A new census of protein tandem repeats and their relationship with intrinsic disorder

Protein tandem repeats (TRs) are often associated with immunity-related functions and diseases. Since that last census of protein TRs in 1999, the number of curated proteins increased more than seven-fold and new TR prediction methods were published. TRs appear to be enriched with intrinsic disorder and vice versa. The significance and the biological reasons for this association are unknown. Here, we characterize protein TRs across all kingdoms of life and their overlap with intrinsic disorder in unprecedented detail. Using state-of-the-art prediction methods, we estimate that 50.9% of proteins contain at least one TR, often located at the sequence flanks. Positive linear correlation between the proportion of TRs and the protein length was observed universally, with Eukaryotes in general having more TRs, but when the difference in length is taken into account the difference is quite small. TRs were enriched with disorder-promoting amino acids and were inside intrinsically disordered regions. Many such TRs were homorepeats. Our results support that TRs mostly originate by duplication and are involved in essential functions such as transcription processes, structural organization, electron transport and iron-binding. In viruses, TRs are found in proteins essential for virulence

A field assessment of a novel rain measurement system based on earth-to-satellite microwave links

This work presents the performance of an innovative environmental monitoring system - Smart Rainfall System (SRS) - that estimates rainfall in real-time by means of the analysis of the attenuation of satellite signals (DVB-S in the microwave Ku band). SRS consists in a set of peripheral microwave sensors placed on the field of interest, and connected to a central processing and analysis node. It has been developed jointly by the University of Genoa, with its departments DITEN and DICCA and the University spin-off \u201cArtys Srl\u201d. The rainfall intensity measurements accuracy and sensitivity performance of SRS are discussed, based on preliminary results from a field comparison experiment at the urban scale. The test-bed is composed by a set of preliminary measurement sites established since Autumn 2016 in the Genoa (Italy) municipality and the data collected from the sensors during a selection of rainfall events is studied. Point-scale rainfall intensity measurements made by calibrated tipping-bucket rain gauges constitute the reference for the comparative analysis of the system performance. The dynamic calibration of the reference rain gauges has been carried out at the laboratories of DICCA using an automatic calibration rig and the measurements have been processed taking advantage of smart algorithms to reduce counting errors. Additional information about the spatial distribution of precipitation have been provided by the WSR radar of Monte Settepani. An objective of this investigation is the optimization of the specific attenuation model parameters for rain with respect to those recommended by the International Telecommunication Union standard ITU-R P.838-3. In addition, the experimental set-up allows a fine tuning of the retrieval algorithm and a full characterization of the accuracy of the rainfall intensity estimates from the microwave signal attenuation as a function of different precipitation regimes

Mapping of Aedes albopictus abundance at a local scale in Italy

Given the growing risk of arbovirus outbreaks in Europe, there is a clear need to better describe the distribution of invasive mosquito species such as Aedes albopictus. Current challenges consist in simulating Ae. albopictus abundance, rather than its presence, and mapping its simulated abundance at a local scale to better assess the transmission risk of mosquito-borne pathogens and optimize mosquito control strategy. During 2014–2015, we sampled adult mosquitoes using 72 BG-Sentinel traps per year in the provinces of Belluno and Trento, Italy. We found that the sum of Ae. albopictus females collected during eight trap nights from June to September was positively related to the mean temperature of the warmest quarter and the percentage of artificial areas in a 250 m buffer around the sampling locations. Maps of Ae. albopictus abundance simulated from the most parsimonious model in the study area showed the largest populations in highly artificial areas with the highest summer temperatures, but with a high uncertainty due to the variability of the trapping collections. Vector abundance maps at a local scale should be promoted to support stakeholders and policy-makers in optimizing vector surveillance and control

An Advanced Real-Time Rainfall Monitoring System Based on Commercial Satellite Broadcasting Service

Correct regulation of meteoric surface and subsurface flow waters is a fundamental goal for the sustainable development of the territories. In this paper, a new system for real-time monitoring of rainfall and cumulated rainfall is resented and discussed. The system implements a Sensor Network based on the IoT paradigm and can cover a wide area with a relatively small number of sensors, strategically placed. A real application case, based on the implementation of the Monte Scarpino pilot plant, is also presented and discussed

TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner

The Tandem Repeat Annotation Library (TRAL) focuses on analyzing tandem repeat units in genomic sequences. TRAL can integrate and harmonize tandem repeat annotations from a large number of external tools, and provides a statistical model for evaluating and filtering the detected repeats. TRAL version 2.0 includes new features such as a module for identifying repeats from circular profile hidden Markov models, a new repeat alignment method based on the progressive Poisson Indel Process, an improved installation procedure and a docker container. TRAL is an open-source Python 3 library and is available, together with documentation and tutorials viavital-it.ch/software/tral

Beyond microsatellite instability : intrinsic disorder as a potential link between protein short tandem repeats and cancer

Short tandem repeats (STRs) are abundant in genomic sequences and are known for comparatively high mutation rates; STRs therefore are thought to be a potent source of genetic diversity. In protein-coding sequences STRs primarily encode disorder-promoting amino acids and are often located in intrinsically disordered regions (IDRs). STRs are frequently studied in the scope of microsatellite instability (MSI) in cancer, with little focus on the connection between protein STRs and IDRs. We believe, however, that this relationship should be explicitly included when ascertaining STR functionality in cancer. Here we explore this notion using all canonical human proteins from SwissProt, wherein we detected 3,699 STRs. Over 80% of these consisted completely of disorder promoting amino acids. 62.1% of amino acids in STR sequences were predicted to also be in an IDR, compared to 14.2% for non-repeat sequences. Over-representation analysis showed STR-containing proteins to be primarily located in the nucleus where they perform protein- and nucleotide-binding functions and regulate gene expression. They were also enriched in cancer-related signaling pathways. Furthermore, we found enrichments of STR-containing proteins among those correlated with patient survival for cancers derived from eight different anatomical sites. Intriguingly, several of these cancer types are not known to have a MSI-high (MSI-H) phenotype, suggesting that protein STRs play a role in cancer pathology in non MSI-H settings. Their intrinsic link with IDRs could therefore be an attractive topic of future research to further explore the role of STRs and IDRs in cancer. We speculate that our observations may be linked to the known dosage-sensitivity of disordered proteins, which could hint at a concentration-dependent gain-of-function mechanism in cancer for proteins containing STRs and IDRs

Spatial ecological complexity measures in GRASS GIS

Good estimates of ecosystem complexity are essential for a number of ecological tasks: from biodiversity estimation, to forest structure variable retrieval, to feature extraction by edge detection and generation of multifractal surface as neutral models for e.g. feature change assessment. Hence, measuring ecological complexity over space becomes crucial in macroecology and geography. Many geospatial tools have been advocated in spatial ecology to estimate ecosystem complexity and its changes over space and time. Among these tools, free and open source options especially offer opportunities to guarantee the robustness of algorithms and reproducibility. In this paper we will summarize the most straightforward measures of spatial complexity available in the Free and Open Source Software GRASS GIS, relating them to key ecological patterns and processes

Energie- und klimabewusste Ernährung in städtischen Verpflegungsbetrieben

Im Projekt wurden Menüvorschläge für Personalrestaurants (PR) und Alterszentren (ASZ) erarbeitet, die in Umweltfreundlichkeit, Ausgewogenheit und Beliebtheit ein möglichst optimales «Set» von Mahlzeiten abbilden und zu einer möglichst grossen Reduktion des Energieverbrauchs und der Treibhausgas-Emissionen beitragen. In Ergänzung zu den bewerteten Menüs wurde untersucht, welche Interventionen für die städtischen Verpflegungsbetriebe besonders erfolgversprechend sind, um eine umweltfreundliche Ernährung zu fördern. Es wurden 149 Menüs für PR und 155 Menüs für ASZ zusammengestellt, welche umweltfreundlich, ernährungsphysiologisch optimiert und relativ beliebt sind. Die Menüs der PR wurden ernährungsphysiologisch für Erwachsene im Alter von 19 bis 65 optimiert, jene der ASZ für Erwachsene im Alter von 80+. Die Menüs liegen in zwei Datenbanken vor, die Küchenverantwortlichen verwenden können. Insgesamt konnte die durchschnittliche Gesamtumweltbelastung pro Menü durch die Menü-Auswahl und -Optimierungen (im Vergleich zum Basis-Menü-Set) um 52 % und das Treibhauspotenzial um 48 % reduziert werden. Unter den je drei Interventionen, die in PR und ASZ getestet wurden, konnte für die Intervention «Menüwechsel», bei der Fleisch- und Vegi-Menüs auf den Menülinien zufällig wechselten, eine punktuelle Steigerung des Verkaufs vegetarischer Menüs verzeichnet werden. Anpassungen im Menüangebot sind entscheidend, um Klimaziele im Bereich Ernährung zu erreichen. Um das Dilemma insbesondere in ASZ zwischen der Erreichung minimaler Umwelt- und Klimabelastungen und einer für die Altersgruppe ausgewogenen Ernährung aufzulösen, sind Kreativität aufseiten der Küchenverantwortlichen und sinnvolle Zielvorgaben nötig. Die im Projekt erarbeiteten Menüs liefern den Küchenverantwortlichen Inspirationen, für den Ersatz bestimmter Menü-Komponenten, ohne dabei die Ausgewogenheit zu vernachlässigen. Eine Plattform zu schaffen, die es Küchenverantwortlichen ermöglicht, Erfahrungen sowie Tipps und Tricks regelmässig zu teilen, sich gegenseitig zu motivieren und zu trainieren, könnte langfristig einen weiteren Beitrag dazu leisten, ein klima- und umweltfreundlicheres Menüangebot zu etablieren, welches gleichzeitig ausgewogen ist und schmeckt

Bayesian network analysis reveals the interplay of intracranial aneurysm rupture risk factors

Clinical decision making regarding the treatment of unruptured intracranial aneurysms (IA) benefits from a better understanding of the interplay of IA rupture risk factors. Probabilistic graphical models can capture and graphically display potentially causal relationships in a mechanistic model. In this study, Bayesian networks (BN) were used to estimate IA rupture risk factors influences. From 1248 IA patient records, a retrospective, single-cohort, patient-level data set with 9 phenotypic rupture risk factors (n=790 complete entries) was extracted. Prior knowledge together with score-based structure learning algorithms estimated rupture risk factor interactions. Two approaches, discrete and mixed-data additive BN, were implemented and compared. The corresponding graphs were learned using non-parametric bootstrapping and Markov chain Monte Carlo, respectively. The BN models were compared to standard descriptive and regression analysis methods. Correlation and regression analyses showed significant associations between IA rupture status and patient’s sex, familial history of IA, age at IA diagnosis, IA location, IA size and IA multiplicity. BN models confirmed the findings from standard analysis methods. More precisely, they directly associated IA rupture with familial history of IA, IA size and IA location in a discrete framework. Additive model formulation, enabling mixed-data, found that IA rupture was directly influenced by patient age at diagnosis besides additional mutual influences of the risk factors. This study establishes a data-driven methodology for mechanistic disease modelling of IA rupture and shows the potential to direct clinical decision-making in IA treatment, allowing personalised prediction