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PubMed2006

Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity.

Exploring the utility of de novo gene synthesis with the aim of designing stably attenuated polioviruses (PV), we followed two strategies to construct PV variants containing synthetic replacements of the capsid coding sequences either by deoptimizing synonymous codon usage (PV-AB) or by maximizing synonymous codon position changes of the existing wild-type (wt) poliovirus codons (PV-SD). Despite 934 nucleotide changes in the capsid coding region, PV-SD RNA produced virus with wild-type characteristics. In contrast, no viable virus was recovered from PV-AB RNA carrying 680 silent mutations, due to a reduction of genome translation and replication below a critical level. After subcloning of smaller portions of the AB capsid coding sequence into the wt background, several viable viruses were obtained with a wide range of phenotypes corresponding to their efficiency of directing genome translation. Surprisingly, when inoculated with equal infectious doses (PFU), even the most replication-deficient viruses appeared to be as pathogenic in PV-sensitive CD155tg (transgenic) mice as the PV(M) wild type. However, infection with equal amounts of virus particles revealed a neuroattenuated phenotype over 100-fold. Direct analysis indicated a striking reduction of the specific infectivity of PV-AB-type virus particles. Due to the distribution effect of many silent mutations over large genome segments, codon-deoptimized viruses should have genetically stable phenotypes, and they may prove suitable as attenuated substrates for the production of poliovirus vaccines.

Animals↗
PubMed1981

Genome structure of Abelson murine leukemia virus variants: proviruses in fibroblasts and lymphoid cells.

We have prepared full-length DNA clones of the Abelson murine leukemia virus (A-MuLV) genome. A specific probe homologous to the central portion of the A-MuLV genome was prepared by nick translation of a subcloned restriction fraction from the cloned DNA. The probe was used to examine the genome structure of several A-MuLV variants. The conclusions are: (i) three viruses coding for Abelson-specific proteins of molecular weight 120,000, 100,000, and 90,000 had genomes indistinguishable in size, suggesting that the shorter proteins are the result of early translational termination; (ii) compared with the genome encoding the 120,000-dalton (120K) protein, a genome coding for a 160K protein was 0.8 kilobase larger in the A-MuLV-specific region; and (iii) a genome coding for a 92K protein had a 700-base pair deletion internal to the coding region. This mutant was transformation defective: its 92K protein lacked the protein kinase activity normally associated with the A-MuLV protein, and cells containing the virus were not morphologically transformed. In addition, we determined the number of A-MuLV proviruses in each of several transformed fibroblast and lymphoid cells prepared by infection in vitro. These experiments show that a single copy of the A-MuLV provirus is sufficient to transform both types of cells and that nonproducer cells generally have only one integrated provirus.

Abelson murine leukemia virus↗
PubMed2000

Generation of cytomegalovirus-specific human T-lymphocyte clones by using autologous B-lymphoblastoid cells with stable expression of pp65 or IE1 proteins: a tool to study the fine specificity of the antiviral response.

Cytotoxic T lymphocytes (CTLs) play a central role in the control of persistent human cytomegalovirus (HCMV) infection in healthy virus carriers. Previous analyses of the specificity of HCMV-reactive CD8(+) CTLs drawn from in vitro models in which antigen-presenting cells were autologous fibroblasts infected with laboratory HCMV strains have shown focusing of CTL responses against the major tegument protein, pp65. By contrast, the 72-kDa major immediate-early protein (IE1) was identified as a minor target for this response. Here we have studied the fine specificity and T-cell-receptor features of T-cell clones generated against autologous B lymphoblastoid cell lines stably transfected with HCMV cDNA coding for either pp65 or a natural variant of IE1. This strategy allowed efficient generation of T-cell clones against IE1 and pp65 and led to the identification of several new IE1 and pp65 epitopes, including some located in polymorphic regions of IE1. Such an approach may provide relevant information about the characteristics of the CTL response to IE1 and the effect of viral polymorphism on the immune response against HCMV.

Alleles↗
PubMed2005

Spastin mutations are frequent in sporadic spastic paraparesis and their spectrum is different from that observed in familial cases.

BACKGROUND: SPG4 encodes spastin, a member of the AAA protein family, and is the major gene responsible for autosomal dominant spastic paraplegia. It accounts for 10-40% of families with pure (or eventually complicated) hereditary spastic paraparesis (HSP). OBJECTIVE: To assess the frequency of SPG4 mutation in patients with spastic paraplegia but without family histories. METHODS: 146 mostly European probands with progressive spastic paraplegia were studied (103 with pure spastic paraplegia and 43 with additional features). Major neurological causes of paraplegia were excluded. None had a family history of paraplegia. DNA was screened by DHPLC for mutations in the 17 coding exons of the SPG4 gene. Sequence variants were characterised by direct sequencing. A panel of 600 control chromosomes was used to rule out polymorphisms. RESULTS: The overall rate of mutations was 12%; 19 different mutations were identified in 18 patients, 13 of which were novel. In one family, where both parents were examined and found to be normal, the mutation was transmitted by the asymptomatic mother, indicating reduced penetrance. The parents of other patients were not available for analysis but were reported to be normal. There was no evidence for de novo mutations. The mutations found in these apparently isolated patients were mostly of the missense type and tended to be associated with a less severe phenotype than previously described in patients with inherited mutations. CONCLUSIONS: The unexpected presence of SPG4 gene mutations in patients with sporadic spastic paraplegia suggests that gene testing should be done in individuals with pure or complicated spastic paraplegia without family histories.

Adenosine Triphosphatases↗
PubMed1997

The rat 5S rRNA bona fide gene repeat maps to chromosome 19q12-->qter and the pseudogene repeat maps to 12q12.

The bona fide 5S rRNA genes in the rat are found in a 1.8-kb tandem repeat and the pseudogenes occur in a 2.5-kb tandem repeat. Three bona fide 5S rRNA genes and one gene variant with one base substitution in the coding region were isolated from the 1.8-kb repeat. Six pseudogenes were isolated from the 2.5-kb repeat. The total number of genes/gene variants/pseudogenes is 700-1200 copies per haploid genome, and the pseudogene repeat contains about 50% more 5S rDNA related sequences compared with the bona fide gene repeat. Various well-defined 5' - and 3'-flanking sequences of the bona fide gene and of the pseudogene were used for in situ hybridization to metaphase chromosomes. The results showed that the bona fide 5S rRNA gene repeat Rn5s maps to chromosome 19q12 and the pseudogene repeat Rn5sp maps to 12q12.

Animals↗
PubMed1997

Probabilistic incremental program evolution

Probabilistic incremental program evolution (PIPE) is a novel technique for automatic program synthesis. We combine probability vector coding of program instructions, population-based incremental learning, and tree-coded programs like those used in some variants of genetic programming (GP). PIPE iteratively generates successive populations of functional programs according to an adaptive probability distribution over all possible programs. Each iteration, it uses the best program to refine the distribution. Thus, it stochastically generates better and better programs. Since distribution refinements depend only on the best program of the current population, PIPE can evaluate program populations efficiently when the goal is to discover a program with minimal runtime. We compare PIPE to GP on a function regression problem and the 6-bit parity problem. We also use PIPE to solve tasks in partially observable mazes, where the best programs have minimal runtime.

Journal Article↗
PubMed1987

Regulation of human IGF-II transcription in fetal and adult tissues.

The insulin-like growth factors are single-chain polypeptides which promote cell multiplication in vitro. Their role in mammalian development is uncertain, although they have been implicated as modulators of cell growth and differentiation. We present evidence that the human IGF-II gene has at least two promoters, and their expression may be developmentally controlled in the liver. Most of the IGF-II transcripts in the fetal organs examined are derived from a promoter which is different to that used for most adult liver IGF-II mRNAs. Steady-state levels of IGF-II transcripts are seen to be dramatically reduced in organs of adult rather than fetal origin. This observation is apparently not linked to promoter usage and therefore suggests a second level of transcriptional control. In addition, we show that an alternative splicing event at an intron/exon boundary, which results in an mRNA with an altered coding potential, is not developmentally regulated. This variant IGF-II mRNA is coexpressed with the major species of IGF-II at a low, but constant, ratio in all fetal and adult organs examined.

Base Sequence↗
PubMed2002

Report of 16 kindreds and one kindred with hMLH1 germline mutation.

AIM: To analyze the diagnosis and treatment of 16 hereditary nonpolyposis colorectal cancer (HNPCC) kindreds, and to report the first kindred with hMLH1 germline mutation in Mainland China. METHODS: The diagnosis, treatment and follow-up study of 16 HNPCC kindreds were retrospectively reviewed. Data concerning site of the malignant tumor, age at the diagnosis, history of synchronous and/or metachronous cancer, and histopathology of tumors were recorded. All treatments had won formal consent. PCR and SSCP were used to screen the coding region of hMLH1 and hMSH2 genes. Variant bands were sequenced by a 377 DNA sequencer. RESULTS: Among sixteen kindreds, sixty-eight patients had a mean age of 50.8 years, including twenty-one multiple cancer patients and forty-six colorectal cancer patients (metachronous colorectal cancers in sixteen). A total of one hundred and one malignant neoplasms were found in these sixty-eight patients, including 50 colonic, 17 rectal, 11 gastric, 7 endometrial, and 4 esophageal cancers. 39.5% colorectal patients had metachronous cancers within ten years who needed reoperations. A germline G265T nonsense mutation was found in the third exon of hMLH1, resulting in a stop codon and truncated protein. Three phenotypically normal family members were also found to carry the mutated gene. CONCLUSION: HNPCC is a typical auto-dominant hereditary disease, the main characteristics include early onset and frequency of cancers; predominance of colorectal, especially right-sided colon cancers; frequency of multiple primary cancers (especially colorectal cancers). Segmental resection for colorectal cancers is not eligible for colorectal cancer patient in HNPCC kindreds. Intensive follow-up is essential for all patients and possible gene carriers. The first HNPCC kindred with hMLH1 gene germline mutation was identified in Mainland China, and three phenotypically normal family members were found to be carriers of the mutated gene. The G265T germline (nonsense) mutation in the third exon of hMLH1 found here had not been reported previously in the literature.

Adaptor Proteins, Signal Transducing↗
PubMed1999

Recovery of upstream cDNA sequences by a PCR-based biotin-capture method.

The world-wide, large-scale sequencing efforts have generated an abundance of partial cDNA sequences, i.e., expressed sequence tags (ESTs), accessible in the public databases. To enable functional characterization of these partial cDNA sequences, general and robust methods for recovery of upstream full-coding cDNA sequences are needed. Here, a novel biotin- and PCR-assisted capture method was used directly on poly(A)+ RNA for the purpose of generating a full-coding sequence of a gene with only partially known sequence and for which a full-length clone of the gene was not found in existing cDNA libraries. The presented method involves linear extension by reverse transciptase from a biotinylated primer annealing in a region with known sequence. After capture of the generated single-stranded cDNA onto paramagnetic beads, unspecifically annealing primers, i.e., arbitrary primers, were used to generate cDNA fragments that could be amplified by PCR and thereafter directly sequenced without subcloning. By using the presented strategy, which is to be seen as a complement to rapid amplification of cDNA ends (RACE)-related methods, we were able to recover full-coding sequence versions of two potential splice variants of the target gene. The general applicability of the novel method for recovery and sequencing of cDNA sequences is discussed.

Animals↗
PubMed2000

[Disorders of thyroid function and fertility disorders].

The treatment of young infertile women and women with menstrual cycle dysfunction by thyroid gland extracts and later by pure thyroid hormones led to improvement of their menstrual cycle and frequently also to desired conception. Therefore a functional connection between thyroid and ovary, i.e. an effect of thyroid hormones on ovarian reproductive function was assumed. However, till recently exact scientific evidence did not exist, which could explain the functional connection between these two endocrine glands. The scientific discoveries of the last years in the area of human reproduction (which continues in experimental work on the superfamily of steroid/thyroid receptors, which have been coded by protoonkogen c-erb-A variants), presented proof of the presence of thyroid stimulating hormone (TSH) as well as of T3-receptors in ovary and thus way of direct TSH- and T3-effect on steroidogenesis and oocyte maturation. The authors present scientific discoveries from recent years, which seem to be crucial for the explanation of the thyroid-ovary relation and present the treatment algorithm for practical clinical application of experimental knowledge of human reproduction.

Female↗
PubMedDate not supplied

[Contribution of genotyping and phenotyping of biotransformation in therapeutic drug monitoring].

Genetic-controlled biotransformation is a factor partly accounting for interindividual variability in drug responses. This control occurs via gene coding for polymorphic enzymes or rare genetic variants. Currently, the clinical relevance of genetically controlled biotransformation concerns only a few drugs. Determinants of clinical relevance depend on the size of the contribution of the metabolic pathway subject to genetic control, the existence of a relationship between the concentration and the therapeutic and/or toxic effect, a low therapeutic index and a pharmacokinetic variability smaller than pharmacodynamic one. Phenotyping using test drugs allows the determination of the activity of the drug-metabolizing enzyme but can be hampered by drug-drug interactions and some pathophysiological states. Genotyping can offer additional information such as the differentiation between ultra rapid metabolizers and patients who comply poorly with drug treatment, and the differentiation between genetic and environmental determinants. Genotyping and phenotyping can help predict dosage requirements. Currently the number of clinical laboratories using these tools in the drug-monitoring approach is small.

Biotransformation↗
PubMed2001

Association of the ADH2*3 allele with a negative family history of alcoholism in African American young adults.

BACKGROUND: Two of the class I alcohol dehydrogenase (ADH) genes (ADH2 and ADH3) encode for multiple isozymes that differ in their kinetic properties. Polymorphisms at both of these gene loci have been linked to alcoholism and/or alcohol-induced disabilities in some populations. At the ADH2 locus, three polymorphisms are present (ADH2*1, ADH2*2, ADH2*3). ADH2*3 allele codes for a high Km and Vmax variant that has been reported to occur exclusively in African Americans and some tribes of Native Americans. In African Americans, the presence of the ADH2*3 allele is associated with protection from alcohol-related birth defects. However, its relationship to risk for alcoholism in African Americans remains relatively unexplored. METHODS: The participants were 97 African American young adults (18-25 years old). A structured interview was used to gather information on demographics, psychiatric diagnoses, personal drinking and drug use history, and familial history of alcohol use disorders. A blood sample was obtained from each participant and leukocyte DNA extracted and genotyped for the presence of ADH2*3 alleles. The specific aim of the study was to investigate the associations between the presence of the ADH2* 3 allele and personal and family history of alcohol use/abuse. RESULTS: Thirty participants (31%) had at least one ADH2*3 allele and two were homozygous for the allele. A significant association between the presence of an ADH2*3 allele and a negative family history of alcoholism was uncovered (p < 0.04). No significant associations of an ADH2*3 allele with personal history of alcohol use disorders or with current drinking were found; however, power to detect associations was limited in this population because half the population did not drink regularly. CONCLUSIONS: Because family history of alcoholism is one of the best predictors of the development of alcohol use disorders, this pilot study suggests that, in this sample of African American young adults, the ADH2*3 allele may be associated with a lowered risk for the development of alcoholism.

Adolescent↗
PubMed2001

Cytochrome P4502C9 genotype in Southeast Anatolia and possible relation with some serum tumour markers and cytokines.

Substrates for CYP2C9 include fluoxetine, phenytoin, warfarin, losartam and numerous nonsteroidal anti-inflammatory drugs. Polymorphisms in the coding region of the CYP2C9 gene produce variants at amino-acid residues 144 Arg/Cys and 359 Ile/Leu of the CYP2C9 protein. Individuals homozygous for Leu359 have markedly diminished metabolic capacities for most CYP2C9 substrates, the frequency of this allele is, however, rather low. Consistently with the modulation of enzyme activity by genetic and other factors, wide interindividual variability occurs in the elimination and/or dosage requirements of prototypic CYP2C9 substrates. The polymorphic enzyme CYP2C9 takes part in the metabolism of alkylating agents and polycyclic aromatic hydrocarbons like benzo(a)pyrene, a carcinogen present in tobacco smoke. Although the impact of impaired enzyme activity in metabolism of carcinogens and procarcinogens has not been fully defined, an association of CYP2C9 variant alleles to DNA adduct levels in lung tissues as well as to lung cancer risk have been reported. In this study 64 healthy subjects (44M/22F) were analysed for CYP2C9 genotype with PCR-RFLP and for serum carcinoembryonic antigen (CEA), alpha-fetoprotein (AFP), CA 19-9, CA 15-3, ferritin, IL-6, IL-8 concentrations by chemiluminescence or electrochemiluminescence methods. CYP2C9*1 was found to be the most prevalent allele and CYP2C9*1/CYP2C9*1 was the most frequent genotype represented in 64% of the population in southeastern Anatolia (Gaziantep). Although slight differences in serum tumour marker and cytokine concentrations were observed for CYP2C9 genotypes the differences were statistically insignificant (P > 0.05). This could be due to the complexity of the role of CYP2C9 in benzo(a)pyrene metabolism as well as from other contributing factors like interindividual variability of diverse enzymes participating in the same metabolic pathway, unequal expression of the variant alleles and differences in exposure to carcinogens. However, determination of CYP2C9 phenotypes in a larger group of subjects might clarify these slight differences.

Adolescent↗
PubMed2005

[Contribution of MODY6 gene in the pathogenesis of familial type 2 diabetes in Chinese population].

OBJECTIVE: To investigate the contribution of MODY6 gene in the pathogenesis of familiar type 2 diabetes in Chinese population. METHODS: PCR and single strand configuration polymorphism (PCR-SSCP) technique was used to screen the coding sequence of NeuroD1/BETA2 gene for DNA variants in 188 probands in the pedigrees of familiar type 2 diabetes and 130 normal persons as controls in Beijing, China. The discovered variants were confirmed by sequencing. RESULTS: A4T5 polymorphism and a novel Gly12Arg mutation were found. The frequency of A4T5 of the patients was 19.7%, significantly higher than that of the controls (10.0%, P < 0.05). In the control group, the Homa-beta of the 13 subjects with T allele was 4.6 +/- 04, significantly lower than that of the 117 subjects without T allele (4.9 +/- 0.5, P < 0.05). Co-segregating with diabetes, Gly12Arg mutation was found in only one pedigree and in none normal subjects. CONCLUSION: A4T5 polymorphism of NeuroD1/BETA2 gene is correlated with familiar type 2 diabetes in Chinese population. NeuroD1/BETA2 gene or its nearby gene may play a role in the pathogenesis of familiar type 2 diabetes. The novel GlyArg mutation may be a genetic cause of some diabetic pedigrees.

Adult↗
PubMed2005

[Mutation screening of GCK gene in Chinese early-onset diabetes population].

OBJECTIVE: To investigate the prevalence of mutations and sequence variations of glucokinase gene GCK in Chinese early-onset diabetes population. METHODS: The study was conducted in 174 unrelated Chinese residents, including 80 nondiabetic controls, 94 probands of early-onset diabetes pedigree. Direct sequencing was performed to screen all 10 exons of glucokinase gene, including promoter and exon/intron junctions. RESULTS: No mutations were identified in coding region, but several previously reported sequence variants were identified. 5'-untranslated region of exon 1a, 84 bp upstream of the translation initiation site GGCGG to GGGGG(early-onset diabetes group G allele frequency 0.106 vs control group 0.075, P=0.355); IVS1b+12 (A-->T) (early-onset diabetes group T allele frequency 0.005 vs non-identity of this variation in control group); IVS 5+29 (G-->T) (early-onset diabetes group T allele frequency 0.027 vs control group 0.019, P=0.731); IVS 9+8 (T-->C) (early-onset diabetes group C allele frequency 0.585 vs 0.694, P=0.044). A novel variation IVS 9+49 (G-->A) (early-onset diabetes group A allele frequency 0.011 vs control 0.006, P=1.000) was identified. There were no significant relationships of the exon 1a 5'-untransted region -84 bp(C-->G), IVS 5+29 (G-->T), IVS 9+8 (T-->C) and IVS 9+49 (G-->A) variants of GCK gene to the clinical variables such as plasma glucose, insulin, C-peptide and fasting lipid profile. CONCLUSION: The prevalence of structural mutations in glucokinase gene responsible for early-onset diabetes appears to be rare among Chinese patients.

Adult↗
PubMed1988

Meth A fibrosarcoma cells express two transforming mutant p53 species.

Expression plasmids directing the synthesis of various forms of the p53 cellular tumor antigen were compared with respect to their biological activities. All plasmids encoding wild type p53, derived from two different cDNA libraries, had absolutely no detectable activity when assayed for transformation of primary rat embryo fibroblasts in collaboration with Ha-ras. In contrast, p53 variants carrying point mutations in the protein coding region exhibited at least some transforming activity. Most notably, this was true for both types of mutant p53 cDNA clones isolated from Meth A cells. The data indicate that these cells, derived from a chemically-induced tumor, carry two independently mutated p53 alleles, each encoding a transformationally activated protein. This may imply that the mutations in the p53 gene played a role in the development of the Meth A tumor. Finally, cells overexpressing a transfected mutant p53 exhibit a physical complex between this exogenous p53 and its endogenous counterpart, possibly resulting in the stabilization of the latter.

Animals↗
PubMedDate not supplied

[Changes in the biological properties of influenza virus (HON1) strains virulent for mice when exposed to homologous antibodies].

A decrease in the virulent properties of two influenza virus strains (A/PR/8/34 and A/Mel/35 (HON1) pathogenic for mice was demonstrated in multiple passages in chick embryos in the presence of homologous antibody. The artificially developed avirulent A/PR/8/240 and A/Mel/375 variants had low immunogenic activity and a marked temperature sensitivity to 40 degrees C. Common ts mutations in the genomes of these avirulent variants located in genes 1 and 7 coding for P3 and M proteins were demonstrated.

Animals↗
PubMed1995

Molecular analysis in three cases of X91- variant chronic granulomatous disease.

Defects in gp91-phox, the large subunit of cytochrome b558 (b-245) give rise to X-linked chronic granulomatous disease (CGD), a rare inherited condition characterized by an extreme susceptibility to bacterial and fungal infection. In the majority of cases, the phagocytes are unable to generate any superoxide owing to complete absence of the flavocytochrome. However, a small minority of these patients do have some phagocytic oxidase activity. We describe here an analysis of the molecular basis of the disease in three such variant patients with lesions in the gene coding for gp91-phox on the X chromosome. Three different genetic lesions were found, resulting in the substitution of tyrosine for cysteine 244, a deletion of one of three lysines 313 through 315, and the deletion of the six C-terminal amino acids, respectively. The functional consequences of these defects on oxidase activity was a reduction to 12%, 3.6%, and 2.1% of the normal levels, respectively. Corresponding levels of gp91-phox were 20%, 8%, and 16% of normal classifying these patients as X91-. Microbicidal assays showed that killing of Staphylococcus aureus was grossly impaired in cells in which there was 12% normal activity. This implies that if gene therapy is to be applied, it must restore oxidase activity to a much higher level than that present in the cells of this patient. The sites of two of the mutations were analyzed on a model of the C-terminal half of the gp91-phox, based on the crystal structure of the homologous protein ferrodoxin NADP reductase. Possible structural consequences of the mutations were examined.

Adolescent↗