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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] 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

• 4. [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

• 5. [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

• 6. [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

• 7. [Article] Isolation of Diverse Members of the Aquificales from Geothermal Springs in Tengchong, China

  The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, ...

  Citation × Citation Citation Abstract Copy Title: Isolation of Diverse Members of the Aquificales from Geothermal Springs in Tengchong, China Author: Hedlund, Brian P., Reysenbach, Anna-Louise, Huang, Liuquin, Ong, John C., Liu, Zizhang, Dodsworth, Jeremy A., Ahmed, Reham, Williams, Amanda J., Briggs, Brandon R., Liu, Yitai, Hou, Weiguo, Dong, Hailiang Year: 2015 The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2–83.3°C and pH 2.6–9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, andSulfurihydrogenibium, including strains distant enough to likely justify new species ofHydrogenobacter and Hydrogenobaculum. The additional strain may represent a new genus in theHydrogenothermaceae. All strains were capable of aerobic respiration under microaerophilic conditions; however, they had variable capacity for chemolithotrophic oxidation of hydrogen and sulfur compounds and nitrate reduction. Title: Isolation of Diverse Members of the Aquificales from Geothermal Springs in Tengchong, China Author: Hedlund, Brian P., Reysenbach, Anna-Louise, Huang, Liuquin, Ong, John C., Liu, Zizhang, Dodsworth, Jeremy A., Ahmed, Reham, Williams, Amanda J., Briggs, Brandon R., Liu, Yitai, Hou, Weiguo, Dong, Hailiang Year: 2015 The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2–83.3°C and pH 2.6–9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, andSulfurihydrogenibium, including strains distant enough to likely justify new species ofHydrogenobacter and Hydrogenobaculum. The additional strain may represent a new genus in theHydrogenothermaceae. All strains were capable of aerobic respiration under microaerophilic conditions; however, they had variable capacity for chemolithotrophic oxidation of hydrogen and sulfur compounds and nitrate reduction. Close

• 8. [Article] Transcriptomic Regulation of Alternative Phenotypic Trajectories in Embryos of the Annual Killifish <i>Austrofundulus limnaeus</i>

  The Annual Killifish, Austrofundulus limnaeus, survives the seasonal drying of their pond habitat in the form of embryos entering diapause midway through development. The diapause trajectory is one of ...

  Citation × Citation Citation Abstract Copy Title: Transcriptomic Regulation of Alternative Phenotypic Trajectories in Embryos of the Annual Killifish <i>Austrofundulus limnaeus</i> Author: Romney, Amie Lynn Thomas Year: 2017 The Annual Killifish, Austrofundulus limnaeus, survives the seasonal drying of their pond habitat in the form of embryos entering diapause midway through development. The diapause trajectory is one of two developmental phenotypes. Alternatively, individuals can "escape" entry into diapause and develop continuously until hatching. The alternative phenotypes of A. limnaeus are a form of developmental plasticity that provides this species with a physiological adaption for surviving stressful environments. The developmental trajectory of an embryo is not distinguishable morphologically upon fertilization and phenotype is believed to be influenced by maternal provisioning within the egg based on observations of offspring phenotype production. However, incubation temperature may override any such maternal pattern suggesting an environmental influence on the regulation of developmental trajectory. We hypothesize that maternally packaged gene products coordinate the cellular events prior to the maternal-to-zygotic transition (MTZ) that determine developmental trajectory in embryos of A. limnaeus. In addition, we propose that environmentally responsive gene expression after the MTZ can sustain or override any such maternal provisioning. Using high-throughput RNA-sequencing, we have generated transcriptomic profiles of protein-coding messenger RNA and noncoding RNA during development in A. limnaeus. Embryos destined for either the diapause or escape phenotypes display unique expression profiles immediately upon fertilization that support hormone synthesis, well before the stage when phenotypes are morphologically distinct. At stages when the trajectories diverge from one another, differential expression of the vitamin D receptor signaling pathway suggests that vitamin D signaling may be a key regulator of developmental phenotype in this species. These data provide a critical link between maternal and environmental influences on the genetic regulation of phenotypic plasticity. These results will not only impact our understanding of the genetic mechanisms that regulate entrance into diapause, but also provide insight into the epigenetic regulation of gene expression and development. Uncovering genetic mechanisms in a system exhibiting alternative developmental trajectories will elucidate the role of maternal packaging in regulating developmental decisions, and in sustaining metabolic depression during diapause. Title: Transcriptomic Regulation of Alternative Phenotypic Trajectories in Embryos of the Annual Killifish <i>Austrofundulus limnaeus</i> Author: Romney, Amie Lynn Thomas Year: 2017 The Annual Killifish, Austrofundulus limnaeus, survives the seasonal drying of their pond habitat in the form of embryos entering diapause midway through development. The diapause trajectory is one of two developmental phenotypes. Alternatively, individuals can "escape" entry into diapause and develop continuously until hatching. The alternative phenotypes of A. limnaeus are a form of developmental plasticity that provides this species with a physiological adaption for surviving stressful environments. The developmental trajectory of an embryo is not distinguishable morphologically upon fertilization and phenotype is believed to be influenced by maternal provisioning within the egg based on observations of offspring phenotype production. However, incubation temperature may override any such maternal pattern suggesting an environmental influence on the regulation of developmental trajectory. We hypothesize that maternally packaged gene products coordinate the cellular events prior to the maternal-to-zygotic transition (MTZ) that determine developmental trajectory in embryos of A. limnaeus. In addition, we propose that environmentally responsive gene expression after the MTZ can sustain or override any such maternal provisioning. Using high-throughput RNA-sequencing, we have generated transcriptomic profiles of protein-coding messenger RNA and noncoding RNA during development in A. limnaeus. Embryos destined for either the diapause or escape phenotypes display unique expression profiles immediately upon fertilization that support hormone synthesis, well before the stage when phenotypes are morphologically distinct. At stages when the trajectories diverge from one another, differential expression of the vitamin D receptor signaling pathway suggests that vitamin D signaling may be a key regulator of developmental phenotype in this species. These data provide a critical link between maternal and environmental influences on the genetic regulation of phenotypic plasticity. These results will not only impact our understanding of the genetic mechanisms that regulate entrance into diapause, but also provide insight into the epigenetic regulation of gene expression and development. Uncovering genetic mechanisms in a system exhibiting alternative developmental trajectories will elucidate the role of maternal packaging in regulating developmental decisions, and in sustaining metabolic depression during diapause. Close

• 9. [Article] Mitochondrial DNA Sequence and Lack of Response to Anoxia in the Annual Killifish <i>Austrofundulus limnaeus</i>

  The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos ...

  Citation × Citation Citation Abstract Copy Title: Mitochondrial DNA Sequence and Lack of Response to Anoxia in the Annual Killifish <i>Austrofundulus limnaeus</i> Author: Wagner, Josiah T., Chavez, Florisela H., Podrabsky, Jason E. Year: 2016 The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos that are able to persist in the desiccated sediment. Previous work has demonstrated that A. limnaeus have a remarkable ability to tolerate extended periods of anoxia and desiccating conditions. After considering temperature, A. limnaeus embryos have the highest known tolerance to anoxia when compared to any other vertebrate yet studied. Oxygen is completely essential for the process of oxidative phosphorylation by mitochondria, the intracellular organelle responsible for the majority of adenosine triphosphate production. Thus, understanding the unique properties of A. limnaeus mitochondria is of great interest. In this work, we describe the first complete mitochondrial genome (mtgenome) sequence of a single adult A. limnaeus individual and compare both coding and non-coding regions to several other closely related fish mtgenomes. Mitochondrial features were predicted using MitoAnnotator and polyadenylation sites were predicted using RNAseq mapping. To estimate the responsiveness of A. limnaeus mitochondria to anoxia treatment, we measure relative mitochondrial DNA copy number and total citrate synthase activity in both relatively anoxia-tolerant and anoxia-sensitive embryonic stages. Our cross-species comparative approach identifies unique features of ND1, ND5, ND6, and ATPase-6 that may facilitate the unique phenotype of A. limnaeus embryos. Additionally, we do not find evidence for mitochondrial degradation or biogenesis during anoxia/reoxygenation treatment in A. limnaeus embryos, suggesting that anoxia-tolerant mitochondria do not respond to anoxia in a manner similar to anoxia-sensitive mitochondria. Title: Mitochondrial DNA Sequence and Lack of Response to Anoxia in the Annual Killifish <i>Austrofundulus limnaeus</i> Author: Wagner, Josiah T., Chavez, Florisela H., Podrabsky, Jason E. Year: 2016 The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos that are able to persist in the desiccated sediment. Previous work has demonstrated that A. limnaeus have a remarkable ability to tolerate extended periods of anoxia and desiccating conditions. After considering temperature, A. limnaeus embryos have the highest known tolerance to anoxia when compared to any other vertebrate yet studied. Oxygen is completely essential for the process of oxidative phosphorylation by mitochondria, the intracellular organelle responsible for the majority of adenosine triphosphate production. Thus, understanding the unique properties of A. limnaeus mitochondria is of great interest. In this work, we describe the first complete mitochondrial genome (mtgenome) sequence of a single adult A. limnaeus individual and compare both coding and non-coding regions to several other closely related fish mtgenomes. Mitochondrial features were predicted using MitoAnnotator and polyadenylation sites were predicted using RNAseq mapping. To estimate the responsiveness of A. limnaeus mitochondria to anoxia treatment, we measure relative mitochondrial DNA copy number and total citrate synthase activity in both relatively anoxia-tolerant and anoxia-sensitive embryonic stages. Our cross-species comparative approach identifies unique features of ND1, ND5, ND6, and ATPase-6 that may facilitate the unique phenotype of A. limnaeus embryos. Additionally, we do not find evidence for mitochondrial degradation or biogenesis during anoxia/reoxygenation treatment in A. limnaeus embryos, suggesting that anoxia-tolerant mitochondria do not respond to anoxia in a manner similar to anoxia-sensitive mitochondria. Close

• 10. [Article] Distribution Drivers and Physiological Responses in Geothermal Bryophyte Communities

  Premise of Study: Our ability to explain community structure rests on our ability to define the importance of ecological niches, including realized ecological niches, in shaping communities, but few studies ...

  Citation × Citation Citation Abstract Copy Title: Distribution Drivers and Physiological Responses in Geothermal Bryophyte Communities Author: García, Estefanía Llaneza, Rosenstiel, Todd N., Graves, Camille Brianne, Shortlidge, Erin E., Eppley, Sarah M. Year: 2016 Premise of Study: Our ability to explain community structure rests on our ability to define the importance of ecological niches, including realized ecological niches, in shaping communities, but few studies of plant distributions have combined predictive models with physiological measures. Methods: Using field surveys and statistical modeling, we predicted distribution drivers in geothermal bryophyte (moss) communities of Lassen Volcanic National Park (California, USA). In the laboratory, we used drying and rewetting experiments to test whether the strong species-specific effects of relative humidity on distributions predicted by the models were correlated with physiological characters. Key Results: We found that the three most common bryophytes in geothermal communities were significantly affected by three distinct distribution drivers: temperature, light, and relative humidity. Aulacomnium palustre, whose distribution is significantly affected by relative humidity according to our model, and which occurs in high-humidity sites, showed extreme signs of stress after drying and never recovered optimal values of PSII efficiency after rewetting. Campylopus introflexus, whose distribution is not affected by humidity according to our model, was able to maintain optimal values of PSII efficiency for 48 hr at 50% water loss and recovered optimal values of PSII efficiency after rewetting. Conclusions: Our results suggest that species-specific environmental stressors tightly constrain the ecological niches of geothermal bryophytes. Tests of tolerance to drying in two bryophyte species corresponded with model predictions of the comparative importance of relative humidity as distribution drivers for these species. Title: Distribution Drivers and Physiological Responses in Geothermal Bryophyte Communities Author: García, Estefanía Llaneza, Rosenstiel, Todd N., Graves, Camille Brianne, Shortlidge, Erin E., Eppley, Sarah M. Year: 2016 Premise of Study: Our ability to explain community structure rests on our ability to define the importance of ecological niches, including realized ecological niches, in shaping communities, but few studies of plant distributions have combined predictive models with physiological measures. Methods: Using field surveys and statistical modeling, we predicted distribution drivers in geothermal bryophyte (moss) communities of Lassen Volcanic National Park (California, USA). In the laboratory, we used drying and rewetting experiments to test whether the strong species-specific effects of relative humidity on distributions predicted by the models were correlated with physiological characters. Key Results: We found that the three most common bryophytes in geothermal communities were significantly affected by three distinct distribution drivers: temperature, light, and relative humidity. Aulacomnium palustre, whose distribution is significantly affected by relative humidity according to our model, and which occurs in high-humidity sites, showed extreme signs of stress after drying and never recovered optimal values of PSII efficiency after rewetting. Campylopus introflexus, whose distribution is not affected by humidity according to our model, was able to maintain optimal values of PSII efficiency for 48 hr at 50% water loss and recovered optimal values of PSII efficiency after rewetting. Conclusions: Our results suggest that species-specific environmental stressors tightly constrain the ecological niches of geothermal bryophytes. Tests of tolerance to drying in two bryophyte species corresponded with model predictions of the comparative importance of relative humidity as distribution drivers for these species. Close