Physical Sciences and Mathematics Commons^™

What Drives Larval Condition For Northern Anchovy (Engraulis Mordax)? Implications For Coastal Pelagic Species Recruitment Fluctuations And Fishery Management Practices, Michelle Robidas

Theses

Discerning the causes of population boom and bust cycles for coastal pelagic species (CPS) has been a major focus of fisheries management research for over a century. Year-class strength is contingent on larval survival and condition, which can be influenced by larval size at age and growth rate. These two factors, in turn, can be affected by maternal investment and environmental variables such as water temperature, salinity, oxygen, and chlorophyll a. We evaluated each of these factors from 127 two to eight week-old Northern Anchovy (Engraulis mordax) larvae off the coast of San Diego to San Francisco, …

Assessing The Effectiveness Of Integrated Multi-Trophic Aquaculture For Growing West Coast Venus Clams, Avery Wallace

Theses

With demand for sustainable sources of seafood on the rise, California is looking to expand aquaculture with a focus on innovative culturing methods and use of native or resident species. Therefore, this study examined the potential for culturing native North American west coast venus clams (Chione californiensis and Chione undatella) using integrated multi-trophic aquaculture (IMTA). An ITMA approach was chosen because it is a culture method that uses species from different but functionally complementary trophic levels that have been found to reduce the potential negative effects of traditional monoculture. California sea cucumber (Parastichopus californicus) and the seaweeds red ogo (Gracilaria …

The Effect Of Different Feeding Regimes On Recent Nutritional And Growth Measurements In Juvenile California Killifish (Fundulus Parvipinnis), Emily Parks

Theses

Gaining a deeper understanding of in-situ growth approximations for juvenile fishes is one way to understand how food consumption may affect fish growth. If variations in growth rate are strongly mirrored by past food status, then the condition (degree of well-being) of fish can be potentially used as a reference for relative prey availability. Furthermore, confirming that there is a positive relationship between food availability and fish growth rate is a critical first step to deepen our understanding of growth rate variation as well as examining if growth can be a proxy for habitat quality.

The California killifish (Fundulus …

The Effect Of Marine Snow Particle Distribution On The Foraging Behavior Of Calanus Pacificus, Elena Beckhaus

Theses

Marine snow is a major component of the biological pump, through which carbon is exported to the deep ocean. The sinking of marine snow can be disrupted by organisms, including many species of zooplankton that ingest or break up aggregates. These processes can have important impacts on planktonic food web dynamics and carbon export. Marine snow can have vertically patchy distributions, occurring in thin layers, which may further affect interactions with zooplankton. In this lab-based study, we examined how the presence of a marine snow layer affects copepod behavior and ingestion.

We conducted a series of experiments in which copepods …

Studying Neurotoxic Effects Of Three Synthetic Insecticides And Two Herbal Infusions On The Nervous System Of The Fruit Fly Drosophila Melanogaster, Sara Khamis Obaid Hamarain Al Dhaheri

Theses

Pesticides applied on plants and animals can reach the human diet once they enter food chains. Insecticides are neurotoxic agents; they have the potential of causing damage to the nervous system in people. The damage could induce or promote neurodegenerative diseases such as the Parkinson’s and Alzheimer's. It is well-documented that the exposure to the insecticide chlorpyrifos (CPF) stimulate the Parkinson disease in humans and experimental animals. Thus, this research project will study effect of three synthetic insecticides pirimicarb, tefluthrin, and CPF on the nervous system of Drosophila melanogaster as a model organism. In addition, the project will evaluate the …

The Red Palm Weevil In The Uae: Morphological Diversity And Rnai-Mediated Gene Silencing Of Two Cuticle-Related Genes, Safa Hashem Mohammed Musaed

Theses

Red Palm Weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), threatens palm trees worldwide. A better understanding of this insect can help with designing an adequate management strategy. This study aimed to a better understand the morphological diversity of RPW and examined RNAi-mediated gene silencing of two cuticle-related genes, vestigial (vg) gene, and Laccase (Lac2) gene by injecting the last larval stage with double-stranded RNA (dsRNA). For the morphological diversity study, adults of RPW were collected and classified by their prothoracic spots. Additional morphological characters were measured such as Pronotum Length (PL), Pronotum Width (PW), Elytra Length (EL), Elytra Width (EW), and …

Developing A Method To Track Marine Snow Aggregation Through Individual Collisions Using Stereoscopic Imaging, Riley Henning

Theses

The aggregation of individual phytoplankton into marine snow allows particles to sink more quickly, thus resulting in the transport of particulate organic carbon from surface waters to the deep ocean. Aggregate formation has previously been measured in experiments indirectly by quantifying how particle size or particle concentration changes over time. Here, I present my thesis in which I applied high-resolution imaging to quantify aggregate formation using two different methodologies.

We conducted experiments to investigate aggregate formation using stereoscopic imaging, tracking individual particles directly in a 3D volume. Phytoplankton cultures were rolled in cylindrical tanks and imaged by two cameras illuminated …

Otolith Microchemistry Reveals Low Habitat Connectivity Of California Killifish (Fundulus Parvipinnis) Across A Range Of Spatial Scales, Lisa Robison

Theses

As wetlands face continued fragmentation worldwide, an understanding of habitat connectivity and how fishes that rely on these environments is imperative to conduct effective marine management. Site fidelity and habitat connectivity are vital measures of the interdependence of fish populations living in neighboring marshes (or in regions of a single marsh).

Here, we examine the habitat connectivity, site fidelity, and movement of California killifish (Fundulus parvipinnis) within and among three estuaries in Southern California through otolith microelemental analysis. Assessing the site fidelity of estuarine fishes is important to determine the level of connectivity between spatially distinct populations within …

The Role Of Software Engineering In Bioinformatics, Brendan Sean Lawlor

Theses

This thesis proposes that by applying state-of-the-art software engineering tools, techniques and frameworks to currently recognised challenges in bioinformatics, improved outcomes can be attained in that field. It begins by decomposing software engineering into two categories, namely process and architecture, and choosing two key challenges in the practice of bioinformatics: reproducibility and scalability. The body of the thesis is an exploration of the intersection between these two software engineering categories and these two bioinformatics challenges. The question is asked: Can best practices in professional software engineering be applied to address key issues in the bioinformatics domain, creating positive outcomes? And …

Predicting Carcass Cut Yields In Cattle From Digitalimages Using Artificial Intelligence, Darragh Matthews

Theses

Beef carcass classification in Europe is predicated on the EUROP grid for both fatness and conformation. Although this system performs well for grouping visually similar carcasses, it cannot be used to accurately predict meat yields from these groups, especially when considered on an individual cut level. Deep Learning (DL) has proven to be a successful tool for many image classification problems but has yet to be fully proven in a regression scenario using carcass images. Here we have trained DL models to predict carcass cut yields and compared predictions to more standard machine learning (ML) methods. Three approaches were undertaken …

New Methods For Deep Learning Based Real-Valued Inter-Residue Distance Prediction, Jacob Barger

Theses

Background: Much of the recent success in protein structure prediction has been a result of accurate protein contact prediction--a binary classification problem. Dozens of methods, built from various types of machine learning and deep learning algorithms, have been published over the last two decades for predicting contacts. Recently, many groups, including Google DeepMind, have demonstrated that reformulating the problem as a multi-class classification problem is a more promising direction to pursue. As an alternative approach, we recently proposed real-valued distance predictions, formulating the problem as a regression problem. The nuances of protein 3D structures make this formulation appropriate, allowing predictions …

The Effect Of Phytoplankton Properties On The Ingestion Of Marine Snow By Calanus Pacificus, Grace Cawley

Theses

The aggregation of phytoplankton into marine snow provides a mechanism by which smaller particles can coagulate to form larger particles, which can be consumed at various depths or readily transported to the deep ocean and sequestered from the atmosphere on time scales of a thousand years or more. Zooplankton interacting with these large carbon-rich aggregates can obtain nutrition in environments where the phytoplankton size spectrum is small and not directly available, enhancing the possibility of obtaining adequate nutrition in environments dominated by small cells. In addition, interactions between zooplankton and marine snow can result in fragmentation, thus affecting the particle …

Comparison Of Longitudinal Changes In Resting State Functional Magnetic Resonance Imaging Between Alzheimer’S And Healthy Controls, Berk Can Yilmaz

Theses

Resting State Functional Magnetic Resonance Imaging (rs-fMRI) is a technique that is widely used for analyzing brain function using different approaches and methods. This study involves rs-fMRI analysis of Blood Oxygenation Level Dependent (BOLD) signals acquired from Alzheimer’s disease (AD) Patients and Healthy Controls (HC). Each subject in the study had both functional and anatomical images with at least one rs-fMRI scan with their Anatomical (T1) scans. Previous rs-fMRI studies have demonstrated that AD shows differences in Amplitude of Low Frequency (<0.1 Hz) Fluctuations (ALFF), and Regional Homogeneity (ReHo) measures according to HCs.

The aim of the study is to investigate individual and group level differences using ReHo and mALFF related …

Protein Inter-Residue Distance Prediction Using Residual And Capsule Networks, Andrew Dillon

Theses

The protein folding problem, also known as protein structure prediction, is the task of building three-dimensional protein models given their one-dimensional amino acid sequence. New methods that have been successfully used in the most recent CASP challenge have demonstrated that predicting a protein's inter-residue distances is key to solving this problem. Various deep learning algorithms including fully convolutional neural networks and residual networks have been developed to solve the distance prediction problem. In this work, we develop a hybrid method based on residual networks and capsule networks. We demonstrate that our method can predict distances more accurately than the algorithms …

Polya Db3: A Database Cataloging Polyadenation Sites(Pas) Across Different Species And Their Conservation, Ram Mohan Nambiar

Theses

Polyadenation is an important process occurring in the messenger RNA that involves cleavage of 3 end nascent mRNAs and addition of poly(A) tails. For this thesis,I present PolyA DB3 ,a database cataloging cleavage and polyadenylation sites (PASs) in several genomes specifically for human,mouse,rat and chicken. This database is based on deep sequencing data. PASs are mapped by the 3’ region extraction and deep sequencing (3’READS) method, ensuring unequivocal PAS identification. Large volume of data based on diverse biological samples is used to increase PAS coverage and provide PAS usage information. Strand-specific RNA-seq data were used to extend annotated 3’ ends …

A Parallelized Implementation Of Cut-And-Solve And A Streamlined Mixed-Integer Linear Programming Model For Finding Genetic Patterns Optimally Associated With Complex Diseases, Michael Yip-Hin Chan

Theses

With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as late-onset Alzheimer’s disease (AD), but it has been a challenge to fully uncover the necessary information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases does not involve single markers working alone, but patterns of genetic markers interacting additively or epistatically. But as we move upwards beyond patterns of size two, it quickly becomes computationally infeasible to examine all combinations in the solution space. A common solution to solving …

Habitat Preferences Of Blue Marlin (Makaira Nigricans) And Black Marlin (Istiompax Indica) In The Eastern Pacific Ocean, Nima Farchadi, Michael G. Hinton, Andrew R. Thompson, Zhi-Yong Yin

Theses

Overexploitation and climate change can reduce the abundance and shift the spatial distribution of marine species. Determining the habitat suitability of a mobile pelagic species, such as Makaira nigricans (BUM) and Istiompax indica (BLM), can help describe their spatiotemporal distribution patterns over a broad spatial scale, which is a crucial need for fisheries management. Using 14 years (1997-2010) of Inter-American Tropical Tuna Commission (IATTC) catch data from purse-seine vessels in the eastern Pacific Ocean (EPO), we modeled the dynamic habitat suitability of BUM and BLM in response to environmental variables within the EPO using a species distribution model (MaxEnt) with …

The Effects Of Density Gradients On The Distribution And Behavior Of Copepods, Connor Cayson

Theses

Observations of fine-scale behavioral dynamics of zooplankton may shed insight into much larger-scale ecosystem patterns and phenomena. Some zooplankton, such as copepods, are known to aggregate near density gradients; however, it is not clear the extent to which density gradients alone affect copepod distribution and behavior, since these gradients are often associated with phytoplankton layers. In this study, we investigated the behavior of Calanus pacificus in response to salinity gradients through laboratory experiments observed with high-resolution video and analyzed using computational techniques. Image data were collected using two cameras recording continuously for a duration of 30 minutes or more, allowing …

Bubble Stream Production By Belugas (Delphinapterus Leucas), Megan Slack

Theses

Bubble stream production in belugas has been poorly characterized and its function is not well understood. I examined behavioral states when producing bubble streams (“bubbling”), and when bubbling calls, to determine whether bubbling was significantly associated with a particular call category or behavioral state. Using 19 hours of video and audio recordings collected over a two-day period, I quantified bubble streams of a 4-month old calf and an unrelated adult female housed together. Based on the overall activity budgets and pool of vocalizations for both animals, I calculated the expected counts of bubble streams with and without vocalizations, assuming that …

Hypoxic And Viral Contributions To The Etiopathogenesis Of Schizophrenia: A Whole Transcriptome Analysis, Kathryn A. Gorski

Theses

Schizophrenia is a mental illness with a complex and as of yet unclear etiology. It is highly heritable and has a strong polygenic character, however, studies examining the genetics of schizophrenia have not sufficiently explained all variability in its prevalence. Environmental causes are theorized to have a non trivial contribution to the pathoetiology of schizophrenia, including interactions with genetic components, but these mechanisms remain unclear. Analyzing schizophrenia dysfunction using transcriptomic approaches is a paradigm still in its infancy, and fewer studies still have examined non neurological contributions to schizophrenia pathology with next generation sequencing technologies. This pilot study uses several …

Efficient Reduced Bias Genetic Algorithm For Generic Community Detection Objectives, Aditya Karnam Gururaj Rao

Theses

The problem of community structure identification has been an extensively investigated area for biology, physics, social sciences, and computer science in recent years for studying the properties of networks representing complex relationships. Most traditional methods, such as K-means and hierarchical clustering, are based on the assumption that communities have spherical configurations. Lately, Genetic Algorithms (GA) are being utilized for efficient community detection without imposing sphericity. GAs are machine learning methods which mimic natural selection and scale with the complexity of the network. However, traditional GA approaches employ a representation method that dramatically increases the solution space to be searched by …

Development Of Multi-Class Analytical Methods For Agrochemical Contaminants, Sarah Tuck

Theses

In this project, cost-effective multi-class analytical methods were developed to detect a range of antiparasitic, feed additive and pesticide substances in foodstuffs of animal origin. These substances have the potential to enter the food chain through their occurrence as residues either through the animals themselves or other routes e.g. contamination. To ensure the continued safety of food destined for human consumption regulatory control limits have been established for permitted levels of these residues in foods of animal origin. Despite these controls the continued monitoring of foodstuffs is necessary to ensure these limits are not breached and that substances are not …

Predicting Energy And Water Consumption On Dairy Farms Through Statistical Analysis And Machine-Learning Methods, Philip Shine

Theses

With the abolishment of milking quotas across all European Union member states in April 2015, dairy farmers must adjust their farming practises to minimise milk production costs to adequately prepare for potential periods of reduced revenue. Milk production is an intense energy and water consuming process. Coupled with challenging European greenhouse gas reduction targets and legislation regarding the prevention of groundwater pollution and deterioration, increasing the production of milk in Ireland must be met with the sustainable consumption of on-farm energy and direct water resources, to ensure the future monetary and environmental sustainability of Ireland’s dairy industry. Thus, this body …

The Use Of Machine Learning To Detect Suckling In Pre-Weaned Calves, Sukumar Katamreddy

Theses

The weaning of cattle is a process which is known to be labour intensive and to have stressful effects on both cow and calf Common methods used in the weaning process include the temporary removal of a mother from the calf and manual observation and intervention. Early and speedy weaning is known to have a number of benefits, including health benefits for both cow and calf, additional weight gains for the calves as well as reduced labour and feed requirements. The process known as Two-Stage Weaning is recognised to be an effective low-stress approach to weaning in which the calf …

2-D Electrophoresis Modeling Of Multienzyme Cutting Of Polypeptides, Howard Mayes

Theses

2-Dimensional Electrophoresis is one of the tools in the identification of proteins by molecular weight and pH. The display of molecular weight allows the researcher to quickly identify whether a specific protein or peptide string is in the sample. The pH measurement allows even better resolution between different species in the sample. The MultiEnzyme ElectroPhoresis (MEEP) program tries to model that by providing a graph that displays separated protein strings by both molecular weight and pH. The ability to cleave the protein with 43 different enzyme variations allows the researcher to analyze appropriate enzymes to isolate a protein subsequence before …

Vertical And Cross-Shore Distributions Of Barnacle Larvae In La Jolla, Ca Nearshore Waters: Implications For Larval Transport Processes, Malloree Lynn Hagerty

Theses

Many marine organisms begin their lives as tiny larvae that are at the mercy of ocean currents. Understanding the transport and subsequent dispersal of larvae is crucial, as it drives population connectivity in the ocean. Larval transport is a complex process involving both physical motions of the water and larval behavior. Vertical positioning is especially important because currents vary throughout the water column, and larvae at different depths will be advected differently. With swimming speeds insufficient to swim against currents, marine larvae can mediate cross-shore transport by controlling their depth distributions. Thus, the overall objective of this study was to …

Rational Drug Design Directed At Blocking The Initial Signaling Events In Lipopolysaccharide-Induced Sepsis., Christopher A. Tipton

Theses

Systemic Inflammatory Response Syndrome (SIRS) is classified as an immune system response to an infectious state. If left untreated, SIRS leads to sepsis, septic shock, end-organ dysfunction, and death. As a patient progresses through these stages, associations of acute respiratory distress, disseminated intravascular coagulation, and acute renal failure persist, resulting in millions of deaths annually. Lipopolysaccharide (LPS), a bacterial endotoxin, is released into the blood stream, triggering SIRS. LPS is found in the outer cell-wall of Gram-negative bacteria and is responsible for initiation of a devastating cytokine storm. One of the regions of LPS, lipid A, is a polyacylated glucosamine …

Larval Rockfish Diversity Abundance Dynamics In Association With A Marine Protected Area In The Southern California Bight, Dustin Chen

Theses

Marine protected areas (MPAs) are areas aimed at protecting natural and cultural resources that are often proposed as a way to alleviate the effects of overfishing on populations of targeted species; these areas have varying degrees of fishing and recreational use restrictions. In order to assess MPA efficacy, it is important to determine the mechanisms by which the presence of MPAs affect reproductive output within and potentially even beyond their boundaries. I attempted to address this through studying the responses of rockfish (Sebastes spp.) larval abundances to the presence of the Cowcod Conservation Areas (CCAs) located within the Southern California …

Network Exploration Of Correlated Multivariate Protein Data For Alzheimer's Disease Association, Matthew J. Lane

Theses

Alzheimer Disease (AD) is difficult to diagnose by using genetic testing or other traditional methods. Unlike diseases with simple genetic risk components, there exists no single marker determining as to whether someone will develop AD. Furthermore, AD is highly heterogeneous and different subgroups of individuals develop the disease due to differing factors. Traditional diagnostic methods using perceivable cognitive deficiencies are often too little too late due to the brain having suffered damage from decades of disease progression. In order to observe AD at early stages prior to the observation of cognitive deficiencies, biomarkers with greater accuracy are required. By using …

Novel Neuroevolution Techniques For The Life Science Domain, Timothy Manning

Theses

The life science domain is a high value research area, both in terms of the benefits in increased knowledge and in societal impact. Much of the research funding has focused on wet lab based approaches to increase visibility into biological processes and producing maximal relevant information on which to make decisions. Given the complexity of biological functions, in many cases this has led to an information overload. Researchers are now able to routinely generate and access petabytes of data as a result of high throughput experiments, and this capability is growing. This data can be difficult to interpret and intractable …