Transcriptomic profile of host response in Japanese encephalitis virus infection

Background

The attenuated Yellow fever (YF) 17D vaccine virus is one of the safest and most effective viral vaccines administered to humans, in which it elicits a polyvalent immune response. Herein, we used the YF 17D backbone to express a Trypanosoma cruzi CD8⁺ T cell epitope from the Amastigote Surface Protein 2 (ASP-2) to provide further evidence for the potential of this virus to express foreign epitopes. The TEWETGQI CD8⁺ T cell epitope was cloned and expressed based on two different genomic insertion sites: in the fg loop of the viral Envelope protein and the protease cleavage site between the NS2B and NS3. We investigated whether the site of expression had any influence on immunogenicity of this model epitope.

Results

Recombinant viruses replicated similarly to vaccine virus YF 17D in cell culture and remained genetically stable after several serial passages in Vero cells. Immunogenicity studies revealed that both recombinant viruses elicited neutralizing antibodies to the YF virus as well as generated an antigen-specific gamma interferon mediated T-cell response in immunized mice. The recombinant viruses displayed a more attenuated phenotype than the YF 17DD vaccine counterpart in mice. Vaccination of a mouse lineage highly susceptible to infection by T. cruzi with a homologous prime-boost regimen of recombinant YF viruses elicited TEWETGQI specific CD8⁺ T cells which might be correlated with a delay in mouse mortality after a challenge with a lethal dose of T. cruzi.

Conclusions

We conclude that the YF 17D platform is useful to express T. cruzi (Protozoan) antigens at different functional regions of its genome with minimal reduction of vector fitness. In addition, the model T. cruzi epitope expressed at different regions of the YF 17D genome elicited a similar T cell-based immune response, suggesting that both expression sites are useful. However, the epitope as such is not protective and it remains to be seen whether expression of larger domains of ASP-2, which include the TEWETGQI epitope, will elicit better T-CD8+ responses to the latter. It is likely that additional antigens and recombinant virus formulations will be necessary to generate a protective response.     

Predictive value of ERCC1 single-nucleotide polymorphism in patients receiving platinum-based chemotherapy for locally-advanced and advanced non-small cell lung cancer--a pilot study

Platinum-based chemotherapy is the main type of I-line treatment of advanced and non-operative NSCLC patients without EGFR gene mutation. The excision repair cross-complementation group 1 (ERCC1) is an enzyme that executes the incision of the damaged DNA strand and removes platinum-induced DNA adducts. We investigated whether ERCC1 gene polymorphism has an effect on the response to chemotherapy and survival in 43 patients with NSCLC treated with platinum-based chemotherapy. ERCC1 19007 T>C SNPs were assessed using a PCR-RFLP methods in DNA isolated from peripheral blood lymphocytes. Disease control occurred significantly (p = 0.045) more frequently in patients with CC or CT genotype compared to patients with TT genotype. Median PFS and OS for CC homozygous were 4 and 10.5 months, 4 and 12.5 months for CT heterozygous, but only 0.3 and 1.5 months for TT homozygous patients, respectively. The probability of PFS was significantly higher (HR = 0.438, 95% CI: 0.084-0.881, p = 0.03) and probability of OS was insignificantlyhigher (HR = 0.503, 95% CI: 0.129-1.137, p = 0.084) in patients with CC or CT genotype than in patients with TT genotype. Uncommon TT genotype of ERCC1 19007 T>C polymorphism could predict poor response and shortening of progression free survival in NSCLC patients treated with platinum-based I-line chemotherapy. The analysis of this polymorphism may serve as a promising tool in the qualification of advanced NSCLC patients for appropriate chemotherapy.     

A comprehensive framework for the study of species co‐occurrences,nestedness and turnover

Binary presence–absence matrices (rows = species, columns = sites) are often used to quantify patterns of species co‐occurrence, and to infer possible biotic interactions from these patterns. Previous classifications of co‐occurrence patterns as nested, segregated, or modular have led to contradictory results and conclusions. These analyses usually do not incorporate the functional traits of the species or the environmental characteristics of the sites, even though the outcomes of species interactions often depend on trait expression and site quality. Here we address this shortcoming by developing a method that incorporates realized functional and environmental niches, and relates them to species co‐occurrence patterns. These niches are defined from n‐dimensional ellipsoids, and calculated from the n eigenvectors and eigenvalues of the variance–covariance matrix of measured environmental or trait variables. Average niche overlap among species and the spatial distribution of niches define a triangle plot with vertices of species segregation (low niche overlap), nestedness (high niche overlap), and modular co‐occurrence (clusters of overlapping niches). Applying this framework to temperate understorey plant communities in southwest Poland, we found a consistent modular structure of species occurrences, a pattern not detected by conventional presence–absence analysis. These results suggest that, in our case study, habitat filtering is the most important process structuring understorey plant communities. Furthermore, they demonstrate how incorporating trait and environmental data into co‐occurrence analysis improves pattern detection and provides a stronger theoretical framework for understanding community structure.     

Reconstructed historical distribution and phylogeography unravels non-steppic origin of <Emphasis Type="Italic">Caucasotachea vindobonensis</Emphasis> (Gastropoda: Helicidae)

Existing data on the phylogeography of European taxa of steppic provenance suggests that species were widely distributed during glacial periods but underwent range contraction and fragmentation during interglacials into “warm-stage refugia.” Among the steppe-related invertebrates that have been examined, the majority has been insects, but data on the phylogeography of snails is wholly missing. To begin to fill this gap, phylogeographic and niche modeling studies on the presumed steppic snail Caucasotachea vindobonensis were conducted. Surprisingly, reconstruction of ancestral areas suggests that extant C. vindobonensis probably originated in the Balkans and survived there during the Late Pleistocene glaciations, with a more recent colonization of the Carpatho-Pannonian and the Ponto-Caspian regions. In the Holocene, C. vindobonensis colonized between the Sudetes and the Carpathians to the north, where its recent and current distribution may have been facilitated by anthropogenic translocations. Together, these data suggest a possible non-steppic origin of C. vindobonensis. Further investigation may reveal the extent to which the steppic snail assemblages consist partly of Holocene newcomers.     

Hierarchically structured scleractinian coral biocrystals

Microscopic (AFM and FESEM) observations show that scleractinian coral biomineral fibers in extant Desmophyllum and Favia, and fossil Jurassic Isastrea are composed of nanocrystalline grains of about 30-100 nm in size. In contrast to these findings, SR diffraction data on the same coral materials exhibit narrow Bragg peaks suggesting much larger crystallite size. These seemingly contradicting results of microscopic and diffraction studies are reconciled within a new, minute-scale model of scleractinian biomineral fibers. In this model, nanocrystalline aragonite units are interconnected by mineral bridges and form aggregates usually larger than 200 nm. Most likely, the size of the aggregates is resulting from physiological biomineralization cycles that control cellular secretion of ions and biopolymeric species. Intercalation of biopolymers into crystal lattice may influence consistently several structural parameters of the scleractinian coral bio-aragonite in all studied samples: (i) the lattice parameters and internal strains of the bio-aragonite are larger than in mineral aragonite, (ii) lattice parameter elongations and internal strains reveal directional anisotropy with respect to crystallographic axes.     

Structural basis of developmental plasticity in the corticostriatal system

Previous studies have shown that in developing monkey corticostriatal fibres terminate around striatal cytoarchitectonic compartments--cell islands, showing transfiguration around 105th embryonic day (E105) of gestation. In the present study we have analyzed these striatal cytoarchitectonic islands and acetylcholinesterase (AChE) rich patches in the developing human brain considering them as structural indicators of the development of the corticostriatal pathways. Postmortal brain tissue of 27 fetuses and prematurely born infants, ranging from 11-34 postovulatory weeks (POW) whose deaths were attributed to non neurological causes, were processed by Nissl method, AChE histochemistry and imunocytochemical technique (synaptophysin). All specimens are part of the Zagreb Neuroembryological Collection. Initial AChE patches, presumably corresponding to the dopaminergic islands, were seen as early as 10 POW whereas cytoarchitectonical cell islands were not observed until 14 POW The main developmental change occurs between 20-24 POW when AChE negative cell poor zones develop around cell islands. This transient AChE pattern of striatal organization reaches its peak around 28 POW being most prominent along lateral border of putamen. In one case of periventricular hemorrhagic lesion with premortem survival period we have found reorganization of AChE patches in the putamen which indicates structural plasticity of corticostriatal pathways. In conclusion we propose that cell poor zones serve as waiting compartments for growing corticostriatal fibers which approach striatum through subcallosal bundle and external capsule. The period of the existence of striatal compartments (14-30 POW) is a sensitive period for structural plasticity and vulnerability after periventricular lesions.     

Contextual alignment of biological sequences (Extended abstract)

We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which we assume that the cost of a substitution depends on the surrounding symbols. In this model the cost of transforming one sequence into another depends on the order of editing operations. We present efficient algorithms for calculating this cost, as well as reconstructing (the representation of) all the orders of operations which yield this optimal cost. A precise characterization of the families of linear orders which can emerge this way is given.     

Current state and vegetation history of spring-fed fens in Western Pomerania (Northern Poland): a case study of the Chociel River valley

Wetlands Ecology and Management - Alkaline spring-fed fens are a rare type of soligeneous wetlands, characterised by an alternating arrangement of layers of peat and calcareous tufa, defined as the...     

Nuclear changes in tongue epithelial cells following panoramic radiography

This study aimed to investigate the effect of radiation from panoramic radiographs on the cells of the lateral border of the tongue by evaluating nuclear changes. Forty-two patients were included: 22 had one radiograph (Group I), and 20 required a repeat radiograph due to error in the first exposure (Group II). Material for the cytopathologic evaluation was collected before radiographs and 10 days later. Smears were stained with the Feulgen reaction and micronuclei, buds, broken eggs, karyorrhexis and binucleate cells were scored. The comparison of nuclear changes before and after radiation exposure in both groups revealed a statistically higher number of broken eggs, buds, karyorrhexis and binucleate cells 10 days after exposure (P=0.01). The number of karyorrhexis and binucleate cells was greater in group II (P=0.01). There was no change in the frequency of micronuclei before and after the radiographs. Radiation emitted during panoramic radiographs increased the number of nuclear anomalies (except micronuclei) in exfoliated cells of the lateral border of the tongue. This effect was more pronounced when the patients were exposed to a repeat radiograph, without however implying increased risk of irreversible tissue damage.     

Volatiles as Chemosystematic Markers for Distinguishing Closely Related Species within the Pinus mugo Complex

Headspace solid‐phase microextraction (HS‐SPME) coupled to GC/MS analysis was used to identify the constituents of pine‐needle volatiles differentiating three closely‐related pine species within the Pinus mugo complex, i.e., P. uncinata Ramond ex DC., P. uliginosa G.E.Neumann ex Wimm ., and P. mugo Turra . Moreover, chemosystematic markers were proposed for the three analyzed pine species. The major constituents of the pine‐needle volatiles were α‐pinene (28.4%) and bornyl acetate (10.8%) for P. uncinata, δ‐car‐3‐ene (21.5%) and α‐pinene (16.1%) for P. uliginosa, and α‐pinene (20%) and δ‐car‐3‐ene (18.1%) for P. mugo. This study is the first report on the application of the composition of pine‐needle volatiles for the reliable identification of closely‐related pine species within the Pinus mugo complex.