title: Review: Fundamental and biotechnological applications of neutron scattering measurements for macromolecular dynamics

authors: Tehei, Moeava

subjects: biology

abstract: To explore macromolecular dynamics on the picosecond timescale, we used neutron spectroscopy. First, molecular dynamics were analyzed for the hyperthermophile malate dehydrogenase from Methanococcus jannaschii and a mesophilic homologue, the lactate dehydrogenase from Oryctolagus cunniculus muscle. Hyperthermophiles have elaborate molecular mechanisms of adaptation to extremely high temperature. Using a novel elastic neutron scattering approach that provides independent measurements of the global flexibility and of the structural resilience (rigidity), we have demonstrated that macromolecular dynamics represents one of these molecular mechanisms of thermoadaptation. The flexibilities were found to be similar for both enzymes at their optimal activity temperature and the resilience is higher for the hyperthermophilic protein. Secondly, macromolecular motions were examined in a native and immobilized dihydrofolate reductase (DHFR) from Escherichia coli. The immobilized mesophilic enzyme has increased stability and decreased activity, so that its properties are changed to resemble those of the thermophilic enzyme. Are these changes reflected in dynamical behavior? For this study, we performed quasielastic neutron scattering measurements to probe the protein motions. The residence time is 7.95 ps for the native DHFR and 20.36 ps for the immobilized DHFR. The average height of the potential barrier to local motions is therefore increased in the immobilized DHFR, with a difference in activation energy equal to 0.54 kcal/mol, which is, using the theoretical rate equation, of the same order than expected from calculation.

text: Review: Fundamental and biotechnological applications of neutron scattering measurements for macromolecular dynamics To explore macromolecular dynamics on the picosecond timescale, we used neutron spectroscopy. First, molecular dynamics were analyzed for the hyperthermophile malate dehydrogenase from Methanococcus jannaschii and a mesophilic homologue, the lactate dehydrogenase from Oryctolagus cunniculus muscle. Hyperthermophiles have elaborate molecular mechanisms of adaptation to extremely high temperature. Using a novel elastic neutron scattering approach that provides independent measurements of the global flexibility and of the structural resilience (rigidity), we have demonstrated that macromolecular dynamics represents one of these molecular mechanisms of thermoadaptation. The flexibilities were found to be similar for both enzymes at their optimal activity temperature and the resilience is higher for the hyperthermophilic protein. Secondly, macromolecular motions were examined in a native and immobilized dihydrofolate reductase (DHFR) from Escherichia coli. The immobilized mesophilic enzyme has increased stability and decreased activity, so that its properties are changed to resemble those of the thermophilic enzyme. Are these changes reflected in dynamical behavior? For this study, we performed quasielastic neutron scattering measurements to probe the protein motions. The residence time is 7.95 ps for the native DHFR and 20.36 ps for the immobilized DHFR. The average height of the potential barrier to local motions is therefore increased in the immobilized DHFR, with a difference in activation energy equal to 0.54 kcal/mol, which is, using the theoretical rate equation, of the same order than expected from calculation.

year: 2006

title: Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs

authors: Stacheter, Astrid

abstract: The role of soil methylotrophs in methanol exchange with the atmosphere has been widely overlooked. Methanol can be derived from plant polymers and be consumed by soil microbial communities. In the current study, methanol-utilizing methylotrophs of 14 aerated soils were examined to resolve their comparative diversities and capacities to utilize ambient concentrations of methanol. Abundances of cultivable methylotrophs ranged from 10 ⁶-10 ⁸gsoilDW ⁻¹. Methanol dissimilation was measured based on conversion of supplemented 14C-methanol, and occurred at concentrations down to 0.002 μmol methanol gsoilDW ⁻¹. Tested soils exhibited specific affinities to methanol (a ⁰ s=0 ⁻¹) that were similar to those of other environments suggesting that methylotrophs with similar affinities were present. Two deep-branching alphaproteobacterial genotypes of mch responded to the addition of ambient concentrations of methanol (≤0.6 μmol methanol gsoilDW ⁻¹) in one of these soils. Methylotroph community structures were assessed by amplicon pyrosequencing of genes of mono carbon metabolism (mxaF, mch and fae). Alphaproteobacteria-affiliated genotypes were predominant in all investigated soils, and the occurrence of novel genotypes indicated a hitherto unveiled diversity of methylotrophs. Correlations between vegetation type, soil pH and methylotroph community structure suggested that plant-methylotroph interactions were determinative for soil methylotrophs.

text: Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs The role of soil methylotrophs in methanol exchange with the atmosphere has been widely overlooked. Methanol can be derived from plant polymers and be consumed by soil microbial communities. In the current study, methanol-utilizing methylotrophs of 14 aerated soils were examined to resolve their comparative diversities and capacities to utilize ambient concentrations of methanol. Abundances of cultivable methylotrophs ranged from 10 ⁶-10 ⁸gsoilDW ⁻¹. Methanol dissimilation was measured based on conversion of supplemented 14C-methanol, and occurred at concentrations down to 0.002 μmol methanol gsoilDW ⁻¹. Tested soils exhibited specific affinities to methanol (a ⁰ s=0 ⁻¹) that were similar to those of other environments suggesting that methylotrophs with similar affinities were present. Two deep-branching alphaproteobacterial genotypes of mch responded to the addition of ambient concentrations of methanol (≤0.6 μmol methanol gsoilDW ⁻¹) in one of these soils. Methylotroph community structures were assessed by amplicon pyrosequencing of genes of mono carbon metabolism (mxaF, mch and fae). Alphaproteobacteria-affiliated genotypes were predominant in all investigated soils, and the occurrence of novel genotypes indicated a hitherto unveiled diversity of methylotrophs. Correlations between vegetation type, soil pH and methylotroph community structure suggested that plant-methylotroph interactions were determinative for soil methylotrophs.

year: 2012

title: Alternative anthropologies: Kete aronui from the Waikato

authors: McCormack, Fiona

abstract: As three anthropologists working at the University of Waikato in Hamilton, Aotearoa (New Zealand), we experience anthropology in our daily work in the context of our local histories, communities and politics. While many anthropologists are familiar with the critiques of anthropology that play out in the USA or Europe, the narratives and practices of anthropology from places such as New Zealand are less well known. We argue that these local, diverse experiences of anthropology can enlarge our international understandings and imaginations of what anthropology can be, as well as the challenges it may face.

Anthropologists working in New Zealand today face the same plethora of academic pressures as those found in their counterparts in North America, Britain and Europe; pressures instigated by decades of neoliberal reform, managerialism, and the impact of new entrepreneurial and corporate models of universities that shape everyday identities and social relationships (Shore 2010). Similarly, the critique of anthropology as a discipline rooted in colonial imperatives and practices, resounds in a society whose imperial history and settler colonial present continues to imprint on educational institutions, pedagogy and research. In New Zealand, no neat historical trajectory marks a path from extractive research, wherein Indigenous knowledge and ways of life are pottled for export to the empire’s core, to one based on mutuality, co-creation and the indigenisation of anthropological knowledge.

text: Alternative anthropologies: Kete aronui from the Waikato As three anthropologists working at the University of Waikato in Hamilton, Aotearoa (New Zealand), we experience anthropology in our daily work in the context of our local histories, communities and politics. While many anthropologists are familiar with the critiques of anthropology that play out in the USA or Europe, the narratives and practices of anthropology from places such as New Zealand are less well known. We argue that these local, diverse experiences of anthropology can enlarge our international understandings and imaginations of what anthropology can be, as well as the challenges it may face.

Anthropologists working in New Zealand today face the same plethora of academic pressures as those found in their counterparts in North America, Britain and Europe; pressures instigated by decades of neoliberal reform, managerialism, and the impact of new entrepreneurial and corporate models of universities that shape everyday identities and social relationships (Shore 2010). Similarly, the critique of anthropology as a discipline rooted in colonial imperatives and practices, resounds in a society whose imperial history and settler colonial present continues to imprint on educational institutions, pedagogy and research. In New Zealand, no neat historical trajectory marks a path from extractive research, wherein Indigenous knowledge and ways of life are pottled for export to the empire’s core, to one based on mutuality, co-creation and the indigenisation of anthropological knowledge.

year: 2025