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• 31. [Article] Enzyme reactions using ureidosuccinate as a substrate during pyrimidine biosynthesis and degradation in Cl. oroticum

  Cells of Clostridium oroticum, an anaerobic bacterium, were grown on orotate as a carbon and energy source. Ureidosuccinase, an inducible enzyme in the pathway for pyrimidine degradation has been shown ...

  Citation × Citation Citation Abstract Copy Title: Enzyme reactions using ureidosuccinate as a substrate during pyrimidine biosynthesis and degradation in Cl. oroticum Author: Amy, Penny Year: 1974 Cells of Clostridium oroticum, an anaerobic bacterium, were grown on orotate as a carbon and energy source. Ureidosuccinase, an inducible enzyme in the pathway for pyrimidine degradation has been shown to convert ureidosuccinate to aspartate, C02 and NH3 as reported by Liebenmm and Kornberg (7). Aspartate and C02 were formed in approximately a 1: 1 ratio from ureidosuccinase activity. Ureidosuccinase was found to be a Mn+2 requiring enzyme with a pH optimum of approximately pH 6.5. Enzyme activity is labile to 02, temperature, pH, dilution and high ionic strength. The optimum conditions for storage of ureidosuccinase were found to be mixtures which contained Mn+2, PO4-3 and ureidosuccinate (the substrate of the enzyme) at -20°C in argon gassed serum vials. Hydantoinase, an enzyme which converts ureidosuccinate to 5'-carboxymethylhydantoin in a ratio of two 5'-carboxymethylhydantoin to one ureidosuccinate, was present in cells grown on orotate. Hydantoinase was able to convert both the D and the L isomers of ureidosuccinate to carboxymethylhydantoin. High levels of a Mg+2 dependent carbamyl phosphate kinase were found in extracts from cells grown on orotate. The activity was dependent upon addition of ADP or AMP to the reaction mixture. The pH optimum of the carbamyl phosphate kinase was approximately pH 6.5. Cells grown on orotate contained high levels of an induced system for the degradation of pyrimidines whereas cells grown on glucose contained a constitutive level of enzymes for pyrimidine biosyntheses. Low levels of ureidosuccinase, carbamyl phosphate kinase and hydantoinase were found in glucose grown cells. Cells grown on glucose showed a high level of a Mn+2 dependent aspartate transcarbamylase (the analogous enzyme to ureidosuccinase which is operative during pyrimidine biosynthesis) which forms ureidosuccinate from aspartate and carbamyl phosphate. A consideration of the energy and reducing power supply and demand was made for cells grown both on glucose and orotate as carbon and energy source. Title: Enzyme reactions using ureidosuccinate as a substrate during pyrimidine biosynthesis and degradation in Cl. oroticum Author: Amy, Penny Year: 1974 Cells of Clostridium oroticum, an anaerobic bacterium, were grown on orotate as a carbon and energy source. Ureidosuccinase, an inducible enzyme in the pathway for pyrimidine degradation has been shown to convert ureidosuccinate to aspartate, C02 and NH3 as reported by Liebenmm and Kornberg (7). Aspartate and C02 were formed in approximately a 1: 1 ratio from ureidosuccinase activity. Ureidosuccinase was found to be a Mn+2 requiring enzyme with a pH optimum of approximately pH 6.5. Enzyme activity is labile to 02, temperature, pH, dilution and high ionic strength. The optimum conditions for storage of ureidosuccinase were found to be mixtures which contained Mn+2, PO4-3 and ureidosuccinate (the substrate of the enzyme) at -20°C in argon gassed serum vials. Hydantoinase, an enzyme which converts ureidosuccinate to 5'-carboxymethylhydantoin in a ratio of two 5'-carboxymethylhydantoin to one ureidosuccinate, was present in cells grown on orotate. Hydantoinase was able to convert both the D and the L isomers of ureidosuccinate to carboxymethylhydantoin. High levels of a Mg+2 dependent carbamyl phosphate kinase were found in extracts from cells grown on orotate. The activity was dependent upon addition of ADP or AMP to the reaction mixture. The pH optimum of the carbamyl phosphate kinase was approximately pH 6.5. Cells grown on orotate contained high levels of an induced system for the degradation of pyrimidines whereas cells grown on glucose contained a constitutive level of enzymes for pyrimidine biosyntheses. Low levels of ureidosuccinase, carbamyl phosphate kinase and hydantoinase were found in glucose grown cells. Cells grown on glucose showed a high level of a Mn+2 dependent aspartate transcarbamylase (the analogous enzyme to ureidosuccinase which is operative during pyrimidine biosynthesis) which forms ureidosuccinate from aspartate and carbamyl phosphate. A consideration of the energy and reducing power supply and demand was made for cells grown both on glucose and orotate as carbon and energy source. Close

• 32. [Article] In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae

  We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic ...

  Citation × Citation Citation Abstract Copy Title: In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae Author: Hicks, Kiley Ann, Howe, Dana K., Leung, Aubrey, Denver, Dee R., Estes, Suzanne Year: 2012 We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among- isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives. Title: In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae Author: Hicks, Kiley Ann, Howe, Dana K., Leung, Aubrey, Denver, Dee R., Estes, Suzanne Year: 2012 We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among- isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives. Close

• 33. [Article] Life Cycle, Additions to Biology, and New Hosts of Apophallus Donicus (Trematoda: Heterophyidae) in Oregon

  Apophallus donicus is examined, its life cycle is described, and certain additions are made to its biology. It is thought, but not proven, that eggs are eaten by the first.intermediate host, the local ...

  Citation × Citation Citation Abstract Copy Title: Life Cycle, Additions to Biology, and New Hosts of Apophallus Donicus (Trematoda: Heterophyidae) in Oregon Author: Niemi, Delbert Raymond Year: 1973 Apophallus donicus is examined, its life cycle is described, and certain additions are made to its biology. It is thought, but not proven, that eggs are eaten by the first.intermediate host, the local stream snail FluI menicola virens, and the miracidia escape internally. Mother and daughter rediae stages result, the later producing cercariae which are shed into the water. After burrowing just beneath the skin in suckers (Catostomus macrocheilus Girard), rainbow trout (Salmo 9airdneri Richardson), coho salmon (Oncorhynchus kisutch (Walbaum) squawfish (Ptychocheilus oregonensis Richardson), blackside dace (Rhinichthys osculus nubilus (Girard), redside shiners (Richardsonius balteatus balteatus (Richardson),and possibly other fish, the cercariae encyst and the resulting metacercariae cause black-spot disease in the host. Natural definitive hosts were not found, but laboratory infections included gerbils, white rats, golden hamsters, chickens, catfish (Ictalurus punctatus (Rafinesque), cats, and the author. A rainbow trout was found which had 33 immature Apophallus in its small intestine. All were alive and active, but their entire posterior ends, including all the sex organs, were degenerate and poorly formed compared to the anterior halves of their bodies, and there was no evidence that adults with eggs would have resulted. This trematode is very hardy and adaptable in all stages of its life cycle, e.g., cercariae lived and were active up until eight days after being shed, metacercariae remained infective in fish which had been dead and out of water for 60 hours, and adults lived in tap water at room temperature for 72 hours. Title: Life Cycle, Additions to Biology, and New Hosts of Apophallus Donicus (Trematoda: Heterophyidae) in Oregon Author: Niemi, Delbert Raymond Year: 1973 Apophallus donicus is examined, its life cycle is described, and certain additions are made to its biology. It is thought, but not proven, that eggs are eaten by the first.intermediate host, the local stream snail FluI menicola virens, and the miracidia escape internally. Mother and daughter rediae stages result, the later producing cercariae which are shed into the water. After burrowing just beneath the skin in suckers (Catostomus macrocheilus Girard), rainbow trout (Salmo 9airdneri Richardson), coho salmon (Oncorhynchus kisutch (Walbaum) squawfish (Ptychocheilus oregonensis Richardson), blackside dace (Rhinichthys osculus nubilus (Girard), redside shiners (Richardsonius balteatus balteatus (Richardson),and possibly other fish, the cercariae encyst and the resulting metacercariae cause black-spot disease in the host. Natural definitive hosts were not found, but laboratory infections included gerbils, white rats, golden hamsters, chickens, catfish (Ictalurus punctatus (Rafinesque), cats, and the author. A rainbow trout was found which had 33 immature Apophallus in its small intestine. All were alive and active, but their entire posterior ends, including all the sex organs, were degenerate and poorly formed compared to the anterior halves of their bodies, and there was no evidence that adults with eggs would have resulted. This trematode is very hardy and adaptable in all stages of its life cycle, e.g., cercariae lived and were active up until eight days after being shed, metacercariae remained infective in fish which had been dead and out of water for 60 hours, and adults lived in tap water at room temperature for 72 hours. Close

• 34. [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

• 35. [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

• 36. [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

• 37. [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

• 38. [Article] Thermosulfuriphilus ammonigenes gen. nov., sp. nov., a Thermophilic, ChemolithoautotrOphic Bacterium Capable of Respiratory Ammonification of Nitrate with Elemental Sulfur

  An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain ST65T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Centre in the south-western ...

  Citation × Citation Citation Abstract Copy Title: Thermosulfuriphilus ammonigenes gen. nov., sp. nov., a Thermophilic, ChemolithoautotrOphic Bacterium Capable of Respiratory Ammonification of Nitrate with Elemental Sulfur Author: Slobodkina, Galina B., Reysenbach, Anna-Louise, Kolganova, Tatyana V., Bronch-Osmolovskaya, Elizaveta A., Slobodkin, Alexander I. Year: 2017 An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain ST65T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Centre in the south-western Pacific Ocean, at a depth of 1870 m. Cells of strain ST65T were non-motile straight or slightly curved short rods, 0.5–0.6 µm in diameter and 0.8–1.5 µm in length. The temperature range for growth was 47–75 °C, with an optimum at 65 °C. The pH range for growth was 5.5–7.5, with an optimum at pH 6.5. Growth of strain ST65T was observed at NaCl concentrations ranging from 1.5 to 4.5 % (w/v), with an optimum at 2.0–2.5 %. Strain ST65T grew anaerobically with inorganic carbon as a carbon source and with elemental sulfur as an electron donor and nitrate as an electron acceptor producing sulfate and ammonium. It was also able to grow by disproportionation of elemental sulfur, thiosulfate and sulfite. Sulfate was not utilized as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to a deep lineage in the phylum Thermodesulfobacteria . On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the isolate represents a novel species of a new genus, Thermosulfuriphilus ammonigenes gen. nov., sp. nov. ST65T (=DSM 102941T=VKM B-2855T) is the type strain of the type species. Title: Thermosulfuriphilus ammonigenes gen. nov., sp. nov., a Thermophilic, ChemolithoautotrOphic Bacterium Capable of Respiratory Ammonification of Nitrate with Elemental Sulfur Author: Slobodkina, Galina B., Reysenbach, Anna-Louise, Kolganova, Tatyana V., Bronch-Osmolovskaya, Elizaveta A., Slobodkin, Alexander I. Year: 2017 An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain ST65T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Centre in the south-western Pacific Ocean, at a depth of 1870 m. Cells of strain ST65T were non-motile straight or slightly curved short rods, 0.5–0.6 µm in diameter and 0.8–1.5 µm in length. The temperature range for growth was 47–75 °C, with an optimum at 65 °C. The pH range for growth was 5.5–7.5, with an optimum at pH 6.5. Growth of strain ST65T was observed at NaCl concentrations ranging from 1.5 to 4.5 % (w/v), with an optimum at 2.0–2.5 %. Strain ST65T grew anaerobically with inorganic carbon as a carbon source and with elemental sulfur as an electron donor and nitrate as an electron acceptor producing sulfate and ammonium. It was also able to grow by disproportionation of elemental sulfur, thiosulfate and sulfite. Sulfate was not utilized as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to a deep lineage in the phylum Thermodesulfobacteria . On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the isolate represents a novel species of a new genus, Thermosulfuriphilus ammonigenes gen. nov., sp. nov. ST65T (=DSM 102941T=VKM B-2855T) is the type strain of the type species. Close

• 39. [Article] Externally-Expressed Fluorescence across Sexes, Life Stages, and Species of Spiders

  Although all spiders possess fluorophores in their hemolymph, the expression of external fluorescence is much more restricted. The purpose of this study was to evaluate differences in externally-expressed ...

  Citation × Citation Citation Abstract Copy Title: Externally-Expressed Fluorescence across Sexes, Life Stages, and Species of Spiders Author: Brandt, Erin Year: 2012 Although all spiders possess fluorophores in their hemolymph, the expression of external fluorescence is much more restricted. The purpose of this study was to evaluate differences in externally-expressed fluorescence between sexes, life stages, and species of spiders. To approach this question, we developed novel instrumentation to capture fluorescence with photographs of our specimens. We paired these fluorescence measurements with spectrometer measurements to attempt to determine the role that fluorescence plays in the overall coloration in spiders. The study was divided into four sections. First, we examined how fluorescence varies in sexes and life stages in Misumena vatia, an ambush predator that typically preys on insects when they are on flowers. We found that adult females possess brighter external fluorescence than males in all body areas that we measured. We also found that external fluorescence remains relatively similar through life stages in females, but darkens over the course of a male's life. It is likely that the differences between males and females relate to differences in feeding ecology. External fluorescence may contribute to a visual signal allowing females to visually blend in with flowers. The second study involved a series of experiments to determine whether freezing spiders at a temperature of -80°C affects their fluorescence intensity. In spiders considered “white thomisids”, fluorescence intensity increased after freezing, whereas fluorescence brightness in darker-pigmented spiders did not change to any similar extent. It seems likely that tissue trauma due to freezing is the cause of increased fluorescence intensity after freezing. The third study examined fluorescence brightness across ages and life stages of Araneus diadematus, a spider which is exposed to the sun, but builds large webs in which to snare prey. We found that, unlike M. vatia, adult males are the more brightly fluorescent sex, with adult females and all immature life stages possessing significantly less bright external fluorescence. It is unclear why these differences exist, but differences in ecology between adult males and all other life stages could play a role. Additionally, dim fluorescence may contribute to subtle patterning and/or convey photoprotection benefits to immatures and adult females. In the final study, we examined external fluorescence across the Thomisidae family. Because of a relatively large number of species with a small sample size, we divided them into “white” and “dark” thomisids based on taxonomy and what is known about ecology. The white thomisids tend to be prey on insects on the exposed surfaces of flowers, whereas dark thomisids more often reside in leaf litter and crevices. We found that white thomisids fluoresce more brightly than dark thomisids. There were no differences between the sexes in either group, however. The differences between white and dark thomisids may be related to differences in feeding ecology, whereas males and females of the same group tend to have similar ecological characteristics, and also possess similar levels of fluorescence brightness. Title: Externally-Expressed Fluorescence across Sexes, Life Stages, and Species of Spiders Author: Brandt, Erin Year: 2012 Although all spiders possess fluorophores in their hemolymph, the expression of external fluorescence is much more restricted. The purpose of this study was to evaluate differences in externally-expressed fluorescence between sexes, life stages, and species of spiders. To approach this question, we developed novel instrumentation to capture fluorescence with photographs of our specimens. We paired these fluorescence measurements with spectrometer measurements to attempt to determine the role that fluorescence plays in the overall coloration in spiders. The study was divided into four sections. First, we examined how fluorescence varies in sexes and life stages in Misumena vatia, an ambush predator that typically preys on insects when they are on flowers. We found that adult females possess brighter external fluorescence than males in all body areas that we measured. We also found that external fluorescence remains relatively similar through life stages in females, but darkens over the course of a male's life. It is likely that the differences between males and females relate to differences in feeding ecology. External fluorescence may contribute to a visual signal allowing females to visually blend in with flowers. The second study involved a series of experiments to determine whether freezing spiders at a temperature of -80°C affects their fluorescence intensity. In spiders considered “white thomisids”, fluorescence intensity increased after freezing, whereas fluorescence brightness in darker-pigmented spiders did not change to any similar extent. It seems likely that tissue trauma due to freezing is the cause of increased fluorescence intensity after freezing. The third study examined fluorescence brightness across ages and life stages of Araneus diadematus, a spider which is exposed to the sun, but builds large webs in which to snare prey. We found that, unlike M. vatia, adult males are the more brightly fluorescent sex, with adult females and all immature life stages possessing significantly less bright external fluorescence. It is unclear why these differences exist, but differences in ecology between adult males and all other life stages could play a role. Additionally, dim fluorescence may contribute to subtle patterning and/or convey photoprotection benefits to immatures and adult females. In the final study, we examined external fluorescence across the Thomisidae family. Because of a relatively large number of species with a small sample size, we divided them into “white” and “dark” thomisids based on taxonomy and what is known about ecology. The white thomisids tend to be prey on insects on the exposed surfaces of flowers, whereas dark thomisids more often reside in leaf litter and crevices. We found that white thomisids fluoresce more brightly than dark thomisids. There were no differences between the sexes in either group, however. The differences between white and dark thomisids may be related to differences in feeding ecology, whereas males and females of the same group tend to have similar ecological characteristics, and also possess similar levels of fluorescence brightness. Close

• 40. [Article] Bayesian Methods for Comparing Species Physiological and Ecological Response Curves

  Many ecological questions require information on species' optimal conditions or critical limits along environmental gradients. These attributes can be compared to answer questions on niche partitioning, ...

  Citation × Citation Citation Abstract Copy Title: Bayesian Methods for Comparing Species Physiological and Ecological Response Curves Author: Ashcroft, Michael B., Casanova-Katny, Angélica, Mengersen, Kerrie, Rosenstiel, Todd N., Turnbull, Johanna D., Wasley, Jane, Waterman, Melinda J., Zúñiga, Gustavo E., Robinson, Sharon A. Year: 2016 Many ecological questions require information on species' optimal conditions or critical limits along environmental gradients. These attributes can be compared to answer questions on niche partitioning, species coexistence and niche conservatism. However, these comparisons are unconvincing when existing methods do not quantify the uncertainty in the attributes or rely on assumptions about the shape of species' responses to the environmental gradient. The aim of this study was to develop a model to quantify the uncertainty in the attributes of species response curves and allow them to be tested for substantive differences without making assumptions about the shape of the responses. We developed a model that used Bayesian penalised splines to produce and compare response curves for any two given species. These splines allow the data to determine the shape of the response curves rather than making a priori assumptions. The models were implemented using the R2OpenBUGS package for R, which uses Markov Chain Monte Carlo simulation to repetitively fit alternative response curves to the data. As each iteration produces a different curve that varies in optima, niche breadth and limits, the model estimates the uncertainty in each of these attributes and the probability that the two curves are different. The models were tested using two datasets of mosses from Antarctica. Both datasets had a high degree of scatter, which is typical of ecological research. This noise resulted in considerable uncertainty in the optima and limits of species response curves, but substantive differences were found. Schistidium antarcticiwas found to inhabit wetter habitats than Ceratodon purpureus, and Polytrichastrum alpinum had a lower optimal temperature for photosynthesis than Chorisodontium aciphyllum under high light conditions. Our study highlights the importance of considering uncertainty in physiological optima and other attributes of species response curves. We found that apparent differences in optima of 7.5 °C were not necessarily substantive when dealing with noisy ecological data, and it is necessary to consider the uncertainty in attributes when comparing the curves for different species. The model introduced here could increase the robustness of research on niche partitioning, species coexistence and niche conservatism. Title: Bayesian Methods for Comparing Species Physiological and Ecological Response Curves Author: Ashcroft, Michael B., Casanova-Katny, Angélica, Mengersen, Kerrie, Rosenstiel, Todd N., Turnbull, Johanna D., Wasley, Jane, Waterman, Melinda J., Zúñiga, Gustavo E., Robinson, Sharon A. Year: 2016 Many ecological questions require information on species' optimal conditions or critical limits along environmental gradients. These attributes can be compared to answer questions on niche partitioning, species coexistence and niche conservatism. However, these comparisons are unconvincing when existing methods do not quantify the uncertainty in the attributes or rely on assumptions about the shape of species' responses to the environmental gradient. The aim of this study was to develop a model to quantify the uncertainty in the attributes of species response curves and allow them to be tested for substantive differences without making assumptions about the shape of the responses. We developed a model that used Bayesian penalised splines to produce and compare response curves for any two given species. These splines allow the data to determine the shape of the response curves rather than making a priori assumptions. The models were implemented using the R2OpenBUGS package for R, which uses Markov Chain Monte Carlo simulation to repetitively fit alternative response curves to the data. As each iteration produces a different curve that varies in optima, niche breadth and limits, the model estimates the uncertainty in each of these attributes and the probability that the two curves are different. The models were tested using two datasets of mosses from Antarctica. Both datasets had a high degree of scatter, which is typical of ecological research. This noise resulted in considerable uncertainty in the optima and limits of species response curves, but substantive differences were found. Schistidium antarcticiwas found to inhabit wetter habitats than Ceratodon purpureus, and Polytrichastrum alpinum had a lower optimal temperature for photosynthesis than Chorisodontium aciphyllum under high light conditions. Our study highlights the importance of considering uncertainty in physiological optima and other attributes of species response curves. We found that apparent differences in optima of 7.5 °C were not necessarily substantive when dealing with noisy ecological data, and it is necessary to consider the uncertainty in attributes when comparing the curves for different species. The model introduced here could increase the robustness of research on niche partitioning, species coexistence and niche conservatism. Close