.

Adolescent↗

Conservation and co-option in developmental programmes: the importance of homology relationships.

One of the surprising insights gained from research in evolutionary developmental biology (evo-devo) is that increasing diversity in body plans and morphology in organisms across animal phyla are not reflected in similarly dramatic changes at the level of gene composition of their genomes. For instance, simplicity at the tissue level of organization often contrasts with a high degree of genetic complexity. Also intriguing is the observation that the coding regions of several genes of invertebrates show high sequence similarity to those in humans. This lack of change (conservation) indicates that evolutionary novelties may arise more frequently through combinatorial processes, such as changes in gene regulation and the recruitment of novel genes into existing regulatory gene networks (co-option), and less often through adaptive evolutionary processes in the coding portions of a gene. As a consequence, it is of great interest to examine whether the widespread conservation of the genetic machinery implies the same developmental function in a last common ancestor, or whether homologous genes acquired new developmental roles in structures of independent phylogenetic origin. To distinguish between these two possibilities one must refer to current concepts of phylogeny reconstruction and carefully investigate homology relationships. Particularly problematic in terms of homology decisions is the use of gene expression patterns of a given structure. In the future, research on more organisms other than the typical model systems will be required since these can provide insights that are not easily obtained from comparisons among only a few distantly related model species.

Journal Article↗

Sequence analysis of tau 3'untranslated region and saitohin gene in sporadic progressive supranuclear palsy.

BACKGROUND: The extended tau H1 haplotype has previously been described in association with progressive supranuclear palsy (PSP). Recently, a new gene called saitohin (STH), nested within an intron of tau, has been discovered. The Q7R polymorphism of STH appears to be related to late onset Alzheimer's disease. OBJECTIVES: To search for genetic changes in the 3'untranslated region (3'UTR) of tau and adjacent sequence LOC147077, and in the coding region of STH in PSP patients. METHODS: The study included 57 PSP patients and 83 healthy controls. The genetic analysis of each region was performed through sequencing. The Q7R polymorphism was studied through restriction enzyme and electrophoresis analysis. RESULTS: No mutations were found in the regions analysed. The QQ genotype of the STH polymorphism was over-represented in participants with PSP (91.5%) compared with control subjects (47%) (p< or =0.00001). This genotype co-segregated with the H1/H1 haplotype in our PSP cases. CONCLUSIONS: Our results do not support a major role for the tau 3'UTR in PSP genetics. The QQ genotype of STH confers susceptibility for PSP and is in linkage disequilibrium with the H1/H1 haplotype.

3' Untranslated Regions↗

The code within the codons.

For the first time it is shown that each of the three codon bases has a general correlation with a different, predictable amino acid property, depending on position within the codon. In addition to the previously recognized link between the mid-base and the hydrophobic-hydrophilic spectrum, we show that, with the exception of G, the first base is generally invariant within a synthetic pathway. G--coded amino acids show a different order, being found only at the head of the synthetic pathways. The redundancy of the nature of the third base has a previously unrecognised relationship with molecular weight. The bases U and A (transversions) are associated with the most sharply defined or opposite states in both the first and second position, C somewhat less so or intermediate, anf G neutral. The apparently systematic nature of these relationships has profound implications for the origin of the genetic code. It appears to be the remains of the first language of the cell, predating the tRNA/ribosome system, persisting with remarkably little change at a deeper level of organisation than the codon language.

Amino Acid Sequence↗

Codon evolution and conservation of the reading phase in genetic code translation.

The description of the optimized evolution of a code based on 4 nucleotides involves a sequential transition of codons, formed firstly by monomers evolving to dimers and then to triplets, in accordance with the progressive increase of the number of amino acids to be coded. The successive increase in the size of these codons during evolution implies changes in the phase reading of the genetic message, which could become chaotic. In order to overcome this constraint, this paper proposes a codon evolution where two things occur simultaneously: codons change in size and there is an alternation of the molecule which holds the information. For example, the nucleotides of the original oligonucleotide are read as monomers when they are translated to an oligopeptide, but further on, this oligopeptide which is read as amino acid dimers, is translated to a nucleotide form (oligonucleotide). Finally, amino acids conforming a peptide are translated from this oligonucleotide, through a reading of triplets. Although plausible, this evolution is a low-probability process due to the fact that it requires a singular sequence of the oligonucleotide and oligopeptide involved. An alternative hypothesis of evolution is also discussed. It proposes that with the exclusion of the establishment of monomer and dimer codons, there is a direct generation of a code of trinucleotides which arises only when a certain number of amino acids has already been generated. Both hypotheses are discussed in terms of the development of a code in which an optimized hardware is maintained through out its evolution.

Amino Acids↗