A5101418672- Silk-based biomaterials and applications
- Viral Infectious Diseases and Gene Expression in Insects
- RNA Research and Splicing
- RNA modifications and cancer
- Silkworms and Sericulture Research
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Genetics, Aging, and Longevity in Model Organisms
- Animal Genetics and Reproduction
- RNA and protein synthesis mechanisms
- Telomeres, Telomerase, and Senescence
- DNA Repair Mechanisms
- Plant Stress Responses and Tolerance
- Planarian Biology and Electrostimulation
- Neuroblastoma Research and Treatments
- Fungal and yeast genetics research
- Bioinformatics and Genomic Networks
- Advanced Proteomics Techniques and Applications
- Body Contouring and Surgery
- Birth, Development, and Health
- Invertebrate Immune Response Mechanisms
- Machine Learning in Bioinformatics
- Plant responses to water stress
- RNA regulation and disease
- Calcium signaling and nucleotide metabolism
Institute of Molecular Biology
2018-2023
University of Applied Sciences Mainz
2022
Institute of Molecular Biology
2022
University Medical Centre Mannheim
2018
Johannes Gutenberg University Mainz
2017-2018
University Medical Center of the Johannes Gutenberg University Mainz
2017
Technion – Israel Institute of Technology
2012-2016
Agricultural Research Organization
2007-2009
Royal Hospital for Children
1986
Hospital for Sick Children
1983
Diversification at the transcriptome 3'end is an important and evolutionarily conserved layer of gene regulation associated with differentiation dedifferentiation processes. Here, we identify extensive 3'end-alterations in neuroblastoma, a tumour entity paucity recurrent somatic mutations unusually high frequency spontaneous regression. Utilising RNAi-screening reveal landscape drivers 3'end-diversification, discovering PCF11 as critical regulator, directing alternative polyadenylation (APA)...
Abstract Background In fungi, environmental pH is an important signal for development, and successful host colonization depends on homeostasis. Surprisingly, little known regarding the role of in fungal-fungal interactions. Species Trichoderma grow as soil saprobes but many are primarily mycotrophic, using other fungi hosts. Therefore, spp . studied their potential biocontrol plant diseases. Particularly alkaline soil, a critical limiting factor these biofungicides, whose optimal growth 4–6....
RNA-Seq enables the efficient transcriptome sequencing of many samples from small amounts material, but analysis these data remains challenging. In particular, in developmental studies, is challenged by morphological staging samples, such as embryos, since often lack clear markers at any particular stage. cases, automatic identification stage a sample would enable previously infeasible experimental designs. Here we present ‘basic linear index determination transcriptomes’ (BLIND) method for...
RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising perturbations of RNA–protein interactions document their critical function. However, deciphering function is complex, limiting general functional elucidation this growing class and contribution (patho)physiology. Here, we present sCLIP, a simplified robust platform genome-wide interrogation interactomes based on crosslinking-immunoprecipitation...
Mitochondrial metabolic remodeling is a hallmark of the Trypanosoma brucei digenetic life cycle because insect stage utilizes cost-effective oxidative phosphorylation (OxPhos) to generate ATP, while bloodstream cells switch aerobic glycolysis. Due difficulties in acquiring enough parasites from tsetse fly vector, dynamics parasite's rewiring vector have remained obscure. Here, we took advantage vitro–induced differentiation follow changes at RNA, protein, and metabolite levels. This...
Telomeres are nucleoprotein structures at the ends of linear chromosomes and present an essential feature for genome integrity. Vertebrate telomeres usually consist hexameric TTAGGG repeats, however, in cells that use alternative lengthening (ALT) mechanism, variant repeat sequences interspersed throughout telomeres. Previously, it was shown NR2C/F transcription factors bind to TCAGGG repeats contribute telomere maintenance ALT cells. While specific binders other have been lacking date, we...
Abstract Telomeres are nucleoprotein structures at the ends of linear chromosomes. In humans, they consist TTAGGG repeats, which bound by dedicated proteins such as shelterin complex. This complex blocks unwanted DNA damage repair telomeres, e.g. suppressing nonhomologous end joining (NHEJ) through its subunit TRF2. Here, we describe ZNF524, a zinc finger protein that directly binds telomeric repeats with nanomolar affinity, and reveal base-specific sequence recognition cocrystallization...
The typical isohydric plant response to low relative humidity involves stomatal closure, followed by long-term responses like adjustment of shoot-to-root ratios. Little information is available on the early root system exposure shoots humidity, nor it clear what extent Arabidopsis thaliana conform model. In this study, A. plants grown hydroponically at high were exposed two constant humidities, 17% and 77%, while remained in aerated nutrient solution. Leaf conductance (gs), transpiration,...
A 5 month old boy died after fever, persistently raised blood pressure, and hypokalaemia. disorder of cortisol metabolism caused by 11 beta-hydroxysteroid dehydrogenase deficiency was detected retrospectively.
The long non-coding RNA Malat1 has been implicated in several human cancers, while the mechanism of action is not completely understood. As RNAs cells function together with RNA-binding proteins (RBPs), composition their RBP complex can shed light on functionality. We here performed quantitative interactomics 14 non-overlapping fragments covering full length to identify possible nuclear interacting proteins. Overall, we identified 35 candidates including already known binders, which are able...
Abstract Protein abundance is controlled at the transcriptional, translational and post-translational levels, its regulatory principles are starting to emerge. Investigating these requires large-scale proteomics data cannot just be done with transcriptional outcomes that commonly used as a proxy for protein abundance. Here, we determine proteome changes resulting from individual knockout of 3308 nonessential genes in yeast Schizosaccharomyces pombe . We use similarity clustering global infer...
Alternative polyadenylation (APA) produces isoforms with distinct 3'-ends, yet their functional differences remain largely unknown. Here, we introduce the APA-seq method to detect expression levels of APA from 3'-end RNA-Seq data by exploiting both paired-end reads for gene isoform identification and quantification. We detected in individual Caenorhabditis elegans embryos at different stages throughout embryogenesis. Examining correlation between temporal profiles led us distinguish two...
Genome maintenance is orchestrated by a highly regulated DNA damage response with specific repair pathways. Here, we investigate the phylogenetic diversity in recognition and of three well-established lesions, primarily repaired base excision (BER) ribonucleotide (RER): (1) 8-oxoguanine, (2) abasic site, (3) incorporated 11 species: Escherichia coli, Bacillus subtilis, Halobacterium salinarum, Trypanosoma brucei, Tetrahymena thermophila, Saccharomyces cerevisiae, Schizosaccharomyces pombe,...
Abstract Background The process of identifying all coding regions in a genome is crucial for any study at the level molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-seq or mass spectrometry. While satisfactory annotation has been made feasible well-studied model organisms through great efforts big consortia, most systems this kind data either absent not adequately precise. Results Combining in-depth transcriptome sequencing and high resolution...
The ability to determine gene expression profiles across distant species presents a unique opportunity identify functional relationships between genes. In particular, transcriptome data may help distinguish whether genes with similar are functionally related or independent. Recent studies on the evolution of have revealed striking amount divergence strains and species, notion which has hitherto not been brought bear problem detecting Here, we introduce evo-links, method by pair linked if...
Nematodes encompass more than 24,000 described species, which were discovered in almost every ecological habitat, and make up >80% of metazoan taxonomic diversity soils. The last common ancestor nematodes is believed to date back ∼650–750 million years, generating a large phylogenetically diverse group be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry–based proteomics...
Abstract Telomeres are nucleoprotein structures at the ends of linear chromosomes. In humans, they consist TTAGGG repeats, which bound by dedicated proteins such as shelterin complex. This complex blocks unwanted DNA damage repair telomeres, e.g. suppressing non-homologous end joining (NHEJ) through its subunit TRF2. We here describe ZNF524, a zinc finger protein that directly binds telomeric repeats with nanomolar affinity and reveal base-specific sequence recognition co-crystallization...
Abstract Diversification at the transcriptome 3’end is an important and evolutionarily conserved layer of gene regulation associated with differentiation dedifferentiation processes. However underlying mechanisms functional consequences are poorly defined. Here, we identify extensive transcriptome-3’end-alterations in neuroblastoma, a tumour entity paucity recurrent somatic mutations unusually high frequency spontaneous regression. Utilising RNAi-screening reveal landscape drivers...
Abstract Background The process of identifying all coding regions in a genome is crucial for any study at the level molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-seq or mass spectrometry. While satisfactory annotation has been made feasible well-studied model organisms through great efforts big consortia, most systems this kind data either absent not adequately precise. Results Combining in-depth transcriptome sequencing and high resolution...