Fast Selection of Spectral Variables with B-Spline Compression

The large number of spectral variables in most data sets encountered in spectral chemometrics often renders the prediction of a dependent variable uneasy. The number of variables hopefully can be reduced, by using either projection techniques or selection methods; the latter allow for the interpretation of the selected variables. Since the optimal approach of testing all possible subsets of variables with the prediction model is intractable, an incremental selection approach using a nonparametric statistics is a good option, as it avoids the computationally intensive use of the model itself. It has two drawbacks however: the number of groups of variables to test is still huge, and colinearities can make the results unstable. To overcome these limitations, this paper presents a method to select groups of spectral variables. It consists in a forward-backward procedure applied to the coefficients of a B-Spline representation of the spectra. The criterion used in the forward-backward procedure is the mutual information, allowing to find nonlinear dependencies between variables, on the contrary of the generally used correlation. The spline representation is used to get interpretability of the results, as groups of consecutive spectral variables will be selected. The experiments conducted on NIR spectra from fescue grass and diesel fuels show that the method provides clearly identified groups of selected variables, making interpretation easy, while keeping a low computational load. The prediction performances obtained using the selected coefficients are higher than those obtained by the same method applied directly to the original variables and similar to those obtained using traditional models, although using significantly less spectral variables

Dual infections of CD163 expressing NPTr epithelial cells with influenza A virus and PRRSV

In the pig, respiratory co-infections involving various pathogens are far more frequent than single infections. Amongst respiratory viruses, swine influenza type A virus (swIAV) and porcine reproductive and respiratory syndrome virus (PRRSV) are frequently associated. Previously, we performed co-infections with swIAV and PRRSV in porcine alveolar macrophages (PAM) and precision cut lung slices (PCLS). With these two approaches it was practically impossible to have co-infections of the same cells as the main target cell of swIAV is the epithelial cell while the main target of PRRSV is the PAM. This constraint makes the study of interference between the two viruses difficult at the cellular level. In the current report, an epithelial cell line expressing, CD163, the main receptor of PRRSV was generated. This cell line receptive for both viruses was used to assess the interference between the two viruses. Results showed that swIAV as well as PRRSV, even if they interacted differently with the modified epithelial cells, were clearly interfering with each other regarding their replication when they infected a same cell with consequences within the cellular antiviral response. Our modified cell line, receptive to both viruses, can be used as a tool to assess interference between swIAV and PRRSV in a same cell as it probably happens in the porcine host

Pathogen-reactive T helper cell analysis in the pig

There is growing interest in studying host-pathogen interactions in human-relevant large animal models such as the pig. Despite the progress in developing immunological reagents for porcine T cell research, there is an urgent need to directly assess pathogen-specific T cells-an extremely rare population of cells, but of upmost importance in orchestrating the host immune response to a given pathogen. Here, we established that the activation marker CD154 (CD40L), known from human and mouse studies, identifies also porcine antigen-reactive CD4(+) T lymphocytes. CD154 expression was upregulated early after antigen encounter and CD4(+)CD154(+) antigen-reactive T cells coexpressed cytokines. Antigen-induced expansion and autologous restimulation enabled a time-and dose-resolved analysis of CD154 regulation and a significantly increased resolution in phenotypic profiling of antigen-responsive cells. CD154 expression identified T cells responding to staphylococcal Enterotoxin B superantigen stimulation as well as T cells responding to the fungus Candida albicans and T cells specific for a highly prevalent intestinal parasite, the nematode Ascaris suum during acute and trickle infection. Antigen-reactive T cells were further detected after immunization of pigs with a single recombinant bacterial antigen of Streptococcus suis only. Thus, our study offers new ways to study antigen-specific T lymphocytes in the pig and their contribution to host-pathogen interactions

Transcription profiling reveals potential mechanisms of dysbiosis in the oral microbiome of rhesus macaques with chronic untreated SIV infection.

A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression. Due to the impracticalities of conducting host-microbe systems-based studies in HIV infected patients, we have evaluated the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease. We present the first description of the rhesus macaque oral microbiota and show that a mixture of human commensal bacteria and "macaque versions" of human commensals colonize the tongue dorsum and dental plaque. Our findings indicate that SIV infection results in chronic activation of antiviral and inflammatory responses in the tongue mucosa that may collectively lead to repression of epithelial development and impact the microbiome. In addition, we show that dysbiosis of the lingual microbiome in SIV infection is characterized by outgrowth of Gemella morbillorum that may result from impaired macrophage function. Finally, we provide evidence that the increased capacity of opportunistic pathogens (e.g. E. coli) to colonize the microbiome is associated with reduced production of antimicrobial peptides

Sexual dimorphism in immune development and in response to nutritional intervention in neonatal piglets

Although sex disparity in immunological function and susceptibility to various inflammatory and infectious disease is recognized in adults, far less is known about the situation in young infants during immune development. We have used an outbred piglet model to explore potential early sex disparity underlying both mucosal immune development and systemic responses to novel antigen. Despite similarities in intestinal barrier function and therefore, presumably, antigen exposure, females had less CD172+ (Sirp-α) antigen presenting cells and expression of MHCIIDR at 28 days old compared to males, along with greater regulatory T-cell numbers. This suggests that, during infancy, females may have greater potential for local immune regulation than their male counterparts. However, females also presented with significantly greater systemic antibody responses to injected ovalbumin and dietary soya. Females also synthesized significantly more IgA in mesenteric lymph nodes, whereas males synthesized more in caecal mucosa, suggesting that plasma cells were retained within the MLN in females, but increased numbers of plasma cells circulated through to the mucosal tissue in males. Significant effects of inulin and Bifidobacterium lactis NCC2818 on the developing immune system were also sex-dependent. Our results may start to explain inconsistencies in outcomes of trials of functional foods in infants, as distinction between males and females is seldom made. Since later functionality of the immune system is highly dependent on appropriate development during infancy, stratifying nutritional interventions by sex may present a novel means of optimizing treatments and preventative strategies to reduce the risk of the development of immunological disorders in later life

Establishing the pig as a large animal model for vaccine development against human cancer

Immunotherapy has increased overall survival of metastatic cancer patients, and cancer antigens are promising vaccine targets. To fulfill the promise, appropriate tailoring of the vaccine formulations to mount in vivo cytotoxic T cell (CTL) responses towards co-delivered cancer antigens is essential. Previous development of therapeutic cancer vaccines has largely been based on studies in mice, and the majority of these candidate vaccines failed to induce therapeutic responses in the subsequent human clinical trials. Given that antigen dose and vaccine volume in pigs are translatable to humans and the porcine immunome is more closely related to the human counterpart, we here introduce pigs as a supplementary large animal model for human cancer vaccine development. IDO and RhoC, both important in human cancer development and progression, were used as vaccine targets and 12 pigs were immunized with overlapping 20-mer peptides spanning the entire porcine IDO and RhoC sequences formulated in CTL-inducing adjuvants: CAF09, CASAC, Montanide ISA 51 VG or PBS. Taking advantage of recombinant swine MHC class I molecules (SLAs), the peptide-SLA complex stability were measured for 198 IDO- or RhoC-derived 9-11mer peptides predicted to bind to SLA-1*04:01, -1*07:02, -2*04:01, -2*05:02 and/or -3*04:01. This identified 89 stable (t½ ≥ 0.5 hour) peptide-SLA complexes. By IFN-γ release in PBMC cultures we monitored the vaccine-induced peptide-specific CTL responses, and found responses to both IDO- and RhoC-derived peptides across all groups with no adjuvant being superior. These findings support the further use of pigs as a large animal model for vaccine development against human cancer

Early intervention with Bifidobacterium lactis NCC2818 modulates the host-microbe interface independent of the sustained changes induced by the neonatal environment

Inflammatory and metabolic diseases can originate during early-life and have been correlated with shifts in intestinal microbial ecology. Here we demonstrate that minor environmental fluctuations during the early neonatal period had sustained effects on the developing porcine microbiota and host-microbe interface. These inter-replicate effects appear to originate during the first day of life, and are likely to reflect very early microbiota acquisition from the environment. We statistically link early systemic inflammation with later local increases in inflammatory cytokine (IL-17) production, which could have important enteric health implications. Immunity, intestinal barrier function, host metabolism and host-microbiota co-metabolism were further modified by Bifidobacterium lactis NCC2818 supplementation, although composition of the in situ microbiota remained unchanged. Finally, our robust model identified novel, strong correlations between urinary metabolites (eg malonate, phenylacetylglycine, alanine) and mucosal immunoglobulin (IgM) and cytokine (IL-10, IL-4) production, thus providing the possibility of the development of urinary ‘dipstick’ tests to assess non-accessible mucosal immune development and identify early precursors (biomarkers) of disease. These results have important implications for infants exposed to neonatal factors including caesarean delivery, antibiotic therapy and delayed discharge from hospital environments, which may predispose to the development of inflammatory and metabolic diseases in later life

Grouping Pig-Specific Responses to Mitogen with Similar Responder Animals may Facilitate the Interpretation of Results Obtained in an Out-Bred Animal Model

Copyright: © 2014 J. Alex Pasternak, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Peer ReviewedPig peripheral blood-derived mononuclear cells (PBMCs) and lamina propria mononuclear cells (LPMCs) stimulated with mitogens ex vivo can show significant animal-to-animal variation lead to difficulty in interpreting responses in an out-bred animal species. Mixed-cell populations were stimulated ex vivo with 2.5 μg/ml Con A or 2.5 ng/ml PMA plus 250 ng/ml ionomycin (PMAi; (LPCMs only)) or media alone for 72 hours. Supernatants were then tested for cytokine production using a Bioplex assay for porcine IFNα, IFNγ, IL-10, and IL-12. Unstimulated PBMCs had significant levels of IL-10 and the median value for this group decreased in the presence of Con A. Con A did, however, induce production of IFNα and IFNγ, but not IL-12 in this cell population. In contrast, unstimulated and Con A-stimulated LPMCs produced negligible IL-10, IFNα, IFNγ, and the majority of animals’ LPMCs showed negligible IL-12 production in response to Con A. In contrast, LPMCs stimulated with PMAi produced IFNγ suggesting cytokine production is mitogen–specific response. When we tracked animal-specific responses, we observed that discrete subsets of animal’s PBMCs responded to Con A with significantly increased or decreased IL-10 production relative to unstimulated cells. Further, in the LPMCs, some cells produced no IL-12 in response to Con A but showed augmented production in response to PMAi, while others showed production of IL-12 in response to Con A but no response to PMAi. Flow cytometric analysis showed that the PBMCs were a mixture of CD3+ T cells>CD21+ B cells>CD172+ myeloid cells whereas the LPMCs consisted of mainly Cytotoxic T cells and Natural Killer cells. The percentage of CD8α+CD4+ antigen-experienced T cells was greater in the LPMCs relative to the PBMCs. As expected in an out-bred species, animal-specific differences in cytokine production in response to stimulants exist and may confound interpretation of results unless tracked individually

Cytolytic DNA vaccine encoding lytic perforin augments the maturation of- and antigen presentation by- dendritic cells in a time-dependent manner

The use of cost-effective vaccines capable of inducing robust CD8+ T cell immunity will contribute significantly towards the elimination of persistent viral infections and cancers worldwide. We have previously reported that a cytolytic DNA vaccine encoding an immunogen and a truncated mouse perforin (PRF) protein significantly augments anti-viral T cell (including CD8+ T cell) immunity. Thus, the current study investigated whether this vaccine enhances activation of dendritic cells (DCs) resulting in greater priming of CD8+ T cell immunity. In vitro data showed that transfection of HEK293T cells with the cytolytic DNA resulted in the release of lactate dehydrogenase, indicative of necrotic/lytic cell death. In vitro exposure of this lytic cell debris to purified DCs from naïve C57BL/6 mice resulted in maturation of DCs as determined by up-regulation of CD80/CD86. Using activation/proliferation of adoptively transferred OT-I CD8+ T cells to measure antigen presentation by DCs in vivo, it was determined that cytolytic DNA immunisation resulted in a time-dependent increase in the proliferation of OT-I CD8+ T cells compared to canonical DNA immunisation. Overall, the data suggest that the cytolytic DNA vaccine increases the activity of DCs which has important implications for the design of DNA vaccines to improve their translational prospects.Danushka K. Wijesundara, Wenbo Yu, Ben J. C. Quah, Preethi Eldi, John D. Hayball, Kerrilyn R. Diener, Ilia Voskoboinik, Eric J. Gowans, and Branka Grubor-Bau

Clinical protection against caprine herpesvirus 1 genital infection by intranasal administration of a live attenuated glycoprotein E negative bovine herpesvirus 1 vaccine

BACKGROUND: Caprine herpesvirus 1 (CpHV-1) is responsible of systemic diseases in kids and genital diseases leading to abortions in goats. CpHV-1 is widespread and especially in Mediterranean countries as Greece, Italy and Spain. CpHV-1 is antigenically and genetically closely related to bovine herpesvirus 1 (BoHV-1). Taking into account the biological properties shared by these two viruses, we decided in the current study to assess the protection of a live attenuated glycoprotein E (gE) negative BoHV-1 vaccine against a genital CpHV-1 infection in goats. RESULTS: The vaccine was inoculated intranasally twice three weeks apart followed by a subsequent CpHV-1 intravaginal challenge which is the natural route of infection in three goats. To analyse the safety and the efficacy of this marker vaccine, two groups of three goats served as controls: one immunised with a virulent CpHV-1 and one uninoculated until the challenge. Goats were clinically monitored and all sampling procedures were carried out in a blind manner. The vaccine did not induce any undesirable local or systemic reaction and goats did not excrete gE-negative BoHV-1. After challenge, a significant reduction in disease severity was observed in immunised goats. Moreover, goats immunised with either gE-negative BoHV-1 or CpHV-1 exhibited a significant reduction in the length and the peak of viral excretion. Antibodies neutralising both BoHV-1 and CpHV-1 were raised in immunised goats. CONCLUSION: Intranasal application of a live attenuated gE-negative BoHV-1 vaccine is able to afford a clinical protection and a reduction of virus excretion in goats challenged by a CpHV-1 genital infection