Some capabilities for model-based and model-free linkage analysis using the program package S.A.G.E. (Statistical Analysis for Genetic Epidemiology).

For both model-free and model-based linkage analysis the S.A.G.E. (Statistical Analysis for Genetic Epidemiology) program package has some unique capabilities in analyzing both continuous traits and binary traits with variable age of onset. Here we highlight model-based linkage analysis of a quantitative trait (plasma dopamine ß hydroxylase) that is known to be largely determined by monogenic inheritance, using a prior segregation analysis to produce the best fitting model for the trait. For a binary trait with variable age of onset (schizophrenia), we illustrate how using age of onset information to obtain a quantitative susceptibility trait leads to more statistically significant linkage signals, suggesting better power.

Genome-wide association identifies SKIV2L and MYRIP as protective factors for age-related macular degeneration.

Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly in the developed world. We conducted a genome-wide association study in a series of families enriched for AMD and completed a meta-analysis of this new data with results from reanalysis of an existing study of a late-stage case-control cohort. We tested the top findings for replication in 1896 cases and 1866 controls and identified two novel genetic protective factors for AMD. In addition to the complement factor H (CFH) (P=2.3 × 10⁻64) and age-related maculopathy susceptibility 2 (ARMS2) (P=1.2 × 10⁻6°) loci, we observed a protective effect at rs429608, an intronic SNP in SKIV2L (P=5.3 × 10⁻¹5), a gene near the complement component 2 (C2)/complement factor B (BF) locus, that indicates the protective effect may be mediated by variants other than the C2/BF variants previously studied. Haplotype analysis at this locus identified three protective haplotypes defined by the rs429608 protective allele. We also identified a new potentially protective effect at rs2679798 in MYRIP (P=2.9 × 10⁻4), a gene involved in retinal pigment epithelium melanosome trafficking. Interestingly, MYRIP was initially identified in the family-based scan and was confirmed in the case-control set. From these efforts, we report the identification of two novel protective factors for AMD and confirm the previously known associations at CFH, ARMS2 and C3.

An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei.

RNA editing in trypanosomes occurs by a series of enzymatic steps that are catalyzed by a macromolecular complex. The TbMP52 protein is shown to be a component of this complex, to have RNA ligase activity, and to be one of two adenylatable proteins in the complex. Regulated repression of TbMP52 blocks editing, which shows that it is a functional component of the editing complex. This repression is lethal in bloodforms of the parasite, indicating that editing is essential in the mammalian stage of the life cycle. The editing complex, which is present in all kinetoplastid parasites, may thus be a chemotherapeutic target.

Uridylate addition and RNA ligation contribute to the specificity of kinetoplastid insertion RNA editing.

RNA editing in Trypanosoma brucei inserts and deletes uridylates (U's) in mitochondrial pre-mRNAs under the direction of guide RNAs (gRNAs). We report here the development of a novel in vitro precleaved editing assay and its use to study the gRNA specificity of the U addition and RNA ligation steps in insertion RNA editing. The 5' fragment of substrate RNA accumulated with the number of added U's specified by gRNA, and U addition products with more than the specified number of U's were rare. U addition up to the number specified occurred in the absence of ligation, but accumulation of U addition products was slowed. The 5' fragments with the correct number of added U's were preferentially ligated, apparently by adenylylated RNA ligase since exogenously added ATP was not required and since ligation was eliminated by treatment with pyrophosphate. gRNA-specified U addition was apparent in the absence of ligation when the pre-mRNA immediately upstream of the editing site was single stranded and more so when it was base paired with gRNA. These results suggest that both the U addition and RNA ligation steps contributed to the precision of RNA editing.

Association of two novel proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA editing complex.

RNA editing in kinetoplastid mitochondria inserts and deletes uridylates at multiple sites in pre-mRNAs as directed by guide RNAs. This occurs by a series of steps that are catalyzed by endoribonuclease, 3'-terminal uridylyl transferase, 3'-exouridylylase, and RNA ligase activities. A multiprotein complex that contains these activities and catalyzes deletion editing in vitro was enriched from Trypanosoma brucei mitochondria by sequential ion-exchange and gel filtration chromatography, followed by glycerol gradient sedimentation. The complex size is approximately 1,600 kDa, and the purified fraction contains 20 major polypeptides. A monoclonal antibody that was generated against the enriched complex reacts with an approximately 49-kDa protein and specifically immunoprecipitates in vitro deletion RNA editing activity. The protein recognized by the antibody was identified by mass spectrometry, and the corresponding gene, designated TbMP52, was cloned. Recombinant TbMP52 reacts with the monoclonal antibody. Another novel protein, TbMP48, which is similar to TbMP52, and its gene were also identified in the enriched complex. These results suggest that TbMP52 and TbMP48 are components of the RNA editing complex.

Four related proteins of the Trypanosoma brucei RNA editing complex.

RNA editing in kinetoplastid mitochondria occurs by a series of enzymatic steps that is catalyzed by a macromolecular complex. Four novel proteins and their corresponding genes were identified by mass spectrometric analysis of purified editing complexes from Trypanosoma brucei. These four proteins, TbMP81, TbMP63, TbMP42, and TbMP18, contain conserved sequences to various degrees. All four proteins have sequence similarity in the C terminus; TbMP18 has considerable sequence similarity to the C-terminal region of TbMP42, and TbMP81, TbMP63, and TbMP42 contain zinc finger motif(s). Monoclonal antibodies that are specific for TbMP63 and TbMP42 immunoprecipitate in vitro RNA editing activities. The proteins are present in the immunoprecipitates and sediment at 20S along with the in vitro editing, and RNA editing ligases TbMP52 and TbMP48. Recombinant TbMP63 and TbMP52 coimmunoprecipitate. These results indicate that these four proteins are components of the RNA editing complex and that TbMP63 and TbMP52 can interact.

Novel regulations of glutamate and aspartate uptake by HeLa cells.

Pathways of L-glutamate and L-aspartate import by HeLa S3 cells were investigated before and after the cells were depleted of internal amino acids by starvation. Two new regulations of transport were observed in starved cells. Aspartate entered nonstarved cells by two routes, one non-saturable and one, an apparent analog of saturable system X-AG, that was sodium-dependent and competitively inhibited by glutamate. Starvation for one hour in saline increased the efficiency of saturable aspartate import, increasing Vmax and decreasing Km, an effect not previously reported for system X-AG. Glutamate uptake by nonstarved cells appeared to occur through system X-AG; through an analog of system X-C, which was sodium-independent, cystine- and quisqualate-inhibitable; as well as through one or more nonsaturable pathways. Starvation in saline for one hour resulted in the appearance of a new low-affinity saturable glutamate uptake system. This new system was sodium-dependent but not inhibited by aspartate.

Numerical analysis reveals complexities of glutamate transport.

The uptake of radiolabeled glutamate into cultured human (HeLa S3) and hamster (CHO-K1) cells was analyzed according to modified Michaelis-Menten models fit by the Marquardt least-squares method. Kinetic parameters not previously reported for these cells were obtained. Some rarely used features available with this fitting method proved to be extremely helpful. Most importantly, a goodness-of-fit measure revealed a significant alteration of glutamate uptake in HeLa cells that was induced by starvation. This apparent regulation, unexpected for glutamate transport, might have been missed if the fit had been judged by eye or by the magnitude of parameter standard deviations. Techniques for analyzing parameter distributions, improving experimental design and performing tests of significance are also described.

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.

New mutations and phenotypes associated with glutamate and aspartate transport in Chinese hamster ovary (CHO-K1) cells.

Two new Chinese hamster ovary cell (CHO-K1) mutants lacking amino acid transport System X-AG activity were isolated by [3H]aspartate suicide selection. These null mutants, Dd-B6 and Dd-B7, were analyzed by somatic cell hybridization, along with previously described partial-function mutants, Ed-A1 and Ed-B8. With respect to System X-AG activity, all four mutations fell into a single complementation group. By quantitative assay, the mutations in Ed-A1 and Ed-B8 behaved as simple recessives in fusions with wild type cells, while those in Dd-B6 and Dd-B7 were codominant. We have discovered that Ed-A1 and Ed-B8 are highly permeable to small neutral molecules. This high permeability phenotype was dominant to wild-type. Northern, Southern, and Western analyses indicated that System X-AG in CHO is not closely related to any of the three well characterized glutamate transporters represented by GLT-1, EAACI or GLAST.

The Na+-dependent glutamate and aspartate transporter supports glutathione maintenance and survival of CHO-K1 cells.

Glutathione synthesis, a vital cellular process, depends on L-cystine uptake by the amino acid transporter, System x-C. Here we show that a second transporter, System X-AG, is required for normal System x-C activity and glutathione maintenance by employing somatic cell mutants of CHO-K1. Uptake by System x-C in two X-AG-null mutants is significantly lower than that of CHO-K1, either under control conditions or after prolonged treatment with an electrophile. In addition, levels of glutathione in control and treated mutant cells are less than half those of wild-type CHO-K1 or of a pseudorevertant. The significance of this reduction was tested by chemical challenge: mutants are twofold more sensitive than wild type to reactive oxygen species generated by phenylbenzoquinone and to damage produced by the anticancer drug, cisplatin. These results suggest that System X-AG provides a significant portion of the glutamate used to energize the uptake of cystine required for the synthesis of glutathione.

Selection of Chinese hamster ovary cells (CHO-K1) with reduced glutamate and aspartate uptake.

Transport of L-[3H]glutamate into Chinese hamster ovary cells (CHO-K1) was characterized and the results used to design a tritium suicide selection for cells with transport defects. Replicas of surviving colonies on polyester cloth disks were screened by autofluorography for reduced uptake and two mutant clones, Ed-A1 and Ed-B8, were obtained. Uptake of glutamate through a sodium-dependent system in both mutants was characterized by significant reductions in Vmax and increases in Km compared to parental cells, but their response to removal of extracellular sodium differed, suggesting distinct mutations in the two lines. The Vmax of aspartate uptake through this system was reduced in both mutants, to one-ninth in the case of Ed-B8. Glutamate uptake through a sodium-independent system was not altered in either mutant. Surprisingly, acid-soluble intracellular pools of several amino acids were higher in both mutants.

The specificity of nucleotide removal during RNA editing in Trypanosoma brucei.

RNA editing in Trypanosoma brucei produces mature mRNAs by posttranscriptional insertion and deletion of uridylates (Us) by a series of catalytic steps, which include endoribonucleolytic cleavage, 3' terminal addition or removal of Us, and RNA ligation. Preedited mRNA (pre-mRNA) and guide RNA (gRNA) that are mutated at or near the editing site (ES) were used to examine the effects on the specificity of in vitro editing. Sequences that are not predicted to form a gRNA/pre-mRNA base pair immediately 5' to the ES still supported accurate editing. Substitution of a non-U nucleotide at various positions within a stretch of Us that are normally removed from the ES resulted in deletion of only the Us that were 3' to the substituted nucleotide. Overall, ES selection by the endoribonuclease, the specificity of the 3' exoribonuclease for Us, and ligation appear to act in concert to ensure the production of accurately edited RNA.