Vaccinology in the era of high-throughput biology

Vaccination has been tremendously successful saving lives and preventing infections. However, the development of vaccines against global pandemics such as HIV, malaria and tuberculosis has been obstructed by several challenges. A major challenge is the lack of knowledge about the correlates and mechanisms of protective immunity. Recent advances in the application of systems biological approaches to analyse immune responses to vaccination in humans are beginning to yield new insights about mechanisms of vaccine immunity, and to define molecular signatures, induced rapidly after vaccination, that correlate with and predict vaccine induced immunity. Here, we review these advances and discuss the potential of this systems vaccinology approach in defining novel correlates of protection in clinical trials, and in infection-induced ‘experimental challenge models'' in humans.     

Local divergence of thermal reaction norms among amphibian populations is affected by pond temperature variation

Although temperature variation is known to cause large‐scale adaptive divergence, its potential role as a selective factor over microgeographic scales is less well‐understood. Here, we investigated how variation in breeding pond temperature affects divergence in multiple physiological (thermal performance curve and critical thermal maximum [CT_max]) and life‐history (thermal developmental reaction norms) traits in a network of Rana arvalis populations. The results supported adaptive responses to face two main constraints limiting the evolution of thermal adaptation. First, we found support for the faster–slower model, indicating an adaptive response to compensate for the thermodynamic constraint of low temperatures in colder environments. Second, we found evidence for the generalist–specialist trade‐off with populations from colder and less thermally variable environments exhibiting a specialist phenotype performing at higher rates but over a narrower range of temperatures. By contrast, the local optimal temperature for locomotor performance and CT_max did not match either mean or maximum pond temperatures. These results highlight the complexity of the adaptive multiple‐trait thermal responses in natural populations, and the role of local thermal variation as a selective force driving diversity in life‐history and physiological traits in the presence of gene flow.     

Chitosan as a Biomaterial: Influence of Degree of Deacetylation on Its Physiochemical,Material and Biological Properties

Chitosan is a biomaterial with a range of current and potential biomedical applications. Manipulation of chitosan degree of deacetylation (DDA) to achieve specific properties appears feasible, but studies investigating its influence on properties are often contradictory. With a view to the potential of chitosan in the regeneration of nerve tissue, the influence of DDA on the growth and health of olfactory ensheathing cells (OECs) was investigated. There was a linear increase in OEC proliferation as the DDA increased from 72 to 85%. This correlated with linear increases in average surface roughness (0.62 to 0.78 μm) and crystallinity (4.3 to 10.1%) of the chitosan films. Mitochondrial activity and membrane integrity of OECs was significantly different for OECs cultivated on chitosan with DDAs below 75%, while those on films with DDAs up to 85% were similar to cells in asynchronous growth. Apoptotic indices and cell cycle analysis also suggested that chitosan films with DDAs below 75% were cytocompatible but induced cellular stress, while OECs grown on films fabricated from chitosan with DDAs above 75% showed no significant differences compared to those in asynchronous growth. Tensile strength and elongation to break varied with DDA from 32.3 to 45.3 MPa and 3.6 to 7.1% respectively. DDA had no significant influence on abiotic and biotic degradation profiles of the chitosan films which showed approximately 8 and 20% weight loss respectively. Finally, perceived patterns in property changes are subject to change based on potential variations in DDA analysis. NMR examination of the chitosan samples here revealed significant differences depending upon which peaks were selected for integration; 6 to 13% in DDA values within individual samples. Furthermore, differences between DDA values determined here and those reported by the commercial suppliers were significant and this may also be a source of concern when selecting commercial chitosans for biomaterial research.     

Natural gum-assisted phthalocyanine immobilization in electroactive nanocomposites: physicochemical characterization and sensing applications

Natural gums have been traditionally applied in cosmetics and the food industry, mainly as emulsification agents. Due to their biodegradability and excellent mechanical properties, new technological applications have been proposed involving their use with conventional polymers forming blends and composites. In this study, we take advantage of the polyelectrolyte character exhibited by the natural gum ChichA (Sterculia striata), extracted in the Northeastern region of Brazil, to produce electroactive nanocomposites. The nanocomposites were fabricated in the form of ultrathin films by combining a metallic phthalocyanine (nickel tetrasulfonated phthalocyanine, NiTsPc) and the ChichA gum in a tetralayer architecture, in conjunction with conventional polyelectrolytes. The presence of the gum led to an efficient adsorption of the phthalocyanine and enhanced the electrochemical response of the films. Upon combining the electrochemical and UV-vis absorption data, energy diagrams of the ChichA/NiTsPc-based system were obtained. Furthermore, modified electrodes based on gum/phthalocyanine films were able to detect dopamine at concentrations as low as 10-5 M.     

Linkage analysis by genotyping of sibling populations: a genetic map for the potato cyst nematode constructed using a “pseudo-F2” mapping strategy

A mapping strategy is described for the construction of a linkage map of a non-inbred species in which individual offspring genotypes are not amenable to marker analysis. After one extra generation of random mating, the segregating progeny was propagated, and bulked populations of offspring were analyzed. Although the resulting population structure is different from that of commonly used mapping populations, we show that the maximum likelihood formula for a normal F2 is applicable for the estimation of recombination. This “pseudo-F2” mapping strategy, in combination with the development of an AFLP assay for single cysts, facilitated the construction of a linkage map for the potato cyst nematode Globodera rostochiensis. Using 12 pre-selected AFLP primer combinations, a total of 66 segregating markers were identified, 62 of which were mapped to nine linkage groups. These 62 AFLP markers are randomly distributed and cover about 65% of the genome. An estimate of the physical size of the Globodera genome was obtained from comparisons of the number of AFLP fragments obtained with the values for Caenorhabditis elegans. The methodology presented here resulted in the first genomic map for a cyst nematode. The low value of the kilobase/centimorgan (kb/cM) ratio for the Globodera genome will facilitate map-based cloning of genes that mediate the interaction between the nematode and its host plant. Received: 7 January 1999 / Accepted: 16 April 1999     

Reproductive strategies of Red-bellied Piranha (<Emphasis Type="Italic">Pygocentrus nattereri</Emphasis> Kner, 1858) in the white waters of the Mamirauá flooded forest,central Brazilian Amazon

Despite being an important member of neotropical fish assemblages, as well as a species with an unenviable reputation, little is known about the reproductive ecology of Red-bellied Piranha, Pygocentrus nattereri, in the wild. We tracked the reproductive activity of piranhas in the flooded forests of Mamirauá Reserve, Central Brazilian Amazon, for 2 years, in an investigation that included over 3,000 individual fish. Contrary to expectation piranhas had not one, but rather two annual reproductive seasons, tuned to water level fluctuation and the flooding pulse. Females were found to have up to 30,000 oocytes, little more than one third of which were mature and available for spawning in a single batch. Sexual maturation (of both males and females) occurred at around 160 mm. At this point sexually active individuals (of both sexes) became dark and lost most of their red coloration. Ontogenetic changes in habitat selection were strongly associated with the spawning behavior of mature adults. We also found that flooded marginal vegetation and marginal grasses inside lakes were the preferred spawning areas. In contrast, non-reproductive individuals were found in open water and under floating meadows.     

Reduced folate carrier-1 G80a gene polymorphism is associated with neuroblastoma’s development

Neuroblastoma is a malignant embryonal tumor of neural crest cells that give rise to the sympathetic nervous system, responsible for 10–70 % of all cases of childhood cancer. Because of its early appearance, it has been suggested that risk factors active in the prenatal can be associated with the pathogenesis of neuroblastoma. The aim of this study was to investigate whether the genetic polymorphisms MTHFR C677T and A1298C, MTR A2756G, TYMS 2R/3R and SLC19A1 G80A, involved in folate metabolism, increase the risk of neuroblastoma in Brazilian children. This study comprised 31 Brazilian children (0–14 years old) diagnosed with neuroblastoma compared with 92 controls. Investigation of polymorphisms MTHFR C677T, MTR A2756G and SLC19A1 A80G was performed using PCR–RFLP, the TYMS 2R/3R using PCR and MTHFR A1298C using AS-PCR. The SLC19A1 A80A genotype was significantly associated with the development of neuroblastoma, compared with the control group (Williams G-Test = 0.0286; OR = 5.1667; 95 % CI = 1.4481–18.4338; p = 0.0175). When analyzed together, the 80AG+AA genotypes showed a trend toward association (OR = 3.3033; 95 % CI = 1.0586–10.3080; p = 0.0563). Our results suggest that individuals carriers of genotype AA for the SLC19A1 gene present risk for the development of neuroblastoma and possibly have difficulty in absorption of folic acid by the cells, and this may adversely affect the metabolism of folate causing genomic instability and promoting the development of cancer. This is the first retrospective/prospective study to examine the relationship between polymorphisms of folate pathway genes and risk of neuroblastoma.     

SSU Ribosomal DNA-Based Monitoring of Nematode Assemblages Reveals Distinct Seasonal Fluctuations within Evolutionary Heterogeneous Feeding Guilds

Soils are among the most complex, diverse and competitive habitats on Earth and soil biota are responsible for ecosystem services such as nutrient cycling, carbon sequestration and remediation of freshwater. The extreme biodiversity prohibits the making of a full inventory of soil life. Hence, an appropriate indicator group should be selected to determine the biological condition of soil systems. Due to their ubiquity and the diverse responses to abiotic and biotic changes, nematodes are suitable indicators for environmental monitoring. However, the time-consuming microscopic analysis of nematode communities has limited the scale at which this indicator group is used. In an attempt to circumvent this problem, a quantitative PCR-based tool for the detection of a consistent part of the soil nematofauna was developed based on a phylum-wide molecular framework consisting of 2,400 full-length SSU rDNA sequences. Taxon-specific primers were designed and tested for specificity. Furthermore, relationships were determined between the quantitative PCR output and numbers of target nematodes. As a first field test for this DNA sequence signature-based approach, seasonal fluctuations of nematode assemblages under open canopy (one field) and closed canopy (one forest) were monitored. Fifteen taxa from four feeding guilds (covering ∼ 65% of the free-living nematode biodiversity at higher taxonomical level) were detected at two trophic levels. These four feeding guilds are composed of taxa that developed independently by parallel evolution and we detected ecologically interpretable patterns for free-living nematodes belonging to the lower trophic level of soil food webs. Our results show temporal fluctuations, which can be even opposite within taxa belonging to the same guild. This research on nematode assemblages revealed ecological information about the soil food web that had been partly overlooked.