title: Characterising the Physiological Responses of Chinook Salmon (Oncorhynchus tshawytscha) Subjected to Heat and Oxygen Stress.

authors: Marcoli, Roberta

subjects: Chinook salmon

abstract: In New Zealand, during the hottest periods of the year, some salmon farms in the Marlborough Sounds reach water temperatures above the optimal range for Chinook salmon. High levels of mortality are recorded during these periods, emphasising the importance of understanding thermal stress in this species. In this study, the responses of Chinook salmon (Oncorhynchus tshawytscha) to chronic, long-term changes in temperature and dissolved oxygen were investigated. This is a unique investigation due to the duration of the stress events the fish were exposed to. Health and haematological parameters were analysed alongside gene expression results to determine the effects of thermal stress on Chinook salmon. Six copies of heat shock protein 90 (HSP90) were discovered and characterised: HSP90AA1.1a, HSP90AA1.2a, HSP90AA1.1b, HSP90AA1.2b, HSP90AB1a and HSP90AB1b, as well as two copies of SOD1, named SOD1a and SOD1b. The amino acid sequences contained features similar to those found in other vertebrate HSP90 and SOD1 sequences, and the phylogenetic tree and synteny analysis provided conclusive evidence of their relationship to other vertebrate HSP90 and SOD1 genes. Primers were designed for qPCR to enable the expression of all copies of HSP90 and SOD1 to be analysed. The expression studies showed that HSP90 and SOD1 were downregulated in the liver and spleen in response to longer term exposure to high temperatures and lower dissolved oxygen. HSP90 was also downregulated in the gill; however, the results for SOD1 expression in the gill were not conclusive. This study provides important insights into the physiological and genetic responses of Chinook salmon to temperature and oxygen stress, which are critical for developing sustainable fish aquaculture in an era of changing global climates.

text: Characterising the Physiological Responses of Chinook Salmon (Oncorhynchus tshawytscha) Subjected to Heat and Oxygen Stress. In New Zealand, during the hottest periods of the year, some salmon farms in the Marlborough Sounds reach water temperatures above the optimal range for Chinook salmon. High levels of mortality are recorded during these periods, emphasising the importance of understanding thermal stress in this species. In this study, the responses of Chinook salmon (Oncorhynchus tshawytscha) to chronic, long-term changes in temperature and dissolved oxygen were investigated. This is a unique investigation due to the duration of the stress events the fish were exposed to. Health and haematological parameters were analysed alongside gene expression results to determine the effects of thermal stress on Chinook salmon. Six copies of heat shock protein 90 (HSP90) were discovered and characterised: HSP90AA1.1a, HSP90AA1.2a, HSP90AA1.1b, HSP90AA1.2b, HSP90AB1a and HSP90AB1b, as well as two copies of SOD1, named SOD1a and SOD1b. The amino acid sequences contained features similar to those found in other vertebrate HSP90 and SOD1 sequences, and the phylogenetic tree and synteny analysis provided conclusive evidence of their relationship to other vertebrate HSP90 and SOD1 genes. Primers were designed for qPCR to enable the expression of all copies of HSP90 and SOD1 to be analysed. The expression studies showed that HSP90 and SOD1 were downregulated in the liver and spleen in response to longer term exposure to high temperatures and lower dissolved oxygen. HSP90 was also downregulated in the gill; however, the results for SOD1 expression in the gill were not conclusive. This study provides important insights into the physiological and genetic responses of Chinook salmon to temperature and oxygen stress, which are critical for developing sustainable fish aquaculture in an era of changing global climates.

year: 2023-10-17

title: How life uses sound to reorganise matter: The role of anharmonic phonon exchange in enzyme catalysis

authors: Batterton, Christopher

subjects: enzyme catalysis

abstract: Biological enzyme catalysis is the name for life's ability to rapidly invoke coordinated rearrangements of molecular structures using highly specialised, relatively-large functional proteins called enzymes. It is well established that enzymes reduce the activation energy barrier, which vastly accelerates the rate of reaction, however the specific dynamics and quantum mechanics are largely uncharted. Recent experimentation and modelling hints that there is a phase transition dynamic that is fundamental to enzymatic catalysis. The hypothesis that I explore in this thesis is that a mathematical model of a substrate molecule based upon anharmonic quantum vibrational modes (molecular phonons) will predict phase transition dynamics due to the presence of the appropriate enzyme. A molecular phonon is one particular individualised wave pattern in the locations of atomic nuclei from the total molecular dance that spans the low-frequency bulk swaying motions, mid-frequency bond stretches, to the high-frequency oscillations of the hydrogen bond network. 


In this thesis, I derive a generalised set of equations of motion for the anharmonic response behaviour of molecular phonons to enzyme stimulus via a dissipative quantum master equation, and I explore the phase transition dynamics by determining the stability bifurcation of the steady states. I then determine the critical minimum stimulus required for a molecular vibrational mode to exhibit a phase transition. The primary catalytic reaction of focus for this thesis is the cleavage of the glycosidic carbon-oxygen bond of the complex sugar isomaltose into two individual glucose molecules via the action of the enzyme MalL. Prior to this thesis, the atomic structure of MalL was obtained experimentally via X-ray diffraction crystallography of prepared MalL crystals, then digitised into the Gromacs software package and energy minimised in a simulated water bath to approximate the vibrational modes of the in vivo configuration. I obtain the substrate molecule's harmonic frequencies and anharmonic shifts via molecular dynamics performed using the Gaussian 09 normal mode analysis and simulated anharmonic infrared spectroscopy packages, respectively. I construct a generalised coding package in Matlab to extract the molecule and enzyme data, perform a quantum anharmonic analysis of the molecule--enzyme complex and their interactions, and then simulate the response of the molecule to stimulus from the enzyme. 

 
I determine that the vibrational modes of isomaltose that significantly contribute to stretching the glycosidic carbon-oxygen bond occur within the 21 to 35 THz (700 to 1,170 cm^{-1}) frequency bandwidth, and the dominant stretching modes are contained within 28 to 33 THz (930 to 1,100cm^{-1}), which is in agreement with the experimental literature of polysaccharides. In the final chapter, I perform numerical simulations of the equations of motion to compute the energy response spectrogram for a proxy substrate (benzene) under conditions that are informed by literature and the theoretical findings of this thesis. In lieu of anharmonic isomaltose data, I selected benzene as it is a small molecule with a high degree of symmetry which has several bond stretching modes within the aforementioned bandwidth. The results show that while the stimulus from water is insufficient, there are vibrational modes pertaining to glycosidic bond stretching that can be selectively excited to phase transition behaviour due to a reasonable stimulus from the supply of phonons from the MalL enzyme.

text: How life uses sound to reorganise matter: The role of anharmonic phonon exchange in enzyme catalysis Biological enzyme catalysis is the name for life's ability to rapidly invoke coordinated rearrangements of molecular structures using highly specialised, relatively-large functional proteins called enzymes. It is well established that enzymes reduce the activation energy barrier, which vastly accelerates the rate of reaction, however the specific dynamics and quantum mechanics are largely uncharted. Recent experimentation and modelling hints that there is a phase transition dynamic that is fundamental to enzymatic catalysis. The hypothesis that I explore in this thesis is that a mathematical model of a substrate molecule based upon anharmonic quantum vibrational modes (molecular phonons) will predict phase transition dynamics due to the presence of the appropriate enzyme. A molecular phonon is one particular individualised wave pattern in the locations of atomic nuclei from the total molecular dance that spans the low-frequency bulk swaying motions, mid-frequency bond stretches, to the high-frequency oscillations of the hydrogen bond network. 


In this thesis, I derive a generalised set of equations of motion for the anharmonic response behaviour of molecular phonons to enzyme stimulus via a dissipative quantum master equation, and I explore the phase transition dynamics by determining the stability bifurcation of the steady states. I then determine the critical minimum stimulus required for a molecular vibrational mode to exhibit a phase transition. The primary catalytic reaction of focus for this thesis is the cleavage of the glycosidic carbon-oxygen bond of the complex sugar isomaltose into two individual glucose molecules via the action of the enzyme MalL. Prior to this thesis, the atomic structure of MalL was obtained experimentally via X-ray diffraction crystallography of prepared MalL crystals, then digitised into the Gromacs software package and energy minimised in a simulated water bath to approximate the vibrational modes of the in vivo configuration. I obtain the substrate molecule's harmonic frequencies and anharmonic shifts via molecular dynamics performed using the Gaussian 09 normal mode analysis and simulated anharmonic infrared spectroscopy packages, respectively. I construct a generalised coding package in Matlab to extract the molecule and enzyme data, perform a quantum anharmonic analysis of the molecule--enzyme complex and their interactions, and then simulate the response of the molecule to stimulus from the enzyme. 

 
I determine that the vibrational modes of isomaltose that significantly contribute to stretching the glycosidic carbon-oxygen bond occur within the 21 to 35 THz (700 to 1,170 cm^{-1}) frequency bandwidth, and the dominant stretching modes are contained within 28 to 33 THz (930 to 1,100cm^{-1}), which is in agreement with the experimental literature of polysaccharides. In the final chapter, I perform numerical simulations of the equations of motion to compute the energy response spectrogram for a proxy substrate (benzene) under conditions that are informed by literature and the theoretical findings of this thesis. In lieu of anharmonic isomaltose data, I selected benzene as it is a small molecule with a high degree of symmetry which has several bond stretching modes within the aforementioned bandwidth. The results show that while the stimulus from water is insufficient, there are vibrational modes pertaining to glycosidic bond stretching that can be selectively excited to phase transition behaviour due to a reasonable stimulus from the supply of phonons from the MalL enzyme.

year: 2024

title: Huikau

authors: Maxwell, Te Kahautu

abstract: Huikau is dedicated to my life long mentor and educator Mrs Ema Rogers who imparted her knowledge of Te Haahi Ringatū and things Māori to me. She housed me for months while I reseearched my MA Thesis Te Kōpura. Mrs Rogers passed away in December 2012. This new composition was performed by Ōpōtiki Mai Tawhiti Kapa Haka at the Mātaatua Regional Kapa Haka Competition. This composition placed first in the Waiata Tira category.

text: Huikau Huikau is dedicated to my life long mentor and educator Mrs Ema Rogers who imparted her knowledge of Te Haahi Ringatū and things Māori to me. She housed me for months while I reseearched my MA Thesis Te Kōpura. Mrs Rogers passed away in December 2012. This new composition was performed by Ōpōtiki Mai Tawhiti Kapa Haka at the Mātaatua Regional Kapa Haka Competition. This composition placed first in the Waiata Tira category.

year: 2012