Epistatic Mechanisms Research Articles

Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape.

In this study, we performed a computational study of binding mechanisms for the SARS-CoV-2 spike Omicron XBB lineages with the host cell receptor ACE2 and a panel of diverse class one antibodies. The central objective of this investigation was to examine the molecular factors underlying epistatic couplings among convergent evolution hotspots that enable optimal balancing of ACE2 binding and antibody evasion for Omicron variants BA.1, BA2, BA.3, BA.4/BA.5, BQ.1.1, XBB.1, XBB.1.5, and XBB.1.5 + L455F/F456L. By combining evolutionary analysis, molecular dynamics simulations, and ensemble-based mutational scanning of spike protein residues in complexes with ACE2, we identified structural stability and binding affinity hotspots that are consistent with the results of biochemical studies. In agreement with the results of deep mutational scanning experiments, our quantitative analysis correctly reproduced strong and variant-specific epistatic effects in the XBB.1.5 and BA.2 variants. It was shown that Y453W and F456L mutations can enhance ACE2 binding when coupled with Q493 in XBB.1.5, while these mutations become destabilized when coupled with the R493 position in the BA.2 variant. The results provided a molecular rationale of the epistatic mechanism in Omicron variants, showing a central role of the Q493/R493 hotspot in modulating epistatic couplings between convergent mutational sites L455F and F456L in XBB lineages. The results of mutational scanning and binding analysis of the Omicron XBB spike variants with ACE2 receptors and a panel of class one antibodies provide a quantitative rationale for the experimental evidence that epistatic interactions of the physically proximal binding hotspots Y501, R498, Q493, L455F, and F456L can determine strong ACE2 binding, while convergent mutational sites F456L and F486P are instrumental in mediating broad antibody resistance. The study supports a mechanism in which the impact on ACE2 binding affinity is mediated through a small group of universal binding hotspots, while the effect of immune evasion could be more variant-dependent and modulated by convergent mutational sites in the conformationally adaptable spike regions.

Linkage and association mapping in multi-parental populations reveal the genetic basis of carotenoid variation in maize kernels.

Carotenoids are indispensable to plants and critical components of the human diet. The carotenoid metabolic pathway is conserved across plant species, but our understanding of the genetic basis of carotenoid variation remains limited for the seeds of most cereal crops. To address this issue, we systematically performed linkage and association mapping for eight carotenoid traits using six recombinant inbred line (RIL) populations. Single linkage mapping (SLM) and joint linkage mapping (JLM) identified 77 unique additive QTLs and 104 pairs of epistatic QTLs. Among these QTLs, we identified 22 overlapping hotspots of additive and epistatic loci, highlighting the important contributions of some QTLs to carotenoid levels through additive or epistatic mechanisms. A genome-wide association study based on all RILs detected 244 candidate genes significantly associated with carotenoid traits, 23 of which were annotated as carotenoid pathway genes. Effect comparisons suggested that a small number of loci linked to pathway genes have substantial effects on carotenoid variation in our tested populations, but many loci not associated with pathway genes also make important contributions to carotenoid variation. We identified ZmPTOX as the causal gene for a QTL hotspot (Q10/JLM10/GWAS019); this gene encodes a putative plastid terminal oxidase that produces plastoquinone-9 used by two enzymes in the carotenoid pathway. Natural variants in the promoter and second exon of ZmPTOX were found to alter carotenoid levels. This comprehensive assessment of the genetic mechanisms underlying carotenoid variation establishes a foundation for rewiring carotenoid metabolism and accumulation for efficient carotenoid biofortification.

Unveiling the Genetic Basis Underlying Rice Anther Culturability via Segregation Distortion Analysis in Doubled Haploid Population.

Anther culture (AC) is a valuable technique in rice breeding. However, the genetic mechanisms underlying anther culturability remain elusive, which has hindered its widespread adoption in rice breeding programs. During AC, microspores carrying favorable alleles for AC are selectively regenerated, leading to segregation distortion (SD) of chromosomal regions linked to these alleles in the doubled haploid (DH) population. Using the AC method, a DH population was generated from the japonica hybrid rice Shenyou 26. A genetic map consisting of 470 SNPs was constructed using this DH population, and SD analysis was performed at both the single- and two-locus levels to dissect the genetic basis underlying anther culturability. Five segregation distortion loci (SDLs) potentially linked to anther culturability were identified. Among these, SDL5 exhibited an overrepresentation of alleles from the female parent, while SDL1.1, SDL1.2, SDL2, and SDL7 displayed an overrepresentation of alleles from the male parent. Furthermore, six pairs of epistatic interactions (EPIs) that influenced two-locus SDs in the DH population were discovered. A cluster of genetic loci, associated with EPI-1, EPI-3, EPI-4, and EPI-5, overlapped with SDL1.1, indicating that the SDL1.1 locus may play a role in regulating anther culturability via both additive and epistatic mechanisms. These findings provide valuable insights into the genetic control of anther culturability in rice and lay the foundation for future research focused on identifying the causal genes associated with anther culturability.

Emergence of Canonical and Noncanonical Genomic Variants following In Vitro Exposure of Clinical Mycobacterium tuberculosis Strains to Bedaquiline or Clofazimine.

In Mycobacterium tuberculosis, bedaquiline and clofazimine resistance occurs primarily through Rv0678 variants, a gene encoding a repressor protein that regulates mmpS5/mmpL5 efflux pump gene expression. Despite the shared effect of both drugs on efflux, little else is known about other pathways affected. We hypothesized that in vitro generation of bedaquiline- or clofazimine-resistant mutants could provide insight into additional mechanisms of action. We performed whole-genome sequencing and determined phenotypic MICs for both drugs on progenitor and mutant progenies. Mutants were induced through serial passage on increasing concentrations of bedaquiline or clofazimine. Rv0678 variants were identified in both clofazimine- and bedaquiline-resistant mutants, with concurrent atpE SNPs occurring in the latter. Of concern was the acquisition of variants in the F420 biosynthesis pathway in clofazimine-resistant mutants obtained from either a fully susceptible (fbiD: del555GCT) or rifampicin mono-resistant (fbiA: 283delTG and T862C) progenitor. The acquisition of these variants possibly implicates a shared pathway between clofazimine and nitroimidazoles. Pathways associated with drug tolerance and persistence, F420 biosynthesis, glycerol uptake and metabolism, efflux, and NADH homeostasis appear to be affected following exposure to these drugs. Shared genes affected by both drugs include Rv0678, glpK, nuoG, and uvrD1. Genes with variants in the bedaquiline resistant mutants included atpE, fadE28, truA, mmpL5, glnH, and pks8, while clofazimine-resistant mutants displayed ppsD, fbiA, fbiD, mutT3, fadE18, Rv0988, and Rv2082 variants. These results show the importance of epistatic mechanisms as a means of responding to drug pressure and highlight the complexity of resistance acquisition in M. tuberculosis.

The effect of the LPA variant P.THR3888PRO on lipoprotein(a) and coronary artery disease is modified by the LPA KIV-2 splice site variant 4925g>A

Background and Aims : Lipoprotein(a) [Lp(a)] plasma concentrations are mainly regulated by the LPA gene. Besides the KIV-2 repeat (a complex copy number variation), multiple SNPs pronouncedly modify Lp(a) levels (e.g. the recently described KIV-2 variant 4925G>A). However, little is known about non-linear and/or epistatic mechanisms and SNP interactions. Thus, we investigated the impact of the interaction between the largely investigated LPA variant p.Thr3888Pro (rs41272110) and the KIV-2 variant 4925G>A on Lp(a) concentration and CAD risk.

Mastering the control of the Rho transcription factor for biotechnological applications

The present review represents an update on the fundamental role played by the Rho factor, which facilitates the process of Rho-dependent transcription termination in the prokaryotic world; it also provides a summary of relevant mutations in the Rho factor and the insights they provide into the functions carried out by this protein. Furthermore, a section is dedicated to the putative future use of Rho (the 'taming' of Rho) to facilitate biotechnological processes and adapt them to different technological contexts. Novel bacterial strains can be designed, containing mutations in the rho gene, that are better suited for different biotechnological applications. This process can obtain novel microbial strains that are adapted to lower temperatures of fermentation, shorter production times, exhibit better nutrient utilization, or display other traits that are beneficial in productive Biotechnology. Additional important issues reviewed here include epistasis, the design of TATA boxes, the role of small RNAs, and the manipulation of clathrin-mediated endocytosis, by some pathogenic bacteria, to invade eukaryotic cells. KEY POINTS: • It is postulated that controlling the action of the prokaryotic Rho factor could generate major biotechnological improvements, such as an increase in bacterial productivity or a reduction of the microbial-specific growth rate. • The review also evaluates the putative impact of epistatic mechanisms on Biotechnology, both as possible responsible for unexpected failures in gene cloning and more important for the genesis of new strains for biotechnological applications • The use of clathrin-coated vesicles by intracellular bacterial microorganisms is included too and proposed as a putative delivery mechanism, for drugs and vaccines.

Unconditional and conditional analysis of epistasis between tillering QTLs based on single segment substitution lines in rice

Epistasis plays an important role in manipulating rice tiller number, but epistatic mechanism still remains a challenge. Here we showed the process of epistatic analysis between tillering QTLs. A half diallel mating scheme was conducted based on 6 single segment substitution lines and 9 dual segment pyramiding lines to allow the analysis of 4 epistatic components. Additive-additive, additive-dominance, dominance-additive, and dominance-dominance epistatic effects were estimated at 9 stages of development via unconditional QTL analysis simultaneously. Unconditional QTL effect (QTL cumulative effect before a certain stage) was then divided into several conditional QTL components (QTL net effect in a certain time interval). The results indicated that epistatic interaction was prevalent, all QTL pairs harboring epistasis and one QTL always interacting with other QTLs in various component ways. Epistatic effects were dynamic, occurring mostly within 14d and 21–35d after transplant and exhibited mainly negative effects. The genetic and developmental mechanism on several tillering QTLs was further realized and perhaps was useful for molecular pyramiding breeding and heterosis utilization for improving plant architecture.

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.

To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.

Altered cytokine profile, pain sensitivity, and stress responsivity in mice with co-disruption of the developmental genes Neuregulin-1 × DISC1

The complex genetic origins of many human disorders suggest that epistatic (gene×gene) interactions may contribute to a significant proportion of their heritability estimates and phenotypic heterogeneity. Simultaneous disruption of the developmental genes and schizophrenia risk factors Neuregulin-1 (NRG1) and Disrupted-in-schizophrenia 1 (DISC1) in mice has been shown to produce disease-relevant and domain-specific phenotypic profiles different from that observed following disruption of either gene alone. In the current study, anxiety and stress responsivity phenotypes in male and female mutant mice with simultaneous disruption of DISC1 and NRG1 were examined. NRG1×DISC1 mutant mice were generated and adult mice from each genotype were assessed for pain sensitivity (hot plate and tail flick tests), anxiety (light-dark box), and stress-induced hypothermia. Serum samples were assayed to measure circulating levels of pro-inflammatory cytokines. Mice with the NRG1 mutation, irrespective of DISC1 mutation, spent significantly more time in the light chamber, displayed increased core body temperature following acute stress, and decreased pain sensitivity. Basal serum levels of cytokines IL8, IL1β and IL10 were decreased in NRG1 mutants. Mutation of DISC1, in the absence of epistatic interaction with NRG1, was associated with increased serum levels of IL1β. Epistatic effects were evident for IL6, IL12 and TNFα. NRG1 mutation alters stress and pain responsivity, anxiety, and is associated with changes in basal cytokine levels. Epistasis resulting from synergistic NRG1 and DISC1 gene mutations altered pro-inflammatory cytokine levels relative to the effects of each of these genes individually, highlighting the importance of epistatic mechanisms in immune-related pathology.

A family-based, genome-wide association study of young-onset breast cancer: inherited variants and maternally mediated effects.

Young-onset breast cancer shows certain phenotypic and etiologic differences from older-onset breast cancer and may be influenced by some distinct genetic variants. Few genetic studies of breast cancer have targeted young women and no studies have examined whether maternal variants influence disease in their adult daughters through prenatal effects. We conducted a family-based, genome-wide association study of young-onset breast cancer (age at diagnosis <50 years). A total of 602 188 single-nucleotide polymorphisms (SNPs) were genotyped for 1279 non-Hispanic white cases and their parents or sisters. We used likelihood-based log-linear models to test for transmission asymmetry within families and for maternally mediated genetic effects. Three autosomal SNPs (rs28373882, P=2.8 × 10(-7); rs879162, P=9.2 × 10(-7); rs12606061, P=9.1 × 10(-7)) were associated with risk of young-onset breast cancer at a false-discovery rate below 0.20. None of these loci has been previously linked with young-onset or overall breast cancer risk, and their functional roles are unknown. There was no evidence of maternally mediated, X-linked, or mitochondrial genetic effects, and no notable findings within cancer subcategories defined by menopausal status, estrogen receptor status, or by tumor invasiveness. Further investigations are needed to explore other potential genetic, epigenetic, or epistatic mechanisms and to confirm the association between these three novel loci and young-onset breast cancer.

Abstract 570: Deficiency of Inhibitory Fcgamma Receptor II Does Not Exacerbate Atherosclerosis

Objective: Functionally, Fcgamma receptors (FcgRs) can be classified as activating (FcgRI, III, and IV) and inhibitory (FcgRII, CD32b) receptors. We have reported that deletion of activating FcgRs in apoE knockout mice decreased atherosclerosis. In this report we investigated the hypothesis that the deficiency of inhibitory CD32b exacerbates atherosclerosis in a hypercholesterolemic mouse model. Approach and Results: ApoE-CD32b double knockout mice congenic to the C57BL/6 (apoE-CD32b B6 -/-) were generated and atherosclerotic lesions were assessed. Contrary to our hypothesis, arterial lesions were significantly decreased in chow or high fat diet fed apoE-CD32b B6 -/- male and female mice, relative to apoE-/- mice . Bone marrow chimera approach using apoE-/- mice transplanted with apoE-CD32b B6 -/- marrow also showed significantly reduced arterial lesions. ApoE-CD32b B6 -/- mice had increased levels of IL-10 and TGF-b by CD4+ T cells, while IFN-g and IL-17 was decreased. As our findings conflict with a previous report using apoE-CD32b 129/6 -/- mixed background, we investigated if strain differences contributed to the anti-inflammatory response. Macrophages from mixed apoE-CD32b 129/B6 -/- mice showed more IL-1b, IL-6 and MCP-1 in response to immune complexes, while congenic CD32b B6 -/- mice showed more IL-10 and significantly reduced IL-1b. Interestingly expression of lupus-associated slam genes, located in close proximity to cd32b in mouse chromosome 1, is upregulated only in mixed CD32b 129/B6 -/- mice. Conclusions: Our findings demonstrate a detrimental role for CD32b signaling in atherosclerosis and the contribution of anti-inflammatory cytokine responses in the attenuated lesions observed in apoE-CD32b B6 -/- mice. As 129/sv genome derived lupus associated genes have been implicated in lupus phenotype in CD32b 129/B6 -/- mice our findings suggest possible epistatic mechanism contributing to the decreased lesions.

Reduced Atherosclerosis in apoE-inhibitory FcγRIIb-Deficient Mice Is Associated With Increased Anti-Inflammatory Responses by T Cells and Macrophages.

Fcγ receptors (FcγRs) are classified as activating (FcγRI, III, and IV) and inhibitory (FcγRII) receptors. We have reported that deletion of activating FcγRs in apolipoprotein E (apoE) single knockout mice attenuated atherosclerosis. In this report, we investigated the hypothesis that deficiency of inhibitory FcγRIIb exacerbates atherosclerosis. ApoE-FcγRIIb double knockout mice, congenic to the C57BL/6 (apoE-FcγRIIbB6 (-/-)), were generated and atherosclerotic lesions were assessed. In contrary to our hypothesis, when compared with apoE single knockout mice, arterial lesions were significantly decreased in apoE-FcγRIIbB6 (-/-) male and female mice fed chow or high-fat diets. Chimeric mice generated by transplanting apoE-FcγRIIbB6 (-/-) marrow into apoE single knockout mice also developed reduced lesions. CD4(+) T cells from apoE-FcγRIIbB6 (-/-) mice produced higher levels of interleukin-10 and transforming growth factor-β than their apoE single knockout counterparts. As our findings conflict with a previous report using apoE-FcγRIIb129/B6 (-/-) mice on a mixed genetic background, we investigated whether strain differences contributed to the anti-inflammatory response. Macrophages from FcγRIIb129/B6 (-/-) mice on a mixed genetic background produced more interleukin-1β and MCP-1 (monocyte chemoattractant protein-1) in response to immune complexes, whereas congenic FcγRIIbB6 (-/-) mice generated more interleukin-10 and significantly less interleukin-1β. Interestingly, the expression of lupus-associated slam genes, located in proximity to fcgr2b in mouse chromosome 1, is upregulated only in mixed FcγRIIb129/B6 (-/-) mice. Our findings demonstrate a detrimental role for FcγRIIb signaling in atherosclerosis and the contribution of anti-inflammatory cytokine responses in the attenuated lesions observed in apoE-FcγRIIbB6 (-/-) mice. As 129/sv genome-derived lupus-associated genes have been implicated in lupus phenotype in FcγRIIb129/B6 (-/-) mice, our findings suggest possible epistatic mechanism contributing to the decreased lesions.

Letter to the Editor regarding: Epistatic effects in pathophysiology of asthma and the “missing heritability” of this disease

We are probably only at the beginning of the road leading to explanation of how some genetic variants can cause chronic disease. It seemed that the so-called “genome-wide association studies” (GWAS) would clarify this issue. Takahiro Yoshikawa et al., however, at the outset of their recent paper wrote that “most of these studies have only managed to explain a small additional percentage of hereditability estimates” [1]. These researchers are convinced that the mechanisms of genetic conditioning of chronic diseases will be explained more effectively by so-called “epistatic analyses” [1]. They remember that, contrary to Mendel’s classical law of heredity in which each gene locus exerts an independent effect on a single phenotype, it has been proven that 2 different gene loci can affect the same phenotype and that the action between 2 loci is classically defined as ‘epistasis’ [1]. It turns out that investigations of the genetic determinants of various chronic diseases (e.g., atherosclerosis, coronary heart disease [CAD], or Parkinson’s disease) encounter similar phenomena [2,3]. This means that the consideration of individual genetic variants, in particular the so-called “single-nucleotide polymorphisms” (SNPs) using the simple additive model of their impacts, does not explain the genetic conditioning of these diseases. Marian drew critical conclusions from all previous genome-wide association studies related to atherosclerosis and CAD [4]. He stressed that GWA studies have successfully led to identification of over 100 different loci for susceptibility to coronary atherosclerosis, yet the clinical outcomes of GAWS studies are modest [4]. He justified his opinion by citing the fact that the identified SNPs account for a relatively small fraction of the heritability of atherosclerosis [4]. In his next paper he raised the question of „missing heritability” and stated that gene-gene (epistasis) and gene-environmental (G-En) interactions might explain only a fraction of the heritability of complex traits [5]. In fact, epistatic analyses is just one of several possible approaches that try to explain the so-called “missing heritability’ [2,6]. The “missing heritability” phenomenon can be defined as the inability of individual genes to account for most heritability of diseases. Most variants of genes identified so far that are specific for a chronic disease often confer relatively small increments of risk and familial clustering [6]. In addition to the epistatic influences and gene-environmental interactions, the “missing heritability” is explained by transgenerational epigenetic changes, regulated in part by microRNAs [2,5]. Eichler et al. hypothesized that a plausible explanation of the “missing heritability” might be the presence of uncommon and rare variants in the genome that have not been discovered by GWAS, but that might have a great effect on the risk of development of chronic diseases [2]. Surprisingly, Eichler et al. included possible deletions, duplications, and inversions of polynucleotides among these possible uncommon variants [2]. They wrote that these large variants are individually rare but collectively common in the human population [2]. They emphasized that multiple genetic variations interact through different layers of genomic complexity and that the modern definition of the epistatic mechanisms recognizes the complexity of gene networks and biochemical systems [2]. This led to the idea that “a significant proportion of the missing heritability is not due to single common variants, nor single rare variants, “but rather to rare combinations of common variants”. Eichler et al. stated that solving a part of the missing heritability problem will require the application of new “statistical and computational methods” that will detect patterns of epistasis across the genome, implemented in a complex biological system [2]. Yoshikawa et al. concluded that: “… a genetic approach using quantitatively measurable parameters is well suited for the identification of risk factors in individuals who are likely to have disease prior to the complete development of significant symptoms and signs. Furthermore, it seems worthy to combine this style of genetic approach with prospective research to follow individuals at risk for disease…”. This is an important and significant statement. Asthma is a clinical condition that is diagnosed or suspected in the course of occurrence of symptoms, which does not allow unequivocal diagnosis of this disease. Such states are often referred to as spastic or obstructive bronchitis, chronic obstructive bronchitis, or bronchitis with an obstructive component. It seems that the precise recognition of the specific genetic profile of these patients (the status of expression of genes recognized as pathogenic, as well as their epistatic interactions) will improve the possibilities of treatment and prevention. It must be realized, however, that such a practical diagnostic approach must be continually modified in light of the results of future trials explaning the “missing heritability”.

Transcriptome Analysis of Epigenetically Modulated Genome Indicates Signature Genes in Manifestation of Type 1 Diabetes and Its Prevention in NOD Mice

Classic genetic studies implicated several genes including immune response genes in the risk of developing type 1 diabetes in humans. However, recent evidence including discordant diabetes incidence among monozygotic twins suggested a role for epigenetics in disease manifestation. NOD mice spontaneously develop type 1 diabetes like humans and serve as an excellent model system to study the mechanisms of type 1 diabetes as well as the efficacy of maneuvers to manipulate the disease. Using this preclinical model, we have recently demonstrated that pharmacological inhibition of histone deacetylases can lead to histone hyperacetylation, selective up-regulation of interferon-γ and its transactivator Tbx21/Tbet, and amelioration of autoimmune diabetes. In the current study, we show that chromatin remodeling can render splenocytes incapable of transferring diabetes into immunodeficient NOD.scid mice. To elucidate the underlying mechanisms of drug-mediated protection against type 1 diabetes, we performed global gene expression profiling of splenocytes using high throughput microarray technology. This unbiased transcriptome analysis unraveled the exaggerated expression of a novel set of closely related inflammatory genes in splenocytes of acutely diabetic mice and their repression in mice cured of diabetes by chromatin remodeling. Analysis of gene expression by qRT-PCR using RNA derived from spleens and pancreata of cured mice validated the suppression of most of these genes, indicating an inverse correlation between the high levels of these inflammatory genes and protection against diabetes in NOD mice. In addition, higher-level expression of genes involved in insulin sensitivity, erythropoiesis, hemangioblast generation, and cellular redox control was evident in spleens of cured mice, indicating their possible contribution to protection against type 1 diabetes. Taken together, these results are consistent with the involvement of epistatic mechanisms in the manifestation of autoimmune diabetes and further indicate the utility of chromatin remodeling in curing this complex autoimmune disorder.

Congenic dissection of a major QTL for methamphetamine sensitivity implicates epistasis

We previously used the C57BL/6J (B6) × A/J mouse chromosome substitution strain (CSS) panel to identify a major quantitative trait locus (QTL) on chromosome 11 influencing methamphetamine (MA)-induced locomotor activity. We then made an F(2) cross between CSS-11 and B6 and narrowed the locus (Bayes credible interval: 79-109 Mb) which was inherited dominantly and accounted for 14% of the phenotypic variance in the CSS panel. In the present study, we created congenic and subcongenic lines possessing heterozygous portions of this QTL to narrow the interval. We identified one line (84-96 Mb) that recapitulated the QTL, thus narrowing the region to 12 Mb. This interval also produced a small decrease in locomotor activity following prior saline treatment. When we generated subcongenic lines spanning the entire 12-Mb region, the phenotypic difference in MA sensitivity abruptly disappeared, suggesting an epistatic mechanism. We also evaluated the rewarding properties of MA (2 mg/kg, i.p.) in the 84- to 96-Mb congenic line using the conditioned place preference (CPP) test. We replicated the locomotor difference in the MA-paired CPP chamber yet observed no effect of genotype on MA-CPP, supporting the specificity of this QTL for MA-induced locomotor activity under these conditions. Lastly, to aid in prioritizing candidate genes responsible for this QTL, we used the Affymetrix GeneChip(®) Mouse Gene 1.0ST Array to identify genes containing expression QTLs (eQTL) in the striatum of drug-naÏve, congenic mice. These findings highlight the difficulty of using congenic lines to fine map QTLs and illustrate how epistasis may thwart such efforts.

Novelty seekers and impulsive subjects are low in morningness

The bipolar dimension of morningness–eveningness refers to the preferred times of day for achieving various activities (i.e. the phase of the circadian clock). It is validated from a biological point of view, associated with at least one gene and heritable through an epistatic mechanism. It has been used as a proxy to study the relationships between the circadian system, personality and psychopathology: there is a correlation between the evening orientation and depression, extraversion and, probably, impulsivity. Furthermore, there is a possible relationship with temperament in children as theorized by Thomas and Chess. In this paper, we expanded on the hypothesis that impulsive subjects are low in morningness by performing a factor analysis of the Composite Scale of Morningness, Cloninger’s temperament and character inventory, and Spielberger’s trait anxiety inventory in a sample of 129 males. The results can probably be extended to women. Morningness is negatively correlated with novelty seeking (which includes an impulsivity facet), positively correlated with persistence, and independent of character dimensions and trait anxiety. Future research may focus in the involvement of the circadian system in these personality dimensions and facets, and the benefits of adding chronotherapic manipulations in the treatment of the personality disorders.

Acute clinical events in 299 homozygous sickle cell patients living in France

A subset of 299 patients with homozygous sickle cell anaemia, enrolled in the cohort of the French Study Group on sickle cell disease (SCD), was investigated in this study. The majority of patients were children (mean age 10.1 +/- 5.8 yr) of first generation immigrants from Western and Central Africa, the others originated from the French West Indies (20.2%). We report the frequency of the main clinical events (mean follow-up 4.2 +/- 2.2 yr). The prevalence of meningitis-septicaemia and osteomyelitis was, respectively, 11.4% and 12% acute chest syndrome was observed in 134 patients (44.8%). Twenty patients (6.7%) developed stroke with peak prevalence at 10-15 yr of age. One hundred and seventy-two patients (58%) suffered from one or more painful sickle cell crises, while the others (42.5%) never suffered from pain. The overall frequency of acute anaemic episodes was 50.5%, (acute aplastic anaemia 46%; acute splenic sequestration 26%). A group of 27 patients were asymptomatic (follow-up > 3 yr). Epistatic mechanisms influencing SCD were studied. Coinherited alpha-thalassemia strongly reduced the risk of stroke (p <0.001) and increased that of painful crises (p < 0.02). There was a low prevalence of Senegal and Bantu (CAR) betas-chromosomes in patients with meningitis (p <0.04) and osteomyelitis (p < 0.03). Prevalence of Senegal betas-chromosomes was lower in the asymptomatic group of 27 patients (p < 0.02). The patients come from a population of unmixed immigrants in whom the beta-globin gene haplotype strongly reflects the geographic origin and identifies subgroups with a homogenous genetic background. Thus the observed effects might result more from differences in as yet unidentified determinants in the genetic background than from the direct linkage with differences in the beta-globin gene locus.

A TEST OF THE ROLE OF EPISTASIS IN DIVERGENCE UNDER UNIFORM SELECTION.

Five populations of Drosophila melanogaster have previously been shown to be replicably different in their responses to artificial selection for knockdown resistance to ethanol fumes (Cohan and Hoffmann, 1986). The present study tests whether this divergence could be attributed to the epistatic mechanism assumed by Wright's shifting-balance model of evolution, in which alleles favored in the genetic background of one population are not favored in that of another. If this were the mechanism of divergence, crosses between selected lines from different populations would be expected to yield an epistatic loss of the selected phenotype. However, all such crosses showed a good fit to an additive model with dominance. Divergence by an epistatic mechanism may also be associated with epistatic variance within populations, but no evidence for such epistasis was found. The populations therefore appear to have responded in different ways to selection not because of epistasis but because knockdown-resistance alleles that were common in some populations were absent (or at least less common) in others.