An in silico modeling approach to understanding the dynamics of sarcoidosis

Background

Sarcoidosis is a polygenic disease with diverse phenotypic presentations characterized by an abnormal antigen-mediated Th1 type immune response. At present, progress towards understanding sarcoidosis disease mechanisms and the development of novel treatments is limited by constraints attendant to conducting human research in a rare disease in the absence of relevant animal models. We sought to develop a computational model to enhance our understanding of the pathological mechanisms of and predict potential treatments of sarcoidosis.

Methodology/Results

Based upon the literature, we developed a computational model of known interactions between essential immune cells (antigen-presenting macrophages, effector and regulatory T cells) and cytokine mediators (IL-2, TNFα, IFNγ) of granulomatous inflammation during sarcoidosis. The dynamics of these interactions are described by a set of ordinary differential equations. The model predicts bistable switching behavior which is consistent with normal (self-limited) and “sarcoidosis-like” (sustained) activation of the inflammatory components of the system following a single antigen challenge. By perturbing the influence of model components using inhibitors of the cytokine mediators, distinct clinically relevant disease phenotypes were represented. Finally, the model was shown to be useful for pre-clinical testing of therapies based upon molecular targets and dose-effect relationships.

Conclusions/Significance

Our work illustrates a dynamic computer simulation of granulomatous inflammation scenarios that is useful for the investigation of disease mechanisms and for pre-clinical therapeutic testing. In lieu of relevant in vitro or animal surrogates, our model may provide for the screening of potential therapies for specific sarcoidosis disease phenotypes in advance of expensive clinical trials.     

Exploring Individual- to Population-Level Impacts of Disease on Coral Reef Sponges: Using Spatial Analysis to Assess the Fate,Dynamics, and Transmission of Aplysina Red Band Syndrome (ARBS)

Background

Marine diseases are of increasing concern for coral reef ecosystems, but often their causes, dynamics and impacts are unknown. The current study investigated the epidemiology of Aplysina Red Band Syndrome (ARBS), a disease affecting the Caribbean sponge Aplysina cauliformis, at both the individual and population levels. The fates of marked healthy and ARBS-infected sponges were examined over the course of a year. Population-level impacts and transmission mechanisms of ARBS were investigated by monitoring two populations of A. cauliformis over a three year period using digital photography and diver-collected data, and analyzing these data with GIS techniques of spatial analysis. In this study, three commonly used spatial statistics (Ripley’s K, Getis-Ord General G, and Moran’s Index) were compared to each other and with direct measurements of individual interactions using join-counts, to determine the ideal method for investigating disease dynamics and transmission mechanisms in this system. During the study period, Hurricane Irene directly impacted these populations, providing an opportunity to assess potential storm effects on A. cauliformis and ARBS.

Results

Infection with ARBS caused increased loss of healthy sponge tissue over time and a higher likelihood of individual mortality. Hurricane Irene had a dramatic effect on A. cauliformis populations by greatly reducing sponge biomass on the reef, especially among diseased individuals. Spatial analysis showed that direct contact between A. cauliformis individuals was the likely transmission mechanism for ARBS within a population, evidenced by a significantly higher number of contact-joins between diseased sponges compared to random. Of the spatial statistics compared, the Moran’s Index best represented true connections between diseased sponges in the survey area. This study showed that spatial analysis can be a powerful tool for investigating disease dynamics and transmission in a coral reef ecosystem.     

Protection of mice against enterotoxigenic E. coli by immunization with a polyvalent enterotoxin comprising a combination of LTB, STa, and STb

Currently available enterotoxigenic Escherichia coli (ETEC) vaccines are based on colonization factors and/or the heat-labile enterotoxin B subunit (LTB). However, the induction of antitoxic responses against heat-stable enterotoxin a (STa) and b (STb) has merit as these two poorly immunogenic toxins are frequently associated with ETEC strains. In this study, we genetically constructed a trivalent enterotoxin fusion protein (STa–LTB–STb, abbreviated to SLS) in an effort to develop a single toxoid containing these three enterotoxins for vaccination against ETEC. Mutagenesis at one disulfide-bridge-forming cysteine in STa led to a dramatic reduction in the STa toxicity of SLS; however, the fusion peptide retained the STb-associated toxicity. Immunization of mice with SLS protein elicited significant antibody responses to LTB, STa, and STb. Significantly, the mice antisera were able to neutralize the biological activity of both STa and STb. In the experiment to assess the protective effect of SLS immunization, the mortality of mice receiving SLS was significantly lower than their control cohorts (P < 0.01) after intraperitoneal challenge with ETEC. These results show that the trivalent fusion enterotoxin SLS has the potential to serve as a useful toxin-based vaccine against ETEC-induced diarrheal disease via a single immunogen.     

Damaging effects of ischemia/reperfusion on intestinal muscle

Periods of ischemia followed by restoration of blood flow cause ischemia/reperfusion (I/R) injury. In the intestine, I/R damage to the mucosa and neurons is prominent. Functionally, abnormalities occur in motility, most conspicuously a slowing of transit, possibly as a consequence of damage to neurons and/or muscle. Here, we describe degenerative and regenerative changes that have not been previously reported in intestinal muscle. The mouse small intestine was made ischemic for 1 h, followed by re-perfusion for 1 h to 7 days. The tissues were examined histologically, after hematoxylin/eosin and Masson’s trichrome staining, and by myeloperoxidase histochemistry to detect inflammatory reactions to I/R. Histological analysis revealed changes in the mucosa, muscle, and neurons. The mucosa was severely but transiently damaged. The mucosal surface was sloughed off at 1–3 h, but re-epithelialization occurred by 12 h, and the epithelium appeared healthy by 1–2 days. Longitudinal muscle degeneration was followed by regeneration, but little effect on the circular muscle was noted. The first signs of muscle change were apparent at 3–12 h, and by 1 and 2 days, extensive degeneration within the muscle was observed, which included clear cytoplasm, pyknotic nuclei, and apoptotic bodies. The muscle recovered quickly and appeared normal at 7 days. Histological evidence of neuronal damage was apparent at 1–7 days. Neutrophils were not present in the muscle layers and were infrequent in the mucosa. However, they were often seen in the longitudinal muscle at 1–3 days and were also present in the circular muscle. Neutrophil numbers increased in the mucosa in both I/R and sham-operated animals and remained elevated from 1 h to 7 days. We conclude that I/R causes severe longitudinal muscle damage, which might contribute to the long-term motility deficits observed after I/R injury to the intestine.     

Effects of variety and storage duration on the nutrient digestibility and the digestible and metabolisable energy content of maize fed to growing pigs

The objective of this research was to determine the effects of variety and storage duration on the nutrient digestibility and the digestible (DE) and metabolisable (ME) energy content in maize when fed to growing pigs. Four maize varieties (LS1, LS2, LS3 and LS4) were hand-harvested from the same growing area in China in early October of 2012. The samples were sun dried to about 14% moisture content and then stored in the warehouse of the Fengning Pig Experiment Base at China Agricultural University for 0, 3 or 10 months. Twenty-four barrows of about 33 kg body weight were used and allotted to a completely randomised block design with four diets and six replicate pigs per diet. Pigs were individually housed in metabolic crates. The four experimental diets were formulated by mixing 96.8% of each variety of maize with 3.2% vitamins and minerals. A 5-day collection period followed a 7-day diet acclimation period. The results indicated that the DE and ME contents of maize and the apparent total tract digestibility (ATTD) of organic matter (OM), dry matter, gross energy (GE), neutral detergent fibre, acid detergent fibre (ADF), crude protein (CP) and ether extract (EE) were significantly (p < 0.05) influenced by maize variety and storage duration. With an extension of storage duration from 0 to 10 months, the DE and ME of maize and the ATTD of OM, GE, ADF, CP and EE changed in a quadratic manner (p < 0.05), and 3 months of storage exceeded 0 months of storage by 1.84%, 1.43%, 0.31%, 0.32%, 15.37%, 2.11% and 5.02%, respectively. The DE, ME of maize and the ATTD of OM, GE, ADF, CP and EE decreased by 3.67%, 6.00%, 0.97%, 1.40%, 30.54%, 3.92% and 20.93%, respectively, at 10 months of storage compared to 3 months of storage. No interaction was observed between maize variety and storage duration in DE and ME contents in maize. In conclusion, under the conditions of this study, most of the nutrient digestibility and the DE and ME contents of maize increased from 0 to 3 months and decreased from 3 to 10 months.     

Ants and Habitat Specificity in Aphids

A number of rare butterflies are known to only utilise their host plant species when they grow in particular situations. Field data are presented showing that two rare species of aphid also only utilised their host plants when they grew in particular situations, namely near ant nests. The oak-feeding aphid Stomaphis quercus only occupied trees within 17 m of a Lasius fulignosus nest. The thyme-feeding aphid Aphis serpylli only occurred in a region of a Breckland grass heath where the sward contained a high density of Lasius niger nests, and then most commonly only in quadrats containing ant nests. The sward that was suitable for A. serpylli was generated by the action of farm traffic. It is concluded that ants indirectly impose habitat specificity on these aphids.     

Phylogenetic analyses of marine sponges within the order Verongida: a comparison of morphological and molecular data

Abstract. Because the taxonomy of marine sponges is based primarily on morphological characters that can display a high degree of phenotypic plasticity, current classifications may not always reflect evolutionary relationships. To assess phylogenetic relationships among sponges in the order Verongida, we examined 11 verongid species, representing six genera and four families. We compared the utility of morphological and molecular data in verongid sponge systematics by comparing a phylogeny constructed from a morphological character matrix with a phylogeny based on nuclear ribosomal DNA sequences. The morphological phylogeny was not well resolved below the ordinal level, likely hindered by the paucity of characters available for analysis, and the potential plasticity of these characters. The molecular phylogeny was well resolved and robust from the ordinal to the species level. We also examined the morphology of spongin fibers to assess their reliability in verongid sponge taxonomy. Fiber diameter and pith content were highly variable within and among species. Despite this variability, spongin fiber comparisons were useful at lower taxonomic levels (i.e., among congeneric species); however, these characters are potentially homoplasic at higher taxonomic levels (i.e., between families). Our molecular data provide good support for the current classification of verongid sponges, but suggest a re-examination and potential reclassification of the genera Aiolochroia and Pseudoceratina . The placements of these genera highlight two current issues in morphology-based sponge taxonomy: intermediate character states and undetermined character polarity.     

Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts

Cyanobacteria are common members of sponge-associated bacterial communities and are particularly abundant symbionts of coral reef sponges. The unicellular cyanobacterium Synechococcus spongiarum is the most prevalent photosynthetic symbiont in marine sponges and inhabits taxonomically diverse hosts from tropical and temperate reefs worldwide. Despite the global distribution of S. spongiarum , molecular analyses report low levels of genetic divergence among 16S ribosomal RNA (rRNA) gene sequences from diverse sponge hosts, resulting either from the widespread dispersal ability of these symbionts or the low phylogenetic resolution of a conserved molecular marker. Partial 16S rRNA and entire 16S–23S rRNA internal transcribed spacer (ITS) genes were sequenced from cyanobacteria inhabiting 32 sponges (representing 18 species, six families and four orders) from six geographical regions. ITS phylogenies revealed 12 distinct clades of S. spongiarum that displayed 9% mean sequence divergence among clades and less than 1% sequence divergence within clades. Symbiont clades ranged in specificity from generalists to specialists, with most (10 of 12) clades detected in one or several closely related hosts. Although multiple symbiont clades inhabited some host sponges, symbiont communities appear to be structured by both geography and host phylogeny. In contrast, 16S rRNA sequences were highly conserved, exhibiting less than 1% sequence divergence among symbiont clades. ITS gene sequences displayed much higher variability than 16S rRNA sequences, highlighting the utility of ITS sequences in determining the genetic diversity and host specificity of S. spongiarum populations among reef sponges. The genetic diversity of S. spongiarum revealed by ITS sequences may be correlated with different physiological capabilities and environmental preferences that may generate variable host–symbiont interactions.     

Potential risk of biologic pollution associated to the introduction of <i>Pinus radiata</i> in grassland areas

Afforestation is a recommended practice to mitigate global warming. However, their implementation may generate undesirable impacts, mostly if exotic species are used. Plantations of Pinus radiata D Don in Ventania (Bs. As., Argentina) soils showed notorious increments of extractable P (Pe), which could affect the dynamic of this element as well as the degree of phosphorus saturation (GSP_Bray). The objectives of this study were: i) to quantify the GSP_Bray in Mollisols afforested with P. radiata comparing the results with those coming from adjacent, natural grassland areas (base line); ii) to evaluate the potential environmental risk induced by afforestation through the identification of a change point (PC) in the GSP_Bray indicative of a phosphate leaching increment. Treatments included mature stands of P. radiata (TB) and adjacent areas with natural grassland vegetation (TP). Samples were taken at 0-15; 15-30 and 30-45 cm soil depth, and texture, pH, total organic carbon (COT), Pe, soluble reactive phosphorus (PSR), phosphorus sorption index (ISP) and GSP_Bray were determined. The results showed a significant acidification in TB and an increase in the COT stock, indicating an additional atmospheric CO₂ sequestration by the trees. The Pe and PSR values were notoriously higher in TB, and they were reflected in a significant increment in the GSP_Bray with respect to TP. The detection of a significant PC in the GSP_Bray-PSR regression indicates higher chances of phosphate leaching in the forest stands, which could reach water courses, lakes and artificial reservoirs promoting their eutrophication. Because of the potential environmental pollution risk of biologic origin derived from the afforestation with P. radiata in Mollisols areas, their inclusion in clean development practices must be reconsidered.