A genome scan in multigenerational families with dyslexia: Identification of a novel locus on chromosome 2q that contributes to phonological decoding efficiency.

Dyslexia is a common and complex developmental disorder manifested by unexpected difficulty in learning to read. Multiple different measures are used for diagnosis, and may reflect different biological pathways related to the disorder. Impaired phonological decoding (translation of written words without meaning cues into spoken words) is thought to be a core deficit. We present a genome scan of two continuous measures of phonological decoding ability: phonemic decoding efficiency (PDE) and word attack (WA). PDE measures both accuracy and speed of phonological decoding, whereas WA measures accuracy alone. Multipoint variance component linkage analyses (VC) and Markov chain Monte-Carlo (MCMC) multipoint joint linkage and segregation analyses were performed on 108 families. A strong signal was observed on chromosome 2 for PDE using both VC (LOD=2.65) and MCMC methods (intensity ratio (IR)=32.1). The IR is an estimate of the ratio of the posterior to prior probability of linkage in MCMC analysis. The chromosome 2 signal was not seen for WA. More detailed mapping with additional markers provided statistically significant evidence for linkage of PDE to chromosome 2, with VC-LOD=3.0 and IR=59.6 at D2S1399. Parametric analyses of PDE, using a model obtained by complex segregation analysis, provided a multipoint maximum LOD=2.89. The consistency of results from three analytic approaches provides strong evidence for a locus on chromosome 2 that influences speed but not accuracy of phonological decoding.

Instructional treatment associated with changes in brain activation in children with dyslexia.

OBJECTIVE: To assess the effects of reading instruction on fMRI brain activation in children with dyslexia. BACKGROUND: fMRI differences between dyslexic and control subjects have most often involved phonologic processing tasks. However, a growing body of research documents the role of morphologic awareness in reading and reading disability. METHODS: The authors developed tasks to probe brain activation during phoneme mapping (assigning sounds to letters) and morpheme mapping (understanding the relationship of suffixed words to their roots). Ten children with dyslexia and 11 normal readers performed these tasks during fMRI scanning. Children with dyslexia then completed 28 hours of comprehensive reading instruction. Scans were repeated on both dyslexic and control subjects using the same tasks. RESULTS: Before treatment, children with dyslexia showed less activation than controls in left middle and inferior frontal gyri, right superior frontal gyrus, left middle and inferior temporal gyri, and bilateral superior parietal regions for phoneme mapping. Activation was significantly reduced for children with dyslexia on the initial morpheme mapping scan in left middle frontal gyrus, right superior parietal, and fusiform/occipital region. Treatment was associated with improved reading scores and increased brain activation during both tasks, such that quantity and pattern of activation for children with dyslexia after treatment closely resembled that of controls. The elimination of group differences at follow-up was due to both increased activation for the children with dyslexia and decreased activation for controls, presumably reflecting practice effects. CONCLUSION: These results suggest that behavioral gains from comprehensive reading instruction are associated with changes in brain function during performance of language tasks. Furthermore, these brain changes are specific to different language processes and closely resemble patterns of neural processing characteristic of normal readers.

Segregation analysis of phenotypic components of learning disabilities. I. Nonword memory and digit span.

Dyslexia is a common and complex disorder with evidence for a genetic component. Multiple loci (i.e., quantitative-trait loci [QTLs]) are likely to be involved, but the number is unknown. Diagnosis is complicated by the lack of a standard protocol, and many diagnostic measures have been proposed as understanding of the component processes has evolved. One or more genes may, in turn, influence these measures. To date, little work has been done to evaluate the mode of inheritance of individual component-as opposed to composite-phenotypes, beyond family or twin correlation studies that initially demonstrate evidence for a genetic basis of such components. Here we use two approaches to segregation analysis in 102 nuclear families to estimate genetic models for component phenotypes associated with dyslexia: digit span and a nonword-repetition task. Both measures are related to phonological skills, one of the key component processes in dyslexia. We use oligogenic-trait segregation analysis to estimate the number of QTLs contributing to each phenotype, and we use complex segregation analysis to identify the most parsimonious inheritance models. We provide evidence in support of both a major-gene mode of inheritance for the nonword-repetition task, with approximately 2.4 contributing QTLs, and for a genetic basis of digit span, with approximately 1.9 contributing QTLs. Results obtained by reciprocal adjustment of measures suggest that genes contributing to digit span may contribute to the nonword-repetition score but that there are additional QTLs involved in nonword repetition. Our study adds to existing studies of the genetic basis of composite phenotypes related to dyslexia, by providing evidence for major-gene modes of inheritance of these single-measure component phenotypes.

Familial aggregation of dyslexia phenotypes.

There is evidence for genetic contributions to reading disability, but the phenotypic heterogeneity associated with the clinical diagnosis may make identification of the underlying genetic basis difficult. In order to elucidate distinct phenotypic features that may be contributing to the genotypic heterogeneity, we assessed the familial aggregation patterns of Verbal IQ and 24 phenotypic measures associated with dyslexia in 102 nuclear families ascertained through probands in grades 1 through 6 who met the criteria for this disorder. Correlations between relatives were computed for all diagnostic phenotypes, using a generalized estimating equation (GEE) approach. GEE is a recently developed semiparametric method for handling correlated data. The method is robust to model misspecification and flexible in adjusting for the subjects' characteristics and pedigree sizes as well as for the ascertainment process, while estimating the correlations between related subjects. The Nonword Memory (NWM) subtest of a prepublication version of the Comprehensive Test of Phonological Processing (CTOPP) and Phonemic Decoding Efficiency (PDE) subtest of a prepublication version of the Test of Word Reading Efficiency (TOWRE) showed correlation patterns in relatives that are strongly supportive of a genetic basis. The Wechsler Scale Digit Span, the Word Attack subtest of the Woodcock Reading Mastery Test--Revised, and the Spelling subtest of the Wide Range Achievement Test--Third Edition had slightly weaker evidence of a genetic basis. Five additional phenotypes (the Spelling subtest of the Wechsler Individual Achievement Test, the Accuracy, Rate, and Comprehension subtests of the Gray Oral Reading Test--Third Edition, and Rapid Automatized Naming of Letters and Numbers) gave suggestive evidence of such a pattern. The results cross-validate in that evidence for a pattern consistent with a genetic basis was obtained for two measures of phonological short-term memory (CTOPP Nonword Memory and WISCIII or WAIS-R Digit Span), for two measures of phonological decoding (WRMT-R Word Attack and TOWRE Phonemic Decoding Efficiency), and for two measures of spelling from dictation (WRAT-3 Spelling and, to a lesser extent, WIAT Spelling). These measures are thus good candidates for more sophisticated segregation analyses that can formulate models for incorporation into linkage analyses.

Chronic tolerance and sensitization to alcohol in sons of alcoholics: II. Replication and reanalysis.

Data from D. B. Newlin and J. B. Thomson (1991) were reanalyzed, and data from an independent replication study were analyzed, relative to tonic (baseline) and phasic (response to alcohol challenge) aspects of drinking alcohol administered at the same dose on several occasions. Among the high-risk men (sons of alcoholic fathers), linear trends across days for resting (predrinking) baselines were opposite to alcohol-evoked changes for finger pulse amplitude, finger temperature, and skin conductance in Study 1 and for pulse transit time and body sway (static ataxia) in Study 2. In contrast, the structure of the low-risk men's (sons of nonalcoholic parents) data was precisely the opposite. Results are discussed in terms of sensitization as a potential mechanism that relates vulnerability to final manifestation of addictive behavior.

The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form.

In the natural form of the hairpin ribozyme the two loop-carrying duplexes that comprise the majority of essential bases for activity form two adjacent helical arms of a four-way RNA junction. In the present work we have manipulated the sequence around the junction in a way known to perturb the global folding properties. We find that replacement of the junction by a different sequence that has the same conformational properties as the natural sequence gives closely similar reaction rate and Arrhenius activation energy for the substrate cleavage reaction. By comparison, rotation of the natural sequence in order to alter the three-dimensional folding of the ribozyme leads to a tenfold reduction in the kinetics of cleavage. Replacement with the U1 four-way junction that is resistant to rotation into the antiparallel structure required to allow interaction between the loops also gives a tenfold reduction in cleavage rate. The results indicate that the conformation of the junction has a major influence on the catalytic activity of the ribozyme. The results are all consistent with a role for the junction in the provision of a framework by which the loops are presented for interaction in order to create the active form of the ribozyme.

Structure and activity of the hairpin ribozyme in its natural junction conformation: effect of metal ions.

The natural form of the hairpin ribozyme consists of a four-way RNA junction of which the single-stranded loop-carrying helices are adjacent arms. The junction can be regarded as providing a framework for constructing the active ribozyme, and the rate of cleavage can be modulated by changing the conformation of the junction. We find that the junction-based form of the hairpin ribozyme is active in magnesium, calcium, or strontium ions, but not in manganese, cadmium, or sodium ions. Using fluorescence resonance energy transfer experiments, we have investigated the global structure of the ribozyme. The basic folding of the construct is based on pairwise helical stacking, so that the two loop-carrying arms are located on opposite stacked helical pairs. In the presence of magnesium, calcium, or strontium ions, the junction of the ribozyme undergoes a rotation into a distorted antiparallel geometry, creating close physical contact between the two loops. Manganese ions induce the same global folding, but no catalytic activity; this change in global conformation is therefore necessary but not sufficient for catalytic activity. Fitting the dependence of the conformation on ionic concentration to a two-state model suggests that cooperative binding of two ions is required to bring about the folding. However, further ion binding is required for cleavage activity. Cobalt hexammine ions also bring about global folding, while spermidine generates a more symmetrical form of the antiparallel structure. Cadmium ions generate a different folded form, interpreted in terms of close loop-loop association while the junction is unfolded. Sodium ions were unable to induce any folding of the ribozyme, which remained slightly parallel. These results are consistent with a folding process induced by the binding of two group IIA metal ions, distributed between the junction and the loop interface.

Prediction of stimulant response in children with attention-deficit/hyperactivity disorder.

Discrimination of stimulant-responding and nonresponding groups of children with attention-deficit/hyperactivity disorder (ADHD) on the basis of demographic, neurophysiologic, or behavioral variables would be beneficial for clinical and theoretical reasons. Previous researchers have identified many predictor variables, but relationships between predictor and criterion variables generally have been subtle. In addition, few investigations have considered the relative predictive power of the variables. The present study evaluated the multivariate relationship between several predictor variables and response to medication in 336 children with ADHD. Neurologic status, inattention, and overactivity were found to be most likely to predict good response to psychostimulants, whether rated by parents or teachers. Although a number of variables predicted a positive psychostimulant response, the strength of the predictive associations suggests only minimal clinical usefulness.

Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops.

The hairpin ribozyme is a self-cleaving motif found in the negatives strand of the satellite RNA of some plant viruses. In its natural context, the ribozyme comprises four helices, two of which contain conserved formally unpaired loops, that are adjacent arms of a four-way RNA junction. We show that the arms that would carry these loops are brought close together in the global conformation of the isolated junction. Using fluorescence resonance energy transfer, we demonstrate a two-magnesium ion-dependent conformational transition of the complete ribozyme that brings the loopbearing arms into close physical proximity. The ribozyme is active as a four-way junction, and the rate of cleavage may be modulated by the conformation of the four-way junction.

In vitro selection of hammerhead ribozymes containing a bulged nucleotide in stem II.

Hammerhead ribozymes were transcribed from a dsDNA template containing four random nucleotides between stems II and III, which replace the naturally occurring GAA nucleotides. In vitro selection was used to select hammerhead ribozymes capable of in cis cleavage using denaturing polyacrylamide gels for the isolation of cleaving sequences. Self-cleaving ribozymes were cloned after the first and second rounds of selection, sequenced and characterised. Only sequences containing 5'-HGAA-3', where H is A, C or U, between stems II and III were active; G was clearly not tolerated at this position. Thus, only three sequences out of the starting pool of 256 (4(4)) were active. The Michaelis-Menten parameters were determined for the in trans cleaving versions of these ribozymes and indicate that selected ribozymes are less efficient than the native sequence. We propose that the selected ribozymes accommodate the extra nucleotide as a bulge in stem II.

Identification and eradication of a denatured DNA isolated during alkaline lysis-based plasmid purification procedures.

Many plasmid isolation procedures use strongly alkaline conditions in the initial stages to facilitate lysis of the host bacteria. We demonstrate that such procedures can give rise to a minor but significantly altered form of plasmid. After electrophoresis and uv transillumination of ethidium bromide-stained agarose gels we and others have noticed a faint band migrating near to the major fluorescent product, covalently closed circular plasmid DNA. This faint band is resistant to cleavage by restriction endonucleases which have recognition sites in the parent plasmid. We were able to show that the contaminating band is able to transform competent Escherichia coli cells and that normal double-stranded plasmids were isolated from such transformants. We were able to selectively hydrolyze the contaminating band using T5 exonuclease which is a 5'-nuclease with a single-strand specific endonuclease activity. Plasmid preparations carried out under nonalkaline conditions failed to produce the contaminant band. We suggest methods for purifying plasmid DNA which remove the denatured band and could improve cloning efficiencies where the largest recombinant libraries are required.

RNA cleavage by small catalytic RNAs.

Recent studies of the hammerhead ribozyme have provided an insight into its three-dimensional structure. In addition, studies using chemical probes, functional-group modification and mutational analysis, in combination with computer modelling, have led to proposals for the structure of both the hairpin and hepatitis delta virus ribozymes. Such structural elucidations will aid understanding of the mechanism of ribozyme catalysis. The discovery that certain RNA-binding proteins can increase the catalytic efficiency of ribozymes in encouraging for their use in the inhibition of gene expression in vivo.

Inhibition of gene expression with ribozymes.

1. Ribozymes can be designed to cleave in trans, i.e. several substrate molecules can be turned over by one molecule of the catalytic RNA. Only small molecular weight ribozymes, or small ribozymes, are discussed in this review with particular emphasis on the hammerhead ribozyme as this has been most widely used for the inhibition of gene expression by cleavage of mRNAs. 2. Cellular delivery of the ribozyme is of crucial importance for the success of inhibition of gene expression by this methodology. Two modes of delivery can be envisaged, endogenous and exogenous delivery. Of the former several variants exist, depending on the vector used. The latter is still in its infancy, even though chemical modification has rendered such ribozymes resistant against degradation by serum nucleases without impairment of catalytic efficiency. 3. Various successful applications of ribozymes for the inhibition of gene expression are discussed, with particular emphasis on HIV1 and cancer targets. These examples demonstrate the promise of this methodology.

Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs.

The crystal structure of the oligonucleotide d(CGCAAATTO8GGCG), containing the chemically modified base 8-hydroxydeoxyguanine (O8G), has been determined at 2.5-A resolution and refined to a crystallographic R-factor of 16.8%. The B-type DNA helix contains standard Watson-Crick base pairs except at the mismatch sites, where O8G adopts a syn conformation and forms hydrogen bonds to adenine in the anti conformation. The thermodynamic stability of the duplex was found by UV melting techniques to be intermediate between the native oligonucleotide d(CGCAAATTTGCG) and an oligonucleotide containing A.G mispairs d(CGCAAATTGGCG). Comparison of the structure of the O8G(syn).A(anti) base pair with those of Watson-Crick base pairs has given a reason why O8G.A base pairs are not well repaired by DNA proofreading enzymes.

Autoantibody associations with MHC class II antigens in scleroderma and autoimmune vasculitis.

HLA-DR haplotypes in patients with scleroderma and vasculitis were compared with those in healthy controls from the Scottish population to investigate whether any associations exist between MHC antigens and development of specific autoantibodies. In patients with systemic vasculitis the presence of any antibodies against neutrophil cytoplasmic antigens (ANCA) was associated with an increased frequency of DR8 [p < 0.004], and no patients expressed the DR5 antigen. However, no significant differences were observed when these patients were subdivided into those with anti-myeloperoxidase (MPO) antibodies or anti-proteinase-3 (PR3) antibodies. Scleroderma patients as a whole showed a lower frequency of DR7 than controls [5.1% cf 28% in control population, p < 0.002]. Following subdivision by autoantibody profile, patients with circulating anti-centromere antibody (ACA) showed an increased frequency of DR1 compared to the control population [p < 0.001]. No scleroderma patient without ACA expressed this haplotype. Associations between MHC and some autoantibodies suggest that antigen presentation could lead to their production.

Activity of hammerhead ribozymes containing non-nucleotidic linkers.

Hammerhead ribozymes were synthesized in which the tetranucleotide loop II was replaced by non-nucleotidic linkers of 7, 13, 17 and 19 atoms length. Ribozymes with 17 and 19 atom linkers, in combination with a 4 base pair stem II, had catalytic efficiencies which were 2 fold increased to that of the parent ribozyme with a tetranucleotide loop. Ribozymes with these linkers, but in combination with a 2 base pair stem II, showed a 2 fold decrease in catalytic efficiency when compared to the parent ribozyme. Prolonged preincubation in the presence of MgCl2 was required for hexaethylene glycol linker-modified ribozymes to obtain maximum activity and reproducible kinetic data.

Chronic tolerance and sensitization to alcohol in sons of alcoholics.

In view of conflicting results concerning differences between sons of alcoholics and sons of nonalcoholics in response to a single alcohol challenge (with a given dose), we exposed these high and low risk groups to several sessions in which they drank alcohol at the same dose in order to measure the development of chronic tolerance or sensitization with repeated doses. Sons of alcoholics and sons of nonalcoholics received a moderate dose of alcohol (0.5 g/kg) in three sessions with alcohol, followed by a placebo session. Sons of alcoholics developed reverse tolerance or chronic sensitization to repeated dosings of alcohol in finger pulse amplitude, while sons of nonalcoholics did not. Sons of alcoholics failed to show chronic tolerance in skin conductance and finger temperature, while sons of alcoholics did show the development of tolerance. Sons of alcoholics demonstrated greater motor activity throughout the sessions, both before and after alcohol. These results indicate that high and low risk groups differ in terms of their developmental adaptation to alcohol, as well as in the temperamental trait of behavioral activity.

Alcohol challenge with sons of alcoholics: a critical review and analysis.

Studies are reviewed in which response to acute administration of alcohol was compared between individuals with and without family histories of alcoholism (FH+, FH-). This research represents a search for a psychobiological marker for alcoholism. A methodological critique of the procedures reported in this literature is then presented. Finally, a conceptual model is suggested in which differences in the response to alcohol between FH+ individuals and FH- individuals must be understood in relation to time after drinking alcohol. This Newtonian differentiator model proposes that sons of alcoholics exhibit acute sensitization as blood alcohol level rises and acute tolerance as blood alcohol level falls, compared with sons of nonalcoholics. Therefore, FH+ subjects find alcohol more rewarding because they accentuate the pleasurable, excitatory aspects of initial intoxication and attenuate the feelings of anxiety and depression that predominate as blood alcohol levels drop.

Effects of alcohol conditioning and expectancy on a visuo-motor integration task.

Two experiments were performed in which the classical conditioning model of tolerance, the habituation theory of tolerance, and state dependent learning theory made conflicting predictions. In the first experiment, alcohol conditioning did not produce a compensatory response under placebo on a visuo-motor integration task, but disguised alcohol produced a large decrement in performance. Since the results were consistent both with habituation and state dependent learning theories, a second experiment was performed in which all subjects received alcohol, but half were told that they were receiving pure tonic water. The finding of no expectancy effect was inconsistent with habituation theory, but fully consistent with state dependent learning theory.