Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density

OBJECTIVE: Analyze the information contained in homozygous haplotypes detected with high density genotyping. METHODS: We analyze the genotypes of approximately 2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium. RESULTS: We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of R(2), as well as the importance of correcting for small sample variation when evaluating D'. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination. CONCLUSIONS: It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers.     

Fluidity of HIV-1-Specific T-Cell Responses during Acute and Early Subtype C HIV-1 Infection and Associations with Early Disease Progression

Deciphering immune events during early stages of human immunodeficiency virus type 1 (HIV-1) infection is critical for understanding the course of disease. We characterized the hierarchy of HIV-1-specific T-cell gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay responses during acute subtype C infection in 53 individuals and associated temporal patterns of responses with disease progression in the first 12 months. There was a diverse pattern of T-cell recognition across the proteome, with the recognition of Nef being immunodominant as early as 3 weeks postinfection. Over the first 6 months, we found that there was a 23% chance of an increased response to Nef for every week postinfection (P = 0.0024), followed by a nonsignificant increase to Pol (4.6%) and Gag (3.2%). Responses to Env and regulatory proteins appeared to remain stable. Three temporal patterns of HIV-specific T-cell responses could be distinguished: persistent, lost, or new. The proportion of persistent T-cell responses was significantly lower (P = 0.0037) in individuals defined as rapid progressors than in those progressing slowly and who controlled viremia. Almost 90% of lost T-cell responses were coincidental with autologous viral epitope escape. Regression analysis between the time to fixed viral escape and lost T-cell responses (r = 0.61; P = 0.019) showed a mean delay of 14 weeks after viral escape. Collectively, T-cell epitope recognition is not a static event, and temporal patterns of IFN-γ-based responses exist. This is due partly to viral sequence variation but also to the recognition of invariant viral epitopes that leads to waves of persistent T-cell immunity, which appears to associate with slower disease progression in the first year of infection.For more than a decade, there has been a wealth of evidence to show that human immunodeficiency virus (HIV)-specific cytotoxic T-cell (CTL) responses play a role in the control of HIV-1 and simian immunodeficiency virus (SIV) infection. In humans, the first appearance of CTL in primary HIV-1 infection coincides with the decline of peak viremia (7, 27), while depletion of CD8⁺ T cells in SIV infection resulted in elevated viremia (45). Additionally, polymorphisms in HLA class I-restricted CTL responses are associated with differential HIV-1 disease outcomes (25), and the emergence of viral escape within CTL epitopes during acute and chronic SIV or HIV-1 infection demonstrates the effectiveness of CD8⁺ T cells to exert viral selection pressure (21). Dissecting the specificity of HIV-1-specific CD8⁺ T-cell responses that associate with the control of viral replication during acute/early infection is thought to be critical for the design of vaccines and potential immunotherapeutic strategies aimed at stimulating these responses.Preferential targeting of class I-restricted CTL epitopes in Gag during early and chronic HIV-1 infection has been associated with lower viral loads (15, 25, 34, 48, 55), whereas Env- and Nef-specific CD8⁺ T-cell responses have been associated with higher viremia (15, 34, 55). Increasing evidence suggests that patterns of immunodominant HIV-specific CD8⁺ T-cell responses restricted by specific HLA alleles are major determinants of the viral set point (47). In addition, Goonetilleke et al. (17) have provided insight into the rapidity of early escape and the contribution of the first HIV-specific CD8⁺ T-cell responses to the transmitted/founder virus in control of acute viremia. The restriction of CTL epitopes by HLA-B*5801, for example, has also been associated with better viral control (16, 24). However, the temporal nature of epitope-specific responses that associate with viral control has not been explored. Recently, we found no association between the magnitude and breadth of gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay responses at a static 3-month time point with the viral set point at 12 months (22). The unpredictability of early T-cell responses with later viral control could be a result of HIV variability resulting in epitope escape from humoral and T-cell pressure (1, 8). For example, the impact of CTL pressure on shaping viral diversity at a human population level has been observed through HLA imprinting (6, 9, 44), and several studies have shown that certain selected escape mutations can compromise viral fitness (10, 29, 33, 39). Other studies have also demonstrated that the selection of escape variants in chronic HIV-1 and SIV infection can result in the loss of immune control and disease progression (3, 20). Assessing the nature of T-cell responses longitudinally and relating the patterns of contemporaneous viral recognition with viral diversity may represent alternative insights into factors associated with set point and disease progression.As the global AIDS epidemic continues to expand in sub-Saharan Africa, and South Africa in particular, the need to implement a preventive vaccine through the public health sector remains paramount. To date, several prototype antibody and T-cell-based candidate vaccine trials have been completed worldwide (37), and the recent failure of a phase IIb Ad5-Gag-Pol-Nef HIV-1 vaccine trial has emphasized the challenge of producing an effective T-cell-based vaccine against HIV. Data from the recent ALVAC and AIDSVAX (RV144) trials in Thailand have provided modest efficacy of a vaccine regimen in reducing HIV infection (42), and while the immune mechanisms for this are as yet unclear, these findings have created a platform for identifying immune responses that correlate with protection.The identification of the earliest targets of T cells during acute HIV-1 infection would be helpful in understanding the evolution of immunity when a host first encounters the virus and also would provide insight into the host-pathogen interplay when there is a rapidly changing target. We describe some of the earliest T-cell responses that occur during acute subtype C HIV-1 infection, how these change over time and associate with early disease progression, as well as the kinetics of these changes in relation to autologous viral escape.     

Frequency of serovars and antimicrobial resistance in Shigella spp. from Brazil

A total of 296 Shigella spp. were received from State Public Health Laboratories, during the period from 1999 to 2004, by National Reference Laboratory for Cholera and Enteric Diseases (NRLCED)--IOC/Fiocruz, Rio de Janeiro, Brazil. The frequency of Shigella spp. was: S. flexneri (52.7%), S. sonnei (44.2%), S. boydii (2.3%), and S. dysenteriae (0.6%). The most frequent S. flexneri serovars were 2a and 1b. The highest incidence rates of Shigella isolation were observed in the Southeast (39%) and Northeast (34%) regions and the lowest rate in the South (3%) of Brazil. Strains were further analyzed for antimicrobial susceptibility by disk diffusion method as part of a surveillance program on antimicrobial resistance. The highest rates of antimicrobial resistance were to trimethoprim-sulfamethozaxole (90%), tetracycline (88%), ampicillin (56%), and chloramphenicol (35%). The patterns of antimicrobial resistance among Shigella isolates pose a major difficulty in the determination of an appropriate drug for shigellosis treatment. Continuous monitoring of antimicrobial susceptibilities of Shigella spp. through a surveillance system is thus essential for effective therapy and control measures against shigellosis.     

Adiponectin and the mediation of HDL-cholesterol change with improved lifestyle: the Look AHEAD Study

Adipose tissue dysfunction plays a key role in the development of the metabolic abnormalities characteristic of type 2 diabetes (T2DM) and participates actively in lipid metabolism. Adiponectin, found abundantly in circulation and a marker of adipose health, is decreased in obese persons with T2DM. We investigated whether the changes in adiponectin with an intensive lifestyle intervention (ILI) for weight loss could potentially mediate the increase in low HDL-cholesterol (HDL-C) with ILI. Adiponectin and its fractions were determined using an ELISA with selective protease treatment in 1,397 participants from Look AHEAD, a trial examining whether ILI will reduce cardiovascular events in overweight/obese subjects with T2DM when compared with a control arm, diabetes support and education (DSE). Multivariable regression and mediational analyses were performed for adiponectin and its high-molecular-weight (HMW) and non-HMW fractions. ILI increased baseline HDL-C by 9.7% and adiponectin by 11.9%; changes with DSE were 1.3% and 0.2%, respectively (P < 0.0001). In a model including changes in weight, fitness, triglycerides, and glucose control and that adjusted for demographics and medical history, adiponectin changes remained significantly associated with HDL-C change. Data supported the contribution of changes in both HMW- and non-HMW-adiponectin to the improvement in HDL-C with ILI     

Nephelometry determined serum immunoglobulin isotypes in healthy Thai children aged 2-15 years

Knowledge of what constitute normal serum immunoglobulin (Ig) concentrations are important for the diagnosis of immunologic disorders. Data on normal Ig evaluated by nephelometry are limited in healthy Asian children, none being available for Thai children. One hundred and forty-eight healthy Thai children aged 2-15 years were tested for serum immunoglobulins G, A, M, G1, G2, G3, and G4 (Ig G, A, M, G1, G2, G3, and G4) by nephelometry. Sixty-three percent were girls of median interquartile range age 6.9 (4.8-9.7) years. The geometric means for each Ig were summarized and categorized by age. Statistical analyses were used to compare Igs between sexes and age groups, and to compare IgG in this study with data from other published studies. The average ratios of IgG subclasses/IgG for Ig G1:2:3:4 were 66:22:5:7%. IgG, IgA, IgG2, and IgG3 concentrations showed a gradual increase with increasing age. There were no significant sex differences for any immunoglobulin isotype (P= 0.971). Our mean IgG concentration was lower than that measured by the radial diffusion method in healthy Thai children (P < 0.05). In all age groups, the mean IgG concentration in our study was significantly higher than that reported in Turkish and USA children, evaluated by the nephelometric and radial diffusion techniques, respectively (both P < 0.001). This study provides information about normal Ig concentrations measured by nephelometry in healthy Asian children and illustrates the importance of ascertaining normal Ig values for age- and ethnic-matched controls using the same assay to diagnose immunologic disorders correctly.     

The effect of maternal multiple micronutrient supplementation on cognition and mood during pregnancy and postpartum in Indonesia: a randomized trial

Maternal caregiving capacity, which is affected in part by cognition and mood, is crucial for the health of mothers and infants. Few interventions aim to improve maternal and infant health through improving such capacity. Multiple micronutrient (MMN) supplementation may improve maternal cognition and mood, since micronutrients are essential for brain function. We assessed mothers who participated in the Supplementation with Multiple Micronutrients Intervention Trial (SUMMIT), a double-blind cluster-randomized trial in Indonesia comparing MMN supplementation to iron and folic acid (IFA) during pregnancy and until three months postpartum. We adapted a set of well-studied tests of cognition, motor dexterity, and mood to the local context and administered them to a random sample of 640 SUMMIT participants after an average of 25 weeks (SD = 9) of supplementation. Analysis was by intention to treat. Controlling for maternal age, education, and socio-economic status, MMN resulted in a benefit of 0.12 SD on overall cognition, compared to IFA (95%CI 0.03-0.22, p = .010), and a benefit of 0.18 SD on reading efficiency (95%CI 0.02-0.35, p = .031). Both effects were found particularly in anemic (hemoglobin<110 g/L; overall cognition: B = 0.20, 0.00-0.41, p = .055; reading: B = 0.40, 0.02-0.77, p = .039) and undernourished (mid-upper arm circumference<23.5 cm; overall cognition: B = 0.33, 0.07-0.59, p = .020; reading: B = 0.65, 0.19-1.12, p = .007) mothers. The benefit of MMN on overall cognition was equivalent to the benefit of one year of education for all mothers, to two years of education for anemic mothers, and to three years of education for undernourished mothers. No effects were found on maternal motor dexterity or mood. This is the first study demonstrating an improvement in maternal cognition with MMN supplementation. This improvement may increase the quality of care mothers provide for their infants, potentially partly mediating effects of maternal MMN supplementation on infant health and survival. The study is registered as an International Standard Randomized Controlled Trial, number ISRCTN34151616. http://www.controlled-trials.com/ISRCTN34151616.