title: Insights into invasive species from whole‐genome resequencing

authors: North, Henry L.

subjects: adaptation

abstract: Studies of invasive species can simultaneously inform management strategies and quantify rapid evolution in the wild. The role of genomics in invasion science is increasingly recognised, and the growing availability of reference genomes for invasive species is paving the way for whole-genome resequencing studies in a wide range of systems. Here, we survey the literature to assess the application of whole-genome resequencing data in invasion biology. For some applications, such as the reconstruction of invasion routes in time and space, sequencing the whole genome of many individuals can increase the accuracy of existing methods. In other cases, population genomic approaches such as haplotype analysis can permit entirely new questions to be addressed and new technologies applied. To date whole-genome resequencing has only been used in a handful of invasive systems, but these studies have confirmed the importance of processes such as balancing selection and hybridization in allowing invasive species to reuse existing adaptations and rapidly overcome the challenges of a foreign ecosystem. The use of genomic data does not constitute a paradigm shift per se, but by leveraging new theory, tools, and technologies, population genomics can provide unprecedented insight into basic and applied aspects of invasion science.

text: Insights into invasive species from whole‐genome resequencing Studies of invasive species can simultaneously inform management strategies and quantify rapid evolution in the wild. The role of genomics in invasion science is increasingly recognised, and the growing availability of reference genomes for invasive species is paving the way for whole-genome resequencing studies in a wide range of systems. Here, we survey the literature to assess the application of whole-genome resequencing data in invasion biology. For some applications, such as the reconstruction of invasion routes in time and space, sequencing the whole genome of many individuals can increase the accuracy of existing methods. In other cases, population genomic approaches such as haplotype analysis can permit entirely new questions to be addressed and new technologies applied. To date whole-genome resequencing has only been used in a handful of invasive systems, but these studies have confirmed the importance of processes such as balancing selection and hybridization in allowing invasive species to reuse existing adaptations and rapidly overcome the challenges of a foreign ecosystem. The use of genomic data does not constitute a paradigm shift per se, but by leveraging new theory, tools, and technologies, population genomics can provide unprecedented insight into basic and applied aspects of invasion science.

year: 2021

title: Protein Dynamics and its Correlation to Protein Activity and Stability

authors: Clement, David

subjects: Incoherent neutron scattering

abstract: The aim of this thesis is to investigate the role of fast protein dynamics (picosecond
timescale) in enzyme activity and stability, and specifically to test the
hypothesis that enzyme activity and stability are inversely related by their internal
dynamics.
Activity   Dynamics (flexibility)   1/Stability
In order to test this hypothesis, the well known anti-cancer drug: methotrexate
was used as an informative ligand in the network established between these
properties. A multidisciplinary approach combining neutron scattering, circular
dichroism, UV absorption, isothermal titration calorimetry and X-ray crystallography
was undertaken to examine the current paradigm using the enzyme: dihydrofolate
reductase as a model.
As inferred by neutron spectroscopy, the binding of MTX influences the
dynamical behavior of DHFR. Macromolecular dynamics such as the resilience: lt;kgt;
(i.e. structural rigidity) was found to be increased and, inversely, the flexibility
decreased upon MTX binding. In addition, as revealed by circular dichroism, this
dynamical dependency upon MTX binding was correlated with an enhanced thermal
stability. Compared to the free enzyme, the melting temperature was found to be
increased by 13.8  C in the presence of MTX. The inhibitory power of MTX was also
examined by steady state kinetics and isothermal titration calorimetry. The Ki for
MTX was found to be in the nanomolar range Ki= 10.9 nM. Using isothermal
titration calorimetry, the binding thermodynamic signature between MTX and DHFR
was characterized. The binding event was found to be largely favourable (DGb=-12.1
Kcal mol-1), enthalpy driven (DHb= -16.8 Kcal mol-1) with an unfavourable entropy
DSb=-15.6 cal K-1mol-1.
In conclusion, the modulation of the macromolecular dynamics may reflect
how specific conformations are favoured for subsequent protein function in response
of the binding of specific ligand and how conformational substates approach to
protein function. In this context the unprecedented power of transition state analogs
such as MTX on protein function might therefore be dependent on fast protein
dynamics.

text: Protein Dynamics and its Correlation to Protein Activity and Stability The aim of this thesis is to investigate the role of fast protein dynamics (picosecond
timescale) in enzyme activity and stability, and specifically to test the
hypothesis that enzyme activity and stability are inversely related by their internal
dynamics.
Activity   Dynamics (flexibility)   1/Stability
In order to test this hypothesis, the well known anti-cancer drug: methotrexate
was used as an informative ligand in the network established between these
properties. A multidisciplinary approach combining neutron scattering, circular
dichroism, UV absorption, isothermal titration calorimetry and X-ray crystallography
was undertaken to examine the current paradigm using the enzyme: dihydrofolate
reductase as a model.
As inferred by neutron spectroscopy, the binding of MTX influences the
dynamical behavior of DHFR. Macromolecular dynamics such as the resilience: lt;kgt;
(i.e. structural rigidity) was found to be increased and, inversely, the flexibility
decreased upon MTX binding. In addition, as revealed by circular dichroism, this
dynamical dependency upon MTX binding was correlated with an enhanced thermal
stability. Compared to the free enzyme, the melting temperature was found to be
increased by 13.8  C in the presence of MTX. The inhibitory power of MTX was also
examined by steady state kinetics and isothermal titration calorimetry. The Ki for
MTX was found to be in the nanomolar range Ki= 10.9 nM. Using isothermal
titration calorimetry, the binding thermodynamic signature between MTX and DHFR
was characterized. The binding event was found to be largely favourable (DGb=-12.1
Kcal mol-1), enthalpy driven (DHb= -16.8 Kcal mol-1) with an unfavourable entropy
DSb=-15.6 cal K-1mol-1.
In conclusion, the modulation of the macromolecular dynamics may reflect
how specific conformations are favoured for subsequent protein function in response
of the binding of specific ligand and how conformational substates approach to
protein function. In this context the unprecedented power of transition state analogs
such as MTX on protein function might therefore be dependent on fast protein
dynamics.

year: 2009

title: “You’re not coming out – you’ve been there all along and just no one’s looked”: Māori LGBT+ youth and identity exploration

authors: Laurence, Rebekah

subjects: Māori

abstract: This research is a Masters-level project on Māori LGBT-plus (lesbian, gay, bisexual, transgender, and other) youths’ experience of exploring their gender and sexual identities, highlighting how whānau (loosely, ‘extended family’) can provide mana (authority, power) such that youth can exercise mana rangatiratanga (a Maniapoto description of ‘autonomy, self-determination’) regarding their identities. This is a novel, exploratory study.
Adapted elements from a Mana Wāhine (Māori feminist) perspective of Kaupapa Māori theory comprised the theoretical framework for this project. These elements were Mana rangatiratanga (adapted from Tino rangatiratanga), Te reo Māori me ōna tikanga (Māori language and its culture), and Whanaungatanga (relationships). The three elements were adapted to fit a Ngāti Maniapoto worldview. 
Qualitative research methods were used for this study. There were five participants aged between 17 and 24 years, who were Māori and had diverse gender or sexual identities. Semi-structured, face-to-face interviews were conducted with participants, which allowed them to share their experiences of exploring their gender and sexual identities and of whānau support. Interviews were analysed using a process of inductive thematic analysis, which identified and analysed patterns across the dataset.
Eight themes were derived from participants’ experiences. These themes were Ko Tūhura, which described the process of discovery that participants have experienced; Ko Matatapu, which described participants’ experience of authenticity and concealment of their gender and sexual identities; Ko Tautoko, which described how whānau have empowered participants to explore their identities, and how participants have been denied empowerment; Ko Mata-ngaro, which described participants’ early lack of exposure to diverse identities, and their having their identities unseen by others; Ko te Ahunga-ki-te-aunoa, which described how diverse identities have been accepted within participants’ whānau; Ko Tauawhi, which described how participants have been embraced for their diverse identities; Ko Mata-pū-take, which describes participants’ experience of finding somewhere to belong; and Ko Kiritau, which describes participants’ becoming settled in their expression of their gender and sexual identities.
The findings of the thesis describe roles that whānau play in participants’ exploration of their gender and sexual identities and some of the effects that colonisation has had within participants’ whānau regarding their gender and sexual identities. Nonetheless, participants actively resisted these aspects of colonisations and found ways to give voice to their gender and sexual identities.
Given that participants shared that there was a dearth of information regarding gender and sexual identities available to them within their whānau and school environments, organisations within psychology and related fields may work to proactively provide all young Māori people and their whānau with information regarding diverse gender and sexual identities. Moreover, to address the dearth of resources designed for Māori LGBT-plus youth, New Zealand-based researchers may collate information specifically regarding Māori LGBT-plus youth experience of identity exploration and Māori knowledges regarding gender and sexual identities. This information may be collated in community-based resources that are designed specifically for members of this group and their whānau, and professionals who work for them.

text: “You’re not coming out – you’ve been there all along and just no one’s looked”: Māori LGBT+ youth and identity exploration This research is a Masters-level project on Māori LGBT-plus (lesbian, gay, bisexual, transgender, and other) youths’ experience of exploring their gender and sexual identities, highlighting how whānau (loosely, ‘extended family’) can provide mana (authority, power) such that youth can exercise mana rangatiratanga (a Maniapoto description of ‘autonomy, self-determination’) regarding their identities. This is a novel, exploratory study.
Adapted elements from a Mana Wāhine (Māori feminist) perspective of Kaupapa Māori theory comprised the theoretical framework for this project. These elements were Mana rangatiratanga (adapted from Tino rangatiratanga), Te reo Māori me ōna tikanga (Māori language and its culture), and Whanaungatanga (relationships). The three elements were adapted to fit a Ngāti Maniapoto worldview. 
Qualitative research methods were used for this study. There were five participants aged between 17 and 24 years, who were Māori and had diverse gender or sexual identities. Semi-structured, face-to-face interviews were conducted with participants, which allowed them to share their experiences of exploring their gender and sexual identities and of whānau support. Interviews were analysed using a process of inductive thematic analysis, which identified and analysed patterns across the dataset.
Eight themes were derived from participants’ experiences. These themes were Ko Tūhura, which described the process of discovery that participants have experienced; Ko Matatapu, which described participants’ experience of authenticity and concealment of their gender and sexual identities; Ko Tautoko, which described how whānau have empowered participants to explore their identities, and how participants have been denied empowerment; Ko Mata-ngaro, which described participants’ early lack of exposure to diverse identities, and their having their identities unseen by others; Ko te Ahunga-ki-te-aunoa, which described how diverse identities have been accepted within participants’ whānau; Ko Tauawhi, which described how participants have been embraced for their diverse identities; Ko Mata-pū-take, which describes participants’ experience of finding somewhere to belong; and Ko Kiritau, which describes participants’ becoming settled in their expression of their gender and sexual identities.
The findings of the thesis describe roles that whānau play in participants’ exploration of their gender and sexual identities and some of the effects that colonisation has had within participants’ whānau regarding their gender and sexual identities. Nonetheless, participants actively resisted these aspects of colonisations and found ways to give voice to their gender and sexual identities.
Given that participants shared that there was a dearth of information regarding gender and sexual identities available to them within their whānau and school environments, organisations within psychology and related fields may work to proactively provide all young Māori people and their whānau with information regarding diverse gender and sexual identities. Moreover, to address the dearth of resources designed for Māori LGBT-plus youth, New Zealand-based researchers may collate information specifically regarding Māori LGBT-plus youth experience of identity exploration and Māori knowledges regarding gender and sexual identities. This information may be collated in community-based resources that are designed specifically for members of this group and their whānau, and professionals who work for them.

year: 2020