A5048575461- Plant Molecular Biology Research
- Plant Disease Resistance and Genetics
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Wheat and Barley Genetics and Pathology
- Rice Cultivation and Yield Improvement
- Plant nutrient uptake and metabolism
- Legume Nitrogen Fixing Symbiosis
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Botanical Research and Chemistry
- Plant-Microbe Interactions and Immunity
- Bryophyte Studies and Records
- Plant Reproductive Biology
- Machine Learning in Bioinformatics
- Plant Stress Responses and Tolerance
- Silicon Effects in Agriculture
- Plant Gene Expression Analysis
- Botany and Plant Ecology Studies
- Bacteriophages and microbial interactions
- Genetic and Environmental Crop Studies
- Nitrogen and Sulfur Effects on Brassica
- Plant Pathogens and Resistance
- Genomics and Chromatin Dynamics
Adam Mickiewicz University in Poznań
2015-2024
Institute of Molecular Biology and Biotechnology
2015-2023
University of Life Sciences in Poznań
2020
Laboratoire des Sciences de l’Information et de la Communication
2010
Bioinformatics Institute
2010
Institute of Bioinformatics and Systems Biology
2004
Translational Genomics Research Institute
2004
Rutgers, The State University of New Jersey
2004
University of Arizona
2004
University of California, Los Angeles
1998-2003
Abstract Receptor-like kinases (RLKs) belong to the large RLK/Pelle gene family, and it is known that Arabidopsis thaliana genome contains >600 such members, which play important roles in plant growth, development, defense responses. Surprisingly, we found rice (Oryza sativa) has nearly twice as many members does, not simply a consequence of larger predicted number rice. From inferred phylogeny all estimated common ancestor had >440 RLK/Pelles large-scale expansions certain...
MicroRNAs are the key post-transcriptional regulators of gene expression in development and stress responses. Thus, precisely quantifying level each particular microRNA is utmost importance when studying biology any organism. The mirEX 2.0 web portal ( http://www.combio.pl/mirex ) provides a comprehensive platform for exploration data based on quantitative Real Time PCR NGS sequencing experiments, covering various developmental stages, from wild-type to mutant plants. includes mature...
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides single access point to 44 resources and >18 million ncRNA from wide range organisms types. now also includes secondary (2D) structure information for >13 sequences, making the world's largest 2D database. The diagrams are displayed using R2DT, new visualization method uses consistent, reproducible recognizable layouts related RNAs. sequence similarity search has been updated with faster interface...
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences all types from broad range organisms. We have recently added new genome mapping pipeline that identifies genomic locations for in 296 species. also several functional annotations, such as tRNA secondary structures, Gene Ontology and miRNA-target interactions. A quality control mechanism based Rfam family assignments potential contamination, incomplete more. The has become...
RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides single entry point for accessing all types organisms. Since its launch in 2014, has integrated twelve new resources, taking the total number collaborating to 22, began importing data, such as modified nucleotides MODOMICS PDB. We created species-specific identifiers refer unique within context species. The website been subject continuous improvements focusing on...
Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of clearly defined benchmarking consensus hampers their performance assessment.Here, we present community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas sequence-based research. We characterize 74 methods available 24 software tools five...
Arabidopsis microRNA expression regulation was studied in a wide array of abiotic stresses such as drought, heat, salinity, copper excess/deficiency, cadmium excess, and sulfur deficiency. A home-built RT-qPCR mirEX platform for the amplification 289 transcripts used to study their response stresses. Small RNA sequencing, Northern hybridization, TaqMan® assays were performed abundance mature microRNAs. broad on level primary miRNAs (pri-miRNAs) observed. However, stress at microRNAs rather...
The influence of the histone variant H2A.Z on transcription remains a long-standing conundrum. Here, by analyzing actin-related protein6 mutant, which is impaired in deposition, and profiling stress conditions, we investigated impact this gene expression Arabidopsis thaliana We demonstrate that arp6 mutant exhibits anomalies response to osmotic stress. Indeed, stress-responsive genes are overrepresented among those hyperactive arp6. In wild-type plants, these exhibit high levels body....
Zea mays L. ssp. , or corn, one of the most important crops and a model for plant genetics, has genome ≈80% size human genome. To gain global insight into organization its genome, we have sequenced ends large insert clones, yielding cumulative length one-eighth with DNA sequence read every 6.2 kb, thereby describing percentage genes transposable elements maize in an unbiased approach. Based on accumulative 307 Mb sequence, repeat sequences occupy 58% genic regions 7.5%. A conservative...
In animals, steroid hormones regulate gene expression by binding to nuclear receptors. Plants lack genes for receptors, yet genetic evidence from Arabidopsis suggests developmental roles lipids/sterols analogous those in animals. contrast the lipid/sterol-binding StAR-related lipid transfer (START) protein domains are conserved, making them candidates involvement both animal and plant lipid/sterol signal transduction.
Here we report on the characterization of rice osa-miR827 and its two target genes, OsSPX-MFS1 OsSPX-MFS2, which encode SPX-MFS proteins predicted to be implicated in phosphate (Pi) sensing or transport. We first show by Northern blot analysis that is strongly induced Pi starvation both shoots roots. Hybridization situ confirms strong induction starvation, with signals concentrated mesophyll, epidermis ground tissues In parallel, analyzed responses OsSPX-MFS2 gene targets starvation. mRNA...
Heat stress is one of the major abiotic factors that can induce severe plant damage, leading to a decrease in crop productivity. Despite barley being cereal great economic importance, few data are available concerning its thermotolerance mechanisms. In this work microRNAs (miRNAs) involved heat response were investigated. The level selected mature miRNAs was examined by hybridization. Quantitative real-time PCR (RT-qPCR) used monitor changes expression profiles primary miRNA (pri-miRNA)...
Summary Liverworts are the most basal group of extant land plants. Nonetheless, molecular biology liverworts is poorly understood. Gene expression has been studied in only one species, Marchantia polymorpha . In particular, no microRNA (miRNA) sequences from have reported. Here, Illumina‐based next‐generation sequencing was employed to identify small RNAs, and analyze transcriptome degradome Pellia endiviifolia Three hundred eleven conserved miRNA plant families were identified, 42 new...
Ribosomal 5S RNA (5S rRNA) is the ubiquitous component found in large subunit of ribosomes all known organisms. Due to its small size, abundance and evolutionary conservation rRNA for many years now used as a model molecule studies on structure, RNA–protein interactions molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) first database that provides high quality reference set ribosomal RNAs across three domains life. Here, we give an overview new developments associated web tools since...
In wheat, adult plant resistance (APR) to leaf rust (Puccinia triticina), is effective in restricting pathogen growth and provides durable against a wide range of virulent forms P. triticina. Despite the importance, there limited knowledge on molecular basis this type resistance. We isolated characterized wall-associated kinase encoding gene assigned it as TaWAK6. Localization TaWAK6 homeologs A B wheat subgenomes was consistent with presence gene's orthologs T. urartu (AA) dicoccoides...
Copy number variations (CNVs) greatly contribute to intraspecies genetic polymorphism and phenotypic diversity. Recent analyses of sequencing data for >1000 Arabidopsis (Arabidopsis thaliana) accessions focused on small did not include CNVs. Here, we performed genome-wide analysis identified large indels (50 499 bp) CNVs (500 bp larger) in these accessions. The fully overlap with 18.3% protein-coding genes, enrichment evolutionarily young genes involved stress defense. By combining both...
MicroRNAs (miRNAs) are major regulators of gene expression during plant development under normal and stress conditions. In this study, we analyzed the 150 conserved miRNAs drought applied to barley ready flower. The dynamics was also observed after rewatering. Target messenger RNA (mRNAs) were experimentally identified for all but two miRNAs, 41 targets not reported before. Drought induced accelerated flowering coordinated by a pair differently expressed originating from single precursor:...
Domains in Arabidopsis proteins NRPE1 and SPT5-like, composed almost exclusively of repeated motifs which only WG or GW sequences an overall amino-acid preference are conserved, have been experimentally shown to bind multiple molecules Argonaute (AGO) protein(s). Domain swapping between the WG/GW domains human protein GW182 showed a conserved function . As classical sequence alignment methods poorly-adapted detect such weakly-conserved motifs, we developed tool carry out systematic analysis...
mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT–qPCR-based gene profiles are stored in universal and expandable database scheme wrapped by an intuitive user-friendly interface. A new way accessing data includes simple mouse operated querying system dynamic graphs mining analyses. In contrast to other publicly available databases, the interface allows simultaneous comparison levels between various genes diverse organs developmental stages....
Abstract Background MicroRNAs (miRNAs) regulate gene expression via mRNA cleavage or translation inhibition. In spite of barley being a cereal great economic importance, very little data is available concerning its miRNA biogenesis. There are 69 and 67 pre-miRNA sequences in the miRBase (release 19). However, no pri-miRNA MIR structures have been shown experimentally. present paper, we examine biogenesis selected miRNAs developmental regulation their processing to learn more about maturation...