Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli

mRNA methylation is an important regulator of many physiological processes in eukaryotes but has not been studied in depth in prokaryotes. Working with bacterial mRNA is challenging because it lacks a poly(A)-tail. However, methods for detecting RNA modifications, both sequencing and mass spectrometry, rely on efficient preparation of mRNA. Here, we compared size-dependent separation by electrophoresis and rRNA depletion for enrichment of Escherichia coli mRNA. The purification success was monitored by qRT-PCR and RNA sequencing. Neither method allowed complete removal of rRNA. Nevertheless, we were able to quantitatively analyze several modified nucleosides in the different RNA types. We found evidence for stress dependent RNA modification reprofiling in rRNA, but also several modified nucleosides in the mRNA enriched fractions showed significant changes

Aufgabenprofile und Handlungsmodi von Fachberaterinnen und Fachberatern. Berufliches Handeln zwischen Personen- und Organisationsbezug

Fachberatung spielt eine Schlüsselrolle für die Qualitätssicherung und -entwicklung im System der Kindertagesbetreuung. Was ihre strukturelle Verankerung, ihr gesetzlich kodifiziertes Mandat sowie ihre Aufgabenprofile betrifft, befindet sie sich als Berufsfeld jedoch nach wie vor in einem Werdeprozess. Die vorliegende Publikation präsentiert erste Ergebnisse der WiFF-Fachberatungsstudie. Sie beleuchtet die Zuständigkeitsbereiche und das berufliche Selbstverständnis von Fachberaterinnen und Fachberatern und leistet damit einen Beitrag zur Professionalisierung der Frühen Bildung. (Verlag

Steuerung der Qualität oder Qualität der Steuerung? Die gesetzliche Rahmung der Kita-Fachberatung in den Bundesländern

In den vergangenen Jahren ließen sich im Rahmen der Fachberatung zunehmende Verrechtlichungsprozesse beobachten, die zugleich als Strategie der Professionalisierung des Kita-Systems interpretiert werden können. Das vorliegende Diskussionspapier stellt die Ergebnisse einer Dokumentenanalyse zur gesetzlichen Rahmung von Fachberatung in den Bundesländern vor und skizziert, wie sich Mandat und Lizenz von Fachberaterinnen und Fachberatern derzeit gestalten. (DIPF/Orig.

The tomato receptor CuRe1 senses a cell wall protein to identify Cuscuta as a pathogen

Parasitic plants of the genus Cuscuta penetrate shoots of host plants with haustoria and build a connection to the host vasculature to exhaust water, solutes and carbohydrates. Such infections usually stay unrecognized by the host and lead to harmful host plant damage. Here, we show a molecular mechanism of how plants can sense parasitic Cuscuta. We isolated an 11 kDa protein of the parasite cell wall and identified it as a glycine-rich protein (GRP). This GRP, as well as its minimal peptide epitope Crip21, serve as a pathogen-associated molecular pattern and specifically bind and activate a membrane-bound immune receptor of tomato, the Cuscuta Receptor 1 (CuRe1), leading to defense responses in resistant hosts. These findings provide the initial steps to understand the resistance mechanisms against parasitic plants and further offer great potential for protecting crops by engineering resistance against parasitic plants

Pollution in the Arctic Ocean: An overview of multiple pressures and implications for ecosystem services

The Arctic is undergoing unprecedented change. Observations and models demonstrate significant perturbations to the physical and biological systems. Arctic species and ecosystems, particularly in the marine environment, are subject to a wide range of pressures from human activities, including exposure to a complex mixture of pollutants, climate change and fishing activity. These pressures affect the ecosystem services that the Arctic provides. Current international policies are attempting to support sustainable exploitation of Arctic resources with a view to balancing human wellbeing and environmental protection. However, assessments of the potential combined impacts of human activities are limited by data, particularly related to pollutants, a limited understanding of physical and biological processes, and single policies that are limited to ecosystem-level actions. This manuscript considers how, when combined, a suite of existing tools can be used to assess the impacts of pollutants in combination with other anthropogenic pressures on Arctic ecosystems, and on the services that these ecosystems provide. Recommendations are made for the advancement of targeted Arctic research to inform environmental practices and regulatory decisions

Evaluation of an in vitro toxicogenetic mouse model for hepatotoxicity

Numerous studies support the fact that a genetically diverse mouse population may be useful as an animal model to understand and predict toxicity in humans. We hypothesized that cultures of hepatocytes obtained from a large panel of inbred mouse strains can produce data indicative of inter-individual differences in in vivo responses to hepato-toxicants. In order to test this hypothesis and establish whether in vitro studies using cultured hepatocytes from genetically distinct mouse strains are feasible, we aimed to determine whether viable cells may be isolated from different mouse inbred strains, evaluate the reproducibility of cell yield, viability and functionality over subsequent isolations, and assess the utility of the model for toxicity screening. Hepatocytes were isolated from 15 strains of mice (A/J, B6C3F1, BALB/cJ, C3H/HeJ, C57BL/6J, CAST/EiJ, DBA/2J, FVB/NJ, BALB/cByJ, AKR/J, MRL/MpJ, NOD/LtJ, NZW/LacJ, PWD/PhJ and WSB/EiJ, males) and cultured for up to 7 days in traditional 2-dimesional culture. Cells from B6C3F1, C57BL/6J, and NOD/LtJ strains were treated with acetaminophen, WY-14,643 or rifampin and concentration-response effects on viability and function were established. Our data suggest that high yield and viability can be achieved across a panel of strains. Cell function and expression of key liver specific genes of hepatocytes isolated from different strains and cultured under standardized conditions is comparable. Strain-specific responses to toxicant exposure have been observed in cultured hepatocytes and these experiments open new opportunities for further developments of in vitro models of hepatotoxicity in a genetically diverse population

DIFFUSE JUVENILE SYSTEMIC SCLEROSIS PATIENTS SHOW DISTINCT ORGAN INVOLVEMENT, ANTIBODY PATTERN AND HAVE SIGNIFICANTLY MORE SEVERE DISEASE IN THE LARGEST JSSC COHORT OF THE WORLD. RESULTS FROM THE JUVENILE SCLERODERMA INCEPTION COHORT

Peer reviewe

Towards computerizing intensive care sedation guidelines: design of a rule-based architecture for automated execution of clinical guidelines

<p>Abstract</p> <p>Background</p> <p>Computerized ICUs rely on software services to convey the medical condition of their patients as well as assisting the staff in taking treatment decisions. Such services are useful for following clinical guidelines quickly and accurately. However, the development of services is often time-consuming and error-prone. Consequently, many care-related activities are still conducted based on manually constructed guidelines. These are often ambiguous, which leads to unnecessary variations in treatments and costs.</p> <p>The goal of this paper is to present a semi-automatic verification and translation framework capable of turning manually constructed diagrams into ready-to-use programs. This framework combines the strengths of the manual and service-oriented approaches while decreasing their disadvantages. The aim is to close the gap in communication between the IT and the medical domain. This leads to a less time-consuming and error-prone development phase and a shorter clinical evaluation phase.</p> <p>Methods</p> <p>A framework is proposed that semi-automatically translates a clinical guideline, expressed as an XML-based flow chart, into a Drools Rule Flow by employing semantic technologies such as ontologies and SWRL. An overview of the architecture is given and all the technology choices are thoroughly motivated. Finally, it is shown how this framework can be integrated into a service-oriented architecture (SOA).</p> <p>Results</p> <p>The applicability of the Drools Rule language to express clinical guidelines is evaluated by translating an example guideline, namely the sedation protocol used for the anaesthetization of patients, to a Drools Rule Flow and executing and deploying this Rule-based application as a part of a SOA. The results show that the performance of Drools is comparable to other technologies such as Web Services and increases with the number of decision nodes present in the Rule Flow. Most delays are introduced by loading the Rule Flows.</p> <p>Conclusions</p> <p>The framework is an effective solution for computerizing clinical guidelines as it allows for quick development, evaluation and human-readable visualization of the Rules and has a good performance. By monitoring the parameters of the patient to automatically detect exceptional situations and problems and by notifying the medical staff of tasks that need to be performed, the computerized sedation guideline improves the execution of the guideline.</p

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.

In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA

The German National Registry of Primary Immunodeficiencies (2012-2017)

Introduction: The German PID-NET registry was founded in 2009, serving as the first national registry of patients with primary immunodeficiencies (PID) in Germany. It is part of the European Society for Immunodeficiencies (ESID) registry. The primary purpose of the registry is to gather data on the epidemiology, diagnostic delay, diagnosis, and treatment of PIDs. Methods: Clinical and laboratory data was collected from 2,453 patients from 36 German PID centres in an online registry. Data was analysed with the software Stata® and Excel. Results: The minimum prevalence of PID in Germany is 2.72 per 100,000 inhabitants. Among patients aged 1–25, there was a clear predominance of males. The median age of living patients ranged between 7 and 40 years, depending on the respective PID. Predominantly antibody disorders were the most prevalent group with 57% of all 2,453 PID patients (including 728 CVID patients). A gene defect was identified in 36% of patients. Familial cases were observed in 21% of patients. The age of onset for presenting symptoms ranged from birth to late adulthood (range 0–88 years). Presenting symptoms comprised infections (74%) and immune dysregulation (22%). Ninety-three patients were diagnosed without prior clinical symptoms. Regarding the general and clinical diagnostic delay, no PID had undergone a slight decrease within the last decade. However, both, SCID and hyper IgE- syndrome showed a substantial improvement in shortening the time between onset of symptoms and genetic diagnosis. Regarding treatment, 49% of all patients received immunoglobulin G (IgG) substitution (70%—subcutaneous; 29%—intravenous; 1%—unknown). Three-hundred patients underwent at least one hematopoietic stem cell transplantation (HSCT). Five patients had gene therapy. Conclusion: The German PID-NET registry is a precious tool for physicians, researchers, the pharmaceutical industry, politicians, and ultimately the patients, for whom the outcomes will eventually lead to a more timely diagnosis and better treatment