570 Biowissenschaften; Biologie
Refine
Has Fulltext
- yes (68)
Is part of the Bibliography
- yes (68)
Year of publication
- 2019 (68) (remove)
Document Type
- Journal article (49)
- Doctoral Thesis (18)
- Preprint (1)
Keywords
- leukemic cells (3)
- apoptosis (2)
- cancer (2)
- cytotoxicity (2)
- dSTORM (2)
- infection (2)
- metagenomics (2)
- optimal drug combination (2)
- 3D tissue model (1)
- ABP1 (1)
- AUX1 (1)
- Accurate (1)
- Acids (1)
- Algorithmus (1)
- Alpine habitats (1)
- Aminerge Nervenzelle (1)
- Aneugene (1)
- Annotation (1)
- Anthropocene (1)
- Antigen CD19 (1)
- Apidae (1)
- Apis mellifera (1)
- Aspergillus fumigalus (1)
- Automated Image Analysis (1)
- Automatisierung (1)
- Automatisierung der Analyse (1)
- B-MYB (1)
- Barrier (1)
- Bees (1)
- Behavioural ecology (1)
- Berberine (1)
- Bildanalyse (1)
- Bildverarbeitung (1)
- Bioinformatik (1)
- Biomarker (1)
- C-60 fullerene (1)
- C60 fullerene (1)
- C\(_{60}\) fullerene (1)
- Caenorhabditis elegans (1)
- Cancer Cell (1)
- Cell stainin (1)
- Cellular neuroscience (1)
- Central nervous system (1)
- Chlamydia trachomatis (1)
- Chronobiologie (1)
- Circular dichroism (1)
- Click Chemie (1)
- CoQ10 (1)
- Colonization (1)
- Computational and Systems Biology (1)
- Computer modelling (1)
- Confocal microscopy (1)
- Conservation (1)
- CpG (1)
- Cytosol (1)
- DLS and AFM measurements (1)
- DNS-Doppelstrangbruch (1)
- DNS-Schädigung (1)
- Dnaschaden (1)
- Dopamine (1)
- Doxorubicin (1)
- Drosophila melanogaster (1)
- Dynamics (1)
- E8 symmetry (1)
- ERK signaling (1)
- Ecology (1)
- Einzelmolekülmikroskopie (1)
- Electron Microscopy (1)
- Elektronenmikroskopie (1)
- Embryonic induction (1)
- Endogene Rhythmik (1)
- Environmental impact (1)
- Evolutionary developmental biology (1)
- Evolutionary emergence (1)
- Extracellular matrix (1)
- Fgf-signalling (1)
- Flowering plants (1)
- Flowers (1)
- Fluorescence spectroscopy (1)
- Fluoreszenzmikroskopie (1)
- Gene expression analysis (1)
- Genotoxicitiy (1)
- Genotoxizität (1)
- Germline (1)
- Gliazelle (1)
- Glioblastom (1)
- Glykane (1)
- Haut (1)
- HeLa cells (1)
- Health (1)
- Herzmuskelzelle (1)
- Hochauflösende Fluoreszenzmikroskopie (1)
- Host-parasite interaction (1)
- Hurwitz theorem (1)
- Hypothalamus (1)
- Immunoprecipitation (1)
- Immuntherapie (1)
- In vitro (1)
- Inhibitor (1)
- Insect flight (1)
- Invertebrate herbivory (1)
- Klassifizierung (1)
- Klastogene (1)
- Leaf traits (1)
- Lee Smolin (1)
- Limb development (1)
- Llullaillaco Volcano (1)
- M14 carboxypeptidasses (1)
- Maculinea butterfly (1)
- Markierungen synaptischer Proteine (1)
- Mc4r (1)
- Melanom (1)
- Melanoma (1)
- Methylation (1)
- Microbiology and Infectious Disease (1)
- Mikroskopie (1)
- Mitochondria (1)
- Modell (1)
- Molekülsystem (1)
- Multiples Myelom (1)
- Myb-MuvB (1)
- Myrmica ant non-equilibrium dynamics (1)
- Neisseria gonorrhoeae (1)
- Neisseria meningitidis (1)
- Neural circuits (1)
- Neurogenese (1)
- Non-coding RNA (1)
- Outer membrane proteins (1)
- PDF neurons (1)
- PI3K/mTOR inhibierung (1)
- Patterns and drivers of invertebrate herbivory (1)
- Patterns and drivers of species diversity of phytophagous beetles (1)
- Patterns and drivers of species richness and community biomass of large mammals (1)
- Pigmentdispergierender Faktor (1)
- Plants (1)
- Plasmamembranorganisation (1)
- Plasmozytom (1)
- Polysaccharide (1)
- Protein folding (1)
- Proteomics Analysis of Complexes (1)
- Proteotype (1)
- Proteus vulgaris (1)
- Quantifizierung (1)
- Quantitative Mikroskopie (1)
- R package (1)
- RNA metabolism (1)
- RNA sequencing (1)
- RNA-seq (1)
- RNA-seq transcriptome (1)
- RNAi (1)
- Registrierung <Bildverarbeitung> (1)
- Reiz (1)
- Research Article (1)
- SSR42 (1)
- Scarabaeidae (1)
- Self-renewal (1)
- Serotonin (1)
- Sex chromosome (1)
- Sex determination (1)
- Sexual development and function (1)
- Small interfering RNAs (1)
- Solution-state NMR (1)
- Species delimitation (1)
- Species richness (1)
- Stammzelle (1)
- Staphylococcus aureus (1)
- Stoffwechsel (1)
- Strains (1)
- Subtercola vilae (1)
- Synaptische Vesikel (1)
- Taufliege (1)
- Transcription (1)
- Transcriptomic (1)
- Translation (1)
- Transposable element (1)
- Tumor (1)
- UV–Vis (1)
- Ustilago maydis (1)
- Wundheilung (1)
- YAP (1)
- Zellmigration (1)
- accessory medulla (1)
- accumulation (1)
- acetate (1)
- alternative splicing (1)
- altitudinal gradients (1)
- aminergic neurons (1)
- aneugens (1)
- animal physiology (1)
- artifacts (1)
- automatisierte Bildanalyse (1)
- autophagy (1)
- auxin (1)
- behavioral plasticity (1)
- bioinformatics tool (1)
- biomarker (1)
- biomarker signature (1)
- biotic interaction (1)
- brain (1)
- burnt-wood (1)
- cancer metabolism (1)
- carabid beetles (1)
- cardiomyocytes (1)
- cell biology (1)
- chlamydia (1)
- circRNA (1)
- circadian clock (1)
- circular transcriptome sequencing (1)
- classification (1)
- clastogens (1)
- click chemistry (1)
- co-culture (1)
- cold adaptation (1)
- colorectal cancer (1)
- comparative genomics (1)
- competition (1)
- conservation (1)
- cosmology (1)
- crystal growth (1)
- crystallization (1)
- dead-wood enrichment (1)
- dendritic cells (1)
- developmental forms (1)
- direct muss spectrometric profiling (1)
- disease modelling (1)
- diversity gradients (1)
- domain-specific language (1)
- doxorubicin (1)
- drivers and patterns of diversity and herbivory (1)
- drug release (1)
- ecology (1)
- ecosystem service (1)
- efficient intervention points (1)
- elementary body (1)
- endocytosis (1)
- enercy-richness hypothesis (1)
- energy homeostasis (1)
- enhancer (1)
- evolution (1)
- evolutionary genetics (1)
- expansion microscopy (1)
- external stimuli (1)
- extinction dynamics (1)
- fertility (1)
- fluxosome (1)
- food resources (1)
- forest fire (1)
- forest management (1)
- friut fly behaviour (1)
- functional analysis (1)
- fungal rhodopsins (1)
- gangliosides and lipid rafts (1)
- gastrointestinal tract (1)
- gene expression analysis (1)
- genetic engineering (1)
- genome analysis (1)
- genome annotation (1)
- genomics (1)
- glia cells (1)
- global change (1)
- ground-dwelling predators (1)
- growth (1)
- heuristics (1)
- hochauflösende Fluoreszenzmikroskopie (1)
- honeybee (1)
- honeybees (1)
- ichthyology (1)
- imaging (1)
- immunocompetent skin (1)
- indole-3-acetic acid (1)
- infection biology (1)
- inflation (1)
- insect abundance (1)
- insect collection (1)
- integrative management strategy (1)
- intervention point analyzing (1)
- knockout (1)
- land sharing (1)
- land use (1)
- localization microscopy (1)
- lowland beech forests (1)
- mRNA (1)
- machine learning (1)
- macrophages (1)
- mating preference (1)
- mechanisms of disease (1)
- mechanistic modelling (1)
- medaka (1)
- meta-analysis (1)
- metabolic flux (1)
- metabolic modeling (1)
- metabolic modelling (1)
- metabolite profiling (1)
- methods (1)
- miR-26 (1)
- microbial rhodopsins (1)
- microbiome (1)
- mitotic genes (1)
- molecular biology (1)
- mutants (1)
- nanocomplex (1)
- native populations (1)
- natural pest control (1)
- neuronal (1)
- next generation sequencing (1)
- next-generation sequencing (1)
- noncovalent complex (1)
- noncovalent nanocomplex (1)
- nuclear envelope (1)
- nuclear export (1)
- oncogenes (1)
- oncology (1)
- optimal drug targeting (1)
- optimal pharmacological modulation (1)
- optimal treatment strategies (1)
- p53 (1)
- parasite biology (1)
- patch-clamp (1)
- peptidomoics (1)
- photodynamic chemotherapy (1)
- piRNA (1)
- plasma membrane depolarization (1)
- plasma membrane organization (1)
- pollination (1)
- population genetics (1)
- post-fire management (1)
- protected forests (1)
- protein processing (1)
- puberty (1)
- resonance theory (1)
- reticulate body (1)
- rheumatoid arthritis (1)
- risk factors (1)
- saproxylic organisms (1)
- secreted effectors (1)
- sentinel prey (1)
- signalling (1)
- single-molecule tracking (1)
- skin model (1)
- sleep (1)
- small intestinal submucosa scaffold (1)
- small-cell lung cancer (1)
- soil fauna (1)
- species richness (1)
- species‐area hypothesis (1)
- sphingolipids (1)
- sporidia (1)
- structured illumination microscopy (1)
- super-resolution fluorescence microscopy (1)
- super-resolution microscopy (1)
- superresolution (1)
- survival analysis (1)
- synapses (1)
- synergistic effect (1)
- systematic affiliation (1)
- systematic drug targeting (1)
- targeted therapies (1)
- temperature‐mediated resource exploitation hypothesis (1)
- temperature‐richness hypothesis (1)
- time lag (1)
- transcription (1)
- transcriptome (1)
- transcriptomics (1)
- transient dynamics (1)
- tree cavities (1)
- trypanosomes (1)
- unmanaged broadleaved forests (1)
- uptake (1)
- vessel wall resident stem cells (1)
- virus (1)
- whole-genome sequencing (1)
- wound healing (1)
- yH2AX-Foci (1)
Institute
- Theodor-Boveri-Institut für Biowissenschaften (68) (remove)
In most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences. In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects. By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.
Icefishes (suborder Notothenioidei; family Channichthyidae) are the only vertebrates that lack functional haemoglobin genes and red blood cells. Here, we report a high-quality genome assembly and linkage map for the Antarctic blackfin icefish Chaenocephalus aceratus, highlighting evolved genomic features for its unique physiology. Phylogenomic analysis revealed that Antarctic fish of the teleost suborder Notothenioidei, including icefishes, diverged from the stickleback lineage about 77 million years ago and subsequently evolved cold-adapted phenotypes as the Southern Ocean cooled to sub-zero temperatures. Our results show that genes involved in protection from ice damage, including genes encoding antifreeze glycoprotein and zona pellucida proteins, are highly expanded in the icefish genome. Furthermore, genes that encode enzymes that help to control cellular redox state, including members of the sod3 and nqo1 gene families, are expanded, probably as evolutionary adaptations to the relatively high concentration of oxygen dissolved in cold Antarctic waters. In contrast, some crucial regulators of circadian homeostasis (cry and per genes) are absent from the icefish genome, suggesting compromised control of biological rhythms in the polar light environment. The availability of the icefish genome sequence will accelerate our understanding of adaptation to extreme Antarctic environments.
Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.
MYC paralogs are frequently activated in small cell lung cancer (SCLC) but represent poor drug targets. Thus, a detailed mapping of MYC-paralog-specific vulnerabilities may help to develop effective therapies for SCLC patients. Using a unique cellular CRISPR activation model, we uncover that, in contrast to MYCN and MYCL, MYC represses BCL2 transcription via interaction with MIZ1 and DNMT3a. The resulting lack of BCL2 expression promotes sensitivity to cell cycle control inhibition and dependency on MCL1. Furthermore, MYC activation leads to heightened apoptotic priming, intrinsic genotoxic stress and susceptibility to DNA damage checkpoint inhibitors. Finally, combined AURK and CHK1 inhibition substantially prolongs the survival of mice bearing MYC-driven SCLC beyond that of combination chemotherapy. These analyses uncover MYC-paralog-specific regulation of the apoptotic machinery with implications for genotype-based selection of targeted therapeutics in SCLC patients.
Animals must slow or halt locomotion to integrate sensory inputs or to change direction. In Caenorhabditis elegans, the GABAergic and peptidergic neuron RIS mediates developmentally timed quiescence. Here, we show RIS functions additionally as a locomotion stop neuron. RIS optogenetic stimulation caused acute and persistent inhibition of locomotion and pharyngeal pumping, phenotypes requiring FLP-11 neuropeptides and GABA. RIS photoactivation allows the animal to maintain its body posture by sustaining muscle tone, yet inactivating motor neuron oscillatory activity. During locomotion, RIS axonal Ca2+ signals revealed functional compartmentalization: Activity in the nerve ring process correlated with locomotion stop, while activity in a branch correlated with induced reversals. GABA was required to induce, and FLP-11 neuropeptides were required to sustain locomotion stop. RIS attenuates neuronal activity and inhibits movement, possibly enabling sensory integration and decision making, and exemplifies dual use of one cell across development in a compact nervous system.
Coordinated regulation of the lysosomal and autophagic systems ensures basal catabolism and normal cell physiology, and failure of either system causes disease. Here we describe an epigenetic rheostat orchestrated by c-MYC and histone deacetylases that inhibits lysosomal and autophagic biogenesis by concomitantly repressing the expression of the transcription factors MiT/TFE and FOXH1, and that of lysosomal and autophagy genes. Inhibition of histone deacetylases abates c-MYC binding to the promoters of lysosomal and autophagy genes, granting promoter occupancy to the MiT/TFE members, TFEB and TFE3, and/or the autophagy regulator FOXH1. In pluripotent stem cells and cancer, suppression of lysosomal and autophagic function is directly downstream of c-MYC overexpression and may represent a hallmark of malignant transformation. We propose that, by determining the fate of these catabolic systems, this hierarchical switch regulates the adaptive response of cells to pathological and physiological cues that could be exploited therapeutically.
Background
Shotgun metagenomes contain a sample of all the genomic material in an environment, allowing for the characterization of a microbial community. In order to understand these communities, bioinformatics methods are crucial. A common first step in processing metagenomes is to compute abundance estimates of different taxonomic or functional groups from the raw sequencing data.
Given the breadth of the field, computational solutions need to be flexible and extensible, enabling the combination of different tools into a larger pipeline.
Results
We present NGLess and NG-meta-profiler. NGLess is a domain specific language for describing next-generation sequence processing pipelines. It was developed with the goal of enabling user-friendly computational reproducibility. It provides built-in support for many common operations on sequencing data and is extensible with external tools with configuration files.
Using this framework, we developed NG-meta-profiler, a fast profiler for metagenomes which performs sequence preprocessing, mapping to bundled databases, filtering of the mapping results, and profiling (taxonomic and functional). It is significantly faster than either MOCAT2 or htseq-count and (as it builds on NGLess) its results are perfectly reproducible.
Conclusions
NG-meta-profiler is a high-performance solution for metagenomics processing built on NGLess. It can be used as-is to execute standard analyses or serve as the starting point for customization in a perfectly reproducible fashion.
NGLess and NG-meta-profiler are open source software (under the liberal MIT license) and can be downloaded from https://ngless.embl.de or installed through bioconda.
Mathematical optimization framework allows the identification of certain nodes within a signaling network. In this work, we analyzed the complex extracellular-signal-regulated kinase 1 and 2 (ERK1/2) cascade in cardiomyocytes using the framework to find efficient adjustment screws for this cascade that is important for cardiomyocyte survival and maladaptive heart muscle growth. We modeled optimal pharmacological intervention points that are beneficial for the heart, but avoid the occurrence of a maladaptive ERK1/2 modification, the autophosphorylation of ERK at threonine 188 (ERK\(^{Thr188}\) phosphorylation), which causes cardiac hypertrophy. For this purpose, a network of a cardiomyocyte that was fitted to experimental data was equipped with external stimuli that model the pharmacological intervention points. Specifically, two situations were considered. In the first one, the cardiomyocyte was driven to a desired expression level with different treatment strategies. These strategies were quantified with respect to beneficial effects and maleficent side effects and then which one is the best treatment strategy was evaluated. In the second situation, it was shown how to model constitutively activated pathways and how to identify drug targets to obtain a desired activity level that is associated with a healthy state and in contrast to the maleficent expression pattern caused by the constitutively activated pathway. An implementation of the algorithms used for the calculations is also presented in this paper, which simplifies the application of the presented framework for drug targeting, optimal drug combinations and the systematic and automatic search for pharmacological intervention points. The codes were designed such that they can be combined with any mathematical model given by ordinary differential equations.
Background
The honeybee (Apis mellifera) represents a model organism for social insects displaying behavioral plasticity. This is reflected by an age-dependent task allocation. The most protruding tasks are performed by young nurse bees and older forager bees that take care of the brood inside the hive and collect food from outside the hive, respectively. The molecular mechanism leading to the transition from nurse bees to foragers is currently under intense research. Circular RNAs, however, were not considered in this context so far. As of today, this group of non-coding RNAs was only known to exist in two other insects, Drosophila melanogaster and Bombyx mori. Here we complement the state of circular RNA research with the first characterization in a social insect.
Results
We identified numerous circular RNAs in the brain of A. mellifera nurse bees and forager bees using RNA-Seq with exonuclease enrichment. Presence and circularity were verified for the most abundant representatives. Back-splicing in honeybee occurs further towards the end of transcripts and in transcripts with a high number of exons. The occurrence of circularized exons is correlated with length and CpG-content of their flanking introns. The latter coincides with increased DNA-methylation in the respective loci. For two prominent circular RNAs the abundance in worker bee brains was quantified in TaqMan assays. In line with previous findings of circular RNAs in Drosophila, circAmrsmep2 accumulates with increasing age of the insect. In contrast, the levels of circAmrad appear age-independent and correlate with the bee's task. Its parental gene is related to amnesia-resistant memory.
Conclusions
We provide the first characterization of circRNAs in a social insect. Many of the RNAs identified here show homologies to circular RNAs found in Drosophila and Bombyx, indicating that circular RNAs are a common feature among insects. We find that exon circularization is correlated to DNA-methylation at the flanking introns. The levels of circAmrad suggest a task-dependent abundance that is decoupled from age. Moreover, a GO term analysis shows an enrichment of task-related functions. We conclude that circular RNAs could be relevant for task allocation in honeybee and should be investigated further in this context.
Conventional anticancer chemotherapy is limited because of severe side effects as well as a quickly evolving multidrug resistance of the tumor cells. To address this problem, we have explored a C\(_{60}\) fullerene-based nanosized system as a carrier for anticancer drugs for an optimized drug delivery to leukemic cells.Here, we studied the physicochemical properties and anticancer activity of C\(_{60}\) fullerene noncovalent complexes with the commonly used anticancer drug doxorubicin. C\(_{60}\)-Doxorubicin complexes in a ratio 1:1 and 2:1 were characterized with UV/Vis spectrometry, dynamic light scattering, and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The obtained analytical data indicated that the 140-nm complexes were stable and could be used for biological applications. In leukemic cell lines (CCRF-CEM, Jurkat, THP1 and Molt-16), the nanocomplexes revealed 3.5 higher cytotoxic potential in comparison with the free drug in a range of nanomolar concentrations. Also, the intracellular drug's level evidenced C\(_{60}\) fullerene considerable nanocarrier function.The results of this study indicated that C\(_{60}\) fullerene-based delivery nanocomplexes had a potential value for optimization of doxorubicin efficiency against leukemic cells.