Quelques objets surprenants en textile non tissé dans les réserves du musée Bénaki

Τα πλεγμένα αντικείμενα που εξετάζονται στην παρούσα μελέτη μαρτυρούν σημαντικά τεχνικά στάδια στην ιστορία του υφάσματος, τα οποία εμφανίστηκαν διαδοχικά αλλά και συνυπήρξαν. Στο πλαίσιο αυτό τα συγκεκριμένα έργα παρουσιάζουν ιδιαίτερο ενδιαφέρον από εθνολογική άποψη. Στα αντικείμενα με αρ. ευρ. 16113 και 16115 χρησιμοποιήθηκε κλωστή περιορισμένου μήκους που, περασμένη σε βελόνα τύπου ραπτικής, δημιούργησε διαπλοκή από θηλιές. Η παλαιότερη αυτή τεχνική πλεξίματος προέρχεται τόσο από τη ραπτική, όσο και από την ψαθοπλεκτική. Με πολλές διαφορές μεταξύ τους, τα δύο αυτά αντικείμενα αποτελούν χαρακτηριστικά δείγματα του είδους που ο R. d’Harcourt ονόμασε το 1934 «δίχτυ με βελόνα» (είναι πλεκτά με την αυστηρή έννοια του όρου. Εδώ χρησιμοποιήθηκε κλωστή “απεριόριστου” μήκους, δηλαδή που δεν είχε κοπεί από πριν, με την οποία ο τεχνίτης δημιούργησε με τα χέρια θηλιές σε δύο βελόνες τύπου πλεξίματος. Τα δείγματα του Μουσείου Μπενάκη είναι από τα παλαιότερα του είδους και βρέθηκαν στα ερείπια του μουσουλμανικού Καΐρου. Ωστόσο, δεν μας επιτρέπουν να θεωρήσουμε ότι το πλεκτό κατάγεται από την Αίγυπτο ή ότι σχετίζεται με κάποια πληθυσμιακή κοινότητα. Σχετικά με τη χρήση των τεσσάρων παραπάνω αντικειμένων, η λειτουργία του γαντιού με αρ. ευρ. 16113 είναι προφανής: το αντικείμενο χρησίμευε για την προστασία των χεριών στο κυνήγι, στην εργασία και από το κρύο. Αντίστοιχα δείγματα πλεκτικής έχουν βρεθεί ανάμεσα σε κάλτσες της κοπτικής Αιγύπτου (από τον 4ο αι.), αλλά και σε γάντια από περιοχές της Βόρειας Ευρώπης (9ος-10ος αι.). Η πυκνοϋφασμένη βαμβακερή ταινία με αρ. ευρ. 16115 θα μπορούσε να έχει διακοσμητική χρήση, ανήκοντας σε μαξιλάρι, κουρτίνα ή κεφαλόδεσμο. Παραπλήσια μοτίβα ψαροκόκκαλου (chevron) σε αντικείμενα που μοιάζει να έχουν την ίδια τεχνική έχουν εντοπιστεί σε απομακρυσμένες χρονικά και γεωγραφικά περιοχές (δαντέλες από την Ιρλανδία (19ος αι.), σκούφοι από το Κονγκό (20ός αι.). Η χρήση των σωληνοειδών πλεκτών με αρ. ευρ. 16114 και 16117 παραμένει άγνωστη. Οι ερμηνευτικές τους προσεγγίσεις ως πορτοφολιών ή παιδικών καλτσών δεν στηρίζονται σε επαρκή τεκμηρίωση. Παρόμοια δείγματα έχουν ανευρεθεί μόνο στην Αίγυπτο. Περίπου 40 αντικείμενα με τις χρωματικές επιλογές του πλεκτού αρ. ευρ. 16117 (μπλε και υπόλευκο) φυλάσσονται σε μουσεία της Αμερικής και της Ευρώπης, και τέσσερα στο Μουσείο Μπενάκη.No abstract

Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription

We analyzed the periodic patterns in E. coli promoters and compared the distributions of the corresponding patterns in promoters and in the complete genome to elucidate their function. Except the three-base periodicity, coincident with that in the coding regions and growing stronger in the region downstream from the transcriptions start (TS), all other salient periodicities are peaked upstream of TS. We found that helical periodicities with the lengths about B-helix pitch ~10.2-10.5 bp and A-helix pitch ~10.8-11.1 bp coexist in the genomic sequences. We mapped the distributions of stretches with A-, B-, and Z- like DNA periodicities onto E.coli genome. All three periodicities tend to concentrate within non-coding regions when their intensity becomes stronger and prevail in the promoter sequences. The comparison with available experimental data indicates that promoters with the most pronounced periodicities may be related to the supercoiling-sensitive genes.Comment: 23 pages, 6 figures, 2 table

Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility

Nucleoid-associated proteins are bacterial proteins that are responsible for chromosomal DNA compaction and global gene regulation. One such protein is Escherichia coli Histone-like nucleoid structuring protein (H-NS) which functions as a global gene silencer. Whereas the DNA-binding mechanism of H-NS is well-characterized, its paralogue, StpA which is also able to silence genes is less understood. Here we show that StpA is similar to H-NS in that it is able to form a rigid filament along DNA. In contrast to H-NS, the StpA filament interacts with a naked DNA segment to cause DNA bridging which results in simultaneous stiffening and bridging of DNA. DNA accessibility is effectively blocked after the formation of StpA filament on DNA, suggesting rigid filament formation is the important step in promoting gene silencing. We also show that >1 mM magnesium promotes higher order DNA condensation, suggesting StpA may also play a role in chromosomal DNA packaging

Selection against Spurious Promoter Motifs Correlates with Translational Efficiency across Bacteria

Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the −10 promoter motifs that bind the σ70 subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of −10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, −10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers. These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also confirms previous results indicating that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

Despite almost 40 years of molecular genetics research in Escherichia coli a major fraction of its Transcription Start Sites (TSSs) are still unknown, limiting therefore our understanding of the regulatory circuits that control gene expression in this model organism. RegulonDB (http://regulondb.ccg.unam.mx/) is aimed at integrating the genetic regulatory network of E. coli K12 as an entirely bioinformatic project up till now. In this work, we extended its aims by generating experimental data at a genome scale on TSSs, promoters and regulatory regions. We implemented a modified 5′ RACE protocol and an unbiased High Throughput Pyrosequencing Strategy (HTPS) that allowed us to map more than 1700 TSSs with high precision. From this collection, about 230 corresponded to previously reported TSSs, which helped us to benchmark both our methodologies and the accuracy of the previous mapping experiments. The other ca 1500 TSSs mapped belong to about 1000 different genes, many of them with no assigned function. We identified promoter sequences and type of σ factors that control the expression of about 80% of these genes. As expected, the housekeeping σ70 was the most common type of promoter, followed by σ38. The majority of the putative TSSs were located between 20 to 40 nucleotides from the translational start site. Putative regulatory binding sites for transcription factors were detected upstream of many TSSs. For a few transcripts, riboswitches and small RNAs were found. Several genes also had additional TSSs within the coding region. Unexpectedly, the HTPS experiments revealed extensive antisense transcription, probably for regulatory functions. The new information in RegulonDB, now with more than 2400 experimentally determined TSSs, strengthens the accuracy of promoter prediction, operon structure, and regulatory networks and provides valuable new information that will facilitate the understanding from a global perspective the complex and intricate regulatory network that operates in E. coli

Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi

We experimentally identified and characterized 97 novel, non-protein-coding RNA candidates (npcRNAs) from the human pathogen Salmonella enterica serovar Typhi (hereafter referred to as S. typhi). Three were specific to S. typhi, 22 were restricted to Salmonella species and 33 were differentially expressed during S. typhi growth. We also identified Salmonella Pathogenicity Island-derived npcRNAs that might be involved in regulatory mechanisms of virulence, antibiotic resistance and pathogenic specificity of S. typhi. An in-depth characterization of S. typhi StyR-3 npcRNA showed that it specifically interacts with RamR, the transcriptional repressor of the ramA gene, which is involved in the multidrug resistance (MDR) of Salmonella. StyR-3 interfered with RamR–DNA binding activity and thus potentially plays a role in regulating ramA gene expression, resulting in the MDR phenotype. Our study also revealed a large number of cis-encoded antisense npcRNA candidates, supporting previous observations of global sense–antisense regulatory networks in bacteria. Finally, at least six of the npcRNA candidates interacted with the S. typhi Hfq protein, supporting an important role of Hfq in npcRNA networks. This study points to novel functional npcRNA candidates potentially involved in various regulatory roles including the pathogenicity of S. typhi

High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria

Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of “alien” elements which probably undergo special temporal–spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these “exotic” regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs) in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased “non-optimal” codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for “alien” regions, but also provide hints to the special evolutionary course and transcriptional regulation of GI regions

Les reliques de Saint Césaire d’Arles (472-542)

Saint Césaire (471-542) fut l’une des grandes figures théologiques, pastorales et politiques de la Gaule du VIe siècle. En 513, il a reçu du pape Symmaque le pallium, symbole du lien privilégié qui s’établit alors entre l’Eglise métropolitaine et le Saint-siège, cette longue écharpe de laine blanche faisant officiellement de son détenteur le « Vicaire des Gaules et d’Espagne ». A sa mort, l’archevêque métropolitain fut enterré avec son pallium selon la coutume et proclamé saint. L’invasion de..