Open Access

Background and methods: Idiopathic autism, suspected to be caused by exposure of genetically susceptible individuals to unknown environmental triggers, has increased dramatically in the past 25 years. The objectives of our study were to determine, using a linear regression model, whether the county prevalence of autism in the Pacific Northwest of the United States was associated with the source of drinking water for that county and whether this relationship was dependent on the level of environmental pollutants and meteorological factors in the county. Results: We found the previously reported relationship between precipitation and autism in a county was dependent on the amount of drinking water derived from surface sources in the county. We also found a positive association between the EPA’s risk of neurological disease and autism, but this relationship was only present in warm areas. Conclusions: Our study provides evidence for the hypothesis that environmental factors are associated with autism and that meteorological factors play a role in this relationship

HIV Controllers Exhibit Enhanced Frequencies of Major Histocompatibility Complex Class II Tetramer+ Gag-Specific CD4+ T Cells in Chronic Clade C HIV-1 Infection

Immune control of viral infections is heavily dependent on helper CD4(+) T cell function. However, the understanding of the contribution of HIV-specific CD4(+) T cell responses to immune protection against HIV-1, particularly in clade C infection, remains incomplete. Recently, major histocompatibility complex (MHC) class II tetramers have emerged as a powerful tool for interrogating antigen-specific CD4(+) T cells without relying on effector functions. Here, we defined the MHC class II alleles for immunodominant Gag CD4(+) T cell epitopes in clade C virus infection, constructed MHC class II tetramers, and then used these to define the magnitude, function, and relation to the viral load of HIV-specific CD4(+) T cell responses in a cohort of untreated HIV clade C-infected persons. We observed significantly higher frequencies of MHC class II tetramer-positive CD4(+) T cells in HIV controllers than progressors (P = 0.0001), and these expanded Gag-specific CD4(+) T cells in HIV controllers showed higher levels of expression of the cytolytic proteins granzymes A and B. Importantly, targeting of the immunodominant Gag41 peptide in the context of HLA class II DRB1*1101 was associated with HIV control (r = −0.5, P = 0.02). These data identify an association between HIV-specific CD4(+) T cell targeting of immunodominant Gag epitopes and immune control, particularly the contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infection. Furthermore, these results highlight the advantage of the use of class II tetramers in evaluating HIV-specific CD4(+) T cell responses in natural infections. IMPORTANCE Increasing evidence suggests that virus-specific CD4(+) T cells contribute to the immune-mediated control of clade B HIV-1 infection, yet there remains a relative paucity of data regarding the role of HIV-specific CD4(+) T cells in shaping adaptive immune responses in individuals infected with clade C, which is responsible for the majority of HIV infections worldwide. Understanding the contribution of HIV-specific CD4(+) T cell responses in clade C infection is particularly important for developing vaccines that would be efficacious in sub-Saharan Africa, where clade C infection is dominant. Here, we employed MHC class II tetramers designed to immunodominant Gag epitopes and used them to characterize CD4(+) T cell responses in HIV-1 clade C infection. Our results demonstrate an association between the frequency of HIV-specific CD4(+) T cell responses targeting an immunodominant DRB1*11-Gag41 complex and HIV control, highlighting the important contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infections

A case study of time-series regression modeling: Risk factors for pond-level mortality of farmed grass carp (Ctenopharyngodon idella) on a southern Chinese farm

Limited research has been done using multivariable statistical methods to assess factors associated with fish mortality in warm-water finfish aquaculture in China. We carried out a case study to test the hypothesized association between pond-level daily mortality of farmed grass carp and predisposing environmental and husbandry factors. Based on logbook data from a single farm in Guangdong province (China) in 2013, two-stage time-series regression (TSR) analyses were conducted to estimate the lagged effect of these predisposing factors on grass carp mortality. Factors assessed included temperature fluctuations, movement of fish into and out of ponds, and 3 types of treatments (antibiotics-antiparasitics, traditional Chinese medicine-probiotics, and chemicals to improve water quality). First, coefficients were estimated using a generalized linear negative-binomial model for each pond, and these coefficient estimates were combined using meta-analytic techniques. Sensitivity analyses were done to compare effects of changes in the 3 modeling components: distributional forms, number of spline knots, and types of autocorrelation terms. Model results in the case study indicated 2 risk factors might be associated with increased mortality of grass carp: (1) movements-in of new fish during the previous 14 days; and (2) increasing water temperature during the previous 7 days. Sensitivity analyses indicated good consistency of the estimates with different modeling components. Our findings highlight the utility of assessing daily farm records using TSR to develop hypotheses about potential risk factors for grass carp mortality in China

Tool for predicting Caligus rogercresseyi abundance on salt water salmon farms in Chile

Caligus rogercresseyi is a host-dependent parasite that affects rainbow trout and Atlantic salmon in Chile. Numbers of sea lice on fish increase over time at relatively predictable rates when the environment is conducive to the parasite's survival and fish are not undergoing treatment. We developed a tool for the salmon industry in Chile that predicts the abundance of adult sea lice over time on farms that are relatively isolated. We used data on sea louse abundance collected through the SalmonChile INTESAL sea lice monitoring program to create series of weekly lice counts between lice treatment events on isolated farms. We defined isolated farms as those with no known neighbors within a 10 km seaway distance and no more than two neighbors within a 20 km seaway distance. We defined the time between sea lice treatments as starting the week immediately post treatment and ending the week before a subsequent treatment. Our final dataset of isolated farms consisted of 65 series from 32 farms, between 2009 and 2015. Given an observed abundance at time t = 0, we built a model that predicted 8 consecutive weekly sea louse abundance levels, based on the preceding week's lice prediction. We calibrated the parameters in our model on a randomly selected subset of training data, choosing the parameter combinations that minimized the absolute difference between the predicted and observed sea louse abundance values. We validated the parameters on the remaining, unseen, subset of data. We encoded our model and made it available as a Web-accessible applet for producers. We determined a threshold, based on the upper 97.5% predictive interval, as a guideline for producers using the tool. We hypothesize that if farms exceed this threshold, especially if the sea lice levels are above this threshold 2 and 4 weeks into the model predictions, the sea louse population on the farm is likely influenced by sources other than lice within the farm

Understanding sources of sea lice for salmon farms in Chile

The decline of fisheries over recent decades and a growing human population has coincided with an increase in aquaculture production. As farmed fish densities increase, so have their rates of infectious diseases, as predicted by the theory of density-dependent disease transmission. One of the pathogen that has increased with the growth of salmon farming is sea lice. Effective management of this pathogen requires an understanding of the spatial scale of transmission. We used a two-part multi-scale model to account for the zero-inflated data observed in weekly sea lice abundance levels on rainbow trout and Atlantic salmon farms in Chile, and to assess internal (farm) and external (regional) sources of sea lice infection. We observed that the level of juvenile sea lice was higher on farms that were closer to processing plants with fish holding facilities. Further, evidence for sea lice exposure from the surrounding area was supported by a strong positive correlation between the level of juvenile sea lice on a farm and the number of gravid females on neighboring farms within 30. km two weeks prior. The relationship between external sources of sea lice from neighboring farms and juvenile sea lice on a farm was one of the strongest detected in our multivariable model. Our findings suggest that the management of sea lice should be coordinated between farms and should include all farms and processing plants with holding facilities within a relatively large geographic area. Understanding the contribution of pathogens on a farm from different sources is an important step in developing effective control strategies

Differential immunodominance hierarchy OF CD8+ T cell responses in HLA-B*27:05 AND B*27:02-mediated control of HIV-1 infection

The well-characterized association between HLA-B*27:05 and protection against HIV disease progression has been linked to immunodominant HLA-B*27:05-restricted CD8+ T-cell responses toward the conserved Gag KK10 (residues 263 to 272) and polymerase (Pol) KY9 (residues 901 to 909) epitopes. We studied the impact of the 3 amino acid differences between HLA-B*27:05 and the closely related HLA-B*27:02 on the HIV-specific CD8+ T-cell response hierarchy and on immune control of HIV. Genetic epidemiological data indicate that both HLA-B*27:02 and HLA-B*27:05 are associated with slower disease progression and lower viral loads. The effect of HLA-B*27:02 appeared to be consistently stronger than that of HLA-B*27:05. In contrast to HLA-B*27:05, the immunodominant HIV-specific HLA-B*27:02-restricted CD8+ T-cell response is to a Nef epitope (residues 142 to 150 [VW9]), with Pol KY9 subdominant and Gag KK10 further subdominant. This selection was driven by structural differences in the F pocket, mediated by a polymorphism between these two HLA alleles at position 81. Analysis of autologous virus sequences showed that in HLA-B*27:02-positive subjects, all three of these CD8+ T-cell responses impose selection pressure on the virus, whereas in HLA-B*27:05-positive subjects, there is no Nef VW9-mediated selection pressure. These studies demonstrate that HLA-B*27:02 mediates protection against HIV disease progression that is at least as strong as or stronger than that mediated by HLA-B*27:05. In combination with the protective Gag KK10 and Pol KY9 CD8+ T-cell responses that dominate HIV-specific CD8+ T-cell activity in HLA-B*27:05-positive subjects, a Nef VW9-specific response is additionally present and immunodominant in HLA-B*27:02-positive subjects, mediated through a polymorphism at residue 81 in the F pocket, that contributes to selection pressure against HIV

A combined prediction strategy increases identification of peptides bound with high affinity and stability to porcine MHC class I molecules SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01

Affinity and stability of peptides bound by major histocompatibility complex (MHC) class I molecules are important factors in presentation of peptides to cytotoxic T lymphocytes (CTLs). In silico prediction methods of peptide-MHC binding followed by experimental analysis of peptide-MHC interactions constitute an attractive protocol to select target peptides from the vast pool of viral proteome peptides. We have earlier reported the peptide binding motif of the porcine MHC-I molecules SLA-1*04:01 and SLA-2*04:01, identified by an ELISA affinity-based positional scanning combinatorial peptide library (PSCPL) approach. Here, we report the peptide binding motif of SLA-3*04:01 and combine two prediction methods and analysis of both peptide binding affinity and stability of peptide-MHC complexes to improve rational peptide selection. Using a peptide prediction strategy combining PSCPL binding matrices and in silico prediction algorithms (NetMHCpan), peptide ligands from a repository of 8900 peptides were predicted for binding to SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01 and validated by affinity and stability assays. From the pool of predicted peptides for SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01, a total of 71, 28, and 38 % were binders with affinities below 500 nM, respectively. Comparison of peptide-SLA binding affinity and complex stability showed that peptides of high affinity generally, but not always, produce complexes of high stability. In conclusion, we demonstrate how state-of-the-art prediction and in vitro immunology tools in combination can be used for accurate selection of peptides for MHC class I binding, hence providing an expansion of the field of peptide-MHC analysis also to include pigs as a livestock experimental model.Fil: Pedersen, Lasse Eggers. Technical University of Denmark; DinamarcaFil: Rasmussen, Michael. Universidad de Copenhagen; DinamarcaFil: Harndahl, Mikkel. Universidad de Copenhagen; DinamarcaFil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús) | Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús); ArgentinaFil: Buus, Søren. Universidad de Copenhagen; DinamarcaFil: Jungersen, Gregers. Technical University of Denmark; Dinamarc

Identification and HLA-Tetramer-Validation of Human CD4(+) and CD8(+) T Cell Responses against HCMV Proteins IE1 and IE2

Human cytomegalovirus (HCMV) is an important human pathogen. It is a leading cause of congenital infection and a leading infectious threat to recipients of solid organ transplants as well as of allogeneic hematopoietic cell transplants. Moreover, it has recently been suggested that HCMV may promote tumor development. Both CD4+ and CD8+ T cell responses are important for long-term control of the virus, and adoptive transfer of HCMV-specific T cells has led to protection from reactivation and HCMV disease. Identification of HCMV-specific T cell epitopes has primarily focused on CD8+ T cell responses against the pp65 phosphoprotein. In this study, we have focused on CD4+ and CD8+ T cell responses against the immediate early 1 and 2 proteins (IE1 and IE2). Using overlapping peptides spanning the entire IE1 and IE2 sequences, peripheral blood mononuclear cells from 16 healthy, HLA-typed, donors were screened by ex vivo IFN-γ ELISpot and in vitro intracellular cytokine secretion assays. The specificities of CD4+ and CD8+ T cell responses were identified and validated by HLA class II and I tetramers, respectively. Eighty-one CD4+ and 44 CD8+ T cell responses were identified representing at least seven different CD4 epitopes and 14 CD8 epitopes restricted by seven and 11 different HLA class II and I molecules, respectively, in total covering 91 and 98% of the Caucasian population, respectively. Presented in the context of several different HLA class II molecules, two epitope areas in IE1 and IE2 were recognized in about half of the analyzed donors. These data may be used to design a versatile anti-HCMV vaccine and/or immunotherapy strategy

Humoral and Cellular CMV Responses in Healthy Donors; Identification of a Frequent Population of CMV-Specific, CD4+ T Cells in Seronegative Donors

CMV status is an important risk factor in immune compromised patients. In hematopoeitic cell transplantations (HCT), both donor and recipient are tested routinely for CMV status by serological assays; however, one might argue that it might also be of relevance to examine CMV status by cellular (i.e., T lymphocyte) assays. Here, we have analyzed the CMV status of 100 healthy blood bank donors using both serology and cellular assays. About half (56%) were found to be CMV seropositive, and they all mounted strong CD8+ and/or moderate CD4+ T cell responses ex vivo against the immunodominant CMV protein, pp65. Of the 44 seronegative donors, only five (11%) mounted ex vivo T cell responses; surprisingly, 33 (75%) mounted strong CD4+ T cell responses after a brief in vitro peptide stimulation culture. This may have significant implications for the analysis and selection of HCT donors