Genetic variation in the Yolk protein expression network of Drosophila melanogaster: sex-biased negative correlations with longevity.

One of the persistent problems in biology is understanding how genetic variation contributes to phenotypic variation. Associations at many levels have been reported, and yet causal inference has remained elusive. We propose to rely on the knowledge of causal relationships established by molecular biology approaches. The existing molecular knowledge forms a firm backbone upon which hypotheses connecting genetic variation, transcriptional variation and phenotypic variation can be built. The sex determination pathway is a well-established molecular network, with the Yolk protein 1-3 (Yp) genes as the most downstream target. Our analyses reveal that genetic variation in expression for genes known to be upstream in the pathway explains variation in downstream targets. Relationships differ between the two sexes, and each Yp has a distinct transcriptional pattern. Yp expression is significantly negatively correlated with longevity, an important life history trait, for both males and females.

Allelic imbalance in Drosophila hybrid heads: exons, isoforms, and evolution.

Unraveling how regulatory divergence contributes to species differences and adaptation requires identifying functional variants from among millions of genetic differences. Analysis of allelic imbalance (AI) reveals functional genetic differences in cis regulation and has demonstrated differences in cis regulation within and between species. Regulatory mechanisms are often highly conserved, yet differences between species in gene expression are extensive. What evolutionary forces explain widespread divergence in cis regulation? AI was assessed in Drosophila melanogaster-Drosophila simulans hybrid female heads using RNA-seq technology. Mapping bias was virtually eliminated by using genotype-specific references. Allele representation in DNA sequencing was used as a prior in a novel Bayesian model for the estimation of AI in RNA. Cis regulatory divergence was common in the organs and tissues of the head with 41% of genes analyzed showing significant AI. Using existing population genomic data, the relationship between AI and patterns of sequence evolution was examined. Evidence of positive selection was found in 30% of cis regulatory divergent genes. Genes involved in defense, RNAi/RISC complex genes, and those that are sex regulated are enriched among adaptively evolving cis regulatory divergent genes. For genes in these groups, adaptive evolution may play a role in regulatory divergence between species. However, there is no evidence that adaptive evolution drives most of the cis regulatory divergence that is observed. The majority of genes showed patterns consistent with stabilizing selection and neutral evolutionary processes.

Direct mapping of density response in a population of B73 x Mo17 recombinant inbred lines of maize (Zea Mays L.).

Maize yield per unit area has dramatically increased over time as have plant population densities, but the genetic basis for plant response to density is unknown as is its stability over environments. To elucidate the genetic basis of plant response to density in maize, we mapped QTL for plant density-related traits in a population of 186 recombinant inbred lines (RILs) derived from the cross of inbred lines B73 and Mo17. All RILs were evaluated for growth, development, and yield traits at moderate (50 000 plants per hectare) and high (100 000 plants per hectare) plant densities. The results show that genetic control of the traits evaluated is multigenic in their response to density. Five of the seven loci significant for final height showed statistical evidence for epistatic interactions. Other traits such as days to anthesis, anthesis-to-silking interval, barrenness, ears per plant, and yield per plant all showed statistical evidence for an epistatic interaction. Locus by density interactions are of critical importance for anthesis-to-silking interval, barrenness, and ears per plant. A second independent experiment to examine the stability of QTL for barrenness in a new environment clearly showed that the multilocus QTL were stable across environments in their differential response to density. In this verification experiment, the four-locus QTL was used to choose lines with the four unfavorable alleles and compare them with the lines with four favorable alleles and the effect was confirmed.

Mapping reciprocal effects and interactions with plant density stress in Zea mays L.

Reciprocal effects are due to genetic effects of the parents (i.e. maternal and paternal effects), cytoplasmic effects and parent-of-origin effects. However, in Zea mays L. the extent to which reciprocal effects exist, or can be attributed to specific underlying components, remains an area of interest and study. Reciprocal effects have been reported by several investigators for various agronomic characters in different types of maize materials for grain and silage usage. Maize geneticists and breeders have recognized reciprocal effects as one source of genetic variability, but the lack of consistency in the observation of these effects, particularly due to stress conditions, has prevented a systematic exploitation of these effects in practical breeding programs. There is mounting molecular evidence for underlying mechanisms in maize, which could be responsible for both the existence, and the instability of reciprocal effects. In this study, we developed population of reciprocal backcrosses based on an initial set of recombinant inbred lines. This population was used for dissecting reciprocal effects into the underlying components (maternal, cytoplasmic and parent-of-origin) effects. We also developed statistical framework to identify and map contributions of specific nuclear chromosomal regions to reciprocal effects. We showed that differences in maternal parents, endosperm DNA and maternally transmitted factors collectively influence reciprocal effects early during the season, and that their influence diluted at later stages. We also found evidence that parent-of-origin effects in the sporophyte DNA existed at all stages and played an important role in establishing differences between reciprocal backcrosses at later developmental stages.

Using mating designs to uncover QTL and the genetic architecture of complex traits.

Analysis of quantitative trait loci (QTL) affecting complex traits is often pursued in single-cross experiments. For most purposes, including breeding, some assessment is desired of the generalizability of the QTL findings and of the overall genetic architecture of the trait. Single-cross experiments provide a poor basis for these purposes, as comparison across experiments is hampered by segregation of different allelic combinations among different parents and by context-dependent effects of QTL. To overcome this problem, we combined the benefits of QTL analysis (to identify genomic regions affecting trait variation) and classic diallel analysis (to obtain insight into the general inheritance of the trait) by analyzing multiple mapping families that are connected via shared parents. We first provide a theoretical derivation of main (general combining ability (GCA)) and interaction (specific combining ability (SCA)) effects on F(2) family means relative to variance components in a randomly mating reference population. Then, using computer simulations to generate F(2) families derived from 10 inbred parents in different partial-diallel designs, we show that QTL can be detected and that the residual among-family variance can be analyzed. Standard diallel analysis methods are applied in order to reveal the presence and mode of action (in terms of GCA and SCA) of undetected polygenes. Given a fixed experiment size (total number of individuals), we demonstrate that QTL detection and estimation of the genetic architecture of polygenic effects are competing goals, which should be explicitly accounted for in the experimental design. Our approach provides a general strategy for exploring the genetic architecture, as well as the QTL underlying variation in quantitative traits.

Genetic architecture of two fitness-related traits in Drosophila melanogaster: ovariole number and thorax length.

In Drosophila melanogaster, ovariole number and thorax length are morphological characters thought to be associated with fitness. Maximum daily egg production in females is positively correlated with ovariole number, while thorax length is correlated with male reproductive success and female fecundity. Though both traits are related to fitness, ovariole number is likely to be under stabilizing selection, while thorax length appears to be under directional selection. Current research has focused on examining the sources of variation for ovariole number in relation to fitness, with a view towards elucidating how segregating variation is maintained in natural populations. Here, we utilize a diallel design to explore the genetic architecture of ovariole number and thorax length in nine isogenic lines derived from a natural population. The full diallel design allows the estimation of general combining ability (GCA), specific combining ability (SCA), and also describes variation due to reciprocal effects (RGCA and RSCA). Ovariole number and thorax length differed with respect to their genetic architecture, reflective of the independent selective forces acting on the traits. For ovariole number, GCA accounted for the majority (67.3%) of variation segregating between the lines, with no evidence of reciprocal effects or inbreeding depression; SCA accounted for a small percentage (3.9%) of the variance, suggesting dominance variation; no reciprocal effects were observed. In contrast, for thorax length, the majority of the non-error variance was accounted for by SCA (17.9%), with only one third as much variance (6.2%) due to GCA. Interestingly, RSCA (nuclear-extranuclear interactions) accounted for slightly more variation (7.5%) than GCA in these data. Thus, genetic variation for thorax length is largely in accord with predictions for a fitness trait under directional selection: little additive genetic variation and substantial dominance variation (including a suggestion of inbreeding depression); while the mechanisms underlying the maintenance of variation for ovariole number are more complex.

Additivity and trans-acting effects on gene expression in male Drosophila simulans.

Understanding how genetic variation is maintained begins with a comprehensive description of what types of genetic variation exist, the extent and magnitude of the variation, and patterns discernable in that variation. However, such studies have focused primarily on DNA sequence data and have ignored genetic variation at other hierarchical levels of genetic information. Microarray technology permits an examination of genetic variation at the level of mRNA abundance. Utilizing a round-robin design, we present a quantitative description of variation in mRNA abundance in terms of GCA (general combining ability or additive variance). We test whether genes significant for GCA are randomly distributed across chromosomes and use a nonparametric approach to demonstrate that the magnitude of the variation is not random for GCA. We find that there is a paucity of genes significant for GCA on the X relative to the autosomes. The overall magnitude of the effects for GCA on the X tends to be lower than that on the autosomes and is contributed by rare alleles of larger effect. Due to male hemizygosity, GCA for X-linked phenotypes must be due to trans-acting factors, while GCA for autosomal phenotypes may be due to cis- or trans-acting factors. The contrast in the amount of variation between the X and the autosomes suggests that both cis and trans factors contribute to variation for expression in D. simulans with the preponderance of effects being trans. This nonrandom patterning of genetic variation in gene expression data with respect to chromosomal context may be due to hemizygosity in the male.

Genome-wide transcription profile of field- and laboratory-selected dichlorodiphenyltrichloroethane (DDT)-resistant Drosophila.

Genome-wide microarray analysis (Affymetrix array) was used (i) to determine whether only one gene, the cytochrome P450 enzyme Cyp6g1, is differentially transcribed in dichlorodiphenyltrichloroethane (DDT)-resistant vs. -susceptible Drosophila; and (ii) to profile common genes differentially transcribed across a DDT-resistant field isolate [Rst(2)DDT(Wisconsin)] and a laboratory DDT-selected population [Rst(2)DDT(91-R)]. Statistical analysis (ANOVA model) identified 158 probe sets that were differentially transcribed among Rst(2)DDT(91-R), Rst(2)DDT(Wisconsin), and the DDT-susceptible genotype Canton-S (P < 0.01). The cytochrome P450 Cyp6a2 and the diazepam-binding inhibitor gene (Dbi) were over transcribed in the two DDT-resistant genotypes when compared to the wild-type Drosophila, and this difference was significant at the most stringent statistical level, a Bonferroni correction. The list of potential candidates differentially transcribed also includes 63 probe sets for which molecular function ontology annotation of the probe sets did not exist. A total of four genes (Cyp6a2, Dbi, Uhg1, and CG11176) were significantly different (P < 5.6 e(-06)) between Rst(2)DDT(91-R) and Canton-S. Additionally, two probe sets encoding Cyp12d1 and Dbi were significantly different between Rst(2)DDT(Wisconsin) and Canton-S after a Bonferroni correction. Fifty-two probe sets, including those associated with pesticide detoxification, ion transport, signal transduction, RNA transcription, and lipid metabolism, were commonly expressed in both resistant lines but were differentially transcribed in Canton-S. Our results suggest that more than Cyp6g1 is overtranscribed in field and laboratory DDT-resistant genotypes, and the number of commonalities suggests that similar resistance mechanisms may exist between laboratory- and field-selected DDT-resistant fly lines.

Expression profile analysis of wild-type and fcc1 mutant strains of Fusarium verticillioides during fumonisin biosynthesis.

Fusarium verticillioides produces a group of mycotoxins known as fumonisins that are associated with a variety of mycotoxicoses in humans and animals. In this study, DNA microarrays were constructed with expressed sequence tags (ESTs) from F. verticillioides. To identify genes with patterns of expression similar to the fumonisin biosynthetic (FUM) genes, the microarray was probed with labeled cDNAs originating from a wild-type strain and a fcc1 mutant grown on maize and in a defined medium adjusted to either pH 3 or pH 8. The comparative analyses revealed differential expression of genes corresponding to 116 ESTs when the fungal strains were grown on maize. Under different pH conditions, 166 ESTs were differentially expressed, and 19 ESTs were identified that displayed expression patterns similar to the FUM ESTs. These results provide candidate genes with potential roles in fumonisin biosynthesis.

Combining mapping and arraying: An approach to candidate gene identification.

A combination of quantitative trait locus (QTL) mapping and microarray analysis was developed and used to identify 34 candidate genes for ovariole number, a quantitative trait, in Drosophila melanogaster. Ovariole number is related to evolutionary fitness, which has been extensively studied, but for which few a priori candidate genes exist. A set of recombinant inbred lines were assayed for ovariole number, and QTL analyses for this trait identified 5,286 positional candidate loci. Forty deletions spanning the QTL were employed to further refine the map position of genes contributing to variation in this trait between parental lines, with six deficiencies showing significant effects and reducing the number of positional candidates to 548. Parental lines were then assayed for expression differences by using Affymetrix microarray technology, and ANOVA was used to identify differentially expressed genes in these deletions. Thirty-four genes were identified that showed evidence for differential expression between the parental lines, one of which was significant even after a conservative Bonferroni correction. The list of potential candidates includes 5 genes for which previous annotations did not exist, and therefore would have been unlikely choices for follow-up from mapping studies alone. The use of microarray technology in this context allows an efficient, objective, quantitative evaluation of genes in the QTL and has the potential to reduce the overall effort needed in identifying genes causally associated with quantitative traits of interest.

The maize Brown midrib1 locus affects cell wall composition and plant development in a dose-dependent manner.

The four brown midrib (bm) mutants of maize have a reduced content and altered subunit composition of the cell wall polymer lignin. The bm mutations have traditionally been considered completely recessive, because the brown midrib phenotype is only apparent in plants homozygous for the mutation. In addition to an effect on cell wall composition, some bm mutations have been shown to affect flowering time. We had preliminary evidence for a dosage effect of the Bm1 locus on flowering time, which prompted this detailed study on the Bm1 locus. In this study, near-isogenic lines (in an A619 background) with zero, one or two bm1 mutant alleles were compared. The bm1 heterozygotes flowered significantly earlier than both the wild-type plants and bm1 mutants. This difference can at least be partly attributed to an accelerated growth rate in the later stages of plant development. Furthermore, Fourier transform infrared spectroscopy revealed that the cell wall composition of the bm1 heterozygous plants is distinct from both the bm1 and wild-type homozygotes. The combination of the data on flowering time and the data on cell wall composition provide evidence for a dosage effect at the Bm1 locus.

Detection and localization of a single binary trait locus in experimental populations.

The advancements made in molecular technology coupled with statistical methodology have led to the successful detection and location of genomic regions (quantitative trait loci; QTL) associated with quantitative traits. Binary traits (e.g. susceptibility/resistance), while not quantitative in nature, are equally important for the purpose of detecting and locating significant associations with genomic regions. Existing interval regression methods used in binary trait analysis are adapted from quantitative trait analysis and the tests for regression coefficients are tests of effect, not detection. Additionally, estimates of recombination that fail to take into account varying penetrance perform poorly when penetrance is incomplete. In this work a complete probability model for binary trait data is developed allowing for unbiased estimation of both penetrance and recombination between a genetic marker locus and a binary trait locus for backcross and F2 experimental designs. The regression model is reparameterized allowing for tests of detection. Extensive simulations were conducted to assess the performance of estimation and testing in the proposed parameterization. The proposed parameterization was compared with interval regression via simulation. The results indicate that our parameterization shows equivalent estimation capabilities, requires less computational effort and works well with only a single marker.

Rater agreement and utility of the mutagen-induced chromosome damage assay.

Chromosomal damage in peripheral blood lymphocytes induced by short-term in vitro exposure to the cytotoxic antibiotic bleomycin was first described in 1983 and proposed as a phenotypic assay for chromosome instability. This assay was subsequently described as potentially useful in assessing an individual's risk to environmental carcinogens in 1989. Since 1995 numerous published studies have used this assay to assess risk for cancer in the aerodigestive tract, particularly lung cancer, in various ethnic populations. Odds ratios up to 8.5 have been reported for individuals deemed "mutagen sensitive" (defined as > or = 1 chromatid break per metaphase averaged in 50 metaphases analyzed). While this phenotypic assay is appealing for lung cancer risk assessment it has not been reproduced by other investigators. Because of our interest in lung cancer biology, epidemiology, and genetics, we sought to independently assess the rater agreement of this assay. We found that 1) the assay is laborious to conduct (8 hours of labor) and relatively expensive (> $100), yet reducing the number of metaphases from 50 to 20 produced a reliable, less expensive, and less laborious test; and 2) the rater agreement of individual metaphase readings is poor, but agreement for a summary measure is high.

Measuring patient expectations: does the instrument affect satisfaction or expectations?

BACKGROUND: Fulfillment of patients' expectations may influence health care utilization, affect patient satisfaction, and be used to indicate quality of care. Several different instruments have been used to measure expectations, yet little is known about how different assessment methods affect outcomes. OBJECTIVE: The object of the study was to determine whether different measurement instruments elicit different numbers and types of expectations and different levels of patient satisfaction. DESIGN: Patients waiting to see their physician were randomly assigned to receive 1 of 2 commonly used instruments assessing expectations or were assigned to a third (control) group that was not asked about expectations. After the visit, patients in all 3 groups were asked about their satisfaction and services they received. SUBJECTS: The study subjects were 290 male, primary care outpatients in a VA general medicine clinic. MEASURES: A "short" instrument asked about 3 general expectations for tests, referrals, and new medications, while a "long" instrument nested similar questions within a more detailed list. Wording also differed between the 2 instruments. The short instrument asked patients what they wanted; the long instrument asked patients what they thought was necessary for the physician to do. Satisfaction was measured with a visit-specific questionnaire and a more general assessment of physician interpersonal skills. RESULTS: Patients receiving the long instrument were more likely to express expectations for tests (83% vs. 28%, P <0.001), referrals (40% vs. 18%, P <0.001), and new medications (45% vs. 28%, P <0.001). The groups differed in the number of unmet expectations: 40% of the long instrument group reported at least 1 unmet expectation compared with 19% of the short instrument group (P <0.001). Satisfaction was similar among the 3 groups. CONCLUSIONS: These different instruments elicit different numbers of expectations but do not affect patient satisfaction.

Dementia with Lewy bodies and Alzheimer's disease.

To investigate similarities and differences between Alzheimer's disease (AD) and dementia with Lewy bodies (DLB), we undertook a demographic analysis of 277 patients from the Kathleen Price Bryan Brain Bank with an antemortem diagnosis of probable AD. Patients with additional, possibly confounding clinical and pathologic diagnoses such as infarcts, hematomas, neoplasms, and other neurodegenerative disorders, were excluded from the analysis. Neuropathologically, AD alone was present in 192 subjects (69%), and DLB was found in 85 subjects (31%). All of the DLB cases had neuropathologic evidence of AD sufficient to meet CERAD criteria for a diagnosis of definite AD plus nigral Lewy bodies. Gender, apolipoprotein E (APOE) genotype, brain weight, age at death, duration of disease and Braak stage were compared between the two groups. Statistical analyses were performed using Fisher's exact test for comparisons of categorical data and Student's t-test for comparison of means for continuous outcomes. The proportion of males and females was balanced in the combined AD and DLB populations. There was a highly statistically significant increased frequency of APOE 3/4 in males with DLB (P = 0.007). We found higher brain weights in males with DLB versus males with AD (P = 0.012). AD was more frequent in females and DLB was more frequent in males (P = 0.019). Our findings with respect to age at death, duration of disease and Braak stage within diagnostic groups confirm previously reported findings. These data suggest that Lewy bodies are more common in males affected with dementia, especially those with the APOE 3/4 genotype.

Incidence of stroke and season of the year: evidence of an association.

Evidence of seasonal variation in the incidence of stroke is inconsistent. This may be a likely consequence of one or more methodological shortcomings of the studies investigating this issue, including inappropriate analytic models, insufficient length of time, small sample size, and a regional (vs. national) focus. The authors' objective was to ascertain whether an association exists between season of the year and the incidence of stroke by using a methodological approach designed to overcome these limitations. The authors used a longitudinal study design involving 72,779 veterans hospitalized for stroke at any Veterans Affairs hospital nationally during the years 1986-1995. These data were analyzed by using time series methods. There was clear evidence of a seasonal occurrence for stroke in general. This seasonal effect was found for ischemic stroke, but not for hemorrhagic stroke. The peak occurrence was in mid-May. Neither the region (i.e., climate) nor the race of the patient substantially modified the seasonal trend. An explanation for this pattern remains to be determined.

In vitro resistance to thrombin-induced platelet microbicidal protein in isolates of Staphylococcus aureus from endocarditis patients correlates with an intravascular device source.

Platelet microbicidal proteins (PMPs) are small antimicrobial peptides secreted by mammalian platelets. In vitro resistance of Staphylococcus aureus strains to PMPs correlates with more extensive disease in experimental infective endocarditis (IE). To determine whether this same relationship exists in human S. aureus IE, we evaluated the in vitro PMP susceptibility phenotype of isolates from 58 prospectively-identified patients with definite S. aureus IE. On multivariate analyses, patients with S. aureus IE complicating an infected intravascular device were significantly more likely to have IE caused by a PMP-resistant strain (P=.0193). No correlations were detected between in vitro PMP resistance among S. aureus strains and the severity of human IE. This work supports the concept that in vitro PMP resistance in clinical S. aureus strains is associated with important clinical characteristics of S. aureus endovascular infections in vivo.

Racial variation in wanting and obtaining mental health services among women veterans in a primary care clinic.

Epidemiologic studies suggest that African-American women may be less likely to obtain mental health services. Racial differences were explored in wanting and obtaining mental health services among women in an equal access primary care clinic setting after adjusting for demographics, mental disorder symptoms, and a history of sexual trauma. Participating in the study were women veterans at a primary care clinic at the Durham Veterans Affairs Medical Center. Consecutive women patients (n = 526) between the ages of 20 and 49 years were screened for a desire to obtain mental health services. Patients were given the Primary Care Evaluation of Mental Disorders questionnaire (PRIME-MD) and a sexual trauma questionnaire. Mental health service utilization was monitored for 12 months. The median age of the women was 35.8 years; 54.4% of them were African-American. African-American women expressed a greater desire for mental health services than whites, yet mental health resources at the clinic were similarly used by both racial groups. African-American women may want more mental health services; however, given an equal access system, there were no racial differences in mental health use.

Circumventing multiple testing: a multilocus Monte Carlo approach to testing for association.

Advances in marker technology have made a dense marker map a reality. If each marker is considered separately, and separate tests for association with a disease gene are performed, then multiple testing becomes an issue. A common solution uses a Bonferroni correction to account for multiple tests performed. However, with dense marker maps, neighboring markers are tightly linked and may have associated alleles; thus tests at nearby marker loci may not be independent. When alleles at different marker loci are associated, the Bonferroni correction may lead to a conservative test, and hence a power loss. As an alternative, for tests of association that use family data, we propose a Monte Carlo procedure that provides a global assessment of significance. We examine the case of tightly linked markers with varying amounts of association between them. Using computer simulations, we study a family-based test for association (the transmission/disequilibrium test), and compare its power when either the Bonferroni or Monte Carlo procedure is used to determine significance. Our results show that when the alleles at different marker loci are not associated, using either procedure results in tests with similar power. However, when alleles at linked markers are associated, the test using the Monte Carlo procedure is more powerful than the test using the Bonferroni procedure. This proposed Monte Carlo procedure can be applied whenever it is suspected that markers examined have high amounts of association, or as a general approach to ensure appropriate significance levels and optimal power.

In search of a good death: observations of patients, families, and providers.

Despite a recent increase in the attention given to improving end-of-life care, our understanding of what constitutes a good death is surprisingly lacking. The purpose of this study was to gather descriptions of the components of a good death from patients, families, and providers through focus group discussions and in-depth interviews. Seventy-five participants-including physicians, nurses, social workers, chaplains, hospice volunteers, patients, and recently bereaved family members-were recruited from a university medical center, a Veterans Affairs medical center, and a community hospice. Participants identified six major components of a good death: pain and symptom management, clear decision making, preparation for death, completion, contributing to others, and affirmation of the whole person. The six themes are process-oriented attributes of a good death, and each has biomedical, psychological, social, and spiritual components. Physicians' discussions of a good death differed greatly from those of other groups. Physicians offered the most biomedical perspective, and patients, families, and other health care professionals defined a broad range of attributes integral to the quality of dying. Although there is no "right" way to die, these six themes may be used as a framework for understanding what participants tend to value at the end of life. Biomedical care is critical, but it is only a point of departure toward total end-of-life care. For patients and families, psychosocial and spiritual issues are as important as physiologic concerns.