Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network.

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 the evolution of prokaryotes. Actually, they can be transferred among different organisms allowing the dissemination of novel functions, thus playing a pivotal role in prokaryotic evolution. However, the study of their evolutionary dynamics is complicated by the absence of universally shared genes, a prerequisite for phylogenetic analyses. RESULTS: To overcome such limitations we developed a bioinformatic package, named Blast2Network (B2N), allowing the automatic phylogenetic profiling and the visualization of homology relationships in a large number of plasmid sequences. The software was applied to the study of 47 completely sequenced plasmids coming from Escherichia, Salmonella and Shigella spps. CONCLUSION: The tools implemented by B2N allow to describe and visualize in a new way some of the evolutionary features of plasmid molecules of Enterobacteriaceae; in particular it helped to shed some light on the complex history of Escherichia, Salmonella and Shigella plasmids and to focus on possible roles of unannotated proteins.The proposed methodology is general enough to be used for comparative genomic analyses of bacteria.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Junior Students’ with Hearing Impairment Psychological Correction of Learning Motivation Development

У статті розглянуто основні методологічні принципи, методи, етапи корекційного процесу. Обґрунтовано використання гуманістичного підходу до корекції мотиваційної сфери учіння та підібрано комплекс корекційних завдань для розвитку цієї сфери в молодших школярів із порушеннями слуху. The article presents basic methodological principles, methods, main stages of correctional process. A humanitarian approach to learning motivation development correction has been grounded and a complex of correctional tasks for junior students with hearing impairment has been selected

Holocene climate variability of the Western Mediterranean: surface water dynamics inferred from calcareous plankton assemblages

A high-resolution study (centennial scale) has been performed on the calcareous plankton assemblage of the Holocene portion of the Ocean Drilling Program Site 976 (Alboran Sea) with the aim to identify the main changes in the surface water dynamic. The dataset also provided a seasonal foraminiferal sea surface water temperatures (SSTs), estimated using the modern analog technique SIMMAX 28, and it was compared with available geochemical and pollen data at the site. Three main climate shifts were identified as (1) the increase in abundance of Syracosphaera spp. and Turborotalita quinqueloba marks the early Holocene humid phase, during maximum summer insolation and enhanced river runoff. It is concomitant with the expansion of Quercus, supporting high humidity on land. It ends at 8.2 ka, registering a sudden temperature and humidity reduction; (2) the rise in the abundances of Florisphaera profunda and Globorotalia inflata, at ca. 8 ka, indicates the development of the modern geostrophic front, gyre circulation, and of a deep nutricline following the sea-level rise; and (3) the increase of small Gephyrocapsa and Globigerina bulloides at 5.3 ka suggests enhanced nutrient availability in surface waters, related to more persistent wind-induced upwelling conditions. Relatively higher winter SST in the last 3.5 ka favored the increase of Trilobatus sacculifer, likely connected to more stable surface water conditions. Over the main trends, a short-term cyclicity is registered in coccolithophore productivity during the last 8 ka. Short periods of increased productivity are in phase with Atlantic waters inflow, and more arid intervals on land. This cyclicity has been related with periods of positive North Atlantic Oscillation (NAO) circulations. Spectral analysis on coccolithophore productivity confirms the occurrence of millennial-scale cyclicity, suggesting an external (i.e. solar) and an internal (i.e. atmospheric/oceanic) forcing.Geoscience PhD scholarship, Universita degli Studi di BariPotenziamento Strutturale dell'Universita degli Studi di Bari, Laboratorio per lo Sviluppo Integrato delle Scienze e delle Tecnologie dei Materiali Avanzati e per dispositivi innovativi (SISTEMA) [PONa3_00369]Fundacao para a Ciencia e a Tecnologia (FCT)Portuguese Foundation for Science and TechnologyEuropean Commission [SFRH/BPD/111433/2015]info:eu-repo/semantics/submittedVersio

The histidine operon of Azospirillum brasilense: organization, nucleotide sequence and functional analysis

A 3457-base pair fragment of Azospirillum brasilense DNA which complemented mutations in the hisA and hisF genes of Escherichia coli was sequenced. The sequence analysis revealed the presence of six major contiguous open reading frames (ORF). The comparison of the predicted amino acid sequence of these ORF with those encoded by the eubacterial, archaebacterial and eukaryotic his genes sequenced thus far revealed that four of them have a significant degree of homology with the E. coli hisH, hisA, hisF and the C-terminal domain of the hisI gene products. S1 mapping experiments indicated that the putative transcription start site coincided with the AUG translational initiation codon of the hisBd gene, the first gene of the A. brasilense his operon. Downstream from the last ORF, a sequence was identified which functions as a Rho-independent transcription terminator. Comparison of amino acid sequences, gene order and organization and evolutionary aspects of the A. brasilense his cluster are discussed

Paleoproductivity modes in central Mediterranean during MIS 20 ‐ MIS 18: Calcareous plankton and alkenone variability

International audiencePaleoproductivity is reconstructed across a Mediterranean benchmark record, the Early/Middle Pleistocene Montalbano Jonico section, cropping out in southern Italy. High-resolution coccolithophore and alkenone data (C37 and C37:2/C38:2 ratio) were collected in order to extend the data set on Mediterranean paleoproductivity pattern and forcing mechanisms. The multi-proxy record indicates low productivity during glacial and stadial phases and enhanced productivity during interglacial and interstadials. Increased surface water turbidity, cold-water temperature and polar-subpolar low salinity water incursion appear as the dominant controls for low productivity during Marine Isotope Stage (MIS) 20. Enhanced productivity during MIS 19c was sustained by warmer surface waters, coupled with a seasonal precipitation regime, providing higher nutrient availability. Productivity increases during interstadials with respect to stadials, in relation with enhanced land-derived nutrient input through river discharge during wetter winters. The productivity scenario we propose is similar to those reconstructed from deep-sea records in the central and western Mediterranean during Dansgaard-Oeschger oscillations over the last 70 ka. This indicates that similar forcing mechanisms acted on productivity dynamics on a regional scale over different times. We suggest that migration of the westerly wind system over the Mediterranean and the polar water inflow influenced productivity on a regional scale. The acquired data set provides new evidences on the environmental significance of the C37:2/C38:2 ratio and on its relation with surface water productivity

DataSheet2_Living coralligenous as geo-historical structure built by coralline algae.PDF

The most important reef of the Mediterranean is the Coralligène (Coralligenous = C), including several types of calcareous algal-invertebrate build-ups growing in normal open marine conditions. We analyzed and compared two C samples from the Ligurian Sea developed in different environmental settings: 1) off Portofino on a rocky cliff, at a depth of about 40 m and 2) in front of Bogliasco, on a sub-horizontal substrate at a depth of 10 m. The maximum AMS radiocarbon dating provided an older age for Bogliasco (about 5 ka BP) than for Portofino (about 3.6 ka BP), and the mean accumulation rate of the Portofino build-up (about 80 µm y−1) was found to be higher than the one in Bogliasco (about 65 µm y−1). The different sides of each build-up showed a remarkable heterogeneity in the dominant cover by living organisms, and the comparison between the two build-ups highlighted an evident diversity in their taxonomic composition and structure, although crustose coralline algae (CCA) are the dominant framework builder and major autogenic ecosystem engineers at both localities, in the present as in the past millennia. Other major components of the structure are bryozoans and serpulids, and an important role is played by sediment filling. In Bogliasco, extreme climate events and major peaks of fine matrix and terrigenous grains are observed, lithologically related to the drainage basin of the Poggio creek and associated with charophyte occurrence and reduced CCA abundance. The occurrence of the rare Sporolithon ptychoides was observed both in Portofino at about 750 BCE and in Bogliasco. These Sporolithon phases are likely related to warm and humid spells punctuating the Holocene climate fluctuations in the Ligurian Sea. Because coralline algae are confirmed to be the most important habitat engineer of the Mediterranean reefs, they deserve more attention in the framework of any monitoring initiative aimed at C management and conservation.</p

Geomorphology of coralligenous reefs offshore southeastern Sicily (Ionian Sea)

ABSTRACTCoralligenous (C) includes calcareous build-ups of biogenic origin, formed since the Holocene transgression. Peculiar columnar-shaped C outcrops were documented offshore Marzamemi village (SE Sicily, Ionian Sea), although the actual extension and distribution were not assessed. Project ‘CRESCIBLUREEF’ produced a new, 17 km2 high-resolution bathymetric map, leading to good knowledge about their extent in this area. C bioconstructions are largely distributed along two depth ranges 36–42 m and 86–102 m water depth. By coupling the documented uplift rate in this region and the Holocene sea-level curve, we were able to interpret the distribution of C outcrops over terraces. However, additional investigation is required to understand: (1) the role of the inherited continental shelf landscape, in creating a favorable substrate for the settlement and growth of C habitats during the Holocene, and (2) the extent to which C bioconstructions can impact the evolution of present-day continental shelf landforms and landscapes

Late quaternary evolution of the continental shelf offshore Marzamemi (southern Sicily, Ionian Sea) and implications on the distribution of associated mesophotic bioconstructions

Coralligenous (C) bioconstructions include calcareous build-ups of biogenic origin that typify selected regions of the Mediterranean Sea. These peculiar habitats thrive from shallow waters (15-20 m of water depth (w.d.) up to the limit of the mesophotic zone, and they formed since the Holocene transgression. They are from few to tens of meters large, displaying variable lateral continuity and thickness. Peculiar C outcrops are present offshore Marzamemi (southeastern Sicily, Ionian Sea). Their extension and distribution across the shelf were investigated within the project CRESCIBLUREEF - Grown in the blue: new technologies for knowledge and conservation of Mediterranean reefs. We produced a new 17 km2 high-resolution bathymetric map using a R2-Sonic 2022 system, ground-truthed by ROV video inspections. From a geomorphological point of view, the shelf is typified by four distinct marine terraces. Climate change and tectonic uplift are the dominant forcing mechanisms responsible for the formation of long and narrow terraced landforms in a variety of geomorphic settings; and marine terraces are largely used to reconstruct the Quaternary glacial and interglacial climates. The coupling of documented uplift rate in this region (ca. 0.2 mm/yr since the Tyrrhenian time) and the evidence reported in literature for late Quaternary relative sea-level curves shows a good correlation between the distribution of C outcrops and local, short stasis of sea level transgression periods, culminated with the rapid Flandrian transgression. C outcrops are mainly spread over the first and last terraces at two specific depth ranges: from 36 to 42 m of w.d., and from 86 to 102 m of w.d., respectively. Settlement and growth were mainly favored by a low sedimentation regime. Indeed, lowstand stages were likely characterized by erosional forces. This is particularly noticeable in the middle of our study area, where we have a paleo-incision typified by peculiar erosional features we were able to map. The role of the inherited continental shelf landscape in creating favorable substrate for the settlement and growth of C during the Holocene is here investigated