Development of Environmental Metabarcoding Analysis for Use in Ecological Studies of Aquatic Fungal and Oomycete Communities Using Nanopore Sequencing

One of several factors contributing to amphibian decline are organisms called water molds (oomycetes), which parasitize and kill amphibian and fish eggs, larvae, and occasionally adults. Amphibian decline is one of the most difficult issues facing ecologists and conservationists to date; half of amphibian species are in severe decline and one third of amphibian species are facing extinction, threatening the stability of ecosystems globally. Multiple oomycete species are known to cause the disease saprolegniasis and contribute to amphibian decline; however, the full range of species involved is not presently known. This study evaluated the Oxford Nanopore minION DNA sequencer (R9.2 chemistry) for use in DNA barcoding multiplexed samples. This study aimed to develop new methods of environmental metabarcoding analysis to assess aquatic oomycete and fungal communities using the internal transcribed spacer (ITS) DNA barcode. A proof-of-concept survey was performed to assess community composition and diversity of aquatic oomycetes and Fungi in 4 freshwater habitats with saprolegniasis present. Samples were taken April 15, 2016 at 4 sites along Interstate-90 near Snoqualmie Pass (Wenatchee National forest, Washington) during Rana cascadae and Anaxyrus boreas breeding season near eggs with saprolegniasis. The minION produced high but uneven throughput across all four sites. The sequence accuracy and error type prevented chimera checking and phylotype assignment. Sequences were matched using NanoOK to the UNITE database to assign operational taxonomic units (OTUs). FUNGuild was used to assign trophic modes to OTUs to evaluate functional diversity. The recovered oomycete OTUs were low (~1% of all reads) and represented plant pathogenic phyla. Fungal recovery was broad with aquatic taxa represented heavily. Diversity analysis showed little difference between sites, with evidence that uneven throughput affected beta-diversity indices from assessing compositional differences. Trophic mode analysis showed little difference between sites. Overall, this study found that the minION sequence data presented multiple bioinformatic challenges for metabarcoding using the ITS region. With low recovery of oomycetes, further study is needed to determine the availability of oomycete zoospores for collection via the sampling methods used in this study. Additionally, oomycete specific primers are recommended for increased recovery

A method for estimating the rate of shedding of tags from yellowfin tuna

ENGLISH: The present paper describes a new method for estimating the shedding rate of tags. The method utilizes not only data on tagging and recovery of fish marked with two tags but also data from those marked with one. One important advantage of the new technique is that the estimates of the shedding rates are free from distortion caused by variations in fishing intensity during the total recovery period. The idea of this method appears to be implicit in a short note by Gulland (1963). This technique has been applied to the data obtained by the Inter-American Tropical Tuna Commission in a tagging cruise off the west coast of southern Baja California, during June 1963, at which time both single and double-tagged yellowfin tuna were released. Details of the tagging procedure and equipment have been described by Fink (1965b). The results presented in the present paper are for yellowfin tuna tagged with dart tags. Estimates of shedding should be made separately for each species investigated and also for each type of tag used, since these rates may be variable and often unexpectedly high (Springer and McErlean 1961, Chadwick 1963). SPANISH: El presente estudio describe un nuevo método para estimar las tasas del desprendimiento de marcas. El método emplea no solamente los datos sobre la marcación y recobro de peces marcados con dos marcas, pero también datos de los peces marcados con una marca. Una ventaja importante de la nueva técnica, es que las estimaciones de las tasas de desprendimiento son libres de alteración, causada por las variaciones en la intensidad de pesca durante el período total de recobro. La idea de este método parece ser implícita en un breve apunte por Gulland (1963). Esta técnica se ha aplicado a los datos obtenidos por la Comisión Interamericana del Atún Tropical, en un crucero de marcación efectuado frente a la costa occidental al sur de Baja California, en junio de 1963, tiempo en el cual fueron liberados atunes aleta amarilla marcados tanto con una como con dos marcas. Los detalles del procedimiento de la marcación y del equipo usado han sido descritos por Fink (1965b). Los resultados presentados en este estudio, pertenecen al atún aleta amarilla marcado con marcas de dardo. Las estimaciones del desprendimiento deben efectuarse separadamente para cada especie que ha sido investigada y también para cada tipo de marca usado, ya que estas tasas pueden ser vaiables, y a menudo inesperadamente altas (Springer y McErlean 1961, Chadwick 1963). (PDF contains 20 pages.

A method for estimating the rate of shedding of tags from yellowfin tuna

ENGLISH: The present paper describes a new method for estimating the shedding rate of tags. The method utilizes not only data on tagging and recovery of fish marked with two tags but also data from those marked with one. One important advantage of the new technique is that the estimates of the shedding rates are free from distortion caused by variations in fishing intensity during the total recovery period. The idea of this method appears to be implicit in a short note by Gulland (1963). This technique has been applied to the data obtained by the Inter-American Tropical Tuna Commission in a tagging cruise off the west coast of southern Baja California, during June 1963, at which time both single and double-tagged yellowfin tuna were released. Details of the tagging procedure and equipment have been described by Fink (1965b). The results presented in the present paper are for yellowfin tuna tagged with dart tags. Estimates of shedding should be made separately for each species investigated and also for each type of tag used, since these rates may be variable and often unexpectedly high (Springer and McErlean 1961, Chadwick 1963). SPANISH: El presente estudio describe un nuevo método para estimar las tasas del desprendimiento de marcas. El método emplea no solamente los datos sobre la marcación y recobro de peces marcados con dos marcas, pero también datos de los peces marcados con una marca. Una ventaja importante de la nueva técnica, es que las estimaciones de las tasas de desprendimiento son libres de alteración, causada por las variaciones en la intensidad de pesca durante el período total de recobro. La idea de este método parece ser implícita en un breve apunte por Gulland (1963). Esta técnica se ha aplicado a los datos obtenidos por la Comisión Interamericana del Atún Tropical, en un crucero de marcación efectuado frente a la costa occidental al sur de Baja California, en junio de 1963, tiempo en el cual fueron liberados atunes aleta amarilla marcados tanto con una como con dos marcas. Los detalles del procedimiento de la marcación y del equipo usado han sido descritos por Fink (1965b). Los resultados presentados en este estudio, pertenecen al atún aleta amarilla marcado con marcas de dardo. Las estimaciones del desprendimiento deben efectuarse separadamente para cada especie que ha sido investigada y también para cada tipo de marca usado, ya que estas tasas pueden ser vaiables, y a menudo inesperadamente altas (Springer y McErlean 1961, Chadwick 1963). (PDF contains 20 pages.

Teacher Efficacy in the Implementation of New Curriculum Supported by Professional Development

A large body of literature regarding professional development and its effects on teaching and student achievement and learning has emerged over the last decade. There are many teachers who either have limited access to professional development activities or who have access and choose not to take part in professional development activities. This qualitative study employed a phenomenological tradition in describing the lived experiences of participants involved in the implementation of new curriculum. Fourteen teachers and seven principals were purposefully selected to be part of this study in a rural school jurisdiction in southern Alberta. Through a qualitative analysis, this study shared teachers\u27 perceptions as they described the role professional development plays in enhancing teacher efficacy and changing teaching practices in the implementation of new curriculum. Data were collected during face-to-face, semi-structured interviews, and the analysis of data revealed six topics: the need for change, professional development and curriculum implementation, professional development and teaching practices, professional development and teacher efficacy, professional development and student learning and motivation. Major findings from this study concluded that teacher participants recognize PD as the common thread that motivates teachers, improves their sense of efficacy, assists them in successful curriculum implementation, heightens their awareness of the need to improve teaching practices and the need to become student-centered and improve student learning. Principal participants concurred with teacher participants, and recognize the role leaders play in motivating teachers to become actively engaged in professional learning activities. Professional development plays a key role in providing teachers with knowledge and skills to hone their teaching practices, to rejuvenate them, and to improve student learning. It also assists teachers in successfully implementing new curricula. As teachers become aware of the need to change teaching practices in order to improve teacher efficacy, professional development provides opportunities to gain confidence and heighten their sense of personal efficacy

Traverse: a novel

Traverse is a Master\u27s thesis in the form of a novel about an engineer traveling back in time as a result of an experimental accident, the efforts to return him to the present, and the trials which the main character goes through in the past. The novel is intended to explore the dynamic interaction and interdependence between society, technology, and the natural world. The thesis consists of 100 pages of completed writing with the rest of the novel in outline form. The form of the thesis is intended to act as a submission to a professional book agent

An optical procedure for the measurement of composition profiles

This thesis is concerned with the development of an optical method, and the design of the appropriate apparatus, to measure composition profiles in a binary solution

Local u'g'r'i'z' Standard Stars in the Chandra Deep Field-South

Because several observing programs are underway in various spectral regimes to explore the Chandra Deep Field South (CDF-S), the value of local photometric standards is obvious. As part of an NOAO Surveys Program to establish u'g'r'i'z' standard stars in the southern hemisphere, we have observed the central region of the CDF-S to create local standards for use by other investigators using these filters. As a courtesy, we present the CDF-S standards to the public now, although the main program will not finish until mid-2005.Comment: Accepted by AJ (scheduled for October 2003 issue). 26 pages, 5 tables, 5 figures. High resolution version of Figure 7 available at http://home.fnal.gov/~dtucker/Southern_ugriz/index.htm

Senior Recital: Douglas Becknell, Baritone; Wanda Bennett, Piano; February 7, 1971

Centennial Recital HallFebruary 7, 19713:00 p.m