In Silico Mining of Conserved miRNAs of Indian Catfish <Emphasis Type="Italic">Clarias batrachus</Emphasis> (Linnaeus, 1758) from the Contigs,ESTs, and BAC End Sequences

MicroRNAs are small non-coding RNAs which play significant role in RNA interference. The present work deals with mining of the conserved miRNA and their target genes from the contigs, ESTs, and BAC end sequences of commercially important catfish, Clarias batrachus, from India. A total of 138, 1 and 1 conserved pre-miRNA sequences, were mined from the contigs, ESTs, and BAC end sequences, respectively. The analysis of families of the conserved pre-miRNA revealed conservation of the fish-specific family mir-430 and other important families, such as mir-455, let-7, mir-133, and mir-137. The mir-455 is involved in hypoxia signaling, let-7 family represents potential anti-tumor molecules involved in human cancer therapy, whereas mir-133 and mir-137 have high therapeutic potentials. Using an alternate computational in silico approach, mining of mature miRNAs resulted in identification of 210 mature miRNAs from contigs, 1 from EST, and 2 each from forward as well as reverse BAC end sequences. Target prediction of these putative miRNAs resulted in the identification of 66,758 and 18,747 target genes in C. batrachus and Danio rerio, respectively. Functional annotation of these miRNAs indicated their involvement in diverse biological functions. The findings of the present study can serve as a valuable resource for further functional genomics studies in C. batrachus.     

Evaluation of factors and current approaches related to computerized design of tillage tools: a review

The objectives of this paper are to evaluate the factors that are involved in the tillage process, and to explore the potential approaches for the computer-aided design of tillage tools. An overview related to the dynamic effect on the performance of tillage operations has been conducted. Compared with the analytical methods, the finite element method (FEM) has some advantages for the computerized design of tillage tools. The artificial neural networks (ANN) may be useful for the integrated evaluation of tillage performance with multi-objectives. ANN can be employed for simulation of a dynamic constitutive model and identification of soil conditions for agricultural soils. The integral approach of ANN analysis with FEM is found to be promising for optimizing design of tillage tools.     

A non-linear 3-D finite element analysis of soil failure with tillage tools

A non-linear 3-D finite element model was developed to study the soil failure under a narrow tillage blade. The weighted residual method was applied to formulate the finite element model. The Duncan and Chang hyperbolic stress-strain model was used in the analysis. This finite element model also takes into account friction at the soil-tool interface, and progressive and continuous cutting. A FORTRAN program was written to carry out the finite element analysis. The results provided soil forces, a progressive developed failure zone, displacement field and stress distribution along the tool surface. Tillage were conducted in the laboratory soil bin to verify soil forces from the finite element analysis. The comparison between the results from the finite element model and those from the soil bin tests was reasonably good.     

Computational Analysis Reveals Monomethylated Triazolopyrimidine as a Novel Inhibitor of SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp)

The human population is still facing appalling conditions due to several outbreaks of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) virus. The absence of specific drugs, appropriate vaccines for mutants, and knowledge of potential therapeutic agents makes this situation more difficult. Several 1, 2, 4-triazolo [1, 5-a] pyrimidine (TP)-derivative compounds were comprehensively studied for antiviral activities against RNA polymerase of HIV, HCV, and influenza viruses, and showed immense pharmacological interest. Therefore, TP-derivative compounds can be repurposed against the RNA-dependent RNA polymerase (RdRp) protein of SARS-CoV-2. In this study, a meta-analysis was performed to ensure the genomic variability and stability of the SARS-CoV-2 RdRp protein. The molecular docking of natural and synthetic TP compounds to RdRp and molecular dynamic (MD) simulations were performed to analyse the dynamic behaviour of TP compounds at the active site of the RdRp protein. TP compounds were also docked against other non-structural proteins (NSP1, NSP2, NSP3, NSP5, NSP8, NSP13, and NSP15) of SARS-CoV-2. Furthermore, the inhibition potential of TP compounds was compared with Remdesivir and Favipiravir drugs as a positive control. Additionally, TP compounds were analysed for inhibitory activity against SARS-CoV RdRp protein. This study demonstrates that TP analogues (monomethylated triazolopyrimidine and essramycin) represent potential lead molecules for designing an effective inhibitor to control viral replication. Furthermore, in vitro and in vivo studies will strengthen the use of these inhibitors as suitable drug candidates against SARS-CoV-2.     

Dynamic modeling of soil–tool interaction: An overview from a fluid flow perspective

The study of tillage tool interaction centers on soil failure patterns and development of force prediction models for design optimization. The force-deformation relationships used in models developed to date have been considering soil as a rigid solid or elasto-plastic medium. Most of the models are based on quasi-static soil failure patterns. In recent years, efforts have been made to improve the conventional analytical and experimental models by numerical approaches. This paper aims at reviewing the existing methods of tillage tool modeling and exploring the use of computational fluid dynamics to deal with unresolved aspects of soil dynamics in tillage. The discussion also focuses on soil rheological behaviour for its visco-plastic nature and its mass deformation due to machine interaction which may be analyzed as a Bingham plastic material using a fluid flow approach. Preliminary results on visco-plastic soil deformation patterns and failure front advancement are very encouraging. For a tool operating speed of 5.5 m s⁻¹, the soil failure front was observed to be about 100-mm forward of the tool.     

Fluorogenic dual click derived bis-glycoconjugated triazolocoumarins for selective recognition of Cu(II) ion

Carbohydrate based fluorescent sensors S1 and S2 have been developed by fluorogenic dual click chemistry and are characterized by various spectroscopic techniques. Both the fluorescent probes displayed highly selective detection of Cu²⁺ ions by means of fluorescence quenching. The job plot experiment suggested 1:1 complexation of probes S1 and S2 with Cu²⁺ ions having detection limit of 6.99 μM and 7.30 μM, respectively. The binding constants for S1-Cu²⁺ and S2-Cu²⁺ complexation were evaluated to be 3.34 × 10³ M⁻¹ and 5.93 × 10³ M⁻¹, respectively.     

Electronic transitions of guanine tautomers, their stacked dimers, trimers and sodium complexes

Planar and nonplanar geometries of the keto-N9H and keto-N7H tautomers of the guanine base of DNA as well as the hydrogen bonded complexes of these species with three water molecules each were optimized using the density functional theory at the B3LYP/6-31G** level. Geometries of the isolated bases were also optimized using the ab initio approach at the MP2/6-31G** level. The isolated keto-N9H and keto-N7H tautomers as well as their hydrogen bonded complexes with three water molecules each were solvated in bulk water employing the polarized continuum model (PCM) of the self-consistent reaction field theory (SCRF). Stacked dimers and trimers of both the tautomers of guanine were generated by placing the planar forms of the species at a fixed distance of 3.5 A from the neighboring one and rotating one molecule with respect to the other by 110 degrees for the keto-N9H form and 90 degrees for the keto-N7H form which corresponded to total energy minima at the B3LYP/6-31G** level. Geometry optimization for the cation of the monomer of guanine was performed at the same level of theory, and its solvation in bulk water was treated using the PCM model of the SCRF theory. The geometries of complexes of the two tautomers of guanine with a Na+ ion each were optimized at the B3LYP/6-31G** level, and the Na+ ion is predicted to bind with the keto-N9H tautomer preferentially. While the complex of the keto-N7H form of guanine with three water molecules in gas phase is slightly more stable than the corresponding complex of the keto-N9H form of guanine, the reverse is true in bulk water. Stacking interactions enhance the relative stability of the keto-N9H tautomer over that of the keto-N7H tautomer, suggesting that in bulk solutions, the former would be dominant. Electronic spectra of the isolated tautomers of guanine, those of their complexes with three water molecules each, the (keto-n9h and keto-n7h) cation of guanine, the complexes of the tautomers with a Na+ ion each, the stacked dimers and trimers of the two tautomers were calculated using configuration interaction involving single electron excitations (CIS). The relative absorption intensities of the two tautomers of guanine near 275 and 248 nm in the monomer, dimer, and trimer are predicated to be in the opposite order. Thus the absorption intensity oscillation observed using a guanine aqueous solution can be explained in terms of oscillation of relative populations of the two tautomers of the molecule. The 248 nm absorption peak would be appreciably red-shifted on formation of the cation of guanine. Binding of the Na+ ion with the two tautomers of guanine reduces intensities of their transitions appreciably and also it causes large red-shifts in the same.     

SAFT-D theory for hard sphere and hard disc chain fluids

SAFT-dimer (SAFT-D) theory is reformulated to yield an improved equation of state for the hard sphere chain fluid. Two sets of the equation of state are proposed by employing Chiew's expressions for the contact values of the m hard sphere site-site correlation function g(σ). Comparison with molecular simulation data shows that the improved SAFT-D equation of state predicts the compressibility factor more accurately than Ghonasgi and Chapman's equation of state. It has been shown that SAFT-dimer theory can be applied readily to fused hard sphere chain fluids by considering the correct value of the effective chain length (m*). SAFT-dimer theory is also extended to the 2-dimensional tangent and fused hard disc chain fluids. For the fused hard disc dimer fluid, the SAFT equation of state is found to be more accurate than the Boublik hard disc dimer equation of state. For tangent hard disc chain fluids, the results obtained from SAFT-dimer theory are compared with Monte Carlo results for 5-mers and with GFD theory for 4-mers, 8-mers and 16-mers.