Alessio Mengoni, Eva Grassi, Marco Bazzicalupo,
... Method for Taxonomic Interpretation of T-RFLP PatternsAlessio Mengoni, Eva Grassi & Marco BazzicalupoAlessio Mengoni*Address correspondence to Dr. Alessio Mengoni, Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy. e-mail: E-mail Address: alessiome@unifi.itUniversità di Firenze, Firenze, Italy, Eva GrassiUniversità di Firenze, Firenze, Italy & Marco BazzicalupoUniversità di Firenze, Firenze, ItalyPublished Online:17 Sep ...
Tópico(s): Environmental DNA in Biodiversity Studies
2002 - Future Science Ltd | BioTechniques
George C. diCenzo, Michelangelo Tesi, Thomas Pfau, Alessio Mengoni, Marco Fondi,
Abstract The mutualistic association between leguminous plants and endosymbiotic rhizobial bacteria is a paradigmatic example of a symbiosis driven by metabolic exchanges. Here, we report the reconstruction and modelling of a genome-scale metabolic network of Medicago truncatula (plant) nodulated by Sinorhizobium meliloti (bacterium). The reconstructed nodule tissue contains five spatially distinct developmental zones and encompasses the metabolism of both the plant and the bacterium. Flux balance ...
Tópico(s): Ammonia Synthesis and Nitrogen Reduction
2020 - Nature Portfolio | Nature Communications
Angelo Porreca, Daniele D’Agostino, D. Dente, Matteo Dandrea, A. Salvaggio, E. Cappa, A. Zuccalà, Alessandro Del Rosso, Francesco Chessa, Daniele Romagnoli, Francesco Mengoni, Marco Borghesi, Riccardo Schiavina,
Objectives The aim of our study is to present early outcomes of our series of retroperitoneal-RAPN (Robot Assisted Partial Nephrectomy). Materials and methods From September 2010 until December 2015, we performed 81 RAPN procedures (44 at left kidney and 37 at right). Average size was 3cm (1-9). Average PADUA score 7.1 (5-10). Average surgical time (overall and only robot time), ischemia time, blood loss, pathological stage, complications and hospital stay have been recorded. Results All of the cases ...
Tópico(s): Bladder and Urothelial Cancer Treatments
2018 - Sociedade Brasileira de Urologia | International braz j urol
Emanuele Bosi, Giovanni Bacci, Alessio Mengoni, Marco Fondi,
Bacteria have evolved to efficiently interact each other, forming complex entities known as microbial communities. These “super-organisms” play a central role in maintaining the health of their eukaryotic hosts and in the cycling of elements like carbon and nitrogen. However, despite their crucial importance, the mechanisms that influence the functioning of microbial communities and their relationship with environmental perturbations are obscure. The study of microbial communities was boosted by ...
Tópico(s): Biofuel production and bioconversion
2017 - Frontiers Media | Frontiers in Genetics
Francesco Pini, Nicole J. De Nisco, Lorenzo Ferri, Jon Penterman, Antonella Fioravanti, Matteo Brilli, Alessio Mengoni, Marco Bazzicalupo, Patrick H. Viollier, Graham C. Walker, Emanuele G. Biondi,
In all domains of life, proper regulation of the cell cycle is critical to coordinate genome replication, segregation and cell division. In some groups of bacteria, e.g. Alphaproteobacteria, tight regulation of the cell cycle is also necessary for the morphological and functional differentiation of cells. Sinorhizobium meliloti is an alphaproteobacterium that forms an economically and ecologically important nitrogen-fixing symbiosis with specific legume hosts. During this symbiosis S. meliloti undergoes ...
Tópico(s): Wastewater Treatment and Nitrogen Removal
2015 - Public Library of Science | PLoS Genetics
Produção Nacional
Revisado por pares
Sangam L. Dwivedi, K. L. Sahrawat, Hari D. Upadhyaya, Alessio Mengoni, Marco Galardini, Marco Bazzicalupo, Emanuele G. Biondi, Mariangela Hungría, Glaciela Kaschuk, Matthew W. Blair, Rodomiro Ortíz,
Legumes form symbiotic relationship with root-nodule, rhizobia. The nitrogen (N2) fixed by legumes is a renewable source and of great importance to agriculture. Symbiotic nitrogen fixation (SNF) is constrained by multiple stresses and alleviating them would improve SNF contribution to agroecosystems. Genetic differences in adaptation tolerance to various stresses are known in both host plant and rhizobium. The discovery and use of promiscuous germplasm in soybean led to the release of high-yielding ...
Tópico(s): Genetic and Environmental Crop Studies
2014 - Elsevier BV | Advances in agronomy
Elisabetta Polazzi, Ilaria Mengoni, Marco Caprini, Emiliano Peña‐Altamira, Ewelina Kurtys, Barbara Monti,
The role so far ascribed to intracellular CuZn superoxide dismutase is that of an intracellular scavenger of oxygen radicals. However, other functions of cytosolic CuZn superoxide dismutase have been hypothesized. For example, CuZn superoxide dismutase incubated with rat hepatocyte cells in culture inhibits 3-hydroxy-3methylglutaryl CoA reductase, thereby reducing cholesterol synthesis. We recently demonstrated the presence of surface membrane receptors for CuZn superoxide dismutase, suggesting ...
Tópico(s): Cholinesterase and Neurodegenerative Diseases
2012 - Karger Publishers | Neurosignals
Roberta Pastorelli, Silvia Landi, Darine Trabelsi, Raimondo Piccolo, Alessio Mengoni, Marco Bazzicalupo, M. Pagliai,
The influx of carbon sources and energy into the grossly oligotrophic soil system is a major driving force in biogeochemical cycles. Differences in these inputs due to the ground-covering plants and agriculture practices, likely influence the activity of the microbial communities. Previously, we have shown that the extent and degree of active bacterial diversity in soils are clearly affected by the type of management. In the present study we have evaluated the effects of different soil managements ( ...
Tópico(s): Protist diversity and phylogeny
2011 - Elsevier BV | Applied Soil Ecology
Lorenzo Ferri, Alessandro Gori, Emanuele G. Biondi, Alessio Mengoni, Marco Bazzicalupo,
Although horizontal gene transfer mediated by plasmids is important to the generation of the genetic variability of Sinorhizobium strains, the barriers which can reduce horizontal gene transfer between bacteria have not yet been studied in Sinorhizobium. We studied the plasmid transfer by electroporation and its restriction in strains of Sinorhizobium meliloti and S. medicae. After conditions for electroporation were established, three S. meliloti strains (including the sequenced type strain Rm1021) ...
Tópico(s): Plant nutrient uptake and metabolism
2010 - Elsevier BV | Plasmid
Majid Talebi, Masoud Bahar, Ghodratollah Saeidi, Alessio Mengoni, Marco Bazzicalupo,
Alfalfa is believed to have originated in north-western Iran and has a long history of coexistence with its bacterial symbiont Sinorhizobium in soils of Iran. However, little is known about the diversity of Sinorhizobium strains nodulating Iranian alfalfa genotypes. In this study, Sinorhizobium populations were sampled from eight different Iranian sites using three cultivars of Medicago sativa as trap host plants. A total of 982 rhizobial strains were isolated and species were identified showing ...
Tópico(s): Agronomic Practices and Intercropping Systems
2008 - Oxford University Press | FEMS Microbiology Letters
Matteo Brilli, Alessio Mengoni, Marco Fondi, Marco Bazzicalupo, Píetro Lió, Renato Fani,
Abstract Background Phylogenetic methods are well-established bioinformatic tools for sequence analysis, allowing to describe the non-independencies of sequences because of their common ancestor. However, the evolutionary profiles of bacterial genes are often complicated by hidden paralogy and extensive and/or (multiple) horizontal gene transfer (HGT) events which make bifurcating trees often inappropriate. In this context, plasmid sequences are paradigms of network-like relationships characterizing ...
Tópico(s): Microbial Community Ecology and Physiology
2008 - BioMed Central | BMC Bioinformatics
Emanuele G. Biondi, Elena Pilli, Elisa Giuntini, Marina L. Roumiantseva, Е. Е. Андронов, Olga P Onichtchouk, О. Н. Курчак, Б. В. Симаров, Nikolay Dzyubenko, Alessio Mengoni, Marco Bazzicalupo,
Sinorhizobium meliloti and Sinorhizobium medicae are two closely related species of the genus Sinorhizobium showing a similar host range, nodulating leguminous species of the genera Medicago, Melilotus and Trigonella, but their phylogenic relationship has not been elucidated yet. In this paper we report the application of three different molecular markers, (i) RFLP of nodD genes, (ii) 16S-23S rDNA intergenic gene spacer fingerprinting and (iii) amplification fragment length polymorphism to S. meliloti ...
Tópico(s): Coastal wetland ecosystem dynamics
2003 - Oxford University Press | FEMS Microbiology Letters
George C. diCenzo, Alessio Mengoni, Marco Fondi,
The design of synthetic cells requires a detailed understanding of the relevance of genes and gene networks underlying complex cellular phenotypes. Transposon-sequencing (Tn-seq) and constraint-based metabolic modeling can be used to probe the core genetic and metabolic networks underlying a biological process. Integrating these highly complementary experimental and in silico approaches has the potential to yield a highly comprehensive understanding of the core networks of a cell. Specifically, it ...
Tópico(s): Genomics and Phylogenetic Studies
2018 - American Chemical Society | ACS Synthetic Biology
A. Bonincontro, Costantino Mari, Marco Mengoni, Gianfranco Risuleo,
The permittivity of ribosomal proteins and ribosomal RNA (rRNA) in solution was measured in the range 100 kHz to 1 GHz at four different temperatures (5, 15, 25 and 35 degrees C). The experimental dielectric relaxation was analysed by the Cole-Cole equation and, from the best-fit parameters, the average values of the dipole moment and molecular radius of the proteins were obtained. The activation enthalpy was calculated from an Arrhenius plot of the relaxation time. The energy involved in the dielectric ...
Tópico(s): Electrostatics and Colloid Interactions
1997 - Elsevier BV | Biophysical Chemistry
Marco Galardini, Alessio Mengoni, Marco Bazzicalupo,
Obtaining bacterial genomic sequences has become a routine task in today’s biology. The emergence of the comparative genomics approach has led to an increasing number of bacterial species having more than one strain sequenced, thus facilitating the annotation process. On the other hand, many genomic sequences are now left in the “draft” status, as a series of contigs, mainly for the labor-intensive finishing task. As a result, many genomic analyses are incomplete (e.g., in their annotation) or impossible ...
Tópico(s): Robotics and Sensor-Based Localization
2014 - Springer Science+Business Media | Methods in molecular biology
Francesca Decorosi, Carlo Viti, Alessio Mengoni, Marco Bazzicalupo, Luciana Giovannetti,
Here the cDNA-fluorescent amplified fragment length polymorphism (cDNA-FAFLP) technique, an improvement of cDNA-AFLP method, was used in order to analyse expression profiling in bacteria. The obtained results were validated by real-time PCR. This is the first report that validates the foreseen transcription pattern by cDNA-FAFLP with the application of real-time PCR in bacteria. This new protocol offers the possibility of quick and reliable analysis of transcription profiles, also avoids the problem ...
Tópico(s): Bacteriophages and microbial interactions
2005 - Elsevier BV | Journal of Microbiological Methods
Matteo Brilli, Marco Fondi, Renato Fani, Alessio Mengoni, Lorenzo Ferri, Marco Bazzicalupo, Emanuele G. Biondi,
Abstract Background In the bacterium Caulobacter crescentus , CtrA coordinates DNA replication, cell division, and polar morphogenesis and is considered the cell cycle master regulator. CtrA activity varies during cell cycle progression and is modulated by phosphorylation, proteolysis and transcriptional control. In a phosphorylated state, CtrA binds specific DNA sequences, regulates the expression of genes involved in cell cycle progression and silences the origin of replication. Although the circuitry ...
Tópico(s): Genomics and Phylogenetic Studies
2010 - Springer Science+Business Media | BMC Systems Biology
A. Bonincontro, Stefania Cinelli, Marco Mengoni, G. Onori, Gianfranco Risuleo, A. Santucci,
We investigated the thermal degradation of E. coli ribosomes by differential scanning microcalorimetry. The 70S particles show two distinctive and irreversible peaks upon thermal degradation. Free rRNA in solution produces, on the contrary, an unstructured denaturation profile. The thermal analysis of 50S particles shows a profile substantially identical to that observed in 70S, while 30S particles produce an unstructured denaturation pattern. Therefore the thermal behavior of the 70S particle is ...
Tópico(s): RNA and protein synthesis mechanisms
1998 - Elsevier BV | Biophysical Chemistry
Alessio Mengoni, Marco Fondi, Marco Galardini,
Bacterial genomics is a mature research interdisciplinary field, which is approached by ecologists, geneticists, bacteriologists, molecular biologists and evolutionary biologists working in medical, i
Tópico(s): Molecular Biology Techniques and Applications
2014 - Springer Science+Business Media | Methods in molecular biology
Alessio Mengoni, Alessio Gori, Marco Bazzicalupo,
Abstract The level of random amplified polymorphic DNA (RAPD) and microsatellite variation present in four ecotypes and two varieties of alfalfa (lucerne) from Italian and Egyptian germplasm sources was evaluated. A sample of 100 plants from 10 populations was analysed by means of 41 RAPD markers and 37 simple sequence repeat (SSR) markers. Both molecular approaches revealed a high degree of genetic diversity within each of the cultivated populations and enabled each of the plants considered to be ...
Tópico(s): Genetic diversity and population structure
2000 - Wiley | Plant Breeding
Silvana Vanucci, D MINERDI, Kenji Kadomatsu, Alessio Mengoni, Marco Bazzicalupo,
A cDNA sequence of a putative midkine (MK) family protein was identified and characterised in the mollusc Patella caerulea. The midkine family consists of two members, midkine and pleiotrophin (PTN), and it is one of the recently discovered cytokines. Our results show that this putative midkine protein is up-regulated in specimens of P. caerulea exposed to sublethal cadmium concentrations (i.e. 0.5 and 1 mg l−1 Cd) over a 10-day exposure period. Semiquantitative RT-PCR and quantitative Real time RT- ...
Tópico(s): Protease and Inhibitor Mechanisms
2005 - Elsevier BV | Aquatic Toxicology
Darine Trabelsi, Alessio Mengoni, Mohamed Elarbi Aouani, Marco Bazzicalupo, Ridha Mhamdi,
Leguminous plants are promising pioneer-species for colonization of marginal areas and soils undergoing desertification. They derive part of their colonization abilities from their symbiotic interaction with nitrogen-fixing bacteria known as rhizobia. In this work, we analyzed total and culturable rhizobium communities from two Tunisian soils in close proximity to each other: one non-salty and cultivated and the other uncultivated and salty. The taxonomic diversity of the Rhizobiaceae family, evaluated ...
Tópico(s): Coastal wetland ecosystem dynamics
2010 - BioMed Central | Annals of Microbiology
George C. diCenzo, Alice Checcucci, Marco Bazzicalupo, Alessio Mengoni, Carlo Viti, Łukasz Dziewit, Turlough M. Finan, Marco Galardini, Marco Fondi,
Abstract The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental adaptations and/or niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological niches ( ...
Tópico(s): Plant nutrient uptake and metabolism
2016 - Nature Portfolio | Nature Communications
Marco Galardini, Alessio Mengoni, Emanuele G. Biondi, Roberto Semeraro, Alessandro Florio, Marco Bazzicalupo, Anna Benedetti, Stéfano Mocali,
Addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological manipulation of metabolic pathways. Over the last years, the OmniLog™ Phenotype Microarray (PM) technology has been used to address many specific issues related to the metabolic functionality of microorganisms. However, computational tools that could directly ...
Tópico(s): Genomics and Phylogenetic Studies
2013 - Elsevier BV | Genomics
Alessio Mengoni, Alan J. M. Baker, Marco Bazzicalupo, Roger D. Reeves, Nezaket Adıgüzel, E. Chianni, Francesca Galardi, R. Gabbrielli, Cristina Gonnelli,
• Molecular phylogeny based on ribosomal internal transcribed spacer (ITS) sequences was studied to investigate the phyletic relationships among some nickel (Ni)-hyperaccumulating and nonhyperaccumulating species of the genus Alyssum in relation to their geographic distribution and Ni-hyperaccumulating phenotype. • Thirty-seven samples belonging to 32 taxa were analysed by sequencing the polymerase chain reaction-amplified ITS region and performing neighbor joining, maximum parsimony and maximum likelihood phylogenetic ...
Tópico(s): Botany, Ecology, and Taxonomy Studies
2003 - Wiley | New Phytologist
Maura Mengoni, Serena Graziosi, Marco Mandolini, Margherita Peruzzini,
Tópico(s): Service-Oriented Architecture and Web Services
2010 - Springer Science+Business Media | International Journal on Interactive Design and Manufacturing (IJIDeM)
Luca Davoli, Marco Martalò, Antonio Cilfone, Laura Belli, Gianluigi Ferrari, Roberta Presta, Roberto Montanari, Maura Mengoni, Luca Giraldi, Elvio Gilberto Amparore, Marco Botta, Idílio Drago, Giuseppe Carbonara, Andrea Castellano, Johan Plomp,
Advanced Driver-Assistance Systems (ADASs) are used for increasing safety in the automotive domain, yet current ADASs notably operate without taking into account drivers’ states, e.g., whether she/he is emotionally apt to drive. In this paper, we first review the state-of-the-art of emotional and cognitive analysis for ADAS: we consider psychological models, the sensors needed for capturing physiological signals, and the typical algorithms used for human emotion classification. Our investigation ...
Tópico(s): Sleep and Work-Related Fatigue
2020 - Multidisciplinary Digital Publishing Institute | Safety
Dario Zuccon, Jean‐Marc Pons, Giovanni Boano, Giorgio Chiozzi, Anita Gamauf, Chiara Mengoni, Davide Nespoli, Georges Olioso, Marco Pavia, Irene Pellegrino, Marko Raković, Ettore Randi, Hamid Rguibi Idrissi, Moez Touihri, Markus Unsöld, Severino Vitulano, Mattia Brambilla,
Abstract We revise the taxonomy of the Sylvia cantillans complex, a group of phenotypically distinct warblers with mainly parapatric distributions around a large part of the Mediterranean basin. We redefine the species limits using a combination of mitochondrial and nuclear markers and we objectively link available names to the genetically defined lineages by genotyping the surviving type specimens. In addition, the study of archival documents clarifies the exact composition of type series and provides ...
Tópico(s): Lepidoptera: Biology and Taxonomy
2019 - Oxford University Press | Zoological Journal of the Linnean Society
Isabel Maida, Carolina Chiellini, Alessio Mengoni, Emanuele Bosi, Fabio Firenzuoli, Marco Fondi, Renato Fani,
Summary In this work we have studied the antagonistic interactions existing among cultivable bacteria isolated from three ecological niches (rhizospheric soil, roots and stem/leaves) of the traditional natural medicinal plant E chinacea purpurea . The three compartments harboured different taxonomic assemblages of strains, which were previously reported to display different antibiotic resistance patterns, suggesting the presence of differential selective pressure due to antagonistic molecules in the ...
Tópico(s): Plant tissue culture and regeneration
2015 - Wiley | Environmental Microbiology
Maria Carelli, S. Gnocchi, Silvia Fancelli, Alessio Mengoni, Donatella Paffetti, Carla Scotti, Marco Bazzicalupo,
ABSTRACT We analyzed the genetic diversity of 531 Sinorhizobium meliloti strains isolated from nodules of Medicago sativa cultivars in two different Italian soils during 4 years of plant growth. The isolates were analyzed for DNA polymorphism with the random amplified polymorphic DNA method. The populations showed a high level of genetic polymorphism distributed throughout all the isolates, with 440 different haplotypes. Analysis of molecular variance allowed us to relate the genetic structure of ...
Tópico(s): Plant Disease Resistance and Genetics
2000 - American Society for Microbiology | Applied and Environmental Microbiology