Heritability within groups is uninformative about differences among groups: Cases from behavioral, evolutionary, and statistical genetics

Without the ability to control or randomize environments (or genotypes), it is difficult to determine the degree to which observed phenotypic differences between two groups of individuals are due to genetic vs. environmental differences. However, some have suggested that these concerns may be limited to pathological cases, and methods have appeared that seem to give-directly or indirectly-some support to claims that aggregate heritable variation within groups can be related to heritable variation among groups. We consider three families of approaches: the "between-group heritability" sometimes invoked in behavior genetics, the statistic [Formula: see text] used in empirical work in evolutionary quantitative genetics, and methods based on variation in ancestry in an admixed population, used in anthropological and statistical genetics. We take up these examples to show mathematically that information on within-group genetic and phenotypic information in the aggregate cannot separate among-group differences into genetic and environmental components, and we provide simulation results that support our claims. We discuss these results in terms of the long-running debate on this topic.

Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations

In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these two fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we derive a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., Genome-Wide Association Studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur using analytical theory and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate this by showing how a standard GWAS technique-including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model-can mitigate spurious correlations in phylogenetic analyses. As a case study of this, we re-examine an analysis testing for co-evolution of expression levels between genes across a fungal phylogeny, and show that including covariance matrix eigenvectors as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.

Heritability within groups is uninformative about differences among groups: cases from behavioral, evolutionary, and statistical genetics

Without the ability to control or randomize environments (or genotypes), it is difficult to determine the degree to which observed phenotypic differences between two groups of individuals are due to genetic vs. environmental differences. However, some have suggested that these concerns may be limited to pathological cases, and methods have appeared that seem to give-directly or indirectly-some support to claims that aggregate heritable variation within groups can be related to heritable variation among groups. We consider three families of approaches: the "between-group heritability" sometimes invoked in behavior genetics, the statistic P S T used in empirical work in evolutionary quantitative genetics, and methods based on variation in ancestry in an admixed population, used in anthropological and statistical genetics. We take up these examples to show mathematically that information on within-group genetic and phenotypic information in the aggregate cannot separate among-group differences into genetic and environmental components, and we provide simulation results that support our claims. We discuss these results in terms of the long-running debate on this topic.

Tree-based QTL mapping with expected local genetic relatedness matrices

Understanding the genetic basis of complex phenotypes is a central pursuit of genetics. Genome-wide association studies (GWASs) are a powerful way to find genetic loci associated with phenotypes. GWASs are widely and successfully used, but they face challenges related to the fact that variants are tested for association with a phenotype independently, whereas in reality variants at different sites are correlated because of their shared evolutionary history. One way to model this shared history is through the ancestral recombination graph (ARG), which encodes a series of local coalescent trees. Recent computational and methodological breakthroughs have made it feasible to estimate approximate ARGs from large-scale samples. Here, we explore the potential of an ARG-based approach to quantitative-trait locus (QTL) mapping, echoing existing variance-components approaches. We propose a framework that relies on the conditional expectation of a local genetic relatedness matrix (local eGRM) given the ARG. Simulations show that our method is especially beneficial for finding QTLs in the presence of allelic heterogeneity. By framing QTL mapping in terms of the estimated ARG, we can also facilitate the detection of QTLs in understudied populations. We use local eGRM to analyze two chromosomes containing known body size loci in a sample of Native Hawaiians. Our investigations can provide intuition about the benefits of using estimated ARGs in population- and statistical-genetic methods in general.

Microsatellites used in forensics are in regions enriched for trait-associated variants

The 20 short tandem repeat (STR) loci of the combined DNA index system (CODIS) are the basis of the vast majority of forensic genetics in the United States. One argument for permissive rules about the collection of CODIS genotypes is that the CODIS loci are thought to contain little information about ancestry or traits. However, in the past 20 years, a growing field has identified hundreds of thousands of genotype-trait associations. Here, we conduct a survey of the landscape of such associations surrounding the CODIS loci as compared with non-CODIS STRs. Although this study cannot establish or quantify associations between CODIS genotypes and phenotypes, we find that the regions around the CODIS loci are enriched for both known pathogenic variants (> 90th percentile) and for trait-associated SNPs identified in genome-wide association studies (GWAS) (≥ 95th percentile in 10kb and 100kb flanking regions), compared with other random sets of autosomal tetranucleotide-repeat STRs.

A likelihood-based framework for demographic inference from genealogical trees

The demographic history of a population drives the pattern of genetic variation and is encoded in the gene-genealogical trees of the sampled alleles. However, existing methods to infer demographic history from genetic data tend to use relatively low-dimensional summaries of the genealogy, such as allele frequency spectra. As a step toward capturing more of the information encoded in the genome-wide sequence of genealogical trees, here we propose a novel framework called the genealogical likelihood (gLike), which derives the full likelihood of a genealogical tree under any hypothesized demographic history. Employing a graph-based structure, gLike summarizes across independent trees the relationships among all lineages in a tree with all possible trajectories of population memberships through time and efficiently computes the exact marginal probability under a parameterized demographic model. Through extensive simulations and empirical applications on populations that have experienced multiple admixtures, we showed that gLike can accurately estimate dozens of demographic parameters when the true genealogy is known, including ancestral population sizes, admixture timing, and admixture proportions. Moreover, when using genealogical trees inferred from genetic data, we showed that gLike outperformed conventional demographic inference methods that leverage only the allele-frequency spectrum and yielded parameter estimates that align with established historical knowledge of the past demographic histories for populations like Latino Americans and Native Hawaiians. Furthermore, our framework can trace ancestral histories by analyzing a sample from the admixed population without proxies for its source populations, removing the need to sample ancestral populations that may no longer exist. Taken together, our proposed gLike framework harnesses underutilized genealogical information to offer exceptional sensitivity and accuracy in inferring complex demographies for humans and other species, particularly as estimation of genome-wide genealogies improves.

Amplification is the primary mode of gene-by-sex interaction in complex human traits

Sex differences in complex traits are suspected to be in part due to widespread gene-by-sex interactions (GxSex), but empirical evidence has been elusive. Here, we infer the mixture of ways in which polygenic effects on physiological traits covary between males and females. We find that GxSex is pervasive but acts primarily through systematic sex differences in the magnitude of many genetic effects ("amplification") rather than in the identity of causal variants. Amplification patterns account for sex differences in trait variance. In some cases, testosterone may mediate amplification. Finally, we develop a population-genetic test linking GxSex to contemporary natural selection and find evidence of sexually antagonistic selection on variants affecting testosterone levels. Our results suggest that amplification of polygenic effects is a common mode of GxSex that may contribute to sex differences and fuel their evolution.

Tree-based QTL mapping with expected local genetic relatedness matrices

Understanding the genetic basis of complex phenotypes is a central pursuit of genetics. Genome-wide Association Studies (GWAS) are a powerful way to find genetic loci associated with phenotypes. GWAS are widely and successfully used, but they face challenges related to the fact that variants are tested for association with a phenotype independently, whereas in reality variants at different sites are correlated because of their shared evolutionary history. One way to model this shared history is through the ancestral recombination graph (ARG), which encodes a series of local coalescent trees. Recent computational and methodological breakthroughs have made it feasible to estimate approximate ARGs from large-scale samples. Here, we explore the potential of an ARG-based approach to quantitative-trait locus (QTL) mapping, echoing existing variance-components approaches. We propose a framework that relies on the conditional expectation of a local genetic relatedness matrix given the ARG (local eGRM). Simulations show that our method is especially beneficial for finding QTLs in the presence of allelic heterogeneity. By framing QTL mapping in terms of the estimated ARG, we can also facilitate the detection of QTLs in understudied populations. We use local eGRM to identify a large-effect BMI locus, the CREBRF gene, in a sample of Native Hawaiians in which it was not previously detectable by GWAS because of a lack of population-specific imputation resources. Our investigations can provide intuition about the benefits of using estimated ARGs in population- and statistical-genetic methods in general.

Microsatellites used in forensics are located in regions unusually rich in trait-associated variants

The 20 short tandem repeat (STR) markers of the combined DNA index system (CODIS) are the basis of the vast majority of forensic genetics in the United States. One argument for permissive rules about the collection of CODIS genotypes is that the CODIS markers are thought to contain information relevant to identification only (such as a human fingerprint would), with little information about ancestry or traits. However, in the past 20 years, a quickly growing field has identified hundreds of thousands of genotype-trait associations. Here we conduct a survey of the landscape of such associations surrounding the CODIS loci as compared with non-CODIS STRs. We find that the regions around the CODIS markers are enriched for both known pathogenic variants (>90th percentile) and for SNPs identified as trait-associated in genome-wide association studies (GWAS) (≥95th percentile in 10kb and 100kb flanking regions), compared with other random sets of autosomal tetranucleotide-repeat STRs. Although it is not obvious how much phenotypic information CODIS would need to convey to strain the "DNA fingerprint" analogy, the CODIS markers, considered as a set, are in regions unusually dense with variants with known phenotypic associations.

Gattaca as a lens on contemporary genetics: Marking 25 years into the film's "not-too-distant" future

The 1997 film Gattaca has emerged as a canonical pop culture reference used to discuss modern controversies in genetics and bioethics. It appeared in theaters a few years prior to the announcement of the "completion" of the human genome (2000), as the science of human genetics was developing a renewed sense of its social implications. The story is set in a near-future world in which parents can, with technological assistance, influence the genetic composition of their offspring on the basis of predicted life outcomes. The current moment-25 years after the film's release-offers an opportunity to reflect on where society currently stands with respect to the ideas explored in Gattaca. Here, we review and discuss several active areas of genetic research-genetic prediction, embryo selection, forensic genetics, and others-that interface directly with scenes and concepts in the film. On its silver anniversary, we argue that Gattaca remains an important reflection of society's expectations and fears with respect to the ways that genetic science has manifested in the real world. In accompanying supplemental material, we offer some thought questions to guide group discussions inside and outside of the classroom.

Open practices in our science and our courtrooms

Advocates of transparency in science often point to the benefits of open practices for the scientific process. Here, we focus on a possibly underappreciated effect of standards for transparency: their influence on non-scientific decisions. As a case study, we consider the current state of probabilistic genotyping software in forensics.

Skin deep: The decoupling of genetic admixture levels from phenotypes that differed between source populations

OBJECTIVES

In genetic admixture processes, source groups for an admixed population possess distinct patterns of genotype and phenotype at the onset of admixture. Particularly in the context of recent and ongoing admixture, such differences are sometimes taken to serve as markers of ancestry for individuals-that is, phenotypes initially associated with the ancestral background in one source population are assumed to continue to reflect ancestry in that population. Such phenotypes might possess ongoing significance in social categorizations of individuals, owing in part to perceived continuing correlations with ancestry. However, genotypes or phenotypes initially associated with ancestry in one specific source population have been seen to decouple from overall admixture levels, so that they no longer serve as proxies for genetic ancestry. Here, we aim to develop an understanding of the joint dynamics of admixture levels and phenotype distributions in an admixed population.

METHODS

We devise a mechanistic model, consisting of an admixture model, a quantitative trait model, and a mating model. We analyze the behavior of the mechanistic model in relation to the model parameters.

RESULTS

We find that it is possible for the decoupling of genetic ancestry and phenotype to proceed quickly, and that it occurs faster if the phenotype is driven by fewer loci. Positive assortative mating attenuates the process of dissociation relative to a scenario in which mating is random with respect to genetic admixture and with respect to phenotype.

CONCLUSIONS

The mechanistic framework suggests that in an admixed population, a trait that initially differed between source populations might serve as a reliable proxy for ancestry for only a short time, especially if the trait is determined by few loci. It follows that a social categorization based on such a trait is increasingly uninformative about genetic ancestry and about other traits that differed between source populations at the onset of admixture.

Attacks on genetic privacy via uploads to genealogical databases

Direct-to-consumer (DTC) genetics services are increasingly popular, with tens of millions of customers. Several DTC genealogy services allow users to upload genetic data to search for relatives, identified as people with genomes that share identical by state (IBS) regions. Here, we describe methods by which an adversary can learn database genotypes by uploading multiple datasets. For example, an adversary who uploads approximately 900 genomes could recover at least one allele at SNP sites across up to 82% of the genome of a median person of European ancestries. In databases that detect IBS segments using unphased genotypes, approximately 100 falsified uploads can reveal enough genetic information to allow genome-wide genetic imputation. We provide a proof-of-concept demonstration in the GEDmatch database, and we suggest countermeasures that will prevent the exploits we describe.

Reconstructing the History of Polygenic Scores Using Coalescent Trees

Genome-wide association studies (GWAS) have revealed that many traits are highly polygenic, in that their within-population variance is governed, in part, by small-effect variants at many genetic loci. Standard population-genetic methods for inferring evolutionary history are ill-suited for polygenic traits: when there are many variants of small effect, signatures of natural selection are spread across the genome and are subtle at any one locus. In the last several years, various methods have emerged for detecting the action of natural selection on polygenic scores, sums of genotypes weighted by GWAS effect sizes. However, most existing methods do not reveal the timing or strength of selection. Here, we present a set of methods for estimating the historical time course of a population-mean polygenic score using local coalescent trees at GWAS loci. These time courses are estimated by using coalescent theory to relate the branch lengths of trees to allele-frequency change. The resulting time course can be tested for evidence of natural selection. We present theory and simulations supporting our procedures, as well as estimated time courses of polygenic scores for human height. Because of its grounding in coalescent theory, the framework presented here can be extended to a variety of demographic scenarios, and its usefulness will increase as both GWAS and ancestral-recombination-graph inference continue to progress.

Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences

Recent analyses of polygenic scores have opened new discussions concerning the genetic basis and evolutionary significance of differences among populations in distributions of phenotypes. Here, we highlight limitations in research on polygenic scores, polygenic adaptation and population differences. We show how genetic contributions to traits, as estimated by polygenic scores, combine with environmental contributions so that differences among populations in trait distributions need not reflect corresponding differences in genetic propensity. Under a null model in which phenotypes are selectively neutral, genetic propensity differences contributing to phenotypic differences among populations are predicted to be small. We illustrate this null hypothesis in relation to health disparities between African Americans and European Americans, discussing alternative hypotheses with selective and environmental effects. Close attention to the limitations of research on polygenic phenomena is important for the interpretation of their relationship to human population differences.

Statistical Detection of Relatives Typed with Disjoint Forensic and Biomedical Loci

In familial searching in forensic genetics, a query DNA profile is tested against a database to determine whether it represents a relative of a database entrant. We examine the potential for using linkage disequilibrium to identify pairs of profiles as belonging to relatives when the query and database rely on nonoverlapping genetic markers. Considering data on individuals genotyped with both microsatellites used in forensic applications and genome-wide SNPs, we find that ∼30%-32% of parent-offspring pairs and ∼35%-36% of sib pairs can be identified from the SNPs of one member of the pair and the microsatellites of the other. The method suggests the possibility of performing familial searches of microsatellite databases using query SNP profiles, or vice versa. It also reveals that privacy concerns arising from computations across multiple databases that share no genetic markers in common entail risks, not only for database entrants, but for their close relatives as well.

Consanguinity Rates Predict Long Runs of Homozygosity in Jewish Populations

OBJECTIVES

Recent studies have highlighted the potential of analyses of genomic sharing to produce insight into the demographic processes affecting human populations. We study runs of homozygosity (ROH) in 18 Jewish populations, examining these groups in relation to 123 non-Jewish populations sampled worldwide.

METHODS

By sorting ROH into 3 length classes (short, intermediate, and long), we evaluate the impact of demographic processes on genomic patterns in Jewish populations.

RESULTS

We find that the portion of the genome appearing in long ROH - the length class most directly related to recent consanguinity - closely accords with data gathered from interviews during the 1950s on frequencies of consanguineous unions in various Jewish groups.

CONCLUSION

The high correlation between 1950s consanguinity levels and coverage by long ROH explains differences across populations in ROH patterns. The dissection of ROH into length classes and the comparison to consanguinity data assist in understanding a number of additional phenomena, including similarities of Jewish populations to Middle Eastern, European, and Central and South Asian non-Jewish populations in short ROH patterns, relative lengths of identity-by-descent tracts in different Jewish groups, and the "population isolate" status of the Ashkenazi Jews.

Evaluation of a Digital Behavioral Counseling Program for Reducing Risk Factors for Chronic Disease in a Workforce

OBJECTIVE

To evaluate a digitally delivered, intensive behavioral counseling program for a workforce at risk for obesity-related chronic disease.

METHODS

Employees were offered a digital health program modeled after the diabetes prevention program (DPP). Annual workforce health assessments were used to examine changes in chronic disease risk factors between participants (n = 634) relative to a matched comparison group (n = 1268).

RESULTS

Overall, employees were gaining an average of 3.5 pounds annually before program inception. Program engagement was positive; 83% completed the majority of the curriculum and 31% lost at least 5% of their starting weight. Compared with non-participating peers, participants demonstrated reduced weight, improved fasting blood glucose, and improved nutritional intake after a year.

CONCLUSIONS

The digital health program was effective for engaging employees in health behavior change. Digital options facilitate widespread implementation.

A General Model of the Relationship between the Apportionment of Human Genetic Diversity and the Apportionment of Human Phenotypic Diversity

Models that examine genetic differences between populations alongside a genotype-phenotype map can provide insight about phenotypic variation among groups. We generalize a simple model of a completely heritable, additive, selectively neutral quantitative trait to examine the relationship between single-locus genetic differentiation and phenotypic differentiation on quantitative traits. In agreement with similar efforts using different models, we show that the expected degree to which two groups differ on a neutral quantitative trait is not strongly affected by the number of genetic loci that influence the trait: neutral trait differences are expected to have a magnitude comparable to the genetic differences at a single neutral locus. We discuss this result with respect to population differences in disease phenotypes, arguing that although neutral genetic differences between populations can contribute to specific differences between populations in health outcomes, systematic patterns of difference that run in the same direction for many genetically independent health conditions are unlikely to be explained by neutral genetic differentiation.

Implications of the apportionment of human genetic diversity for the apportionment of human phenotypic diversity

Researchers in many fields have considered the meaning of two results about genetic variation for concepts of "race." First, at most genetic loci, apportionments of human genetic diversity find that worldwide populations are genetically similar. Second, when multiple genetic loci are examined, it is possible to distinguish people with ancestry from different geographical regions. These two results raise an important question about human phenotypic diversity: To what extent do populations typically differ on phenotypes determined by multiple genetic loci? It might be expected that such phenotypes follow the pattern of similarity observed at individual loci. Alternatively, because they have a multilocus genetic architecture, they might follow the pattern of greater differentiation suggested by multilocus ancestry inference. To address the question, we extend a well-known classification model of Edwards (2003) by adding a selectively neutral quantitative trait. Using the extended model, we show, in line with previous work in quantitative genetics, that regardless of how many genetic loci influence the trait, one neutral trait is approximately as informative about ancestry as a single genetic locus. The results support the relevance of single-locus genetic-diversity partitioning for predictions about phenotypic diversity.

The mind, the lab, and the field: Three kinds of populations in scientific practice

Scientists use models to understand the natural world, and it is important not to conflate model and nature. As an illustration, we distinguish three different kinds of populations in studies of ecology and evolution: theoretical, laboratory, and natural populations, exemplified by the work of R. A. Fisher, Thomas Park, and David Lack, respectively. Biologists are rightly concerned with all three types of populations. We examine the interplay between these different kinds of populations, and their pertinent models, in three examples: the notion of "effective" population size, the work of Thomas Park on Tribolium populations, and model-based clustering algorithms such as Structure. Finally, we discuss ways to move safely between three distinct population types while avoiding confusing models and reality.

Windfalls and pitfalls: Applications of population genetics to the search for disease genes

Association mapping can be viewed as an application of population genetics and evolutionary biology to the problem of identifying genes causally connected to phenotypes. However, some population-genetic principles important to the design and analysis of association studies have not been widely understood or have even been generally misunderstood. Some of these principles underlie techniques that can aid in the discovery of genetic variants that influence phenotypes (‘windfalls’), whereas others can interfere with study design or interpretation of results (‘pitfalls’). Here, considering examples involving genetic variant discovery, linkage disequilibrium, power to detect associations, population stratification and genotype imputation, we address misunderstandings in the application of population genetics to association studies, and we illuminate how some surprising results in association contexts can be easily explained when considered from evolutionary and population-genetic perspectives. Through our examples, we argue that population-genetic thinking—which takes a theoretical view of the evolutionary forces that guide the emergence and propagation of genetic variants—substantially informs the design and interpretation of genetic association studies. In particular, population-genetic thinking sheds light on genetic confounding, on the relationships between association signals of typed markers and causal variants, and on the advantages and disadvantages of particular strategies for measuring genetic variation in association studies.

Iowa Gambling Task performance in euthymic bipolar I disorder: a meta-analysis and empirical study

BACKGROUND

The Iowa Gambling Task (IGT) has been recommended as an index of reward sensitivity, which is elevated in bipolar disorder. We conducted a meta-analysis of IGT performance in euthymic bipolar I disorder compared with control participants. Findings indicated that people with bipolar disorder make more risky choices than control participants, though the effect is small (g=0.35). It is not clear which of the many processes involved in IGT performance are involved in producing the observed group difference.

METHODS

Fifty-five euthymic people with bipolar disorder and 39 control participants completed the IGT. The Expectancy Valence Model was used to examine differences in IGT. We also examined whether variation in IGT performance within the bipolar group was related to current mood, illness course, impulsivity, or demographics.

RESULTS

Bipolar and control groups did not differ on the total number of risky choices, rate of learning, or any of the parameters of the Expectancy Valence Model. IGT performance in bipolar disorder was not related to any of the examined individual differences.

LIMITATIONS

It is possible that there are group differences that are too small to detect at our sample size or that are not amenable to study via the Expectancy Valence Model.

CONCLUSIONS

We were unable to identify group differences on the IGT or correlates of IGT performance within bipolar disorder. Though the IGT may serve as a useful model for decision-making, its structure may make it unsuitable for behavioral assessment of reward sensitivity independent of punishment sensitivity.

People with bipolar I disorder report avoiding rewarding activities and dampening positive emotion

BACKGROUND

Researchers have linked bipolar disorder to elevations in reward sensitivity and positive affect. Little is known, however, about how people with bipolar disorder respond to rewards and positive affect and how these tendencies relate to functioning or quality of life.

METHODS

Persons diagnosed with bipolar I disorder and matched controls completed the Responses to Positive Affect (RPA) measure and the Brief Quality of Life in Bipolar Disorder scale. Bipolar participants also completed the Reward Responses Inventory, which we designed to assess the extent to which participants avoid rewarding activities to prevent mania. A subsample of participants with bipolar disorder completed a positive mood induction procedure to examine the validity of the Response to Positive Affect scale.

RESULTS

The majority of bipolar participants reported avoiding at least one rewarding activity as a means of preventing mania. In addition, people with bipolar I disorder reported more dampening responses to positive affect than did control participants. Dampening positive emotions was related to lower quality of life.

LIMITATIONS

This study does not address whether responses to affect and reward are related to the longitudinal course of symptoms.

CONCLUSIONS

These findings suggest that people with bipolar I disorder seem to be aware of the potential of goal achievements to trigger mania, and many people with bipolar disorder seem to take steps to avoid positive emotion and reward.

Neural mechanisms underlying 5-HTTLPR-related sensitivity to acute stress

OBJECTIVE

Many studies have shown that 5-HTTLPR genotype interacts with exposure to stress in conferring risk for psychopathology. However, the specific neural mechanisms through which this gene-by-environment interaction confers risk remain largely unknown, and no study to date has directly examined the modulatory effects of 5-HTTLPR on corticolimbic circuit responses during exposure to acute stress.

METHOD

An acute laboratory stressor was administered to 51 healthy women during blood-oxygen-level-dependent functional magnetic resonance imaging. In this task, participants were threatened with electric shocks of uncertain intensity, which were unpredictably delivered to the wrist after a long anticipatory cue period of unpredictable duration.

RESULTS

Relative to women carrying the L allele, those with the SS genotype showed enhanced activation during threat anticipation in a network of regions, including the amygdala, hippocampus, anterior insula, thalamus, pulvinar, caudate, precuneus, anterior cingulate cortex, and medial prefrontal cortex. Individuals with the SS genotype also displayed enhanced positive coupling between medial prefrontal cortex activation and anxiety experience, whereas enhanced negative coupling between insula activation and perceived success at regulating anxiety was observed in individuals carrying the L allele.

CONCLUSIONS

These findings suggest that during stress exposure, neural systems that enhance fear and arousal, modulate attention toward threat, and perseverate on emotional salience of the threat may be engaged preferentially in individuals with the SS genotype. This may be one mechanism underlying the risk for psychopathology conferred by the S allele upon exposure to life stressors.

The behavioral activation system and mania

For over two decades, theorists have suggested that mania relates to heightened sensitivity of the behavioral activation system (BAS). In this article, we review a burgeoning empirical literature on this model, drawing on both cross-sectional and prospective studies. As evidence has emerged for this model, we argue that it is time to consider more specific aspects of BAS sensitivity in this disorder. We review evidence that bipolar disorder relates to an increased willingness to expend effort toward reward and to increases in energy and goal pursuit after an initial reward. We conclude by considering the strengths and weaknesses of this literature, with an eye toward future directions and implications for treatment.

The behavioral activation system and mania

For over two decades, theorists have suggested that mania relates to heightened sensitivity of the behavioral activation system (BAS). In this article, we review a burgeoning empirical literature on this model, drawing on both cross-sectional and prospective studies. As evidence has emerged for this model, we argue that it is time to consider more specific aspects of BAS sensitivity in this disorder. We review evidence that bipolar disorder relates to an increased willingness to expend effort toward reward and to increases in energy and goal pursuit after an initial reward. We conclude by considering the strengths and weaknesses of this literature, with an eye toward future directions and implications for treatment.

Healthy young women with serotonin transporter SS polymorphism show a pro-inflammatory bias under resting and stress conditions

The study of functionally relevant biological effects of serotonin transporter gene promoter region (5-HTTLPR) polymorphisms is especially important given the current controversy about the clinical relevance of these polymorphisms. Here we report an intrinsic immunobiological difference between individuals carrying two short (SS) versus long (LL) 5-HTTLPR alleles, that is observed in healthy subjects reporting low exposure to life stress. Given that 5-HTTLPR polymorphisms are thought to influence susceptibility to depression and are associated with robust neurobiological effects, that depression is associated with higher pro-inflammatory and lower anti-inflammatory cytokines, and that acute stressors increase circulating concentrations of pro-inflammatory cytokines, we hypothesized that compared to LL individuals, SS individuals may show a pro-inflammatory bias under resting conditions and/or during stress. 15 LL and 11 SS individuals participated in the Trier Social Stress Test (TSST). Serum IL-6 and IL-10 were quantified at baseline and 30, 60, 90, and 120min after beginning the 20-min stress test. Compared to LL individuals, SS individuals showed a higher IL-6/IL-10 ratio at baseline and during stress. Importantly, this pro-inflammatory bias was observed despite both groups being healthy, reporting similar intensities of stress and negative emotionality during the TSST, and reporting similar low exposures to early and recent life stress. To our knowledge, this is the first report of a pro-inflammatory bias/phenotype in individuals carrying the SS genotype of 5-HTTLPR. Thus, healthy SS individuals may be chronically exposed to a pro-inflammatory physiological burden under resting and stress conditions, which could increase their vulnerability to disorders like depression and other diseases that can be facilitated/exacerbated by a chronic pro-inflammatory state.

For better or worse? Stress inoculation effects for implicit but not explicit anxiety

BACKGROUND

Severe early life stress (ELS) is associated with negative outcomes. It is not clear, however, what impact moderate ELS has. A growing stress inoculation literature suggests that moderate (vs. low or high) ELS is associated with diminished behavioral and physiological anxiety responses. At the same time, studies of trait anxiety suggest that moderate (vs. low) ELS is associated with greater self-reported anxiety. This study tested the hypothesis that stress inoculation effects are evident for implicit (nonconscious) but not explicit (conscious) aspects of anxiety.

METHODS

Ninety-seven healthy women were assessed for ELS and explicit anxiety using questionnaires and assessed for implicit anxiety using a version of the Implicit Association Test.

RESULTS

Results indicated a quadratic relation between ELS and implicit anxiety, such that moderate ELS was associated with lower implicit anxiety levels than low or high ELS. By contrast, the relation between ELS and explicit anxiety was linear.

CONCLUSION

These findings support the stress inoculation hypothesis and suggest that stress inoculation applies for implicit but not explicit aspects of anxiety.

Endoscopic retrograde cholangiopancreatography after a liquid fatty meal: effect on deep common bile duct cannulation time

BACKGROUND AND STUDY AIM

Endoscopic retrograde cholangiopancreatography (ERCP) is an important gastrointestinal endoscopic procedure in the study and treatment of pancreaticobiliary diseases. The critical step of the procedure is cannulation of the common bile duct (CBD) and/or the pancreatic duct. Cannulation can be a technical challenge at times. Fat is a natural stimulator for bile secretion and relaxation of the sphincter of Oddi. The objective of this study was to determine the effect of a liquid fatty meal on deep CBD cannulation during ERCP.

PATIENTS AND METHODS

We performed a randomized double-blind study in 84 patients to examine the effect of a liquid fatty meal on deep CBD cannulation during ERCP, in a teaching medical center. In the study group, each patient had a liquid fatty meal orally about 1 hour before the procedure. In the control group, each patient had the same volume of a non-fat meal. The appearance of the major papilla, the cannulation rate, the cannulation time, and the fluoroscopy time during cannulation were compared for the two groups.

RESULTS

The orifice of the CBD/pancreatic duct was much more easily identified in the group who ingested the fatty meal. Compared with the non-fat meal group, in the fatty meal group the mean and the median deep CBD cannulation times were shorter, at 8.0 minutes vs. 14.7 minutes ( P = 0.005) and 8.0 minutes vs. 11.5 minutes ( P = 0.008), respectively. Additionally, in the fatty meal group, the mean and the median fluoroscopy times during deep CBD cannulation were lower, at 3.3 minutes vs. 6.1 minutes ( P = 0.040) and 2.5 minutes vs. 3.9 minutes ( P = 0.013), respectively. There were no complications, such as aspiration, associated with the liquid meals given shortly before the ERCP procedure.

CONCLUSIONS

To avoid prolonged cannulation and unnecessary radiation exposure, patients should have a liquid fatty meal before ERCP procedures.

Continuous affinity-based selection: rapid screening and simultaneous amplification of bacterial surface-display libraries

A new method for continuous biopanning has been developed. We have combined the power of affinity chromatography with the fecundity of bacteria in a unique process that mimics clonal selection. Mixed populations of bacteria were applied to a fermenter containing the immobilized ligand of interest. Bacteria retained in this affinity fermenter were allowed to grow under continuous washout conditions, such that weakly bound organisms were selectively lost. Those initially rare founder bacteria expressing a receptor for the immobilized ligand (R+ve) were thus enriched and amplified simultaneously. From an initial culture containing 1 x 10(10) R-ve cells spiked with fewer than 30 R+ve bacteria (<1 in 10(8)), final ratios of R+ve/R-ve bacteria as high as 1 in 12 were observed, representing an enrichment factor of 55 million-fold. This technology has considerable potential for rapid screening of bacterial surface-display libraries and in facilitating directed-evolution studies.

Evidence for heterotypic interaction between the receptor tyrosine kinases TIE-1 and TIE-2

The orphan receptor tyrosine kinase Tie-1 is expressed in endothelial cells and is essential for vascular development. Nothing is known about the signaling pathways utilized by this receptor. In this study we have used chimeric receptors composed of the TrkA ectodomain fused to the transmembrane and intracellular domains of Tie-1, or the related receptor Tie-2, to examine Tie-1 signaling capacity. In contrast to TrkA/Tie-2, the Tie-1 chimera was unable to phosphorylate cellular proteins or undergo autophosphorylation. Consistent with this Tie-1 exhibited negligible kinase activity. Co-immunoprecipitation analysis revealed Tie-1 was present in endothelial cells bound to Tie-2. Full-length Tie-1 and truncated receptor, formed by regulated endoproteolytic cleavage, were found to complex with Tie-2. Association was mediated by the intracellular domains of the receptors and did not require Tie-1 to be membrane-localized. Tie-1 bound to Tie-2 was not tyrosine-phosphorylated under basal conditions or following Tie-2 stimulation. This study provides the first evidence for the existence of a pre-formed complex of Tie-1 and Tie-2 in endothelial cells. The data suggest Tie-1 does not signal via ligand-induced kinase activation involving homo-oligomerization. The physical association between Tie-1 and Tie-2 is consistent with Tie-1 having a role in modulating Tie-2 signaling.

Community-acquired bacteremia in HIV-positive patients: protective benefit of co-trimoxazole

OBJECTIVE

To evaluate the effect of the type of Pneumocystis carinii pneumonia (PCP) prophylaxis on the development of community-acquired bacteremia.

DESIGN

Case-control study using all cases of community-acquired bacteremia identified prospectively during a longitudinal study of all infections in a cohort of HIV-infected persons.

SETTING

University-affiliated Department of Veterans Affairs Medical Center HIV program.

PATIENTS

All patients with community-acquired bacteremia seen at the facility between January 1990 and December 1995 were included. Controls, seen at the same facility and matched by date and CD4 count, were used to assess risk factors. A total of 57 cases and 114 controls were analysed.

MAIN OUTCOME MEASURES

Risk of development of bacteremia, distribution of organisms, and effect of specific prophylactic regimens for PCP.

RESULTS

Bacteremia was caused by Staphylococcus aureus (23%), Pseudomonas aeruginosa (18%), Escherichia coli (16%), Streptococcus pneumoniae (14%) and others (31%). Groups were similar by age, race, HIV risk factors and CD4 count. The presence of an intravenous catheter was mildly predictive of the development of bacteremia [odds ratio (OR), 2.67; P = 0.024]. Type of PCP prophylaxis in cases and controls with CD4 < 200 x 10(6)/l included co-trimoxazole (trimethoprim-sulfamethoxazole, TMP-SMX; 31 and 60%, respectively), dapsone (33 and 24%, respectively) and aerosolized pentamidine (27 and 13%, respectively). Use of TMP-SMX (but not dapsone or aerosolized pentamidine) was associated with the absence of bacteremia (OR, 0.28; P = 0.001). A similar protective effect was found when controlling for the presence of an intravenous catheter.

CONCLUSION

PCP prophylaxis with TMP-SMX apparently protects against community-acquired bacteremia in HIV-infected persons.

The production of PCR products with 5' single-stranded tails using primers that incorporate novel phosphoramidite intermediates

We have prepared several novel phosphoramidites and have synthesised oligonucleotides incorporating them internally. The presence of these residues in an oligonucleotide template presents an impossible barrier to primed synthesis by Taq DNA polymerase. When extended as polymerase chain reaction products, these oligonucleotides no longer serve as templates for the polymerase beyond the insertion sites of the modified intermediates, thereby producing single-stranded tails on amplification products. These tails can then be used for solid phase capture and colorimetric detection of PCR products.

Lipocortin 1 fragment modifies pyrogenic actions of cytokines in rats

Lipocortins form a group of proteins that have been proposed as mediators of the anti-inflammatory actions of glucocorticoids. Intracerebroventricular injection of a recombinant fragment of lipocortin 1 (NH2-terminal 1-188) caused dose-dependent (0.4-1.2 micrograms) reductions in the acute increases in colonic temperature and oxygen consumption, which occurred in response to central injections of recombinant interleukin 1 beta and gamma-interferon in conscious rats. In contrast the lipocortin fragment did not affect the response to prostaglandin E2, and its activity was prevented by heat treatment or by pretreatment of animals with polyclonal antiserum raised to the fragment. Central injection of antiserum significantly enhanced the thermogenic responses to interleukin 1 beta in rats treated with dexamethasone without affecting the responses in normal animals. These results support a physiological role for lipocortin in the central effects of glucocorticoids.

Analysis of A-MuLV transformed fibroblast lines for amplification of the c-myc, p53 and c-fos nuclear proto-oncogenes

Aberrations in nuclear proto-oncogene organisation and/or gene expression have been implicated in cell transformation mediated by the v-abl gene. For example, it has been suggested that amplification of the c-myc proto-oncogene is a co-operative event in v-abl induced fibroblast transformation. We have investigated amplification of the c-myc, p53 and c-fos nuclear proto-oncogenes in several Abelson murine leukaemia virus (A-MuLV) transformed fibroblast lines. None of these proto-oncogenes were detectably rearranged or amplified in v-abl transformed Swiss 3T3 lines. In contrast, NIH3T3 fibroblasts transformed by the v-abl gene consistently showed a 4 to 16-fold amplification of the c-myc gene. These data show that c-myc gene amplification is not an obligatory event associated with A-MuLV transformation, but may be restricted to cell lines derived from NIH3T3. c-myc gene amplification also did not correlate with a reduced latency period for tumour induction in nude mice. In addition, c-myc amplification was not selected during tumourigenesis, indicating that this event is not required for A-MuLV transformed Swiss 3T3 cells to display a full tumourigenic phenotype.

Hybridisation detection of single nucleotide changes with enzyme labelled oligonucleotides

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Human complement factor I: analysis of cDNA-derived primary structure and assignment of its gene to chromosome 4

Factor I is a serine proteinase of complement which together with one of several specific cofactors cleaves activation products of the third and fourth components of complement (C3b and C4b) and modulates the activity of C3 convertase. A heterodimer glycoprotein (Mr = 88,000), factor I is synthesized as a single-chain precursor, prepro-I, which undergoes intracellular proteolytic processing. The human hepatoma line HepG2, however, secretes predominantly the single-chain precursor pro-I. In order to determine the molecular basis for this apparent processing defect, factor I cDNA clones were isolated from a HepG2 mRNA-derived library. Sequencing of the largest insert, HI1971, revealed that it contains 14 base pairs of 5' untranslated region, the complete coding sequence for the 583-residue prepro-I (NH2-signal peptide-heavy chain-linking peptide-light chain-COOH), two polyadenylation signals within the 200-base pair 3' untranslated region, and a portion of poly(A) tail. Analysis of the derived protein structure 1) reveals a mosaic multidomain structure of the heavy chain; 2) demonstrates structural similarity between intracellular conversion of pro-I and activation of other serine proteinase zymogens; and 3) indicates that the light chain of factor I resembles most closely the active subunit of tissue plasminogen activator among all serine proteinases and factor D among complement proteinases. Furthermore, this protein sequence was compared to the sequences of factor I cDNA clones isolated from normal human liver libraries and found to be identical. By exclusion, this defines as cellular the basis for the inefficient processing of pro-I by the HepG2 line. Chromosomal localization by the somatic cell hybrid method maps the factor I gene to chromosome 4.

Extensive mutagenesis of the nuclear location signal of simian virus 40 large-T antigen

Site-directed mutagenesis was used to change Lys-128 of the simian virus 40 large-T nuclear location signal to Met, Ile, Arg, Gln, Asn, Leu, or His. Except for the large-T antigen of the Arg mutation, which was present in cytoplasmic and nuclear compartments, the resultant proteins were unable to enter the nucleus. By contrast, mutations at other sites within the signal were generally less severe in their effect. In some cases (Lys-128 to Gln, Asn, and His), the apparently cytoplasmic variants were able to support limited plasmid DNA replication, suggesting that low levels of large-T antigen undetectable by immunofluorescence were present in the nucleus. Such mutants did not support viral DNA replication. We conclude that there is a strong requirement for a basic residue at position 128 in the large-T nuclear location signal, with Lys the preferred residue.

Functionally important conserved amino-acids in interferon-alpha 2 identified with analogues produced from synthetic genes

A gene was chemically synthesised and expressed in Escherichia coli to produce [Ala30,32,33]IFN-alpha 2, an analogue of human alpha 2-interferon (IFN-alpha 2) which is devoid of activity on human cells. Eight additional analogues provided single changes in IFN-alpha 2 at each of these three conserved positions. No one residue is essential for activity, but both antiviral and anti-proliferative activity are particularly sensitive to changes in the side-chain of Arg33.

Human serum amyloid P component. cDNA isolation, complete sequence of pre-serum amyloid P component, and localization of the gene to chromosome 1

Complementary DNA clones corresponding to the human serum amyloid P component (SAP) were isolated, and the complete nucleotide and derived amino acid sequence of preSAP was determined. PreSAP biosynthesis is directed by a 1.1-kilobase mRNA. Synthesis and postsynthetic processing of preSAP in Xenopus oocytes result in secretion of a protein with mobility similar to native purified SAP when analyzed by sodium dodecyl sulfate gel electrophoresis. The human SAP gene is on chromosome 1, probably closely linked to the gene for C-reactive protein which encodes the related acute phase reactant found in human plasma.

Human serum amyloid A (SAA): biosynthesis and postsynthetic processing of preSAA and structural variants defined by complementary DNA

To study structural variants of human serum amyloid A (SAA), an apoprotein of high-density lipoprotein, complementary DNA clones were isolated from a human liver library with the use of two synthetic oligonucleotide mixtures containing sequences that could code for residues 33-38 and 90-95 of the protein sequence. The SAA-specific cDNA clone (pA1) contains the nucleotide sequence coding for the mature SAA and 10 amino acids of the 18-residue signal peptide. It also includes a 70 nucleotide long 3'-untranslated region and approximately 120 bases of the poly(A) tail. The derived amino acid sequence of pA1 is identical with the alpha form of apoSAA1. A fragment of pA1 containing the conserved (residues 33-38) region of SAA also hybridized with RNA from human acute phase liver and acute phase stimulated, but not unstimulated, mouse and rabbit liver. In contrast, a fragment corresponding to the variable region hybridized to a much greater extent with human than with rabbit or murine RNA. Human acute phase liver SAA mRNA (approximately 600 nucleotides in length) directs synthesis of preSAA (Mr 14 000) in a cell-free translating system. In a Xenopus oocyte translation system preSAA is synthesized and processed to the mature Mr 12 000 product. The complete 18 amino acid signal peptide sequence of preSAA was derived from sequencing cDNA synthesized by "primer extension" from the region of SAA mRNA corresponding to the amino terminus of the mature product. Two other SAA-specific cDNA clones (pA6 and pA10) differed from pA1 in that they lack the internal PstI restriction enzyme site spanning residues 54-56 of pA1.(ABSTRACT TRUNCATED AT 250 WORDS)

Cloning of human prealbumin complementary DNA. Localization of the gene to chromosome 18 and detection of a variant prealbumin allele in a family with familial amyloid polyneuropathy

Prealbumin, a 55,000 Mr protein, is a normal constituent of human serum. In patients with familial amyloid polyneuropathy (FAP), an autosomal dominant disease, variant prealbumin molecules are found in association with systemic amyloid deposits. One variant prealbumin has a methionine for valine substitution at amino acid 30 and has been implicated in the pathogenesis of type 1 FAP. A prealbumin-specific complementary DNA clone has been isolated from an adult human liver library and used in Southern blot hybridization experiments to identify a unique NsiI restriction endonuclease site in the variant allele carried by type 1 FAP patients with the methionine for valine substitution. The complementary DNA clone has been used to analyse a panel of human-mouse and human--hamster somatic cell hybrid DNAs and localize the prealbumin gene to chromosome 18.

Isolation of a complementary DNA clone for the human complement protein C2 and its use in the identification of a restriction fragment length polymorphism

Complementary DNA (cDNA) clones corresponding to the major histocompatibility (MHC) class III antigen, complement protein C2, have been isolated from human liver cDNA libraries with the use of a complex mixture of synthetic oligonucleotides (17 mer) that contains 576 different oligonucleotide sequences. The C2 cDNA were used to identify a DNA restriction enzyme fragment length polymorphism that provides a genetic marker within the MHC that was not detectable at the protein level. An extensive search for genomic polymorphisms using a cDNA clone for another MHC class III gene, factor B, failed to reveal any DNA variants. The genomic variants detected with the C2 cDNA probe provide an additional genetic marker for analysis of MHC-linked diseases.