title: Retroviruses in the common brush-tailed possum (Trichosurus vulpecula)

authors: Baillie, Gregory John

abstract: This study details the search for, and characterisation of, retroviruses in a marsupial, the common brush-tailed possum (Trichosurus vulpecula). Initial efforts were directed at detecting exogenous retroviruses in possums, but the majority of the work described in this thesis involved the isolation and characterisation of a possum endogenous retrovirus.

Endogenous retroviruses were detected in possum genomic DNA by PCR amplification using degenerate primers derived from the retroviral pol gene. Cloning, sequencing, and analysis of these PCR products revealed the presence of several families of endogenous retroviruses in the possum genome.

Reverse transcriptase activity was detected in the blood of all possums tested using the product enhanced reverse transcriptase (PERT) assay. RT-PCR was performed on RNA isolated from possum blood plasma using the pol-derived degenerate primers. Cloning and sequencing of the products indicated that a homogeneous retroviral RNA species was present in the blood of possums, and that this RNA was related to, but not identical to, the endogenous possum retroviruses already detected.

A 3'-RACE approach was used to amplify the majority of the 3' end of the possum retroviral RNA. The subsequent discovery that this RNA species was derived from an endogenous retrovirus in the possum genome allowed amplification of the remainder of the genome by a combination of PCR, single primer PCR, and RT-PCR. The sequences were assembled into a contiguous sequence, the TvERV-K1 contig. In addition, a near-full-length TvERV-K1-related fragment, was amplified from possum genomic DNA, cloned, and sequenced. It was named pTvERV-K2. The TvERV-K elements are the first full-length marsupial retrovirus sequences to be reported.

Analysis of the sequences of the TvERV-K1 contig and pTvERV-K2 revealed most of the regulatory regions required for replication of a retroviral genome, as well as uninterrupted, or minimally interrupted, open reading frames (ORFs) for the gag, pro, and pol genes. Only a short region of sequence with homology to the Env proteins of other retroviruses was detected. All of the TvERV-K proteins displayed highest homology to those of the simian type D retroviruses. Likewise, phylogenetic analysis using the deduced amino acid sequences of the Pro and Pol proteins, placed the possum endogenous retrovirus with the exogenous and endogenous type D retroviruses of Old World and New World monkeys. Thus, a cross-species transmission event - from marsupials to primates, from primates to marsupials, or from an unidentified source to both marsupials and primates - appears to have occurred.

There are 15-20 copies of the TvERV-K element in the possum genome, as determined by Southern hybridisation. However, integration sites appeared to be variable between possums, suggesting recent (or ongoing) retrotranspositional activity. Both PCR and Southern hybridisation analyses suggest that TvERV-K elements shorter than those from which the TvERV-K1 contig and pTvERV-K2 were derived are present in the possum genome. 

The implications of these findings are discussed.

text: Retroviruses in the common brush-tailed possum (Trichosurus vulpecula) This study details the search for, and characterisation of, retroviruses in a marsupial, the common brush-tailed possum (Trichosurus vulpecula). Initial efforts were directed at detecting exogenous retroviruses in possums, but the majority of the work described in this thesis involved the isolation and characterisation of a possum endogenous retrovirus.

Endogenous retroviruses were detected in possum genomic DNA by PCR amplification using degenerate primers derived from the retroviral pol gene. Cloning, sequencing, and analysis of these PCR products revealed the presence of several families of endogenous retroviruses in the possum genome.

Reverse transcriptase activity was detected in the blood of all possums tested using the product enhanced reverse transcriptase (PERT) assay. RT-PCR was performed on RNA isolated from possum blood plasma using the pol-derived degenerate primers. Cloning and sequencing of the products indicated that a homogeneous retroviral RNA species was present in the blood of possums, and that this RNA was related to, but not identical to, the endogenous possum retroviruses already detected.

A 3'-RACE approach was used to amplify the majority of the 3' end of the possum retroviral RNA. The subsequent discovery that this RNA species was derived from an endogenous retrovirus in the possum genome allowed amplification of the remainder of the genome by a combination of PCR, single primer PCR, and RT-PCR. The sequences were assembled into a contiguous sequence, the TvERV-K1 contig. In addition, a near-full-length TvERV-K1-related fragment, was amplified from possum genomic DNA, cloned, and sequenced. It was named pTvERV-K2. The TvERV-K elements are the first full-length marsupial retrovirus sequences to be reported.

Analysis of the sequences of the TvERV-K1 contig and pTvERV-K2 revealed most of the regulatory regions required for replication of a retroviral genome, as well as uninterrupted, or minimally interrupted, open reading frames (ORFs) for the gag, pro, and pol genes. Only a short region of sequence with homology to the Env proteins of other retroviruses was detected. All of the TvERV-K proteins displayed highest homology to those of the simian type D retroviruses. Likewise, phylogenetic analysis using the deduced amino acid sequences of the Pro and Pol proteins, placed the possum endogenous retrovirus with the exogenous and endogenous type D retroviruses of Old World and New World monkeys. Thus, a cross-species transmission event - from marsupials to primates, from primates to marsupials, or from an unidentified source to both marsupials and primates - appears to have occurred.

There are 15-20 copies of the TvERV-K element in the possum genome, as determined by Southern hybridisation. However, integration sites appeared to be variable between possums, suggesting recent (or ongoing) retrotranspositional activity. Both PCR and Southern hybridisation analyses suggest that TvERV-K elements shorter than those from which the TvERV-K1 contig and pTvERV-K2 were derived are present in the possum genome. 

The implications of these findings are discussed.

year: 1999

title: Tidal inlet configuration and bathymetric changes resulting from active sedimentation, Buffalo Bay, New Zealand.

authors: Steeghs, Lauren

subjects: accretion

abstract: The Whitianga tidal inlet lies within Mercury Bay, on the northeast coast of New Zealand. The Whitianga Estuary harbours many recreational and commercial vessels. Terrestrial sediment inputs into the Whitianga Estuary catchment are high, due to the erodible tertiary sediments and the steep nature of the catchment, which suffers intense rainfall that results in high sediment influxes, much of which becomes deposited within the estuary. In recent years active shoals have appeared in Buffalo Bay and the inlet channel has noticeably shallowed, both of which inhibit the use of the inlet by boat traffic. The past and present bathymetry of Buffalo Bay is compared to establish changes in morphology and zones of accretion and erosion within Buffalo Bay. The outcomes of this research contribute to a larger research programme which aims to use numerical model simulations to identify sediment transport pathways and patterns within Buffalo Bay. This research will particularly provide information which can be used to calibrate a sediment transport model. Comparison of the Buffalo Bay bathymetries over the 38 year period from 1938 to 1979 and Whitianga inlet bathymetries between 1979 and 1995, show extensive accretion in the ebb discharge channel which is predominantly associated with the migration of the tidal inlet channel and growth of the ebb delta, and within the inner inlet area which are attributed to the growth of the flood delta system.

text: Tidal inlet configuration and bathymetric changes resulting from active sedimentation, Buffalo Bay, New Zealand. The Whitianga tidal inlet lies within Mercury Bay, on the northeast coast of New Zealand. The Whitianga Estuary harbours many recreational and commercial vessels. Terrestrial sediment inputs into the Whitianga Estuary catchment are high, due to the erodible tertiary sediments and the steep nature of the catchment, which suffers intense rainfall that results in high sediment influxes, much of which becomes deposited within the estuary. In recent years active shoals have appeared in Buffalo Bay and the inlet channel has noticeably shallowed, both of which inhibit the use of the inlet by boat traffic. The past and present bathymetry of Buffalo Bay is compared to establish changes in morphology and zones of accretion and erosion within Buffalo Bay. The outcomes of this research contribute to a larger research programme which aims to use numerical model simulations to identify sediment transport pathways and patterns within Buffalo Bay. This research will particularly provide information which can be used to calibrate a sediment transport model. Comparison of the Buffalo Bay bathymetries over the 38 year period from 1938 to 1979 and Whitianga inlet bathymetries between 1979 and 1995, show extensive accretion in the ebb discharge channel which is predominantly associated with the migration of the tidal inlet channel and growth of the ebb delta, and within the inner inlet area which are attributed to the growth of the flood delta system.

year: 2007

title: Different coloured tears: Dual cultural identity and Tangihanga – A directed study

authors: Edge, Kiri

subjects: bereavement

abstract: Although whānau/family that are configured by both Pākehā and Māori identities number significantly within New Zealand, there has been little or no attention paid to the ways in which these identities influence the bereavement processes that will inevitably impact upon the lives of these whānau/family. The present study explored the experiences of an individual, whose whānau/family included two life ways; Māori and Pākehā. Of specific focus was the ways in which these identities influenced his bereavement subsequent to the death of his beloved wife, who was of Māori descent. One elderly male Pākehā participant was interviewed, using an open-ended narrative approach. The interview was semi structured around five broad themes, but the focus was upon the participant’s experiences and his preference in expressing these. The data analysis utilised a thematic process, which allowed the participant’s experiences to determine the emergent themes. The results depicted the diversity of issues that may be raised for dual cultural whānau/family within bereavement processes. Two central themes are discussed in relation to intercultural conflict and the eventual resolution that was created. Decision making processes, cultural and language differences played significant roles within the conflict and exclusion experienced by the participant. Communication and compromise provided resolution to the prior conflicts experienced. This created positive and unexpected outcomes which resulted in increased understandings and the strengthening of links between the participant, his whānau/family and his wife’s marae.

text: Different coloured tears: Dual cultural identity and Tangihanga – A directed study Although whānau/family that are configured by both Pākehā and Māori identities number significantly within New Zealand, there has been little or no attention paid to the ways in which these identities influence the bereavement processes that will inevitably impact upon the lives of these whānau/family. The present study explored the experiences of an individual, whose whānau/family included two life ways; Māori and Pākehā. Of specific focus was the ways in which these identities influenced his bereavement subsequent to the death of his beloved wife, who was of Māori descent. One elderly male Pākehā participant was interviewed, using an open-ended narrative approach. The interview was semi structured around five broad themes, but the focus was upon the participant’s experiences and his preference in expressing these. The data analysis utilised a thematic process, which allowed the participant’s experiences to determine the emergent themes. The results depicted the diversity of issues that may be raised for dual cultural whānau/family within bereavement processes. Two central themes are discussed in relation to intercultural conflict and the eventual resolution that was created. Decision making processes, cultural and language differences played significant roles within the conflict and exclusion experienced by the participant. Communication and compromise provided resolution to the prior conflicts experienced. This created positive and unexpected outcomes which resulted in increased understandings and the strengthening of links between the participant, his whānau/family and his wife’s marae.

year: 2010-01