Computational methods for single cell RNA and genome assembly resolution using genetic variation

Genetic variation and natural selection have driven the evolutionary history on this planet and are responsible for creating us and all other life as we know it. Over the past several decades, the genomic revolution has allowed us to assess population variation across humans and other species and use that to link genotypes with phenotypes and infer evolutionary histories. In this thesis, I explore computational methods for using genetic variation to demultiplex and disambiguate complex data. In single cell RNAseq, problems of batch effects, doublets, and ambient RNA are each sources of noise that impede our ability to infer the functional states of cells and compare them between experiments. One new popular new experimental design promising to solve each of these while also reducing experimental costs is mixturing multiple individuals' cells into a single experiment. In chapter 2, I present a method for clustering cells by genotype, calling doublets, and using the cross-genotype signal in singletons to estimate and remove ambient RNA. I compare this methods to other existing methods including one that requires \textit{a priori} information about the genotypes, and two which do not. I find that my method outperforms each of these methods across a wide range of data parameters and sample types. In genome assembly, the recent higher throughput and lower cost of long read sequencing has revolutionized our ability to create reference quality genomes and has revitalized the assembly community. Now, massive efforts are taking place in the Darwin Tree of Life project and the Earth Biogenome project to create reference genomes for all multicelular eukaryotic life. This will create a scientific resource for the next generation of biological science, will serve as a conservation of data that could otherwise be lost in this time of mass extinction, and will allow for a much more broad understanding of evolution and the evolutionary history of life on Earth. While much progress has been made in data quality and assembly algorithms, some problems still exist. Until recently, the DNA input requirements for long read sequencing technologies made it impossible to sequence single individuals of these species with long reads. Also, high heterozygosity makes assembly more difficult due to the inherent ambiguity between heterozygous sequence versus paralogous sequence when confronted with inexact homology. One solution to the DNA input requirements would be to pool individuals, but this only increases the heterozygosity of the sample and reduces assembly quality. In chapter 3, we present the first high quality assembly of a single mosquito using new library preparation methods with reduced DNA requirements. This reduces the number of haplotypes to two, improving the assembly quality. In chapter 4, we further address the problems brought on by heterozygosity in assembly. I present a suite of tools that use the phasing consistency of multiple heterozygous sequences as a signal for physical linkage, thus using genetic variation to our advantage rather than as a challenge to overcome. This tool creates phased, linked assemblies and phasing aware scaffolding. Further, I provide a tool for phasing aware scaffolding on existing assemblies. This includes a novel haplotype phasing algorithm with some unique beneficial properties. It is robust to non-heterozygous variants as input and can detect and correct those genotypes. And it naturally extends to polyploid genomes.Wellcome Trus

Evaluation of Blue Tilapia (Oreochromis aureus) for Duckweed (Lemna minor) Control in South Carolina\u27s Private Waters

ABSTRACT We investigated the potential of Blue Tilapia (Oreochromis aureus) as a means for biological control of duckweed in agricultural impoundments, and assessed the potential for naturalization of this non-native fish in coastal regions of South Carolina. Additionally, we studied growth characteristics and nutrient accumulation abilities of duckweed (Lemna minor) growing in agricultural impoundments in the piedmont and coastal plain. Observations of tank feeding trials indicated juvenile Blue Tilapia consumed 36 – 86% of their body weight in fresh duckweed every 24 hours. Tilapia were stocked in agricultural impoundments in the piedmont and coastal plain during the 2012 and 2013 growing seasons. Duckweed population densities (19, 310 kg/ha) at time of stocking prevented survival of tilapia due to anoxic conditions. As a result, we were unable to measure duckweed control by tilapia in impoundments. Cold tolerance trials were conducted using juvenile Blue Tilapia (38 – 54 mm TL) to determine LT50 and LT100. Observed lethal temperatures were LT50 = 8.8° C and LT100 = 6° C. Investigations of duckweed growth characteristics in agriculture impoundments from April to October revealed monthly changes in duckweed water surface coverage and biomass. Duckweed coverage of ponds was highest in August (98.75%) and lowest in October (77.8%). Duckweed biomass was highest in July (2.93 kg/m2) and lowest in October (1.76 kg/m2). Attempts to predict duckweed biomass in terms of percent surface coverage were unsuccessful due to variability of biomass as surface coverage neared 100%. Duckweed tissue was analyzed to determine nutritional quality, nutrient concentrations, and bioconcentration ability. Observed crude protein (20.38%) and fat (2.38%) contents indicate duckweed was comparable to other plant sources of protein in livestock feeds. Nutrient concentrations observed in duckweed tissue in descending order were: K, Ca, Fe, Mn, P, Mg, Zn, and Cu. Analysis of nutrient accumulation indicated duckweed bioconcentration was significant for all measured nutrients. We ranked nutrient accumulation for macro and micro nutrients. Rankings were as follows: primary macro (P \u3e K), secondary macro (S \u3e Ca \u3e Mg), and micro (Mn \u3e Fe \u3e Zn \u3e Cu). Based on results of this study, Blue tilapia have potential as a biological control option for duckweed when used responsibly. Additionally, duckweed has potential as a feed source for livestock, biomass production, and bioremediation of waters

Evaluation of Conservation Management Practices for Northern Bobwhites and Shrub-Scrub Songbirds

ABSTRACT We evaluated the effect of early-successional habitat management practices on vegetation structure and composition, shrub-scrub songbird nesting, wintering songbird habitat use, and Northern Bobwhite habitat use in the lower Coastal Plain of South Carolina. The response of vegetation was measured for 18 different disturbance treatments at the end of each growing season from 2000 to 2006. The response of vegetation to disturbance was different among treatments. However, similarities existed between burn and disk treatments with the same season and frequency. We found 76 shrub-scrub songbird nests during the 2005 and 2006 nesting seasons. Painted buntings, indigo buntings, and blue grosbeaks were the most commonly found nesting species in the study. Nesting success and productivity experienced variation between years. Nest failures were the most commonly caused by storms, snakes, and raccoons. Hedgerows and field borders were the most commonly used habitat for nesting. Winter songbird use of early-successional habitat was studied in January and February of 2006. Birds were counted in treatment plots during man drives. Bird numbers were highest in plots that received spring and winter burning treatments. Northern bobwhites (n=11) were tracked using a modified homing technique from February thru August of 2006. Locations (n=951) were recorded based on the habitat type birds were in 3 times daily. Bobwhite use of the study area indicated that ditchlines, hedgerows, and food plots were important field components for the species. Based on our results land managers in the lower Coastal Plain may achieve the greatest results in early-successional habitat management with the use of prescribed burns applied in the spring at least every two years

An evaluation of the evolution of attitudes of certain employees of the Waltham Watch Company

Thesis (M.S.)--Boston Universit

The impact of worldview on the process of administration : a study of Shona and Ndebele Christians in Zimbabwe

As a Euro-African I wish to explore the validity of the idea that worldview factors are fundamental in determining the praxis of administration. From observation and experience, problems with the practice of administration appear to be generic, rather than primarily personal. (It was noted, however, that personality and temperament also play a role.) The enquiry focuses on Shona and Ndebele Christians in Zimbabwe. As the field of study is Practical Theology and to give a theological foundation for and, perhaps, at least a partial solution to some of the perceived problems, a nascent theological approach to administration is presented, together with proposed training courses in administration and leadership for Bible colleges. Because the notion of administration is somewhat abstract, a fivefold framework was used comprising Planning, Organising, Leading and Controlling, all performed within Time. Questions on the connections, values, perceptions, expectations and use of these components by Shona and Ndebele Christians were discussed in light of their worldviews. Although the intended research approach was social construction, the need for the framework undercut this approach somewhat. I also came from a moderately soft postfoundationalist viewpoint, using narrative practical theology. Six Christian leaders as co-researchers – three Shona and three Ndebele; three Pentecostal and three non-Pentecostal – shared their multicultural insights through personal anecdotes and narrative interaction. Chapter One, in two parts, begins with a personal anecdote and other illustrations highlighting some of the difficulties experienced with administration and its processes in a multicultural African context. The research question – whether worldview shapes the praxis of administration – together with sub-problems, is then outlined. The second section explains the research methodology. Chapter Two defines worldview and administration from both the natural and Christian perspectives, to clarify their nature and praxis. Some underlying problems are introduced. Chapter Three explores what constitutes administration in Christian ministry. Here, values and tasks are itemised to reveal the actual content of administration (at least from a local church pastor’s perspective) and some assumptions behind it. Chapter Four presents individual conversations with the six co-researchers. These personal responses begin to highlight the connection of worldview to administrative praxis and some initial issues arising there from. Chapter Five reflects group dialogues, which allow for cross-cultural and cross-theological views. Gender is introduced as a woman para-church ministry leader replaces a pastor. This provides further fusion of views. From there, Chapter Six examines the Shona, Ndebele and Christian worldviews in more depth. Two case studies are explored narratively, to identify how worldview factors impact the praxis of administration in specific settings. Chapter Seven discusses the group’s understanding of the Biblical perspective of administration. A tentative theological approach to administration is offered. And lastly, Chapter Eight summarises the findings, identifies the issues and presents some solutions. The focus for the latter is on possible administration courses for Bible colleges. Although not directly social constructionist, the team affirmed this approach. The intention here is to enhance this training and thus improve administration in Christian ministry for the wider benefit of the Church community.Thesis (PhD (Practical Theology))--University of Pretoria, 2007.Practical TheologyPhDunrestricte

Exploring relationships between stress and olfaction as mediated by neuropeptide y

The negative correlation between olfactory sensitivity and depression has been well documented, but the biological processes underpinning the relationship are not understood. This study explored a potential relationship between olfactory sensitivity, stress, and resilience to stress, specifically examining neuropeptide y (NPY) as a mediator. In phase I, 197 UTC students participated in a survey measuring stress and resilience among other factors. Of this sample, 25 students volunteered for phase II, in which they took an olfactory threshold test and gave blood. Serum levels of cortisol and NPY were analyzed from blood samples. Correlational analyses suggest a positive effect of stress (p=.013) and a negative effect of resilience (p=.003) on olfactory thresholds, while biological markers were inconclusive. Future studies should incorporate the diagnosis of stress disorders, as biological markers may not significantly fluctuate based on non-clinical levels of stress

Scientific Value of Real-Time Global Positioning System Data

The Global Positioning System (GPS) is an example of a Global Navigation Satellite System (GNSS) that provides an essential complement to other geophysical networks because of its high precision, sensitivity to the longest‐period bands, ease of deployment, and ability to measure displacement and atmospheric properties over local to global scales. Recent and ongoing technical advances, combined with decreasing equipment and data acquisition costs, portend rapid increases in accessibility of data from expanding global geodetic networks. Scientists and the public are beginning to have access to these high‐rate, continuous data streams and event‐specific information within seconds to minutes rather than days to months. These data provide the opportunity to observe Earth system processes with greater accuracy and detail, as they occur

Prospectus, October 24, 2019

APO PLANS ANNUAL PENNIES FOR PUMPKINS; Costume Shop Provides Last-minute Halloween Ideas; Students Reveal Halloween Traditions & Superstitions; Annual U of I Homecoming Parade: A Long-lasting Tradition; A teacher, creator, and mentor of theatre; Fall festivities anyone?; History of the holiday: What is Halloween?https://spark.parkland.edu/prospectus_2019/1046/thumbnail.jp

National Seismic System Science Plan

Recent developments in digital communication and seismometry are allowing seismologists to propose revolutionary new ways to reduce vulnerability from earthquakes, volcanoes, and tsunamis, and to better understand these phenomena as well as the basic structure and dynamics of the Earth. This document provides a brief description of some of the critical new problems that can be addressed using modem digital seismic networks. It also provides an overview of existing seismic networks and suggests ways to integrate these together into a National Seismic System. A National Seismic System will consist of a number of interconnected regional networks (such as southern California, central and northern California, northeastern United States, northwestern United States, and so on) that are jointly operated by Federal, State, and private seismological research institutions. Regional networks will provide vital information concerning the hazards of specific regions. Parts of these networks will be linked to provide uniform rapid response on a national level (the National Seismic Network). A National Seismic System promises to significantly reduce societal risk to earthquake losses and to open new areas of fundamental basic research. The following is a list of some of the uses of a National Seismic System