title: Malware Propagation and Prevention Model for Time-Varying Community Networks within Software Defined Networks

authors: Liu, Lan

subjects: Science & Technology

abstract: As the adoption of Software Defined Networks (SDNs) grows, the security of SDN still has several unaddressed limitations. A key network security research area is in the study of malware propagation across the SDN-enabled networks. To analyze the spreading processes of network malware (e.g., viruses) in SDN, we propose a dynamic model with a time-varying community network, inspired by research models on the spread of epidemics in complex networks across communities. We assume subnets of the network as communities and links that are dense in subnets but sparse between subnets. Using numerical simulation and theoretical analysis, we find that the efficiency of network malware propagation in this model depends on the mobility rate q of the nodes between subnets. We also find that there exists a mobility rate threshold 𝑞𝑐. The network malware will spread in the SDN when the mobility rate 𝑞 > 𝑞𝑐. The malware will survive when 𝑞 > 𝑞𝑐 and perish when 𝑞 < 𝑞𝑐. The results showed that our model is effective, and the results may help to decide the SDN control strategy to defend against network malware and provide a theoretical basis to reduce and prevent network security incidents.

text: Malware Propagation and Prevention Model for Time-Varying Community Networks within Software Defined Networks As the adoption of Software Defined Networks (SDNs) grows, the security of SDN still has several unaddressed limitations. A key network security research area is in the study of malware propagation across the SDN-enabled networks. To analyze the spreading processes of network malware (e.g., viruses) in SDN, we propose a dynamic model with a time-varying community network, inspired by research models on the spread of epidemics in complex networks across communities. We assume subnets of the network as communities and links that are dense in subnets but sparse between subnets. Using numerical simulation and theoretical analysis, we find that the efficiency of network malware propagation in this model depends on the mobility rate q of the nodes between subnets. We also find that there exists a mobility rate threshold 𝑞𝑐. The network malware will spread in the SDN when the mobility rate 𝑞 > 𝑞𝑐. The malware will survive when 𝑞 > 𝑞𝑐 and perish when 𝑞 < 𝑞𝑐. The results showed that our model is effective, and the results may help to decide the SDN control strategy to defend against network malware and provide a theoretical basis to reduce and prevent network security incidents.

year: 2017

title: Cultivating microbial dark matter - A combination of traditional and molecular techniques

authors: King, Charlotte

abstract: The services bacteria offer the world are immense and impact people's lives daily. They were first described by Antoni van Leeuwenhoek in 1676, but bacteria have been utilised in the medical, agricultural, and food and beverage industries even before they were formally identified. Microbes’ roles in the environment for cycling of nutrients, climate regulation and pollution are becoming more well understood, and they are also utilised to answer a wide variety of research questions in disparate fields. Traditional cultivation techniques were initially developed to study bacteria and understand their functions as isolates. Such cultivation techniques have become rarer as new molecular and bioinformatic tools have been developed. These cultivation- independent techniques have allowed the study of microbial life genetic data which led to the finding that 99% of all microbial species were yet to be cultured and studied in a laboratory. The applications of these unstudied organisms could be unprecedented, though their cultivation remains challenging due to the requirement of specific nutrients that are hard to identify, very slow growth rates, environmental conditions that are difficult to replicate in a laboratory setting, live in symbiosis with other organisms, or live in extreme climates. Therefore, much of the information may be overlooked and hidden in this microbial dark matter. Methods such as metagenomics, metagenome-assembled genomes (MAGs), and single amplified genomes (SAGs) have provided us with genomic data for previously uncharacterised microbes from diverse environments. However, such data is still limited. Omics tools can provide insights into what is living there and what it can potentially do. However, this data is regularly incomplete due to the processes involved in sequencing, and conclusions are often drawn from associations relating to cultured organisms. This can lead to potentially spurious conclusions as a gene may behave differently in different species, and the absence of genes may depend on how the data was analysed. Therefore, cultured isolates of the organism are vital. To combat this issue of an uncultivated majority, it is important to have a targeted approach to culture, what is wanted, not just what is easy.

This thesis aimed to provide an easy-to-follow, straightforward workflow to cultivate target environmental organisms using standard molecular tools and methods readily accessible in any standard microbiological laboratory. The idea is to isolate and culture what is specifically wanted or needed, not just what is easy. Specifically, it combined classical cultivation and molecular techniques to target a sulphur-reducing, obligate anaerobe from an environmental sample— namely a Desulfurella sp. from a geothermal pool in Rotorua, New Zealand.
In order to provide the desired targeted approach, specific primers needed to be designed and assessed to first find the right sampling site for the initial inoculum and second to ensure the target is not lost throughout the culturing process. I designed and evaluated primers for targeting specific taxa at different stringency levels. Initially, I tested published primers (EPS_F/EPS_R, Gittel et al., 2012) aimed at Epsilonproteobacteria, which were reclassified into the Campylobacterota phylum (including Desulfurella sp.). These primers did not target Desulfurella sp., so I modified them (EPS_FM/EPS_RL) to produce a longer amplicon for broader Campylobacterota detection. However, these also amplified non-target species (e.g., Desulfobacterota). Finally, I designed a third set of primers (DS_F/DS_R) specific to Desulfurella sp., confirmed by in silico testing. These primers allow assessment of Desulfurella sp. and broader Campylobacterota before sequencing.
The second experimental chapter focuses on enriching the target using the previously described primers, classical cultivation techniques, and molecular tools. Site selection was based on the 1000 Springs Project (Power et al., 2018). Culturing was performed originally with DSMZ Desulfurella medium and later modified, investigating pH (4 and 6) and temperature (50°C and 30°C) variations and adapting it for solid media by replacing elemental sulphur with sodium polysulfide. I used a vacuum food sealer to cultivate anaerobes, an accessible and portable alternative to expensive anaerobic chambers. Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to assess axenicity before sending samples for 16S rRNA gene and whole genome sequencing. Desulfurella was detected in each culture using species-specific primers (DS_F/DS_R), enabling its phylogenetic placement. However, despite Desulfurella presence in the 16S rRNA gene amplicon sequencing, a metagenome-assembled genome (MAG) could not be produced. This thesis discusses lessons learned and suggests improvements for future studies.

text: Cultivating microbial dark matter - A combination of traditional and molecular techniques The services bacteria offer the world are immense and impact people's lives daily. They were first described by Antoni van Leeuwenhoek in 1676, but bacteria have been utilised in the medical, agricultural, and food and beverage industries even before they were formally identified. Microbes’ roles in the environment for cycling of nutrients, climate regulation and pollution are becoming more well understood, and they are also utilised to answer a wide variety of research questions in disparate fields. Traditional cultivation techniques were initially developed to study bacteria and understand their functions as isolates. Such cultivation techniques have become rarer as new molecular and bioinformatic tools have been developed. These cultivation- independent techniques have allowed the study of microbial life genetic data which led to the finding that 99% of all microbial species were yet to be cultured and studied in a laboratory. The applications of these unstudied organisms could be unprecedented, though their cultivation remains challenging due to the requirement of specific nutrients that are hard to identify, very slow growth rates, environmental conditions that are difficult to replicate in a laboratory setting, live in symbiosis with other organisms, or live in extreme climates. Therefore, much of the information may be overlooked and hidden in this microbial dark matter. Methods such as metagenomics, metagenome-assembled genomes (MAGs), and single amplified genomes (SAGs) have provided us with genomic data for previously uncharacterised microbes from diverse environments. However, such data is still limited. Omics tools can provide insights into what is living there and what it can potentially do. However, this data is regularly incomplete due to the processes involved in sequencing, and conclusions are often drawn from associations relating to cultured organisms. This can lead to potentially spurious conclusions as a gene may behave differently in different species, and the absence of genes may depend on how the data was analysed. Therefore, cultured isolates of the organism are vital. To combat this issue of an uncultivated majority, it is important to have a targeted approach to culture, what is wanted, not just what is easy.

This thesis aimed to provide an easy-to-follow, straightforward workflow to cultivate target environmental organisms using standard molecular tools and methods readily accessible in any standard microbiological laboratory. The idea is to isolate and culture what is specifically wanted or needed, not just what is easy. Specifically, it combined classical cultivation and molecular techniques to target a sulphur-reducing, obligate anaerobe from an environmental sample— namely a Desulfurella sp. from a geothermal pool in Rotorua, New Zealand.
In order to provide the desired targeted approach, specific primers needed to be designed and assessed to first find the right sampling site for the initial inoculum and second to ensure the target is not lost throughout the culturing process. I designed and evaluated primers for targeting specific taxa at different stringency levels. Initially, I tested published primers (EPS_F/EPS_R, Gittel et al., 2012) aimed at Epsilonproteobacteria, which were reclassified into the Campylobacterota phylum (including Desulfurella sp.). These primers did not target Desulfurella sp., so I modified them (EPS_FM/EPS_RL) to produce a longer amplicon for broader Campylobacterota detection. However, these also amplified non-target species (e.g., Desulfobacterota). Finally, I designed a third set of primers (DS_F/DS_R) specific to Desulfurella sp., confirmed by in silico testing. These primers allow assessment of Desulfurella sp. and broader Campylobacterota before sequencing.
The second experimental chapter focuses on enriching the target using the previously described primers, classical cultivation techniques, and molecular tools. Site selection was based on the 1000 Springs Project (Power et al., 2018). Culturing was performed originally with DSMZ Desulfurella medium and later modified, investigating pH (4 and 6) and temperature (50°C and 30°C) variations and adapting it for solid media by replacing elemental sulphur with sodium polysulfide. I used a vacuum food sealer to cultivate anaerobes, an accessible and portable alternative to expensive anaerobic chambers. Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to assess axenicity before sending samples for 16S rRNA gene and whole genome sequencing. Desulfurella was detected in each culture using species-specific primers (DS_F/DS_R), enabling its phylogenetic placement. However, despite Desulfurella presence in the 16S rRNA gene amplicon sequencing, a metagenome-assembled genome (MAG) could not be produced. This thesis discusses lessons learned and suggests improvements for future studies.

year: 2024

title: Whanau Whakapakari: a Māori-centred approach to child rearing and Parent-training programmes

authors: Herbert, Averil May Lloyd

subjects: Whanau Whakapakari

abstract: The goal of this Whanau Whakapakari (Strengthening Families) research was to define critical aspects of Māori experiences and views on child-rearing practices, and to describe whanau (extended family) values and expectations for tamariki (children) and mokopuna (grandchildren).  Furthermore, these Māori views were included in culturally adapted parent-training programmes.  The overall aim was to devise an approach to emphasise client strengths and provide best outcomes for research participants.  Qualitative aspects included discussing the research processes in the Māori community by acknowledging the roles of whanau, hapu (sub-tribal), and iwi (tribal) structures.  I also identified the importance of pan-tribal and urban Māori groups in the current research.  As the project developed, an ongoing consultation and feedback protocol was established to ensure that Māori views on the research and the written outcomes were recognised.  In-depth interviews with kaumatua (elders), and focus groups with Māori service providers and Māori parents were analysed qualitatively to establish Māori values in child rearing and parenting, and the knowledge and skills that contribute to effective parenting and family functioning.  Values identified from these participants confirmed the central role of whanaungatanga (family connections), whakapapa (genealogy), and awhinatanga (support) for Māori. Two culturally adapted parent-training programmes, the Matuatanga (Parenting) Relationships Model and the Matuatanga Values Model programmes, were developed and compared with a Standard Parent Training programme.  The Matuatanga Relationships Model programme emphasised the importance of child, parent and whanau relationships and interactions.  The Matuatanga Values Model programme emphasised Māori values derived from the qualitative data - whanaungatanga, whakapapa and awhinatanga.  A range of pre- and post-training measures were undertaken to identify acceptable and appropriate measures for quantifying parent-training outcomes.  These included questions on support networks, parent expectations of children, parental self-efficacy, parental self-rating, critical-incident scenarios, and programme evaluation.  While 78 participants attended at least one of the research sessions 22 participants provided pre- and post-training measures for the Whanau Whakapakari programmes.  Results showed that there was a medium effect size improvement across all Standard Parent Training and Matuatanga Model programmes and a statistically significant improvement in the Standard Parent Training and Matuatanga Relationship Model programmes.  There were no statistically significant differences between the outcomes of the different programmes but qualitative differences from evaluation and feedback data were considered in identifying specific skills acquisition, general understanding and enjoyment components in the programmes.  Results from the different measures indicated that parent expectations and critical-incident scenario measures provided the most information on post-training changes.  Analysis of the outcome data with the attendance patterns confirmed the value of parent-training programmes per se and indicated that at least in the short term, parent effectiveness scores continued to improve for participants who continued to attend for more than one programme.  Programme follow-ups considered natural whanau supports in the Māori community and issues of social and cultural validity.  Integration of standard parent-training concepts and cultural concepts suggest a multi-dimensional approach which recognises parenting skills acquisition and cultural validation of whanau concepts relevant to parenting for Māori.

text: Whanau Whakapakari: a Māori-centred approach to child rearing and Parent-training programmes The goal of this Whanau Whakapakari (Strengthening Families) research was to define critical aspects of Māori experiences and views on child-rearing practices, and to describe whanau (extended family) values and expectations for tamariki (children) and mokopuna (grandchildren).  Furthermore, these Māori views were included in culturally adapted parent-training programmes.  The overall aim was to devise an approach to emphasise client strengths and provide best outcomes for research participants.  Qualitative aspects included discussing the research processes in the Māori community by acknowledging the roles of whanau, hapu (sub-tribal), and iwi (tribal) structures.  I also identified the importance of pan-tribal and urban Māori groups in the current research.  As the project developed, an ongoing consultation and feedback protocol was established to ensure that Māori views on the research and the written outcomes were recognised.  In-depth interviews with kaumatua (elders), and focus groups with Māori service providers and Māori parents were analysed qualitatively to establish Māori values in child rearing and parenting, and the knowledge and skills that contribute to effective parenting and family functioning.  Values identified from these participants confirmed the central role of whanaungatanga (family connections), whakapapa (genealogy), and awhinatanga (support) for Māori. Two culturally adapted parent-training programmes, the Matuatanga (Parenting) Relationships Model and the Matuatanga Values Model programmes, were developed and compared with a Standard Parent Training programme.  The Matuatanga Relationships Model programme emphasised the importance of child, parent and whanau relationships and interactions.  The Matuatanga Values Model programme emphasised Māori values derived from the qualitative data - whanaungatanga, whakapapa and awhinatanga.  A range of pre- and post-training measures were undertaken to identify acceptable and appropriate measures for quantifying parent-training outcomes.  These included questions on support networks, parent expectations of children, parental self-efficacy, parental self-rating, critical-incident scenarios, and programme evaluation.  While 78 participants attended at least one of the research sessions 22 participants provided pre- and post-training measures for the Whanau Whakapakari programmes.  Results showed that there was a medium effect size improvement across all Standard Parent Training and Matuatanga Model programmes and a statistically significant improvement in the Standard Parent Training and Matuatanga Relationship Model programmes.  There were no statistically significant differences between the outcomes of the different programmes but qualitative differences from evaluation and feedback data were considered in identifying specific skills acquisition, general understanding and enjoyment components in the programmes.  Results from the different measures indicated that parent expectations and critical-incident scenario measures provided the most information on post-training changes.  Analysis of the outcome data with the attendance patterns confirmed the value of parent-training programmes per se and indicated that at least in the short term, parent effectiveness scores continued to improve for participants who continued to attend for more than one programme.  Programme follow-ups considered natural whanau supports in the Māori community and issues of social and cultural validity.  Integration of standard parent-training concepts and cultural concepts suggest a multi-dimensional approach which recognises parenting skills acquisition and cultural validation of whanau concepts relevant to parenting for Māori.

year: 2001