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: Difference in details: transfer learning case study of "cryptic" plants and moths

authors: Vetrova, Varvara

subjects: Machine learning

abstract: Can we classify species of very similar looking organisms quickly and accurately using only out of the box feature transfer? What if we only have small number of images? This experimental paper is part of on-going project on species recognition research and evaluates transfer learning and fine-tuning approaches on two highly specialized fine-grained datasets. The two fine-grained datasets were specifically assembled for the purpose of this research. These datasets consist of images of New Zealand native species of moths and ”cryptic” plants of Genus Corposma found also in New Zealand. We compare results from finetuning experiments with performance of transfer learning without fine-tuning. The latter results are based on features extracted from various levels of depth in the InceptionV3 network, including fully connected layers. The extracted features serve as inputs to a number of classification algorithms. We observe contrasting results for the two datasets. For the dataset of moths, the method based on features extracted from deep levels of the InceptionV3 network outperforms fine-tuning in accuracy (90.09% versus 87.18%). This is not the case for the dataset of cryptic plants (60.46% versus 74.37%). Despite both datasets being fine-grained in nature, these experimental differences could be attributed to intrinsically different morphology of organisms and warrant further investigation.

text: Difference in details: transfer learning case study of "cryptic" plants and moths Can we classify species of very similar looking organisms quickly and accurately using only out of the box feature transfer? What if we only have small number of images? This experimental paper is part of on-going project on species recognition research and evaluates transfer learning and fine-tuning approaches on two highly specialized fine-grained datasets. The two fine-grained datasets were specifically assembled for the purpose of this research. These datasets consist of images of New Zealand native species of moths and ”cryptic” plants of Genus Corposma found also in New Zealand. We compare results from finetuning experiments with performance of transfer learning without fine-tuning. The latter results are based on features extracted from various levels of depth in the InceptionV3 network, including fully connected layers. The extracted features serve as inputs to a number of classification algorithms. We observe contrasting results for the two datasets. For the dataset of moths, the method based on features extracted from deep levels of the InceptionV3 network outperforms fine-tuning in accuracy (90.09% versus 87.18%). This is not the case for the dataset of cryptic plants (60.46% versus 74.37%). Despite both datasets being fine-grained in nature, these experimental differences could be attributed to intrinsically different morphology of organisms and warrant further investigation.

year: 2018

title: Ngati Rahiri versus Ngati Tamatera

authors: Hart, Philip

abstract: Conflict between Ngati Tamatera, of Ohinemuri, and Ngati Rahiri, of Te Aroha, was provoked by the latter believing that members of other hapu had received money for the Aroha Block to which they were not entitled. In addition, the two hapu disagreed over the block’s northern boundary. In early 1877 Ngati Rahiri threatened violence and even fired over the heads of several rangatira passing through their land, thereby challenging their right to intrude on it. In response, Ngati Tamatera, with the assistance of Ngati Koi, blocked the road to Te Aroha and also the Waihou River against Ngati Rahiri, although they permitted Pakeha to pass. Pakeha took a relaxed attitude to the conflict, not expecting any real battles occurring during a squabble they understood to have been caused by members of an inferior hapu having their names wrongly included in Crown grants.
After Ngati Tamatera erected two small and unimpressive pa to block both road and river, Ngati Rahiri retaliated by constructing a similarly unimpressive pa at Omahu, their settlement at Te Aroha. Apart from much posturing, the only actions taken were Ngati Tamatera sending back to Omahu an aged woman who had come down the river in a canoe and Ngati Rahiri stealing pigs and peaches and firing shots near a settlement. The Native Minister and various officials, notably James Mackay, intervened to resolve the conflict, which was ended with a reconciliation initiated by Ngati Tamatera and formalized by a large meeting of both hapu at Omahu.
Once this quarrel was settled, negotiations to enable the Crown to purchase the Aroha Block were resumed.

text: Ngati Rahiri versus Ngati Tamatera Conflict between Ngati Tamatera, of Ohinemuri, and Ngati Rahiri, of Te Aroha, was provoked by the latter believing that members of other hapu had received money for the Aroha Block to which they were not entitled. In addition, the two hapu disagreed over the block’s northern boundary. In early 1877 Ngati Rahiri threatened violence and even fired over the heads of several rangatira passing through their land, thereby challenging their right to intrude on it. In response, Ngati Tamatera, with the assistance of Ngati Koi, blocked the road to Te Aroha and also the Waihou River against Ngati Rahiri, although they permitted Pakeha to pass. Pakeha took a relaxed attitude to the conflict, not expecting any real battles occurring during a squabble they understood to have been caused by members of an inferior hapu having their names wrongly included in Crown grants.
After Ngati Tamatera erected two small and unimpressive pa to block both road and river, Ngati Rahiri retaliated by constructing a similarly unimpressive pa at Omahu, their settlement at Te Aroha. Apart from much posturing, the only actions taken were Ngati Tamatera sending back to Omahu an aged woman who had come down the river in a canoe and Ngati Rahiri stealing pigs and peaches and firing shots near a settlement. The Native Minister and various officials, notably James Mackay, intervened to resolve the conflict, which was ended with a reconciliation initiated by Ngati Tamatera and formalized by a large meeting of both hapu at Omahu.
Once this quarrel was settled, negotiations to enable the Crown to purchase the Aroha Block were resumed.

year: 2016