Genome-scale analyses of health-promoting bacteria: probiogenomics

The human body is colonized by an enormous population of bacteria (microbiota) that provides the host with coding capacity and metabolic activities. Among the human gut microbiota are health-promoting indigenous species (probiotic bacteria) that are commonly consumed as live dietary supplements. Recent genomics-based studies (probiogenomics) are starting to provide insights into how probiotic bacteria sense and adapt to the gastrointestinal tract environment. In this Review, we discuss the application of probiogenomics in the elucidation of the molecular basis of probiosis using the well-recognized model probiotic bacteria genera Bifidobacterium and Lactobacillus as examples.

The Irish House of Lords, 1780-1800: politics and ideology

This thesis covers the Irish House of Lords in the last two decades of its life. A number of important themes run through the work - the regency crisis, patronage, the management of the Lords, the relationship between the Lords and Commons. These themes, explored from different angles, are vital to an understanding of the political role of the upper house in the 1780s and 1790s. This study is confined to the Lords as a political institution and thus its judicial role as final court of appeal, which was restored to it in 1782, will not be explored here. The thesis consists of two parts. Part one examines the structure and powers of the House of Lords while part two looks at the parties and policies of the house. Chapter one discusses the British constitution as imposed upon Ireland. Chapter two suggests the reasons why constitutional changes were introduced in 1782, and looks at the contribution made by the Irish House of Lords in securing these changes. Chapter three explores the various channels of influence which the peers enjoyed. Chapter four explores the sometimes tense relationship between Lords and Commons. Chapter five examines management of the House of Lords by Dublin Castle. Part two, begins at chapter six. This chapter explores the leadership of both parties within the Lords. Chapter seven looks at how patronage was used to reward those who were loyal to the government. Chapter eight explores the influence of the Whig opposition. Chapter nine looks at the controversial attempts made by Pitt and his ministry during the 1790s to win the support of catholics and turn them from the lure of French ideas, and of the response of the peers to these attempts. Chapter ten is concerned with the relationship between the peers of the House of Lords and the lords lieutenant during the 1790s. Chapter eleven looks at the Union and the House of Lords and attempts to answer the question historians have long asked: why did the Irish parliament and the House of Lords in particular, look favourably on the proposed union of the two kingdoms and the end of their own institution? The House of Lords in the closing decades of the eighteenth century was an institution within which the wealth and power of the kingdom could be found. Its members were politically active, both inside and outside the house. It contained a majority who saw the Crown as the source of stability, but it was a living and evolving political organism and therefore it contained men who believed that the Crown should have its influence limited. This evolution is also demonstrated in its desire for political change in 1782 and 1788. Its last, and perhaps most radical decision, was to vote for its own demise in 1900.

Nuove intersezioni: crimine e storia nella narrativa Italiana al cambio di millennio

My research investigates a recent tendency in Italian literature, characterized by elements of renewal within the novel-writing tradition and of discontinuity with postmodern culture. It proposes an interpretation of the genres of the historical novel and crime fiction in the last fifteen years, in order to underline the important role played by these types of narrative in revitalizing contemporary Italian literature. These modalities of writing are considered both individually and in their connections beyond a traditional notion of genre, emphasizing those characteristics which may be assumed as irreconcilable with a postmodern approach to fiction and those which, furthermore, seem to indicate attempts to take a new course. In particular, my study analyses the recent literary tendency to combine the elements of ‘crime’ and ‘history’ in order to represent political and social reality, and how the works examined relate to postmodern narrative. For this reason, I pay particular attention to the relationship between literature and the past and to the socio-political aspects connected with the praxis of narrating, offering an original interpretation of the way in which the authors studied engage with these characteristics.

Azione destabilizzante e impegno politico. Le figure femminili tra il giallo e il nero Italiani dal 1980 a oggi

My thesis analyses female figures in Italian crime fiction since 1980, from narratological, sociological and gender-studies perspectives. It considers the narrative structure of the giallo and the noir, taking into account the difficulties, particularly in Italy, of establishing what noir fiction is and if/how it is possible to frame it in a specific narrative scheme. This discourse connects to the extraordinary success of Italian giallo and noir fiction over the past fifteen-twenty years. In this scenario, I examine the place of female writers in relation to this phenomenon, especially since the 1980s: in terms of the level of visibility/acceptance of their work, in a narrative space traditionally considered as a male territory, and with regard to their writings, which introduce different narrative perspectives. Specifically, I consider selected texts by leading female Italian writers, in which female elements (writers/characters) become destabilizing factor both on the narrative level, by undermining the schemes of ‘formulaic’ fiction, and on the political one, through their implicit potential (as women) for disrupting the rigid models inherited from processes of social conditioning and from political structures. In terms of gender identities, such texts offer scope to question conventional social constructions of the subject: by empowering the female narrative voice and by embodying it in characters (investigators/killers) traditionally personified by male figures. These texts offer themselves as a critical space where, potentially, readers can rethink static gendered relationships and stereotypical symbolical categories.

Identification of RNA editing in the human exome and development of DARNED DatabaseSF

RNA editing is a biological phenomena that alters nascent RNA transcripts by insertion, deletion and/or substitution of one or a few nucleotides. It is ubiquitous in all kingdoms of life and in viruses. The predominant editing event in organisms with a developed central nervous system is Adenosine to Inosine deamination. Inosine is recognized as Guanosine by the translational machinery and reverse-transcriptase. In primates, RNA editing occurs frequently in transcripts from repetitive regions of the genome. In humans, more than 500,000 editing instances have been identified, by applying computational pipelines on available ESTs and high-throughput sequencing data, and by using chemical methods. However, the functions of only a small number of cases have been studied thoroughly. RNA editing instances have been found to have roles in peptide variants synthesis by non-synonymous codon substitutions, transcript variants by alterations in splicing sites and gene silencing by miRNAs sequence modifications. We established the Database of RNA EDiting (DARNED) to accommo-date the reference genomic coordinates of substitution editing in human, mouse and fly transcripts from published literatures, with additional information on edited genomic coordinates collected from various databases e.g. UCSC, NCBI. DARNED contains mostly Adenosine to Inosine editing and allows searches based on genomic region, gene ID, and user provided sequence. The Database is accessible at http://darned.ucc.ie RNA editing instances in coding region are likely to result in recoding in protein synthesis. This encouraged me to focus my research on the occurrences of RNA editing specific CDS and non-Alu exonic regions. By applying various filters on discrepancies between available ESTs and their corresponding reference genomic sequences, putative RNA editing candidates were identified. High-throughput sequencing was used to validate these candidates. All predicted coordinates appeared to be either SNPs or unedited.

Theme and variations: Christianity and regional landscapes in early medieval Ireland

This thesis explores the impact of Christianity on the landscape in Ireland from the conversion period to the coming of the Anglo-Normans. The premise is that ecclesiastical and secular settlement formed a cohesive whole which characterised the societal organisation of early medieval Ireland. The matter of the thesis is to isolate some of the agents of cohesion to see was this homogenous or did it vary in different areas. One of these agents was the ownership of land and the thesis undertakes to identify ecclesiastical landholding and examine the manner of settlement on it. A corollary is to explore the contribution of the genealogical link between kin-group, founding saint and territory to the construction of local identities. This necessitated a narrow focus; thus small study areas were chosen, which approximated to early medieval kingdoms in North Louth, Rathdown, Co Dublin and Ross, Co Cork. A multidisciplinary approach was taken using both archaeological and documentary evidence. The thesis found ecclesiastical sites were at the same density through the study areas, but there were considerable regional variations in related secular settlement. Ecclesiastical estates were identified in the three study areas and common settlement patterns were found in two of them. Settlement in all areas indicated the foundation of minor churches by local groups. Ecclesiastical sites were found to be integral to kin-group identity and status, but the manner in which each group negotiated this, was very different. Finally the thesis examined material evidence for a change from diffused to concentrated power in the political organisation of Irish society, a process entwined with developments of the Viking Age. This centralisation of power and associated re-formation of identity was still often mediated through the ecclesiastical sphere but the thesis demonstrates diversity in the materialising of the mediation.

Fundamental studies on the application of enzymes when brewing with unmalted oats and sorghum

The use of unmalted oats or sorghum in brewing has great potential for creating new beer types/flavors and saving costs. However, the substitution of barley malt with oat or sorghum adjunct is not only innovative but also challenging due to their specific grain characteristics. The overall objectives of this Ph.D. project were: 1) to investigate the impact of various types and levels of oats or sorghum on the quality/processability of mashes, worts, and beers; 2) to provide solutions as regards the application of industrial enzymes to overcome potential brewing problems. For these purposes, a highly precise rheological method using a controlled stress rheometer was developed and successfully applied as a tool for optimizing enzyme additions and process parameters. Further, eight different oat cultivars were compared in terms of their suitability as brewing adjuncts and two very promising types identified. In another study, the limitations of barley malt enzymes and the benefits of the application of industrial enzymes in high-gravity brewing with oats were determined. It is recommended to add enzymes to high-gravity mashes when substituting 30% or more barley malt with oats in order to prevent filtration and fermentation problems. Pilot-scale brewing trials using 10–40% unmalted oats revealed that the sensory quality of oat beers improved with increasing adjunct level. In addition, commercially available oat and sorghum flours were implemented into brewing. The use of up to 70% oat flour and 50% sorghum flour, respectively, is not only technically feasible but also economically beneficial. In a further study on sorghum was demonstrated that the optimization of industrial mashing enzymes has great potential for reducing beer production costs. A comparison of the brewing performance of red Italian and white Nigerian sorghum clearly showed that European grown sorghum is suitable for brewing purposes; 40% red sorghum beers were even found to be very low in gluten.

Landscapes of kingship in early medieval Ireland, AD 400–1150

This thesis explores the evolution of kingship in early medieval Ireland (AD 400–1150) through a kingdom based and multi-scalar approach to royal landscapes. Through exploring the role of place and landscape in the construction of early medieval Irish kingship, this study will assess the relationship between the social, economic and ideological roles of the king in Irish society. Kingship in Ireland was vested in places, such that royal landscapes were the pre-eminent symbol of regality and authority. As such, an interdisciplinary study of kingship grounded in archaeological methodologies has a unique potential to contribute to our knowledge of the practice of kingship. Consequently, this research considers the material apparatus of different scales of kingships and explores the role of landscape in the construction of kingship and the evolution of kingdoms. It takes two major case studies; (i) Cashel, Munster and the Éoganachta federation; and (ii) the Uí Néill, Tara and the Síl nÁedo Sláine kingdom of Brega. Through interdisciplinary methodologies it charts the genesis and development of political federations, focusing specifically on the role that royal landscapes’ played in their evolution. Similarly, this thesis engages critically with the nature of assembly places and practices in Ireland, and focuses specifically on issues pertaining to the nature of assembly and the archaeological manifestation of such practices. It includes a list of 115 landscapes identified as assembly places, and through the analysis of this material, this thesis examines the ways in which different types of royal sites articulated together to create royal landscapes implicated in the exercise of kingship, and the construction and maintenance of authority. Moreover, through the analysis of assembly places within the context of the development of kingdoms, and structures of jurisdiction and administration, it also investigates the evolution of supra-regional scales of identity and community associated with the emergence of major political federations in early medieval Ireland.

Locating the transnational: representations and aesthetics of the city in contemporary European cinemas

This thesis focuses on two Western European cinematic cities, and two unique periods of their respective nations’ histories, in a bid to “locate” the transnational within a contemporary European milieu. I argue that my geo-cinematic case studies are emblematic of broader questions of the problematics of national identity in contemporary Europe in the face of cross-national flows yet, as a result of their representations as cities both “anchored” and “in flux”, they reject a European postnational identity. Through its engagement with cinematic Rome as the “Eternal City” of Europe and cinematic Dublin as the “newly Europeanised” city, my thesis traces how representations and aesthetics of the urban spaces of these two cities correspond with the tensions at the heart of the respective eras in question. Via the figures that inhabit it, navigate it and search for it, the city is utilised to highlight fixity and mobility, centrality and dislocation, in explicit and implicit ways, amid the rapidly changing landscape of its national terrain. It is through my analyses of the filmed places and sociopolitical, socioeconomic and sociocultural spaces of these capital cities under the rubric of the transnational that this research demonstrates the “pluralities” of the construct in its cinematic manifestations. It is also my aim to evaluate the concept of cinematic transnationalism when identifying and accounting for representations of a specific national, historical timeframe, when the momentousness of the changes that occur is not bound by the national, but rather is reflective of the influence of both domestic and external forces. To this end, my thesis draws attention to instances in which the nation is shown to persist and resist dilution, arguing that it is only against the backdrop and continuity of the nation (in its evershifting guises) that the transnational can be conceived in representative and aesthetic terms.

Recasting 'Black Venus' in the new African Diaspora

This article explores the ways in which transnational feminist analysis can be deployed to reconfigure new gendered and racialized cartographies of the African Diaspora in Europe. First, I position contemporary film representations of trafficked Nigerian sex workers in Italy in dialogical relation to 19th century discourses of black sexuality - in particular, Sharpley-Whiting's (1999) reinscribed 'Black Venus Master Narrative' - and assess historical and geographical (dis)continuities in their modes of signification. Second, by linking endemic factors feeding the supply of Nigerian women for the purposes of (in)voluntary participation in the Italian sex industry, such as the localized feminization of poverty and regionally specific perceptions of sex work as a temporary economic strategy, I engage with broader feminist debates on victimization and agency in global sex work and migration literatures. In doing so, this dialectical think piece highlights the gendered complexities of new African diasporic formations and the ways in which their growth is facilitated by broader illegal networks that shape and are shaped by vicissitudes in glocalized economies. © 2004 Elsevier Ltd. All rights reserved.

Three Hundred Years in Annapolis: Phase III Archaeological Investigations of the Anne Arundel County Courthouse Site (18AP63), Annapolis, Maryland

During the summer of 1994, Archaeology in Annapolis conducted archaeological investigations of the city block bounded by Franklin, South and Cathedral Streets in the city of Annapolis. This Phase III excavation was conducted as a means to identify subsurface cultural resources in the impact area associated with the proposed construction of the Anne Arundel County Courthouse addition. This impact area included both the upper and lower parking lots used by Courthouse employees. Investigations were conducted in the form of mechanical trenching and hand excavated units. Excavations in the upper lot area yielded significant information concerning the interior area of the block. Known as Bellis Court, this series of rowhouses was constructed in the late nineteenth century and was used as rental properties by African-Americans. The dwellings remained until the middle of the twentieth century when they were demolished in preparation for the construction of a Courthouse addition. Portions of the foundation of a house owned by William H. Bellis in the 1870s were also exposed in this area. Construction of this house was begun by William Nicholson around 1730 and completed by Daniel Dulany in 1732/33. It was demolished in 1896 by James Munroe, a Trustee for Bellis. Excavations in the upper lot also revealed the remains of a late seventeenth/early eighteenth century wood-lined cellar, believed to be part of the earliest known structure on Lot 58. After an initially rapid deposition of fill around 1828, this cellar was gradually covered with soil throughout the remainder of the nineteenth century. The fill deposit in the cellar feature yielded a mixed assemblage of artifacts that included sherds of early materials such as North Devon gravel-tempered earthenware, North Devon sgraffito and Northem Italian slipware, along with creamware, pearlware and whiteware. In the lower parking lot, numerous artifacts were recovered from yard scatter associated with the houses that at one time fronted along Cathedral Street and were occupied by African- Americans. An assemblage of late seventeenth century/early eighteenth century materials and several slag deposits from an early forge were recovered from this second area of study. The materials associated with the forge, including portions of a crucible, provided evidence of some of the earliest industry in Annapolis. Investigations in both the upper and lower parking lots added to the knowledge of the changing landscape within the project area, including a prevalence of open space in early periods, a surprising survival of impermanent structures, and a gradual regrading and filling of the block with houses and interior courts. Excavations at the Anne Arundel County Courthouse proved this to be a multi-component site, rich in cultural resources from Annapolis' Early Settlement Period through its Modern Period (as specified by Maryland's Comprehensive Historic Preservation Plan (Weissman 1986)). This report provides detailed interpretations of the archaeological findings of these Phase III investigations.

Exploring Musical Diversity in the Collaborative Repertoire from 1880 through 1963

It is essential in musical performance not only to convey the unique language of the composers but also to approach each composition from the perspective of its style. During the 20th century, diverse musical idioms co-existed, sometimes mixing or fusing, yet retaining recognizable characteristics and thereby remaining distinctive. This dissertation explores myriad examples from Late Romanticism/Post- Romanticism, Naturalism, Neo-Classicism, Nationalism and Impressionism composed during this unusually rich period. In order to explore a broad range of collaborative repertoire and to deepen my knowledge of the styles and performance practices relating to these pieces, I studied and performed the repertoire with pianist Eunae Baik–Kim, clarinetist Jihoon Chang, and singers Joshua Brown and Young Joo Lee. The first program featured Post-Romantic, Neo-Classic and Impressionist two-piano works composed by Debussy, Rachmaninoff, and Stravinsky. Each of the three composers used their own distinctive harmonies, rhythms, melodic inventions, pedaling and figurations. In all of the works, both piano parts were densely interwoven, having equal importance. Lied and operatic aria was the focus of the second recital. Brahms’ Vier Ernste Gesänge Op. 121, Ravel’s Don Quichotte a Dulcineé and Italian, French and German operatic arias were the examples of Post-Romanticism and Nationalism. The representative composers were Verdi, Massenet, Korngold, Leoncavallo, Ravel and Wagner. Despite the fact that all of the repertoire was written in traditional musical forms, the composers’ unique voices mark each work as belonging to a particular genre. The third recital focused on Post-Romantic and Impressionistic music written for clarinet and piano: the Première Rhapsodie by Debussy, the Sonata by Poulenc and Brahms’ Sonata in F minor Op. 120, No. 1. These works, although profoundly different in style, share elements of simplicity, clarity and elegance as well as technical virtuosity, articulation and profound musical depth. The three recitals which comprise this dissertation project were performed at the University of Maryland Gildenhorn Recital Hall on February 27, 2010, October 25, 2010, and January 31, 2011. The recitals were recorded on compact disc and are archived within the Digital Repository at the University of Maryland (DRUM).

AUSTRO-GERMAN VIOLIN REPERTORIE FROM BAROQUE THROUGH ROMANTIC PERIOD

At the end of the sixteenth century, Germany had become one of the most active centers of early Baroque music, and therefore Austro-German music came to dominate Western music. An investigation of violin works written during this period reveals the ways in which Austro-German compositions are extraordinary contributions to the violin repertoire. This research warranted further study and performance of these works in order to determine what influence these composers had on the violin repertoire as a whole. For my dissertation recital project, I trace the history of works for violin focusing the violin concerto repertoire in particular. A genre which remained popular throughout the century, the nineteenth-century concerto served primarily as a vehicle for virtuosic display of the violin and piano as never before. For my research I studied and performed works selected from the Baroque through the Romantic period in three recorded recitals with collaborative pianists Ilya Sinaisky, Sun-ha Yun, and Seyon Lee at the Gildenhorn Recital Hall, Clarice Smith Performing Arts Center. I selected particularly prominent pieces which represent the work of significant composers from each period. The composers discussed include Johann Sebastian Bach (1685-1750), owing to the fact that his works are the culmination of the Baroque era during the first half of the eighteenth century; from the Classical period, Wolfgang Amadeus Mozart (1756-1791) all of whom emerged mixing German and Italian traditions into his own style, and Ludwig van Beethoven (1770-1827), the bridge composer between the Classical and the Romantic periods; Romantic composers, Franz Schubert (1979-1828), Johannes Brahms (1833-1897), Robert Schumann (1810-1856), Felix Mendelssohn (1809-1847), and Max Bruch (1838-1920), all who tended to mix Classic and Romantic elements. As a violinist, I learned that their own original sound, rich harmonies and unique expression made these works worthy of becoming masterpieces. I have relished the opportunity for musical and professional growth in exploring these substantial compositions.

The Voyage of Impressionism in Three Violin Recitals: To See the World in Different Colors

Impressionism serves as the transition between romantic and modern music. This dissertation examines the varying characteristics and colors of Impressionism in the works of late-romantic French composers, French Impressionistic composers, and composers with Impressionistic influence from countries other than France. Violin Sonata in g minor, L. 140 (1917) is the last work composed by Claude Debussy. The impressionistic characters in this work includes the ambiguous yet innovative and variant sonority and form. As a work also written in 1917, Ottorino Respighi's Violin Sonata in b minor is deeply rooted in Italian Romanticism. Some of the Impressionistic characters can be found in the second movement where the harmonies are in parallel motion. César Franck, a forerunner of impressionism, heavily influenced Debussy with the use of cyclic form. The Violin Sonata in A major (1886) is rich in harmonic language. Ernest Chausson's works mark the transition between Franck and Debussy. The Poème portrays a love story, Song of Love Triumphant by Turgenev. The work is a symphonic poem for violin and orchestra. The Mythes, Op. 30 (1915) by Karol Szymanowski is based on Greek mythology. Ravel's Sonata for Violin and Cello (1922), dedicated to Debussy, points to the future with a sophisticated harmonic language extending into atonality, spare texture, and expanded palate of impressionistic colors and techniques. Ernest Bloch's Violin Sonata No. 1 (1920) portrays the feeling of torment. Beneath the soaring cries of the violin, the harmonic sonority of Impressionism are present. Gabriel Fauré's Violin Sonata No. 1 in A major, op. 13 (1876) is the earliest work of this project. The scherzo movement became a prototype for future scherzo movements for Ravel and Debussy. Ravel's Tzigane (1924), at once a paragon of French impressionism, a delightful gypsy-style dance-fantasy, and a breathtaking virtuoso piece, is the perfect conclusion to my dissertation project. The pieces discussed above were presented in three recitals. Compact disc recordings of these recitals are available in the Michelle Smith Performing Arts Library of the Clarice Smith Performing Arts Center at the University of Maryland.

Laparoscopic Appendectomy in Italy: An Appraisal of 26,863 Cases

Objective: To evaluate the practice of laparoscopic appendectomy (LA) in Italy. Methods: On behalf of the Italian Society of Young Surgeons (SPIGC), an audit of LA was carried out through a written questionnaire sent to 800 institutions in Italy. The questions concerned the diffusion of laparoscopic surgery and LA over the period 1990 through 2001, surgery-related morbidity and mortality rates, indications for LA, the diagnostic algorithm adopted prior to surgery, and use of LA among young surgeons (<40 years). Results: A total of 182 institutions (22.7%) participated in the current audit, and accounted for a total number of 26863 LA. Laparoscopic surgery is performed in 173 (95%) institutions, with 144 (83.2%) routinely performing LA. The mean interval from introduction of laparoscopic surgery to inception of LA was 3.4 ± 2.5 years. There was an emergent basis for 8809 (32.8%) LA procedures (<6 hours of admission); 10314 (38.4%) procedures were performed on an urgent basis (<24 hours of admission); while 7740 (28.8%) procedures were elective. The conversion rate was 2.1% (561 cases) and was due to intraoperative complications in 197 cases (35.1%). Intraoperative complications ranged as high as 0.32%, while postoperative complications were reported in 1.2% of successfully completed LA. The mean hospital stay for successfully completed LA was 2.5 ± 1.05 days. The highest rate of intraoperative complications was reported as occurring during the learning curve phase of their experience (in their first 10 procedures) by 39.7% of the surgeons. LA was indicated for every case of suspected acute appendiceal disease by 51.8% of surgeons, and 44.8% order abdominal ultrasound (US) prior to surgery. A gynecologic counseling is deemed necessary only by 34.5% surgeons, while an abdominal CT scan is required only by 1.5%. The procedure is completed laparoscopically in the absence of gross appendiceal inflammation by 83%; 79.8% try to complete the procedure laparoscopically in the presence of concomitant disease; while 10.4% convert to open surgery in cases of suspected malignancy. Of responding surgeons aged under 40, 76.3% can perform LA, compared to 47.3% surgeons of all age categories. Conclusions: The low response rate of the present survey does not allow us to assess the diffusion of LA in Italy, but rather to appraise its practice in centers routinely performing laparoscopic surgery. In the hands of experienced surgeons, LA has morbidity rates comparable to those of international series. The higher diagnostic yield of laparoscopy makes it an invaluable tool in the management algorithm of women of childbearing age; its advantages in the presence of severe peritonitis are less clear-cut. Surgeons remain the main limiting factor preventing a wider diffusion of LA in our country, since only 47.3% of surgeons from the audited institutions can perform LA on a routine basis.