A5064227397- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Antibiotic Resistance in Bacteria
- Genetic diversity and population structure
- Mycorrhizal Fungi and Plant Interactions
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Plant Pathogens and Fungal Diseases
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Machine Learning in Bioinformatics
- Chromosomal and Genetic Variations
- Vibrio bacteria research studies
- Bacterial biofilms and quorum sensing
- CRISPR and Genetic Engineering
- Identification and Quantification in Food
- Lichen and fungal ecology
- Escherichia coli research studies
- Fungal and yeast genetics research
- Marine Biology and Ecology Research
- Epigenetics and DNA Methylation
- Parasite Biology and Host Interactions
- Protist diversity and phylogeny
- Plant Genetic and Mutation Studies
- Genomics and Chromatin Dynamics
Goethe University Frankfurt
2015-2024
Senckenberg Biodiversity and Climate Research Centre
2016-2024
LOEWE Centre for Translational Biodiversity Genomics
2019-2024
Institute of Cell Biology
2019-2024
University of Göttingen
2023
Goethe Institute
2023
Max Planck Institute for Chemical Ecology
2023
Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI)
2023
Medical University of Vienna
2007-2013
Max Perutz Labs
2007-2012
Summary The nuclear ribosomal internal transcribed spacer ( ITS ) region is the primary choice for molecular identification of fungi. Its two highly variable spacers 1 and 2) are usually species specific, whereas intercalary 5.8S gene conserved. For sequence clustering blast searches, it often advantageous to rely on either one but not conserved gene. To identify extract 2 from large taxonomic environmental data sets is, however, difficult, many sequences incorrectly delimited in public...
Arthropods were the first animals to conquer land and air. They encompass more than three quarters of all described living species. This extraordinary evolutionary success is based on an astoundingly wide array highly adaptive body organizations. A lack robustly resolved phylogenetic relationships, however, currently impedes reliable reconstruction underlying processes. Here, we show that phylogenomic data can substantially advance our understanding arthropod evolution resolve several...
EST sequencing is a versatile approach for rapidly gathering protein coding sequences. They provide direct access to an organism's gene repertoire bypassing the still error-prone procedure of prediction from genomic data. Therefore, ESTs are often only source biological sequence data taxa outside mainstream interest. The widespread use in evolutionary studies and particularly molecular systematics hindered by lack efficient reliable approaches automated ortholog predictions ESTs. Existing...
Innate Immunity in the Fly Gut Drosophila melanogaster is an important model system to study innate immunity, being both easy manipulate and lacking adaptive immune system. In order identify genes that regulate Cronin et al. (p. 340 ; published online 11 June) performed RNA interference screen on flies infected with oral bacterial pathogen, Serratia marcescens . Genes involved intestinal immunity regulation of hemocytes, macrophage-like cells critical for phagocytosis killing bacteria, were...
Remipedes are a small and enigmatic group of crustaceans, first described only 30 years ago. Analyses both morphological molecular data have recently suggested close relationship between Remipedia Hexapoda. If true, the remipedes occupy an important position in pancrustacean evolution may be pivotal for understanding evolutionary history crustaceans hexapods. However, it is to test this hypothesis using new types analytical approaches. Here, we assembled phylogenomic set 131 taxa,...
The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture biology. However, despite recent progress, many deep within the remain unclear. Here, we present first phylogenomic study an entire eukaryotic that uses consistency criterion to strengthen conclusions. We reason branches (splits)...
Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed sources incongruence in by using an extended transcriptome data set. Our analyses showed unevenly distributed missing can be severely misleading inflating node support despite absence phylogenetic signal. In consequence, only decisive sets...
Abstract Tumor-immune cell interactions shape the immune phenotype, with microRNAs (miRs) being crucial components of this crosstalk. How they are transferred and how affect their target landscape, especially in tumor-associated macrophages (TAMs), is largely unknown. Here we report that breast cancer cells have a high constitutive expression miR-375, which released as non-exosome entity during apoptosis. Deep sequencing miRome pointed to enhanced accumulation miR-375 TAMs, facilitated by...
Within the complex metazoan phylogeny, relationships of three lophophorate lineages, ectoprocts, brachiopods and phoronids, are particularly elusive. To shed further light on this issue, we present phylogenomic analyses 196 genes from 58 bilaterian taxa, paying particular attention to influence compositional heterogeneity. The phylogenetic strongly support monophyly Lophophorata a sister-group relationship between Ectoprocta Phoronida. Our results contrast previous findings based rDNA...
Abstract The blunt snout bream Megalobrama amblycephala is the economically most important cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, large number of intermuscular bones in trunk musculature adverse to meat processing consumption. a first towards optimizing this aquatic livestock, we present 1.116-Gb draft genome M. amblycephala, with 779.54 Mb anchored on 24 linkage groups. Integrating spatiotemporal transcriptome...
Acinetobacter baumannii causes a broad range of opportunistic infections in humans. Its success as an emerging pathogen is due to combination increasing antibiotic resistance, environmental persistence and adaptation the human host. To date very little known about molecular basis latter. Here we demonstrate that A. can use phosphatidylcholine, integral part cell membranes, sole carbon energy source. We report on identification three phospholipases belonging PLD superfamily. PLD1 PLD2 appear...
Abstract Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal transfer (xenologs), in addition to sequence divergence loss. Orthologs particular play an essential role comparative genomics phylogenomic analyses. With continued sequencing organisms across tree life, data are available reconstruct unique evolutionary histories tens thousands families. Accurate reconstruction these histories, however, is a challenging...
To better understand the evolutionary forces that affect human genes, we sequenced 5055 expressed sequence tags from chimpanzee and compared them to their counterparts. In conjunction with intergenic DNA sequences data on single-nucleotide polymorphisms in genes studied, this allows us gauge extent which selection affects at a genome-wide scale. The comparison indicates about 39% of silent sites protein-coding regions are deleterious subject negative selection. Further, when divergence...
The human genome is a mosaic with respect to its evolutionary history. Based on phylogenetic analysis of 23,210 DNA sequence alignments from human, chimpanzee, gorilla, orangutan, and rhesus, we present map genetic ancestry. For about 23% our genome, share no immediate ancestry closest living relative, the chimpanzee. This encompasses genes exons same extent as intergenic regions. We conclude that 1/3 started evolve human-specific lineages before differentiation chimps, gorillas took place....
Ribosome biogenesis is fundamental for cellular life, but surprisingly little known about the underlying pathway. In eukaryotes a comprehensive collection of experimentally verified ribosome factors (RBFs) exists only Saccharomyces cerevisiae. Far less other fungi, animals or plants, and insights are even more limited archaea. Starting from 255 yeast RBFs, we integrated ortholog searches, domain architecture comparisons and, in part, manual curation to investigate inventories RBF candidates...
Translation fidelity and efficiency require multiple ribosomal (r)RNA modifications that are mostly mediated by small nucleolar (sno)RNPs during ribosome production. Overlapping basepairing of snoRNAs with pre-rRNAs often necessitates sequential efficient association dissociation the snoRNPs, however, how such hierarchy is established has remained unknown so far. Here, we identify several late-acting bind pre-40S particles in human cells show their function complexes regulated RNA helicase...
AMPK and TOR protein kinases are the major control points of energy signaling in eukaryotic cells organisms. They form core a complex regulatory network to co-ordinate metabolic activities cytosol with those mitochondria plastids. Despite its relevance, it is still unclear when how this pathway was formed during evolution, what extent representations lineages resemble each other. Here we have traced 153 essential proteins forming human AMPK–TOR pathways across 412 species representing all...