Effects Of Proline And Glycine On The Cnidocyte Discharge Of Hydra Magnipapillata, 2015 University of New Hampshire
Effects Of Proline And Glycine On The Cnidocyte Discharge Of Hydra Magnipapillata, Janine R. Appleton
Honors Theses and Capstones
The sense of taste enables animals to utilize environmental cues to detect favorable foods. Through specialized sensory receptors, Cnidarians employ stinging cells called cnidocytes to perform a variety of activities such as locomotion, capturing prey, inducing of feeding responses, and defense. Their discharge is highly regulated by mechanical and chemical signals that are mediated by a complex system including the opsin and taste pathways. Taste 1 Receptors (T1R) have previously been isolated in vertebrates but only until recently, have been noted in invertebrates. Receptors specific to L- amino acids corresponding to the taste sensation of umami, were studied to determine …
Primer Efficacy In The Dna Barcoding Of Spiders, 2015 University of Northern Iowa
Primer Efficacy In The Dna Barcoding Of Spiders, Rhennetta Jo Bork
Honors Program Theses
DNA barcoding is the process of amplifying a 650 base pair segment of the sequence of the mitochondrial gene cytochrome c oxidase (COI), and amplifying this gene with a polymerase chain reaction (PCR). It is used to help identify and distinguish animal species and also to help determine genetic differences in species. DNA barcoding can be especially useful when working with spiders since they tend to be very small and hard to distinguish. However, achieving a DNA barcode can be difficult and thus techniques to improve the method of DNA barcoding can be helpful. This research looked into the different …
Developing A Gene Editing System To Study Haplodiploidy In The Jewel Wasp, Nasonia Vitripennis, 2015 Scripps College
Developing A Gene Editing System To Study Haplodiploidy In The Jewel Wasp, Nasonia Vitripennis, Emily A. Muller
Scripps Senior Theses
Hymenopteran insects, which include all ants, bees and wasps, reproduce through a poorly understood form of reproduction known as haplodiploidy. A promising experimental system for understanding this developmental process is the jewel wasp, Nasonia vitripennis. A critical aspect of using Nasonia as a model is establishing an effective means for editing specific genes of interest so that their functions can be studied through genetic means. For my thesis research, I performed a pilot study of the gene editing method known as CRISPR in Nasonia. I targeted the single heterochromatin protein 1 (HP1) gene present in the Nasonia genome …
High-Throughput Comparison, Functional Annotation, And Metabolic Modeling Of Plant Genomes Using The Plantseed Resource, 2015 University of Chicago
High-Throughput Comparison, Functional Annotation, And Metabolic Modeling Of Plant Genomes Using The Plantseed Resource, Samuel M. D. Seaver, Svetlana Gerdes, Océane Frelin, Claudia Lerma-Ortiz, Louis M. T. Bradbury, Rémi Zallot, Ghulam Hasnain, Thomas D. Niehaus, Basma El Yacoubi, Shiran Pasternak, Robert Olson, Gordon Pusch, Ross Overbeek, Valérie De Crécy-Lagarde, Doreen Ware, Andrew D. Hanson, Christopher S. Henry
Publications and Research
There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and …
Genetically Based Low Oxygen Affinities Of Felid Hemoglobins: Lack Of Biochemical Adaptation To High-Altitude Hypoxia In The Snow Leopard, 2015 Duquesne University, Pittsburgh
Genetically Based Low Oxygen Affinities Of Felid Hemoglobins: Lack Of Biochemical Adaptation To High-Altitude Hypoxia In The Snow Leopard, Jan E. Janecka, Simone S. E. Nielsen, Sidsel D. Andersen, Federico G. Hoffmann, Roy E. Weber, Trevor Anderson, Jay F. Storz, Angela Fago
School of Biological Sciences: Faculty Publications
Genetically based modifications of hemoglobin (Hb) function that increase blood–O2 affinity are hallmarks of hypoxia adaptation in vertebrates. Among mammals, felid Hbs are unusual in that they have low intrinsic O2 affinities and reduced sensitivities to the allosteric cofactor 2,3-diphosphoglycerate (DPG). This combination of features compromises the acclimatization capacity of blood–O2 affinity and has led to the hypothesis that felids have a restricted physiological niche breadth relative to other mammals. In seeming defiance of this conjecture, the snow leopard (Panthera uncia) has an extraordinarily broad elevational distribution and occurs at elevations above 6000 m in the Himalayas. Here, …
Smoking Patterns Among Vcu Students, 2015 Virginia Commonwealth University
Smoking Patterns Among Vcu Students, Jasmine Saini
Undergraduate Research Posters
For some individuals, college can be a high risk time for the development of problems associated with alcohol use and other substances. The purpose of this study is to examine these initiation and use patterns as they relate to nicotine use among college students 18 years of age and older enrolled in Spit for Science: The VCU Student Survey. The Spit for Science research project evaluates how genetic and environmental factors contribute to substance use and emotional health among college students at VCU. This study uses data from the Spit for Science 2011 cohort (n=2007) to investigate smoking patterns among …
Cellular Defects Caused By Hypomorphic Variants Of The Bloom Syndrome Helicase Gene Blm, 2015 University of South Florida
Cellular Defects Caused By Hypomorphic Variants Of The Bloom Syndrome Helicase Gene Blm, Vivek M. Shastri, Kristina H. Schmidt
Molecular Biosciences Faculty Publications
BACKGROUND: Bloom syndrome is an autosomal recessive disorder characterized by extraordinary cancer incidence early in life and an average life expectancy of ~27 years. Premature stop codons in BLM, which encodes a DNA helicase that functions in DNA double-strand-break repair, make up the vast majority of Bloom syndrome mutations, with only 13 single amino acid changes identified in the syndrome. Sequencing projects have identified nearly one hundred single nucleotide variants in BLM that cause amino acid changes of uncertain significance.
METHODS AND RESULTS: Here, in addition to identifying five BLM variants incapable of complementing certain defects of Bloom syndrome cells, …
Altered Fire Regimes And The Persistence Of Quaking Aspen In The Rocky Mountains: A Literature Review, 2015 Utah State University
Altered Fire Regimes And The Persistence Of Quaking Aspen In The Rocky Mountains: A Literature Review, Aaron Rosenblum
Aspen Bibliography
The persistence of quaking aspen (Populus tremuloides Michx.) is of significant importance to land managers in the Rocky Mountain region. Fire suppression in the past century has been implicated as a mechanism influencing aspen population dynamics, as aspen are generally considered an early seral disturbance adapted species. The heterogeneity of aspen community assemblages and fire regimes makes it difficult to discern what the result of fire suppression has been at large spatial and temporal scales. Decision makers should investigate the questions at hand at the stand level in their study location to best determine the mechanisms at play, as well …
Investigating The Influence Of Chd1 On Gene Expression In Drosophila Melanogaster Using Position Effect Variegation, 2015 Scripps College
Investigating The Influence Of Chd1 On Gene Expression In Drosophila Melanogaster Using Position Effect Variegation, Phuongngan Thi Bui
Scripps Senior Theses
Position Effect Variegation (PEV) is the mosaic expression of a gene that has been moved out of its optimal environment and into a different area on the chromosome. Changing a gene’s environment may have profound effects on its eligibility for proper expression, which is a complicated process regulated by many factors. The PEV phenomenon is used as an assay to study gene expression as regulated by chromatin structure. In this study, the Drosophila melanogaster white gene was used as a reporter to study the various effects of CHD1, a chromatin regulating factor, on PEV gene expression. Inspired by preliminary data …
Global Analysis Of Gene Expression And Projection Target Correlations In The Mouse Brain, 2015 Old Dominion University
Global Analysis Of Gene Expression And Projection Target Correlations In The Mouse Brain, Ahmed Fakhry, Tao Zeng, Hanchuan Peng, Shuiwang Ji
Computer Science Faculty Publications
Recent studies have shown that projection targets in the mouse neocortex are correlated with their gene expression patterns. However, a brain-wide quantitative analysis of the relationship between voxel genetic composition and their projection targets is lacking to date. Here we extended those studies to perform a global, integrative analysis of gene expression and projection target correlations in the mouse brain. By using the Allen Brain Atlas data, we analyzed the relationship between gene expression and projection targets. We first visualized and clustered the two data sets separately and showed that they both exhibit strong spatial autocorrelation. Building upon this initial …
Long-Term Vegetation Change In Utah's Henry Mountains: A Study In Repeat Photography, 2015 Utah State University
Long-Term Vegetation Change In Utah's Henry Mountains: A Study In Repeat Photography, Charles E. Kay
Aspen Bibliography
An extensive search was conducted of archival and other sources to locate as many historical photographs as possible for the Henry Mountains in south-central Utah. Those images were then taken into the field, the original camera stations relocated, and modern pictures made of the historical scenes to evaluate long-term vegetation change and land management activities. In all, 626 repeat photo sets were compiled—608 by the author and 18 by Earl Hindley. This book includes 126 photo sets that were representative of the areas studied.
Fungicide Resistance Genetics Of Apple Scab Fungus Venturia Inaequalis, 2015 University of New Hampshire - Main Campus
Fungicide Resistance Genetics Of Apple Scab Fungus Venturia Inaequalis, Alexis Lt Reddel
Honors Theses and Capstones
Apple scab, caused by the ascomycete fungus Venturia inaequalis, is considered the most devastating disease on domestic apple crops. Apples are the most important cultivated crop in temperate regions and the United States produced about 4.6 million tons of apples in 2010. Traditional methods to control fungal plant diseases like apple scab are based on the use of chemical compounds that may produce serious negative effects, mainly related with environmental pollution and the development of fungicide resistance. Identifying genes and mechanisms of fungicide resistance in V. inaequalis is imperative to developing new and more effective defenses against the spread …
Erratum To: Hclp46 Increases Smad3 Protein Stability Via Inhibiting Its Ubiquitin-Proteasomal Degradation, 2015 Edith Cowan University
Erratum To: Hclp46 Increases Smad3 Protein Stability Via Inhibiting Its Ubiquitin-Proteasomal Degradation, Yingying Xing, Qiaoyun Chu, Run Feng, Wei Wang, Lixin Lu
Research outputs 2014 to 2021
No abstract provided.
Influence Of Landscape On Gene Differentiation In The American Pika (Ochotona Princeps) Within The Interstate 90 Snoqualmie Pass Corridor, 2015 Central Washington University
Influence Of Landscape On Gene Differentiation In The American Pika (Ochotona Princeps) Within The Interstate 90 Snoqualmie Pass Corridor, Craig P. Fergus
All Master's Theses
Understanding the impact of different landscape features on the movement of genes among populations can be helpful in managing wildlife populations. Our study used GIS tools to compare genetic connectivity among 13 American pika (Ochotona princeps) habitat patches across an approximately 77 square km area adjacent to Interstate 90 near Snoqualmie Pass, WA. Tissue samples were collected from 85 individuals and genotyped at six microsatellite loci to determine genetic differentiation among each pair of patches. A variety of models estimating the influence of landscape factors on gene flow were then used to find “resistance scores” between each pair …
Up Regulation Of Heat Shock Protein 70b (Hsp70b) And Ssa1 In Chlamydomonas Reinhardtii Via Hsp70a-Rbcs2 And Psad Promoter, 2015 University of Kentucky
Up Regulation Of Heat Shock Protein 70b (Hsp70b) And Ssa1 In Chlamydomonas Reinhardtii Via Hsp70a-Rbcs2 And Psad Promoter, B. Kirtley Amos
Theses and Dissertations--Biosystems and Agricultural Engineering
Fabrication of effective algae cultivation systems adjacent to coal-fired power plants to fixate waste CO2 would represent a sizable step towards achieving a carbon neutral energy cycle. However, emission gas would elevate the algal cultivation system temperature and decreases its pH without expensive preprocessing. Increased temperature and acidity constitutes a profound stress on the algae. Although stressed algae produce heat shock proteins (HSPs) that promote protein folding and protect against stress, the ordinary biological response is insufficient to protect against coal flue gas. Experimental upregulation of HSPs could make algae respond to the stress caused by high temperatures and …
Quaking Aspen At The Residential-Wildland Interface: Elk Herbivory Hinders Forest Conservation., 2015 Utah State University
Quaking Aspen At The Residential-Wildland Interface: Elk Herbivory Hinders Forest Conservation., Paul C. Rogers, Allison Jones, James Catlin, James Shuler, Arthur Morris, Michael R. Kuhns
Aspen Bibliography
T: Quaking aspen (Populus tremuloides) forests are experiencing numerous impediments across North America. In the West, recent drought, fire suppression, insects, diseases, climate trends, inappropriate management, and ungulate herbivory are impacting these high biodiversity forests. Additionally, ecological tension zones are sometimes created at residential-wildland interfaces with divergent management directives. For example, private conservation reserves bordering public land may be degraded from browsing where game species find refuge from hunting and plentiful forage. We examined putative herbivore impacts to nearly pure aspen forests at Wolf Creek Ranch (WCR), a sparsely developed residential landscape in northern Utah. Forty-three one-hectare monitoring …
Regeneration Dynamics Of White Spruce, Trembling Aspen, And Balsam Poplar In Response To Disturbance, Climatic, And Edaphic Factors In The Cold, Dry Boreal Forests Of The Southwest Yukon, Canada, 2015 Utah State University
Regeneration Dynamics Of White Spruce, Trembling Aspen, And Balsam Poplar In Response To Disturbance, Climatic, And Edaphic Factors In The Cold, Dry Boreal Forests Of The Southwest Yukon, Canada, Shyam K. Paudel, Craig R. Nitschke, Suzanne W. Simard, John L. Innes
Aspen Bibliography
The southwestern region of the Yukon Territory of Canada has experienced an unprecedented spruce bark beetle outbreak (Dendroctonus rufipennis) and an increase in the frequency of forest fires that extend beyond historical trends and that have caused significant impacts on forest structure and composition. A Strategic Forest Management Plan (SFMP) for the Champagne and Aishihik Traditional Territory located in the southwest Yukon was implemented in 2004 in response to the spruce bark beetle (D. rufipennis) infestation and increased fire risk. The plan has recommended salvage harvesting of beetle-killed stands as a strategy to facilitate the development …
An Investigation Of Hermaphroditism In R Sp Sb 347, 2015 College of William & Mary - Arts & Sciences
An Investigation Of Hermaphroditism In R Sp Sb 347, Maureen Catherine Farrell
Dissertations, Theses, and Masters Projects
No abstract provided.
Cloning Of Ribosomal Its Pcr Products Creates Frequent, Non-Random Chimeric Sequences – A Test Involving Heterozygotes Between Gymnopus Dichrous Taxa I And Ii., 2015 Ecology and Evolutionary Biology, University of Tennessee, Knoxville
Cloning Of Ribosomal Its Pcr Products Creates Frequent, Non-Random Chimeric Sequences – A Test Involving Heterozygotes Between Gymnopus Dichrous Taxa I And Ii., Karen Hughes, Samuel D. Morris, Ana L. Reboredo-Segovia
Faculty Publications and Other Works -- Ecology and Evolutionary Biology
Gymnopus dichrous exists in the southern Appalachians as two distinct entities with essentially identical nuclear ribosomal ITS1 sequences but differing ITS2 and LSU sequences (for convenience, called G. dichrous I and II). F1 ITS heterozygotes between the two are routinely collected from nature. Cloning of ITS PCR products from F1 heterozygotes produced sequences of both parental haplotypes but also numerous chimeric sequences (21.9%). The location of template switching was non-random leading to recovery of the same chimera several times and the chimeric region varied from 45bp to 300bp. By comparison, single-basidiospore isolates from heterozygote F1 fruitbodies showed …
Robust Optimization Of Biological Protocols, 2015 University of Massachusetts - Amherst
Robust Optimization Of Biological Protocols, Patrick Flaherty, Ronald W. Davis
Mathematics and Statistics Department Faculty Publication Series
When conducting high-throughput biological experiments, it is often necessary to develop a protocol that is both inexpensive and robust. Standard approaches are either not cost-effective or arrive at an optimized protocol that is sensitive to experimental variations. Here, we describe a novel approach that directly minimizes the cost of the protocol while ensuring the protocol is robust to experimental variation. Our approach uses a risk-averse conditional value-at-risk criterion in a robust parameter design framework. We demonstrate this approach on a polymerase chain reaction protocol and show that our improved protocol is less expensive than the standard protocol and more robust …