Modelling the influence of land-use changes on biophysical and biochemical interactions at regional and global scales

Land-use changes since the start of the industrial era account for nearly one-third of the cumulative anthropogenic CO2 emissions. In addition to the greenhouse effect of CO2 emissions, changes in land use also affect climate via changes in surface physical properties such as albedo, evapotranspiration and roughness length. Recent modelling studies suggest that these biophysical components may be comparable with biochemical effects. In regard to climate change, the effects of these two distinct processes may counterbalance one another both regionally and, possibly, globally. In this article, through hypothetical large-scale deforestation simulations using a global climate model, we contrast the implications of afforestation on ameliorating or enhancing anthropogenic contributions from previously converted (agricultural) land surfaces. Based on our review of past studies on this subject, we conclude that the sum of both biophysical and biochemical effects should be assessed when large-scale afforestation is used for countering global warming, and the net effect on global mean temperature change depends on the location of deforestation/afforestation. Further, although biochemical effects trigger global climate change, biophysical effects often cause strong local and regional climate change. The implication of the biophysical effects for adaptation and mitigation of climate change in agriculture and agroforestry sectors is discussed. center dot Land-use changes affect global and regional climates through both biochemical and biophysical process. center dot Climate effect from biophysical process depends on the location of land-use change. center dot Climate mitigation strategies such as afforestation/reforestation should consider the net effect of biochemical and biophysical processes for effective mitigation. center dot Climate-smart agriculture could use bio-geoengineering techniques that consider plant biophysical characteristics such as reflectivity and water use efficiency.

Biochemical Characterization of Nonamer Binding Domain of RAG1 Reveals its Thymine Preference with Respect to Length and Position

RAG complex consisting of RAG1 and RAG2 is a site-specific endonuclease responsible for the generation of antigen receptor diversity. It cleaves recombination signal sequence (RSS), comprising of conserved heptamer and nonamer. Nonamer binding domain (NBD) of RAG1 plays a central role in the recognition of RSS. To investigate the DNA binding properties of the domain, NBD of murine RAG1 was cloned, expressed and purified. Electrophoretic mobility shift assays showed that NBD binds with high affinity to nonamer in the context of 12/23 RSS or heteroduplex DNA. NBD binding was specific to thymines when single stranded DNA containing poly A, C, G or T were used. Biolayer interferometry studies showed that poly T binding to NBD was robust and comparable to that of 12RSS. More than 23 nt was essential for NBD binding at homothymidine stretches. On a double-stranded DNA, NBD could bind to A:T stretches, but not G:C or random sequences. Although NBD is indispensable for sequence specific activity of RAGs, external supplementation of purified nonamer binding domain to NBD deleted cRAG1/cRAG2 did not restore its activity, suggesting that the overall domain architecture of RAG1 is important. Therefore, we define the sequence requirements of NBD binding to DNA.

Mutations in the nucleotide binding and hydrolysis domains of Helicobacter pylori MutS2 lead to altered biochemical activities and inactivation of its in vivo function

Background: Helicobacter pylori MutS2 (HpMutS2), an inhibitor of recombination during transformation is a non-specific nuclease with two catalytic sites, both of which are essential for its anti-recombinase activity. Although HpMutS2 belongs to a highly conserved family of ABC transporter ATPases, the role of its ATP binding and hydrolysis activities remains elusive. Results: To explore the putative role of ATP binding and hydrolysis activities of HpMutS2 we specifically generated point mutations in the nucleotide-binding Walker-A (HpMutS2-G338R) and hydrolysis Walker-B (HpMutS2-E413A) domains of the protein. Compared to wild-type protein, HpMutS2-G338R exhibited similar to 2.5-fold lower affinity for both ATP and ADP while ATP hydrolysis was reduced by similar to 3-fold. Nucleotide binding efficiencies of HpMutS2-E413A were not significantly altered; however the ATP hydrolysis was reduced by similar to 10-fold. Although mutations in the Walker-A and Walker-B motifs of HpMutS2 only partially reduced its ability to bind and hydrolyze ATP, we demonstrate that these mutants not only exhibited alterations in the conformation, DNA binding and nuclease activities of the protein but failed to complement the hyper-recombinant phenotype displayed by mutS2-disrupted strain of H. pylori. In addition, we show that the nucleotide cofactor modulates the conformation, DNA binding and nuclease activities of HpMutS2. Conclusions: These data describe a strong crosstalk between the ATPase, DNA binding, and nuclease activities of HpMutS2. Furthermore these data show that both, ATP binding and hydrolysis activities of HpMutS2 are essential for the in vivo anti-recombinase function of the protein.

Biochemical and Behavioral Evaluation of Human MAPT Mutations in Transgenic Drosophila melanogaster

Mutations in the human microtubule-associated protein tau (hMAPT) gene including R406W and V337M result in autosomal dominant neurodegenerative disorder. These mutations lead to hyperphosphorylation and aggregation of Tau protein which is a known genetic factor underlying development of Alzheimer's disease (AD). In the present study, transgenic Drosophila models of AD expressing wild-type and mutant forms of hMAPT exhibit a progressive neurodegeneration which was manifested in the form of early death and impairment of cognitive ability. Moreover, they were also found to have significantly decreased activity of neurotransmitter enzymes accompanied by decreased cellular endogenous antioxidant profile. The extent of neurodegeneration, memory impairment, and biochemical profiles was different in the tau transgenic strains which indicate multiple molecular and cellular responses underlie each particular form of hMAPT.

Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue96 in the Plasmodial Enzyme

Despite extensive research into triosephosphate isomerases (TIMs), there exists a gap in understanding of the remarkable conjunction between catalytic loop-6 (residues 166-176) movement and the conformational flip of Glu165 (catalytic base) upon substrate binding that primes the active site for efficient catalysis. The overwhelming occurrence of serine at position96 (98% of the 6277 unique TIM sequences), spatially proximal to E165 and the loop-6 residues, raises questions about its role in catalysis. Notably, Plasmodium falciparum TIM has an extremely rare residuephenylalanineat this position whereas, curiously, the mutant F96S was catalytically defective. We have obtained insights into the influence of residue96 on the loop-6 conformational flip and E165 positioning by combining kinetic and structural studies on the PfTIM F96 mutants F96Y, F96A, F96S/S73A, and F96S/L167V with sequence conservation analysis and comparative analysis of the available apo and holo structures of the enzyme from diverse organisms.

Influences of strain rate and temperature variation on material intrinsic length of plasticity strain gradient theory

Cowper-Symonds and Johnson-Cook dynamic constitutive relations are used to study the influence of both strain rate effect and temperature variation on the material intrinsic length scale in strain gradient plasticity. The material intrinsic length scale decreases with increasing strain rates, and this length scale increases with temperature.

Characters of variation of LURR during the earthquake sequence of Xinjiang

The theory of the loading/unloading response ratio (LURR) was applied to the Jiashi earthquake sequence which occurred at the beginning of 1997 in Xinjiang, and found that, before the earthquakes with relatively high magnitudes In the sequence, the ratio showed anomalies of high values. That is to say, the LURR theory can be applied to the short-term earthquake prediction in some cases, especially in the early period after a strong earthquake, such as the forecasts for some strong earthquakes in the Jiashi sequence.

Variation of drag coefficient with wind wave development

Turbulent air flows over developing wind waves in the air-sea boundary layer are numerically simulated without considering wave breaking. Influences of wind waves on air flows are considered using a model of significant wave and surface roughness, with a formula proposed for calculating the surface roughness, k - epsilon model is adopted to simulate turbulent flows. The results of the drag coefficient and turbulence characteristics agree well with the observations.

Variation Of Flexural Strength Of Cement Mortar Attacked By Sulfate Ions

Under the environment of seawater, durability of concrete materials is one of the chief factors considered in the design of structures. The decrease of durability of structures is induced by the evolution of micro-damage due to the erosion of chlorine and sulfate ions, which is characterized by the reduction of modulus, strength, and toughness of the material. In this paper, the variation of the flexural strength of cement mortar under sulfate erosion is investigated. The results obtained in present work indicate that the erosion time, concentration of sulfate solution, and water-to-cement ratio will significantly affect the flexural strength. Crown Copyright (c) 2008 Published by Elsevier Ltd. All rights reserved.

Variation of added mass and its application to the calculation of amplitude response for a circular cylinder

In the present study, analyzed are the variation of added mass for a circular cylinder in the lock-in ( synchronization) range of vortex-induced vibration (VIV) and the relationship between added mass and natural frequency. A theoretical minimum value of the added mass coefficient for a circular cylinder at lock-in is given. Developed are semi-empirical formulas for the added mass of a circular cylinder at lock-in as a function of flow speed and mass ratio. A comparison between experiments and numerical simulations shows that the semi-empirical formulas describing the variation of the added mass for a circular cylinder at lock-in are better than the ideal added mass. In addition, computation models such as the wake oscillator model using the present formulas can predict the amplitude response of a circular cylinder at lock-in more accurately than those using the ideal added mass.