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• 1. [Article] Temperature Dependent Transcription Initiation in Archaea: Interplay between Transcription Factor B and Promoter Sequence

  In Pyrococcus furiosus (Pfu), a hyperthermophile archaeon, two transcription factor Bs, TFB1 and TFB2 are encoded in the genomic DNA. TFB1 is the primary TFB in Pfu, and is homologous to transcription ...

  Citation × Citation Citation Abstract Copy Title: Temperature Dependent Transcription Initiation in Archaea: Interplay between Transcription Factor B and Promoter Sequence Author: Wu, Ming-Hsiao Year: 2014 In Pyrococcus furiosus (Pfu), a hyperthermophile archaeon, two transcription factor Bs, TFB1 and TFB2 are encoded in the genomic DNA. TFB1 is the primary TFB in Pfu, and is homologous to transcription factor IIB (TFIIB) in eukaryotes. TFB2 is proposed to be a secondary TFB that is compared to TFB1, TFB2 lacks the conserved B-finger / B-reader / B-linker regions which assist RNA polymerase in transcription start site selection and promoter opening functions respectively. P. furiosus, like all Archaea, encodes a single transcription factor E (TFE), that is homologous to the N-terminus of transcription factor II E (TFIIE) α subunit in eukaryotes. TFE stabilizes the transcription bubble when present, although it is not required for in vitro transcription. In this study, in vitro transcription is used to reveal how TFB2 responds to different temperature (65 °C, 70 °C, 75 °C, 80 °C, and 85 °C) at promoters for three different kinds of gene: non-temperature responsive, heat-shock induced, and cold-shock induced in the absence or presence of TFE. The activity of transcription complexes formed by TFB2 is always lower than by TFB1 in all temperatures and promoters. However, with heat-shock gene promoters, the activity of transcription complexes formed by TFB2 increases more than those formed with TFB1 with increasing temperatures. The temperature-dependent activities of TFB1 and TFB2 are similar with the non-temperature responsive gene promoter. With the cold-shock gene promoter, the activity of transcription complexes formed by both TFB1 and TFB2 has the highest activity in lower temperatures. When TFE is present, the activity of transcription complexes formed by TFB2 is enhanced with heat-shock gene promoters particularly at lower temperatures, and makes TFB2 behave more similarly to TFB1. With the non-temperature responsive gene promoter, TFB2 still behaves similarly to TFB1 when TFE is present. However, with the cold-shock gene promoter, most of the activity of transcription complexes formed by TFB1 and TFB2 remain the same, but only the activity of TFB1 decreases at 75 °C. The results suggest that TFB2 may play a role in heat-shock response through its increased sensitivity to temperature, and that TFE can modulate this temperature response. Title: Temperature Dependent Transcription Initiation in Archaea: Interplay between Transcription Factor B and Promoter Sequence Author: Wu, Ming-Hsiao Year: 2014 In Pyrococcus furiosus (Pfu), a hyperthermophile archaeon, two transcription factor Bs, TFB1 and TFB2 are encoded in the genomic DNA. TFB1 is the primary TFB in Pfu, and is homologous to transcription factor IIB (TFIIB) in eukaryotes. TFB2 is proposed to be a secondary TFB that is compared to TFB1, TFB2 lacks the conserved B-finger / B-reader / B-linker regions which assist RNA polymerase in transcription start site selection and promoter opening functions respectively. P. furiosus, like all Archaea, encodes a single transcription factor E (TFE), that is homologous to the N-terminus of transcription factor II E (TFIIE) α subunit in eukaryotes. TFE stabilizes the transcription bubble when present, although it is not required for in vitro transcription. In this study, in vitro transcription is used to reveal how TFB2 responds to different temperature (65 °C, 70 °C, 75 °C, 80 °C, and 85 °C) at promoters for three different kinds of gene: non-temperature responsive, heat-shock induced, and cold-shock induced in the absence or presence of TFE. The activity of transcription complexes formed by TFB2 is always lower than by TFB1 in all temperatures and promoters. However, with heat-shock gene promoters, the activity of transcription complexes formed by TFB2 increases more than those formed with TFB1 with increasing temperatures. The temperature-dependent activities of TFB1 and TFB2 are similar with the non-temperature responsive gene promoter. With the cold-shock gene promoter, the activity of transcription complexes formed by both TFB1 and TFB2 has the highest activity in lower temperatures. When TFE is present, the activity of transcription complexes formed by TFB2 is enhanced with heat-shock gene promoters particularly at lower temperatures, and makes TFB2 behave more similarly to TFB1. With the non-temperature responsive gene promoter, TFB2 still behaves similarly to TFB1 when TFE is present. However, with the cold-shock gene promoter, most of the activity of transcription complexes formed by TFB1 and TFB2 remain the same, but only the activity of TFB1 decreases at 75 °C. The results suggest that TFB2 may play a role in heat-shock response through its increased sensitivity to temperature, and that TFE can modulate this temperature response. Close

• 2. [Article] A Metabolic Hypothesis for the Evolution of Temperature Effects on the Arterial PCO2 and pH of Vertebrate Ectotherms

  Body temperature increases in ectothermic vertebrates characteristically lead to both increases in arterial PCO2 (PaCO2) and declines in resting arterial pH (pHa) of about 0.017 pH units/°C increase in ...

  Citation × Citation Citation Abstract Copy Title: A Metabolic Hypothesis for the Evolution of Temperature Effects on the Arterial PCO2 and pH of Vertebrate Ectotherms Author: Hillman, Stanley S., Hedrick, Michael Scott Year: 2017 Body temperature increases in ectothermic vertebrates characteristically lead to both increases in arterial PCO2 (PaCO2) and declines in resting arterial pH (pHa) of about 0.017 pH units/°C increase in temperature. This ‘alphastat’ pH pattern has previously been interpreted as being evolutionarily-driven by the maintenance of a constant protonation state on the imidazole moiety of histidine protein residues, hence stabilizing protein structure-function. Analysis of the existing data for interclass responses of ectothermic vertebrates show different degrees of PaCO2 increases and pH declines with temperature between the classes with reptiles>amphibians>fish. The PaCO2 at the temperature where maximal aerobic metabolism (VO2max) is achieved is significantly and positively correlated with temperature for all vertebrate classes. For ectotherms, the PaCO2 where VO2max is greatest is also correlated with VO2max indicating there is an increased driving force for CO2 efflux that is lowest in fish, intermediate in amphibians and highest in reptiles. The pattern of increased PaCO2 and the resultant reduction of pHa to increased body temperature would serve to increase CO2 efflux, O2 delivery, blood buffering capacity and maintain ventilatory scope. This represents a new hypothesis for the selective advantage of arterial pH regulation from a systems physiology perspective in addition to the advantages of maintenance of protein structure-function. Title: A Metabolic Hypothesis for the Evolution of Temperature Effects on the Arterial PCO2 and pH of Vertebrate Ectotherms Author: Hillman, Stanley S., Hedrick, Michael Scott Year: 2017 Body temperature increases in ectothermic vertebrates characteristically lead to both increases in arterial PCO2 (PaCO2) and declines in resting arterial pH (pHa) of about 0.017 pH units/°C increase in temperature. This ‘alphastat’ pH pattern has previously been interpreted as being evolutionarily-driven by the maintenance of a constant protonation state on the imidazole moiety of histidine protein residues, hence stabilizing protein structure-function. Analysis of the existing data for interclass responses of ectothermic vertebrates show different degrees of PaCO2 increases and pH declines with temperature between the classes with reptiles>amphibians>fish. The PaCO2 at the temperature where maximal aerobic metabolism (VO2max) is achieved is significantly and positively correlated with temperature for all vertebrate classes. For ectotherms, the PaCO2 where VO2max is greatest is also correlated with VO2max indicating there is an increased driving force for CO2 efflux that is lowest in fish, intermediate in amphibians and highest in reptiles. The pattern of increased PaCO2 and the resultant reduction of pHa to increased body temperature would serve to increase CO2 efflux, O2 delivery, blood buffering capacity and maintain ventilatory scope. This represents a new hypothesis for the selective advantage of arterial pH regulation from a systems physiology perspective in addition to the advantages of maintenance of protein structure-function. Close

• 3. [Article] Temperature Changes in Human Skeletal Muscle during Single Leg Dynamic Knee Extension Exercise

  49 pages. A thesis presented to the Department of Uman Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Arts, Summer ...

  Citation × Citation Citation Abstract Copy Title: Temperature Changes in Human Skeletal Muscle during Single Leg Dynamic Knee Extension Exercise Author: Peck, Mairin Year: 2015 49 pages. A thesis presented to the Department of Uman Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Arts, Summer 2015. Title: Temperature Changes in Human Skeletal Muscle during Single Leg Dynamic Knee Extension Exercise Author: Peck, Mairin Year: 2015 49 pages. A thesis presented to the Department of Uman Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Arts, Summer 2015. Close

• 4. [Article] Reproductive Output of Mosses Under Experimental Warming on Fildes Peninsula, King George Island, Maritime Antarctica

  Background: Mosses dominate much of the vegetation in the Antarctic, but the effect of climatic change on moss growth and sexual reproduction has scarcely been studied. In Antarctica, mosses infrequently ...

  Citation × Citation Citation Abstract Copy Title: Reproductive Output of Mosses Under Experimental Warming on Fildes Peninsula, King George Island, Maritime Antarctica Author: Casanova-Katny, Angélica, Torres-Mellado, G. A., Eppley, Sarah M. Year: 2016 Background: Mosses dominate much of the vegetation in the Antarctic, but the effect of climatic change on moss growth and sexual reproduction has scarcely been studied. In Antarctica, mosses infrequently produce sporophytes; whether this is due to physiological limitation or an adaptive response is unknown. We studied the effect of experimental warming (with Open Top Chambers, OTCs) on sporophyte production on Fildes Peninsula, King George Island for four moss species (Bartramia patens, Hennediella antarctica, Polytrichastrum alpinum, and Sanionia georgicouncinata). To determine whether reducing cold stress increases sexual reproduction as would be predicted if sex is being constrained due to physiological limitations, we counted sporophytes for these four moss species in OTC and control plots during two years. Also, we measured sporophyte size for a smaller sample of sporophytes of two species, B. patens and H. antarctica, in the OTC and control plots. Results: After 2 years of the experimental treatment, maximum daily air temperature, but not daily mean air temperature, was significantly higher inside OTCs than outside. We found a significant species by treatment effect for sporophyte production, with more sporophytes produced in OTCs compared with controls for B. patens and P. alpinum. Also, sporophytes of B. patens and H. antarctica were significantly larger in the OTCs compared with the control plots. Conclusions: Our results suggest that the lack of sexual reproduction in these Antarctic mosses is not adaptive but is constrained by current environmental conditions and that ameliorating conditions, such as increased temperature may affect sexual reproduction in many Antarctic mosses, altering moss population genetics and dispersal patterns. Title: Reproductive Output of Mosses Under Experimental Warming on Fildes Peninsula, King George Island, Maritime Antarctica Author: Casanova-Katny, Angélica, Torres-Mellado, G. A., Eppley, Sarah M. Year: 2016 Background: Mosses dominate much of the vegetation in the Antarctic, but the effect of climatic change on moss growth and sexual reproduction has scarcely been studied. In Antarctica, mosses infrequently produce sporophytes; whether this is due to physiological limitation or an adaptive response is unknown. We studied the effect of experimental warming (with Open Top Chambers, OTCs) on sporophyte production on Fildes Peninsula, King George Island for four moss species (Bartramia patens, Hennediella antarctica, Polytrichastrum alpinum, and Sanionia georgicouncinata). To determine whether reducing cold stress increases sexual reproduction as would be predicted if sex is being constrained due to physiological limitations, we counted sporophytes for these four moss species in OTC and control plots during two years. Also, we measured sporophyte size for a smaller sample of sporophytes of two species, B. patens and H. antarctica, in the OTC and control plots. Results: After 2 years of the experimental treatment, maximum daily air temperature, but not daily mean air temperature, was significantly higher inside OTCs than outside. We found a significant species by treatment effect for sporophyte production, with more sporophytes produced in OTCs compared with controls for B. patens and P. alpinum. Also, sporophytes of B. patens and H. antarctica were significantly larger in the OTCs compared with the control plots. Conclusions: Our results suggest that the lack of sexual reproduction in these Antarctic mosses is not adaptive but is constrained by current environmental conditions and that ameliorating conditions, such as increased temperature may affect sexual reproduction in many Antarctic mosses, altering moss population genetics and dispersal patterns. Close

• 5. [Article] THE EFFECT OF A PATENT FORAMEN OVALE ON THERMOREGULATORY AND VENTILATORY RESPONSES DURING PASSIVE HEATING AND COOLING

  41 pages. A thesis presented to the Department of Human Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, ...

  Citation × Citation Citation Abstract Copy Title: THE EFFECT OF A PATENT FORAMEN OVALE ON THERMOREGULATORY AND VENTILATORY RESPONSES DURING PASSIVE HEATING AND COOLING Author: Hay, Madeline Year: 2016 41 pages. A thesis presented to the Department of Human Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2016. Title: THE EFFECT OF A PATENT FORAMEN OVALE ON THERMOREGULATORY AND VENTILATORY RESPONSES DURING PASSIVE HEATING AND COOLING Author: Hay, Madeline Year: 2016 41 pages. A thesis presented to the Department of Human Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2016. Close

• 6. [Article] Epigenetic Regulation of Alternative Developmental Trajectories

  The annual killifish, Austrofundulus limnaeus, is capable of entering into a state of metabolic and developmental dormancy during embryogenesis termed diapause. However, individuals may also follow an ...

  Citation × Citation Citation Abstract Copy Title: Epigenetic Regulation of Alternative Developmental Trajectories Author: Romney, Arnie Lynn T., Podrabsky, Jason E. Year: 2017 The annual killifish, Austrofundulus limnaeus, is capable of entering into a state of metabolic and developmental dormancy during embryogenesis termed diapause. However, individuals may also follow an alternative phenotypic trajectory and instead "escaped" entry into diapause and develop continuously until hatching. Early development along the two trajectories is morphologically indistinguishable, and gene regulatory mechanisms are currently unknown. Phenotype appears to be influenced by maternal provisioning based on the observation that young females produce predominately escape embryos and older females produce diapausing embryos. Additionally, the incubation temperature of embryos can override this maternal pattern and alter trajectory. Maternal provisioning is known in many vertebrates to direct early development prior to the initiation of embryonic gene transcription. Using RNA-seq, we have generated transcriptomic profiles of messenger RNAs (mRNAs) during embryogenesis of A. limnaeus. Embryos that are destined for either the diapause or escape phenotypes have unique profiles of mRNA isoforms at fertilization; well before they are morphologically distinct. We hypothesize that maternally packaged gene products coordinate the cellular events that determine developmental trajectory in A. limnaeus. In addition, we propose the expression of environmentally responsive microRNAs during development that can override maternal provisioning. RNA-seq data during early development, after the maternal-to-zygotic transition, suggest distinct profiles of microRNA expression that are phenotype specific. Our findings suggest maternal programming of diapause through the packaging of specific mRNAs as well as temperature induced microRNAs that target maternal transcripts allowing an escape from the diapause trajectory. This presents a novel example of maternal-embryonic-conflict in gene regulation that provides the embryo with alternatives in developmental trajectories in the face of fluctuating environmental patterns. These results will not only impact our understanding of genetic mechanisms that regulate entrance into diapause, but will also provide insight into epigenetic control of development. Title: Epigenetic Regulation of Alternative Developmental Trajectories Author: Romney, Arnie Lynn T., Podrabsky, Jason E. Year: 2017 The annual killifish, Austrofundulus limnaeus, is capable of entering into a state of metabolic and developmental dormancy during embryogenesis termed diapause. However, individuals may also follow an alternative phenotypic trajectory and instead "escaped" entry into diapause and develop continuously until hatching. Early development along the two trajectories is morphologically indistinguishable, and gene regulatory mechanisms are currently unknown. Phenotype appears to be influenced by maternal provisioning based on the observation that young females produce predominately escape embryos and older females produce diapausing embryos. Additionally, the incubation temperature of embryos can override this maternal pattern and alter trajectory. Maternal provisioning is known in many vertebrates to direct early development prior to the initiation of embryonic gene transcription. Using RNA-seq, we have generated transcriptomic profiles of messenger RNAs (mRNAs) during embryogenesis of A. limnaeus. Embryos that are destined for either the diapause or escape phenotypes have unique profiles of mRNA isoforms at fertilization; well before they are morphologically distinct. We hypothesize that maternally packaged gene products coordinate the cellular events that determine developmental trajectory in A. limnaeus. In addition, we propose the expression of environmentally responsive microRNAs during development that can override maternal provisioning. RNA-seq data during early development, after the maternal-to-zygotic transition, suggest distinct profiles of microRNA expression that are phenotype specific. Our findings suggest maternal programming of diapause through the packaging of specific mRNAs as well as temperature induced microRNAs that target maternal transcripts allowing an escape from the diapause trajectory. This presents a novel example of maternal-embryonic-conflict in gene regulation that provides the embryo with alternatives in developmental trajectories in the face of fluctuating environmental patterns. These results will not only impact our understanding of genetic mechanisms that regulate entrance into diapause, but will also provide insight into epigenetic control of development. Close

• 7. [Article] DROSOPHILA SUZUKII DEVELOPMENT & ATTRACTION

  36 pages. A thesis presented to the Department of Environmental Science and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, ...

  Citation × Citation Citation Abstract Copy Title: DROSOPHILA SUZUKII DEVELOPMENT & ATTRACTION Author: McIntosh, Hanna Year: 2016 36 pages. A thesis presented to the Department of Environmental Science and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2016. Title: DROSOPHILA SUZUKII DEVELOPMENT & ATTRACTION Author: McIntosh, Hanna Year: 2016 36 pages. A thesis presented to the Department of Environmental Science and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2016. Close

• 8. [Article] Phenotypic Variation in the Model Organism, Danio Rerio

  Model organisms are used to study evolutionary conserved traits. Zebrafish (Danio rerio) are used a model organism because of their highly fecundity, external fertilization, and robust nature, making them ...

  Citation × Citation Citation Abstract Copy Title: Phenotypic Variation in the Model Organism, Danio Rerio Author: Champaigne, Rachel D, Brown, Kim H. Year: 2014 Model organisms are used to study evolutionary conserved traits. Zebrafish (Danio rerio) are used a model organism because of their highly fecundity, external fertilization, and robust nature, making them highly adaptable to environmental and genetic variation. In an effort to limit data variation that lies outside of topic interest, phenotypic measures of variation must be performed, understood, and taken into consideration for future studies. A common measurement of phenotypic variation in fish is in the maximum (Ucrit) swimming speeds. Inter and intra-strain variation in zebrafish Ucrit swimming speeds will be observed in a swim tunnel. Baseline values will be recorded from ten fish from each of two families in each of three strains: WIK, Tubigan and AB. Environmental variation in zebrafish raised (beginning at one month of age) in tanks with various volumes and densities of fish will also be recorded from each strain. Mitochondrial density in white muscle will be compared in each strain in each condition. Diet, take salinity, pH, temperature, and light exposure will all remain constant for all fish. Title: Phenotypic Variation in the Model Organism, Danio Rerio Author: Champaigne, Rachel D, Brown, Kim H. Year: 2014 Model organisms are used to study evolutionary conserved traits. Zebrafish (Danio rerio) are used a model organism because of their highly fecundity, external fertilization, and robust nature, making them highly adaptable to environmental and genetic variation. In an effort to limit data variation that lies outside of topic interest, phenotypic measures of variation must be performed, understood, and taken into consideration for future studies. A common measurement of phenotypic variation in fish is in the maximum (Ucrit) swimming speeds. Inter and intra-strain variation in zebrafish Ucrit swimming speeds will be observed in a swim tunnel. Baseline values will be recorded from ten fish from each of two families in each of three strains: WIK, Tubigan and AB. Environmental variation in zebrafish raised (beginning at one month of age) in tanks with various volumes and densities of fish will also be recorded from each strain. Mitochondrial density in white muscle will be compared in each strain in each condition. Diet, take salinity, pH, temperature, and light exposure will all remain constant for all fish. Close

• 9. [Article] Modeling Microvirus Capsid Protein Evolution Utilizing Metagenomic Sequence Data

  The Microviridae are increasingly becoming recognized as one of the most globally ubiquitous and highly diverse virus families, and as such, provide an advantageous model for studying virus evolution and ...

  Citation × Citation Citation Abstract Copy Title: Modeling Microvirus Capsid Protein Evolution Utilizing Metagenomic Sequence Data Author: Diemer, Geoffrey S., Stedman, Kenneth M. Year: 2016 The Microviridae are increasingly becoming recognized as one of the most globally ubiquitous and highly diverse virus families, and as such, provide an advantageous model for studying virus evolution and adaptation. Here, we utilize microvirus sequences from diverse physiochemical environments, including novel sequences from a high-temperature acidic lake, to chart the outcome of natural selection in the main structural protein of the virus. Each icosahedral microvirus virion is composed of sixty identical capsid proteins that interact along twofold, threefold and fivefold symmetry axis interfaces to encapsidate a small, circular, single-stranded DNA genome. Viable assembly of the virus is guided by scaffolding proteins, which coordinate inter-subunit contacts between the capsid proteins. Structure-based analysis indicates that amino acid sequence conservation is predominantly localized to the twofold axis interface. While preservation of this quaternary interface appears to be essential, tertiary and secondary structural features of the capsid protein are permissive to considerable sequence variation. Title: Modeling Microvirus Capsid Protein Evolution Utilizing Metagenomic Sequence Data Author: Diemer, Geoffrey S., Stedman, Kenneth M. Year: 2016 The Microviridae are increasingly becoming recognized as one of the most globally ubiquitous and highly diverse virus families, and as such, provide an advantageous model for studying virus evolution and adaptation. Here, we utilize microvirus sequences from diverse physiochemical environments, including novel sequences from a high-temperature acidic lake, to chart the outcome of natural selection in the main structural protein of the virus. Each icosahedral microvirus virion is composed of sixty identical capsid proteins that interact along twofold, threefold and fivefold symmetry axis interfaces to encapsidate a small, circular, single-stranded DNA genome. Viable assembly of the virus is guided by scaffolding proteins, which coordinate inter-subunit contacts between the capsid proteins. Structure-based analysis indicates that amino acid sequence conservation is predominantly localized to the twofold axis interface. While preservation of this quaternary interface appears to be essential, tertiary and secondary structural features of the capsid protein are permissive to considerable sequence variation. Close

• 10. [Article] Identifying Genes Required for Cell Division in the Early C. elegans Embryo

  42 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Fall 201...

  Citation × Citation Citation Abstract Copy Title: Identifying Genes Required for Cell Division in the Early C. elegans Embryo Author: Standage, Hayley Year: 2014, 2013 42 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Fall 2013. Title: Identifying Genes Required for Cell Division in the Early C. elegans Embryo Author: Standage, Hayley Year: 2014, 2013 42 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Fall 2013. Close