title: Repair eXtreme - DNA repair proteins from Antarctic extremophiles

authors: Rzoska-Smith, Elizabeth

abstract: The McMurdo Dry valleys (DV) in Antarctica are one of the harshest environments on Earth, with high levels of UV radiation, freeze-thaw cycles, low moisture, and nutrient content. Bacteria in this extreme environment have adapted to slow growth and low-nutrient conditions. It is proposed that bacteria from Antarctic DV systems may possess unique DNA repair enzymes and pathways that enable their survival in such extreme conditions. Exploring these DNA repair systems may offer valuable insights into microbial survival in extreme environments or even extra-terrestrial settings. To investigate this, DNA repair enzymes were identified from Antarctic DV microbial metagenomes using in silico analysis and in vivo characterisation of recombinantly produced proteins.

Four candidate enzymes were chosen for structural and biological characterisation. Three of these enzymes are characterised as LigB type ATP-dependent DNA ligases, with the typical arrangement of a DNA binding domain, adenylation domain and an OB-fold domain. These ligases can utilise both ATP and ADP nucleotide cofactors for the ligation of nick and mismatch DNA substrates, requiring the addition of magnesium or manganese metal ions. One LigB ligase stands out due to its interesting fusion with an N-terminally located nuclease domain, which resembles an extensively studied MBL-β-CASP domain found in all domains of life. The recombinantly expressed nuclease domain can coordinate several types of metal ions and shows nuclease activity against a diverse range of DNA substrates. Nuclease activity favoured single-stranded DNA substrates, in a 5’ to 3’ direction, and was particularly active on substrates with abasic sites or 5’ flaps. The fourth protein was initially annotated as a hypothetical protein, however in silico analysis revealed that it exhibited homology to NucS nucleases identified in archaea and bacteria. This NucS homolog is a monomeric enzyme, made up of four domains, which is different from other proteins in this family. This enzyme shows a preference for single-stranded DNA and has a broad range of nuclease activity on damaged and mismatched DNA substrates. It can utilise both magnesium and manganese metal ions for activity on DNA substrates. Overall, these findings suggest that the described enzymes will play a role in DNA repair pathways, potentially in high-damage environments like the DVs of Antarctica.

text: Repair eXtreme - DNA repair proteins from Antarctic extremophiles The McMurdo Dry valleys (DV) in Antarctica are one of the harshest environments on Earth, with high levels of UV radiation, freeze-thaw cycles, low moisture, and nutrient content. Bacteria in this extreme environment have adapted to slow growth and low-nutrient conditions. It is proposed that bacteria from Antarctic DV systems may possess unique DNA repair enzymes and pathways that enable their survival in such extreme conditions. Exploring these DNA repair systems may offer valuable insights into microbial survival in extreme environments or even extra-terrestrial settings. To investigate this, DNA repair enzymes were identified from Antarctic DV microbial metagenomes using in silico analysis and in vivo characterisation of recombinantly produced proteins.

Four candidate enzymes were chosen for structural and biological characterisation. Three of these enzymes are characterised as LigB type ATP-dependent DNA ligases, with the typical arrangement of a DNA binding domain, adenylation domain and an OB-fold domain. These ligases can utilise both ATP and ADP nucleotide cofactors for the ligation of nick and mismatch DNA substrates, requiring the addition of magnesium or manganese metal ions. One LigB ligase stands out due to its interesting fusion with an N-terminally located nuclease domain, which resembles an extensively studied MBL-β-CASP domain found in all domains of life. The recombinantly expressed nuclease domain can coordinate several types of metal ions and shows nuclease activity against a diverse range of DNA substrates. Nuclease activity favoured single-stranded DNA substrates, in a 5’ to 3’ direction, and was particularly active on substrates with abasic sites or 5’ flaps. The fourth protein was initially annotated as a hypothetical protein, however in silico analysis revealed that it exhibited homology to NucS nucleases identified in archaea and bacteria. This NucS homolog is a monomeric enzyme, made up of four domains, which is different from other proteins in this family. This enzyme shows a preference for single-stranded DNA and has a broad range of nuclease activity on damaged and mismatched DNA substrates. It can utilise both magnesium and manganese metal ions for activity on DNA substrates. Overall, these findings suggest that the described enzymes will play a role in DNA repair pathways, potentially in high-damage environments like the DVs of Antarctica.

year: 2023

title: Quality, quantity, and nutritional impacts of rice price changes in Vietnam

authors: Gibson, John

subjects: Asia

abstract: Asian governments intervene in the world rice market to protect domestic consumers. Whether consumers are nutritionally vulnerable depends on the elasticity of calories with respect to rice prices. Common demand models applied to household survey and market price data ignore quality substitution and force all adjustment onto the quantity (calorie) margin. This paper uses data from Vietnam on market prices, food quantity and quality. A 10% increase in the relative price of rice reduces household calorie consumption by less than 2% but this elasticity would be wrongly estimated to be more than twice as large if quality substitution is ignored.

text: Quality, quantity, and nutritional impacts of rice price changes in Vietnam Asian governments intervene in the world rice market to protect domestic consumers. Whether consumers are nutritionally vulnerable depends on the elasticity of calories with respect to rice prices. Common demand models applied to household survey and market price data ignore quality substitution and force all adjustment onto the quantity (calorie) margin. This paper uses data from Vietnam on market prices, food quantity and quality. A 10% increase in the relative price of rice reduces household calorie consumption by less than 2% but this elasticity would be wrongly estimated to be more than twice as large if quality substitution is ignored.

year: 2013

title: Listening at dawn: Trans* storywork for all my relations

authors: Luna-Pizano, Rafaela

subjects: Transgender

abstract: This is a love letter to trans* people: a reminder of our place and legacy of trans*formation. In the form of collaborative and ceremonial research, this PhD with creative practice component is an affirmation of embodied, elemental storytelling as a necessary practice for unearthing and grounding the traditional knowledge that Indigenous-Trans* (Indigi-Trans*) people carry within our body-spirits. This creative practice (co)research uplifts liminal states of being, as given to us by our elemental ancestors, in the decolonial project of Indigenous (encompassing Black and Trans*) body-land reclamation and restoration. By recognizing and nourishing the power of the between, this thesis remembers practices of place that are rooted in the body, often our last piece of ancestral land as displaced and diasporic Indigi-Trans* people. Spanning the coasts of Aotearoa-NZ to the west coast of Ixtlán (Turtle Island-US), this creative project listened to the somatic presence of Indigi-Trans* creators (co-researchers) who are in varying states of connection to their ancestral lands and traditions. To account for sudden and extreme shifts in safety and access due to the COVID-19 pandemic, I created online and on-site rituals to sustain connection and retrace our ancestors’ techniques of time and space travel. By engaging with body-awareness practices or ritual performances offered in this project, co-researchers and storytellers were able to experiment with ‘knew’ ways of engaging the ancestral power of place. As a member of the communities contributing to this project, I witnessed an important transformation within co-researchers from a sense of landlessness to a sense of infinite place. This transformation gave co-researchers and storytellers a new source of power, strengthening their spiritual-mental capacity to receive and grow (especially during the height of the COVID-19 pandemic). In a political climate of increasing backlash to trans* and Indigenous sovereignty, this creative project is a unique contribution to the kete, or basket of knowledge that we offer to the coming generations of trans*formational practitioners and scholars.
Situated within the realms of Indigenous, Queer, Xicana and Critical Black Trans* Feminist theories, this creative project also draws upon performance, sound, and poetic practice to hatch another creative methodology that centers place-based ritual. As I created this thesis in a liminal waterscape, crossing back and forth between Aotearoa and Ixtlán, colliding with the onset of the COVID-19 pandemic, I opened myself to theories generated by the lands that nourished me. Thus, a Kaupapa Māori and Mana Wahine informed approach emerges as the prow of this banka, or canoe that carries other Black, Indigenous and Trans* lineages of scholarship. From this fluid place of theory, my practice as an Indigi-
Trans* ritualist, poet, and sound artist grounds these theories in my body and the body-lands of my co-researchers. Together, we create a Kappi (Ilocano crab motif referencing Maui’s fishing up of our islands) methodology, or the underwater reflections of celestial movement as mapped by Indigi-Trans* freedom strategies. As the co-researchers and storytellers of this project demonstrate, many Indigi-Trans* people are (re)birthing and (re)creating life and possibility just by existing. Our power of place, in body and land, can link and strengthen all Indigenous sovereignty movements when our communities take up the call to foster each person’s fluid potential.
Although this entire project is creative, as a PhD with creative practice component, this project is an ebb and flow of written and other media components. Most of the ‘creative component’ occurred during the co-research stage of this thesis and has been documented via photographs, video, participant testimony, soundscapes, and poetry on a separate, companion website (https://transjoy.cargo.site/). These artifacts of ritual research are also discussed within the harvest (data) section of the written portion, but reader/listeners are encouraged to view the website in tandem. Poetry, narrative, and soundscapes (hyperlinks or bone icons) weave throughout the written portion to create a multi-sensory experience that privileges my roots in aural tradition. Together, the performances, website, poetry, and soundscapes constitute roughly thirty percent of the final thesis, weighing more heavily on a written portion of seventy percent. Listener/readers are encouraged to experience the written and multi-media portions in tandem, cycling back and forth in a playful spirit as the next step of creative practice: listener participation. Please enter this project with the care and excitement invited of all listeners when the storyteller asks, “are you ready to hear a story?”

text: Listening at dawn: Trans* storywork for all my relations This is a love letter to trans* people: a reminder of our place and legacy of trans*formation. In the form of collaborative and ceremonial research, this PhD with creative practice component is an affirmation of embodied, elemental storytelling as a necessary practice for unearthing and grounding the traditional knowledge that Indigenous-Trans* (Indigi-Trans*) people carry within our body-spirits. This creative practice (co)research uplifts liminal states of being, as given to us by our elemental ancestors, in the decolonial project of Indigenous (encompassing Black and Trans*) body-land reclamation and restoration. By recognizing and nourishing the power of the between, this thesis remembers practices of place that are rooted in the body, often our last piece of ancestral land as displaced and diasporic Indigi-Trans* people. Spanning the coasts of Aotearoa-NZ to the west coast of Ixtlán (Turtle Island-US), this creative project listened to the somatic presence of Indigi-Trans* creators (co-researchers) who are in varying states of connection to their ancestral lands and traditions. To account for sudden and extreme shifts in safety and access due to the COVID-19 pandemic, I created online and on-site rituals to sustain connection and retrace our ancestors’ techniques of time and space travel. By engaging with body-awareness practices or ritual performances offered in this project, co-researchers and storytellers were able to experiment with ‘knew’ ways of engaging the ancestral power of place. As a member of the communities contributing to this project, I witnessed an important transformation within co-researchers from a sense of landlessness to a sense of infinite place. This transformation gave co-researchers and storytellers a new source of power, strengthening their spiritual-mental capacity to receive and grow (especially during the height of the COVID-19 pandemic). In a political climate of increasing backlash to trans* and Indigenous sovereignty, this creative project is a unique contribution to the kete, or basket of knowledge that we offer to the coming generations of trans*formational practitioners and scholars.
Situated within the realms of Indigenous, Queer, Xicana and Critical Black Trans* Feminist theories, this creative project also draws upon performance, sound, and poetic practice to hatch another creative methodology that centers place-based ritual. As I created this thesis in a liminal waterscape, crossing back and forth between Aotearoa and Ixtlán, colliding with the onset of the COVID-19 pandemic, I opened myself to theories generated by the lands that nourished me. Thus, a Kaupapa Māori and Mana Wahine informed approach emerges as the prow of this banka, or canoe that carries other Black, Indigenous and Trans* lineages of scholarship. From this fluid place of theory, my practice as an Indigi-
Trans* ritualist, poet, and sound artist grounds these theories in my body and the body-lands of my co-researchers. Together, we create a Kappi (Ilocano crab motif referencing Maui’s fishing up of our islands) methodology, or the underwater reflections of celestial movement as mapped by Indigi-Trans* freedom strategies. As the co-researchers and storytellers of this project demonstrate, many Indigi-Trans* people are (re)birthing and (re)creating life and possibility just by existing. Our power of place, in body and land, can link and strengthen all Indigenous sovereignty movements when our communities take up the call to foster each person’s fluid potential.
Although this entire project is creative, as a PhD with creative practice component, this project is an ebb and flow of written and other media components. Most of the ‘creative component’ occurred during the co-research stage of this thesis and has been documented via photographs, video, participant testimony, soundscapes, and poetry on a separate, companion website (https://transjoy.cargo.site/). These artifacts of ritual research are also discussed within the harvest (data) section of the written portion, but reader/listeners are encouraged to view the website in tandem. Poetry, narrative, and soundscapes (hyperlinks or bone icons) weave throughout the written portion to create a multi-sensory experience that privileges my roots in aural tradition. Together, the performances, website, poetry, and soundscapes constitute roughly thirty percent of the final thesis, weighing more heavily on a written portion of seventy percent. Listener/readers are encouraged to experience the written and multi-media portions in tandem, cycling back and forth in a playful spirit as the next step of creative practice: listener participation. Please enter this project with the care and excitement invited of all listeners when the storyteller asks, “are you ready to hear a story?”

year: 2023