title: Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility

authors: Grzymski, Joseph J.

subjects: Epsilonproteobacteria

abstract: Hydrothermal vent ecosystems support diverse life forms, many of which rely on symbiotic associations to perform functions integral to survival in these extreme physicochemical environments. Epsilonproteobacteria, found free-living and in intimate associations with vent invertebrates, are the predominant vent-associated microorganisms. The vent-associated polychaete worm, Alvinella pompejana, is host to a visibly dense fleece of episymbionts on its dorsal surface. The episymbionts are a multispecies consortium of Epsilonproteobacteria present as a biofilm. We unraveled details of these enigmatic, uncultivated episymbionts using environmental genome sequencing. They harbor wide-ranging adaptive traits that include high levels of strain variability analogous to Epsilonproteobacteria pathogens such as Helicobacter pylori, metabolic diversity of free-living bacteria, and numerous orthologs of proteins that we hypothesize are each optimally adapted to specific temperature ranges within the 10–65 °C fluctuations characteristic of the A. pompejana habitat. This strategic combination enables the consortium to thrive under diverse thermal and chemical regimes. The episymbionts are metabolically tuned for growth in hydrothermal vent ecosystems with genes encoding the complete rTCA cycle, sulfur oxidation, and denitrification; in addition, the episymbiont metagenome also encodes capacity for heterotrophic and aerobic metabolisms. Analysis of the environmental genome suggests that A. pompejana may benefit from the episymbionts serving as a stable source of food and vitamins. The success of Epsilonproteobacteria as episymbionts in hydrothermal vent ecosystems is a product of adaptive capabilities, broad metabolic capacity, strain variance, and virulent traits in common with pathogens.

text: Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility Hydrothermal vent ecosystems support diverse life forms, many of which rely on symbiotic associations to perform functions integral to survival in these extreme physicochemical environments. Epsilonproteobacteria, found free-living and in intimate associations with vent invertebrates, are the predominant vent-associated microorganisms. The vent-associated polychaete worm, Alvinella pompejana, is host to a visibly dense fleece of episymbionts on its dorsal surface. The episymbionts are a multispecies consortium of Epsilonproteobacteria present as a biofilm. We unraveled details of these enigmatic, uncultivated episymbionts using environmental genome sequencing. They harbor wide-ranging adaptive traits that include high levels of strain variability analogous to Epsilonproteobacteria pathogens such as Helicobacter pylori, metabolic diversity of free-living bacteria, and numerous orthologs of proteins that we hypothesize are each optimally adapted to specific temperature ranges within the 10–65 °C fluctuations characteristic of the A. pompejana habitat. This strategic combination enables the consortium to thrive under diverse thermal and chemical regimes. The episymbionts are metabolically tuned for growth in hydrothermal vent ecosystems with genes encoding the complete rTCA cycle, sulfur oxidation, and denitrification; in addition, the episymbiont metagenome also encodes capacity for heterotrophic and aerobic metabolisms. Analysis of the environmental genome suggests that A. pompejana may benefit from the episymbionts serving as a stable source of food and vitamins. The success of Epsilonproteobacteria as episymbionts in hydrothermal vent ecosystems is a product of adaptive capabilities, broad metabolic capacity, strain variance, and virulent traits in common with pathogens.

year: 2008

title: Detecting sequential structure

authors: Nevill-Manning, Craig G.

subjects: PBD

abstract: Programming by demonstration requires detection and analysis of sequential patterns in a user’s input, and the synthesis of an appropriate structural model that can be used for prediction. This paper describes SEQUITUR, a scheme for inducing a structural description of a sequence from a single example. SEQUITUR integrates several different inference techniques: identification of lexical subsequences or vocabulary elements, hierarchical structuring of such subsequences, identification of elements that have equivalent usage patterns, inference of programming constructs such as looping and branching, generalisation by unifying grammar rules, and the detection of procedural substructure., Although SEQUITUR operates with abstract sequences, a number of concrete illustrations are provided.

text: Detecting sequential structure Programming by demonstration requires detection and analysis of sequential patterns in a user’s input, and the synthesis of an appropriate structural model that can be used for prediction. This paper describes SEQUITUR, a scheme for inducing a structural description of a sequence from a single example. SEQUITUR integrates several different inference techniques: identification of lexical subsequences or vocabulary elements, hierarchical structuring of such subsequences, identification of elements that have equivalent usage patterns, inference of programming constructs such as looping and branching, generalisation by unifying grammar rules, and the detection of procedural substructure., Although SEQUITUR operates with abstract sequences, a number of concrete illustrations are provided.

year: 1995

title: A trans-national analysis of equitable utilisation and minimisation of environmental harm under environmental laws at international, federal and national levels

authors: Hasan, Qaraman

subjects: International Environmental Law

abstract: Due to increasing demand for various human needs and climate change issues, rivers are now under enormous pressure. With increasing pressure on these valuable natural resources, responses among state and non-state actors are insufficient in the Anthropocene. To fill the gap, International Environmental Law (IEL) provides several principles for better management of these resources. Equitable utilisation and minimisation of environmental harm are among the most important principles of the IEL. From a theoretical perspective, these principles should lead to the sustainability of these resources and promote cooperation among relevant actors.

However, many river basins are still not allocated equitably and suffer from environmental damage. By using comparative, doctrinal, and empirical research methods, this thesis evaluates the two principles at the international level in Tigris and Euphrates River Basin, the federal level in Murray Darling Basin and at the local level in the Waikato River catchment. The research discovered major challenges for implementing the two principles. One major challenge is sovereignty, another is a lack or weakness of local voices and transparency. As the nature and status of all basins are different, the challenges are not exactly the same. For example, hearing local voices and better information transparency have significantly improved in the Waikato River.

As the challenges for implementing the two principles are not purely legal, the responses should blend legal solutions with political and socio-economic solutions. Therefore, this thesis strongly supports shared sovereignty among states at the international level as well as shared sovereignty with indigenous and minority groups at the national level. Cooperation among national and international actors in the river basins is also crucial for implementing the two principles effectively. Finally, there is the opportunity to establish basin institutions or organisations to manage river basins integrated and sustainable. This is vital in the case of TE-RB because the basin still lacks an institution. Furthermore, the basin institution in the MDB requires more robust compliance and monitoring power because the provisions of the Water Act 2007 and the basin plan still have not been implemented effectively.

Finally, the thesis concludes with two common lessons in comparing these cases. The first lesson is that equitable utilisation cannot be implemented effectively if it is not accepted by the local community in a broad and deep meaning. It means that the equitable allocation should be extended from only the riparian states to equitable allocation among the people within each state. The second lesson is that the minimisation of environmental harm cannot be implemented without determining the minimum flow of rivers, particularly transboundary rivers. Determining an environmental impact assessment for water projects and taking advantage of available solutions of nature contributes significantly in implementing the two principles and sustainable management of our rivers.

text: A trans-national analysis of equitable utilisation and minimisation of environmental harm under environmental laws at international, federal and national levels Due to increasing demand for various human needs and climate change issues, rivers are now under enormous pressure. With increasing pressure on these valuable natural resources, responses among state and non-state actors are insufficient in the Anthropocene. To fill the gap, International Environmental Law (IEL) provides several principles for better management of these resources. Equitable utilisation and minimisation of environmental harm are among the most important principles of the IEL. From a theoretical perspective, these principles should lead to the sustainability of these resources and promote cooperation among relevant actors.

However, many river basins are still not allocated equitably and suffer from environmental damage. By using comparative, doctrinal, and empirical research methods, this thesis evaluates the two principles at the international level in Tigris and Euphrates River Basin, the federal level in Murray Darling Basin and at the local level in the Waikato River catchment. The research discovered major challenges for implementing the two principles. One major challenge is sovereignty, another is a lack or weakness of local voices and transparency. As the nature and status of all basins are different, the challenges are not exactly the same. For example, hearing local voices and better information transparency have significantly improved in the Waikato River.

As the challenges for implementing the two principles are not purely legal, the responses should blend legal solutions with political and socio-economic solutions. Therefore, this thesis strongly supports shared sovereignty among states at the international level as well as shared sovereignty with indigenous and minority groups at the national level. Cooperation among national and international actors in the river basins is also crucial for implementing the two principles effectively. Finally, there is the opportunity to establish basin institutions or organisations to manage river basins integrated and sustainable. This is vital in the case of TE-RB because the basin still lacks an institution. Furthermore, the basin institution in the MDB requires more robust compliance and monitoring power because the provisions of the Water Act 2007 and the basin plan still have not been implemented effectively.

Finally, the thesis concludes with two common lessons in comparing these cases. The first lesson is that equitable utilisation cannot be implemented effectively if it is not accepted by the local community in a broad and deep meaning. It means that the equitable allocation should be extended from only the riparian states to equitable allocation among the people within each state. The second lesson is that the minimisation of environmental harm cannot be implemented without determining the minimum flow of rivers, particularly transboundary rivers. Determining an environmental impact assessment for water projects and taking advantage of available solutions of nature contributes significantly in implementing the two principles and sustainable management of our rivers.

year: 2023