- MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. [Journal Article]
- MPMol Plant 2019 Jan 09
- Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assemble…
Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.
- The transcriptional regulator FUBP1 influences disease outcome in murine and human myeloid leukemia. [Journal Article]
- LLeukemia 2019 Jan 11
- The transcriptional regulator far upstream element binding protein 1 (FUBP1) acts as an oncoprotein in solid tumor entities and plays a role in the maintenance of hematopoietic stem cells. However, i…
The transcriptional regulator far upstream element binding protein 1 (FUBP1) acts as an oncoprotein in solid tumor entities and plays a role in the maintenance of hematopoietic stem cells. However, its potential function in leukemia is unknown. In murine models of chronic (CML) and acute myeloid leukemia (AML) induced by BCR-ABL1 and MLL-AF9, respectively, knockdown of Fubp1 resulted in prolonged survival, decreased numbers of CML progenitor cells, decreased cell cycle activity and increased apoptosis. Knockdown of FUBP1 in CML and AML cell lines recapitulated these findings and revealed enhanced DNA damage compared to leukemia cells expressing wild type FUBP1 levels. FUBP1 was more highly expressed in human CML compared to normal bone marrow cells and its expression correlated with disease progression. In AML, higher FUBP1 expression in patient leukemia cells was observed with a trend toward correlation with shorter overall survival. Treatment of mice with AML with irinotecan, known to inhibit topoisomerase I and FUBP1, significantly prolonged survival alone or in combination with cytarabine. In summary, our data suggest that FUBP1 acts as cell cycle regulator and apoptosis inhibitor in leukemia. We demonstrated that FUBP1 might play a role in DNA repair, and its inhibition may improve outcome in leukemia patients.
- Activating mutations in the MAP-kinase pathway define non-ossifying fibroma of bone. [Journal Article]
- JPJ Pathol 2019; 248(1):116-122
- Non-ossifying fibroma (NOF), which occasionally results in pathologic fracture, is considered the most common benign and self-limiting lesion of the growing skeleton. By DNA sequencing we have identi…
Non-ossifying fibroma (NOF), which occasionally results in pathologic fracture, is considered the most common benign and self-limiting lesion of the growing skeleton. By DNA sequencing we have identified hotspot KRAS, FGFR1 and NF1 mutations in 48 of 59 patients (81.4%) with NOF, at allele frequencies ranging from 0.04 to 0.61. Our findings define NOF as a genetically driven neoplasm caused in most cases by activated MAP-kinase signalling. Interestingly, this driving force either diminishes over time or at least is not sufficient to prevent autonomous regression and resolution. Beyond its contribution to a better understanding of the molecular pathogenesis of NOF, this study adds another benign lesion to the spectrum of KRAS- and MAP-kinase signalling-driven tumours. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
- Human-directed behaviour in goats is not affected by short-term positive handling. [Journal Article]
- ACAnim Cogn 2018; 21(6):795-803
- In addition to domestication, interactions with humans or task-specific training during ontogeny have been proposed to play a key role in explaining differences in human-animal communication across s…
In addition to domestication, interactions with humans or task-specific training during ontogeny have been proposed to play a key role in explaining differences in human-animal communication across species. In livestock, even short-term positive interactions with caretakers or other reference persons can influence human-animal interaction at different levels and over different periods of time. In this study, we investigated human-directed behaviour in the 'unsolvable task' paradigm in two groups of domestic goats (Capra aegagrus hircus). One group was positively handled and habituated to a plastic box by the experimenter to retrieve a food reward, while the other group only received standard husbandry care and was habituated to the box without human assistance. In the unsolvable task, the lid was fixed to the box, with the reward inaccessible to the subjects. The goats were confronted with the unsolvable task three times. We observed no difference between the two groups regarding gaze and contact alternations with the experimenter when confronted with the task they cannot solve by themselves. The goats did not differ in their expression rates of both gaze and contact alternations over three repetitions of the unsolvable task; however, they showed earlier gaze and contact alternations in later trials. The results do not support the hypothesis that short-term positive handling or task-specific training by humans facilitates human-directed behaviour in goats. In contrast, standard husbandry care might be sufficient to establish humans as reference persons for farm animals in challenging situations.
- A versatile platform for activity determination of cytokines and growth factors based on the human TSLP (thymic stromal lymphopoietin) receptor. [Journal Article]
- CCytokine 2019; 113:228-237
- Cytokines and growth factors are signaling proteins involved in communication processes between cells. They are involved in the control of numerous essential physiological processes such as cell prol…
Cytokines and growth factors are signaling proteins involved in communication processes between cells. They are involved in the control of numerous essential physiological processes such as cell proliferation, gene transcription and differentiation; therefore being in the focus of basic and applied research. Many of them are also of relevance for human diseases. When observed as potential targets for pharmacological intervention and objects of structure/function studies, it is important to measure their biological activities, optionally along with potential inhibitors, in a convenient and rational manner. Such tests are frequently laborious to set up and their establishment is complicated by the necessity to employ problematic cell types and sophisticated assays. Here we present a robust and modular activity assay system which can be adapted to virtually all ligands that signal through dimerization of membrane receptors from different families. The technique rests on fusing ligand-binding domains of specific receptors to the transmembrane and intracellular components of the thymic stromal lymphopoietin (TSLP) receptor which translates signals into readily quantifiable luciferase expression in reporter cells. We show that the activation of various hematopoietic cytokine receptors, of receptor tyrosine kinases as well as of receptors bearing serine/threonine kinase domains by their respective ligands was faithfully reflected both upon transient and stable introduction of hybrid receptor and reporter gene constructs into the murine pro-B cell line Ba/F3. Moreover, we demonstrate the suitability of this platform for the functional characterization of cytokine/growth factor receptor inhibitors.
- Multimessenger observations of a flaring blazar coincident with high-energy neutrino IceCube-170922A. [Journal Article]
- SciScience 2018 07 13; 361(6398)
- Previous detections of individual astrophysical sources of neutrinos are limited to the Sun and the supernova 1987A, whereas the origins of the diffuse flux of high-energy cosmic neutrinos remain uni…
Previous detections of individual astrophysical sources of neutrinos are limited to the Sun and the supernova 1987A, whereas the origins of the diffuse flux of high-energy cosmic neutrinos remain unidentified. On 22 September 2017, we detected a high-energy neutrino, IceCube-170922A, with an energy of ~290 tera-electron volts. Its arrival direction was consistent with the location of a known γ-ray blazar, TXS 0506+056, observed to be in a flaring state. An extensive multiwavelength campaign followed, ranging from radio frequencies to γ-rays. These observations characterize the variability and energetics of the blazar and include the detection of TXS 0506+056 in very-high-energy γ-rays. This observation of a neutrino in spatial coincidence with a γ-ray-emitting blazar during an active phase suggests that blazars may be a source of high-energy neutrinos.
- Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris. [Journal Article]
- NCNat Commun 2018 06 28; 9(1):2515
- A parasitic lifestyle, where plants procure some or all of their nutrients from other living plants, has evolved independently in many dicotyledonous plant families and is a major threat for agricult…
A parasitic lifestyle, where plants procure some or all of their nutrients from other living plants, has evolved independently in many dicotyledonous plant families and is a major threat for agriculture globally. Nevertheless, no genome sequence of a parasitic plant has been reported to date. Here we describe the genome sequence of the parasitic field dodder, Cuscuta campestris. The genome contains signatures of a fairly recent whole-genome duplication and lacks genes for pathways superfluous to a parasitic lifestyle. Specifically, genes needed for high photosynthetic activity are lost, explaining the low photosynthesis rates displayed by the parasite. Moreover, several genes involved in nutrient uptake processes from the soil are lost. On the other hand, evidence for horizontal gene transfer by way of genomic DNA integration from the parasite's hosts is found. We conclude that the parasitic lifestyle has left characteristic footprints in the C. campestris genome.
- High Kynurenine (a Tryptophan Metabolite) Predicts Remission in Patients with Major Depression to Add-on Treatment with Celecoxib. [Journal Article]
- FPFront Psychiatry 2017; 8:16
- CONCLUSIONS: The high KYN/TRP ratio predicted remission after treatment with celecoxib in this small sample of depressed patients. Eventually, the KYN/TRP ratio might be a marker for those patients, which benefit from an additional anti-inflammatory treatment.
- High-dose methotrexate-based immuno-chemotherapy for elderly primary CNS lymphoma patients (PRIMAIN study). [Clinical Trial, Phase II]
- LLeukemia 2017; 31(4):846-852
- To investigate immuno-chemotherapy for elderly immuno-competent patients (⩾65 years) with newly diagnosed primary central nervous system lymphoma, we conducted a multicentre single-arm trial. One cyc…
To investigate immuno-chemotherapy for elderly immuno-competent patients (⩾65 years) with newly diagnosed primary central nervous system lymphoma, we conducted a multicentre single-arm trial. One cycle consisted of rituximab (375 mg/m2, days 1, 15, 29), high-dose methotrexate (3 g/m2 days 2, 16, 30), procarbazine (60 mg/m2 days 2-11) and lomustine (110 mg/m2, day 2)-R-MPL protocol. Owing to infectious complications, we omitted lomustine during the study and consecutive patients were treated with the R-MP protocol. Three cycles were scheduled and repeated on day 43. Subsequently, patients commenced 4 weekly maintenance treatment with procarbazine (100 mg for 5 days). Primary end point was complete remission (CR) after 3 cycles. We included 107 patients (69 treated with R-MPL and 38 with R-MP). In all, 38/107 patients achieved CR (35.5%) and 15 (14.0%) achieved partial remission. R-MP was associated with a lower CR rate (31.6%) compared with R-MPL (37.7%), but respective 2-year progression-free survival (All 37.3%; R-MP 34.9%; R-MPL 38.8%) and overall survival (All 47.0%; R-MP 47.7%; R-MPL 46.0%) rates were similar. R-MP was associated with less ⩾grade 3 toxicities compared with R-MPL (71.1% vs 87.0%). R-MP is more feasible while still associated with similar efficacy compared with R-MPL and warrants further improvement in future studies.
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- Association of lectin pathway proteins with intra-abdominal Candida infection in high-risk surgical intensive-care unit patients. A prospective cohort study within the fungal infection network of Switzerland. [Journal Article]
- JIJ Infect 2016; 72(3):377-85
- CONCLUSIONS: Lectin pathway protein levels and MBL2 genotype investigated in this study were not associated with heavy Candida colonization or IAC in a cohort of high-risk ICU patients.