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At least 199 records · Page 11Linked to original sources
PubMed2002

Differential genetic etiology of reading component processes as a function of IQ.

Results obtained from previous studies of word recognition, reading component skills, and reading composite measures suggest that genetic factors may be more important as a cause for reading disability among children with higher IQ scores than among those with lower IQ scores. To investigate the genetic etiology of reading disability further, measures of word recognition, phonological decoding, orthographic coding, and phoneme awareness were obtained from a total of 465 twin pairs with a positive school history of reading problems. The basic and extended DeFries and Fulker (DF) multiple regression models for the analysis of selected twin data were employed to investigate the etiology of group deficits in reading and language skills, as well as to assess differential genetic etiology for the reading-related measures as a function of IQ. Data from 168 sibling pairs (drawn from the twins' families), including fraternal twin pairs and their siblings, as well as non-twin siblings of identical twins were subjected to single-marker analyses using the DF basic linkage model to examine evidence for linkage of a quantitative-trait locus (QTL) for reading and language deficits to the short arm of chromosome 6. Lastly, to investigate the possible differential influence of this QTL as a function of IQ, the sibling pair data were fitted to an extension of the DF basic linkage model. Results indicated that reading and language deficits are significantly heritable and that differential genetic influences as a function of IQ are evident for measures of word recognition and phonological decoding. Results obtained from linkage analyses confirmed the presence of a QTL on chromosome 6p that influences phonological and orthographic skills, as well as phoneme awareness measures, and suggest that this QTL may influence phoneme awareness differentially as a function of IQ: however, future analyses with considerably larger samples are needed to test the hypothesis of differential QTL influence more rigorously.

Adolescent↗
PubMed2000

Decoding of tandem quadruplets by adjacent tRNAs with eight-base anticodon loops.

To expand the genetic code for specification of multiple non-natural amino acids, unique codons for these novel amino acids are needed. As part of a study of the potential of quadruplets as codons, the decoding of tandem UAGA quadruplets by an engineered tRNA(Leu) with an eight-base anticodon loop, has been investigated. When GCC is the codon immediately 5' of the first UAGA quadruplet, and release factor 1 is partially inactivated, the tandem UAGAs specify two leucines with an overall efficiency of at least 10%. The presence of a purine at anticodon loop position 32 of the tRNA decoding the codon 5' to the first UAGA seems to influence translation of the following codon. Another finding is intraribosomal dissociation of anticodons from codons and their re-pairing to mRNA at overlapping or nearby codons. In one case where GCC is replaced by CGG, only a single Watson-Crick base pair can form upon re-pairing when decoding is resumed. This has implications for the mechanism of some cases of programmed frameshifting.

Anticodon↗
PubMed2004

Yeast as a model organism for studying the evolution of non-standard genetic codes.

During the last 30 years, a number of alterations to the standard genetic code have been uncovered both in prokaryotes and eukaryotic nuclear and mitochondrial genomes. But, the study of the evolutionary pathways and molecular mechanisms of codon identity redefinition has been largely ignored due to the assumption that non-standard genetic codes can only evolve through neutral evolutionary mechanisms and that they have no functional significance. The recent discovery of a genetic code change in the genus Candida that evolved through an ambiguous messenger RNA decoding mechanism is bringing that naive assumption to an abrupt end by showing, in a rather dramatic way, that genetic code changes have profound physiological and evolutionary consequences for the species that redefine codon identity. In this paper, the recent data on the evolution of the Candida genetic code are reviewed and an experimental framework based on forced evolution, molecular genetics and comparative and functional genomics methodologies is put forward for the study of non-standard genetic codes and genetic code ambiguity in general. Additionally, the importance of using Saccharomyces cerevisiae as a model organism for elucidating the evolutionary pathway of the Candida and other genetic code changes is emphasised.

Candida↗
PubMed2006

[A database of available DNA tests in the dog].

For genetic counseling this report presents a database of canine hereditary diseases and coat color characteristics, which have been solved on the molecular level. The database facilitates access to appropriate diagnostic laboratories for specific phenotypes. The recent decoding of the dog genome provides ideal conditions for the molecular genetic analysis of hereditary traits and diseases. Therefore the authors would like to encourage veterinary surgeons in particular to report cases to assist the molecular analysis of further phenotypes in future.

Animals↗
PubMed1999

Genetic probing of the interaction between the translation factor SelB and its mRNA binding element in Escherichia coli.

Decoding of the UGA codon in mRNAs for selenoproteins as selenocysteine requires interaction of the translation factor SelB with an mRNA structure, the SECIS element. A genetic analysis of this interaction was performed by selecting for intergenic suppressor mutations in selB which counteracted the detrimental effect of defined mutations in the SECIS element. Both allele-nonspecific and allele-specific mutations, as judged by readthrough of the UGA into the LacZ-encoding segment of fdhF'-'lacZ fusions and by incorporation of selenium, were isolated. selB genes from ten suppressor mutants were sequenced and the corresponding mutations were localized to five positions within the protein. Four of the suppressors had amino acid exchanges within a 23-amino acid stretch in domain 4b of SelB, which probably represent sites of contact between the protein and the mRNA. A fifth mutation was localized in domain 4a of SelB; it promoted allele-nonspecific readthrough. Since a truncated SelB species lacking domain 4b did not show complex formation with the SECIS element, we speculate that the latter mutation affects the interaction between the tRNA-binding and the mRNA-binding domains. None of the SelB variants was able to promote UGA readthrough when major structural changes that altered the length of the helical part or enlarged the apical loop were introduced into the SECIS element. The results obtained also show that novel pairs of SelB/SECIS derivatives can be generated which may be useful for the targeted insertion of selenocysteine into proteins.

Amino Acid Sequence↗
PubMed2003

Segregation analysis of phenotypic components of learning disabilities. II. Phonological decoding.

Dyslexia is a common, complex disorder, which is thought to have a genetic component. The study of the genetics of dyslexia is complicated by a lack of consensus on diagnostic criteria, and the probability of genetic heterogeneity-it is possible that deficits in different language processes are caused by different underlying genes. In order to address these difficulties, we study continuous phenotypes that are part of the psychometric test batteries often used to diagnose dyslexia. Prior to embarking on a linkage study, it is helpful to employ segregation analysis, both to identify phenotypes that may be amenable to mapping by linkage analysis, and to determine the best models to use for model based analyses. We study 409 people in 102 nuclear families, and employ (1) oligogenic segregation analysis to estimate the number of quantitative trait loci (QTLs) contributing to each phenotype, and (2) complex segregation analysis in order to identify the most parsimonious inheritance model. In this paper, we consider two measures of phonological decoding ability-word attack and phonemic decoding efficiency. We find evidence for one or two genes of at least modest effect contributing to phonemic decoding efficiency, and the best fitting model is a dominant major gene model with residual familial correlations. For word attack, we find evidence for one or two genes of at least modest effect, and the variation in the trait is best explained by a polygenic model.

Data Interpretation, Statistical↗
PubMed2002

Stop codon decoding in Candida albicans: from non-standard back to standard.

The human pathogen Candida albicans translates the standard leucine-CUG codon as serine. This genetic code change is mediated by a novel ser-tRNA(CAG), which induces aberrant mRNA decoding in vitro, resulting in retardation of the electrophoretic mobility of the polypeptides synthesized in its presence. These non-standard decoding events have been attributed to readthrough of the UAG and UGA stop codons encoded by the Brome Mosaic Virus RNA 4, which codes for the virion coat protein, and the rabbit globin mRNAs, respectively. In order to fully elucidate the behaviour of the C. albicans ser-tRNA(CAG) towards stop codons, we have used other cell-free translation systems and reporter genes. However, the reporter systems used encode several CUG codons, making it impossible to distinguish whether the slow migration of the polypeptides is caused by the replacement of leucines by serines at the CUG codons, readthrough, or a combination of both. Therefore, we have constructed new reporter systems lacking CUG codons and have used them to demonstrate that aberrant mRNA decoding in vitro is not a result from stop codon readthrough or any other non-standard translational event. Our data show that a single leucine to serine replacement at only one of the four CUG codons encoded by the BMV RNA-4 gene is responsible for the aberrant migration of the BMV coat protein on SDS-PAGE, suggesting that this amino acid substitution (ser for leu) significantly alters the structure of the virion coat protein. The data therefore show that the only aberrant event mediated by the ser-tRNA(CAG) is decoding of the leu-CUG codon as serine.

Amino Acid Substitution↗
PubMedDate not supplied

Reading skills in early readers: genetic and shared environmental influences.

The present study combined parallel data from the Northeast-Northwest Collaborative Adoption Projects (N2CAP) and the Western Reserve Reading Project (WRRP) to examine sibling similarity and quantitative genetic model estimates for measures of reading skills in 272 school-age sibling pairs from three family types (monozygotic twins, dizygotic twins, and unrelated adoptive siblings). The study included measures of letter and word identification, phonological awareness, phonological decoding, rapid automatized naming, and general cognitive ability. Estimates of additive genetic effects and shared environmental effects were moderate and significant. Furthermore, shared environmental effects estimated in twins were generally similar in magnitude to adoptive sibling correlations, suggesting highly replicable estimates across different study designs.

Adoption↗
PubMed2002

Omnipotent decoding potential resides in eukaryotic translation termination factor eRF1 of variant-code organisms and is modulated by the interactions of amino acid sequences within domain 1.

In eukaryotes, a single translational release factor, eRF1, deciphers three stop codons, although its decoding mechanism remains puzzling. In the ciliate Tetrahymena thermophila, UAA and UAG codons are reassigned to Gln codons. A yeast eRF1-domain swap containing Tetrahymena domain 1 responded only to UGA in vitro and failed to complement a defect in yeast eRF1 in vivo at 37 degrees C. This finding demonstrates that decoding specificity of eRF1 from variant code organisms resides at domain 1. However, the wild-type eRF1 hybrid fully restored the growth of eRF1-deficient yeast at 30 degrees C. Tetrahymena eRF1 contains a variant sequence, KATNIKD, at the tip of domain 1. The TASNIKD variant of hybrid eRF1 rendered the eRF1-nullified yeast viable, although in an in vitro assay, the same hybrid eRF1 responded only to UGA. Nevertheless, the yeast eRF1 bearing the KATNIKD motif instead of the TASNIKS heptapeptide present in higher eukaryotes remains omnipotent in vivo. Collectively, these data suggest that variant genetic code organisms like Tetrahymena have an intrinsic potential to decode three stop codons in vivo, and that interaction within domain 1 between the KAT tripeptide and other sequences modulates the decoding specificity of Tetrahymena eRF1.

Amino Acid Sequence↗
PubMed2003

A genetic algorithm for detecting target geometric figures.

A genetic algorithm is proposed to detect target geometric figures in an given image. Float-point encoding was adopted to process the parameters of a geometric figures to be detected. On the basis of classical Hough transform, a fitness function was obtained for each individual task, and the individuals with the highest fitness function were identified and copied into the cohort of the next generation. For the rest of the individuals, operation with multi-point crossover or uniform mutation was performed to form new individuals in the next generation. When the termination conditions for this genetic algorithm were met, the best-fitted individual was decoded and output as the parameters of the detected geometric figures. This algorithm can eliminate noise interference with good convergence and accurate results, and may save time and storage space during relatively easily programmed computation in comparison with classical Hough transform.

Algorithms↗
PubMed2005

Selenocysteine in proteins-properties and biotechnological use.

Selenocysteine (Sec), the 21st amino acid, exists naturally in all kingdoms of life as the defining entity of selenoproteins. Sec is a cysteine (Cys) residue analogue with a selenium-containing selenol group in place of the sulfur-containing thiol group in Cys. The selenium atom gives Sec quite different properties from Cys. The most obvious difference is the lower pK(a) of Sec, and Sec is also a stronger nucleophile than Cys. Proteins naturally containing Sec are often enzymes, employing the reactivity of the Sec residue during the catalytic cycle and therefore Sec is normally essential for their catalytic efficiencies. Other unique features of Sec, not shared by any of the other 20 common amino acids, derive from the atomic weight and chemical properties of selenium and the particular occurrence and properties of its stable and radioactive isotopes. Sec is, moreover, incorporated into proteins by an expansion of the genetic code as the translation of selenoproteins involves the decoding of a UGA codon, otherwise being a termination codon. In this review, we will describe the different unique properties of Sec and we will discuss the prerequisites for selenoprotein production as well as the possible use of Sec introduction into proteins for biotechnological applications. These include residue-specific radiolabeling with gamma or positron emitters, the use of Sec as a reactive handle for electophilic probes introducing fluorescence or other peptide conjugates, as the basis for affinity purification of recombinant proteins, the trapping of folding intermediates, improved phasing in X-ray crystallography, introduction of 77Se for NMR spectroscopy, or, finally, the analysis or tailoring of enzymatic reactions involving thiol or oxidoreductase (redox) selenolate chemistry.

Biotechnology↗
PubMed2006

Cloned sequence repertoires for small- and large-scale biology.

How to assign function to the tens of thousands of genes discovered in the chromosomes of a few model species? How to complement the classical genetic approaches that are not always ideally suited to decode complex mechanisms? The solutions to these pressing questions are not simple and rely on the development of novel resources and technologies. Here I critically review what clone collections are available and how they can be exploited for the systematic analysis of gene functions in plants.

Cloning, Molecular↗
PubMedDate not supplied

Melanocortin and leptin signaling systems: central regulation of catabolic energy balance.

The recent cloning of the ob gene (leptin) has revolutionized our understanding of obesity and the underlying factors that govern weight homeostasis. There is growing evidence that long term food intake regulation is controlled by the central nervous system by a number of peptide hormones in response to changes in leptin levels. Studies of these hormones, using both genetic and pharmacological approaches, have provided a foundation for decoding the molecular logic of the neuronal circuits which regulate food intake control and energy balance. A review of the current progress in the melanocortin-4 receptor pathway, with particular emphasis on its relation to leptin, neuropeptide Y and other obesity hormones known to modulate weight homeostasis, is presented.

Animals↗
PubMed1991

Decoding signals for membrane protein assembly using alkaline phosphatase fusions.

We have used genetic methods to investigate the role of the different domains of a bacterial cytoplasmic membrane protein, MalF, in determining its topology. This was done by analyzing the effects of MalF topology of deleting various domains of the protein using MalF-alkaline phosphatase fusion proteins. Our results show that the cytoplasmic domains of the protein are the pre-eminent topogenic signals. These domains contain information that determines their cytoplasmic location and, thus, the orientation of the membrane spanning segments surrounding them. Periplasmic domains do not appear to have equivalent information specifying their location and membrane spanning segments do not contain information defining their orientation in the membrane. The strength of cytoplasmic domains as topogenic signals varies, correlated with the density of positively charged amino acids within them.

ATP-Binding Cassette Transporters↗
PubMed2005

From mapping to sequencing, post-sequencing and beyond.

The Rice Genome Research Program (RGP) in Japan has been collaborating with the international community in elucidating a complete high-quality sequence of the rice genome. As the pioneer in large-scale analysis of the rice genome, the RGP has successfully established the fundamental tools for genome research such as a genetic map, a yeast artificial chromosome (YAC)-based physical map, a transcript map and a phage P1 artificial chromosome (PAC)/bacterial artificial chromosome (BAC) sequence-ready physical map, which serve as common resources for genome sequencing. Among the 12 rice chromosomes, the RGP is in charge of sequencing six chromosomes covering 52% of the 390 Mb total length of the genome. The contribution of the RGP to the realization of decoding the rice genome sequence with high accuracy and deciphering the genetic information in the genome will have a great impact in understanding the biology of the rice plant that provides a major food source for almost half of the world's population. A high-quality draft sequence (phase 2) was completed in December 2002. Since then, much of the finished quality sequence (phase 3) has become available in public databases. With the completion of sequencing in December 2004, it is expected that the genome sequence would facilitate innovative research in functional and applied genomics. A map-based genome sequence is indispensable for further improvement of current rice varieties and for development of novel varieties carrying agronomically important traits such as high yield potential and tolerance to both biotic and abiotic stresses. In addition to genome sequencing, various related projects have been initiated to generate valuable resources, which could serve as indispensable tools in clarifying the structure and function of the rice genome. These resources have been made available to the scientific community through the Rice Genome Resource Center (RGRC) of the National Institute of Agrobiological Sciences (NIAS) to enable rapid progress in research that will lead to thorough understanding of the rice plant. As the next trend in rice genome research will focus on determining the function of about 40,000-50,000 genes predicted in the genome as well as applying various genomics tools in rice breeding, an unlimited access to rice DNA and seed stocks will provide a broad community of scientists with the necessary materials for formulating new concepts, developing innovative research and making new scientific discoveries in rice genomics.

Centromere↗
PubMed2003

Genetic and environmental influences on individual differences in printed word recognition.

The genetic and environmental etiologies of individual differences in printed word recognition and related skills were explored in 440 identical and fraternal twin pairs between 8 and 18 years of age. A theoretically driven measurement model identified five latent variables: IQ, phoneme awareness, word recognition, phonological decoding, and orthographic coding. Cholesky decomposition models on these five latent constructs revealed the existence of both common and independent genetic effects, as well as non-shared environmental influences. There was evidence for moderate genetic influences common between IQ, phoneme awareness, and word-reading skills, and for stronger IQ-independent genetic influences that were common between phoneme awareness and word-reading skills, particularly phonological decoding. Phonological and orthographic coding skills in word recognition had both significant common and significant independent genetic influences, with implications for "dual-route" and "connectionist" reading models, subtypes of reading disabilities, and the remediation of reading disabilities.

Awareness↗