165 research outputs found
Coping with Iberian monopolies: Genoese trade networks and formal institutions in Spain and Portugal during the second half of the eighteenth century
No full textThis article explores Genoese trade interests in Cadiz and Lisbon, the two capitals of Iberian colonial trade at the end of the early-modern period. The author aims to explain the persisting intermediary role of a merchant community that has been largely overlooked by historians. The structure of the trade networks established in the two cities will be reconstructed by using the primary sources conserved in the archive of the Durazzos, a powerful aristocratic family of the Republic which has left a unique collection of private correspondence. This sizeable and largely unexplored documentation illuminates the different strategies used to access the Spanish and Portuguese monopolistic systems, the main actors who traded in both contexts, their relations with the local elite, and the nature of the business networks linking Genoese investors in the mother city with the expatriated agents. The author concludes with a comparative analysis of the institutional resources that Genoese used to maintain their interests, with particular attention paid to the religious institutions established by the 'nation' in the two port cities
Perché c’è una scena anziché il nulla? Componenti relazionali della scena performativa italiana (1959-1979)
No full textOn the interaction of replication and transcriptional regulation
No full textDNA replication introduces a gradient of gene copy numbers, and in Bacteria it affects gene expression accordingly. In E. coli and other species, the slope of the gradient averaged over the population can be predicted on the basis of its relationship with growth rate. In this work we integrated this growth- and position-dependent gradient into a classical transcriptional regulation model, to highlight their interaction. The theoretical treatment of our model highlights that the sensitivity to transcription factor-mediated regulations acquires an additional dimension related to the position of a locus on the oriter axis and to division time. This reinforces the idea of replication as an additional layer in gene regulation. We highlight here that replication- and transcription factor-mediated regulations can in theory work in concert or counteract each other, and we discuss why this is important from an evolutionary point of view with respect to both steady state transcript abundance and its variance across conditions. Finally, we note that this treatment may improve the estimation of kinetic parameters for transcription factor activity using RNA-seq data, and the estimation of the dispersion factor in differential gene expression analysis when division time across conditions changes significantly
Dante’s New Lives: Biography and Autobiography
No full textInternational audienceNumerous books have attempted to chronicle the life of Dante Alighieri, yet essential questions remain unanswered. How did a self-taught Florentine become the celebrated author of the Divine Comedy? Was his exile from Florence so extraordinary? How did Dante make himself the main protagonist in his works, in a literary context that advised against it? And why has his life interested so many readers? In Dante’s New Lives, eminent scholars Elisa Brilli and Giuliano Milani answer these questions and many more. Their account reappraises Dante’s life and work by assessing archival and literary evidence and examining the most recent scholarship. The book is a model of interdisciplinary biography, as fascinating as it is rigorous
Dante’s New Lives: Biography and Autobiography
No full textInternational audienceNumerous books have attempted to chronicle the life of Dante Alighieri, yet essential questions remain unanswered. How did a self-taught Florentine become the celebrated author of the Divine Comedy? Was his exile from Florence so extraordinary? How did Dante make himself the main protagonist in his works, in a literary context that advised against it? And why has his life interested so many readers? In Dante’s New Lives, eminent scholars Elisa Brilli and Giuliano Milani answer these questions and many more. Their account reappraises Dante’s life and work by assessing archival and literary evidence and examining the most recent scholarship. The book is a model of interdisciplinary biography, as fascinating as it is rigorous
Flooding responses on grapevine: a physiological, transcriptional and molecular perspective
No full textA highly specific microRNA-mediated mechanism silences LTR retrotransposons of strawberry
No full textSmall RNAs are involved in a plethora of functions in plant genomes. In general, transcriptional gene silencing is mediated by 24-nucleotide siRNAs and is required for keeping transposable elements in a silenced state while microRNAs are not commonly associated with transposon silencing. In this study we performed small RNA transcriptome and degradome analyses of the Rosaceae model plant Fragaria vesca (the woodland strawberry) at the genome-wide level and identified miRNA families and their targets. We report a highly specific mechanism of LTR retrotransposon silencing mediated by an abundant, ubiquitously expressed fve-miR1511 generated from a single locus. This miRNA specifically targets LTR retroelements, silencing them post-transcriptionally by perfectly pairing to the highly conserved primer binding site (PBS) for methionyl-initiator tRNA essential for reverse transcription. We investigated possible origins of this miRNA and we present evidence that the pre-miR1511 hairpin structure likely derived from a locus coding for tRNA(iM) (et) through a single microinversion event. Our study shows that miRNA can target retrotransposons specifically and constitutively and contribute to features such as genome stability, size and architecture in a far more direct way than previously considered
The CAI Analyser Package: inferring gene expressivity from raw genomic data
No full textThe Codon Adaptation Index (CAI) was introduced by Sharp and Li in 1987 to quantify codon usage similarities between a coding sequence and a set of reference sequences. When synonymous codons for a given amino acid exist, highly expressed genes seem to prefer some of them, according to tRNA abundance and thermodynamic issues. Some authors have described CAI-based methods to derive expressivity measures for all genes in a genome, in a computational framework.
Here we present the CAIAP (CAI Analyser Package), a platform independent package of computer programs allowing the calculation of the CAI and a deep study of gene expressivity from raw gene sequences. Our approach implements and optimizes a procedure to derive the reference sequences from whole genomes and use their codon usage for CAI estimation. Moreover, a set of analysis tools are provided to perform statistical analyses and therefore to give robustness to results. Objective: Our efforts were aimed to produce an easy-to-use and fully automatic set of programs specifically designed for the analysis of gene expressivity and inter-species comparisons on a great number of genomes. Moreover, the output integrates information coming from functional annotations of genes.
We are maintaining a web server storing our analyses for hundreds of genomes, allowing intergenomic comparison of data thanks to dedicated search engines. The CAIAP server is hosted at www4.unifi.it/scibio/bioinfo/caiap/html. The programs (maintained as Perl scripts) are also available for download at the same location
The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case
No full textBackground: Histidine biosynthesis is one of the best characterized anabolic pathways. There is a large body of genetic and biochemical information available, including operon structure, gene expression, and increasingly larger sequence databases. For over forty years this pathway has been the subject of extensive studies, mainly in Escherichia coli and Salmonella enterica, in both of which details of histidine biosynthesis appear to be identical. In these two enterobacteria the pathway is unbranched, includes a number of unusual reactions, and consists of nine intermediates; his genes are arranged in a compact operon (hisGDC [NB] HAF [IE]), with three of them (hisNB, hisD and hisIE) coding for bifunctional enzymes. We performed a detailed analysis of his gene fusions in available genomes to understand the role of gene fusions in shaping this pathway.
Results: The analysis of HisA structures revealed that several gene elongation events are at the root of this protein family: internal duplication have been identified by structural superposition of the modules composing the TIM-barrel protein.
Several his gene fusions happened in distinct taxonomic lineages; hisNB originated within gamma-proteobacteria and after its appearance it was transferred to Campylobacter species (epsilon-proteobacteria) and to some Bacteria belonging to the CFB group. The transfer involved the entire his operon. The hisIE gene fusion was found in several taxonomic lineages and our results suggest that it probably happened several times in distinct lineages.
Gene fusions involving hisIE and hisD genes (HIS4) and hisH and hisF genes (HIS7) took place in the Eukarya domain; the latter has been transferred to some delta-proteobacteria.
Conclusion: Gene duplication is the most widely known mechanism responsible for the origin and evolution of metabolic pathways; however, several other mechanisms might concur in the process of pathway assembly and gene fusion appeared to be one of the most important and common
A new selective force driving metabolic gene clustering
No full textABSTRACT The evolution of operons has puzzled evolutionary biologists since their discovery, and many theories exist to explain their emergence, spreading, and evolutionary conservation. In this work, we suggest that DNA replication introduces a selective force for the clustering of functionally related genes on chromosomes, which we interpret as a preliminary and necessary step in operon formation. Our reasoning starts from the observation that DNA replication produces copy number variations of genomic regions, and we propose that such changes perturb metabolism. The formalization of this effect by exploiting concepts from metabolic control analysis suggests that the minimization of such perturbations during evolution could be achieved through the formation of gene clusters and operons. We support our theoretical derivations with simulations based on a realistic metabolic network, and we confirm that present-day genomes have a degree of compaction of functionally related genes, which is significantly correlated to the proposed perturbations introduced by replication. The formation of clusters of functionally related genes in microbial genomes has puzzled microbiologists since their first discovery. Here, we suggest that replication, and the copy number variations due to the replisome passage, might play a role in the process through a perturbation in metabolite homeostasis. We provide theoretical support to this hypothesis, and we found that both simulations and genomic analysis support our hypothesis.IMPORTANCEThe formation of clusters of functionally related genes in microbial genomes has puzzled microbiologists since their discovery. Here, we suggest that replication, and the copy number variations due to the replisome passage, might play a role in the process through a perturbation in metabolite homeostasis. We provide theoretical support to this hypothesis, and we found that both simulations and genomic analysis support our hypothesis
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