Study on important diffusion parameters of binary Ni3Sn4 phase

Important diffusion parameters, such as-parabolic growth constant, integrated diffusivity, ratio of intrinsic diffusivities of species Ni and Sn, Kirkendall marker velocity and the activation energy for diffusion kinetics of binary Ni3Sn4 phase have been investigated with the help of incremental diffusion couple technique (Sn/Ni0.57Sn0.43) in the temperature range 200-150 degrees C. Low activation energy extracted from Arrhenius plot indicates grain boundary controlled diffusion process. The species Sn is three times faster than Ni at 200 degrees C. Further, the activation energy of Sn tracer diffusivity is greater than that of Ni.

Nitrogen deposition: how important is it for global terrestrial carbon uptake?

Global carbon budget studies indicate that the terrestrial ecosystems have remained a large sink for carbon despite widespread deforestation activities. CO2 fertilization, N deposition and re-growth of mid-latitude forests are believed to be key drivers for land carbon uptake. In this study, we assess the importance of N deposition by performing idealized near-equilibrium simulations using the Community Land Model 4.0 (CLM4). In our equilibrium simulations, only 12-17% of the deposited nitrogen is assimilated into the ecosystem and the corresponding carbon uptake can be inferred from a C : N ratio of 20 : 1. We calculate the sensitivity of the terrestrial biosphere for CO2 fertilization, climate warming and N deposition as changes in total ecosystem carbon for unit changes in global mean atmospheric CO2 concentration, global mean temperature and Tera grams of nitrogen deposition per year, respectively. Based on these sensitivities, it is estimated that about 242 PgC could have been taken up by land due to the CO2 fertilization effect and an additional 175 PgC taken up as a result of the increased N deposition since the pre-industrial period. Because of climate warming, the terrestrial ecosystem could have lost about 152 PgC during the same period. Therefore, since pre-industrial times terrestrial carbon losses due to warming may have been more or less compensated by effects of increased N deposition, whereas the effect of CO2 fertilization is approximately indicative of the current increase in terrestrial carbon stock. Our simulations also suggest that the sensitivity of carbon storage to increased N deposition decreases beyond current levels, indicating that climate warming effects on carbon storage may overwhelm N deposition effects in the future.

RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state

Flaviviral RNA-dependent RNA polymerases (RdRps) initiate replication of the single-stranded RNA genome in the absence of a primer. The template sequence 5'-CU-3' at the 3'-end of the flaviviral genome is highly conserved. Surprisingly, flaviviral RdRps require high concentrations of the second incoming nucleotide GTP to catalyze de novo template-dependent RNA synthesis. We show that GTP stimulates de novo RNA synthesis by RdRp from Japanese encephalitis virus (jRdRp) also. Crystal structures of jRdRp complexed with GTP and ATP provide a basis for specific recognition of GTP. Comparison of the jRdRp(GTP) structure with other viral RdRp-GTP structures shows that GTP binds jRdRp in a novel conformation. Apo-jRdRp structure suggests that the conserved motif F of jRdRp occupies multiple conformations in absence of GTP. Motif F becomes ordered on GTP binding and occludes the nucleotide triphosphate entry tunnel. Mutational analysis of key residues that interact with GTP evinces that the jRdRp(GTP) structure represents a novel pre-initiation state. Also, binding studies show that GTP binding reduces affinity of RdRp for RNA, but the presence of the catalytic Mn2+ ion abolishes this inhibition. Collectively, these observations suggest that the observed pre-initiation state may serve as a check-point to prevent erroneous template-independent RNA synthesis by jRdRp during initiation.

Identifying functionally important cis-peptide containing segments in proteins and their utility in molecular function annotation

Cis-peptide embedded segments are rare in proteins but often highlight their important role in molecular function when they do occur. The high evolutionary conservation of these segments illustrates this observation almost universally, although no attempt has been made to systematically use this information for the purpose of function annotation. In the present study, we demonstrate how geometric clustering and level-specific Gene Ontology molecular-function terms (also known as annotations) can be used in a statistically significant manner to identify cis-embedded segments in a protein linked to its molecular function. The present study identifies novel cis-peptide fragments, which are subsequently used for fragment-based function annotation. Annotation recall benchmarks interpreted using the receiver-operator characteristic plot returned an area-under-curve >0.9, corroborating the utility of the annotation method. In addition, we identified cis-peptide fragments occurring in conjunction with functionally important trans-peptide fragments, providing additional insights into molecular function. We further illustrate the applicability of our method in function annotation where homology-based annotation transfer is not possible. The findings of the present study add to the repertoire of function annotation approaches and also facilitate engineering, design and allied studies around the cis-peptide neighborhood of proteins.