Thesis (Ph. D.)--University of Washington, 1993. / Vita. Includes bibliographical references (leaves [236]-244).

Thesis (Ph.D.)--Duquesne University, 2009. / Title from document title page. Abstract included in electronic submission form. Includes bibliographical references and abstracts.

Thesis (M.A.)--Villanova University, 2007. / English Department. Includes bibliographical references.

Malaria is one of the most serious tropical infectious diseases affecting mankind. The prevention of the disease is hampered by the increasing resistance of the parasite to existing chemotherapy and -prophylaxis drugs. The need for novel therapeutic targets and drugs is therefore enormous and the understanding of the biochemistry of the parasite is imperative. The aim of this study was the identification and molecular characterisation of the eDNA of one such metabolic target protein, ornithine decarboxylase (ODC), in the human malaria parasite P. falciparum. The P. falciparum ODC eDNA was isolated by means of a modified RT-PCR technique, RACE. No sequence data were available and the primers used were based on consensus areas identified in the protein sequences from other related organisms. The isolation and identification of the eDNA with degenerate primers was successful in 3' -RACE, but necessitated the optimisation of the eDNA synthesis protocol and the use of total RNA as starting material. The sequence obtained facilitated the application of 5' -RACE with ODC-specific primers based on the 3' -RACE sequence data. The full-length ODC eDNA sequence was obtained by overlap-alignment of various segments. A novel suppression PCR technology was applied during the 5' -RACE in order to create an uncloned eDNA library of amplified cDNAs representing only the mRNA population. The P. falciparum ODC eDNA contains an open reading frame of ---2847 bp and translates to a large 939 amino acid protein. The protein contained large internal insertions and was extended by '""273 N-terminal residues compared to ODCs from other organisms. Several possible signature motifs were identified for phosphorylation, glycosylation and transamidation. The P. falciparum ODC protein seems to contain more hydrophilic and a-helix forming residues. These characteristics should be further investigated after expression of the recombinant protein. The isolation of the P. falciparum ODC eDNA facilitates the validation of this protein as an antimalarial target. / Dissertation (MSc)--University of Pretoria, 1998. / gm2014 / Biochemistry / unrestricted

Subsistence fishing is a vital component of Alaska’s North Slope borough economy and culture that is being threatened by human disturbance. These threats mean the fish must be protected, but the size of the region makes conservation planning difficult. Fortunately, advances in species distribution models (SDMs), environmental DNA (eDNA), and remote sensing technologies provide potential to better understand species’ needs and guide management. The objectives of my study were to: (1) map the current habitat suitability for twelve fish species, occurring in Alaska’s North Slope,(2) determine if SDMs based on eDNA data performed similarly to, or improved, models based on traditional sampling data, and (3) predict how species distributions will shift in the future in response to climate change. I was able to produce robust models for 8 of 12 species that relate environmental characteristics to a species’ presence or absence and identify stream reaches where species are likely to occur. Unfortunately, the use of eDNA data did not produce useful models in Northern Alaskan rivers. However, I was able to generate predictions of species distributions into the future that should help inform management for years to come.

Recent years have seen an explosion of interest in the use of freely available DNA present in aquatic systems, otherwise known as environmental DNA (eDNA), as a tool for monitoring aquatic organisms. However, much remains unknown about the behavior of eDNA over a range of environmental conditions. This is particularly true in high gradient headwater streams, which have received less attention than other types of water bodies. In the summer of 2011, a headwater stream system with well established species distributions was sampled using eDNA techniques. Though species were detected where known to be present, detections also occurred where traditional techniques failed to detect species. This suggests that a cautious approach to positive eDNA detections is advisable. In 2012 a second study was conducted to better understand the dynamics of eDNA concentration in lotic systems. Caged brook trout (Salvelinus fontinalis) were introduced into two otherwise fishless headwater streams, and eDNA samples were collected at evenly spaced intervals downstream of the cage. This was repeated 19 times from mid-summer through autumn, over flows ranging from approximately 1 to 96 l/sec. Quantitative PCR was used to relate DNA copy number to distance from source for each of these 19 sampling events. In all cases, DNA was detectable at 239.5 m from the cage. Increasing flows generally decreased eDNA copy number near the cage but had relatively little effect at downstream sites. Additionally, the presence of leaf biomass during the fall period had the potential to completely erase otherwise high DNA levels.

The global aquaculture industry is expanding to support increased demand in global markets and supplement traditional fisheries. The rapid increase of aquaculture production relies on introducing and using species outside their native range, posing significant regional environmental and socio-economic risks. Non-native species are selected based on transferable large-scale production protocols, fast growth, and existing market demand. Aquaculture is an important sector within Saudi Arabia’s Vision 2030 (anticipated >400% production increase by 2030). Barramundi (Lates calcarifer) was introduced into the Red Sea for open sea-cage farming in 2008, with large-scale production beginning in 2014. Regionally, there are numerous anecdotal reports of escape events of this species, including an incident in 2015 involving the release of ~300,000 fish. Since then, local fishers have caught up to 15 wild individuals per month in Al Lith, central Saudi Arabia. This study presents the first biological information on L. calcarifer aquaculture escapees in the Saudi Arabian Red Sea. Wild-caught L. calcarifer (n=5) were collected from a local fish landing and measured up to 10 kg, eight years of age, were sexually mature, and consumed benthic and coral reef fishes. In contrast, individuals in aquaculture facilities are harvested at < 1 kg and < 400 mm. In their native range, L. calcarifer can reach up to 200 cm and 60 kg. To assist in detecting and monitoring escapees within the Red Sea, I designed and validated a species-specific SYBR-based environmental DNA quantitative PCR assay targeting a 16S mitochondrial region of L. calcarifer rRNA (Barramundi_16S assay). Preliminary results, using DNA metabarcoding and environmental (seawater) samples, detected L. calcarifer near active/historical aquaculture farms and north/south of areas where this species has not been reported previously in the Red Sea (10–250 km from aquaculture facilities). In the future, the Barramundi_16S assay can screen additional eDNA samples (n=250) collected for this study to delineate the geographic range of barramundi in the Red Sea. Cumulatively, this study highlights the need to consider the ecological impacts of aquaculture escapees and provides managers and industry with valuable information and a novel molecular monitoring tool for detecting aquaculture escapees.

The aim of this report is to contribute to the base of knowledge on environmental monitoring by increasing understanding of how eDNA, electrofishing and sampling fishing may be used to examine fish biodiversity. It also aims at understanding if fish indexes developed within the Water Framework Directive reflect biodiversity, as well as the potential of eDNA data to serve as input to these indexes. This was done by using three different approaches. Firstly, in order to establish which of the methods eDNA, electrofishing and sampling fishing is more suitable to measure the different dimensions of biodiversity (species richness, species evenness and genetic diversity), a literature review comparing the different methods was carried out. It was found that eDNA yields a more detailed results for species richness, electrofishing yields better results for species evenness and sampling fishing is outperformed by eDNA and electrofishing alike. Both electrofishing and sampling fishing may collect data for genetic diversity analysis, however electrofishing outperforms sampling fishing with regards to amount of species caught, making electrofishing a more suitable data collection method. Secondly, in order to gain insight on practical usage of eDNA, a case study of Spjutmo (Dalarna county) was reviewed. It was established that eDNA generated more detailed information of species richness in the case of Spjutmo (as compared to electrofishing). The relative abundance data generated by the eDNA study might be seen as a measure of species evenness. However, electrofishing yielded data which may serve as input to species evenness indices. To the best knowledge of the author, none of the methods generated data on genetic diversity in this specific case. Officials from the energy company Fortum and the county board of Dalarna were also interviewed in order to get insight on what potential they see for eDNA to contribute to environmental monitoring. Both officials point at the ability to estimate abundance as a desired feature, hence a better understanding of what the relative abundance results indicates is wanted. The two interviews indicate that this understanding is an important feature to develop in order to make metabarcoding studies effective in current environmental monitoring. Thirdly, in order to understand if fish indexes developed within the Water Framework Directive reflect biodiversity, a literature review was performed. It was found that, all but one of the compared indexes incorporates or somewhat incorporates species richness. However, only five indexes are indicative or somewhat indicative of species richness. Species evenness is incorporated or somewhat incorporated by two indexes, which are also indicative or somewhat indicative of species evenness. None of the indexes incorporate or indicate genetic diversity. Within the third literature review, the potential of eDNA data to serve as input to current fish-based indexes developed within the Water Framework Directive, was studied. It was found that eDNA data may serve as input to only one index in its present form. However, five indexes also use proportional information (e.g. proportion of tolerant species), which possibly could be provided by eDNA data. The index where usage of eDNA data is currently possible uses presence-absence information. / Målet med denna rapport är att bidra till kunskapsläget kring miljöövervakning genom att öka förståelsen för hur eDNA, elfiske och provfiske kan användas för att undersöka fisk biodiversitet. Målet är också att förstå om fisk-index utvecklade inom ramen för det Europeiska vattendirektivet reflekterar biodiversitet samt om data från eDNA kan utgöra input till dessa index. För att uppfylla dessa mål användes tre metoder. För att etablera vilken av metoderna eDNA, elfiske och provfiske är mer lämpad att mäta de olika dimensionerna av biodiversitet (artrikedom, distribution av arter och genetisk diversitet), genomfördes en litteraturstudie. Slutsatsen kunde dras att eDNA mäter artrikedom med högst noggrannhet, elfiske mäter distribution av arter mer detaljerat och att provfiske överträffas av både eDNA och elfiske i alla dimensioner. Både elfiske och provfiske kan samla data för analys av genetisk diversitet, men elfiske överträffar provfiske gällande hur många arter som fångas, vilket gör elfiske mer lämpligt som metod att samla in data för genetisk analys. För att få praktisk insikt i ett fall där eDNA använts, granskades en fallstudie från Spjutmo (i Dalarnas län). eDNA genererade mer detaljerad information om artrikedom än elfiske i detta fall. Datan genererad av eDNA kring relativ abundans mellan arter skulle kunna tolkas som ett mått på distribution av arter. Data genererad av elfiske kan å andra sidan användas som input till olika index för distribution av arter. Författaren veterligen, genererade varken eDNA eller elfiske mått på genetisk diversitet i detta specifika fall. Två personer, en från Fortum och en från länsstyrelsen Dalarna intervjuades också för att få insikt i deras syn på potentialen av att använda eDNA som ett miljöövervakningsverktyg. Båda intervjupersonerna pekade på att en bättre förståelse av de relativa abundansvärdena indikerar är önskad. Båda intervjupersonerna pekade på att det är en viktig aspekt för att metabarcoding studier ska vara effektiva i nuvarande miljöövervakning. För att förstå om fisk-index utvecklade för EU’s vattendirektiv reflekterar biodiversitet, genomfördes en komparativ litteraturstudie av index. Alla index förutom ett inkorporerar eller delvis inkorporerar artrikedom. Bara fem indikerar eller delvis indikerar artrikedom. Distribution av arter inkorporeras eller delvis inkorporeras av två index som också indikerar eller delvis indikerar distribution av arter. Inom den komparativa litteraturstudien av index, studerades även potential att fungera som input av data genererad av eDNA till indexen. Data genererad av eDNA kan i dagsläget fungera som input till ett av indexen. Fem index använder någon form av proportionell data (t.ex. proportion av toleranta arter), som möjligen skulle kunna ges av eDNA. Indexet till vilket det är möjligt att använda eDNA data använder närvarande-ej närvarande information som input.

Foreword to Aria Da Capo The libretto of the opera is a verbatim setting of Edna St. Vincent Millay's one act play "Aria da Capo." World events, especially World War II and the current Korean War influenced the choice of this timely, yet timeless play. Miss Millay's death occurred during the composition of the opera. She never knew, therefore, of the composition or performance of her play as an opera. The form of the opera is that of the "da capo" aria. he form, of course, was determined by the play which ends exactly as it started. Thematic material consists mainly of two themes: the opening theme or Scene I (Pierrot and Columbine's scene) and the opening theme of Scene II (the Shepherd's scene). All of the significant motivic material used in Scene I is derived from the opening theme of that scene. In the shepherd's scene, material derived from both of the above mentioned themes is used. The musical style of the two scenes is intentionally contrasting. In Pierrot and Columbine's scene an attempt was made to express their characters by means of a pseudo-popular music style which is rhythmic and lively but has no real depth of emotional feeling. In the shepherd's scene an attempt was made to express their changing characters by means of a very simple style eventually evolving into a more complex style. In order to make the score more easily understood all the orchestrated parts are written in concert. For the same reason all directions to the musicians are given in English instead of the usual Italian. The opera was produced under the direction of Dr. Lucas Underwood. Thomas Haynes, musical assistant to Dr. Underwood, deserves special recognition, not only for his excellent job of conducting the opera, but also for designing the set and staging the opera and for his untiring efforts in rehearsing the cast and the orchestra.

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