MRI Features of Histologically Diagnosed Supratentorial Primitive Neuroectodermal Tumors and Pineoblastomas in Correlation with Molecular Diagnoses and Outcomes: A Report from the Children's Oncology Group ACNS0332 Trial

BACKGROUND AND PURPOSE

Supratentorial primitive neuroectodermal tumors and pineoblastomas have traditionally been grouped together for treatment purposes. Molecular profiling of these tumors has revealed a number of distinct entities and has led to the term "CNS-primitive neuroectodermal tumors" being removed from the 2016 World Health Organization classification. The purpose of this study was to describe the MR imaging findings of histologically diagnosed primitive neuroectodermal tumors and pineoblastomas and correlate them with molecular diagnoses and outcomes.

MATERIALS AND METHODS

Histologically diagnosed primitive neuroectodermal tumors and pineoblastomas were enrolled in this Children's Oncology Group Phase III trial, and molecular classification was retrospectively completed using DNA methylation profiling. MR imaging features were systematically studied and correlated with molecular diagnoses and survival.

RESULTS

Of the 85 patients enrolled, 56 met the inclusion criteria, in whom 28 tumors were in pineal and 28 in nonpineal locations. Methylation profiling revealed a variety of diagnoses, including pineoblastomas (n = 27), high-grade gliomas (n = 17), embryonal tumors (n = 7), atypical teratoid/rhabdoid tumors (n = 3), and ependymomas (n = 2). Thus, 39% overall and 71% of nonpineal tumor diagnoses were discrepant with histopathology. Tumor location, size, margins, and edema were predictors of embryonal-versus-nonembryonal tumors. Larger size and ill-defined margins correlated with poor event-free survival, while metastatic disease by MR imaging did not.

CONCLUSIONS

In nonpineal locations, only a minority of histologically diagnosed primitive neuroectodermal tumors are embryonal tumors; therefore, high-grade glioma or ependymoma should be high on the radiographic differential. An understanding of molecularly defined tumor entities and their relative frequencies and locations will help the radiologist make more accurate predictions of the tumor types.

The effects of obesity classification method on select kinematic gait variables in adult females

AIM

Obesity has been associated with gait alterations, but most studies have utilized BMI for classification. This study examined gait alterations based on body fat and BMI.

METHOD

Participants (N.=22) had BMI and body fat percentage determined and underwent gait analysis. Body fat percentage was determined using dual energy x-ray absorptiometry (DEXA). Gait variables were examined in 3 groups: step width, preferred walking speed, and stride length; angular displacement at the knee and angular displacement at the ankle; and peak knee flexion velocity and peak knee extension velocity. A multivariate approach with follow-up univariate tests was used.

RESULTS

Based on BMI, there was a significant effect for step width, preferred walking speed, and stride length (F[3, 16]=3.47, P=0.04). Univariate tests were significant for preferred walking speed and stride length (both P<0.03). Overweight by BMI participants had a lower preferred walking speed (1.31±0.16 m/s vs. 1.53±0.18 m/s) and shorter stride length (1.23±0.11 m vs. 1.38±0.11 m). Based on body fat percentage, there was a significant effect for peak knee flexion velocity and peak knee extension velocity (F[2, 19]=4.08, P=0.03). Overweight by body fat participants had lower peak knee flexion velocity (295.99±21.32 o/s vs. 320.25±27.67 o/s; P=0.04).

CONCLUSION

Gait alterations were found for both methods of classifying obesity. However, the alterations were different for each method. The method of determining obesity appears to affect where gait alterations are found.

Measurement of Stress In CVD Diamond Films

Measurement of stress in CVD diamond by Raman spectroscopy and by the substrate curvature method is discussed. A correction to the commonly applied Stoney thin-film equation for the substrate curvature technique is presented for coatings with a large stiffness mismatch with the substrate. Stress measurement by Raman spectroscopy is complicated by factors such as temperature, domain size, non-hydrostatic stress, and degeneracy lifting. With proper consideration of these complicating factors, substrate curvature and Raman spectroscopy stress measurement results can be reconciled with the predictions based on thermal modeling.

Passivation of Interfaces in High-Efficiency Photovoltaic Devices

Solar cells made from III–V materials have achieved efficiencies greater than 30%. Effectively ideal passivation plays an important role in achieving these high efficiencies. Standard modeling techniques are applied to Ga0.5In0.5P solar cells to show the effects of passivation. Accurate knowledge of the absorption coefficient is essential (see appendix). Although ultralow (<2 cm/s) interface recombination velocities have been reported, in practice, it is difficult to achieve such low recombination velocities in solar cells because the doping levels are high and because of accidental incorporation of impurities and dopant diffusion. Examples are given of how dopant diffusion can both help and hinder interface passivation, and of how incorporation of oxygen or hydrogen can cause problems.

Step structures on III-V phosphide (001) surfaces: how do steps and Sb affect CuPt ordering of GaInP2?

The observation of III-V phosphide (001)-(2 x 2) surfaces makes it possible to solve a long standing mystery of step structures. First-principles calculations show that a bulklike type-B step on a hydrogenated 2 x 2 surface is more stable than a rebonded one by 1.1 eV/unit step. In contrast, this energy difference for a H-free beta(2 x 4) surface is only 0.5 eV/unit step. The large difference explains why the CuPt ordering of GaInP is stronger in metal-organic chemical vapor deposition than in molecular beam epitaxy. However, a minute amount of Sb will preferentially attach to the 2 x 2 surface steps and induce additional step structures that cause ordering disruption.

A genome screen of systemic lupus erythematosus using affected-relative-pair linkage analysis with covariates demonstrates genetic heterogeneity

Systemic lupus erythematosus (SLE) appears to be the consequence of complex genetics and of only partly understood environmental contributions. Previous work by ourselves and by others has established genetic effects on 1q, 2q, 4p, 6p, and 16p using SLE as the phenotype. However, individual SLE affecteds are extraordinarily different from one another by clinical and laboratory measures. This variation may have a genetic basis; if so, it is advantageous to incorporate measures of between-family clinical variability as covariates in a genetic linkage analysis of affected relative pairs (ARPs) to allow for locus heterogeneity. This approach was applied to genome scan marker data from 160 pedigrees multiplex for SLE and containing 202 ARPs. Because the number of potential covariates was large, we used both ad hoc methods and formal principal components analysis to construct four composite covariates using the SLE classification criteria plus age of onset, ethnicity, and sex. Linkage analysis without covariates has detected evidence for linkage at 1q22-24, 2q37, 4p16, 12p12-11, and 17p13. Linkage analysis with these covariates uncovered linkage at 13p11, 17q11-25, and 20q12 and greatly improved evidence for linkage at 1q22-24, 2q37, 12p12-11, and 17p13. Follow-up analysis identified the original variables contributing to locus heterogeneity in each of these locations. In conclusion, allowing for locus heterogeneity through the incorporation of covariates in linkage analysis is a useful way to dissect the genetic contributions to SLE and uncover new genetic effects.

Strain-driven mesoscopic reconstruction of the As/Ge(111) surface

Periodic arrays of large hexagonal tiles (up to 170 A in size) are observed on As/Ge(111) surfaces. First-principles total energy calculations combined with scanning tunneling microscopy reveal a (5-7-5)-ringed structure for the trenches that separate the tiles. We find that trenches form via an exothermic process. The calculated equilibrium trench spacing of approximately 104 A agrees with experiment. Comparison between first-principles calculations and continuum elasticity theory suggests that the observed mesoscopic reconstruction is driven entirely by long-range surface strain relaxation.

Locating the genes underlying a simulated complex disease by discriminant analysis

The purpose of this study was to propose and evaluate a novel multivariate approach for genetic mapping of complex binary human diseases. This approach uses the application of either of two methods of standard (stepwise) discriminant analysis to detect linkage based on the differential marker identity-by-descent distributions among the three affection groups of sib pairs (concordantly affected, discordant, and concordantly unaffected). One of the advantages of this approach is that it allows for simultaneously testing all markers, as well as other genetic and environmental factors, in a single multivariate setting. We have explored its properties and behaviors via an application to the simulated data in Genetic Analysis Workshop 12.

Comparison of three methods for obtaining principal components from family data in genetic analysis of complex disease

Three multivariate techniques used to derive principal components (PCs) from family data were compared for their ability to model family data and power to detect linkage. Using the simulated data from Genetic Analysis Workshop 12, the five quantitative traits were first adjusted for age, sex, and environmental factors 1 and 2. Then, standard PCs, PCs obtained from between-family covariance, and PCs obtained from within-family genetic covariance were derived and subjected to multivariate sib pair linkage analysis. The standard PCs obtained from the overall correlation matrix allowed identification of key features of the true genetic model more readily than did the other methods. For detection of linkage, standard PCs and PCs obtained from the between-family genetic covariance performed similarly in terms of both power and type 1 error, and both methods performed better than the PCs obtained from within-family genetic covariance.

Linkage analysis of human systemic lupus erythematosus-related traits: a principal component approach

OBJECTIVE

To identify chromosomal regions containing genes involved in the susceptibility to human systemic lupus erythematosus (SLE)-related traits.

METHODS

In the context of a genome scan, we analyzed 101 SLE-affected sibpairs with respect to dermatologic, renal, immunologic, hematologic, neurologic, cardiopulmonary, and arthritic characteristics. Phenotypes were redefined in terms of principal components, which are synthetic variables composed of linear combinations of the original traits. Using 9 principal components obtained from these 7 traits plus age at SLE onset and race, we analyzed genome scan data with the multivariate version of the new Haseman-Elston regression model.

RESULTS

The largest linkage for an individual trait was on chromosome 2 at 228 cM (immunologic; P = 0.00048). The most significant linkage to an individual principal component was on chromosome 4 at 208 cM (P = 0.00007). The largest multivariate linkage was on chromosome 7 at 69 cM (P = 0.0001). Of the individual organ systems, dermatologic involvement had the largest effect (P = 0.0083) at this peak at 7p13 on chromosome 7. Further analyses revealed that malar rash, a subtype of dermatologic involvement, was linked significantly (P = 0.00458) to this location.

CONCLUSION

These results provide evidence of the presence and locations of genes that are involved in the genetic susceptibility to SLE-related traits in humans.

Altered transcription in yeast expressing expanded polyglutamine

Expanded polyglutamine tracts are responsible for at least eight fatal neurodegenerative diseases. In mouse models, proteins with expanded polyglutamine cause transcriptional dysregulation before onset of symptoms, suggesting that this dysregulation may be an early event in polyglutamine pathogenesis. Transcriptional dysregulation and cellular toxicity may be due to interaction between expanded polyglutamine and the histone acetyltransferase CREB-binding protein. To determine whether polyglutamine-mediated transcriptional dysregulation occurs in yeast, we expressed polyglutamine tracts in Saccharomyces cerevisiae. Gene expression profiles were determined for strains expressing either a cytoplasmic or nuclear protein with 23 or 75 glutamines, and these profiles were compared to existing profiles of mutant yeast strains. Transcriptional induction of genes encoding chaperones and heat-shock factors was caused by expression of expanded polyglutamine in either the nucleus or cytoplasm. Transcriptional repression was most prominent in yeast expressing nuclear expanded polyglutamine and was similar to profiles of yeast strains deleted for components of the histone acetyltransferase complex Spt/Ada/Gcn5 acetyltransferase (SAGA). The promoter from one affected gene (PHO84) was repressed by expanded polyglutamine in a reporter gene assay, and this effect was mitigated by the histone deacetylase inhibitor, Trichostatin A. Consistent with an effect on SAGA, nuclear expanded polyglutamine enhanced the toxicity of a deletion in the SAGA component SPT3. Thus, an early component of polyglutamine toxicity, transcriptional dysregulation, is conserved in yeast and is pharmacologically antagonized by a histone deacetylase inhibitor. These results suggest a therapeutic approach for treatment of polyglutamine diseases and provide the potential for yeast-based screens for agents that reverse polyglutamine toxicity.

Steps on As-terminated Ge(001) revisited: theory versus experiment

We examine the double-layer B-type steps on As-terminated vicinal Ge(001) surfaces. The currently accepted structure is a chemically inert bulklike structure without any gap state, and with all the chemical bonds of the Ge and As atoms being satisfied. However, we show that the need for optimizing the p(3) pyramidal angles of the threefold coordinated As atoms drives unusual atomic rearrangement. This leads to a more stable reconstruction involving odd-membered (5-7-5) rings at the step edge. Comparison between theoretical and experimental scanning tunneling microscopy images yields excellent agreement.

The amyloid precursor protein locus and very-late-onset Alzheimer disease

Although mutations in the amyloid-beta precursor protein (APP) gene are known to confer high risk of Alzheimer disease (AD) to a small percentage of families in which it has early onset, convincing evidence of a major role for the APP locus in late-onset AD has not been forthcoming. In this report, we have used a covariate-based affected-sib-pair linkage method to analyze the chromosome 21 clinical and genetic data obtained on affected sibships by the National Institute of Mental Health Alzheimer Disease Genetics Initiative. The baseline model (without covariates) gave a LOD score of 0.02, which increases to 1.43 when covariates representing the additive effects of E2 and E4 are added. Larger increases in LOD scores were found when age at last examination/death (LOD score 5.54; P=.000002) or age at onset plus disease duration (LOD score 5.63; P=.000006) were included in the linkage model. We conclude that the APP locus may predispose to AD in the very elderly.

Ontogeny of catabolic and morphological properties of skeletal muscle of the red-winged blackbird (Agelaius phoeniceus)

Thermogenic capabilities of red-winged blackbirds improve markedly during their 10-12-day nestling period, especially between day 5 and day 8. The time course of improvements may be determined by the maturation of skeletal muscles involved in shivering thermogenesis, particularly the pectoralis muscles. To test this hypothesis, morphological and biochemical changes in pectoral and leg muscles were measured in young and adult blackbirds. Both muscles grew disproportionately relative to body mass. The pectoralis consisted entirely of fast-twitch fibers, predominantly fast oxidative glycolytic. In contrast, the gastrocnemius muscle consisted of a mixture of slow and fast fibers (predominantly fast glycolytic). Although fiber composition was constant, both cross-sectional area and density of fibers increased with age in both muscles. Catabolic capacities of the pectoralis increased significantly (approximately 7-8-fold) throughout the nestling period, most abruptly after day 3 (citrate synthase, CS) or day 4 (3-hydroxacyl-CoA-dehydrogenase, HOAD). Myofibrillar ATPase activities in the pectoralis were initially low, but increased after day 5. Further increases in CS and myofibrillar ATPase activities occurred in the pectoralis after fledging. CS and HOAD activities in the leg were much lower, but myofibrillar ATPase activities were remarkably similar in the two muscles, differing only in adults. These results are consistent with the hypothesis that the development of endothermy is dependent on the morphological and biochemical maturation of skeletal muscles important in thermogenesis.

No excess of early onset cancer in family members of Wilms tumor patients

BACKGROUND

Wilms tumor is one of the few pediatric cancers with well-defined familial and genetic components. The authors assessed the risk of early-onset cancers in first- and second-degree relatives of patients enrolled by the National Wilms Tumor Study Group.

METHODS

Using a stratified sampling scheme that targeted 530 families of patients who were believed a priori to have a genetic contribution to their disease, the authors conducted interviews regarding cancer occurrence in 4258 family members from 296 families of patients with Wilms tumor. Reports of malignant neoplasms that occurred before 55 years of age were confirmed by review of medical records wherever possible. A period of risk was defined for each family member based on calendar time and his or her relationship to the proband.

RESULTS

Ninety-nine cancers were observed, whereas 126.8 were expected by applying standard cancer rates for age and calendar period to the 120,885 person-years at risk. The standardized incidence ratio (SIR) was O-E = 0.78 with 95% confidence interval (CI) of (0.64, 0.95). In subgroup analyses, the highest relative risks were observed for parents of the index case (O/E = 21/13.0 = 1.6, 95% CI = 1.0, 2.5) and for leukemia (O/E = 9/4.9 = 1.9, 95% CI= 0.85,3.5).

CONCLUSIONS

The results of this study may provide reassurance to families of children who have had Wilms tumor. Potential sources of bias included the low (56%) rate of participation of targeted families. In general, the biases might have led to the underreporting of some cancers, especially in more distant relatives. The possibility of a slight excess of cancer in parents of Wilms tumor patients could not be excluded.

An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles

We have developed a statistical regression modeling approach to discover genes that are differentially expressed between two predefined sample groups in DNA microarray experiments. Our model is based on well-defined assumptions, uses rigorous and well-characterized statistical measures, and accounts for the heterogeneity and genomic complexity of the data. In contrast to cluster analysis, which attempts to define groups of genes and/or samples that share common overall expression profiles, our modeling approach uses known sample group membership to focus on expression profiles of individual genes in a sensitive and robust manner. Further, this approach can be used to test statistical hypotheses about gene expression. To demonstrate this methodology, we compared the expression profiles of 11 acute myeloid leukemia (AML) and 27 acute lymphoblastic leukemia (ALL) samples from a previous study (Golub et al. 1999) and found 141 genes differentially expressed between AML and ALL with a 1% significance at the genomic level. Using this modeling approach to compare different sample groups within the AML samples, we identified a group of genes whose expression profiles correlated with that of thrombopoietin and found that genes whose expression associated with AML treatment outcome lie in recurrent chromosomal locations. Our results are compared with those obtained using t-tests or Wilcoxon rank sum statistics.

NeuroD2 is necessary for development and survival of central nervous system neurons

NeuroD2 is sufficient to induce cell cycle arrest and neurogenic differentiation in nonneuronal cells. To determine whether this bHLH transcription factor was necessary for normal brain development, we used homologous recombination to replace the neuroD2 coding region with a beta-galactosidase reporter gene. The neuroD2 gene expressed the reporter in a subset of neurons in the central nervous system, including in neurons of the neocortex and hippocampus and cerebellum. NeuroD2(-/-) mice showed normal development until about day P14, when they began exhibiting ataxia and failure to thrive. Brain areas that expressed neuroD2 were smaller than normal and showed higher rates of apoptosis. Cerebella of neuroD2-null mice expressed reduced levels of genes encoding proteins that support cerebellar granule cell survival, including brain-derived neurotrophic factor (BDNF). Decreased levels of BDNF and higher rates of apoptosis in cerebellar granule cells of neuroD2(-/-) mice indicate that neuroD2 is necessary for the survival of specific populations of central nervous system neurons in addition to its known effects on cell cycle regulation and neuronal differentiation.

The heritability of attitudes: a study of twins

The genetic basis of individual differences in attitudes was examined in a survey of 195 pairs of monozygotic twins and 141 pairs of same-sex dizygotic twins. A principal components analysis of the 30 attitude items in the survey identified 9 attitude factors, of which 6 yielded significant heritability coefficients. Nonshared environmental factors accounted for the most variance in the attitude factors. Possible mediators of attitude heritability were also assessed, including personality traits, physical characteristics, and academic achievement. Analyses showed that several of these possible mediators correlated at a genetic level with the heritable attitude factors, suggesting that the heritability of the mediator variables might account for part of the heritable components of some attitudes. There was also some evidence that highly heritable attitudes were psychologically "stronger" than less heritable attitudes.

Model-free linkage analysis with covariates confirms linkage of prostate cancer to chromosomes 1 and 4

As with many complex genetic diseases, genome scans for prostate cancer have given conflicting results, often failing to provide replication of previous findings. One factor contributing to the lack of consistency across studies is locus heterogeneity, which can weaken or even eliminate evidence for linkage that is present only in a subset of families. Currently, most analyses either fail to account for locus heterogeneity or attempt to account for it only by partitioning data sets into smaller and smaller portions. In the present study, we model locus heterogeneity among affected sib pairs with prostate cancer by including covariates in the linkage analysis that serve as surrogate measures of between-family linkage differences. The model is a modification of the Olson conditional logistic model for affected relative pairs. By including Gleason score, age at onset, male-to-male transmission, and/or number of affected first-degree family members as covariates, we detected linkage near three locations that were previously identified by linkage (1q24-25 [HPC1; LOD score 3.25, P=.00012], 1q42.2-43 [PCAP; LOD score 2.84, P=.0030], and 4q [LOD score 2.80, P=.00038]), near the androgen-receptor locus on Xq12-13 (AR; LOD score 3.06, P=.00053), and at five new locations (LOD score > 2.5). Without covariates, only a few weak-to-moderate linkage signals were found, none of which replicate findings of previous genome scans. We conclude that covariate-based linkage analysis greatly improves the likelihood that linked regions will be found by incorporation of information about heterogeneity within the sample.

Therapeutic opportunities in polyglutamine disease

Polyglutamine diseases comprise a class of familial neurodegenerative disorders caused by expression of proteins containing expanded polyglutamine tracts. Great progress has been made in elucidating the molecular mechanisms contributing to polyglutamine pathology, and in identifying potential drug targets. Although much remains to be learned, these advances provide an opportunity for rational approaches to target-based drug discovery.

A novel UDP-glucose transferase is part of the callose synthase complex and interacts with phragmoplastin at the forming cell plate

Using phragmoplastin as a bait, we isolated an Arabidopsis cDNA encoding a novel UDP-glucose transferase (UGT1). This interaction was confirmed by an in vitro protein--protein interaction assay using purified UGT1 and radiolabeled phragmoplastin. Protein gel blot results revealed that UGT1 is associated with the membrane fraction and copurified with the product-entrapped callose synthase complex. These data suggest that UGT1 may act as a subunit of callose synthase that uses UDP-glucose to synthesize callose, a 1,3-beta-glucan. UGT1 also interacted with Rop1, a Rho-like protein, and this interaction occurred only in its GTP-bound configuration, suggesting that the plant callose synthase may be regulated by Rop1 through the interaction with UGT1. The green fluorescent protein--UGT1 fusion protein was located on the forming cell plate during cytokinesis. We propose that UGT1 may transfer UDP-glucose from sucrose synthase to the callose synthase and thus help form a substrate channel for the synthesis of callose at the forming cell plate.

Catabolic capacity of the muscles of shorebird chicks: maturation of function in relation to body size

Newly hatched precocial chicks of arctic shorebirds are able to walk and regulate their body temperatures to a limited extent. Yet, they must also grow rapidly to achieve independence before the end of the short arctic growing season. A rapid growth rate may conflict with development of mature function, and because of the allometric scaling of thermal relationships, this trade-off might be resolved differently in large and small species. We assessed growth (mass) and functional maturity (catabolic enzyme activity) in leg and pectoral muscles of chicks aged 1-16 d and adults of two scolopacid shorebirds, the smaller dunlin (Calidris alpina: neonate mass 8 g, adult mass 50 g) and larger whimbrel (Numenius phaeopus; neonate mass 34 g, adult mass 380 g). Enzyme activity indicates maximum catabolic capacity, which is one aspect of the development of functional maturity of muscle. The growth rate-maturity hypothesis predicts that the development of catabolic capacity should be delayed in faster-growing muscle masses. Leg muscles of both species were a larger proportion of adult size at hatching and grew faster than pectoral muscles. Pectoral muscles grew more rapidly in the dunlin than in the whimbrel, whereas leg muscles grew more rapidly in the whimbrel. In both species and in both leg and pectoral muscles, enzyme activities generally increased with age, suggesting increasing functional maturity. Levels of citrate synthase activity were similar to those reported for other species, but l-3-hydroxyacyl-CoA-dehydrogenase and pyruvate kinase (PK) activities were comparatively high. Catabolic capacities of leg muscles were initially high compared to those of pectoral muscles, but with the exception of glycolytic (PK) capacities, these subsequently increased only modestly or even decreased as chicks grew. The earlier functional maturity of the more rapidly growing leg muscles, as well as the generally higher functional maturity in muscles of the more rapidly growing dunlin chicks, contradicts the growth rate-maturity function trade-off and suggests that birds have considerable latitude to modify this relationship. Whimbrel chicks, apparently, can rely on allometric scaling of power requirements for locomotion and the thermal inertia of their larger mass to reduce demands on their muscles, whereas dunlin chicks require muscles with higher metabolic capacity from an earlier age. Thus, larger and smaller species may adopt different strategies of growth and tissue maturation.

A family-based strategy to identify genes for diabetic nephropathy

Diabetic nephropathy (DN) clusters in families and specific ethnic groups, suggesting a genetic basis of disease transmission. Identification of DN susceptibility loci should reveal new therapeutic targets but requires accurate phenotyping. A powerful family-based strategy, which is novel to the pursuit of nephropathy genes in type 2 diabetes, is being used to collect a sample for candidate gene and genome scan analyses. Sib pairs that include DN index cases plus (1) sibs concordant for type 2 diabetes and DN (affected sib pairs [ASPs]) and (2) sibs concordant for type 2 diabetes but discordant for DN (discordant sib pairs [DSPs]) are targeted specifically for recruitment. Type 2 diabetes and DN phenotype criteria for index cases include diabetes onset after 38 years of age, duration 10 years or longer, no initial insulin treatment, diabetic retinopathy, end-stage renal disease (ESRD), and history of nephrotic proteinuria. ESRD patients were screened by questionnaire and medical record review (n = 2114). Of 666 patients with ESRD secondary to DN, 227 had a family history of ESRD, 150 had a living diabetic sib, and 124 families were enrolled. Sixty-five families, with 86 diabetic relative pairs (69 sibs, 17 children), have been completely phenotyped. If nephropathy in diabetic sibs is defined as albuminuria greater than 0.3 g/24 h, 31 ASPs and 26 DSPs (diabetic sib with albuminuria <0.3 g/24 h) were identified. Applying more stringent criteria, only 12 ASPs (sib with diabetes >10 years, diabetic retinopathy, and nephrotic proteinuria) and 9 DSPs (sib with diabetes >10 years and normal urine albumin excretion) were identified. Extrapolating from the number of subjects recruited using stringent phenotyping criteria, nearly 10,000 ESRD patients are required for screening to achieve adequate statistical power for linkage analysis (80% power to detect locus-specific relative risk of 2.2 at a lod score of 3.0). Careful phenotyping requires a large recruitment effort but is necessary to reduce population heterogeneity, a strategy that increases the likelihood of identifying DN loci.

;Evolution of Photosynthesis' (1970), re-examined thirty years later

I have re-examined my 1970 article 'Evolution of Photosynthesis' (Olson JM, Science 168: 438-446) to see whether any of my original proposals still survive. My original conviction that the evolution of photosynthesis was intimately connected with the origin of life has been replaced with the realization that photosynthesis may have been invented by the Bacteria after their divergence from the Archea. The common ancestor of all extant photosynthetic bacteria and cyanobacteria probably contained bacteriochlorophyll a, rather than chlorophyll a as originally proposed, and may have carried out CO(2) fixation instead of photoassimilation. The first electron donors were probably reduced sulfur compounds and later ferrous iron. The common ancestor of all extant reaction centers was probably similar to the homodimeric RC1 of present-day green sulfur bacteria (Chlorobiaceae) and heliobacteria. In the common ancestor of proteobacteria and cyanobacteria, the gene for the primordial RC1 was apparently duplicated and one copy split into two genes, one for RC2 and the other for a chlorophyll protein similar to CP43 and CP47 in extant cyanobacteria and chloroplasts. Homodimeric RC1 and homodimeric RC2 functioned in series as in the Z-scheme to deliver electrons from Fe(OH)(+) to NADP(+), while RC1 and/or RC2 separately drove cyclic electron flow for the production of ATP. In the line of evolution leading to proteobacteria, RC1 and the chlorophyll protein were lost, but RC2 was retained and became heterodimeric. In the line leading to cyanobacteria, both RC1 and RC2 replaced bacteriochlorophyll a with chlorophyll a and became heterodimeric. Heterodimeric RC2 further coevolved with a Mn-containing complex to utilize water as the electron donor for CO(2) fixation. The chlorophyll-protein was also retained and evolved into CP43 and CP47. Heliobacteria are the nearest photosynthetic relatives of cyanobacteria. The branching order of photosynthetic genes appears to be (1) proteobacteria, (2) green bacteria (Chlorobiaceae plus Chloroflexaceae), and (3) heliobacteria plus cyanobacteria.

Genome scan of human systemic lupus erythematosus by regression modeling: evidence of linkage and epistasis at 4p16-15.2

Systemic lupus erythematosus (SLE) is a complex autoimmune disorder involving at least hormonal, environmental, and genetic factors. Familial aggregation, a 2%-3% sibling recurrence rate, monozygotic twin concordance >20%, association with several candidate genes, as well as the results of five genome scans support a genetic component. We present here the results of a genome scan of 126 pedigrees multiplex for SLE, including 469 sibling pairs (affected and unaffected) and 175 affected relative pairs. Using the revised multipoint Haseman-Elston regression technique for concordant and discordant sibling pairs and a conditional logistic regression technique for affected relative pairs, we identify a novel linkage to chromosome 4p16-15.2 (P=.0003 and LOD=3.84) and present evidence of an epistatic interaction between chromosome 4p16-15.2 and chromosome 5p15 in our European American families. We confirm the evidence of linkage to chromosome 4p16-15.2 in European American families using data from an independent pedigree collection. In addition, our data support the published results of three independent studies for nine purportedly linked regions and agree with the previously published results from a subset of these data for three regions. In summary, results from two new analytical techniques establish and confirm linkage with SLE at 4p16-15.2, indicate epistasis between 4p16-15.2 and 5p15, and confirm other linkage effects with SLE that have been reported elsewhere.

Ascertainment adjustment: where does it take us?

It is commonly assumed that the parameter estimates of a statistical genetics model that has been adjusted for ascertainment will estimate parameters in the general population from which the ascertained subpopulation was originally drawn. We show that this is true only in certain restricted circumstances. More generally, ascertainment-adjusted parameter estimates reflect parameters in the ascertained subpopulation. In many situations, this shift in perspective is immaterial: the parameters of interest are the same in the ascertained sample and in the population from which it was drawn, and it is therefore irrelevant to which population inferences are presumed to apply. In other circumstances, however, this is not so. This has important implications, particularly for studies investigating the etiology of complex diseases.

Haseman and Elston revisited

Haseman and Elston (H-E) [1972] proposed a method to detect quantitative trait loci by linkage to a marker. The squared sib-pair trait difference is regressed on the proportion of marker alleles the pair is estimated to share identical by descent: a significantly negative regression coefficient suggests linkage. It has been shown that a maximum likelihood method that directly models the sib-pair covariance has more power. This increase in power can also be obtained using the H-E regression procedure by changing the dependent variable from the squared difference to the mean-corrected product of the sibs' trait values. Multiple sibs in a sibship can be accommodated by allowing for the correlations between pairs of products in a generalized least squares procedure. Multiple trait loci, including epistatic interactions, involve only multiple linear regression. Multivariate traits can use the method of Amos et al. [1990] to find the linear function of the traits that maximizes the evidence for linkage, which now leads more simply to a test of significance. Multiple markers can be the basis of a multipoint analysis. Results of simulation studies for a continuous trait are presented that investigate Type I error and power. A similar general scheme can be used to study affected sib pairs, testing whether their identity by descent sharing probabilities are greater than would be expected in the absence of linkage, and to study other types of relative pairs.

Exact transmission-disequilibrium tests with multiallelic markers

The transmission-disequilibrium (TD) test is a powerful method for detecting linkage between marker and disease loci in the presence of linkage disequilibrium. For multiallelic markers, we propose the use of exact tests, which are implemented using both an exact algorithm and Markov chain Monte Carlo simulation. Simulation studies show that exact tests improve both the small sample validity and the power of the TD method. We also compared the usual single-affected-offspring sampling scheme to one in which pairs of affected siblings are sampled. Affected-sib-pair sampling greatly increases the power of the TD method and will be most useful when a sample of affected sib pairs is available from prior linkage studies.

Confidence intervals for relative risk estimates from affected-sib-pair data

Confidence intervals for relative risk parameters estimated using affected-sib-pair data are derived and evaluated for two markers showing previous evidence of linkage to bipolar illness. For D18S41 we found some evidence, and for D18S37 stronger evidence, of relative risks greater than 1, although in both cases the estimated confidence intervals for the parameters are wide.

Model-free age-of-onset methods applied to the linkage of bipolar disorder

We performed Haseman-Elston regression on a set of bipolar pedigrees using each of three dependent variables: a binary trait indicating disease concordance or discordance, a binary trait adjusted for age-of-onset, and the residuals from a survival analysis. The latter two methods, which both adjust for age-of-onset, gave smaller p-values when previous analyses suggested linkage between disease and marker, but not when previous analyses were not suggestive of linkage.

Using family history information to distinguish true and false positive model-free linkage results

Genome scans that test for increased marker identity-by-descent sharing between pairs of affected siblings have become increasingly common. These methods do not specify a priori a genetic model for the disease locus and as such lose the ability to specify the parental source of the disease allele. We propose a method that uses family history information to build a more complete model of disease and marker inheritance, while still avoiding specification of the parameters of the disease model of inheritance. One important use for such a model is to test whether a positive linkage result obtained during the course of a genome scan is a true or false positive result. The key to the new test statistics is the interaction between gender-specific marker identity-by-descent sharing and gender-specific family history of disease. The method is useful when the disease locus of interest has a dominant mode of inheritance and a sufficient number of parents are genotyped at the marker locus. If these conditions are met, the proposed tests have good power to differentiate between true and false positive linkage results.

Decreased expression of striatal signaling genes in a mouse model of Huntington's disease

To understand gene expression changes mediated by a polyglutamine repeat expansion in the human huntingtin protein, we used oligonucleotide DNA arrays to profile approximately 6000 striatal mRNAs in the R6/2 mouse, a transgenic Huntington's disease (HD) model. We found diminished levels of mRNAs encoding components of the neurotransmitter, calcium and retinoid signaling pathways at both early and late symptomatic time points (6 and 12 weeks of age). We observed similar changes in gene expression in another HD mouse model (N171-82Q). These results demonstrate that mutant huntingtin directly or indirectly reduces the expression of a distinct set of genes involved in signaling pathways known to be critical to striatal neuron function.

Correcting for ascertainment bias of relative-risk estimates obtained using affected-sib-pair linkage data

Locus-specific sibling relative risk is often estimated using affected-sib-pair lod score analysis of affected sibships and may be used to decide whether to continue or discontinue the search for additional susceptibility genes. We showed that relative-risk estimates obtained using affected-sib-pair data are asymptotically unbiased when each pair is given a weight inversely proportional to the sibship ascertainment probability. Here we show by simulation that the extent of the bias of relative risks estimated using the incorrect ascertainment weights is small for dominant models, but large for single-locus recessive models and some two-locus heterogeneity models. Since in practice the ascertainment scheme is often unknown, we investigate methods for jointly estimating ascertainment and relative risks from affected-sibship data. Given a sufficient sample size, a reasonable estimate of relative risk may always be obtained using only affected pairs from sibships with two affected and no unaffected siblings. This estimate, which has a large variance, may then be used in a three-stage procedure (which we call the alpha method) to estimate consistently both the ascertainment probabilities and the relative risks with greater precision. We additionally propose correction factors to eliminate small-sample bias of relative risks and investigate the bias due to error in the estimate of disease locus location.

Ascertainment bias in the estimation of sibling genetic risk parameters

The sibling recurrence risk, sibling relative risk, and locus-specific sibling relative risk are fundamental quantities in genetic epidemiologic research and are often estimated without accounting for the sampling scheme. For data generated under some genetic models, bias of estimates may be large if the sampling method is incorrectly modeled. In this paper, we explore the relationship between ascertainment of sibships and estimation and interpretation of genetic risk parameters. In particular, we observe that, although traditional definitions of these population parameters are consistent with each other, implied assumptions about ascertainment and the nature of ascertainment correction differ. In the absence of ascertainment correction, unbiased estimation of sibling recurrence risk and overall sibling relative risk requires single ascertainment, while unbiased estimation of locus-specific sibling relative risk requires complete ascertainment.

Generation of neurons by transient expression of neural bHLH proteins in mammalian cells

Basic helix-loop-helix (bHLH) transcription factors are known to function during mammalian neurogenesis. Here we show that transient transfection of vectors expressing neuroD2, MASH1, ngn1 or related neural bHLH proteins, with their putative dimerization partner E12, can convert mouse P19 embryonal carcinoma cells into differentiated neurons. Transfected cells express numerous neuron-specific proteins, adopt a neuronal morphology and are electrically excitable. Thus, the expression of neural bHLH proteins is sufficient to confer a neuronal fate on uncommitted mammalian cells. Neuronal differentiation of transfected cells is preceded by elevated expression of the cyclin-dependent kinase inhibitor p27(Kip1) and cell cycle withdrawal. This demonstrates that the bHLH proteins can link neuronal differentiation to withdrawal from the cell cycle, possibly by activating the expression of p27(Kip1). The ability to generate mammalian neurons by transient expression of neural bHLH proteins should create new opportunities for studying neurogenesis and devising neural repair strategies.

Linkage of chromosome 1 markers to alcoholism-related phenotypes by sib pair linkage analysis of principal components

Using the Collaborative Study on the Genetics of Alcoholism data and affected-sib-pair linkage methods, Reich et al. [1998] reported linkage of alcohol dependence to a region near D1S1588 on chromosome 1. In this paper, we assessed the ability of multivariate sib-pair linkage analysis of the neurophysiologic measurements (including age and sex) to evaluate evidence for linkage to chromosome 1. Principal components of 16 neurophysiologic measurements, plus age and sex, were analyzed separately using sib-pair linkage analysis, and a cumulative sum of the resulting t2-statistics computed at each point on the chromosome. The first four principal components, which accounted for 74% of the total variation, showed little or no evidence for linkage in the D1S1588 region, while the remaining components showed substantial evidence for linkage. We conclude that potentially important linkage results can be missed if investigators limit attention only to major sources of variability.

A general conditional-logistic model for affected-relative-pair linkage studies

Model-free LOD-score methods are often employed to detect linkage between marker loci and common diseases, with samples of affected sib pairs. Although extensions of the basic one-disease-locus model have been proposed that allow separate inclusion of other types of affected relative pairs, discordant relative pairs, covariates, or additional disease loci, a unified framework that can handle all of these features has been lacking. In this report, I propose a conditional-logistic parameterization that generalizes easily to include all of these features. Two data examples, one using simulated data and one using type 1 diabetes, illustrate applications of the models.

Genetic mapping of complex traits

Statistical genetic mapping methods are powerful tools for finding genes that contribute to complex human traits. Mapping methods combine knowledge of the biological mechanisms of inheritance and the randomness inherent in those mechanisms to locate, with increasing precision, trait genes on the human genome. We provide an overview of the two major classes of mapping methods, genetic linkage analysis and linkage disequilibrium analysis, and related concepts of genetic inheritance.

Thyroid development in relation to the development of endothermy in the red-winged blackbird (Agelaius phoeniceus)

We investigated the development of thyroid function during the transition to endothermy in red-winged blackbirds (Agelaius phoeniceus). Thermoregulatory capabilities of blackbirds improve markedly over their relatively short nestling period (10-12 days), with the most striking improvements occurring between days 6 and 8. We hypothesized that the development of endothermy in these birds is dependent in part on the development of thyroid function. We assessed thyroid development by measuring changes in thyroid gland histology and plasma concentrations of thyroxine (T4) and triiodothyronine (T3) during the nestling period. To gain insight into the role of thyroid maturation in the context of thermoregulation, we compared plasma thyroid hormone profiles in nestlings exposed to cold temperatures to those maintained at thermoneutral temperatures. The overall size of the thyroid (as cross-sectional area) increased during nestling development, with the fastest growth occurring just before the development of endothermy. By day 8, it reached the size typical of that in adults. Follicular cell height of the thyroid glands increased in nestlings up to day 6 and then decreased for the rest of the nestling period. The mean area of individual follicles increased up to day 8 of nestling life and then decreased. Individual nestlings were capable of strong endothermic responses at 7 to 8 days of age and had significantly decreased plasma T4 concentrations following cold exposure, suggesting increased T4 to T3 deiodination to maintain the plasma concentrations of the more metabolically active T3. The patterns of plasma T4 and T3 during nestling development were consistent with those of nestlings of other altricial species of birds that have been studied. Overall, the patterns of thyroid development observed were consistent with the hypothesis that the functional development of the thyroid is critical to the development of endothermic capabilities and that thyroid hormones play a role in endothermic responses to cold temperatures.

Relationship estimation by Markov-process models in a sib-pair linkage study

The results of sib-pair linkage studies may be compromised if a substantial number of putative sib pairs are not actually sib pairs. For classification of pairs in a sib-pair genome scan, I propose multipoint methods that are based on a Markov-process model of allele sharing along the chromosome. These methods can be implemented by standard algorithms that compute multipoint marker allele-sharing probabilities for sib pairs. When marker data from at least half the genome are used, misclassification rates are small. The methods will be implemented in an upcoming version of the computer software package S.A.G.E.

Overview of QTL mapping software and introduction to map manager QT

At least ten software packages are available for marker-based detection and localization of loci contributing to quantitative traits in experimental animals and plants. Many of these have unique strengths or situations in which they are particularly useful. Six were developed by or in collaboration with plant geneticists and may not be well known to mammalian geneticists. These software packages are reviewed here and compared with a previously undescribed program, Map Manager QT, a Mac OS microcomputer program for mapping quantitative trait loci in populations derived from backcrosses, intercrosses, and recombinant inbred lines. Map Manager QT is an enhanced version of Map Manager Classic (Map Manager v2.6.5, Manly 1993), designed for mapping Mendelian loci. This review describes the methods Map Manager QT uses for mapping quantitative trait loci and describes other features that differ from those in Map Manager Classic. A complete description of both Map Manager Classic and Map Manager QT is available in the user manual, the on-line version of which can be found at http://mcbio.med.buffalo.edu/MMM/MMM.ht ml.

The central cannabinoid receptor (CB1) mediates inhibition of nitric oxide production by rat microglial cells

Upon activation, brain microglial cells release proinflammatory mediators, such as nitric oxide (NO), which may play an important role in the central nervous system antibacterial, antiviral, and antitumor activities. However, excessive release of NO has been postulated to elicit immune-mediated neurodegenerative inflammatory processes and to cause brain injury. In the present study, the effect of cannabinoids on the release of NO from endotoxin/cytokine-activated rat cortical microglial cells was evaluated. A drug dose-dependent (0.1 microM-8 microM) inhibition of NO release from rat microglial cells was exerted by the cannabinoid receptor high-affinity binding enantiomer (-)-CP55940. In contrast, a minimal inhibitory effect was exerted by the lower affinity binding paired enantiomer (+)-CP56667. Pretreatment of microglial cells with the Galphai/Galphao protein inactivator pertussis toxin, cyclic AMP reconstitution with the cell-permeable analog dibutyryl-cAMP, or treatment of cells with the Galphas activator cholera toxin, resulted in reversal of the (-)-CP55940-mediated inhibition of NO release. A similar reversal in (-)-CP55940-mediated inhibition of NO release was effected when microglial cells were pretreated with the central cannabinoid receptor (CB1) selective antagonist SR141716A. Mutagenic reverse transcription-polymerase chain reaction, Western immunoblot assay using a CB1 receptor amine terminal domain-specific antibody, and cellular colocalization of CB1 and the microglial marker Griffonia simplicifolia isolectin B4 confirmed the expression of the CB1 receptor in rat microglial cells. Collectively, these results indicate a functional linkage between the CB1 receptor and cannabinoid-mediated inhibition of NO production by rat microglial cells.

Genetic linkage analysis of multicase families with fibromyalgia syndrome

OBJECTIVE

Based on the reports of familial aggregation of fibromyalgia (FM) syndrome, we investigated its possible genetic linkage to HLA by studying multicase families.

METHODS

Forty Caucasian multicase families with a diagnosis of FM (American College of Rheumatology criteria) in 2 or more first degree relatives were investigated. Eighty-five affected and 21 unaffected members of 41 sibships were studied. Depression symptomology was assessed by Zung Self-rating Depression Scale (SDS). HLA typing was performed for A, B, and DRB 1 alleles, and haplotypes were determined with no knowledge of the subject's diagnosis. We investigated genetic linkage to the HLA region by evaluating sibships in multicase families.

RESULTS

Sibship analysis showed significant genetic linkage of FM to the HLA region (p = 0.028). Subgroup analysis was also performed for 17 families where the proband was also noted to have depression (with an SDS index value > or =60). We found that the presence of depression did not influence the observed results (p = 0.22).

CONCLUSION

. Our study of 40 multicase families confirms existence of a possible gene for FM that is linked with the HLA region. Our results should be regarded as preliminary and their independent confirmation by other studies is warranted.

Activation patterns and length changes in hindlimb muscles of the bullfrog Rana catesbeiana during jumping

We measured the electromyographic (EMG) activity of seven hindlimb muscles during jumping in the bullfrog Rana catesbeiana. The semimembranosus, gracilis major, gluteus magnus, adductor magnus, cruralis and plantaris longus were consistently active approximately 20-40 ms before any perceptible movement, as indicated by simultaneous video recordings. Activity ended before full extension of the hindlimb and take-off. Activity in the semitendinosus was variable among the jumps recorded. Simultaneous measurements of EMG activity and length changes (via sonomicrometry) in the semimembranosus (SM) and gluteus magnus (GM) muscles indicated that the performance characteristics of these two muscles differed. The SM muscle (a hip extensor) shortens and is activated in a manner consistent with its producing power during a significant fraction of the take-off phase. It shortened by a mean of 26.2% of the resting length during the propulsive phase of the two longest jumps for each frog. The delay between the onset of EMG activity and the beginning of shortening averaged 24 ms, which was brief compared with that found for the GM. The total strain and mean shortening velocity of the SM increased with jumping distance. Contrary to our initial expectations, the GM muscle does not shorten as one would expect of a muscle involved in powering the jump throughout take-off. This muscle has an extensor action at the knee, but also has a flexor action at the hip. A long delay existed between the onset of EMG activity and the beginning of shortening (46-116 ms among the individuals tested). Shortening during take-off by the GM (a mean of 16.7% for all jumps) was much less than by the SM, and in many jumps most of this shortening occurred late in the take-off period. Although the GM cannot contribute directly to power output early in take-off, it may contribute to powering the jump indirectly by transferring energy from the hip extensors to the knee joint. We conclude that muscles previously assumed (on the basis of anatomical criteria) by ourselves and others to be powering the jump may show considerable diversity of function. We hypothesize that elastic energy storage is used to help power jumping, and therefore suggest that muscles in series with major tendinous elements should be targeted for further study.