Mining the genetic riches of human populations.
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Bioethics↗
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Results for “deCode Genetics”
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[Knowledge and destiny or longevity and old age: the heritage of Homo sapiens].
Several theories have been proposed to explain ageing: limitation of the number of cell divisions or Hayflick's limit, the genetic theory, the action of free radicals, immune deficiency, etc. All of these theories share several points in common: their genetic determinism or repercussions which appear to be part of the heritage of complex organisms. Progress in genetics with chromosome decoding to localise genes and genetic manipulations or control of gene expression will probably allow an increased life expectancy, perhaps in the near future.
Aged↗
The Human Genome Diversity Project: medical benefits versus ethical concerns.
By the year 2005 the entire human genome should have been sequenced and the genes identified. But the resulting genomic sequence, although a marvelous accomplishment, will be a composite of just a handful of individuals selected at random. The Human Genome Diversity Project was proposed as a means to overcome these limitations by obtaining genetic information from many diverse populations of the world. This would give medical geneticists a handle on the variations in susceptibility to disease among different populations, as well as being of anthropological value. But would such a project risk exploiting the indigenous populations involved?
Bioethics↗
Human tissue research in the genomic era of medicine: balancing individual and societal interests.
Advances in DNA sequencing technology and in our understanding of the human genome are ushering in a new era of genomic medicine, one with dramatic potential to not only benefit society through research involving human tissue, but also to cause economic or psychosocial harms to tissue donors and their families. This delicate situation requires that the needs of tissue donors be carefully considered and balanced with those of the medical research community, especially on issues concerning confidentiality, consent, and compensation. We analyzed the tensions between tissue donors and researchers over the research use of human tissue. We also reviewed several approaches, including the establishment of tissue-trustee infrastructures at academic medical centers, aimed at achieving a more equitable balance between individual donor protection and societal benefits derived from tissue-based research. Arch Intern Med. 2000;160:3377-3384.
Academic Medical Centers↗
Genetically modified mice: tools to decode the functions of connexins in the heart-new models for cardiovascular research.
It has long been known that gap junctions are required for the propagation of electrical impulse in the heart. A good deal later, the connexins (Cxs), which are probably exclusive components of the junctional channels that constitute the gap junctions, were identified. More recently, the in vivo functions of cardiac Cxs have been investigated by the analysis of genetically modified mice. These studies have confirmed that Cxs are involved in cardiac impulse conduction, and, unexpectedly, in heart morphogenesis. In addition, cardiac abnormalities described in mice genetically modified for Cx genes, and those observed in certain human cardiac diseases, have been proven to be similar.
Animals↗
Suppression and the code: beyond codons and anticodons.
Specificity and accuracy in the decoding of genetic information during mRNA-programmed, ribosome-dependent polypeptide synthesis (translation) involves more than just hydrogen bonding between two anti-parallel trinucleotides, the mRNA codon and the tRNA anticodon. Other macromolecules are also involved, and translational suppression has been and continues to be an appropriate and effective way to identify them, as well as other parts of mRNA and tRNA, and to elucidate the structural determinants of their functions and interactions. Experimental results are presented that bear upon codon context effects, the role of tRNA structural features in aminoacyl-tRNA selection and in codon selection (reading-frame maintenance), determinants of tRNA identity, elongation factor suppressor mutants, and termination codon recognition by the ribosomal RNA of the small subunit. The examples presented illustrate the complexity of the decoding process and the interconnectedness of translational macromolecules in achieving specificity and accuracy in polypeptide synthesis.
Anticodon↗
Ethics briefings: confidentiality; organ donation; insurance; the Icelandic database.
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Bioethical Issues↗
Association of an aminoacyl-tRNA synthetase with a putative metabolic protein in archaea.
Aminoacyl-tRNA synthetases are essential enzymes that catalyze attachment of amino acids to tRNAs for decoding of genetic information. In higher eukaryotes, several synthetases associate with non-synthetase proteins to form a high-molecular mass complex that may improve the efficiency of protein synthesis. This multi-synthetase complex is not found in bacteria. Here we describe the isolation of a non-synthetase protein from the archaeon Methanocaldococcus jannaschii that was copurified with prolyl-tRNA synthetase (ProRS). This protein, Mj1338, also interacts with several other tRNA synthetases and has an affinity for general tRNA, suggesting the possibility of forming a multi-synthetase complex. However, unlike the non-synthetase proteins in the eukaryotic complex, the protein Mj1338 is predicted to be a metabolic protein, related to members of the family of H(2)-forming N(5),N(10)-methylene tetrahydromethanopterin (5,10-CH(2)-H(4)MP) dehydrogenases that are involved in the one-carbon metabolism of the archaeon. The association of Mj1338 with ProRS, and with other components of the protein synthesis machinery, thus suggests the possibility of a closer link between metabolism and decoding in archaea than in eukarya or bacteria.
Amino Acid Sequence↗
[Formation and genetic structure of polylysogens for lambda and phi 80 and their lambda att80 hybrid infecting wild-type Escherichia coli].
The frequency of polylysogeny and the genetic structure of polylysogens were studied for phages lambda, phi 80 and lambda att80. For none of these phages does frequency of polylysogeny vary by more than a factor of 2 within a wide range of multiplicities of infection (from 10(-3) up to 10) but the relative location of the prophages on the host chromosome is different. In the case of lambda, polylysogens are formed with a high frequency (0.20-0.41) and the prophages are inserted in tandem into the primary (normal) att site. In the case of phi 80 and lambda att80, polylysogens occur about 10 times less frequently and usually have one prophage inserted into the primary attachment site and another (sometimes, also a third) in one of the secondary ones. Wild-type Escherichia coli was shown to possess at least four secondary att80 sites, two of which (close to the his and tolC loci) are preferred. The frequency of secondary integration of phi 80 and lambda att80 does not differ significantly in the wild-type host and in cells deleted for the primary att site (0.041 and 0.045, respectively, among surviving cells at MOI 10). Certain properties of the phi 80 lysogens make it more difficult to decode their genetic structure.
Attachment Sites, Microbiological↗
Lessons from knockout and transgenic mice for infertility in men.
This review concentrates on the clear cases where knocking out a gene in mice has caused male infertility and thus comes near to proving that the gene plays a role in the development of sperm. Knockout mice have been created with primary defects at every stage of spermatogenesis thus creating a framework for decoding the genetic hierarchy that causes male germ cell differentiation. As well as defining essential genes in vivo experiments have defined promoter and untranslated sequences responsible for the expression of proteins at all the spermatogenic stages. In conclusion knockout mice remain the ultimate test of spermatogenic hypotheses as well as providing detailed information about this complex process.
Animals↗
Optimized polymerase chain reaction-based single-strand conformation polymorphism analysis of p53 gene applied to Bulgarian patients with invasive breast cancer.
During the last few decades a substantial amount of evidence has accumulated proving that the abrogation of the normal p53 pathway is a critical step in the initiation and progression of tumors. Decoding the genetic mechanisms involved in carcinogenesis requires screening for consistent genetic tumor alterations, including those concerning the p53 gene. Thus, practical, efficient, and inexpensive techniques for accurate determination of p53 mutational status are needed. Polymerase chain reaction/single-strand conformation polymorphism (PCR-SSCP) analysis is considered to be a useful tool to investigate the role of the p53 gene in the development and progression of human cancers. The sensitivity of the method can be increased considerably by varying the experimental conditions. Here we demonstrate a scheme of PCR-SSCP optimization for detection of p53 gene mutations of patients with various cancers. Optimal conditions for PCRSSCP of p53 exons 4-9 are reported. Such PCR-SSCP optimization could allow an increase in the sensitivity and reproducibility of the technique and facilitates screening of large series of patients to assess the clinical significance of p53 mutations in human cancers. Using the optimized PCR-SSCP analysis we screened Bulgarian patients with invasive breast cancer for p53 gene mutations and registered a 33.33% frequency of mutations. To date, there are no data concerning the p53 status of Bulgarian breast cancer patients. Screening for p53 gene mutations enables an accurate and routine determination of the p53 status of patients with cancer and may be applied in clinical oncology to cancer diagnosis, prediction of prognosis and response to treatment.
Base Sequence↗
An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA.
The AUA codon-specific isoleucine tRNA (tRNA(Ile)) in eubacteria has the posttranscriptionally modified nucleoside lysidine (L) at the wobble position of the anticodon (position 34). This modification is a lysine-containing cytidine derivative that converts both the codon specificity of tRNA(Ile) from AUG to AUA and its amino acid specificity from methionine to isoleucine. We identified an essential gene (tilS; tRNA(Ile)-lysidine synthetase) that is responsible for lysidine formation in both Bacillus subtilis and Escherichia coli. The recombinant enzyme complexed specifically with tRNA(Ile) and synthesized L by utilizing ATP and lysine as substrates. The lysidine synthesis of this enzyme was shown to directly convert the amino acid specificity of tRNA(Ile) from methionine to isoleucine in vitro. Partial inactivation of tilS in vivo resulted in an AUA codon-dependent translational defect, which supports the notion that TilS is an RNA-modifying enzyme that plays a critical role in the accurate decoding of genetic information.
Amino Acid Sequence↗
Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3.
The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3. The crystal structure analysis of the complex with tetracycline revealed the functionally important site responsible for the blockage of the A-site. Five additional tetracycline sites resolve most of the controversial biochemical data on the location of tetracycline. The interaction of edeine with the small subunit indicates its role in inhibiting initiation and shows its involvement with P-site tRNA. The location of the C-terminal domain of IF3, at the solvent side of the platform, sheds light on the formation of the initiation complex, and implies that the anti-association activity of IF3 is due to its influence on the conformational dynamics of the small ribosomal subunit.
Binding Sites↗
INE: a rice genome database with an integrated map view.
The Rice Genome Research Program (RGP) launched a large-scale rice genome sequencing in 1998 aimed at decoding all genetic information in rice. A new genome database called INE (INtegrated rice genome Explorer) has been developed in order to integrate all the genomic information that has been accumulated so far and to correlate these data with the genome sequence. A web interface based on Java applet provides a rapid viewing capability in the database. The first operational version of the database has been completed which includes a genetic map, a physical map using YAC (Yeast Artificial Chromosome) clones and PAC (P1-derived Artificial Chromosome) contigs. These maps are displayed graphically so that the positional relationships among the mapped markers on each chromosome can be easily resolved. INE incorporates the sequences and annotations of the PAC contig. A site on low quality information ensures that all submitted sequence data comply with the standard for accuracy. As a repository of rice genome sequence, INE will also serve as a common database of all sequence data obtained by collaborating members of the International Rice Genome Sequencing Project (IRGSP). The database can be accessed at http://www. dna.affrc.go.jp:82/giot/INE. html or its mirror site at http://www.staff.or.jp/giot/INE.html
Chromosomes, Artificial, Yeast↗
Low-salt crystallization of T7 RNA polymerase: a first step towards the transcription bubble complex.
DNA-dependent RNA polymerase is the key enzyme responsible for the biosynthesis of RNA, a process known as transcription. This process, which decodes the genetic information from DNA, is one of the most significant events in a biological system. The crystallization of both native and a chimeric T7/T3 RNAP using high salt conditions has been reported previously but these conditions proved unsuitable for DNA-RNAP complex formation since at high salt concentrations the DNA binding affinity to RNAP is reduced. A search for low-salt crystallization conditions has yielded new low-salt crystals of native T7-RNAP, a chimeric T7-RNAP (T7/T3 RNAP) which contains the T3 promoter recognition sequence, and a T7-RNAP containing an N-terminal histidine tag. The crystals, which are better suited for DNA-RNAP complex formation, belong to space group P3121 with a = 136, c = 156 A, contain a single molecule per asymmetric unit and diffract to 2.7 A resolution. Packing analysis shows that the new low-salt crystals have packing contacts similar to those observed in the high-salt T7-RNAP crystals reported previously. The diffraction anisotropicity observed in crystals of T7 RNAP is explained in term of crystal packing.
Base Sequence↗
Global gene expression analysis of developing neocortex using SAGE.
The mammalian brain is estimated to contain about a hundred billion neurons, making it the most complex biological structure on earth. Trying to understand the assembly and function of this elaborate organ is a formidable task. Yet the information to build a brain is encoded by no more than a subset of the 80,000 genes present in the genome, a more manageable number. This review describes the use of SAGE technology (Serial Analysis of Gene Expression) to decode the genetic repertoire of genes that are differentially expressed in time and in space during development of the neocortex, the part of the mammalian brain responsible for complex traits. We demonstrate that SAGE is not only powerful for generating comprehensive molecular portraits from the developing cortex but can also assist in discovering new genes.
Animals↗
[Genetics and arterial hypertension: 3 approaches to decode a complex disease].
Human arterial hypertension is a complex trait, partly determined by genetic factors. From the analysis of familial studies, it has been estimated that approximately 30% of the blood pressure variance within a population was of genetic origin. Three main types of human studies have been undertaken to try to identify susceptibility genes to hypertension. The first one corresponds to the systematic analysis of the so-called candidate genes, i.e. genes encoding proteins, enzymes, receptors, which are known to belong to pathways controlling blood pressure. Up to now, the most interesting results have been obtained on genes encoding the renin angiotensin system, the a adducin, the G protein subunit beta 3, and adrenergic receptors. The genome wide scan approach corresponds to a systematic analysis of evenly spaced markers throughout the genome in sibling pairs or in more complex families. This second strategy has shown that there was not a single locus that was regularly found by several studies, but rather several possible loci which most often have not been replicated from one study to another one. Among those, the long arm of the human chromosome 17 (17q12-q21) is in synteny with a blood pressure locus found in spontaneously hypertensive rats. The third approach, up to now the most successful, corresponds to the identification of major genes involved in rare Mendelian forms of hypertension. For example, genes responsible for Liddle syndrome, glucocorticoid remediable aldosteronism, apparent mineralocorticoid excess have been characterized and have demonstrated the importance of sodium and water homeostasis in blood pressure control.
Animals↗
AUA codon decoding by preferential use of tRNAIle(UAU) in Lactobacillus casei.
Modified nucleosides at the first (wobble) position of tRNA anticodons play critical roles in accurate decoding of the genetic code. In bacteria, the isoleucine AUA codon is typically decoded by tRNAIle(LAU), in which lysidine (L) at the wobble position of tRNAIle with a CAU anticodon ensures discrimination from the methionine AUG codon. However, some bacteria, such as Mycoplasma mobile, lack tRNAIle(LAU) and instead utilize tRNAIle(UAU). In this organism, the unmodified uridine at the wobble position is thought to enable specific decoding of AUA while avoiding AUG recognition. In our previous study, we identified a lactic acid bacterium in which both tRNAIle(LAU) and tRNAIle(UAU) coexist. Here, we show that tRNAIle(LAU) is scarcely aminoacylated in vivo, whereas tRNAIle(UAU) is efficiently aminoacylated. Notably, the presence of 4-thiouridine (s4U) at position 8 inhibits IleRS-dependent aminoacylation of tRNAIle(UAU) in vitro, suggesting a regulatory role of tRNA modification in this process. Moreover, tRNAIle(LAU) exhibits incomplete discrimination between AUA and AUG codons and binds to AUG in the ribosomal A-site binding assays. In contrast, tRNAIle(UAU) containing N 6-threonylcarbamoyladenosine (t6A) at position 37 showed a tendency toward improved discrimination between AUA and AUG codons and preferentially recognized AUA at the ribosomal A site. These results indicate that AUA decoding is predominantly mediated by preferential use of tRNAIle(UAU) rather than canonical tRNAIle(LAU), revealing an alternative mechanism of codon decoding based on differential utilization of tRNA isoacceptors, and providing an additional layer of translational control in bacteria.
RNA, Transfer, Ile↗