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Doctoral Dissertations

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Metabolic Cost And Stability Of Locomotion In People With Lower Limb Amputation, Ryan Wedge Jan 2019

Metabolic Cost And Stability Of Locomotion In People With Lower Limb Amputation, Ryan Wedge

Doctoral Dissertations

It is generally accepted that metabolic energy expenditure and gait stability are key factors that influence the selection of able-bodied locomotor patterns. It is unclear how energy expenditure and gait stability are prioritized during walking in people with lower limb amputation. People with lower limb amputation generally have greater metabolic energy expenditure during walking and increased incidence of falls. People with unilateral lower limb amputation spend more time on the intact limb compared with the prosthetic limb, while able-bodied individuals generally walk with symmetrical timing between limbs. Restoring symmetry is often a goal of rehabilitation and assistive devices, yet the ...


Chemoreceptor Dynamics And Signaling: Nmr Measurements Within Functional Complexes, Maryam Kashefi Jan 2019

Chemoreceptor Dynamics And Signaling: Nmr Measurements Within Functional Complexes, Maryam Kashefi

Doctoral Dissertations

Bacteria employ remarkable membrane-bound nanoarrays to sense their environment and direct their swimming. Arrays consist of chemotaxis receptor trimers of dimers that are bridged at their membrane-distal tips by rings of two cytoplasmic proteins, a kinase CheA and a coupling protein CheW. It is widely accepted that ligand binding to the receptor causes a 2 Å piston motion of a helix that extends through the periplasmic and transmembrane domains. However, it is not clear how the signal propagates 200 Å further to control activity of the kinase bound at the tip of the receptor. Dynamic changes within the cytoplasmic domain ...


Feasibility And Efficacy Of A Recess-Based Combined Fitness Intervention On Cognition And Academic Performance In Elementary School Children, Christine St Laurent Jan 2019

Feasibility And Efficacy Of A Recess-Based Combined Fitness Intervention On Cognition And Academic Performance In Elementary School Children, Christine St Laurent

Doctoral Dissertations

Youth physical activity and fitness have been reported to influence cognition and academic related outcomes. Despite the potential benefits of muscular fitness, few intervention studies have examined the impact of an intervention that has incorporated both cardiorespiratory and muscular fitness training on cognition and academic performance in children. Previous studies have mainly been implemented either during the school day or immediately after-school. Although recess may be an ideal time to promote physical activity because it does not compete with other academic demands, it has been an understudied setting. Therefore, the purpose of this dissertation project was to examine the feasibility ...


Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold Jan 2019

Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold

Doctoral Dissertations

Soils serve as massive carbon sinks, but their ability to continue this ecological service is contingent on how the resident soil microbial community will respond to the ongoing climate crisis. One key dimension of the microbial response to warming is its carbon use efficiency (CUE), or the fraction of carbon taken up by an organism which is allocated to growth rather than respiration. However, the scientific community is still in the early stages of understanding the drivers, consequences - and even accurate measurements of - CUE. In this dissertation, I first quantified the variability of CUE and its responsiveness to temperature and ...


Silver Mirror Substrate And Rolling Method For Improved Surface-Enhanced Raman Spesctroscopic Analysis In Food, Yanqi Qu Jan 2019

Silver Mirror Substrate And Rolling Method For Improved Surface-Enhanced Raman Spesctroscopic Analysis In Food, Yanqi Qu

Doctoral Dissertations

Surface-enhanced Raman spectroscopy, short for SERS, is an emerging technology with great potential in food analysis due to rapid detection, high sensitivity, portable instrumentation, and simple sample preparation. However, it is always a bottleneck to obtain reproducible SERS measurements in real analytical cases due to the complicity of food systems and inhomogeneous aggregation of colloidal nanoparticles. To improve its performance for practical applications in food analysis, efforts have been made in improving the reproducibility, enhancing the selectivity and reducing the matrix interference to the analyte. Herein, a self-assembly silver nanoparticles mirror substrate was fabricated to improve the and the quantitative ...


Factors Influencing Spartina Alterniflora Productivity In Relationship To Estuary Inlet Opening Ellisville Marsh, Plymouth, Ma, Ellen K. Russell Jan 2019

Factors Influencing Spartina Alterniflora Productivity In Relationship To Estuary Inlet Opening Ellisville Marsh, Plymouth, Ma, Ellen K. Russell

Doctoral Dissertations

A scientific basis for understanding the health of salt marsh vegetation, primarily Spartina alterniflora, in apposition to dredging of the tidal inlet to Ellisville Marsh in Plymouth, Massachusetts was determined. A three-hectare S. alterniflora loss, and coincident coastal bank erosion occurred; ostensibly due to inlet blockage from sand deposition, prolonged inundation, and meandering of inlet channel into coastal bank. This warranted dredging the tidal inlet, whereby tidal flushing would restore growth or discontinue die-off, and deter coastal bank erosion. A pre- and post dredge study was conducted assessing environmental factors related to plant productivity. Following dredging, an increase in tidal ...


Multiscale Simulations Of Intrinsically Disordered Proteins, Xiaorong Liu Jan 2019

Multiscale Simulations Of Intrinsically Disordered Proteins, Xiaorong Liu

Doctoral Dissertations

Intrinsically disordered proteins (IDPs) lack stable secondary and/or tertiary structures under physiological conditions. The have now been recognized to play important roles in numerous biological processes, particularly cellular signaling and regulation. Mutation of IDPs are frequently associated with human diseases, such as cancers and neuron degenerative diseases. Therefore, it is important to understand the structure, dynamics, and interactions of IDPs, so as to establish the mechanistic basis of how intrinsic disorder mediates versatile functions and how such mechanisms may fail in human diseases. However, the heterogeneous structural ensembles of IDPs are not amenable to high resolution characterization solely through ...


Physical And Biological Drivers Of Juvenile Fish Distributions In Unstructured Shallow Tropical Nearshore Habitats, Christopher Haak Jan 2019

Physical And Biological Drivers Of Juvenile Fish Distributions In Unstructured Shallow Tropical Nearshore Habitats, Christopher Haak

Doctoral Dissertations

The structural complexity of aquatic habitats can influence the ecological processes that occur within them, as fine-scale topographic features act as refugia for small fishes, buffering the effects of environmental stressors. Accordingly, the habitat requirements of juvenile demersal fishes in shallow littoral zones are often defined by their associations with distinct benthic microhabitats, such as densely vegetated substrates. However, an array of ecologically-important juvenile fishes also associate with topographically-homogeneous, sparsely-vegetated substrata. Absent the benefits offered by structural refugia, such fishes may be more affected by environmental variability and may have evolved distinct strategies for coping with stressors. I examined this ...


Population Viability And Connectivity Of The Federally Threatened Eastern Indigo Snake In Central Peninsular Florida, Javan Bauder Jan 2019

Population Viability And Connectivity Of The Federally Threatened Eastern Indigo Snake In Central Peninsular Florida, Javan Bauder

Doctoral Dissertations

Understanding the factors influencing the likelihood of persistence of real-world populations requires both an accurate understanding of the traits and behaviors of individuals within those populations (e.g., movement, habitat selection, survival, fecundity, dispersal) but also an understanding of how those traits and behaviors are influenced by landscape features. The federally threatened eastern indigo snake (EIS, Drymarchon couperi) has declined throughout its range primarily due to anthropogenically-induced habitat loss and fragmentation making spatially-explicit assessments of population viability and connectivity essential for understanding its current status and directing future conservation efforts.

The primary goal of my dissertation was to understand how ...


Nascent Dna Proteomics Analysis Uncovers Dna Replication Dynamics In The Human Pathogen Trypanosoma Brucei, Maria Rocha Granados Jan 2019

Nascent Dna Proteomics Analysis Uncovers Dna Replication Dynamics In The Human Pathogen Trypanosoma Brucei, Maria Rocha Granados

Doctoral Dissertations

DNA is the substrate of many cellular processes including DNA replication, transcription and chromatin remodeling. These processes are coordinated to maintain genome integrity and ensure accurate duplication of genetic and epigenetic information. Genome-wide studies have provided evidence of the relationship between transcription and DNA replication timing. A global analysis of DNA replication initiation in T. brucei showed that TbORC1 (subunit of the origin recognition complex, ORC) binding sites are located at the boundaries of transcription units. Although recent studies in T. brucei indicate functional links among DNA replication and transcription, the underlying mechanisms remain unknown. In this study, we adapted ...


Small Fruit Phenolics: Phenolic Variations And Related Health Relevance, Susan Cheplick Jan 2019

Small Fruit Phenolics: Phenolic Variations And Related Health Relevance, Susan Cheplick

Doctoral Dissertations

Berries, specifically, strawberries, raspberries, blackberries, and blueberries, are considered an integral part of a healthy plant-based diet. Berries contain high levels of phenolic compounds, which contribute to the health benefits of berry consumption. Many phenolic compounds exhibit high levels of antioxidant activity and other health related benefits, including anti- microbial, anti-inflammatory and cardio-vascular related functional capabilities.

Strawberry and raspberry fruit were screened and evaluated for potential in dietary management of type 2 diabetes and related hypertension using in vitro assay models. There were differences between cultivars within each crop related to antioxidant activity. Inhibition of α- amylase, α-glucosidase, and ACE-1 ...


The Spatial Organization Of Mycobacterial Membrane, Julia Puffal Jan 2019

The Spatial Organization Of Mycobacterial Membrane, Julia Puffal

Doctoral Dissertations

Mycobacteria comprises a large group of organisms including the pathogenic species Mycobacterium tuberculosis, the causative agent of tuberculosis. A fast- growing saprophytic member of this genus, however, Mycobacterium smegmatis, is oftentimes used as a model organism for the pathogenic species. With a unique cell envelope architecture and unconventional polar growth, spatial coordination of cell envelope biosynthesis is vital for proper assembly of this complex structure. Here, we provide a comprehensive overview of known lateral heterogeneities in mycobacterial plasma membrane, with a particular focus on the intracellular membrane domain (IMD), a spatially distinct region of the plasma membrane with diverse functions ...


Acute Estrogen Synthesis And Action In The Auditory Cortex Of Developing Male Zebra Finches (Taeniopygia Guttata), Daniel Vahaba Jan 2019

Acute Estrogen Synthesis And Action In The Auditory Cortex Of Developing Male Zebra Finches (Taeniopygia Guttata), Daniel Vahaba

Doctoral Dissertations

Birdsong, as with human speech, is learned during an age- and experience-dependent sensitive period early in life. Songbirds must first memorize their parents’ song during a sensory phase, then refine their own burgeoning vocalizations to match the auditory memory of their parents’ song during a sensorimotor phase. While the error-correction aspect of the sensorimotor phase of song learning is comparatively well understood, it is largely unknown how auditory memories are formed and how auditory processing may change across development to facilitate song memorization. The songbird caudomedial nidopallium (NCM) is a brain region that encodes complex communication signals like song and ...


Walking For Object Transport: An Examination Of The Coordinative Adaptations To Locomotor, Perceptual, And Manual Task Constraints, Avelino Amado Jan 2019

Walking For Object Transport: An Examination Of The Coordinative Adaptations To Locomotor, Perceptual, And Manual Task Constraints, Avelino Amado

Doctoral Dissertations

The goal of this dissertation was to understand how the intrinsic dynamics of gait adapt to support the performance of an ecologically relevant object transport task. A common object transport task is walking with a cup of water. Because the water can move relatively independent of the cup, the cup and water system is classified as a complex object. To model this task participants carried a cup with a wooden lid placed on top. On the lid there was a circular region with the same circumference as the cup and a ball. The object of the task was to keep ...


Effects Of Fertilization And Drying Conditions On The Quality Of Selected Chinese Medicinal Plants, Zoe Gardner Jan 2019

Effects Of Fertilization And Drying Conditions On The Quality Of Selected Chinese Medicinal Plants, Zoe Gardner

Doctoral Dissertations

Demand for Chinese medicinal herbs in the U.S. is increasing and American acupuncturists and farmers are interested in domestic production of these plants. Little is known about the feasibility of production of these species outside of China. Four species of herbs were selected for cultivation trials. The purposes of this research were to evaluate the feasibility of cultivation of these species in the northeastern United States, to develop basic agronomic data for each species, and to determine the effects of nitrogen fertilizer on plant growth, yield, and secondary metabolites. Agastache rugosa, Schizonepeta tenuifolia, Leonurus japonicus, and Leonurus sibiricus were ...


Cytochrome P450 Monooxygenase-Mediated Lipid Metabolism In Obesity And Colon Tumorigenesis, Weicang Wang Jan 2019

Cytochrome P450 Monooxygenase-Mediated Lipid Metabolism In Obesity And Colon Tumorigenesis, Weicang Wang

Doctoral Dissertations

Colon cancer is a major public health issue: it is expected to have 140,250 new cases and 50,630 deaths during 2018, making colon cancer the third most common type of cancer and the second leading cause of cancer death in the United States. Obesity is associated with enhanced colonic inflammation, which is a major risk factor of colorectal cancer. Currently, more than 35% of adults and nearly 17% of children are obese. Considering the obesity and colon cancer epidemic in the United States, there is an urgent need to identify novel therapeutic targets for obesity and colon cancer ...


Protein Degradation Regulates Phospholipid Biosynthetic Gene Expression In Saccharomyces Cerevisiae, Bryan Salas-Santiago Jan 2019

Protein Degradation Regulates Phospholipid Biosynthetic Gene Expression In Saccharomyces Cerevisiae, Bryan Salas-Santiago

Doctoral Dissertations

Transcriptional regulation of most phospholipid biosynthetic genes in Saccharomyces cerevisiae is coordinated by inositol and choline. Inositol affects phosphatidic acid (PA) intracellular levels. Opi1p interacts physically with PA and is the main repressor of the phospholipid biosynthetic genes. It is localized in the endoplasmic reticulum (ER) bound to the ER membrane protein Scs2p. When PA levels drop, Opi1p is translocated into the nucleus repressing most phospholipid biosynthetic genes. The OPI1 locus was identified in a screen looking for overproduction and excretion of inositol (Opi-). Opi- mutants are generally associated with a defect in repression of the ...


Determining Kinetic Parameters Of Thiamine Degradation In Three Nasa Spaceflight Foods In Thermal Processing And Long-Term Storage And Methods For Analyzing Microstructure And Precipitant Development In Real And Model Wines, Timothy R. Goulette Jan 2019

Determining Kinetic Parameters Of Thiamine Degradation In Three Nasa Spaceflight Foods In Thermal Processing And Long-Term Storage And Methods For Analyzing Microstructure And Precipitant Development In Real And Model Wines, Timothy R. Goulette

Doctoral Dissertations

The current NASA spaceflight food program encompasses a wide variety of commercial and custom-made edible products. These foods are designed to ensure each crewmember receives the Recommended Dietary Allowance (RDA) of vitamins and minerals to maintain adequate health during the entire spaceflight mission. With the desire for long-duration and exploration-class missions, such as the impending mission to Mars, the retention of important nutrients such as labile vitamins in spaceflight foods is critically important. For this reason, multiple studies were conducted to determine the vitamin degradation behavior of thiamine (vitamin B1) within three spaceflight foods which demonstrated both significant presence ...


Ecology Of The Elusive: Genome-Informed Investigation Of Soil Microbial Diversity, Lauren Alteio Jan 2019

Ecology Of The Elusive: Genome-Informed Investigation Of Soil Microbial Diversity, Lauren Alteio

Doctoral Dissertations

Soil is considered one of the most diverse ecosystems on Earth, harboring diversity of organisms across the three domains of life. It is spatially and chemically heterogeneous: properties that intertwine in a complex matrix to support organismal diversity and function across different scales. Soil microorganisms both respond to and drive changes in ecosystems through metabolic activities. A single gram of soil is teeming with millions of cells comprised of thousands of species. Much of this diversity remains uncharacterized due to technical and methodological challenges faced by soil ecologists. Due to the complex physicochemical properties of soil and cross-feeding interactions between ...


Multi-Level Barriers To Art Adherence Among Hiv-Infected Women In Rural Eswatini: A Mixed Methods Approach, Nozipho Becker Jan 2019

Multi-Level Barriers To Art Adherence Among Hiv-Infected Women In Rural Eswatini: A Mixed Methods Approach, Nozipho Becker

Doctoral Dissertations

Eswatini has the highest global prevalence of HIV despite universal access to free treatment. Lack of compliance continues to be a significant challenge for HIV care and management programs throughout the country. Studies investigating barriers to antiretroviral therapy (ART) adherence, particularly in women, who are the most vulnerable to HIV infections, are limited. The disproportionate impact of HIV on women can be attributed to multiple risk factors at the individual, household, and community/structural levels. Women living in rural settings are particularly at risk as a result of socio-cultural and environmental vulnerabilities such as oppressive traditional practices, intimate partner violence ...


Improving Chinese Mothers’ Health Literacy: A Wechat Intervention, Qiong Chen Jan 2019

Improving Chinese Mothers’ Health Literacy: A Wechat Intervention, Qiong Chen

Doctoral Dissertations

The health literacy and eHealth literacy of women during the reproductive age is crucial, as it can affect their health and the health of their children. Promoting health literacy is essential to achieve mothers’ empowerment by improving access to and capacity of using health information effectively. However, functional, interactive, and critical health literacy and eHealth literacy have never been assessed among Chinese women.

The first study during this dissertation assessed functional, interactive, and critical health literacy and eHealth literacy among 421 of Chinese mothers with children under 3 years old. The results revealed overall less than optimal level of health ...


Function And Dissipation In Finite State Automata - From Computing To Intelligence And Back, Natesh Ganesh Jan 2019

Function And Dissipation In Finite State Automata - From Computing To Intelligence And Back, Natesh Ganesh

Doctoral Dissertations

Society has benefited from the technological revolution and the tremendous growth in computing powered by Moore's law. However, we are fast approaching the ultimate physical limits in terms of both device sizes and the associated energy dissipation. It is important to characterize these limits in a physically grounded and implementation-agnostic manner, in order to capture the fundamental energy dissipation costs associated with performing computing operations with classical information in nano-scale quantum systems. It is also necessary to identify and understand the effect of quantum in-distinguishability, noise, and device variability on these dissipation limits. Identifying these parameters is crucial to ...


Protein Detection And Structural Characterization By Mass Spectrometry Using Supramolecular Assemblies And Small Molecules, Bo Zhao Jan 2019

Protein Detection And Structural Characterization By Mass Spectrometry Using Supramolecular Assemblies And Small Molecules, Bo Zhao

Doctoral Dissertations

Mass spectrometry (MS) has played an increasingly prominent role in proteomics and structure biology because it shows superior capabilities in identification, quantification and structural characterization of proteins. To realize its full potential in protein analysis, significant progress has been made in developing innovative techniques and reagents that can couple to MS detection. This dissertation demonstrates the use of polymeric supramolecular assemblies for enhanced protein detection in complex biological mixtures by MS. An amphiphilic random co-polymer scaffold is developed to form functional supramolecular assemblies for protein/ peptide enrichment. The influences of charge density and functional group pKa on host-guest interactions ...


Spatiotemporal Modeling And Model Restructuration Approaches In Studies Of Intracellular Signalling Pathways, Md Shahinuzzaman Jan 2019

Spatiotemporal Modeling And Model Restructuration Approaches In Studies Of Intracellular Signalling Pathways, Md Shahinuzzaman

Doctoral Dissertations

"The main focus of the research is to understand the complex phenomena of cell transduction pathways and cell biology in a single cell. Mathematical modeling and experimental evaluation are widely used approaches for this kind of research. Firstly, A multiscale framework for protein-protein interaction has been established using Brownian dynamics algorithm. Sit specific feature, steric collision, diffusion, co-localization and complex formation with time and space has been included in this spatial modeling framework. By implementation of the time adaptive feature in this framework, the computation time reduces in an order of magnitude compared with traditional modeling framework. This multiscale Brownian ...


Engineered Coating Of Natural Fibers And Oil-Water Interfaces With Self-Assembly Of Clay Nanotubes, Abhishek Panchal Nov 2018

Engineered Coating Of Natural Fibers And Oil-Water Interfaces With Self-Assembly Of Clay Nanotubes, Abhishek Panchal

Doctoral Dissertations

Taking into consideration two different types of surfaces, this dissertation proposes techniques to coat the surface of natural fibers and oil-water interfaces by spontaneous self-assembly of halloysite clay nanotubes. The material of choice, halloysite clay, is a widely available natural resource and can be used after minimal processing. In regards to chemical composition, halloysite clay resembles aluminosilicate mineral kaolin; physically, a defect in the crystal structure ordering causes the sheets of kaolinite to roll into halloysite nanotubes. The dimensions of halloysite nanotubes are dependent on the source, but generally vary from 200 nm to 3 µm in length, 100-150 nm ...


The Interplay Between Polarity Regulators, Calcium, And The Actin Cytoskeleton During Tip Growth, Carlisle Bascom Jr Jan 2018

The Interplay Between Polarity Regulators, Calcium, And The Actin Cytoskeleton During Tip Growth, Carlisle Bascom Jr

Doctoral Dissertations

Plant cell growth is a meticulously regulated process whereby the cell wall is selectively loosened to allow for turgor-pressure driven expansion. The rate of expansion must equal delivery of new material, or the cell will lyse. In many plant cells, this process happens diffusely around the cell. However, a number of plant cells have anisotropic shapes that require exquisite spatial control of secretion. One simple example of anisotropic patterning is tip growth; highly polarized cell expansion utilized by pollen tubes, root hairs, and moss protonemata. Investigating the role various molecules have in tip growth sheds light on how plant cells ...


Integration Of Robotic Perception, Action, And Memory, Li Yang Ku Jan 2018

Integration Of Robotic Perception, Action, And Memory, Li Yang Ku

Doctoral Dissertations

In the book "On Intelligence", Hawkins states that intelligence should be measured by the capacity to memorize and predict patterns. I further suggest that the ability to predict action consequences based on perception and memory is essential for robots to demonstrate intelligent behaviors in unstructured environments. However, traditional approaches generally represent action and perception separately---as computer vision modules that recognize objects and as planners that execute actions based on labels and poses. I propose here a more integrated approach where action and perception are combined in a memory model, in which a sequence of actions can be planned based on ...


Dissecting Regulatory Mechanisms Of Coma-Dependent And Coma-Independent Quorum Sensing Pathways In Bacillus Subtilis, Emily Roy Jan 2018

Dissecting Regulatory Mechanisms Of Coma-Dependent And Coma-Independent Quorum Sensing Pathways In Bacillus Subtilis, Emily Roy

Doctoral Dissertations

Virtually all living organisms are capable of sensing individuals within a population and communicating amongst themselves to coordinate group behavior. This group coordination holds true for all living organisms, from multi-cellular organisms like humans down to the single-celled microbes including bacteria. In order to survive in everchanging environments, bacteria have developed strategies to determine their current surroundings and communicate with individuals in the population to respond to environmental changes. Bacteria have many different forms of communication similar to the many different human languages. These signals are used to coordinate a variety of biological processes in a density-dependent manner in a ...


Structure-Property Relationships Of Polymer Films And Hydrogels To Control Bacterial Adhesion, Kristopher W. Kolewe Jan 2018

Structure-Property Relationships Of Polymer Films And Hydrogels To Control Bacterial Adhesion, Kristopher W. Kolewe

Doctoral Dissertations

The emergence and spread of antibiotic resistance across microbial species necessitates the need for alternative approaches to mitigate the risk of infection without relying on commercial antibiotics. Biofilm-related infections are a class of notoriously difficult to treat healthcare-associated infections that frequently develop on the surface of implanted medical devices. As biofilm formation is a surface-associated phenomenon, understanding how the intrinsic properties of materials affect bacterial adhesion enables the development of structure-property relationships that can guide the future design of infection-resistant materials. Despite lacking visual, auditory, and olfactory perception, bacteria still manage to sense and attach to surfaces. Previously, it has ...


Impacts Of Genome And Nuclear Architecture On Molecular Evolution In Eukaryotes, Xyrus Maurer-Alcalá Jan 2018

Impacts Of Genome And Nuclear Architecture On Molecular Evolution In Eukaryotes, Xyrus Maurer-Alcalá

Doctoral Dissertations

The traditional view of genomes suggests that they are static entities changing slowly in sequence and structure through time (e.g. evolving over geological time-scales). This outdated view has been challenged as our understanding of the dynamic nature of genomes has increased. Changes in DNA content (i.e. polyploidy) are common to specific life-cycle stages in a variety of eukaryotes, as are changes in genome content itself. These dramatic genomic changes include chromosomal deletions (i.e. paternal chromosome deletion in insects; Goday and Esteban 2001; Ross, et al. 2010), developmentally regulated genome rearrangements (e.g. the V(D)J system ...