The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

Background Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL. Results In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL. Conclusions NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the “arms race” with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.

Cultural safety and diversity: Refocusing our energies in mental health nursing practice, education and research

INTRODUCTION AND BACKGROUND: This presentation draws on a body of work assessing cultural safety's potential to generate change in mental health nursing research (Cox and Simpson 2015), in education and in clinical practice (Cox and Taua 2013, 2016; Happell, Cowin, Roper, Lakeman & Cox 2013). It presents evidence to suggest that cultural safety could resolve the conceptual confusion surrounding culture and diversity in nursing curricular, in clinical and in research practice. The history and nature of mental health work recommend cultural safety to focus attention on diversity, power imbalance, racism, cultural dominance, and structural inequality, identified as barriers and tensions in clinical practice and in service user participation. Cultural safety gives mental health nursing a well theorized and articulated model, which is evolving to improve practice into the future. DESCRIPTION: This work involved an immersion in the literature on cultural safety and the Service User Research movement. It draws on 5 months' work with a service users' research group in the UK and reflections on 9 years of cultural safety teaching. POLICY/PRACTICE CHANGE: This work provokes a crucial change of emphasis from locating the source of issues in the diversity of people to locating it in how society responds to diversity: a change from individualistic to systemic concerns. IMPLICATIONS FOR MENTAL HEALTH NURSING: Cultural safety in clinical practice, education, and research is specifically concerned with awareness of the impact of systemic workplace cultures and with staff cultural self-awareness to bring about cultural change and person-centred care of individuals' unique needs and aspirations within their life context.

Social objectives of fisheries management: What are managers' priorities?

Increasingly, social considerations are having an influence on fisheries policy as well as day-to-day management decision making. Social objectives, unlike economic or conservation objectives, are often poorly defined in fisheries policy, providing substantial leeway for managers to develop management plans in response to the perceived importance of different social outcomes, and potential inconsistencies between different fisheries and jurisdictions. In this paper, through a literature review and workshop with managers across different Australian jurisdictions, we develop a set of social objectives that may be applicable in Australian fisheries. We assess the importance of these different objectives using the Analytic Hierarchy Process, and find considerable diversity in opinion as to which social objectives fisheries management should prioritise to achieve. This diversity of opinion is not directly related to jurisdiction, but does seem related to the context and social environment in which fisheries managers are operating.

Identification of pathotypes of the sorghum rust pathogen, Puccinia purpurea, in Australia

This study aimed to determine if pathotypic diversity of the sorghum rust pathogen, P. purpurea, exists in eastern Australia. A differential set of 10 Sorghum bicolor genotypes was used to identify four putative pathotypes from the 28 P. purpurea isolates that were tested. Pathotypes 1 and 3 were the most common, together comprising 85.7 % of the isolates tested, while pathotype 2 comprised 10.7 % of isolates, and pathotype 4 the remainder. Based on the limited number of isolates that were tested, there was evidence of geographic specialization amongst the pathotypes, with pathotype 1 not being found in north Queensland. This work has provided conclusive evidence that pathotypes of P. purpurea exist in the sorghum growing regions of Australia and has resulted in the development of a protocol for identifying pathotypes and screening breeding and experimental lines for resistance to these pathotypes. However, further investigations on the pathotypic diversity of P. purpurea and on the temporal and geographic distribution of these four as well as any additional undiscovered pathotypes are needed.

Floristic composition and pasture condition of Aristida/Bothriochloa pastures in central Queensland. II. Soil and pasture condition interactions

Sustainable management of native pastures requires an understanding of what the bounds of pasture composition, cover and soil surface condition are for healthy pastoral landscapes to persist. A survey of 107 Aristida/Bothriochloa pasture sites in inland central Queensland was conducted. The sites were chosen for their current diversity of tree cover, apparent pasture condition and soil type to assist in setting more objective bounds on condition ‘states’ in such pastures. Assessors’ estimates of pasture condition were strongly correlated with herbage mass (r = 0.57) and projected ground cover (r = 0. 58), and moderately correlated with pasture crown cover (r = 0.35) and tree basal area (r = 0.32). Pasture condition was not correlated with pasture plant density or the frequency of simple guilds of pasture species. The soil type of Aristida/Bothriochloa pasture communities was generally hard-setting, low in cryptogam cover but moderately covered with litter and projected ground cover (30–50%). There was no correlation between projected ground cover of pasture and estimated ground-level cover of plant crowns. Tree basal area was correlated with broad categories of soil type, probably because greater tree clearing has occurred on the more fertile, heavy-textured clay soils. Of the main perennial grasses, some showed strong soil preferences, for example Tripogon loliiformis for hard-setting soils and Dichanthium sericeum for clays. Common species, such as Chrysopogon fallax and Heteropogon contortus, had no strong soil preference. Wiregrasses (Aristida spp.) tended to be uncommon at both ends of the estimated pasture condition scale whereas H. contortus was far more common in pastures in good condition. Sedges (Cyperaceae) were common on all soil types and for all pasture condition ratings. Plants identified as increaser species were Tragus australianus, daisies (Asteraceae) and potentially toxic herbaceous legumes such as Indigofera spp. and Crotalaria spp. Pasture condition could not be reliably predicted based on the abundance of a single species or taxon but there may be scope for using integrated data for four to five ecologically contrasting plants such as Themeda triandra with daisies, T. loliiformis and flannel weeds (Malvaceae).

Floristic composition and pasture condition of Aristida/Bothriochloa pastures in central Queensland. I. Pasture floristics

A survey was conducted in central inland Queensland, Australia of 108 sites that were deemed to contain Aristida/Bothriochloa native pastures to quantitatively describe the pastures and attempt to delineate possible sub-types. The pastures were described in terms of their floristic composition, plant density and crown cover. There were generally ~20 (range 5–33) main pasture species at a site. A single dominant perennial grass was rare with three to six prominent species the norm. Chrysopogon fallax (golden-beard grass) was the perennial grass most consistently found in all pastures whereas Aristida calycina (dark wiregrass), Enneapogon spp. (bottlewasher grasses), Brunoniella australis (blue trumpet) and Panicum effusum (hairy panic) were all regularly present. The pastures did not readily separate into broad floristic sub-groups, but three groups that landholders could recognise from a combination of the dominant tree and soil type were identified. The three groups were Eucalyptus crebra (narrow-leaved ironbark), E. melanophloia (silver-leaved ironbark) and E. populnea (poplar box). The pastures of the three main sub-groups were then characterised by the prominent presence, singly or in combination, of Bothriochloa ewartiana (desert bluegrass), Eremochloa bimaculata (poverty grass), Bothriochloa decipiens (pitted bluegrass) or Heteropogon contortus (black speargrass). The poplar box group had the greatest diversity of prominent grasses whereas the narrow-leaved ironbark group had the least. Non-native Cenchrus ciliaris (buffel grass) and Melinis repens (red Natal grass) were generally present at low densities. Describing pastures in terms of frequency of a few species or species groups sometimes failed to capture the true nature of the pasture but plant abundance for most species, as density, herbage mass of dry matter or plant crown cover, was correlated with its recorded frequency. A quantitative description of an average pasture in fair condition is provided but it was not possible to explain why some species often occur together or fail to co-exist in Aristida/Bothriochloa pastures, for example C. ciliaris and E. bimaculata rarely co-exist whereas Tragus australianus (small burrgrass) and Enneapogon spp. are frequently recorded together. Most crown cover was provided by perennial grasses but many of these are Aristida spp. (wiregrasses) and not regarded as useful forage for livestock. No new or improved categorisation of the great variation evident in the Aristida/Bothriochloa native pasture type can be given despite the much improved detail provided of the floristic composition by this survey.

Mapping the carriage of flaA-restriction fragment length polymorphism Campylobacter genotypes on poultry carcasses through the processing chain and comparison to clinical isolates

Poultry are considered a major source for campylobacteriosis in humans. A total of 1866 Campylobacter spp. isolates collected through the poultry processing chain were typed using flaA-restriction fragment length polymorphism to measure the impact of processing on the genotypes present. Temporally related human clinical isolates (n = 497) were also typed. Isolates were obtained from whole chicken carcass rinses of chickens collected before scalding, after scalding, before immersion chilling, after immersion chilling and after packaging as well as from individual caecal samples. A total of 32 genotypes comprising at least four isolates each were recognised. Simpson's Index of Diversity (D) was calculated for each sampling site within each flock, for each flock as a whole and for the clinical isolates. From caecal collection to after packaging samples the D value did not change in two flocks, decreased in one flock and increased in the fourth flock. Dominant genotypes occurred in each flock but their constitutive percentages changed through processing. There were 23 overlapping genotypes between clinical and chicken isolates. The diversity of Campylobacter is flock dependant and may alter through processing. This study confirms that poultry are a source of campylobacteriosis in the Australian population although other sources may contribute.

Understandings of higher education curriculum in Vietnam

The Vietnamese higher education context is characterised by state control including the state’s development of curriculum frameworks and materials. Institutional autonomy has been ratified by the government, however, in practice universities seem to have little control over curriculum. In order for universities to develop more ownership of curriculum, it is necessary to explore the foundational understandings of curriculum held by stakeholders. Thus, this paper explores the understandings of curriculum expressed by a group of senior staff, academics and students at a Vietnamese university. We found a diversity of understandings that tended to be product-focused, teacher-focused and textbook-driven. We propose that our findings can be used as a starting point for developing more innovative and student-focused understandings of curriculum.

Crime Justice and Social Democracy: Proceedings of the 3rd International Conference, 9-10 July 2015

We are pleased to present these selected papers from the proceedings of the 3rd Crime, Justice and Social Democracy International Conference, held in July 2015 in Brisbane, Australia. Over 350 delegates attended the conference from 19 countries. The papers collected here reflect the diversity of topics and themes that were explored over three days. The Crime, Justice and Social Democracy International Conference aims to strengthen the intellectual and policy debates concerning links between justice, social democracy, and the reduction of harm and crime, through building more just and inclusive societies and proposing innovative justice responses. In 2015, attendees discussed these issues as they related to ideas of green criminology; indigenous justice; gender, sex and justice; punishment and society; and the emerging notion of ‘Southern criminology’. The need to build global connections to address these challenges is more evident than ever and the conference and these proceedings reflect a growing attention to interdisciplinary, novel, and interconnected responses to contemporary global challenges. Authors in these conference proceedings engaged with issues of online fraud, queer criminology and law, Indigenous incarceration, youth justice, incarceration in Brazil, and policing in Victoria, Australia, among others. The topics explored speak to the themes of the conference and demonstrate the range of challenges facing researchers of crime, harm, social democracy and social justice and the spaces of possibility that such research opens. Our thanks to the conference convenor, Dr Kelly Richards, for organising such a successful conference, and to all those presenters who subsequently submitted such excellent papers for review here. We would also particularly like to thank Jess Rodgers for their tireless editorial assistance, as well as the panel of international scholars who participated in the review process, often within tight timelines.

4QMMT - The Problem of the Epilogue

The main focus of this study is the epilogue of 4QMMT (4QMiqsat Ma aseh ha-Torah), a text of obscure genre containing a halakhic section found in cave 4 at Qumran. In the official edition published in the series Discoveries of the Judaean Desert (DJD X), the extant document was divided by its editors, Elisha Qimron and John Strugnell, into three literary divisions: Section A) the calendar section representing a 364-day solar calendar, Section B) the halakhot, and Section C) an epilogue. The work begins with text critical inspection of the manuscripts containing text from the epilogue (mss 4Q397, 4Q398, and 4Q399). However, since the relationship of the epilogue to the other sections of the whole document 4QMMT is under investigation, the calendrical fragments (4Q327 and 4Q394 3-7, lines 1-3) and the halakhic section also receive some attention, albeit more limited and purpose oriented. In Ch. 2, after a transcription of the fragments of the epilogue, a synopsis is presented in order to evaluate the composite text of the DJD X edition in light of the evidence provided by the individual manuscripts. As a result, several critical comments are offered, and finally, an alternative arrangement of the fragments of the epilogue with an English translation. In the following chapter (Ch. 3), the diversity of the two main literary divisions, the halakhic section and the epilogue, is discussed, and it is demonstrated that the author(s) of 4QMMT adopted and adjusted the covenantal pattern known from biblical law collections, more specifically Deuteronomy. The question of the genre of 4QMMT is investigated in Ch. 4. The final chapter (Ch. 5) contains an analysis of the use of Scripture in the epilogue. In a close reading, both the explicit citations and the more subtle allusions are investigated in an attempt to trace the theology of the epilogue. The main emphases of the epilogue are covenantal faithfulness, repentance and return. The contents of the document reflect a grave concern for the purity of the cult in Jerusalem, and in the epilogue Deuteronomic language and expressions are used to convince the readers of the necessity of a reformation. The large number of late copies found in cave 4 at Qumran witness the significance of 4QMMT and the continuous importance of the Jerusalem Temple for the Qumran community.

Aspects of Arminian Soteriology in Methodist-Lutheran Ecumenical Dialogues in 20th and 21st Century

The aim of this thesis is to analyse the key ecumenical dialogues between Methodists and Lutherans from the perspective of Arminian soteriology and Methodist theology in general. The primary research question is defined as: "To what extent do the dialogues under analysis relate to Arminian soteriology?" By seeking an answer to this question, new knowledge is sought on the current soteriological position of the Methodist-Lutheran dialogues, the contemporary Methodist theology and the commonalities between the Lutheran and Arminian understanding of soteriology. This way the soteriological picture of the Methodist-Lutheran discussions is clarified. The dialogues under analysis were selected on the basis of versatility. Firstly, the sole world organisation level dialogue was chosen: The Church – Community of Grace. Additionally, the document World Methodist Council and the Joint Declaration on the Doctrine of Justification is analysed as a supporting document. Secondly, a document concerning the discussions between two main-line churches in the United States of America was selected: Confessing Our Faith Together. Thirdly, two dialogues between non-main-line Methodist churches and main-line Lutheran national churches in Europe were chosen: Fellowship of Grace from Norway and Kristuksesta osalliset from Finland. The theoretical approach to the research conducted in this thesis is systematic analysis. The Remonstrant articles of Arminian soteriology are utilised as an analysis tool to examine the soteriological positions of the dialogues. New knowledge is sought by analysing the stances of the dialogues concerning the doctrines of partial depravity, conditional election, universal atonement, resistible grace and conditional perseverance of saints. This way information is also provided for approaching the Calvinist-Arminian controversy from new perspectives. The results of this thesis show that the current soteriological position of the Methodist-Lutheran dialogues is closer to Arminianism than Calvinism. The dialogues relate to Arminian soteriology especially concerning the doctrines of universal atonement, resistible grace and conditional perseverance of saints. The commonalities between the Lutheran and Arminian understanding of soteriology exist mainly in these three doctrines as they are uniformly favoured in the dialogues. The most discussed area of soteriology is human depravity, in which the largest diversity of stances occurs as well. On the other hand, divine election is the least discussed topic. The overall perspective, which the results of the analysis provide, indicates that the Lutherans could approach the Calvinist churches together with the Methodists with a wider theological perspective and understanding when the soteriological issues are considered as principal. Human depravity is discovered as the area of soteriology which requires most work in future ecumenical dialogues. However, the detected Lutheran hybrid notion on depravity (a Calvinist-Arminian mixture) appears to provide a useful new perspective for Calvinist-Arminian ecumenism and offers potentially fruitful considerations to future ecumenical dialogues.

Consensus statement on the role of Accredited Exercise Physiologists within the treatment of mental disorders: A guide for mental health professionals

- Objective The aim is to identify the role and scope of Accredited Exercise Physiologist (AEP) services in the mental health sector and to provide insight as to how AEPs can contribute to the multidisciplinary mental health team. - Methods A modified Delphi approach was utilised. Thirteen AEPs with experience in mental health contributed to the iterative development of a national consensus statement. Six mental health professionals with expertise in psychiatry, mental health nursing, general practice and mental health research participated in the review process. Reviewers were provided with a template to systematically provide feedback on the language, content, structure and relevance to their professional group. - Results This consensus statement outlines how AEPs can contribute to the multidisciplinary mental health team, the aims and scope of AEP-led interventions in mental health services and examples of such interventions, the range of physical and mental health outcomes possible through AEP-led interventions and common referral pathways to community AEP services. - Outcome AEPs can play a key role in the treatment of individuals experiencing mental illness. The diversity of AEP interventions allows for a holistic approach to care, enhancing both physical and mental health outcomes.

Causes and consequences of inbreeding in the ant Formica exsecta

Human actions cause destruction and fragmentation of natural habitats, predisposing populations to loss of genetic diversity and inbreeding, which may further decrease their fitness and survival. Understanding these processes is a main concern in conservation genetics. Yet data from natural populations is scarce, particularly on invertebrates, owing to difficulties in measuring both fitness and inbreeding in the wild. Ants are social insects, and a prime example of an ecologically important group for which the effects of inbreeding remain largely unstudied. Social insects serve key roles in all terrestrial ecosystems, and the division of labor between the females in the colonies queens reproduce, workers tend to the developing brood probably is central to their ecological success. Sociality also has important implications for the effects of inbreeding. Despite their relative abundance, the effective population sizes of social insects tend to be small, owing to the low numbers of reproductive individuals relative to the numbers of sterile workers. This may subject social insects to loss of genetic diversity and subsequent inbreeding depression. Moreover, both the workers and queens can be inbred, with different and possibly multiplicative consequences. The aim of this study was to investigate causes and consequences of inbreeding in a natural population of ants. I used a combination of long-term field and genetic data from colonies of the narrow-headed ant Formica exsecta to examine dispersal, mating behavior and the occurrence of inbreeding, and its consequences on individual and colony traits. Mating in this species takes place in nuptial flights that have been assumed to be population-wide and panmictic. My results, however, show that dispersal is local, with queens establishing new colonies as close as 60 meters from their natal colony. Even though actual sib-mating was rare, individuals from different but related colonies pair, which causes the population to be inbred. Furthermore, multiple mates of queens were related to each other, which also indicates localized mating flights. Hence, known mechanisms of inbreeding avoidance, dispersal and multiple mating, were not effective in this population, as neither reduced inbreeding level of the future colony. Inbreeding had negative consequences both at the individual and colony level. A queen that has mated with a related male produces inbred workers, which impairs the colony s reproductive success. The inbred colonies were less productive and, specifically, produced fewer new queens, possibly owing to effects of inbreeding on the caste determination of female larvae. A striking finding was that males raised in colonies with inbred workers were smaller, which reflects an effect of the social environment as males, being haploid, cannot be inbred themselves. The queens produced in the inbred colonies, in contrast, were not smaller, but their immune response was up-regulated. Inbreeding had no effect on queen dispersal, but inbred queens had a lower probability of successfully founding a new colony. Ultimately, queens that survived through the colony founding phase had a shorter lifespan. This supports the idea that inbreeding imposes a genetic stress, leading to inbreeding depression on both the queen and the colony level. My results show that inbreeding can have profound consequences on insects in the wild, and that in social species the effects of inbreeding may be multiplicative and mediated through the diversity of the social environment, as well as the genetic makeup of the individuals themselves. This emphasizes the need to take into account all levels of organization when assessing the effects of genetic diversity in social animals.

Spatial and temporal determinants of Finnish farmland bird populations

During the past decades agricultural intensification has caused dramatic population declines in a wide range of taxa related to farmland habitats, including farmland birds. In this thesis, I studied how boreal farmland landscape characteristics and agricultural land use affect the abundance and diversity of farmland birds using extensive field data collected by territory mapping of breeding farmland birds in various parts of Finland. My results show that the area and openness of agricultural areas are key determinants of farmland bird abundance and distribution. A landscape composition with enough open farmland combined with key habitats such as farmyards and wetland is likely to provide essential prerequisites for the occurrence of a rich farmland avifauna. In Finland, the majority of large areas suitable for open habitat specialists are located in southern and western parts of the country. However, the diversity of the species with an unfavourable conservation status in Europe (SPECs) had notable hotspot areas in northern and north-western agricultural areas. I found that in boreal agroecosystems farmland birds favour fields with springtime vegetative cover, especially agricultural grasslands and set-asides. Hence, in the spring cereal dominated Finnish agroecosystems it is the absence of field vegetation that may limit populations of many farmland bird species. It is likely that the decrease of crops providing vegetative cover in the spring, such as permanent grasslands, cultivated grass, and autumn-sown cereals, has greatly contributed to the declines of Finnish farmland birds. Grass crops have persistently declined in Finland as a consequence of specialization in crop production and the large-scale decline in livestock husbandry. Small-scale non-crop habitats, especially ditches and ditch margins, are also important for many bird species in the Finnish agroecosystems, but have dramatically declined during the last decades. A major problem for farmland bird conservation in Finland is the conflict between landscape structure and agricultural management. Areas with mixed and cattle farming are virtually absent from the large agricultural plains of southern and south-western Finland, where the landscape structure is more likely to be favourable for rich farmland bird assemblages. On the other hand, mixed and cattle farming is still rather frequent in northern and central parts of the country, where the landscape structure is not suitable for many farmland specialist birds requiring open landscapes. My results provide useful guidelines for farmland bird conservation, and imply that considerable attention needs to be paid to landscape factors when selecting areas for various conservational management actions, such as agri-environment schemes. Actions promoting the abundance of set-asides, grass crops, and ditches would markedly benefit Finnish farmland bird populations. Organic farming may benefit farmland birds, but it is not clear how general its beneficial effect is in boreal agroecosystems. The most urgent action aiming to preserve farmland biodiversity would be to support re-introducing and sustaining cattle farming by environmental subsidies. This would be especially beneficial in the southern parts of Finland, where the landscape characteristics and abundance of agricultural areas are most suitable for farmland birds and where cattle farming is currently rare.

Characterization of the molecular components and function of BARE-1, Hin-Mu and Mu transposition machineries

Transposable elements, transposons, are discrete DNA segments that are able to move or copy themselves from one locus to another within or between their host genome(s) without a requirement for DNA homology. They are abundant residents in virtually all the genomes studied, for instance, the genomic portion of TEs is approximately 3% in Saccharomyces cerevisiae, 45% in humans, and apparently more than 70% in some plant genomes such as maize and barley. Transposons plays essential role in genome evolution, in lateral transfer of antibiotic resistance genes among bacteria and in life cycle of certain viruses such as HIV-1 and bacteriophage Mu. Despite the diversity of transposable elements they all use a fundamentally similar mechanism called transpositional DNA recombination (transposition) for the movement within and between the genomes of their host organisms. The DNA breakage and joining reactions that underlie their transposition are chemically similar in virtually all known transposition systems. The similarity of the reactions is also reflected in the structure and function of the catalyzing enzymes, transposases and integrases. The transposition reactions take place within the context of a transposition machinery, which can be particularly complex, as in the case of the VLP (virus like particle) machinery of retroelements, which in vivo contains RNA or cDNA and a number of element encoded structural and catalytic proteins. Yet, the minimal core machinery required for transposition comprises a multimer of transposase or integrase proteins and their binding sites at the element DNA ends only. Although the chemistry of DNA transposition is fairly well characterized, the components and function of the transposition machinery have been investigated in detail for only a small group of elements. This work focuses on the identification, characterization, and functional studies of the molecular components of the transposition machineries of BARE-1, Hin-Mu and Mu. For BARE-1 and Hin-Mu transpositional activity has not been shown previously, whereas bacteriophage Mu is a general model of transposition. For BARE-1, which is a retroelement of barley (Hordeum vulgare), the protein and DNA components of the functional VLP machinery were identified from cell extracts. In the case of Hin-Mu, which is a Mu-like prophage in Haemophilus influenzae Rd genome, the components of the core machinery (transposase and its binding sites) were characterized and their functionality was studied by using an in vitro methodology developed for Mu. The function of Mu core machinery was studied for its ability to use various DNA substrates: Hin-Mu end specific DNA substrates and Mu end specific hairpin substrates. The hairpin processing reaction by MuA was characterized in detail. New information was gained of all three machineries. The components or their activity required for functional BARE-1 VLP machinery and retrotransposon life cycle were present in vivo and VLP-like structures could be detected. The Hin-Mu core machinery components were identified and shown to be functional. The components of the Mu and Hin-Mu core machineries were partially interchangeable, reflecting both evolutionary conservation and flexibility within the core machineries. The Mu core machinery displayed surprising flexibility in substrate usage, as it was able to utilize Hin-Mu end specific DNA substrates and to process Mu end DNA hairpin substrates. This flexibility may be evolutionarily and mechanistically important.