Grotta dell\u2019Acqua Mintina a peculiar geosite with the smell of sulfur

Riassunto La grotta dell\u2019Acqua Mintina (comune di Butera, Caltanissetta, Sicilia) si estende per una lunghezza totale di 140 m nel Calcare di Base di et\ue0 messiniana (Miocene superiore) ed \ue8 caratterizzata dalla spettacolare presenza di concrezioni e cristalli di zolfo nativo e gesso secondario. Lo zolfo si \ue8 formato sulle pareti e sul soffitto della grotto in cristalli fino a 1 cm di lunghezza e in concrezioni microcristalline di forma botroidale, a nuvola, a popcorn e a \u201cmensola\u201d. Il gesso \ue8 presente in aggregati cristallini aciculari, prismatici e fibrosi con cristalli fino a 3 cm di lunghezza. La grotta mostra morfologie non compatibili con i consueti fenomeni carsici ma legate ad attacco acido su calcare. L\u2019acido solforico \ue8 stato generato in corrispondenza della falda acquifera per miscelazione di acque ricche di H2S risalite dai sedimenti sottostanti con acque ricche in ossigeno infiltrate dalla superficie. Il gesso si \ue8 formato attraverso il fenomeno della condensazione-corrosione di acido solforico sulle pareti calcaree della grotta, mentre lo zolfo si \ue8 formato per degassamento di H2S e CO2 al di sotto della superficie dell\u2019acqua, con parziale ossidazione dell\u2019acido solfidrico. L\u2019acido solfidrico \ue8 stato a sua volta generato dalla degradazione dei sedimenti ricchi in materia organica del Tripoli che si trovano immediatamente al di sotto del Calcare di Base e/o per riduzione batterica del gesso primario della Formazione di Pasquasia affiorante al di sopra. La grotta, per la presenza di spettacolari concrezioni di zolfo e gesso, rappresenta un geosito di interesse nazionale da tutelare e conservare attivamente.The Acqua Mintina cave (Butera, Caltanissetta, Sicily) cuts for a total length of 140 m the Messinian Calcare di base unit and is characterized by the spectacular, and fortunately still poorly degraded, presence of native sulfur and secondary gypsum. The sulfur occurs on the walls and ceiling in crystals up to 1 cm in length and centimeter-thick microcrystalline botroydal, cloud, popcorn, and folia concretions. Gypsum is present in acicular, prismatic and fibrous crystal aggregates consisting of crystals of up to 3 cm in length. The cave shows karst morphologies due to acid attack on limestone and not the usual dissolution by water flow. The organic-rich Tripoli sediments below the Calcare di Base unit and/or the bacterial reduction of gypsum from the Upper Gypsum unit probably provided the original H2S. Sulfuric acid was generated when H2S-rich water encountered oxygen-rich water at or near the water table. Gypsum formed by condensation-corrosion of sulfuric acid on the cave walls, while the sulfur concretion probably formed where H2S and CO2 were outgassing below the water surface, with the H2S partially oxidizing to sulfur. The cave for its widespread presence of spectacular crusts of sulfur and gypsum crystals represents a rare and valuable geosite to be actively protected and preserved

Fragon: rapid high-resolution structure determination from ideal protein fragments

Correctly positioning ideal protein fragments by molecular replacement presents an attractive method for obtaining preliminary phases when no template structure for molecular replacement is available. This has been exploited in several existing pipelines. This paper presents a new pipeline, named Fragon, in which fragments (ideal α-helices or β-strands) are placed using Phaser and the phases calculated from these coordinates are then improved by the density-modification methods provided by ACORN. The reliable scoring algorithm provided by ACORN identifies success. In these cases, the resulting phases are usually of sufficient quality to enable automated model building of the entire structure. Fragon was evaluated against two test sets comprising mixed α/β folds and all-β folds at resolutions between 1.0 and 1.7 Å. Success rates of 61% for the mixed α/β test set and 30% for the all-β test set were achieved. In almost 70% of successful runs, fragment placement and density modification took less than 30 min on relatively modest four-core desktop computers. In all successful runs the best set of phases enabled automated model building with ARP/wARP to complete the structure

Reflux and dyspeptic symptom patterns in patients with non erosive reflux disease (NERD) subclassified using 24-hour ambulatory intraluminal pH-Impedance

Ample evidence supports that prostate tumor metastasis originates from a rare population of cancer cells, known as cancer stem cells (CSCs). Unfortunately, little is known about the identity of these cells, making it difficult to target the metastatic prostate tumor. Here, for the first time, we report the identification of a rare population of prostate cancer cells that express the Tie-2 protein. We found that this Tie-2High population exists mainly in prostate cancer cell lines that are capable of metastasizing to the bone. These cells not only express a higher level of CSC markers but also demonstrate enhanced resistance to the chemotherapeutic drug Cabazitaxel. In addition, knockdown of the expression of the Tie-2 ligand angiopoietin (Ang-1) led to suppression of CSC markers, suggesting that the Ang-1/Tie-2 signaling pathway functions as an autocrine loop for the maintenance of prostate CSCs. More importantly, we found that Tie-2High prostate cancer cells are more adhesive than the Tie-2Low population to both osteoblasts and endothelial cells. Moreover, only the Tie-2High, but not the Tie-2Low cells developed tumor metastasis in vivo when injected at a low number. Taken together, our data suggest that Tie-2 may play an important role during the development of prostate tumor metastasis

Recent developments in MrBUMP : better search-model preparation, graphical interaction with search models, and solution improvement and assessment

Increasing sophistication in molecular-replacement (MR) software and the rapid expansion of the PDB in recent years have allowed the technique to become the dominant method for determining the phases of a target structure in macromolecular X-ray crystallography. In addition, improvements in bioinformatic techniques for finding suitable homologous structures for use as MR search models, combined with developments in refinement and model-building techniques, have pushed the applicability of MR to lower sequence identities and made weak MR solutions more amenable to refinement and improvement. MrBUMP is a CCP4 pipeline which automates all stages of the MR procedure. Its scope covers everything from the sourcing and preparation of suitable search models right through to rebuilding of the positioned search model. Recent improvements to the pipeline include the adoption of more sensitive bioinformatic tools for sourcing search models, enhanced model-preparation techniques including better ensembling of homologues, and the use of phase improvement and model building on the resulting solution. The pipeline has also been deployed as an online service through CCP4 online, which allows its users to exploit large bioinformatic databases and coarse-grained parallelism to speed up the determination of a possible solution. Finally, the molecular-graphics application CCP4mg has been combined with MrBUMP to provide an interactive visual aid to the user during the process of selecting and manipulating search models for use in MR. Here, these developments in MrBUMP are described with a case study to explore how some of the enhancements to the pipeline and to CCP4mg can help to solve a difficult case

Soldiers’ physical activity of daily life : a systematic literature review

Purpose High physical fitness and good health are not only essential for the civilian population but also for persons working in physically and psychologically demanding professions, such as armed forces personnel. To date there is no scientific summary of studies dealing with the physical activity of daily life in armed forces personnel, but this is necessary for a targeted intervention. Methods A systematic review was performed in the PubMed database (target date: 24 May 2020), using the search terms “military personnel” and “exercise” or “(physical) activity of daily life” including the assigned MESH words. Results Seven original papers have focused on the daily physical activity of military personal, and they were all conducted in different countries. The activity of daily life was on average 11,540 steps per day. Conclusions It could be shown that soldiers performed more physical activity than the civilian population and that the recommended 10,000 steps per day were slightly exceeded on average. However, the number of steps performed was very low in fields of activity with limited physical activity options, such as on board a ship. Altogether, it thus seems that additional healthpromoting physical activity programs are not required for most of the soldiers, but that, in contrast, corresponding offers for physical activity alternatives, e.g., in the form of fitness equipment, are urgently required in specific task areas (e.g., on board ships).Projekt DEAL 202

Automating tasks in protein structure determination with the Clipper Python module

Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalised for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language. We shall also place an emphasis on best practices in automation, illustrating how this can be achieved with this new Python module. This article is protected by copyright. All rights reserved

Vaccinia virus immunomodulator A46 : a lipid and protein-binding scaffold for sequestering host TIR-domain proteins

TS received Austrian Science Fund (FWF) grants P24038, W1221 and W1258. GAB is a member of Max F. Perutz Laboratories and the Vienna International PostDoctoral Program (VIPS). TKS is a holder of Wellcome Trust grant 097831. IU has Spanish Ministry of Economy and Competitiveness grant BIO2013-49604-EXP.Vaccinia virus interferes with early events of the activation pathway of the transcriptional factor NF-kB by binding to numerous host TIR-domain containing adaptor proteins. We have previously determined the X-ray structure of the A46 C-terminal domain; however, the structure and function of the A46 N-terminal domain and its relationship to the C-terminal domain have remained unclear. Here, we biophysically characterize residues 1-83 of the N-terminal domain of A46 and present the X-ray structure at 1.55 Å. Crystallographic phases were obtained by a recently developed ab initio method entitled ARCIMBOLDO_BORGES that employs tertiary structure libraries extracted from the Protein Data Bank; data analysis revealed an all β-sheet structure. This is the first such structure solved by this method which should be applicable to any protein composed entirely of β-sheets. The A46(1-83) structure itself is a β-sandwich containing a co-purified molecule of myristic acid inside a hydrophobic pocket and represents a previously unknown lipid-binding fold. Mass spectrometry analysis confirmed the presence of long-chain fatty acids in both N-terminal and full-length A46; mutation of the hydrophobic pocket reduced the lipid content. Using a combination of high resolution X-ray structures of the N-and C-terminal domains and SAXS analysis of full-length protein A46(1-240), we present here a structural model of A46 in a tetrameric assembly. Integrating affinity measurements and structural data, we propose how A46 simultaneously interferes with several TIR-domain containing proteins to inhibit NF-κB activation and postulate that A46 employs a bipartite binding arrangement to sequester the host immune adaptors TRAM and MyD88.Publisher PDFPeer reviewe

Update: factors influencing heart rate variability–a narrative review

ObjectiveHeart rate variability (HRV) is an important non-invasive marker for the assessment of an organism’s autonomic physiological regulatory pathways. Lower HRV has been shown to correlate with increased mortality. HRV is influenced by various factors or diseases. The aim of this narrative review is to describe the current state of knowledge on factors influencing HRV and their significance for interpretation.MethodsThe narrative review only included reviews, meta-analyses, and cohort studies which were published until 2021. HRV confounders were grouped into four categories (non-influenceable physiological factors, diseases, influenceable lifestyle factors and external factors).ResultsThe review found that HRV was decreased not only in non-influenceable physiological factors (e.g., age, gender, ethnicity) but also in connection with various number of acute and chronic diseases (e.g., psychiatric diseases, myocardial infarction, heart failure), influenceable lifestyle factors (e.g., alcohol abuse, overweight, physical activity), and external factors (e.g., heat, noise, shift work, harmful- and hazardous substances).ConclusionIn order to improve the quality of HRV studies and to ensure accurate interpretation, it is recommended that confounders be taken into account in future diagnostic measurements or measurements in the workplace (e.g., as part of health promotion measures) in order to counteract data bias