Accurate Cytogenetic Biodosimetry Through Automated Dicentric Chromosome Curation And Metaphase Cell Selection, Jin Liu, Yanxin Li, Ruth Wilkins, Canadian Nuclear Laboratories, Joan H. Knoll, Peter Rogan
Accurate digital image analysis of abnormal microscopic structures relies on high quality images and on minimizing the rates of false positive (FP) and negative objects in images. Cytogenetic biodosimetry detects dicentric chromosomes (DCs) that arise from exposure to ionizing radiation, and determines radiation dose received based on DC frequency. Improvements in automated DC recognition increase the accuracy of dose estimates by reclassifying FP DCs as monocentric chromosomes or chromosome fragments. We also present image segmentation methods to rank high quality digital metaphase images and eliminate suboptimal metaphase cells. A set of chromosome morphology segmentation methods selectively filtered out FP DCs ...
Examining The Neuronal Dopaminergic Pathway Underlying Sleep Behavior And Related Dopamine Sleep Disorders, 2017 University of San Diego
Examining The Neuronal Dopaminergic Pathway Underlying Sleep Behavior And Related Dopamine Sleep Disorders, Mary Beth Putz
Undergraduate Honors Theses
The human brain is an extremely complex organ with approximately 100 billion different neurons that are constantly sending and receiving messages. These messages are sent using the chemical messengers of the brain: neurotransmitters and neuromodulators. Mechanisms of neural control of sleep are substantially conserved across species. Evidence from multiple animal models including flies, zebrafish, and mice shows that the arousal, or wake phase, is regulated by conserved neuromodulators such as dopamine, norepinephrine, and serotonin. Since these neurotransmitter systems are distributed throughout the brain and sub-serve many functions in addition to sleep, the precise circuit mechanisms by which these neurotransmitters regulate ...
Divergent Responses Of Larval And Juvenile Blue Mussels To Low Salinity Exposure, 2017 University of Maine
Divergent Responses Of Larval And Juvenile Blue Mussels To Low Salinity Exposure, Melissa A. May
Electronic Theses and Dissertations
In this study, we compared the osmotic stress response of larval and juvenile blue mussels (Mytilus edulis) at the transcriptomic, metabolomic, and whole organism levels. Blue mussels inhabit coastal areas, where they face climate-induced reductions in nearshore salinity. Despite their ecological and economic importance, scientists do not fully understand the underlying transcriptomic and cellular mechanisms of the osmotic stress response in blue mussels or how the ability to respond to stress changes throughout development. Blue mussels spend the first weeks of life developing through several larval stages in the plankton. These early life history stages are more vulnerable to environmental ...
Lymphoid Hematopoiesis And The Role Of B-Cells In Transgenic Mouse Model Of Sickle Cell Disease, 2017 University of Connecticut - Storrs
Lymphoid Hematopoiesis And The Role Of B-Cells In Transgenic Mouse Model Of Sickle Cell Disease, Christina Cotte
University Scholar Projects
Sickle cell disease (SCD) has been shown to be associated with decreased baseline immunity and thus increased susceptibility to infection. I sought to discern possible causes of this by looking into the correlations between SCD and hematopoiesis, the immune system and the neuroendocrine system, and ultimately by conducting experiments surrounding the impaired immune system of SCD. These experiments focused on the potential causes and effects of the diminution of B-1a cells in the SCD spleen. Adoptive transfers, infections with Streptococcus pneumoniae, and histologic imaging were conducted to establish if the diminution of the B-1a cells in the SCD spleen is ...
Ethical Consequences Of Full Human Genome Testing, 2017 Bond University
Ethical Consequences Of Full Human Genome Testing, Michael Lupton
Law Faculty Publications
A Genome is the entire set of hereditary instructions for building, running, maintaining an organism and passing on life to the next generation. A Genome is divided into chromosomes, the chromosomes contain genes and the genes are made of DNA. Genomes are found in cells; which are the microscopic structures that make up all organisms. With few exceptions, each of your body’s trillions of cells contains a copy of your genome. The human genome may be commonplace but it is quite powerful, because the information in the genome affects every aspect of a person’s behaviour and physiology. The ...
Genome Analysis Of Clostridium Difficile Pcr Ribotype 014 Lineage In Australian Pigs And Humans Reveals A Diverse Genetic Repertoire And Signatures Of Long-Range Interspecies Transmission, 2017 Edith Cowan University
Genome Analysis Of Clostridium Difficile Pcr Ribotype 014 Lineage In Australian Pigs And Humans Reveals A Diverse Genetic Repertoire And Signatures Of Long-Range Interspecies Transmission, Daniel R. Knight, Michael M. Squire, Deirdre A. Collins, Thomas V. Riley
ECU Publications Post 2013
Clostridium difficile PCR ribotype (RT) 014 is well-established in both human and porcine populations in Australia, raising the possibility that C. difficile infection (CDI) may have a zoonotic or foodborne etiology. Here, whole genome sequencing and high-resolution core genome phylogenetics were performed on a contemporaneous collection of 40 Australian RT014 isolates of human and porcine origin. Phylogenies based on MLST (7 loci, STs 2, 13, and 49) and core orthologous genes (1260 loci) showed clustering of human and porcine strains indicative of very recent shared ancestry. Core genome single nucleotide variant (SNV) analysis found 42% of human strains showed a ...
Phylogenomic Analysis Of Copepoda (Arthropoda, Crustacea) Reveals Unexpected Similarities With Earlier Proposed Morphological Phylogenies, 2017 University of Nebraska - Lincoln
Phylogenomic Analysis Of Copepoda (Arthropoda, Crustacea) Reveals Unexpected Similarities With Earlier Proposed Morphological Phylogenies, Seong-Il Eyun
Papers from the Nebraska Center for Biotechnology
Background: Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level.
Results: This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of ...
Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, 2017 SUNY Stony Brook
Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest
Interdisciplinary Research Data
To develop broadly useful methods for the genetic manipulation of Labyrinthulomycetes (a diverse group of ubiquitous osmoheterotrophic marine protists), it is essential to understand the similarities and differences in regulation of gene expression among them. Toward this end we have used FIMO from the MEME suite (http://meme-suite.org/doc/fimo.html) to identify potential transcription factor binding sites in each of the three available genome sequences: Aplanochytrium kerguelense PBS07, Schizochytrium aggregatum ATCC 28209, and Aurantiochytrium limacinum ATCC MYA-1381
Neutral And Adaptive Genetic Variation In North American Hardwood Tree Species, 2017 Michigan Technological University
Neutral And Adaptive Genetic Variation In North American Hardwood Tree Species, Sudhir Khodwekar
Dissertations, Master's Theses and Master's Reports
'Northern Hardwoods,’ are a characteristic composition of multiple tree species and a part of the rich and diverse northeastern forests. Hardwoods e.g. oaks (Quercus: Fagaceae and Sugar maple), serve as foundation species and offer ecological and economical gains to wildlife and humans. Most of the forest trees go through many biotic and abiotic stresses, for example climate change in their long life span. To overcome these threats and to adapt to changing conditions, tree species need to maintain variation especially in adaptive genes. Therefore, it is necessary to analyze genetic diversity within forest tree populations and take appropriate forest ...
Denatured: Emergent Realities Of Encyclopedic Dna Elements, 2017 Bard College
Denatured: Emergent Realities Of Encyclopedic Dna Elements, Amelia Leeya Goldstein
Senior Projects Spring 2017
The Human Genome Project was the center of much controversy in the 1990's, as creating a map of the human genome drew into question the boundaries between nature and nurture, or science and society. Fifteen years have now passed since the Human Genome Project's completion, and the new paradigm of genetics is no longer governed by a strict nature/nurture dualism. This project looks at one of the Human Genome Project's successors: the Encyclopedia of DNA Elements (ENCODE) project, which has created new boundaries and limitations in this new phase of genetic thinking. Using a frame analysis ...
K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, 2017 University of Montana
K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, Russell Kaehler
Graduate Student Theses, Dissertations, & Professional Papers
Biological sequence datasets are increasing at a prodigious rate. The volume of data in these datasets surpasses what is observed in many other fields of science. New developments wherein metagenomic DNA from complex bacterial communities is recovered and sequenced are producing a new kind of data known as metagenomic data, which is comprised of DNA fragments from many genomes. Developing a utility to analyze such metagenomic data and predict the sample class from which it originated has many possible implications for ecological and medical applications. Within this document is a description of a series of analytical techniques used to process ...
Male Facial Appearance And Offspring Mortality In Two Traditional Societies, 2017 University of Durham
Male Facial Appearance And Offspring Mortality In Two Traditional Societies, Lynda G Boothroyd, Alan W Gray, Thomas N Headland, Ray T Uehara, David Waynforth, D Michael Burt, Nicholas Pound
Faculty of Health Sciences & Medicine Publications
It has been hypothesised that facial traits such as masculinity and a healthy appearance may indicate heritable qualities in males (e.g. immunocompetence) and that, consequently, female preferences for such traits may function to increase offspring viability and health. However, the putative link between paternal facial features and offspring health has not previously been tested empirically in humans. Here we present data from two traditional societies with little or no access to modern medicine and family planning technologies. Data on offspring number and offspring survival were analysed for the Agta of the Philippines and the Maya of Belize, and archive ...
Exploring Molecular Mechanisms Of Paradoxical Activation In The Braf Kinase Dimers: Atomistic Simulations Of Conformational Dynamics And Modeling Of Allosteric Communication Networks And Signaling Pathways, 2016 Chapman University
Exploring Molecular Mechanisms Of Paradoxical Activation In The Braf Kinase Dimers: Atomistic Simulations Of Conformational Dynamics And Modeling Of Allosteric Communication Networks And Signaling Pathways, Amanda Tse, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We ...
Genetic Contamination Of Traditional Products, 2016 Iowa State University
Genetic Contamination Of Traditional Products, E. Kwan Choi
E. Kwan Choi
Cross-pollination can be caused by birds, insects and wind. Genetically modified (GM) seeds are produced each year in a controlled environment to maintain their purity. However, pollen from the GM crop can be transferred to traditional crops. When the GM crop producers are in long-run equilibrium and buy seeds from a monopolistic seed producer, the resulting market equilibrium is identical to that when a seed monopolist produces the GM crop directly. When involuntary genetic contamination occurs, the monopolist eventually loses its advantage and stops its protection of GM seeds. A terminator gene can stop genetic contamination but imposes spillover costs ...
Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, 2016 California State University, Chico
Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots
STAR (STEM Teacher and Researcher) Presentations
The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few ...
Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, 2016 University of Nebraska-Lincoln
Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James Van Etten, Kenneth Nickerson
Kenneth Nickerson Papers
Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and ...
Genetic Analysis Reveals A Hierarchy Of Interactions Between Polycystin-Encoding Genes And Genes Controlling Cilia Function During Left-Right Determination, Daniel T. Grimes, Jennifer L. Keynton, Maria T. Buenavista, Xingjian Jin, Saloni H. Patel, Shinohara Kyosuke, Jennifer Vibert, Debbie J. Williams, Hiroshi Hamada, Rohana Hussain, Surya M. Nauli, Dominic P. Norris
Pharmacy Faculty Articles and Research
During mammalian development, left-right (L-R) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This ‘nodal flow’ is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca2+ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM). Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we ...
The Role Of Daf-19 In Non-Ciliated Neurons: How Is Neural Development Regulated By Different Daf-19 Isoforms?, Zabdiel Ek Vazquez
Lawrence University Honors Projects
A degenerative disease-like phenotype, specifically reduction in synaptic protein levels in adult worms, is correlated with loss-of-function of the only RFX transcription factor gene, daf-19, in C. elegans. This gene encodes four known transcription factor isoforms, two of which are correlated with particular functions. The DAF-19C isoform activates genes responsible for cilia development, while DAF-19M is needed for cilia specification in males. A comparison of the transcriptome of daf-19 null and isogenic wild type adult worms suggests both positive and negative regulation of gene expression is correlated with the presence of DAF-19 proteins. We have assessed DAF-19 regulation of gene ...
Identification Of Qtls For Resistance Against Rhizoctonia Solani And Phoma Glycinicola In Soybeans (Glycine Max L. Merr), 2016 University of Nebraska-Lincoln
Identification Of Qtls For Resistance Against Rhizoctonia Solani And Phoma Glycinicola In Soybeans (Glycine Max L. Merr), Herbert Sserunkuma
Theses, Dissertations, and Student Research in Agronomy and Horticulture
A QTL (Quantitative trait locus) is a chromosome location of a gene controlling a specific phenotypic trait. The trait maybe governed by multiple genes. Fungal pathogens are responsible for over 50% of all soybean diseases. Rhizoctonia solani Kühn causes seedling dumping off, root and hypocotyl rots and other disease in soybeans. Phoma glycinicola de Gruyter & Boerema causes Red leaf blotch disease, predominantly in Sub-Saharan Africa. There is no reported complete resistance against these fungal pathogens in soybeans. Reaction to R.solani is reportedly a quantitative trait controlled by major and minor genes. Three QTLs contributing to reaction to R. solani ...
The Effects Of Epigenetics On Stress Response, 2016 San Jose State University
The Effects Of Epigenetics On Stress Response, Kevin Suddarth
Themis: Research Journal of Justice Studies and Forensic Science
Despite the vast amount of resources at the disposal of humanity today, the intricacies of human biology are often a mystery. The chemical and biological products of the human genome have been well studied and documented, but many of the chemical and neurological pathways are missing quite a few details. The human stress response is one of the most primal and valuable functions of this code that developed as a self- preservation mechanism (Hans, 1975) to naturally increase the odds of procreation. However, this function is prone to overload, particularly in individuals with certain epigenetic traits instilled by early life ...