Arum-type of arbuscular mycorrhizae, dark septate endophytes and Olpidium spp. in fine roots of container-grown seedlings of Sorbus torminalis (Rosaceae)

The aim of this study was to determine the mycorrhizal status of nursery seedlings of the wild service tree (Sorbus torminalis), which belongs to the Rosaceae family. Its mycorrhizal associations are still fragmentarily known, and data from the few existing studies indicate that it forms ectomycorrhizal symbiosis (ECM). We analyzed the degree of mycorrhizal colonization of thirty 2-year-old container-grown S. torminalis nursery seedlings, which belonged to three single-tree progenies. The roots were dominated by arbuscular mycorrhizae (AM), with the morphology of the Arum-type containing arbuscules, vesicles and hyphae; however, no ECM structures were found. The degree of root colonization of the analyzed seedlings by AM fungi was 83.6% and did not differ significantly between the three single-tree progenies. In addition to AM, structures of dark septate endophytes (0.7%) and sporangia of Olpidium spp. (1.1%) were found in wild service tree roots. In agreement with previous studies, we confirmed arbuscular mycorrhizae for S. torminalis. Moreover, this is the first report that roots of this Sorbus species show the Arum-type morphology of AM and are associated with Olpidium species

openBIS: a flexible framework for managing and analyzing complex data in biology research

<p>Abstract</p> <p>Background</p> <p>Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.</p> <p>Results</p> <p>We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.</p> <p>Conclusions</p> <p>openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.</p

Nonlinear control of transcription through enhancer-promoter interactions.

Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops and topologically associating domains (TADs)1-4. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. Here, to address this question, we use an assay to position an enhancer at large numbers of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. A quantitative analysis of hundreds of cell lines reveals that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship. Mathematical modelling suggests that nonlinearity might arise from transient enhancer-promoter interactions being translated into slower promoter bursting dynamics in individual cells, therefore uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism of how distal enhancers act from large genomic distances, and of how topologically associating domain boundaries block distal enhancers. Finally, we show that enhancer strength also determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation. Our measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation

Abschätzung der technischen und wirtschaftlichen Potentiale des Beitrags zur Energieversorgung und zur Minderung klimarelevanter Spurengase durch Kernenergie in der Bundesrepublik Deutschland : Studie A.4.2.a und A.4.2.b

In diesem Arbeitspaket A.4.2 werden die Möglichkeiten der Minderung von CO2-Emissionen durch den Einsatz der Kernenergie untersucht. Dabei werden sechs Einsatzbereiche betrachtet, in denen die Kernenergie eine CO2-Emissionsminderung durch Substitution fossiler Energieerzeugung bewirken kann. In Kapitel 2 werden mögliche CO2-Emissionsminderungen im Bereich der Stromerzeugung, in Kapitel 3 bei der Fern- bzw. Nahwärmeerzeugung diskutiert. In den Kapiteln 4 bis 7 werden die CO2-Minderungspotentiale durch die Nutzung der Kernenergie zur Veredelung fossiler Energieträger, zur Prozeßdampf- und Prozeßwärmeerzeugung, zur Wasserstofferzeugung über Elektrolyse und bei der tertiären Erdölförderung in der Bundesrepublik Deutschland untersucht

Sensing the Worst: Neurophenomenological Perspectives on Neutral Stimuli Misperception in Schizophrenia Spectrum

While investigating social cognitive impairments in schizophrenia, prominent evidence has been found that patients with schizophrenia show a tendency to misclassify neutral stimuli as negatively valenced. Within this population, patients presenting delusions are more prone to this phenomenon. In a previous study, Schizophrenia spectrum (SzSp) patients rated positive, negative and neutral stimuli that were multimodally presented, while assessed with a checklist exploring anomalous subjective experiences and evaluated for positive and negative symptomatology. In the present work, we aimed to further explore the relationship between neutral stimuli misperception, anomalous experiences and positive/negative symptoms in SzSp patients. To this end, we adopted a dimensional approach by reconstructing from available data: (1) four a priori scales representing essential dimensions of SzSp experiential pathology following Parnas et al. (2005); and (2) five clinically meaningful factors to describe illness severity derived by Toomey et al. (1997). Results showed that although overall patients correctly recognized the target emotions, those who misinterpreted neutral auditory cues as negatively valenced also presented higher scores in Perplexity (PY), Bizarre Delusions (BD) and Disorganization (Di) dimensions. Moreover, a positive association between BD and both PY and Self-Disorder (SD) dimensions emerged, suggesting that psychotic symptoms may be directly linked to patients’ subjectivity. In an attempt to comprehensively capture the multilayered neutral stimuli misperception phenomenon in SzSp, we aimed at bridging phenomenology and neurobiology by connecting the levels of molecular neurochemistry (i.e., altered dopaminergic neurotransmission), system neuroscience (aberrant salience of perceptual details) and psychopathology (the chain involving hyper-reflexivity, self-disorders and the emergence of delusions)

T-cell recognition of chemicals, protein allergens and drugs: towards the development of in vitro assays

Chemicals can elicit T-cell-mediated diseases such as allergic contact dermatitis and adverse drug reactions. Therefore, testing of chemicals, drugs and protein allergens for hazard identification and risk assessment is essential in regulatory toxicology. The seventh amendment of the EU Cosmetics Directive now prohibits the testing of cosmetic ingredients in mice, guinea pigs and other animal species to assess their sensitizing potential. In addition, the EU Chemicals Directive REACh requires the retesting of more than 30,000 chemicals for different toxicological endpoints, including sensitization, requiring vast numbers of animals. Therefore, alternative methods are urgently needed to eventually replace animal testing. Here, we summarize the outcome of an expert meeting in Rome on 7 November 2009 on the development of T-cell-based in vitro assays as tools in immunotoxicology to identify hazardous chemicals and drugs. In addition, we provide an overview of the development of the field over the last two decades

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues