Mobilomics in Saccharomyces cerevisiae Strains

Background: Mobile Genetic Elements (MGEs) are selfish DNA integrated in the genomes. Their detection is mainly based on consensus-like searches by scanning the investigated genome against the sequence of an already identified MGE. Mobilomics aims at discovering all the MGEs in a genome and understanding their dynamic behavior: The data for this kind of investigation can be provided by comparative genomics of closely related organisms. The amount of data thus involved requires a strong computational effort, which should be alleviated.Results: Our approach proposes to exploit the high similarity among homologous chromosomes of different strains of the same species, following a progressive comparative genomics philosophy. We introduce a software tool based on our new fast algorithm, called regender, which is able to identify the conserved regions between chromosomes. Our case study is represented by a unique recently available dataset of 39 different strains of S.cerevisiae, which regender is able to compare in few minutes. By exploring the non-conserved regions, where MGEs are mainly retrotransposons called Tys, and marking the candidate Tys based on their length, we are able to locate a priori and automatically all the already known Tys and map all the putative Tys in all the strains. The remaining putative mobile elements (PMEs) emerging from this intra-specific comparison are sharp markers of inter-specific evolution: indeed, many events of non-conservation among different yeast strains correspond to PMEs. A clustering based on the presence/absence of the candidate Tys in the strains suggests an evolutionary interconnection that is very similar to classic phylogenetic trees based on SNPs analysis, even though it is computed without using phylogenetic information.Conclusions: The case study indicates that the proposed methodology brings two major advantages: (a) it does not require any template sequence for the wanted MGEs and (b) it can be applied to infer MGEs also for low coverage genomes with unresolved bases, where traditional approaches are largely ineffective

Compression and diffusion: a joint approach to detect complexity

The adoption of the Kolmogorov-Sinai (KS) entropy is becoming a popular research tool among physicists, especially when applied to a dynamical system fitting the conditions of validity of the Pesin theorem. The study of time series that are a manifestation of system dynamics whose rules are either unknown or too complex for a mathematical treatment, is still a challenge since the KS entropy is not computable, in general, in that case. Here we present a plan of action based on the joint action of two procedures, both related to the KS entropy, but compatible with computer implementation through fast and efficient programs. The former procedure, called Compression Algorithm Sensitive To Regularity (CASToRe), establishes the amount of order by the numerical evaluation of algorithmic compressibility. The latter, called Complex Analysis of Sequences via Scaling AND Randomness Assessment (CASSANDRA), establishes the complexity degree through the numerical evaluation of the strength of an anomalous effect. This is the departure, of the diffusion process generated by the observed fluctuations, from ordinary Brownian motion. The CASSANDRA algorithm shares with CASToRe a connection with the Kolmogorov complexity. This makes both algorithms especially suitable to study the transition from dynamics to thermodynamics, and the case of non-stationary time series as well. The benefit of the joint action of these two methods is proven by the analysis of artificial sequences with the same main properties as the real time series to which the joint use of these two methods will be applied in future research work.Comment: 27 pages, 9 figure

Underdiagnosis of osteoporotic vertebral fractures in patients with fragility fractures: retrospective analysis of over 300 patients

Osteoporosis (OP) is a silent disease unless a fracture occurs; it is a major health problem, mainly due to fragility fractures, that occur at vertebral and peripheral sites. Vertebral fractures (VF) are probably the most common fragility fractures, but they go often unrecognized. The main clinical symptoms of VF are acute and chronic back pain, spinal deformity, reduced mobility and impaired quality of life. They are frequently associated with other fragility fractures. We examined 478 patients at our outpatient clinic, who were referred for fragility fracture occurrence. The most common fragility fractures was hip fractures. However, after execution of spine X-rays in patients who had sustained hip fracture, we found that a large proportion of them had VF, which had not been reported in their medical history

A proposal of a new methodology for best location of environmentally sustainable roads infrastructures. Validation along the Fabriano-Muccia road

El trabajo contempla la creación de un modelo para definir la mejor localización en el territorio de nuevos proyectos de infraestructuras viarias y su convalidación en una carretera que forma parte de un proyecto de gran envergadura denominado Cuadrilátero Marcas-Umbría, en vías de realización. El objetivo del trabajo consiste en la puesta a punto de una herramienta ágil y versátil, capaz de sopesar, interpretándolos de forma correlacionada, los distintos aspectos de carácter medioambiental, socioeconómico, técnico y operativo, ligados a la construcción de una obra viaria. Se ha prestado especial atención a las dinámicas de uso y consumo de los hábitats naturales y a las problemáticas vinculadas a los fenómenos de fragmentación ecológica provocados por la red viaria y los asentamientos. La metodología que se ha puesto a punto prevé la recogida y la implementación, dentro de un sistema de información territorial dedicado, de un amplio abanico de datos capaces de definir las características peculiares del ámbito que es objeto del estudio, posteriormente interpretados y reconducidos a síntesis mediante la aplicación de una serie de indicadores específicos. Los indicadores definidos se incorporan posteriormente mediante la aplicación de técnicas de análisis multicriterio para definir un índice de evaluación sintético capaz de estimar de forma correlacionada la sensibilidad del territorio ante la introducción de nuevas infraestructuras viarias. Para convalidar la metodología, los índices propuestos se han aplicado a un área de estudio donde se está construyendo una infraestructura viaria de importancia considerable para las conexiones transversales de Italia central

Assessment of Biological and Sanitary Condition of Alien Fish from a High-Mountain Lake (Cottian Alps)

This study aimed to assess the biological and sanitary conditions of alien fish in a high-mountain lake (Balma Lake) located in the Cottian Alps. A single fish sampling session (August 2018) using gillnets collected 90 specimens of brook trout (Salvelinus fontinalis). Sex and age were determined (59 females and 31 males, age class 0+ to 4+). Regression analysis showed no difference in total weight and total length between males and females (ANCOVA: F = 0.453; p = 0.954). The mean condition factor (Kmean) decreased with increasing age for males and females. Terrestrial insects were the main prey found in the fish stomachs. The parasitological exam was negative, and the bacteriological exam was positive for Carnobacterium maltaromaticum and C. divergens in 33% of specimens. The total mercury, cadmium, and lead concentration in muscle tissue was within the maximum limit established by the European Commission for human consumption. The brook trout population was found to be well structured; these findings may help local administrations in the implementation of eradication measures

Anticancer effects against colorectal cancer models of chloro(triethylphosphine)gold(I) encapsulated in PLGA–PEG nanoparticles

Chloro(triethylphosphine)gold(I), (Et(3)PAuCl hereafter), is an Auranofin (AF)-related compound showing very similar biological and pharmacological properties. Like AF, Et(3)PAuCl exhibits potent antiproliferative properties in vitro toward a variety of cancer cell lines and is a promising anticancer drug candidate. We wondered whether Et(3)PAuCl encapsulation might lead to an improved pharmacological profile also considering the likely reduction of unwanted side-reactions that are responsible for adverse effects and for drug inactivation. Et(3)PAuCl was encapsulated in biocompatible PLGA–PEG nanoparticles (NPs) and the new formulation evaluated in colorectal HCT-116 cancer cells in comparison to the free gold complex. Notably, encapsulated Et(3)PAuCl (nano-Et(3)PAuCl hereafter) mostly retains the cellular properties of the free gold complex and elicits even greater cytotoxic effects in colorectal cancer (CRC) cells, mediated by apoptosis and autophagy. Moreover, a remarkable inhibition of two crucial signaling pathways, i.e. ERK and AKT, by nano-Et(3)PAuCl, was clearly documented. The implications of these findings are discussed. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10534-021-00313-0

The unusual isolation of carnobacteria in eyes of healthy salmonids in high‑mountain lakes

Carnobacteria are common bacteria in cold and temperate environments; they are also reported during fsh mortality events. In a previous study, carnobacteria were isolated from the eyes of healthy wild salmonids from a high-mountain lake. To better understand these fndings, salmonids were captured from three high-mountain lakes (Lower and Upper Balma Lake, Rouen Lake; northwest Italy) during August 2019 and subjected to bacteriological and histological examination. Although all were healthy, 8.7% (Lower Balma Lake), 24% (Upper Balma Lake), and 32.6% (Rouen Lake) were positive for carnobacteria colonization of the eyes. A Trojan-horse efect was hypothesized to explain carnobacteria isolation in the eye. This immune-escaping macrophage-mediated mechanism has been identifed in other Gram-positive bacteria. Biochemical, molecular, and phylogenetic analysis were carried out on isolated bacteria (Carnobacterium maltaromaticum and C. divergens). Based on previous references for carnobacteria isolated from fsh, C. maltaromaticum strains were tested for the pisA precursor gene of the bacteriocin piscicolin 126. Carnobacterium maltaromaticum strains were found to display genotypic heterogeneity and a low percentage of pisA positive amplifcation. Features of geomorphology, geographic isolation, and microbiota common to the three lakes are thought to be possibly related to our fndings. Moreover, terrestrial insects collected from the lake shoreline and the stomach contents were screened for the presence of carnobacteria. The salmonids in these high-mountain environments feed mainly on terrestrial insects, which are considered possible vectors for carnobacteria that might catabolize the exoskeleton chitin. All insects tested negative for carnobacteria, but as a small number of samples were analyzed, their role as possible vectors of infection cannot be excluded. Further studies are needed to corroborate our research hypothesis

Deep Energy Retrofit of Residential Buildings in the Mediterranean Area: The MedZEB Approach

Publicado en : Green Energy and TechnologyMediterranean deep retrofit markets are characterized by common barriers and bottlenecks, which barely have been identified as shared challenges, and this has led to a lack of dedicated solutions and to a substantial delay in achieving the 2020 EU policy targets. This situation is addressed by the H2020 HAPPEN project by proposing a new MedZEB approach characterized by the following features: Holistic, i.e., aimed at integrating the most relevant aspects of the retrofitting supply chain;Transparent, i.e., aimed at putting on the market novel tools for enhancing investors’ trust;Adaptive, i.e., aimed at enhancing “added values” of the retrofitting such as flexibility, well-being, etc. Having arrived at its midpoint, HAPPEN has produced an advanced version of its main outputs, among which are: the HAPPEN cost-optimal technical solutions, developed according to a step-by-step logic;the HAPPEN financial solution, fully integrated with the step-by-step logic, and aimed at funding the retrofitting process by relying on the energy savings achieved;the MedZEB protocol conceived as a guarantee scheme for the achievement of retrofit targets;the HAPPEN platform, an assisted digital marketplace aimed at matching demand and offer according to a one-stop-shop logic, at defragmenting the retrofit value chain, and at supporting actors with dedicated tools. These outputs have been developed also thanks to an extensive living laboratory and pilot-building program, carried out within ten pilot sites across seven EU Med countries; this has made it possible for a large engagement of potential users, which resulted in the ideation of the HAPPEN program, an overall framework aimed at integrating project outputs into an exploitable renovation procedure powered by the HAPPEN platform. This paper describes the first simulation of such a procedure in its entirety based on a real case study. After characterizing the building according to the HAPPEN reference buildings and climates lists, a step-by-step cost-optimal package of solutions was calculated, followed by the application of the HAPPEN financial solution, and by the draft issue of the MedZEB protocol. Results provide the first evidence of the effectiveness of the MedZEB approach in potentially unlocking the deep retrofit market in the Med area, with special attention to the possibility of funding the interventions by relying on the economies generated by the energy savings achieved. Further, the project activities will be aimed at co-creating, together with relevant stakeholders, a go-to-market strategy for the HAPPEN program.Horizonte 2020 (Unión Europea) 78507