Refine
Has Fulltext
- yes (107)
Is part of the Bibliography
- yes (107)
Year of publication
- 2016 (107) (remove)
Document Type
- Journal article (88)
- Doctoral Thesis (19)
Keywords
- Drosophila (5)
- Taufliege (4)
- DNA methylation (3)
- Drosophila melanogaster (3)
- biodiversity (3)
- circadian rhythms (3)
- vision (3)
- DNA damage (2)
- DNS-Sequenz (2)
- Spermatogenesis (2)
- Staphylococcus aureus (2)
- Tagesrhythmus (2)
- Trypanosoma brucei (2)
- biological locomotion (2)
- breast cancer (2)
- circadian clock (2)
- cytotoxicity (2)
- database (2)
- gastric cancer (2)
- gene expression (2)
- genome (2)
- honey bees (2)
- host-pathogen interactions (2)
- insect brain (2)
- lung cancer (2)
- natural language processing (2)
- neurons (2)
- next generation sequencing (2)
- photoperiodism (2)
- phylogenetic trees (2)
- sexual selection (2)
- visualization (2)
- AP-1 (1)
- Abscisinsäure (1)
- Ackerschmalwand (1)
- Action potentials (1)
- Acyrthosiphon pisum (1)
- Adultschlupfes (1)
- Agricultural intensification (1)
- Altern (1)
- Alvis (1)
- Alzheimers disease (1)
- Ameisenoogenese (1)
- Amphibians (1)
- Amyotrophic-lateral-sclerosis (1)
- Angiopoietin-2 (1)
- Angiopoietin-like 4 (1)
- Anionenkanal (1)
- Anionentranslokator (1)
- Annotation (1)
- Anpassung (1)
- Antimikrobielle Peptide (1)
- Antralfollikel (1)
- Arabidopsis-thaliana (1)
- Arthropods (1)
- Aufmerksamkeit (1)
- Autism (1)
- Autism spectrum disorders (1)
- Axon degeneration (1)
- Axonal transport (1)
- Bacterial community analysis (1)
- Bacterial symbionts (1)
- Bauchspeicheldrüsenkrebs (1)
- Bee abundance (1)
- Biodiversity assessment (1)
- Biodiversität (1)
- Bioinformatic (1)
- Bioinformatik (1)
- Blochmannia floridanus (1)
- Blut-Hirn-Schranke (1)
- Bone disease (1)
- Camponotus floridanus (1)
- Cancer genetics (1)
- Candida albicans (1)
- Cervical cancer (1)
- ChIP-sequencing (1)
- Chromosomes (1)
- Chronobiologie (1)
- Cimex lectularius (1)
- Circadian clock (1)
- Cocalodinae (1)
- Coleoptera: Chrysomelidae (1)
- Colony growth (1)
- Context (1)
- Cytotoxic (1)
- DNA methylation dynamics (1)
- DNA-based species delimitation (1)
- DNS-Bindung (1)
- DNS-Methyltransferase (1)
- Danio-rerio (1)
- Darmflora (1)
- Densities (1)
- Dionaea-muscipula ellis (1)
- Down syndrome (1)
- Drosha (1)
- E3 ligase (1)
- ERK (1)
- Ecologically important traits (1)
- Endosymbiosen (1)
- Endothelial growth-factor (1)
- Endothelzelle (1)
- Environment (1)
- Epidermal growth-factor (1)
- Epigenetics (1)
- Epigenetik (1)
- Epitope (1)
- Event (1)
- Exosome (1)
- FISH-CLEM (1)
- FOSL1 (1)
- FWGE (1)
- Fertilität (1)
- Fetal brain development (1)
- Fish Sex determination (1)
- Flabarin (1)
- Flow cytometry (1)
- Foragers (1)
- Frontal cortex (1)
- Funktion (1)
- Geißel <Biologie> (1)
- Gelatine (1)
- Gene (1)
- Gene expression profiling (1)
- Gene-expression (1)
- Genetics research (1)
- Genmutation (1)
- Genom (1)
- Genome (1)
- Genome assembly (1)
- Genome comparison (1)
- Genomics data sets (1)
- Geschlechtsdifferenzierung (1)
- HKT transporter (1)
- HPV (1)
- Habitats (1)
- Holstein <Rind> (1)
- Horizontal transfer (1)
- Human prefrontal cortex (1)
- Hydrogel (1)
- Hymenoptera (1)
- Identifizierungspipeline (1)
- Immungene (1)
- In vitro (1)
- Insect hosts (1)
- Insects (1)
- Interactive Tree Of Life (iTOL) (1)
- Intermediate filaments (1)
- Intracellular virulence (1)
- Jasmonate perception (1)
- Kernhülle (1)
- Kernproteine (1)
- Kristallstruktur (1)
- LASP1 (1)
- LINC complex (1)
- Lachsartige <Familie> (1)
- Lacking neurofilaments (1)
- Lepidoptera (1)
- Locomotor activity (1)
- Locus (1)
- Lynx lynx (1)
- MDSCs (1)
- MIZ1 (1)
- MRSA (1)
- MYC (1)
- MYCN (1)
- Male intromittent organ (1)
- Maus (1)
- Mechanisms (1)
- Meiosis (1)
- Melanom (1)
- Melanoma Maintenance (1)
- Mensch (1)
- Mesenchymal stem cells (1)
- Mesocestoides corti (1)
- Meta-barcoding (1)
- Metagenom (1)
- Methylome (1)
- Microorganisms (1)
- Microtubules (1)
- Missense mutation (1)
- Molekularbiologie (1)
- Molekulargenetik (1)
- Motoneuron (1)
- Motoneuron disease (1)
- Mouse model (1)
- Mt. Kinabalu (1)
- Multiple myeloma (1)
- Mutations (1)
- Myc (1)
- NGS (1)
- NMD (1)
- NO (1)
- Nanda-Hamner (1)
- Nasonia courtship (1)
- Natural Language Processing (1)
- Nesting resources (1)
- Neurale Stammzellen (1)
- Neurofilament (1)
- Neurovaskuläre Einheit (1)
- Next Generation Sequencing (1)
- Non-ribosomal peptide synthetase (1)
- Nurses (1)
- Oilseed rape (1)
- OmoMYC (1)
- Oogenese (1)
- Oogenesis (1)
- Oozyte (1)
- Opsins (1)
- Osteogenic precursor cells (1)
- Ovarielle Alterung (1)
- PICD (1)
- PLGA (1)
- Pain (1)
- Partikel (1)
- Patterns (1)
- Peptidoglycan recognition (1)
- Pipeline-Rechner (1)
- Plant utricularia-gibba (1)
- Podocarpus National Park (1)
- Poecilia reticulata (1)
- Polistine wasps (1)
- Polycistronic mRNA (1)
- Polylactid-co-Glycolid (1)
- Poor-prognosis (1)
- Postovulatorische Alterung (1)
- Primary endosymbiont (1)
- Programmed cell-death (1)
- Progressive motor neuronopathy (1)
- QTL analysis (1)
- QUAC1 (1)
- R-Typ (1)
- RNA interference (1)
- RNA-SEQ data (1)
- RNAseq (1)
- RSK (1)
- Relapse (1)
- Reproduction (1)
- Reveals (1)
- Rhodopsins (1)
- Richness (1)
- SCD (1)
- SUN domain proteins (1)
- Saccharomyces cerevisiae (1)
- Schizophrenia (1)
- Schließzelle (1)
- SdY (1)
- Selektive Wahrnehmung (1)
- Sequenzierung (1)
- Si-rhodamine (1)
- Single nucleotide change (1)
- Social entrainment (1)
- Somatische Mutation (1)
- Spermatogenese (1)
- Spermienbildung (1)
- Spermiogenese (1)
- Stammzelle (1)
- Stat3 (1)
- Stathmin (1)
- Stress responses (1)
- Struktur (1)
- Symbiose (1)
- T lymphocytes (1)
- TEVC (1)
- Temperature rhythms (1)
- Text analysis (1)
- Textanalyse (1)
- Tissue Engineering (1)
- Transcription (1)
- Transcriptome (1)
- Transgenic mice (1)
- Transkription <Genetik> (1)
- Transkriptionsfaktor (1)
- Transovarial transmission (1)
- Trinidadian guppy (1)
- Trypanosomes (1)
- USA300 (1)
- VACV (1)
- Vaccine (1)
- Variantcalling (1)
- Venusfliegenfalle (1)
- Virulenz (1)
- Visueller Reiz (1)
- WDR5 (1)
- Wallemia ichthyophaga (1)
- Williamsia sp. ARP1 (1)
- Wirt (1)
- Wonderful plants (1)
- X. couchianus (1)
- X. hellerii (1)
- Xiphophorus (1)
- Xiphophorus fish (1)
- Yield (1)
- Zebrafish (1)
- Zelldifferenzierung (1)
- achaete-scute homolog 1 (1)
- adaption (1)
- adipose (1)
- adipose tissue (1)
- adipose tissue dysfunction (1)
- adjuvant (1)
- agri-environment schemes (1)
- algorithm (1)
- anastomotic leakage (1)
- angiogenesis (1)
- angiogenic cytokines (1)
- animal behavior (1)
- animals (1)
- annotation (1)
- ant oogenesis (1)
- ant-mimicking spiders (1)
- anterior optic tubercle (1)
- anthropogenic activities (1)
- antimicrobial peptides (1)
- antimycotics (1)
- antioxidants (1)
- antitumor immune response (1)
- antiviral immunity (1)
- ants (1)
- apoptosis (1)
- arabidopsis (1)
- arabidopsis thaliana (1)
- army ants (1)
- artificial diet (1)
- assembly (1)
- astrocytes (1)
- attraction (1)
- autophagy (1)
- axonaler Transport (1)
- bed bug (1)
- bee community (1)
- bees (1)
- behavioral conditioning (1)
- benzoquinone (1)
- bevacizumab (1)
- biodiversity assessment (1)
- bioenergetics (1)
- biofuels (1)
- bioinformatics (1)
- biomarker (1)
- blood (1)
- body weight (1)
- brain-injury (1)
- breast-cancer (1)
- brefeldin-a (1)
- broodtranslocation (1)
- bug riptortus-pedestris (1)
- c-Fos (1)
- caenorhabditis elegans (1)
- calyx (1)
- camponotus ants (1)
- cancer biology (1)
- cancer cells (1)
- canopy spiders (1)
- capacitance (1)
- cell biology (1)
- cell compartmentation (1)
- cell cycle and cell division (1)
- cell cycle arrest (1)
- cell death (1)
- cell differentiation (1)
- cell membranes (1)
- cell motility (1)
- cell staining (1)
- cellular imaging (1)
- central complex (1)
- central nervous system (1)
- chemotherapy (1)
- chromatin (1)
- chronobiology (1)
- climate factors (1)
- cognition (1)
- cognitive functions (1)
- colony survival (1)
- color vision (1)
- colorectal cancer (1)
- community ecology (1)
- complication (1)
- computer-assisted (1)
- confocal laser microscopy (1)
- correlative light and electron microscopy (1)
- crop pollination (1)
- cytokines (1)
- cytokinins (1)
- cytosol (1)
- cytostatic (1)
- damped-oscillator-model of photoperiodic clock (1)
- data mining/methods (1)
- depreissia decipiens (1)
- deuterostomes (1)
- developmental biology (1)
- diapause (1)
- dichthadiigynes (1)
- direct stochasticoptical reconstruction microscopy (1)
- draft genome (1)
- drug-minded protein (1)
- early diagnosis (1)
- early secretory pathway (1)
- ecosystem services (1)
- ectotherms (1)
- endemism (1)
- endoplasmic-reticulum (1)
- endosomes (1)
- endosponge (1)
- endosymbiosis (1)
- enzyme regulation (1)
- epithelial cells (1)
- ethanol (1)
- excretory-secretory (1)
- exocrine glands (1)
- export (1)
- extracellular matrix (1)
- female choice (1)
- fertility (1)
- fetal brain development (1)
- field boundaries (1)
- finger protein 11 (1)
- fish model (1)
- flagella (1)
- flagellum (1)
- fluorescence recovery after photobleaching (1)
- fluorescent-probes (1)
- fluorophore (1)
- food consumption (1)
- foraging (1)
- forest edges (1)
- forest fragmentation (1)
- forest hedges (1)
- forest specialists (1)
- frontal cortex (1)
- fungicide (1)
- gap junction (1)
- gastrointestinal tract (1)
- gene-expression (1)
- genetic dissection (1)
- genetics (1)
- genome assembly (1)
- genotype (1)
- geographic biases (1)
- geographical variation (1)
- global dataset (1)
- gonad development (1)
- gut microbiota (1)
- halophilic fungus (1)
- heterozygosity (1)
- high resolution visualisation (1)
- high-osmolarity glycerol (HOG) (1)
- histone γH2AX (1)
- honeybee (1)
- host cells (1)
- hour-glass (1)
- hourglass clock (1)
- human (1)
- human ectoparasite (1)
- humans (1)
- hyperexpression techniques (1)
- hypothalamus (1)
- hypoxia-inducible factor 3A (1)
- iNOS (1)
- image data (1)
- image processing (1)
- immune genes (1)
- immune response (1)
- immunoreactive neurons (1)
- in vitro Modell (1)
- in-vitro (1)
- induziert pluripotente Stammzelle (1)
- inflammation (1)
- inflammatory bowel disease (1)
- innate immune system (1)
- innexins (1)
- insects (1)
- insulin (1)
- insulin resistance (1)
- intensification (1)
- interaction (1)
- intracellular membranes (1)
- jumping spiders (1)
- junction proteins (1)
- land-use change (1)
- landscape compositionv (1)
- leaf beetle (1)
- learning (1)
- legionary ants (1)
- light-induced gene expression (1)
- light-trapping (1)
- lipid desaturation (1)
- lipidomics (1)
- liver metastasis (1)
- lncRNAs (1)
- localization micoscopy (1)
- locomotor activity (1)
- lungfish (1)
- lymphocytes (1)
- mRNA (1)
- macroecology (1)
- macrophages (1)
- marrow stromal cells (1)
- mathematical modeling (1)
- matrix metalloproteinases (1)
- melanoma (1)
- meliponines (1)
- membrane biophysics (1)
- membrane proteins (1)
- memory (1)
- memory formation (1)
- mesenchymal stem-cells (1)
- metabolism (1)
- metagenomics (1)
- miRNAs (1)
- mice (1)
- microRNA (1)
- microbiology (1)
- microglomeruli (1)
- microscopy (1)
- mitogen activated protein kinase (MAPK) (1)
- modeling (1)
- molecular biology (1)
- monoclonial gammopathy (1)
- monocytes (1)
- moths (1)
- mouse (1)
- mouse models (1)
- mouse-brain (1)
- multimodal (1)
- multiple sequence alignments (1)
- multipotente Stammzelle (1)
- mushroom body (1)
- mutation detection (1)
- neoadjuvant (1)
- nervous-system (1)
- nervous-sytem (1)
- neural circuits (1)
- neural stem-cells (1)
- neurogenic locus notch homolog (1)
- neuroimaging (1)
- neuronal plasticity (1)
- neuropeptides (1)
- neutrophils (1)
- non-crop habitats (1)
- non-invasive biomarkers (1)
- nurses (1)
- obesity (1)
- olfaction (1)
- oncolytic virus therapy (1)
- oxidative stress (1)
- pacbio correction (1)
- parasitic cell cycles (1)
- parasitic diseases (1)
- parasitic life cycles (1)
- parasitology (1)
- peripheral-blood (1)
- phenotype (1)
- phosphorylation (1)
- photoactivation (1)
- photoperiodic time mesurement (1)
- phototransduction (1)
- phyllosphere (1)
- physiological traits (1)
- piRNA (1)
- pitcher-plant mosquito (1)
- plasticity (1)
- polarization vision (1)
- pollen analysis (1)
- potassium (1)
- precedes multiple-myeloma (1)
- prey selection (1)
- progenitors (1)
- promoter affinity (1)
- promoter invasion (1)
- prostate cancer (1)
- protein phosphorylation (1)
- protein-protein interaction (1)
- proteomes (1)
- proteomic analysis (1)
- protocadherin gamma cluster (1)
- protophormia terraenovae (1)
- pyramidal neurons (1)
- queens (1)
- radiation sensitivity (1)
- rainforest (1)
- reactive oxygen species (1)
- receptor tyrosine kinase (1)
- receptor tyrosine kinases (1)
- recombinat-human-erythropoietin (1)
- reconstruction (1)
- repeats (1)
- reproductive character displacement (1)
- reproductive diapause (1)
- resolution limit (1)
- resource availability (1)
- retinal dystrophies (1)
- retinoblastoma protein (1)
- rhythmic components (1)
- risk factor (1)
- salinity stress (1)
- salmonids (1)
- sampling bias (1)
- sampling method (1)
- sarcopterygian fish (1)
- semi-natural habitats (1)
- sequestration (1)
- serotonin transporter (1)
- sex pheromone (1)
- signal peptides (1)
- signaling (1)
- signaling pathway (1)
- single-molecule biophysics (1)
- sky-compass orientation (1)
- sleep (1)
- small RNA-sequencing (1)
- small cell lung cancer (1)
- sodium (1)
- software (1)
- somatic mutations (1)
- somatische Mutationen (1)
- speciation (1)
- species diversification (1)
- sperm head formation (1)
- spermiogenesis (1)
- spillover (1)
- stage specific regulation (1)
- stalking predators (1)
- structure (1)
- structured illumination microscopy (1)
- super-resolution imaging (1)
- super-resolution microscopy (1)
- survival (1)
- swimming (1)
- synaptic connections (1)
- synapticplasticity (1)
- synaptische Funktion (1)
- systemic inflammatory response syndrome (1)
- targets (1)
- taxonomic biases (1)
- taxonomy (1)
- temperature (1)
- thermal adaptation (1)
- tool (1)
- trafficking (1)
- trans-splicing (1)
- transcriptional profiling (1)
- transcriptome (1)
- transcriptome analysis (1)
- transposable elements (1)
- trisomy 21 (1)
- tropical ecology (1)
- trypanosoma brucei gambiense (1)
- undetermined significance (1)
- unstructured data (1)
- unstrukturierte Daten (1)
- urbanization (1)
- vertebrates (1)
- vesicles (1)
- viscosity (1)
- visuell (1)
- wasp-mimicking (1)
- whole genome duplications (1)
- whole genome sequencing (1)
- whole-genome shotgun sequencing (1)
- wild plant pollination (1)
- wyeomyia smithii (1)
- xylem loading (1)
Institute
- Theodor-Boveri-Institut für Biowissenschaften (107) (remove)
Sonstige beteiligte Institutionen
Mutations are the basis of the clonal evolution of most cancers. Nevertheless, a systematic analysis of whether mutations are selected in cancer because they lead to the deregulation of specific biological processes independent of the type of cancer is still lacking. In this study, we correlated the genome and transcriptome of 1,082 tumors. We found that nine commonly mutated genes correlated with substantial changes in gene expression, which primarily converged on metabolism. Further network analyses circumscribed the convergence to a network of reactions, termed AraX, that involves the glutathione- and oxygen-mediated metabolism of arachidonic acid and xenobiotics. In an independent cohort of 4,462 samples, all nine mutated genes were consistently correlated with the deregulation of AraX. Among all of the metabolic pathways, AraX deregulation represented the strongest predictor of patient survival. These findings suggest that oncogenic mutations drive a selection process that converges on the deregulation of the AraX network.
Background
Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species.
Results
We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus.
Conclusions
Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.
Background
Spermatogenesis is a complex differentiation process that involves the successive and simultaneous execution of three different gene expression programs: mitotic proliferation of spermatogonia, meiosis, and spermiogenesis. Testicular cell heterogeneity has hindered its molecular analyses. Moreover, the characterization of short, poorly represented cell stages such as initial meiotic prophase ones (leptotene and zygotene) has remained elusive, despite their crucial importance for understanding the fundamentals of meiosis.
Results
We have developed a flow cytometry-based approach for obtaining highly pure stage-specific spermatogenic cell populations, including early meiotic prophase. Here we combined this methodology with next generation sequencing, which enabled the analysis of meiotic and postmeiotic gene expression signatures in mouse with unprecedented reliability. Interestingly, we found that a considerable number of genes involved in early as well as late meiotic processes are already on at early meiotic prophase, with a high proportion of them being expressed only for the short time lapse of lepto-zygotene stages. Besides, we observed a massive change in gene expression patterns during medium meiotic prophase (pachytene) when mostly genes related to spermiogenesis and sperm function are already turned on. This indicates that the transcriptional switch from meiosis to post-meiosis takes place very early, during meiotic prophase, thus disclosing a higher incidence of post-transcriptional regulation in spermatogenesis than previously reported. Moreover, we found that a good proportion of the differential gene expression in spermiogenesis corresponds to up-regulation of genes whose expression starts earlier, at pachytene stage; this includes transition protein-and protamine-coding genes, which have long been claimed to switch on during spermiogenesis. In addition, our results afford new insights concerning X chromosome meiotic inactivation and reactivation.
Conclusions
This work provides for the first time an overview of the time course for the massive onset and turning off of the meiotic and spermiogenic genetic programs. Importantly, our data represent a highly reliable information set about gene expression in pure testicular cell populations including early meiotic prophase, for further data mining towards the elucidation of the molecular bases of male reproduction in mammals.
Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases
(2016)
Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.
Depreissia is a little known genus comprising two hymenopteran-mimicking species, one found in Central Africa and one in the north of Borneo. The male of D. decipiens is redescribed, the female is described for the first time. The carapace is elongated, dorsally flattened and rhombus-shaped, the rear of the thorax laterally depressed and transformed, with a pair of deep pits; the pedicel is almost as long as the abdomen. The male palp is unusual, characterized by the transverse deeply split membranous tegulum separating a ventral part which bears a sclerotized tegular apophysis and a large dagger-like retrodirected median apophysis. The female epigyne consists of one pair of large adjacent spermathecae and very long copulatory ducts arising posteriorly and rising laterally alongside the spermathecae continuing in several vertical and horizontal coils over the anterior surface. Relationships within the Salticidae are discussed and an affinity with the Cocalodinae is suggested. Arguments are provided for a hypothesis that D. decipiens is not ant-mimicking as was previously believed, but is a mimic of polistinine wasps. The species was found in the canopy in the Kinabalu area only, in primary and old secondary rainforest at 200–700 m.a.s.l. Overlap of canopy-dwelling spider species with those in the understorey are discussed and examples of species richness and endemism in the canopy are highlighted. Canopy fogging is a very efficient method of collecting for most arthropods. The canopy fauna adds an extra dimension to the known biodiversity of the tropical rainforest. In southeast Asia, canopy research has been neglected, inhibiting evaluation of comparative results of this canopy project with that from other regions. More use of fogging as a collecting method would greatly improve insight into the actual species richness and species distribution in general.
Agricultural intensification often leads to fragmentation of natural habitats, such as forests, and thereby negatively affects forest specialist species. However, human introduced habitats, such as hedges, may counteract negative effects of forest fragmentation and increase dispersal, particularly of forest specialists. We studied effects of habitat type (forest edge versus hedge) and hedge isolation from forests (connected versus isolated hedge) in agricultural landscapes on abundance, species richness and community composition of mice, voles and shrews in forest edges and hedges. Simultaneously to these effects of forest edge/hedge type we analysed impacts of habitat structure, namely percentage of bare ground and forest edge/hedge width, on abundance, species richness and community composition of small mammals. Total abundance and forest specialist abundance (both driven by the most abundant species Myodes glareolus, bank vole) were higher in forest edges than in hedges, while hedge isolation had no effect. In contrast, abundance of habitat generalists was higher in isolated compared to connected hedges, with no effect of habitat type (forest edge versus hedge). Species richness as well as abundance of the most abundant habitat generalist Sorex araneus (common shrew), were not affected by habitat type or hedge isolation. Decreasing percentage of bare ground and increasing forest edge/hedge width was associated with increased abundance of forest specialists, while habitat structure was unrelated to species richness or abundance of any other group. Community composition was driven by forest specialists, which exceeded habitat generalist abundance in forest edges and connected hedges, while abundances were similar to each other in isolated hedges. Our results show that small mammal forest specialists prefer forest edges as habitats over hedges, while habitat generalists are able to use unoccupied ecological niches in isolated hedges. Consequently even isolated hedges can be marginal habitats for forest specialists and habitat generalists and thereby may increase regional farmland biodiversity.
Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.
Recently, a genome-wide analysis identified DNA methylation of the HIF3A (hypoxia-inducible factor 3A) as strongest correlate of BMI. Here we tested the hypothesis that HIF3A mRNA expression and CpG-sites methylation in adipose tissue (AT) and genetic variants in HIF3A are related to parameters of AT distribution and function. In paired samples of subcutaneous AT (SAT) and visceral AT (VAT) from 603 individuals, we measured HIF3A mRNA expression and analyzed its correlation with obesity and related traits. In subgroups of individuals, we investigated the effects on HIF3A genetic variants on its AT expression (N = 603) and methylation of CpG-sites (N = 87). HIF3A expression was significantly higher in SAT compared to VAT and correlated with obesity and parameters of AT dysfunction (including CRP and leucocytes count). HIF3A methylation at cg22891070 was significantly higher in VAT compared to SAT and correlated with BMI, abdominal SAT and VAT area. Rs8102595 showed a nominal significant association with AT HIF3A methylation levels as well as with obesity and fat distribution. HIF3A expression and methylation in AT are fat depot specific, related to obesity and AT dysfunction. Our data support the hypothesis that HIF pathways may play an important role in the development of AT dysfunction in obesity.
Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal. Cellular 3D reconstructions revealed bipolar, spherical granules of low electron density, which likely represent carbon reserves. Poribacterial activity profiles were retrieved from prokaryotic enriched sponge metatranscriptomes using simulation-based optimised mapping. We observed high transcriptional activity for proteins related to bacterial microcompartments (BMC) and we resolved their subcellular localisation by combining FISH-CLEM with immunohistochemistry (IHC) on ultra-thin sponge tissue sections. In terms of functional relevance, we propose that the BMC-A region may be involved in 1,2-propanediol degradation. The FISH-IHC-CLEM approach was proven an effective toolkit to combine -omics approaches with functional studies and it should be widely applicable in environmental microbiology.
Mutation Detection in Patients with Retinal Dystrophies Using Targeted Next Generation Sequencing
(2016)
Retinal dystrophies (RD) constitute a group of blinding diseases that are characterized by clinical variability and pronounced genetic heterogeneity. The different nonsyndromic and syndromic forms of RD can be attributed to mutations in more than 200 genes. Consequently, next generation sequencing (NGS) technologies are among the most promising approaches to identify mutations in RD. We screened a large cohort of patients comprising 89 independent cases and families with various subforms of RD applying different NGS platforms. While mutation screening in 50 cases was performed using a RD gene capture panel, 47 cases were analyzed using whole exome sequencing. One family was analyzed using whole genome sequencing. A detection rate of 61% was achieved including mutations in 34 known and two novel RD genes. A total of 69 distinct mutations were identified, including 39 novel mutations. Notably, genetic findings in several families were not consistent with the initial clinical diagnosis. Clinical reassessment resulted in refinement of the clinical diagnosis in some of these families and confirmed the broad clinical spectrum associated with mutations in RD genes.