Mapping of the Influenza-A Hemagglutinin Serotypes Evolution by the ISSCOR Method

Analyses and visualizations by the ISSCOR method of influenza virus hemagglutinin genes of different A-subtypes revealed some rather striking temporal relationships between groups of individual gene subsets. Based on these findings we consider application of the ISSCOR-PCA method for analyses of large sets of homologous genes to be a worthwhile addition to a toolbox of genomics - allowing for a rapid diagnostics of trends, and ultimately even aiding an early warning of newly emerging epidemiological threats.Comment: 26 pages with figures (Figs. 1-4 in the main text, and Figs. S1-S5 in supplementary materials

Effect of genomic and subgenomic leader sequences of potato leafroll virus on gene expression

AbstractThe effect of the genomic and subgenomic leader sequence of potato leafroll polerovirus on the efficiency of translation of the downstream located genes has been studied. The results obtained in vitro and in vivo indicate that neither leader sequence functions as translational enhancer, a generally important feature of leader sequences. Deletion analyses demonstrated that both leader sequences not only decrease translation of the downstream located genes but also alter the ratio of the synthesized proteins. A correlation between the in vitro and in vivo results can be established in the case of the subgenomic leader sequence

Antibody response to DNA vaccine against H5N1 avian influenza virus in broilers immunized according to three schedules.

Broiler type chickens were immunized intramuscularly with a DNA vaccine encoding hemagglutinin (HA) from H5N1 avian influenza virus. The chickens were divided into four groups: control group which was not immunized, a group which obtained only one dose, and two groups which were immunized twice, one group with a boost two weeks after the priming and the other four weeks. Blood samples were collected at several time points and the dynamics of the humoral response to the vaccine was studied. High level of anti-HA antibodies was detected only in the last two groups, that is in chickens immunized according to the prime-boost strategy, regardless of the schedule. An additional interesting observation of this study was detection of the cross-reactivity of an anti-H5 HA positive serum with H5N2 and H1N1 viruses, suggesting that the DNA vaccine tested can induce antibodies of a broad specificity

A highly sensitive electrochemical genosensor based on Co-porphyrin-labelled DNA

We report the use of Co-porphyrins as electrochemical tags for a highly sensitive and selective genosensor. An avian influenza virus-based DNA sequence characteristic of H5N1 was detected at femtomolar levels from competing non-complementary sequences through hybridisation with the labeled DNA

Time-Course Microarray Analysis Reveals Differences between Transcriptional Changes in Tomato Leaves Triggered by Mild and Severe Variants of Potato Spindle Tuber Viroid

Viroids are small non-capsidated non-coding RNA replicons that utilize host factors for efficient propagation and spread through the entire plant. They can incite specific disease symptoms in susceptible plants. To better understand viroid-plant interactions, we employed microarray analysis to observe the changes of gene expression in ‘Rutgers’ tomato leaves in response to the mild (M) and severe (S23) variants of potato spindle tuber viroid (PSTVd). The changes were analyzed over a time course of viroid infection development: (i) the pre-symptomatic stage, (ii) early symptoms, (iii) full spectrum of symptoms and (iv) the so-called ‘recovery’ stage, when stem regrowth was observed in severely affected plants. Gene expression profiles differed depending on stage of infection and variant. In S23-infected plants, the expression of over 3,000 genes was affected, while M-infected plants showed 3-fold fewer differentially expressed genes, only 20% of which were specific to the M variant. The differentially expressed genes included many genes related to stress; defense; hormone metabolism and signaling; photosynthesis and chloroplasts; cell wall; RNA regulation, processing and binding; protein metabolism and modification and others. The expression levels of several genes were confirmed by nCounter analysis

Electrochemical genosensor based on disc and screen printed goldelectrodes for detection of specific DNA and RNA sequences derivedfrom Avian Influenza Virus H5N1

tThe genosensors based on thiolated ssDNA probe deposited on the two types of gold electrodes: screen-printed (miniaturized) and disc electrodes destined for determination of specific sequences of DNA andRNA derived from Avian Influenza Virus H5N1 have been proposed. The working principle of genosensor isbased on the ion-channel mechanism. The analytical signals generated upon hybridization processes wererecorded using electrochemical technique – Osteryoung square wave voltammetry in the presence of aredox active marker [Fe(CN)6]3−/4−in the sample solution. The miniaturized genosensor based on screenprinted gold electrodes was able to detect the 20-mer complementary DNA oligonucleotide sequence aswell as ∼280-mer RNA sequences containing the complementary 20-mer sequence in various positions:at 3�-terminus, at 5�-terminus and in the middle of the RNA transcript at the 1 pM concentration. Themeasuring systems were selective. Non-complementary 20-mer oligonucleotide sequence as well asRNA transcript without complementary region generated weak response. The RNA transcripts were alsotested with gold disc electrodes modified in the same manner. This device was able to detect ∼280-mer RNA sequences, but at higher concentration of 10 pM. The good discrimination of the position ofcomplementary part in the ∼280-mer RNA sequences was observed with using both types of modifiedelectrodes

Root Transcriptomic Analysis Reveals Global Changes Induced by Systemic Infection of Solanum lycopersicum with Mild and Severe Variants of Potato Spindle Tuber Viroid

Potato spindle tuber viroid (PSTVd) causes systemic infection in plant hosts. There are many studies on viroid-host plant interactions, but they have predominantly focused on the aboveground part of the plant. Here, we investigated transcriptomic profile changes in tomato roots systemically infected with mild or severe PSTVd variants using a combined microarray/RNA-seq approach. Analysis indicated differential expression of genes related to various Gene Ontology categories depending on the stage of infection and PSTVd variant. A majority of cell-wall-related genes were down-regulated at early infection stages, but at the late stage, the number of up-regulated genes increased significantly. Along with observed alterations of many lignin-related genes, performed lignin quantification indicated their disrupted level in PSTVd-infected roots. Altered expression of genes related to biosynthesis and signaling of auxin and cytokinin, which are crucial for lateral root development, was also identified. Comparison of both PSTVd infections showed that transcriptional changes induced by the severe variant were stronger than those caused by the mild variant, especially at the late infection stage. Taken together, we showed that similarly to aboveground plant parts, PSTVd infection in the underground tissues activates the plant immune response