A5089616013- Gut microbiota and health
- Dermatology and Skin Diseases
- RNA modifications and cancer
- Circular RNAs in diseases
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Livestock and Poultry Management
- Animal Nutrition and Physiology
- Diverse Educational Innovations Studies
- MicroRNA in disease regulation
- Cancer Immunotherapy and Biomarkers
- Cancer-related molecular mechanisms research
- Education and Critical Thinking Development
- Genomics and Phylogenetic Studies
- Engineering Education and Pedagogy
- Nonmelanoma Skin Cancer Studies
- Pharmaceutical and Antibiotic Environmental Impacts
- Forensic Anthropology and Bioarchaeology Studies
- Engineering Education and Curriculum Development
- Antibiotic Resistance in Bacteria
- Bacteriophages and microbial interactions
- Computational Drug Discovery Methods
- Design Education and Practice
- Forensic and Genetic Research
- Oral Health Pathology and Treatment
Institute of Bioorganic Chemistry, Polish Academy of Sciences
2016-2025
University of Memphis
2020
International Institute of Molecular and Cell Biology
2011-2013
Adam Mickiewicz University in Poznań
2012-2013
Purdue University West Lafayette
1919-1923
American Jewish Committee
1918
We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess leading edge techniques; compare existing methods and tools; evaluate their relative strengths, weaknesses, limitations terms sequence length structural complexity. should give potential users insight into suitability available for different applications facilitate efforts community ongoing improve tools. also...
Recent studies revealed a significant role of the gut fungal community in human health. Here, we investigated content and variation mycobiota among subjects from European population. We explored interplay between fungi various host-related sociodemographic, lifestyle, health, dietary factors. The study included 923 participants. Fecal DNA samples were analyzed by whole-metagenome high-throughput sequencing. Subsequently, taxonomic profiles determined accompanied computational statistical...
Abstract A growing body of evidence indicates an important role miRNAs in cancer; however, there is no definitive, convenient-to-use list cancer-related or miRNA genes that may serve as a reference for analyses cancer. To this end, we created 165 called the Cancer Census (CMC). The based on score, built various types functional and genetic particular cancer, e.g. miRNA–cancer associations reported databases, with cancer hallmarks, signals positive selection alterations presence...
Abstract Recent research indicates that gut microbiota may be vital in the advancement of melanoma. In this study, we found melanoma patients exhibited a distinct mycobiota structure compared with healthy participants. Candida albicans, dubliniensis, and Neurospora crassa were more abundant samples from melanoma, whereas Saccharomyces cerevisiae Debaryomyces hansenii less abundant. During anti–PD-1 treatment, relative amount Malassezia restricta C. albicans increased. A higher level...
Background The gut microbiome and diet are important factors in the pathogenesis management of Crohn’s disease (CD). However, role phageome under dietary influences is unknown. Objective We aim to explore effect on phageome-bacteriome interaction linking CD protection. Design recruited patients healthy subjects (n=140) conducted a multiomics investigation, including paired ileal mucosa bacteriome profiling, survey phenome interrogation. screened for bacteriome, as well its epidemiological...
RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase number experimentally determined 3D structures enabled structure-based searches for small that can specifically bind defined sites molecules, thereby blocking or otherwise modulating function. However, yet, computational methods docking molecule ligands are not well established analogous protein-ligand docking. This motivated us...
Abstract In recent years, the number of metagenomic studies increased significantly. Wide range factors, including tremendous community complexity and variability, is contributing to challenge in reliable microbiome profiling. Many approaches have been proposed overcome these problems making hardly possible compare results different studies. The significant differences between procedures used research are reflected a variation obtained results. This calls for need standardisation procedure,...
Abstract Motivation: Metal ions are essential for the folding of RNA molecules into stable tertiary structures and often involved in catalytic activity ribozymes. However, positions metal 3D difficult to determine experimentally. This motivated us develop a computational predictor ion sites structures. Results: We developed statistical potential predicting (magnesium, sodium potassium), based on analysis binding experimentally solved The MetalionRNA program is available as web server that...
Abstract Myotonic dystrophy type 1 (DM1) and 2 (DM2) are autosomal dominant neuromuscular disorders associated with expansions of microsatellites, respectively, in DMPK CNBP . Their pathogenesis is linked to the global aberrant alternative splicing (AAS) many genes marks mostly muscular neuronal tissues, while blood least affected. Recent data DM1 skeletal muscles indicated that abnormalities RNA metabolism also include upregulation circular RNAs (circRNAs). CircRNAs a heterogeneous group...
Abstract Research has shown that the microbiome can influence how immune system responds to melanoma cells, affecting course of disease and outcome therapy. Here, we used metagenomic approach flow cytometry analyses blood cells discover correlations between gut fungi metastatic patients enrolled in anti-PD-1 therapy lymphocytes their blood. We analyzed patterns associations before first administration (BT, n = 61) third month (T3, 37), allowing us track changes during treatment. To...
There is a growing interest in the genetic variation of noncoding genomic elements, including miRNAs, and several mutations miRNA genes implicated human diseases, cancer, have already been detected. However, lack dedicated analytical tools severely hampers progress this area. In study, we developed whole-miRNome sequencing (WMS), which enables targeted all (n~2000) 28 biogenesis genes. Herein, by almost 600 samples, ~300 tumor/normal pairs samples from different cancer types, identified...
Splicing aberrations induced as a consequence of the sequestration MBNL splicing factors on DMPK transcript, which contains expanded CUG repeats, present major pathomechanism myotonic dystrophy type 1 (DM1). As MBNLs may also be important involved in biogenesis circular RNAs (circRNAs), we hypothesized that level circRNAs would decreased DM1. To test this hypothesis, selected twenty well-validated and analyzed their levels several experimental systems (e.g., cell lines, DM muscle tissues,...
Abstract Metagenome analysis has become a common source of information about microbial communities that occupy wide range niches, including archaeological specimens. It been shown the vast majority DNA extracted from ancient samples come bacteria (presumably modern contaminants). However, characterization accompanying human remains never done systematically for different samples. We used metagenomic approaches to perform comparative analyses microorganism present in 161 remains. were...
A pool of small RNA fragments (RFs) derived from diverse cellular RNAs has recently emerged as a rich source functionally relevant molecules. Although their formation and accumulation been connected to various stress conditions, the knowledge on RFs produced upon viral infections is very limited. Here, we applied next generation sequencing (NGS) characterize generated in hepatitis C virus (HCV) cell culture model (HCV-permissive Huh-7.5 line). We found that both infected non-infected cells...
Abstract LINE-1 (L1) retrotransposons are mobile genetic elements that create new genomic insertions by a copy-paste mechanism involving L1 RNA/RNP intermediates. encodes two ORFs, of which L1-ORF2p nicks DNA and reverse transcribes mRNA using the nicked as primer base-pairs with poly(A) tail mRNA. To better understand importance non-templated 3′ ends’ dynamics interplay between 5′ ends, we investigated effects knock-outs temporal knock-downs XRN1, DCP2, other factors. We hypothesized in...
Abstract Background Recent advances in the next-generation sequencing (NGS) allowed metagenomic analyses of DNA from many different environments and sources, including thousands years old skeletal remains. It has been shown that most extracted ancient samples is microbial. There are several reports demonstrating considerable fraction belonged to bacteria accompanying studied individuals before their death. Results In this study we scanned 344 microbiomes 1000- 2000- year-old human teeth. The...
RNA-seq is currently the only method that can provide a comprehensive landscape of circular RNA (circRNAs) in whole organism and its particular organs. Recent years have brought an increasing number RNA-seq-based reports on plant circRNAs. Notably, picture they revealed questionable depends applied circRNA identification quantification techniques. In consequence, little known about biogenesis functions circRNAs plants. this work we tested two experimental six bioinformatics procedures...