1,721,157 research outputs found
Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination
Full text linkThe prevailing view of the nuclear genetic code is that it is largely frozen and unambiguous. Flexibility in the nuclear genetic code has been demonstrated in ciliates that reassign standard stop codons to amino acids, resulting in seven variant genetic codes, including three previously undescribed ones reported here. Surprisingly, in two of these species, we find efficient translation of all 64 codons as standard amino acids and recognition of either one or all three stop codons. How, therefore, does the translation machinery interpret a “stop” codon? We provide evidence, based on ribosomal profiling and “stop” codon depletion shortly before coding sequence ends, that mRNA 3′ ends may contribute to distinguishing stop from sense in a context-dependent manner. We further propose that such context-dependent termination/readthrough suppression near transcript ends enables genetic code evolution
Temporal characterization of bacterial communities in a phytoremediation pilot plant aimed at decontaminating polluted sediments dredged from Leghorn harbor, Italy
Full text linkThe AGRIPORT project (Agricultural Reuse of Polluted Dredged Sediments, Eco-innovation EU Project n. ECO/08/239065) aims at developing a new technology for the treatment of polluted sediments dredged from the seabed of commercial ports through phytoremediation processes. Through plant activities and microorganism metabolisms, it is possible to recover dredged saline sediments by decontaminating them until an artificially prepared soil that is reusable in the terrestrial environment is obtained. This is an important advantage from the environmental point of view, and allows to partially solve one of the main problems of most commercial ports, that is the accumulation, storage and disposal of polluted dredged sediments. Considering that bacteria provide a significant contribution to phytoremediation process. Aim of the present study is the monitoring of temporal variation of microbial communities developing in an experimental phytoremediation plant during the decontamination process. The treatment plant consists of a sealed 80m(3) basin that is filled with a mixture of dredged sediments (75%) and natural soil (25%). It was planted with three plant species, and has been properly cultivated and fertilized for two years. Terminal Restriction Fragment Length Polymorphism (T-RFLP) on 16S rRNA gene was used to study the composition of bacterial communities at different times and points in the basin. Cluster Analysis (CA) and Non Metric Multidimensional Scaling (NMDS) multivariate statistics were applied for data interpretation. At the onset, the bacterial communities were heterogeneous and discrete, reflecting those inherited from the sediment-soil mixture, from compost and from plant's rhizospheres. The communities' composition rapidly changed to become stabilized after one year
Novel evolutionary insights on the interactions of the Holosporales (Alphaproteobacteria) with eukaryotic hosts from comparative genomics
No full textHolosporales are an alphaproteobacterial order engaging in obligate and complex associations with eukaryotes, in particular protists. The functional and evolutionary features of those interactions are still largely undisclosed. Here, we sequenced the genomes of two members of the species Bealeia paramacronuclearis (Holosporales, Holosporaceae) intracellularly associated with the ciliate protist Paramecium, which resulted in high correspondence. Consistent with the short-branched early-divergent phylogenetic position, Bealeia presents a larger functional repertoire than other Holosporaceae, comparable to those of other Holosporales families, particularly for energy metabolism and motility. Our analyses indicate that different Holosporales likely experienced at least partly autonomous genome reduction and adaptation to host interactions, for example regarding dependence on host biotin driven by multiple independent horizontal acquisitions of transporters. Among Alphaproteobacteria, this is reminiscent of the convergently evolved Rickettsiales, which however appear more diverse, possibly due to a probably more ancient origin. We identified in Bealeia and other Holosporales the plasmid-encoded putative genetic determinants of R-bodies, which may be involved in a killer trait towards symbiont-free hosts. While it is not clear whether these genes are ancestral or recently horizontally acquired, an intriguing and peculiar role of R-bodies is suggested in the evolution of the interactions of multiple Holosporales with their hosts
Survey of Paramecium duboscqui using three markers and assessment of the molecular variability in the genus Paramecium.
No full textThe genus Paramecium (phylum Ciliophora) is one of the best-known among protozoa. Nevertheless, the
knowledge on the diversity and distribution of species within this genus was remarkably scarce until
recent times. In the last years a constantly growing amount of data has formed, especially on the distribution
of species and the characterization of molecular markers. Much effort has been made on detecting
clades inside each morphospecies, which could suggest the presence of sibling species complexes as in
the famous case of Paramecium aurelia. In this work we present new data on Paramecium duboscqui,
one of the morphospecies that have not yet been surveyed employing DNA sequences as markers. We
obtained data from nine strains sampled around the world, using the three most commonly employed
markers (18S rRNA gene, ITS1-5.8S-ITS2 and COI gene sequences). Moreover, we compared our results
with those already available for other Paramecium species, and performed phylogenetic analyses for
the entire genus. We also expanded the knowledge on the ITS2 secondary structure and its usefulness
in studies on Paramecium. Our approach, that considers the data of all the species together, highlighted
some characteristic patterns as well as some ambiguities that should be further investigated
Apofrontonia dohrni sp. n. and the phylogenetic relationships within Peniculia (Protista, Ciliophora, Oligohymenophorea)
No full textAbstract: Apofrontonia dohrni, a new peniculine ciliate, was discovered in a slightly brackish water sample from Mediterranean coastline puddle in Naples, Italy. Its morphology was studied in vivo, in silver- and Feulgen-stained preparations, as well as at the scanning electron microscope; 18S rRNA gene sequence was also determined. The species is characterized by a medium cell size (118 x 61 mu m - fixed cell) and an oval-extended body, flattened dorsoventrally; a very long sausage-like macronucleus rolled up into almost a ring; a comparatively large compact micronucleus; relatively small number of vestibular kineties (4) and a peculiar structure of 3 peniculi, consisting of 5-6, 4-5 and 3 ciliary rows, respectively. The ciliate always has about 20 contractile vacuoles distributed beneath its entire body surface. Using these features, A. dohrni, definitely, can be easily discriminated from the two other species of the genus: Apofrontonia lametschwandtneri and Apofrontonia obtusa. T..
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