2,205 research outputs found
Data for the synthesis of oligo-gamma-glutamylglutamines as model compounds for gamma-glutamyltransferases (GGTs) and for normalization of activities of different GGTs
No full textgamma-Glutamyltransferases (GGTs) are widespread, conserved enzymes that catalyze the transfer of the gamma-glutamyl moiety from a donor substrate to water (hydrolysis) or to an acceptor amino acid (transpeptidation) through the formation of a gamma-glutamyl enzyme intermediate.
Although the vast majority of the known GGTs has a short sequence called lid-loop covering the glutamate binding site, B. subtilis GGT and some other enzymes from Bacillus spp. lack the lid loop. In order to assess the possible role of the lid loop of GGTs in substrate selection, synthetic oligo-gamma-glutamylglutamines containing up to three gamma-glutamyl residues were used as model substrates. The activities of the enzymes under investigation were standardized with respect to a common reaction to ensure comparable results. The activity of an engineered mutant enzyme containing the amino acid sequence of the lid loop from E. coli GGT inserted into the backbone of B. subtilis GGT was compared to that of the lid loop-deficient B. subtilis GGT and the lid loop-carrier E. coli GGT (Calvio, Romagnuolo, Vulcano, Speranza, Morelli Enz. Micr. Technol. 2018 [1]). Here we report the experimental procedures for the synthesis of model substrates gamma-glutamylglutamines through the method of the N-phtaloyl-L-glutamic acid anhydride and the spectral data of the synthetized compounds. The data obtained in the normalization procedure of the activities of the three enzymes are also reported
Calcites at Vulcano island (Italy): Isotopic and geochronological data bearing on the timing of the La Fossa Caldera collapse
No full textSeveral samples of calcites, filling fractures in a restricted area of the southern volcano deposits at Vulcano island, were investigated. Data referring to isotope composition of U, C, O, Sr and fluid inclusions, give a solution, by indirect observations, to the chronostratigraphic problem of the trachybasaltic welded scoriae blankets (WSB) outcropping on Vulcano island. Th-230 ages, close to a value of 50 ka, d(13)C, d(18)O and Sr isotope composition suggest for the calcite deposition a unique event, correlated with a fast degassing, quickly draining deep fluids and probably connected with the first phase of the La Fossa Caldera collapse. The WSB connected to this first collapsed phase should have been deposited at 50 ka, and consequently they could be actually contemporary with the Piano Luccia WSB dated at 48 ka. (C) 1998 INQUA/Elsevier Science Ltd. All rights reserved
"The love that made hell, paradise." Ouida re-writing the Paolo and Francesca theme in Held in Bondage
No full textThe bestselling Victorian author Ouida reveals in her novels, and, in particular, Held in Bondage, an extraordinary knowledge od Dante, by using characters and themes from the Commedia. The Paolo and Francesca theme actually constitutes part of the plot of the novel and is to be found in many of her other works, short stories and non-fiction writing
Evidences on the role of the lid loop of γ-glutamyltransferases (GGT) in substrate selection
No full textγ-Glutamyltransferase (GGT) catalyzes the transfer of the γ-glutamyl moiety from a donor substrate such as glutathione to water (hydrolysis) or to an acceptor amino acid (transpeptidation) through the formation of a γ-glutamyl enzyme intermediate.
The vast majority of the known GGTs has a short sequence covering the glutamate binding site, called lid-loop. Although being conserved enzymes, both B. subtilis GGT and the related enzyme CapD from B. anthracis lack the lid loop and, differently from other GGTs, both accept poly-γ-glutamic acid (γ-PGA) as a substrate. Starting from this observation, in this work the activity of an engineered mutant enzyme containing the amino acid sequence of the lid loop from E. coli GGT inserted into the backbone of B. subtilis GGT was compared to that of the lid loop-deficient B. subtilis GGT and the lid loop-carrier E. coli GGT. Results indicate that the absence of the lid loop seems not to be the sole structural feature responsible for the recognition of a polymeric substrate by GGTs. Nevertheless, time course of hydrolysis reactions carried out using oligo-γ-glutamylglutamines as substrates showed that the lid loop acts as a gating structure, allowing the preferential selection of the small glutamine with respect to the oligomeric substrates. In this respect, the mutant B. subtilis GGT revealed to be more similar to E. coli GGT than to its wild-type counterpart. In addition, the transpeptidase activity of the newly produced mutant enzyme revealed to be higher with respect to that of both E. coli and wild-type B. subtilis GGT. These findings can be helpful in selecting GGTs intended as biocatalysts for preparative purposes as well as in designing mutant enzymes with improved transpeptidase activity
HERStory Makers 2023: Francesca Fotheringham
No full textFrancesca Fotheringham is a postdoctoral research associate at the University of Edinburgh studying educational psychology with a focus on neurodiversity. She took part in HERStory Makers 2023.What is HERStory Makers?HERStory Makers is a social media competition for female-identifying early career researchers to share their research, their career journeys, and to inspire the next generation. Winners are selected by public vote. HERStory Makers is also part of EXPLORATHON, Scotland's contribution to European Researchers' Night.In 2022-23, EXPLORATHON Francescasupported by the Engineering & Physical Sciences Research Council [grant number EP/X020762/1].Author contributions to contentFrancesca conceived, planned, and recorded the video content. Kirsty Ross edited the video content to insert HERStory Maker credits, added subtitles, and reduce video length to below Twitter/X limit of 2 mins and 20 secs.</p
Medicina illuminata. La Biblioteca Lancisiana di Roma
No full textL'articolo presenta i codici miniati della Biblioteca Lancisiana di Roma. La prima parte, del coautore, è dedicata alla Biblioteca. La seconda parte, di F. Manzari, tratta dei manoscritti miniati, costituiti da due codici con le opere di Avicenna e dal Liber fraternitatis della Confraternita dell'Ospedale di Santo Spirito in Sassia a Roma.The article introduces the illuminated manuscripts of the Biblioteca Lancisiana in Rome. The first part of the article, by the co-author, is dedicated to the Library. The second part, by Francesca Manzari, illustrates the manuscipts; these are two manuscripts with the works of Avicenna and the Liber fraternitatis of the Confraternity of the Hospital of Santo Spirito in Sassia in Rome
Metagenomics-driven predictions in Archaea from hydrocarbon-rich Arctic hydrothermal systems: Phylogenetic and metabolic analyses of methane and short-chain alkane-degrading lineages
No full textMetan og hydrokarboner er potente klimagasser som produseres og nedbrytes hovedsakelig biotisk. I havet akkumuleres metan og hydrokarboner i sedimenter og hydrotermiske systemer. Nylige metagenomstudier har utvidet mangfoldet av slektslinjer av arker involvert i metan- og hydrokarbonsyklus. De har vist at metabolske moduler for omsetningsreaksjoner i hydrokarbonsyklus er vanlige i arker og kan forekomme i heterotrofe slektslinjer som bestemmer en mixotrofisk livsstil. Ytterligere metagenomstudier kan bidra til å øke forståelsen av den miljømessige rollen mikroorganismer involvert i omsetning av hydrokarboner har. I løpet av det siste tiåret har hydrokarbon-anrikede hydrotermiske systemer blitt oppdaget langs de arktiske midthavsryggene. I dette studiet har fokuset vært å beskrive det fylogenetiske og metabolske mangfoldet av anaerobe hydrokarbonnedbrytende slektslinjer i disse systemene, hovedsakelig ved å analysere genomer rekonstruert fra metagenomdata. Flere nye slektslinjer av anaerobe metanotrofe arker av typen ANME-1, ble identifisert, inkludert en ny familie. To slektslinjer som kunne oksidere kortkjedede hydrokarboner, henholdsvis etan og propan/butan ble også identifisert. Samtlige av slektslinjene benyttet etablerte metabolismeveier for syntrof anaerob oksidasjon av metan og hydrokarboner. Tidligere ubeskrevne funksjonelle forskjeller ble imidlertid identifisert mellom ulike ANME-1. Basert på tidligere funn i terrestriske hydrotermiske systemer, ble potensialet for metanoksidasjon også evaluert i rekonstruerte genomer av Korarchaeia. Korarchaeia fra marine hydrotermiske system, ble funnet å mangle gen for anaerob oksidasjon av metan. De ble i stedet identifisert som fermenterende mikroorganismer med evne til å benytte sukker og aminosyrer. En komplett Wood-Ljungdahl metabolismevei ble identifisert i dypforgrenede slektslinjer av Korarchaeia og gir sannsynligvis grunnlag for homoacetogenese. Totalt sett har denne studien bekreftet at hydrokarbonrike hydrotermiske systemer ved de arktiske midthavsryggene er tilholdssted for slektslinjer med potensial for hydrokarbonnedbrytning og bidrar til å utvide det fylogenetiske og funksjonelle mangfoldet av slektslinjer som bryter ned hydrokarboner i marine hydrotermiske systemer.Methane and short chain alkanes are potent greenhouse gases generated and degraded mainly biotically. In the ocean, methane and hydrocarbons accumulate in sediments and hydrothermal vents. Recent metagenomic studies have dramatically expanded the diversity of archaeal lineages involved in methane and hydrocarbon cycling. They also have revealed that metabolic modules at the basis of hydrocarbon cycling are relatively conserved and common in Archaea and can occur in heterotrophic lineages determining a mixotrophic lifestyle. Further metagenomic studies can contribute to expand such diversity and describe the environmental role of microorganisms involved in cycling of hydrocarbons. In the last decade, hydrocarbon-enriched hydrothermal vents have been discovered along the Arctic Mid Ocean Ridges (AMOR). This project aimed at identifying lineages of anaerobic hydrocarbon-degraders in these vents and describe their phylogenetic and metabolic diversity, mainly by reconstructing and analyzing metagenome-assembled genomes (MAGs) from various anoxic and actively venting hydrothermal locations. Potential for methane oxidation was also evaluated in MAGs of Korarchaeia since they have been previously proposed as methane oxidizers in terrestrial environments. Overall, several new lineages of anaerobic methanotrophic archaea ANME-1 were identified, including one new family. Two lineages of short-chain alkane oxidizers were found, one an ethane oxidizer and the other a butane/propane oxidizer. All encoded canonical routes for syntrophic anaerobic oxidation of methane and short-chain alkanes. Previously undescribed functional differences were found between ANME-1 lineages. Marine hydrothermal Korarchaeia did not encode genes for anaerobic oxidation of methane. They were instead identified as sugars and amino acids fermenters. Deep-branching lineages of Korarchaeia encoded a complete Wood-Ljungdahl pathway that is likely used reductively as electron sink during fermentation resulting in a homoacetogenic metabolism. Overall, this study confirms that hydrocarbon-rich hydrothermal vents at AMOR host microbial lineages with the potential for degradation of hydrocarbons and contributes to expanding the known phylogenetic and functional diversity of hydrocarbon-degrading lineages in marine hydrothermal systems.Doktorgradsavhandlin
Seasonal blooms of the HAB dinoflagellate Alexandrium taylori Balech in a new Mediterranean Area (Vulcano, Aeolian Islands)
No full textHigh-biomass blooms of A. taylori Balech have recently been spreading over new Mediterranean areas, with evident adverse effects on the marine ecosystem. In 1999-2000, a new Mediterranean locality was affected by blooms of A. taylori: the West Bay of Vulcano (Aeolian Islands, Tyrrhenian Sea), with maximum cell densities of 1.2 x 10(7)cells 1(-1) in August 1999 and 4.0 x 10(6) cells 1(-1) in August 2000 observed together with yellowish water discoloration. The seawater samples contained high concentrations of nutrients as DIN (Dissolved Inorganic Nitrogen), especially NH3-N with values of 14.4 mu M and TOT-P (Total Phosphorus) with values of 3.2 mu M due to the anthropic presence and discharge of untreated sewage. The climatic conditions also seem to influence the occurrence and spreading of the A. taylori blooms in the Vulcano Bay. Clonal cultures of A. taylori, established from Italian and Spanish seawater samples, were used for the sequence analyses of the 5.8S rDNA gene and ITS regions in order to study the genetic variability of different geographical populations of Alexandrium species in the Mediterranean area and to further develop the molecular markers for HAB key-species
A DH-Leavened Musicological Toolbox
No full textGraduate-level training in music research methodologies tends to ignore digital humanities work and overlook the use of digital tools created in support of new forms of reading. Training instead focuses on source material in the student’s area of interest. This material includes secondary and primary (archival) resources, as well as information resources, such as: monuments of music and critical editions; indexes; bibliographies and thematic catalogs; dictionaries and encyclopedias; digital libraries of scores or editions; and databases of period-specific newspapers or journals. Graduate students taking research methods courses already have a toolbox built from their experiences as musicians and students of music, including the ability to read and interpret music notation, to understand theoretical and analytical concepts in music, as well as a command of music history, including the canon of musical works.
Digital humanities has become a major area of academic endeavor at the “interface of technological development, epistemological change and methodological concerns." An important characteristic of digital humanities research has been its interdisciplinarity. We argue that graduate training in musicology needs to include coverage of methodologies applied by digital humanists in support of new forms of reading, not only to broaden the canon of research topics in musicology, but also to build common ground with researchers of other disciplines. We propose that librarians are well positioned to provide this expertise and training
A Twitter Case Study for Assessing Digital Sound
No full textAcademic and cultural heritage institutions around the world have made measurable strides in the development of digital sound archives oriented towards research and access, but their impact on scholarship and society has been little studied. Traditionally, impact has been measured by citations; yet these are problematic metrics for non-traditional outputs like sound recordings. Social media data provide a promising avenue of investigation for measuring scholarly as well as societal impact. Twitter in particular has been shown to provide a high number of references for cultural and research outputs in all disciplines. This study analyzes Twitter references pertaining to the collections of five digital sound archives: British Library Sounds, Europeana Sounds, the Internet Archive Audio Archive, PennSound and UbuWeb. Using text analysis methods to identify high frequency events and trends, and labeling them with a rubric designed for measuring the impact of digital heritage resources, this study provides preliminary insights on user values as they relate to digital sound collections. Despite the limitations of using social media data, the evidence gathered in this case study characterizes aspects of the use of digital sound collections, and may point to future priorities for the digital preservation of sound.Peer reviewe
- …
