A universal BMV-based RNA recombination system—how to search for general rules in RNA recombination

At present, there is no doubt that RNA recombination is one of the major factors responsible for the generation of new RNA viruses and retroviruses. Numerous experimental systems have been created to investigate this complex phenomenon. Consequently, specific RNA structural motifs mediating recombination have been identified in several viruses. Unfortunately, up till now a unified model of genetic RNA recombination has not been formulated, mainly due to difficulties with the direct comparison of data obtained for different RNA-based viruses. To solve this problem, we have attempted to construct a universal system in which the recombination activity of various RNA sequences could be tested. To this end, we have used brome mosaic virus, a model (+)RNA virus of plants, for which the structural requirements of RNA recombination are well defined. The effectiveness of the new homomolecular system has been proven in an experiment involving two RNA sequences derived from the hepatitis C virus genome. In addition, comparison of the data obtained with the homomolecular system with those generated earlier using the heteromolecular one has provided new evidence that the mechanisms of homologous and non-homologous recombination are different and depend on the virus' mode of replication

Multi-agent model of hepatitis C virus infection

Objectives: The objective of this study is to design a method for modeling hepatitis C virus (HCV) infection using multi-agent simulation and to verify it in practice. Methods and materials: In this paper, first, the modeling of HCV infection using a multi-agent system is compared with the most commonly used model type, which is based on differential equations. Then, the implementation and results of the model using a multi-agent simulation is presented. To find the values of the parameters used in the model, a method using inverted simulation flow and genetic algorithm is proposed. All of the data regarding HCV infection are taken from the paper describing the model based on the differential equation to which the proposed method is compared. Results: Important advantages of the proposed method are noted and demonstrated; these include flexibility, clarity, re-usability and the possibility to model more complex dependencies. Then, the simulation framework that uses the proposed approach is successfully implemented in C++ and is verified by comparing it to the approach based on differential equations. The verification proves that an objective function that performs the best is the function that minimizes the maximal differences in the data. Finally, an analysis of one of the already known models is performed, and it is proved that it incorrectly models a decay in the hepatocytes number by 40%. Conclusions: The proposed method has many advantages in comparison to the currently used model types and can be used successfully for analyzing HCV infection. With almost no modifications, it can also be used for other types of viral infections

A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Plastids are small organelles equipped with their own genomes (plastomes). Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (PlasTi-microarray) consisting of 1629 oligonucleotide probes. The oligonucleotides were designed based on the cucumber chloroplast genomic sequence and targeted both strands of the plastome in a non-contiguous arrangement. Up to 4 specific probes were designed for each gene/exon, and the intergenic regions were covered regularly, with 70-nt intervals. We also developed a protocol for direct chemical labeling and hybridization of as little as 2 micrograms of chloroplast RNA. We used this protocol for profiling the expression of the cucumber chloroplast plastome on the PlasTi-microarray. Owing to the high sequence similarity of plant plastomes, the newly constructed microarray can be used to study plants other than cucumber. Comparative hybridization of chloroplast transcriptomes from cucumber, Arabidopsis, tomato and spinach showed that the PlasTi-microarray is highly versatile

Pulmonary presentation of Toxocara sp. infection in children

Wstęp: Celem pracy jest ocena związku pomiędzy zmianami radiologicznymi, eozynofilią obwodową, hiperimmunoglobulinemią E i G oraz Toxocara sp. seropozytywnością u dzieci polskich z nowo rozpoznawanymi zmianami płucnymi. Materiał i metody: Retrospektywnie przeanalizowano dokumentację 119 pacjentów w wieku 1 do 18 lat (średnio: 7,21 ± 4,82) z dodatnimi przeciwciałami w kierunku Toxocara sp. Oceniono eozynofilię obwodową, liczbę leukocytów, stężenie IgE całkowitych, IgG oraz specyficznych przeciwciał przeciw antygenowi wydzielniczemu Toxocara, które badano w chwili rozpoznania zakażenia. U wszystkich dzieci przeprowadzono rutynowe badanie radiologiczne płuc. Wyniki: W dokumentacji 23 dzieci (średnia wieku: 3,58 ± 2,63) stwierdzono nieprawidłowości obrazu radiologicznego płuc. Piętnaścioro dzieci, u których występowały zmiany radiologiczne prezentowało: przewlekły kaszel, świsty, astmę i krwioplucie. U 8 dzieci nie stwierdzono objawów klinicznych zakażenia. Analiza poziomu eozynofilii obwodowej, ilości leukocytów, poziomu IgE całkowitych oraz specyficznych IgG wykazała, iż mają one wartości wyższe u dzieci ze zmianami radiologicznymi niż u dzieci bezobjawowych. Stężenie IgG całkowitych oraz gammaglobulin nie były statystycznie znamiennie różne. U 10 pacjentów KT wykazało obecność owalnych, nieregularnych guzków o średnicy 1 do 13 mm, z lub bez “otoczki halo. Liczba guzków wahała się od pojedynczej zmiany do licznych, rozsianych. Wszystkie zlokalizowane były w częściach obwodowych płuc. 13 pacjentów prezentowało zmiany lokalne o typie mlecznej szyby". U żadnego  z badanych dzieci nie występowała limfadenopatia i nacieki opłucnej. Wnioski: Zmiany płucne z wysoką eozynofilią oraz hiperimunoglobulinemią E mogą być związane z toksokarozą i dlatego w przypadku ich stwierdzenia należy rozważać wdrożenie leczenia z długofalową obserwacją następczą, niż agresywne procedury onkologiczne.Introduction: The aim of this study was to investigate the associations between radiological findings, blood eosinophilia, hyperimmunoglobulinemia E and G and Toxocara seropositivity in Polish children with newly diagnosed pulmonary infiltration. Material and methods: We retrospectively analyzed the documentation of 119 patients, aged 1 to 18 years (mean age: 7.21 ± 4.82), who were seropositive in Toxocara sp. antibodies. In all cases, peripheral blood eosinophils and leukocyte counts, serum total IgE, IgG levels and specific IgG antibodies against excretory and secretory Toxocara sp. antigens were measured at the first presentation. After the confirmation of seropositivity, all children had a routine radiological examination. Results: In the documentation of 23 children (mean age 3.58 ± 2.63 years) we found abnormalities in the radiological examination of their lungs. Fifteen children who had abnormalities in radiological findings presented clinical respiratory complaints such as chronic cough, wheezing, asthma and haemoptysis. Eight children were asymptomatic. The analysis of peripheral eosinophils and leukocyte number, the level of IgE and specific anti-Toxocara IgG presented significantly higher values in children with radiological lesions than in children who had correct radiology. The concentrations of total IgG and gamma globulins were not significantly different. In 10 patients CT showed irregular round nodules with and without halo ranging from 1 to 13 mm. The number of nodules varied from a single lesion to multiple, disseminated ones. All nodules were located in peripheral areas of the lungs. None of them were found in the central areas. In 13 patients, CT images showed ground-glass opacities with ill-defined margins. None of the CT images presented lymphadenopathy and pleural effusion. Conclusion: The pulmonary lesions in small children with high eosinophilia and hyperimmunoglobulinemia E could be related to toxocariasis and for this reason they are eligible to undergo therapy with prolonged observation for several months, rather than start invasive malignancy investigations

Hepatitis C virus quasispecies in chronically infected children subjected to interferon–ribavirin therapy

Accumulating evidence suggests that certain features of hepatitis C virus (HCV), especially its high genetic variability, might be responsible for the low efficiency of anti-HCV treatment. Here, we present a bioinformatic analysis of HCV-1a populations isolated from 23 children with chronic hepatitis C (CHC) subjected to interferon–ribavirin therapy. The structures of the viral quasispecies were established based on a 132-amino-acid sequence derived from E1/E2 protein, including hypervariable region 1 (HVR1). Two types of HCV populations were identified. The first type, found in non-responders, contained a small number of closely related variants. The second type, characteristic for sustained responders, was composed of a large number of distantly associated equal-rank variants. Comparison of 445 HVR1 sequences showed that a significant number of variants present in non-responding patients are closely related, suggesting that certain, still unidentified properties of the pathogen may be key factors determining the result of CHC treatment