Biomedical subjects

David B Allison

Publications and source records attributed to David B Allison.

107 records · Page 6Linked to original sources

PubMed2002

Beneficial influences of systemic cooperation and sociological behavior on longevity.

During his long research career in the field of aging, Dr Bernard Strehler developed a series of theories concerning the identity of genes that can promote longevity and their role in natural selection. As a tribute to Dr Strehler, we have taken this opportunity to summarize a selection of these theories and to illustrate how these insights have influenced our search for longevity genes within the immune system. The identification of longevity genes has proven difficult. We believe that, at least in part, this reflects the emphasis on the concept of survival of the 'physically' fittest. We have used the immune system as a model to demonstrate that, over and above the self-evident advantage of those genes that contribute the attributes commonly associated with survival of the 'physically' fittest, those genes that lead to a predisposition to cooperate also confer a competitive survival advantage. As the acquisition of cooperativity in a society is linked to support mechanisms provided by older individuals, the search for longevity genes should not be limited to those genes that are associated with extended expression of a youthful phenotype. Rather these studies should be expanded to include identification of those genes that regulate physiologic parameters that affect individual longevity, even if they do not correspond with the traditional view of reproductive competitiveness. At the societal level, longevity genes may encode attributes that regulate sociologic or psychological parameters that may contribute to a tendency to non-aggressive or cooperative behavior that leads to achievement of common goals necessary for the survival of the species. This view of the selection for longevity impacts the analysis of longevity genes and aging at the organismal level. Dr Strehler viewed organismal aging as an integrated functional state, in which he conceived the outcome as reflecting the net balance of functional decrementers and evolved compensatory features. We propose that, in more evolved species, the longevity genes will be those genes, or sets of genes, that counterbalance of age-related functional decrementers with the age-related manifestation of evolved compensatory features. Thus, as illustrated here through analysis of the immune system, the longevity genes may well be those genes that promote overall systemic cooperation and compensation within the immune system and associated systems, rather than the genes that prevent age-related alterations in only one or a limited number of pathways.

Aging↗

PubMed2002

Bias in estimates of quantitative-trait-locus effect in genome scans: demonstration of the phenomenon and a method-of-moments procedure for reducing bias.

An attractive feature of variance-components methods (including the Haseman-Elston tests) for the detection of quantitative-trait loci (QTL) is that these methods provide estimates of the QTL effect. However, estimates that are obtained by commonly used methods can be biased for several reasons. Perhaps the largest source of bias is the selection process. Generally, QTL effects are reported only at locations where statistically significant results are obtained. This conditional reporting can lead to a marked upward bias. In this article, we demonstrate this bias and show that its magnitude can be large. We then present a simple method-of-moments (MOM)-based procedure to obtain more-accurate estimates, and we demonstrate its validity via Monte Carlo simulation. Finally, limitations of the MOM approach are noted, and we discuss some alternative procedures that may also reduce bias.

Bias↗

PubMed2002

Power and sample sizes for linkage with extreme sampling under an oligogenic model for quantitative traits.

Extreme sampling of sibling pairs has been shown to be efficient in terms of statistical power and sample sizes (in number of sibling pairs needed to genotype) to detect a quantitative trait locus (QTL) when the residual distribution is normal. In the present study, the efficiency of extreme sampling strategies to detect each locus under an oligogenic model is analytically explored with a test statistic based on identical-by-descent (IBD) statuses of independent sibling pairs. In the oligogenic model, the joint effect of oligogenes is the sum of the effects of each locus. Under this model, detecting each single locus will depend, in part, on the allele frequencies and magnitudes of effect of the other loci. Effects of two QTLs with different magnitudes of displacement and acting nonepistatically are considered. Three types of extreme sampling-that is, extreme concordant high (ECH), extreme concordant low (ECL), and extreme discordant (ED)-are primarily considered herein. Among these, ED sampling under the oligogenic model is shown to be most efficient in most situations considered here in terms of allele frequency and mode of inheritance. Differences in results between ECH and ECL sampling are purely arbitrary, brought up mostly by the directions of displacement effects. However, power to detect a locus with the lesser (in magnitude) displacement effect does not necessarily increase with extremity of sampling. Combinations of extreme discordant and extreme concordant sibling pairs are briefly discussed.

Alleles↗

PubMed2002

Bupropion SR vs. placebo for weight loss in obese patients with depressive symptoms.

OBJECTIVE: This randomized, double-blind, placebo-controlled study evaluated the efficacy and tolerability of bupropion sustained-release (bupropion SR) in reducing weight and depressive symptoms in obese adults. RESEARCH METHODS AND PROCEDURES: Obese adults (body mass index, 30 to 44 kg/m(2)) not currently meeting criteria for major depression but with depressive symptoms (Beck Depression Inventory score 10-30) received bupropion SR 300 mg/d or placebo for 26 weeks with a 500 kcal/d-deficit diet. Patients who lost <5% of baseline weight at week 12 had bupropion SR dosage or placebo increased to 400 mg/d in a blinded fashion. RESULTS: The bupropion SR group (n = 193) lost an average of 4.4 kg (4.6% of baseline weight) vs. 1.7 kg (1.8% of baseline weight) on placebo (n = 191, p < 0.001, last-observation-carried-forward analysis). More patients in the bupropion SR group than in the placebo group (40% vs. 16% of intent-to-treat sample, 50% vs. 28% of completers, respectively) lost at least 5% of baseline weight (p < 0.05 at week 4, p < 0.001 at weeks 6 to 26). The percentage of patients reporting > or =50% decrease in depressive symptoms did not differ between groups, but depressive symptoms improved more with bupropion SR than with placebo among patients with a history of major depression (p < 0.05, weeks 4 to 26). In the sample as a whole, improvement in depressive symptoms was related to weight loss of > or =5% regardless of treatment (p < 0.0001). Bupropion SR was well-tolerated. DISCUSSION: Bupropion SR in combination with a 500 kcal/d-deficit diet facilitated weight loss. Weight loss of > or =5% may improve mood in obese patients with depressive symptoms.

Adolescent↗

PubMed2002

Body mass index and waist circumference independently contribute to the prediction of nonabdominal, abdominal subcutaneous, and visceral fat.

BACKGROUND: It is unknown whether the ability of waist circumference (WC) to predict health risk beyond that predicted by body mass index (BMI) alone is explained in part by the ability of WC to identify those with elevated concentrations of total or abdominal fat. OBJECTIVE: We sought to determine whether BMI and WC independently contribute to the prediction of non-abdominal (total fat - abdominal fat), abdominal subcutaneous, and visceral fat. DESIGN: Fat distribution was measured by magnetic resonance imaging in 341 white men and women. Multiple regression analysis was performed to measure whether the combination of BMI and WC explained a greater variance in non-abdominal, abdominal subcutaneous, and visceral fat than did BMI or WC alone. These fat depots were also compared after a subdivision of the cohort into 3 BMI (normal, overweight, and class I obese) and 3 WC (low, intermediate, and high) categories according to the classification system used to identify associations between BMI, WC, and health risk. RESULTS: Independent of age and sex, the combination of BMI and WC explained a greater variance in non-abdominal, abdominal subcutaneous, and visceral fat than did either BMI or WC alone (P < 0.05). For non-abdominal and abdominal subcutaneous fat, BMI was the strongest correlate; thus, by adding BMI to WC, the variance accrued was greater than when WC was added to BMI. However, when WC was added to BMI, the added variance explained for visceral fat was greater than when BMI was added to WC. Furthermore, within each of the 3 BMI categories studied, an increase in the WC category was associated with an increase in visceral fat (P < 0.05). CONCLUSIONS: BMI and WC independently contribute to the prediction of non-abdominal, abdominal subcutaneous, and visceral fat in white men and women. These observations reinforce the importance of using both BMI and WC in clinical practice.

Abdomen↗

PubMed2002

Two-stage testing in microarray analysis: what is gained?

Microarray technology for gene expression studies offers powerful new technology for understanding changes in gene expression as a function of other observable or manipulable variables. However, microarrays also pose a number of new challenges. One of the most prominent of these is the difficulty in establishing a procedure for declaring whether a gene's expression level is associated with the independent variable that offers reasonable and specifiable false-positive (type 1 error) and false-negative (type 2 error) rates. A recent article described a two-stage testing procedure to address these goals. However, information was not provided to indicate whether this procedure would or would not meet its objectives. Herein, we show mathematically that the two-stage procedure proposed does not provide benefits in terms of minimizing false-negatives while controlling the false-positive rate relative to standard single-stage testing. Therefore, investigators are encouraged to consider alternative analytic approaches.

Animals↗

PubMed2002

Human adenovirus Ad-36 promotes weight gain in male rhesus and marmoset monkeys.

Although obesity has multiple etiologies, an overlooked possibility is an infectious origin. We previously identified two viruses, SMAM-1, an avian adenovirus (Ad), and Ad-36, a human adenovirus, that produce a syndrome of visceral obesity, with paradoxically decreased serum cholesterol and triglycerides in chickens and mice. In the two studies presented in this paper, we used nonhuman primates to investigate the adiposity-promoting potential of Ad-36. In study 1, we observed spontaneously occurring Ad-36 antibodies in 15 male rhesus monkeys, and a significant longitudinal association of positive antibody status with weight gain and plasma cholesterol lowering during the 18 mo after viral antibody appearance. In study 2, which was a randomized controlled experiment, three male marmosets inoculated with Ad-36 had a threefold body weight gain, a greater fat gain and lower serum cholesterol relative to baseline (P <0.05) than three uninfected controls at 28 wk postinoculation. These studies illustrate that the adiposity-promoting effect of Ad-36 occurs in two nonhuman primate species and demonstrates the usefulness of nonhuman primates for further evaluation of Ad-36-induced adiposity.

Adenoviridae Infections↗

PubMed2002

Immunization of rhesus macaques with a DNA prime/modified vaccinia virus Ankara boost regimen induces broad simian immunodeficiency virus (SIV)-specific T-cell responses and reduces initial viral replication but does not prevent disease progression following challenge with pathogenic SIVmac239.

Producing a prophylactic vaccine for human immunodeficiency virus (HIV) has proven to be a challenge. Most biological isolates of HIV are difficult to neutralize, so that conventional subunit-based antibody-inducing vaccines are unlikely to be very effective. In the rhesus macaque model, some protection was afforded by DNA/recombinant viral vector vaccines. However, these studies used as the challenge virus SHIV-89.6P, which is neutralizable, making it difficult to determine whether the observed protection was due to cellular immunity, humoral immunity, or a combination of both. In this study, we used a DNA prime/modified vaccinia virus Ankara boost regimen to immunize rhesus macaques against nearly all simian immunodeficiency virus (SIV) proteins. These animals were challenged intrarectally with pathogenic molecularly cloned SIVmac239, which is resistant to neutralization. The immunization regimen resulted in the induction of virus-specific CD8(+) and CD4(+) responses in all vaccinees. Although anamnestic neutralizing antibody responses against laboratory-adapted SIVmac251 developed after the challenge, no neutralizing antibodies against SIVmac239 were detectable. Vaccinated animals had significantly reduced peak viremia compared with controls (P < 0.01). However, despite the induction of virus-specific cellular immune responses and reduced peak viral loads, most animals still suffered from gradual CD4 depletion and progressed to disease.

AIDS Vaccines↗

PubMed2002

Dominance of CD8 responses specific for epitopes bound by a single major histocompatibility complex class I molecule during the acute phase of viral infection.

Cytotoxic T-lymphocyte (CTL) responses are thought to control human immunodeficiency virus replication during the acute phase of infection. Understanding the CD8(+) T-cell immune responses early after infection may, therefore, be important to vaccine design. Analyzing these responses in humans is difficult since few patients are diagnosed during early infection. Additionally, patients are infected by a variety of viral subtypes, making it hard to design reagents to measure their acute-phase immune responses. Given the complexities in evaluating acute-phase CD8(+) responses in humans, we analyzed these important immune responses in rhesus macaques expressing a common rhesus macaque major histocompatibility complex class I molecule (Mamu-A*01) for which we had developed a variety of immunological assays. We infected eight Mamu-A*01-positive macaques and five Mamu-A*01-negative macaques with the molecularly cloned virus SIV(mac)239 and determined all of the simian immunodeficiency virus-specific CD8(+) T-cell responses against overlapping peptides spanning the entire virus. We also monitored the evolution of particular CD8(+) T-cell responses by tetramer staining of peripheral lymphocytes as well as lymph node cells in situ. In this first analysis of the entire CD8(+) immune response to autologous virus we show that between 2 and 12 responses are detected during the acute phase in each animal. CTL against the early proteins (Tat, Rev, and Nef) and against regulatory proteins Vif and Vpr dominated the acute phase. Interestingly, CD8(+) responses against Mamu-A*01-restricted epitopes Tat(28-35)SL8 and Gag(181-189)CM9 were immunodominant in the acute phase. After the acute phase, however, this pattern of reactivity changed, and the Mamu-A*01-restricted response against the Gag(181-189)CM9 epitope became dominant. In most of the Mamu-A*01-positive macaques tested, CTL responses against epitopes bound by Mamu-A*01 dominated the CD8(+) cellular immune response.

Acute Disease↗

PubMed2002

Effects of cytotoxic T lymphocytes (CTL) directed against a single simian immunodeficiency virus (SIV) Gag CTL epitope on the course of SIVmac239 infection.

Vaccine-induced cytotoxic T lymphocytes (CTL) have been implicated in the control of virus replication in simian immunodeficiency virus (SIV)-challenged and simian-human immunodeficiency virus-challenged macaques. Therefore, we wanted to test the impact that vaccine-induced CTL responses against an immunodominant Gag epitope might have in the absence of other immune responses. By themselves, these strong CTL responses failed to control SIVmac239 replication.

Animals↗

PubMed2002

Tat-vaccinated macaques do not control simian immunodeficiency virus SIVmac239 replication.

The regulatory proteins of human immunodeficiency virus may represent important vaccine targets. Here we assessed the role of Tat-specific cytotoxic T lymphocytes (CTL) in controlling pathogenic simian immunodeficiency virus SIVmac239 replication after using a DNA-prime, vaccinia virus Ankara-boost vaccine regimen. Despite the induction of Tat-specific CTL, there was no significant reduction in either peak or viral set point compared to that of controls.

AIDS Vaccines↗

PubMed2002

Body-size dependence of resting energy expenditure can be attributed to nonenergetic homogeneity of fat-free mass.

An enduring enigma is why the ratio of resting energy expenditure (REE) to metabolically active tissue mass, expressed as the REE/fat-free mass (FFM) ratio, is greater in magnitude in subjects with a small FFM than it is in subjects with a large FFM. This study tested the hypothesis that a higher REE/FFM ratio in subjects with a small body mass and FFM can be explained by a larger proportion of FFM as high-metabolic-rate tissues compared with that observed in heavier subjects. REE was measured by indirect calorimetry, FFM by dual-energy X-ray absorptiometry (DEXA), and tissue/organ contributions to FFM by whole body magnetic resonance imaging (MRI) in healthy adults. Four tissue heat-producing contributions to FFM were evaluated, low-metabolic-rate fat-free adipose tissue (18.8 kJ/kg), skeletal muscle (54.4 kJ/kg), and bone (9.6 kJ/kg); and high-metabolic-rate residual mass (225.9 kJ/kg). Initial evaluations in 130 men and 159 women provided strong support for two key, developed models, one linking DEXA FFM with MRI FFM estimates and the other linking REE predicted from the four MRI-derived components with measured REE. There was an inverse association observed between measured REE/FFM and FFM (r(2) = 0.17, P < 0.001). Allometric models revealed a similar pattern of tissue change relative to body mass across males and females with greater proportional increases in fat-free adipose tissue and skeletal muscle than in FFM and a smaller proportional increase in residual mass than in FFM. When examined as a function of FFM, positive slopes were observed for skeletal muscle/FFM and pooled low-metabolic-rate components, and a negative slope for residual mass. Our linked REE-body composition models and associations strongly support the hypothesis that FFM varies systematically in the proportion of thermogenic components as a function of body mass and FFM. These observations have important implications for the interpretation of between-individual differences in REE expressed relative to metabolically active tissue mass.

Adult↗

PubMed2002

Improving the power of sib pair quantitative trait loci detection by phenotype winsorization.

OBJECTIVES: In sib pair studies, quantitative trait loci (QTL) identification may be adversely affected by non-normality in the phenotypic distribution, particularly when subjects falling in the tails of the distribution bias the trait mean or variance. We evaluated the robustness and power of reducing the influence of subjects with extreme phenotypic values by Winsorizing non-normal distributions in three versions of Haseman-Elston regression-based methods of QTL linkage analysis. METHODS: Data were simulated for normal and non-normal distributions. Phenotypic values that correspond to cutoff points at the omega and 1 - omega percentiles of the distribution were identified, and phenotypic values falling outside the boundaries of the omega and 1 - omega cutoff points were replaced by the omega and 1 - omega values, respectively. One million replications were performed for the three tests of linkage for Winsorized and non-Winsorized data. RESULTS: Winsorization reduced conservatism in the tails of the empirical type I error rate for the vast majority of the tests of linkage, increased the power of QTL detection in non-normal data and created a slight negative bias in symmetrical phenotypic distributions. CONCLUSIONS: Winsorizing can improve the power of QTL detection with certain non-normal distributions but can also introduce bias into the estimate of the QTL effect.

Genetic Predisposition to Disease↗

PubMed2002

Project Grow-2-Gether: a study of the genetic and environmental influences on child eating and obesity.

"Project Grow-2-Gether" is a child nutrition study of same-sex, 3- to 7-year-old monozygotic and dizygotic twin pairs. The study attempts to bridge two bodies of literature that have rarely interfaced with respect to obesity and ingestive behavior: the first being behavioral genetic approaches to obesity-related traits, and the second being developmental approaches focusing on parent-child relationships. The overarching aim of Project Grow-2-Gether is to disentangle genetic from potential home-environmental influences on child eating behavior and body fat. This paper reviews the rationale for Project Grow-2-Gether, its procedures, and core phenotypic measurement battery. A focus of the study is acquisition of controlled food intake measurements obtained in the laboratory, measurement of specific home environmental variables, and multi-method evaluation of parent-child feeding relations. Future directions may involve longitudinal assessment of child growth and molecular analyses for specific genes that influence child eating behavior.

Absorptiometry, Photon↗

PubMed2002

YMD: a microarray database for large-scale gene expression analysis.

The use of microarray technology to perform parallel analysis of the expression pattern of a large number of genes in a single experiment has created a new frontier of medical research. The vast amount of gene expression data generated from multiple microarray experiments requires a robust database system that allows efficient data storage, retrieval, secure access, data dissemination, and integrated data analyses. To address the growing needs of microarray researchers at Yale and their collaborators, we have built the Yale Microarray Database (YMD). YMD is Web-accessible with the following features: (i) a Web program that tracks DNA samples between source plates and arrays, (ii) the capability of finding common genes/clones across different array platforms, (iii) an image file server, (iv) laboratory-based user management and access privileges, (v) project management, (vi) template data entry, (vii) linking gene expression data to annotation databases for functional analysis. YMD is currently being used on a pilot basis by several laboratories for different organisms and array platforms.

Databases, Nucleic Acid↗

PubMedDate not supplied

A design and statistical perspective on microarray gene expression studies in nutrition: the need for playful creativity and scientific hard-mindedness.

OBJECTIVES: Our purpose is to highlight some of the past and potential future uses of microarray in nutrition research, while also commenting on some aspects of the design conduct and analysis of microarray data that will leave to improved data quality. METHODS: In this review article we outline some of the aspects of microarray experimentation that must be considered before and during these experiments. These topics include: identification of the experiment's objective (hypothesis), the experimental design, sample size, statistical analysis, data verification, data handling, and experimental interpretation. RESULTS: In order to illustrate the principles we outline in this article we use the methods to layout the design of a microarray experiment to study one aspect of the observation that a diet high in soy is associated with lower rates of breast cancer. CONCLUSIONS: Microarrays are a very powerful tool for studying virtually every nutrition-related disease and trait and can provide valuable insights that are not obtainable with other techniques. However, unless nutrition researchers conduct their studies with scientific hard-mindedness, the studies will be of lower power at least if not completely misleading.

Animals↗

PubMedDate not supplied

Joint tests for quantitative trait loci in experimental crosses.

Selective genotyping is common because it can increase the expected correlation between QTL genotype and phenotype and thus increase the statistical power of linkage tests (i.e., regression-based tests). Linkage can also be tested by assessing whether the marginal genotypic distribution conforms to its expectation, a marginal-based test. We developed a class of joint tests that, by constraining intercepts in regression-based analyses, capitalize on the information available in both regression-based and marginal-based tests. We simulated data corresponding to the null hypothesis of no QTL effect and the alternative of some QTL effect at the locus for a backcross and an F2 intercross between inbred strains. Regression-based and marginal-based tests were compared to corresponding joint tests. We studied the effects of random sampling, selective sampling from a single tail of the phenotypic distribution, and selective sampling from both tails of the phenotypic distribution. Joint tests were nearly as powerful as all competing alternatives for random sampling and two-tailed selection under both backcross and F2 intercross situations. Joint tests were generally more powerful for one-tailed selection under both backcross and F2 intercross situations. However, joint tests cannot be recommended for one-tailed selective genotyping if segregation distortion is suspected.

Computer Simulation↗