Molecular Mechanism Underlying ATP-Induced Conformational Changes in the Nucleoprotein Filament of Mycobacterium smegmatis RecA

RecA plays a central role in bacterial DNA repair, homologous recombination, and restoration of stalled replication forks by virtue of its active extended nucleoprotein filament. Binding of ATP and its subsequent recognition by the carboxamide group of a highly conserved glutamine (GIn196 in MsRecA) have been implicated in the formation of active RecA nucleoprotein filaments. Although the mechanism of ATP-dependent structural transitions in RecA has been proposed on the basis of low-resolution electron microscopic reconstructions, the precise sequence of events that constitute these transitions is poorly understood. On the basis of biochemical and crystallographic analyses of MsRecA variants carrying mutations in highly conserved Gln196 and Arg198 residues, we propose that the disposition of the interprotomer interface is the structural basis of allosteric activation of RecA. Furthermore, this study accounts, for the contributions of several conserved amino acids to ATP hydrolysis and to the transition from collapsed to extended filament forms in Mycobacterium smegmatis RecA (MsRecA). In addition to their role in the inactive compressed state, the study reveals a role for GIn196 and Arg198 along with Phe219 in ATP hydrolysis in the active extended nucleoprotein filament. Finally, our data suggest that the primary, but not secondary, nucleotide binding site in MsRecA isomerizes into the ATP binding site present in the extended nucleoprotein filament.

Structural Evolution and Property Changes in Nd_{60}Al_{10}Fe_{20}Co_{10} Bulk Metallic Glass During Crystallization

The structural evolution and property changes in Nd60Al10Fe20Co10 bulk metallic glass (BMG) upon crystallization are investigated by the ultrasonic method, x-ray diffraction, density measurement, and differential scanning calorimetry. The elastic constants and Debye temperature of the BMG are obtained as a function of annealing temperature. Anomalous changes in ultrasonic velocities, elastic constants, and density are observed between 600–750 K, corresponding to the formation of metastable phases as an intermediate product in the crystallization process. The changes in acoustic velocities, elastic constants, density, and Debye temperature of the BMG relative to its fully crystallized state are much smaller, compared with those of other known BMGs, the differences being attributed to the microstructural feature of the BMG.

Cell shape changes indicate a role for extrinsic tensile forces in Drosophila germ-band extension.

Drosophila germ-band extension (GBE) is an example of the convergence and extension movements that elongate and narrow embryonic tissues. To understand the collective cell behaviours underlying tissue morphogenesis, we have continuously quantified cell intercalation and cell shape change during GBE. We show that the fast, early phase of GBE depends on cell shape change in addition to cell intercalation. In antero-posterior patterning mutants such as those for the gap gene Krüppel, defective polarized cell intercalation is compensated for by an increase in antero-posterior cell elongation, such that the initial rate of extension remains the same. Spatio-temporal patterns of cell behaviours indicate that an antero-posterior tensile force deforms the germ band, causing the cells to change shape passively. The rate of antero-posterior cell elongation is reduced in twist mutant embryos, which lack mesoderm. We propose that cell shape change contributing to germ-band extension is a passive response to mechanical forces caused by the invaginating mesoderm.

Analysis of Temperature and Pressure Changes in Liquefied Natural Gas (LNG) Cryogenic Tanks

Liquefied natural gas (LNG) is being developed as a transportation fuel for heavy vehicles such as trucks and transit buses, to lessen the dependency on oil and to reduce greenhouse gas emissions. The LNG stations are properly designed to prevent the venting of natural gas (NG) from LNG tanks, which can cause evaporative greenhouse gas emissions and result in fluctuations of fuel flow and changes of fuel composition. Boil-off is caused by the heat added into the LNG fuel during the storage and fueling. Heat can leak into the LNG fuel through the shell of tank during the storage and through hoses and dispensers during the fueling. Gas from tanks onboard vehicles, when returned to LNG tanks, can add additional heat into the LNG fuel. A thermodynamic and heat transfer model has been developed to analyze different mechanisms of heat leak into the LNG fuel. The evolving of properties and compositions of LNG fuel inside LNG tanks is simulated. The effect of a number of buses fueled each day on the possible total fuel loss rate has been analyzed. It is found that by increasing the number of buses, fueled each day, the total fuel loss rate can be reduced significantly. It is proposed that an electric generator be used to consume the boil-off gas or a liquefier be used to re-liquefy the boiloff gas to reduce the tank pressure and eliminate fuel losses. These approaches can prevent boil-off of natural gas emissions, and reduce the costs of LNG as transportation fuel.

Case Study: Influence Of Morphological Changes On Flooding In Jingjiang River

The middle reach of the Yangtze River, customarily called the Jingjiang River, together with its diversion channels and Dongting Lake, form a large complicated drainage system. In the last five decades, significant geomorphological changes have occurred in the drainage system, including the shrinkage of diversion channels, contraction of Dongting Lake, changes in the rating curve at the Luoshan station, and cutoffs of the lower Jingjiang River. These changes are believed to be the cause of the occurrence of abnormal floods in the Jingjiang River. Qualitative analyses suggest that the first three factors aggravate the flood situation in the lower Jingjiang River, while the last factor seems beneficial for flood prevention. To quantitatively evaluate these conclusions, a finite-volume numerical model was constructed. A series of numerical simulations were carried out to test the individual and combined effects of the aforementioned four factors, and these simulations showed that high flood stages in the Jingjiang River clearly are related to the geomorphological changes.

Examination of the LBM in simulation of microchannel flow in transitional regime

The gas flows in micro-electro-mechanical systems possess relatively large Knudsen number and usually belong to the slip flow and transitional flow regimes. Recently the lattice Boltzmann method (LBM) was proposed by Nie et al. in Journal of Statistical Physics, vol. 107, pp. 279-289, in 2002 to simulate the microchannel and microcavity flows in the transitional flow regime. The present article intends to test the feasibility of doing so. The results of using the lattice Boltzmann method and the direct simulation Monte Carlo method show good agreement between them for small Kn (Kn = 0.0194), poor agreement for Kn = 0.194, and large deviation for Kn = 0.388 in simulating microchannel flows. This suggests that the present version of the lattice Boltzmann method is not feasible to simulate the transitional channel flow.