Project description:Analysis of the covalent attachment of GMP to the RNA dependent RNA polymerase proteins of equine arteritis virus and SARS-CoV-2 proteins using heavy-isotope assisted MS and MS/MS peptide sequencing.
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
Project description:Fruit trees, as apricots, can be infected by and are constantly exposed to the attack of viruses. As they are propagated on a vegetative way, this risk is present not only at the field, where they exists for decades, but also during propagation. Metagenomic diagnostic methods, based on next generation sequencing, offer unique possibilities to reveal all the presenting pathogens in the investigated sample. Using small RNA NGS, a special fields of this technique, we tested leaf samples of different varieties of apricot in isolator house and at open air stock nursery. As a result, we identified Cherry Virus A (CVA) and Little Cherry Virus1 (LChV1) first time in Hungary. Gained results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral PCR products enabled us to investigate their phylogenetic relationships. Our results demonstrate, that small RNA NGS can offer a sensitive virus diagnostics method, moreover beside obligatory tested viruses we could detect CVA and LChV1. However as these pathogens haven’t been described in our country before, their role in symptom development and modification during coinfection with other viruses requires further investigations.
Project description:Virus elimination is indispensable for the maintenance of stone fruit plantations, because these pathogens can cause serious crop damage and crop losses. Currently we do not possess efficient plant protection methods against viruses therefore prevention has a prominent role. In order to prevent infections, pathogen-free propagation material production and application of effective diagnostic methods have essential role. Our examined peach samples derived from isolator houses and stock nurseries of Fruitculture Research Institute of NARIC. With the help of highly sensitive metagenomic diagnostic methods: such as next generation sequencing of small RNAs, we are able to detect all of the presenting pathogens within our samples. During preparation steps, total RNA was isolated from leaf samples, RNA pools were made from the varieties, and then small RNA libraries were prepared. Sequencing was performed on Illumina platform and we used CLC Genomics Workbench for the bioinformatics evaluation. Results were verified by RT-PCR and Northern-blot. PCR products were cloned into pJET vector and Sanger sequenced. As a result, we detected nectarine stem pitting-associated virus (NSPaV), peach associated luteovirus (PaLV) and also peach latent mosaic viroid (PLMVd) which presence has to be checked regularly. Moreover we proved the incidence of PLMVd and PaLV first time in Hungary. We suspect, that the source of the viral infection might be the propagation material, which was used as a base for the variety collection in this isolator house.
Project description:Human mucosal surfaces contain a wide range of microorganisms. The biological effects of these organisms are largely unknown. Large-scale metagenomic sequencing is emerging as a method to identify novel microbes. Unexpectedly, we identified DNA sequences homologous to virus ATCV-1, an algal virus not previously known to infect humans, in oropharyngeal samples obtained from healthy adults. The presence of ATCV-1 was associated with a modest but measurable decrease in cognitive functioning. A relationship between ATCV-1 and cognitive functioning was confirmed in a mouse model, which also indicated that exposure to ATCV-1 resulted in changes in gene expression within the brain. Our study indicates that viruses in the environment not thought to infect humans can have biological effects.
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.