title: Microbial abundance and diversity surrounding mummified seals in Miers Valley, Antarctica

authors: Robson, Lisa Marie

subjects: Dry Valleys

abstract: The presence of a number of mummified seal carcasses have been reported in the Dry Valleys of Antarctica. The location of seal carcasses were observed up to 240km in-land, and approximately 1500m above sea level. The extremely cold and dry conditions in the Dry Valleys act to mummify the seal remams, preserving these anomalies for an undetermined length of time.
Given the virtual absence of above ground plant biomass in the Dry Valleys, the primary source of soil organic matter sustaining microbial ecosystems was not obvious. It was hypothesised that these large sources of organic contamination, in the form of a seal carcass, may act to enrich the localised environment surrounding the carcasses with carbon and nitrogen. The increased levels of organic carbon and nitrogen would result in increased microbial abundance and diversity.
A total of 100 environmental samples were taken by Professors S.C. Cary, and D.A. Cowan, surrounding, and directly beneath eleven mummified seals located in Miers Valley, the Antarctic Dry Valleys, on Event D023 Terrestrial Microbiology Antarctic New Zealand 2001/2002. Three of these seals (MVSl, MVS3 and MVS 13) and the areas surrounding, were sampled extensively, and were the basis of research in this Master of Science thesis.
Microbial diversity was investigated using molecular cloning and sequence analysis, and Denaturing Gradient Gel Electrophoresis, of 16S and 18S rDNA amplicons. A large diversity in bacterial populations present in the environmental samples taken from directly beneath the Miers Valley seal carcasses was observed in comparison to control samples of Miers Valley soils.
The levels of microbial abundance were determined by luciferase-dependent luminometric ATP analysis, and analysis of the total quantities of double stranded DNA extracted from the environmental samples. Microbial abundance was found to be increased in samples taken in closer proximity to a seal carcass.
Carbon and nitrogen analysis were conducted on all samples, using a fully automated Europa Scientific 20/20 isotope analyser. The level of carbon present in an environmental sample appeared not to influence the abundance of microorganisms. The levels of nitrogen measured were higher in environmental samples collected in close proximity to the seal carcasses. These samples displayed the greatest microbial abundance, and indicated large differences in the bacterial diversity compared to Miers Valley control samples.
On the basis of these results, and ATP data, the hypothesis of this MSc thesis was determined to be correct. Microbial abundance was found to increase with enrichment of nitrogen surrounding MVS 1 and MVS 13 seal carcasses, and large differences in bacterial diversity were found in environmental samples showing the highest levels of nitrogen enrichment, compared to samples taken further away from the seal, or in Miers Valley control samples.
This thesis effectively described the utilisation of cloning and sequence analysis, and denaturing gradient gel electrophoresis to investigate microbial diversity in Antarctic environmental samples. This study gave a greater understanding in microbial ecology in Miers Valley, Antarctica.

text: Microbial abundance and diversity surrounding mummified seals in Miers Valley, Antarctica The presence of a number of mummified seal carcasses have been reported in the Dry Valleys of Antarctica. The location of seal carcasses were observed up to 240km in-land, and approximately 1500m above sea level. The extremely cold and dry conditions in the Dry Valleys act to mummify the seal remams, preserving these anomalies for an undetermined length of time.
Given the virtual absence of above ground plant biomass in the Dry Valleys, the primary source of soil organic matter sustaining microbial ecosystems was not obvious. It was hypothesised that these large sources of organic contamination, in the form of a seal carcass, may act to enrich the localised environment surrounding the carcasses with carbon and nitrogen. The increased levels of organic carbon and nitrogen would result in increased microbial abundance and diversity.
A total of 100 environmental samples were taken by Professors S.C. Cary, and D.A. Cowan, surrounding, and directly beneath eleven mummified seals located in Miers Valley, the Antarctic Dry Valleys, on Event D023 Terrestrial Microbiology Antarctic New Zealand 2001/2002. Three of these seals (MVSl, MVS3 and MVS 13) and the areas surrounding, were sampled extensively, and were the basis of research in this Master of Science thesis.
Microbial diversity was investigated using molecular cloning and sequence analysis, and Denaturing Gradient Gel Electrophoresis, of 16S and 18S rDNA amplicons. A large diversity in bacterial populations present in the environmental samples taken from directly beneath the Miers Valley seal carcasses was observed in comparison to control samples of Miers Valley soils.
The levels of microbial abundance were determined by luciferase-dependent luminometric ATP analysis, and analysis of the total quantities of double stranded DNA extracted from the environmental samples. Microbial abundance was found to be increased in samples taken in closer proximity to a seal carcass.
Carbon and nitrogen analysis were conducted on all samples, using a fully automated Europa Scientific 20/20 isotope analyser. The level of carbon present in an environmental sample appeared not to influence the abundance of microorganisms. The levels of nitrogen measured were higher in environmental samples collected in close proximity to the seal carcasses. These samples displayed the greatest microbial abundance, and indicated large differences in the bacterial diversity compared to Miers Valley control samples.
On the basis of these results, and ATP data, the hypothesis of this MSc thesis was determined to be correct. Microbial abundance was found to increase with enrichment of nitrogen surrounding MVS 1 and MVS 13 seal carcasses, and large differences in bacterial diversity were found in environmental samples showing the highest levels of nitrogen enrichment, compared to samples taken further away from the seal, or in Miers Valley control samples.
This thesis effectively described the utilisation of cloning and sequence analysis, and denaturing gradient gel electrophoresis to investigate microbial diversity in Antarctic environmental samples. This study gave a greater understanding in microbial ecology in Miers Valley, Antarctica.

year: 2004

title: Model checking for cloud autoscaling using WATERS

authors: van Zijl, Martin

subjects: cloud computing

abstract: This thesis investigates the use of formal methods to verify cloud system designs against Service Level Agreements (SLAs), towards providing guarantees under uncertainty. We used WATERS (the Waikato Analysis Toolkit for Events in Reactive Systems), which is a model-checking tool based on discrete event systems. We created models for one aspect of cloud computing, horizontal autoscaling, and used this to verify cloud system designs against an SLA that specifies the maximum request response time.

To evaluate the accuracy of the WATERS models, the cloud system designs are simulated on a private Kubernetes cluster, using JMeter to drive the workload. The results from Kubernetes are compared to the verification results from WATERS. A key research goal was to have these match as closely as possible, and to explain the discrepancies between the two. This process is followed for two applications: a default installation of NGINX, a web server with a fast but variable response time, and a hand-written Node.js program enforcing a fixed response time.

The results suggest that WATERS can be used to predict potential SLA violations. Lessons learned include that the state space must be constrained to avoid excessive checking times, and we provide a method for doing so. An advantage of our model checking-based technique is that it verifies against all possible patterns of arriving requests (up to a given maximum), which would be impractical to test with a load testing tool such as JMeter.

A key difference from existing work is our use non-probabilistic finite state machines, as opposed to probabilistic models which are prevalent in existing research. In addition, we have attempted to model the detail of the autoscaling process (a “white-box” approach), whereas much existing research attempts to find patterns between autoscaling parameters and SLA violation, effectively viewing autoscaling as a black-box process.

Future work includes refining the WATERS models to more closely match Kubernetes, and modelling other SLO types. Other methods may also be used to limit the compilation and verification time for the models. This includes attempting different algorithms and perhaps editing the models to reduce the state space.

text: Model checking for cloud autoscaling using WATERS This thesis investigates the use of formal methods to verify cloud system designs against Service Level Agreements (SLAs), towards providing guarantees under uncertainty. We used WATERS (the Waikato Analysis Toolkit for Events in Reactive Systems), which is a model-checking tool based on discrete event systems. We created models for one aspect of cloud computing, horizontal autoscaling, and used this to verify cloud system designs against an SLA that specifies the maximum request response time.

To evaluate the accuracy of the WATERS models, the cloud system designs are simulated on a private Kubernetes cluster, using JMeter to drive the workload. The results from Kubernetes are compared to the verification results from WATERS. A key research goal was to have these match as closely as possible, and to explain the discrepancies between the two. This process is followed for two applications: a default installation of NGINX, a web server with a fast but variable response time, and a hand-written Node.js program enforcing a fixed response time.

The results suggest that WATERS can be used to predict potential SLA violations. Lessons learned include that the state space must be constrained to avoid excessive checking times, and we provide a method for doing so. An advantage of our model checking-based technique is that it verifies against all possible patterns of arriving requests (up to a given maximum), which would be impractical to test with a load testing tool such as JMeter.

A key difference from existing work is our use non-probabilistic finite state machines, as opposed to probabilistic models which are prevalent in existing research. In addition, we have attempted to model the detail of the autoscaling process (a “white-box” approach), whereas much existing research attempts to find patterns between autoscaling parameters and SLA violation, effectively viewing autoscaling as a black-box process.

Future work includes refining the WATERS models to more closely match Kubernetes, and modelling other SLO types. Other methods may also be used to limit the compilation and verification time for the models. This includes attempting different algorithms and perhaps editing the models to reduce the state space.

year: 2020

title: Mana Takatāpui: Self-determination for queer rangatahi Māori

authors: Doyle, Benjamin Kauri

subjects: Takatāpui

abstract: Here is a Master’s thesis crafted with, by, and for Rangatahi Takatāpui. It represents a labour of love for the community to which I belong, and seeks to generate understanding about the factors that enable LGBTQI+ Māori youth to embody and enact Tino Rangatiratanga. Principles of Kaupapa Māori Theory provide a paradigm through which this research is conducted, with particular attention paid to the Indigenous Research Agenda. Importantly, this rangahau seeks to offer an alternative to the conventions of hegemonic empirical academia by centering the voices and lived experiences of those who have historically been subjected to the dehumanising objectification of western research practices.

Through the methodological approach of wānanga, and within a Tikanga Māori framework of Āta, or cultural safety, twelve Rangatahi Takatāpui participated in a two day workshop at Te Kohinga Mārama Marae. Over the course of both days, co-researchers shared personal testimonies about their experiences navigating the world as Queer Indigenous peoples, as well as the dreams and aspirations they have for collective self-determination. These accounts ultimately inform the narrative storying employed to convey the key findings of this research, which are described as Mana Tuakiri (identity), Mana Hapori (belonging), Mana Moemoeā (vision), and Mana Wero (challenges).

To make sense of the findings presented in this rangahau, a model is developed which takes inspiration from Te Takarangi, the double spiral motif common in both Toi Māori and Te Tai Ao. Utilising the cyclical and intersecting patterns of Te Takarangi, the four main themes of this research are explored through a progressive layering of personal, interpersonal, and societal relationships in order to provide insight into how best Rangatahi Takatāpui can be supported to enact Tino Rangatiratanga. Ultimately, this research present nine key factors to be addressed and implemented in order to achieve this aspiration, including a call for conscientisation (both the self and the collective), resourcing and support, the removal of barriers to access, community intersectional reflexivity, space for collective Indigenous dreaming, and an ongoing commitment to Te Tiriti justice.

text: Mana Takatāpui: Self-determination for queer rangatahi Māori Here is a Master’s thesis crafted with, by, and for Rangatahi Takatāpui. It represents a labour of love for the community to which I belong, and seeks to generate understanding about the factors that enable LGBTQI+ Māori youth to embody and enact Tino Rangatiratanga. Principles of Kaupapa Māori Theory provide a paradigm through which this research is conducted, with particular attention paid to the Indigenous Research Agenda. Importantly, this rangahau seeks to offer an alternative to the conventions of hegemonic empirical academia by centering the voices and lived experiences of those who have historically been subjected to the dehumanising objectification of western research practices.

Through the methodological approach of wānanga, and within a Tikanga Māori framework of Āta, or cultural safety, twelve Rangatahi Takatāpui participated in a two day workshop at Te Kohinga Mārama Marae. Over the course of both days, co-researchers shared personal testimonies about their experiences navigating the world as Queer Indigenous peoples, as well as the dreams and aspirations they have for collective self-determination. These accounts ultimately inform the narrative storying employed to convey the key findings of this research, which are described as Mana Tuakiri (identity), Mana Hapori (belonging), Mana Moemoeā (vision), and Mana Wero (challenges).

To make sense of the findings presented in this rangahau, a model is developed which takes inspiration from Te Takarangi, the double spiral motif common in both Toi Māori and Te Tai Ao. Utilising the cyclical and intersecting patterns of Te Takarangi, the four main themes of this research are explored through a progressive layering of personal, interpersonal, and societal relationships in order to provide insight into how best Rangatahi Takatāpui can be supported to enact Tino Rangatiratanga. Ultimately, this research present nine key factors to be addressed and implemented in order to achieve this aspiration, including a call for conscientisation (both the self and the collective), resourcing and support, the removal of barriers to access, community intersectional reflexivity, space for collective Indigenous dreaming, and an ongoing commitment to Te Tiriti justice.

year: 2023