Computational analysis of bacterial sulfatases and their modifying enzymes

AbstractThe sequence analysis of enzymes that might modify bacterial sulfatases should be useful in the task of identifying the human sulfatase-modifying homologs — enzymes that are defective in the rare inherited disease multi-sulfatase deficiency

Fine-tuning structural RNA alignments in the twilight zone

Bremges A, Schirmer S, Giegerich R. Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics. 2010;11(1): 222

Everyone’s Going to be an Architect: Design Principles for Architectural Thinking in Agile Organizations

Organizational agility is a prominent aim for companies to thrive in today’s volatile business environments. One common building block of agility are (semi-) autonomous teams for continuously fulfilling and surpassing customers’ needs. However, these teams still need to see the enterprise’s ‘big picture’ of strategic objectives, business processes, and IT landscape to prevent organizational inertia or technical debt. This requires architectural thinking to inform these ‘non’-architects’ decision-making. To aid companies towards achieving sustainable agility, we propose six design principles as underlying logic on how to realize architectural thinking in agile organizations. The results are based on insights from interviews with sixteen employees and consultants with expertise on architecture management and organizational agility across several industries. Our work closes a gap in the agility literature, which so far mainly focused on non-generalizable blueprints for agile setups without showing their underlying logics, or approaches and role set-ups for enterprise-level architecture management

Agrárpiaci Jelentések Zöldség, gyümölcs és bor

Kiadványunk a következő témákban ad információkat: gyümölcspiac, zöldségpiac, borpiac, értékesítési árak, termelői árak, nagybani piac, kereslet-kínálat, fogyasztói piac, nemzetközi árinformációk

Mass fluxes of xenobiotics below cities: challenges in urban hydrogeology

Urban areas are the focus of major ecological, social and economical activity. They are thus also prime locations of increasing conflict with regard to water use and water protection. As a direct and/or indirect consequence of urban land use and human activity, urban water systems are frequently polluted with organic contaminants including waste water-born xenobiotics such as pharmaceuticals, personal care products (collectively known as PPCPs) and endocrine-active substances. This study reviews new integrated methodologies including flux calculations as well as chemical investigations for determining the impact of human activities on urban water systems and on processes within the urban watershed. The use of indicator substances, representing different contaminant sources and pathways, integral pumping tests and mass balance approaches are suitable alternatives within these environments. The issues are explored using contaminant mass balance examples from Halle/Saale and Leipzig, German

MALDI mass spectrometry imaging workflow for the aquatic model organisms Danio rerio and Daphnia magna

Lipids play various essential roles in the physiology of animals. They are also highly dependent on cellular metabolism or status. It is therefore crucial to understand to which extent animals can stabilize their lipid composition in the presence of external stressors, such as chemicals that are released into the environment. We developed a MALDI MS imaging workflow for two important aquatic model organisms, the zebrafish (Danio rerio) and water flea (Daphnia magna). Owing to the heterogeneous structure of these organisms, developing a suitable sample preparation workflow is a highly non-trivial but crucial part of this work and needs to be established first. Relevant parameters and practical considerations in order to preserve tissue structure and composition in tissue sections are discussed for each application. All measurements were based on high mass accuracy enabling reliable identification of imaged compounds. In zebrafish we demonstrate that a detailed mapping between histology and simultaneously determined lipid composition is possible at various scales, from extended structures such as the brain or gills down to subcellular structures such as a single axon in the central nervous system. For D. magna we present for the first time a MALDI MSI workflow, that demonstrably maintains tissue integrity during cryosectioning of non-preserved samples, and allows the mapping of lipids in the entire body and the brood chamber inside the carapace. In conclusion, the lipid signatures that we were able to detect with our method provide an ideal basis to analyze changes caused by pollutants in two key aquatic model organisms

Imaging the Electrostatic Potential of Transmembrane Channels: Atomic Probe Microscopy of OmpF Porin

This is the published version. Copyright 2002 by Elsevier.The atomic force microscope (AFM) was used to image native OmpF porin and to detect the electrostatic potential generated by the protein. To this end the OmpF porin trimers from Escherichia coli was reproducibly imaged at a lateral resolution of ∼0.5 nm and a vertical resolution of ∼0.1 nm at variable electrolyte concentrations of the buffer solution. At low electrolyte concentrations the charged AFM probe not only contoured structural details of the membrane protein surface but also interacted with local electrostatic potentials. Differences measured between topographs recorded at variable ionic strength allowed mapping of the electrostatic potential of OmpF porin. The potential map acquired by AFM showed qualitative agreement with continuum electrostatic calculations based on the atomic OmpF porin embedded in a lipid bilayer at the same electrolyte concentrations. Numerical simulations of the experimental conditions showed the measurements to be reproduced quantitatively when the AFM probe was included in the calculations. This method opens a novel avenue to determine the electrostatic potential of native protein surfaces at a lateral resolution better than 1 nm and a vertical resolution of ∼0.1 nm

Diagnostic accuracy of heart auscultation for detecting valve disease: a systematic review

Objective The objective of this study was to determine the diagnostic accuracy in detecting valvular heart disease (VHD) by heart auscultation, performed by medical doctors. Design/methods A systematic literature search for diagnostic studies comparing heart auscultation to echocardiography or angiography, to evaluate VHD in adults, was performed in MEDLINE (1947–November 2021) and EMBASE (1947–November 2021). Two reviewers screened all references by title and abstract, to select studies to be included. Disagreements were resolved by consensus meetings. Reference lists of included studies were also screened. The results are presented as a narrative synthesis, and risk of bias was assessed using Quality Assessment of Diagnostic Accuracy Studies-2. Main outcome measures Sensitivity, specificity and likelihood ratios (LRs). Results We found 23 articles meeting the inclusion criteria. Auscultation was compared with full echocardiography in 15 of the articles; pulsed Doppler was used as reference standard in 2 articles, while aortography and ventriculography was used in 5 articles. One article used point-of-care ultrasound. The articles were published from year 1967 to 2021. Sensitivity of auscultation ranged from 30% to 100%, and specificity ranged from 28% to 100%. LRs ranged from 1.35 to 26. Most of the included studies used cardiologists or internal medicine residents or specialists as auscultators, whereas two used general practitioners and two studied several different auscultators. Conclusion Sensitivity, specificity and LRs of auscultation varied considerably across the different studies. There is a sparsity of data from general practice, where auscultation of the heart is usually one of the main methods for detecting VHD. Based on this review, the diagnostic utility of auscultation is unclear and medical doctors should not rely too much on auscultation alone. More research is needed on how auscultation, together with other clinical findings and history, can be used to distinguish patients with VHD