Land Cover Change and Its Impact in Crop Yield: A Case Study from Western Nepal.

This study was conducted in Tanahun district of Gandaki Province, Nepal, to analyze the land cover change over two decades, the migration effect in land cover, and the impact caused in crop production by Rhesus macaque. Landsat TM/ETM+ for land use of 2000 and 2010 extracted by ICIMOD and Landsat 8 OLI/TIRS satellite images for land cover 2019 were downloaded from the USGS website. A purposive sample for household survey was carried out based on crops damaged by the monkey. Two hundred and fifty households were taken as samples. The Landsat images were analyzed by ArcGIS, and the social data were analyzed using SPSS and MS Excel. Land cover change data revealed increment of forest cover from 36.57% to 40.91% and drastic decrease in agriculture crops from 57.52% to 43.78% in the period of 20 years. The accuracy of the data showed overall classification accuracy of 86.11%, 81.08%, and 75% with overall kappa statistics 0.83, 0.77, and 0.74, respectively. The migration effect in the land cover was related to remittance and migrated members and found a significant positive relationship. Analyzing the trend of production with an increase in the forest cover, 21% decrease in paddy, 5% decrease in maize, and 26% decrease in millet were found as compared to the production in 2000. The econometric model concluded that the quantity of crop damage was negatively significant in relation to distance from forest and distance from water body while positively significant to distance from settlements and distance from owner's home. The quantity of crop damage was estimated 113.89 kg per household, and the cost was 78.82 USD. This study recommends active forest management; regular thinning, and weeding. Remittance generated should be invested in the agriculture field by the households. Damage relief should be made available for the damage cost by Rhesus macaque.

Effect of monovalent ion binding on molecular dynamics of the S100-family calcium-binding protein calbindin D9k.

Calbindin D9k is a member of the S100 subfamily of EF-hand calcium binding proteins, and has served as an important model system for biophysical studies. The fast timescale dynamics of the calcium-free (apo) state is characterized using molecular dynamics simulations. Order parameters for the backbone NH bond vectors are determined from the simulations and compared with experimentally derived values, with a focus on the dynamics of calcium-binding site I. There is a significant discrepancy between simulated and experimental order parameters for site I residues in the case of no ion bound in site I. However, it was found in the simulations that a Na+ ion can bind in site I, and the resulting order parameters determined from the simulations are in excellent agreement with experiment. Comparisons are made to X-ray structures of other S100 family members in which Na+ ions were observed or suggested to be bound in site I. © 2019 Wiley Periodicals, Inc.

Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.

An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is the loss of entropy that occurs from restricting the conformational freedom of amino acid side chains. The effect of restricting the flexibility of several side chains at a protein-DNA interface may be comparable in many cases to the other factors that determine the binding thermodynamics and may, therefore, play a key role in dictating the binding affinity and/or specificity. Because the entropic contributions, including the presence and influence of side-chain dynamics, are especially difficult to estimate based on structural information, it is important to pursue experimental and theoretical studies that can provide direct information regarding these issues. We report on studies of a model system, the homeodomain/DNA complex, focusing on the Lys50 class of homeodomains where a key lysine residue in position 50 was shown previously to be critical for binding site specificity. NMR methodology was employed for determining the dynamics of lysine side-chain amino groups via 15N relaxation measurements in the Lys50-class homeodomains from the Drosophila protein Bicoid and the human protein Pitx2. In the case of Pitx2, complexes with both a consensus and a nonconsensus DNA binding site were examined. NMR-derived order parameters indicated moderate to substantial conformational freedom for the lysine NH3+ group in the complexes studied. To complement the experimental NMR measurements, molecular dynamics simulations were performed for the consensus complexes to gain further, detailed insights regarding the dynamics of the Lys50 side chain and other important residues in the protein-DNA interface.

Transport by OATP1B1 and OATP1B3 enhances the cytotoxicity of epigallocatechin 3-O-gallate and several quercetin derivatives.

Organic anion transporting polypeptides (OATPs) 1B1 and 1B3 are transporters that are expressed selectively in human hepatocytes under normal conditions. OATP1B3 is also expressed in certain cancers. Flavonoids such as green tea catechins and quercetin glycosides have been shown to modulate the function of some OATPs. In the present study, the extent to which six substituted quercetin derivatives (1-6) affected the function of OATP1B1 and OATP1B3 was investigated. Uptake of the radiolabeled model substrates estradiol 17ß-glucuronide, estrone 3-sulfate, and dehydroepiandrosterone sulfate (DHEAS) was determined in the absence and presence of compounds 1-6 using Chinese hamster ovary (CHO) cells stably expressing either OATP1B1 or OATP1B3. Several of compounds 1-6 inhibited OATP-mediated uptake of all three model substrates, suggesting that they could also be potential substrates. Compound 6 stimulated OATP1B3-mediated estradiol 17ß-glucuronide uptake by increasing the apparent affinity of OATP1B3 for its substrate. Cytotoxicity assays demonstrated that epigallocatechin 3-O-gallate (EGCG) and most of compounds 1-6 killed preferentially OATP-expressing CHO cells. EGCG, 1, and 3 were the most potent cytotoxic compounds, with EGCG and 3 selectively killing OATP1B3-expressing cells. Given that OATP1B3 is expressed in several cancers, EGCG and some of the quercetin derivatives studied might be promising lead compounds for the development of novel anticancer drugs.

Synthesis and antiviral activity of substituted quercetins.

Influenza viruses are important pathogens that cause respiratory infections in humans and animals. In addition to vaccination, antiviral drugs against influenza virus play a significant role in controlling viral infections by reducing disease progression and virus transmission. Plant derived polyphenols are associated with antioxidant activity, anti-carcinogenic, and cardio- and neuro-protective actions. Some polyphenols, such as resveratrol and epigallocatechin gallate (EGCG), showed significant anti-influenza activity in vitro and/or in vivo. Recently we showed that quercetin and isoquercetin (quercetin-3-ß-d-glucoside), a glucoside form of quercetin, significantly reduced the replication of influenza viruses in vitro and in vivo (isoquercetin). The antiviral effects of isoquercetin were greater than that of quercetin with lower IC(50) values and higher in vitro therapeutic index. Thus, we investigated the synthesis and antiviral activities of various quercetin derivatives with substitution of C3, C3', and C5 hydroxyl functions with various phenolic ester, alkoxy, and aminoalkoxy moieties. Among newly synthesized compounds, quercetin-3-gallate which is structurally related to EGCG showed comparable antiviral activity against influenza virus (porcine H1N1 strain) to that of EGCG with improved in vitro therapeutic index.

Synthesis of 2,24-Diene-12,13,15,16,34,35,37,38-octaphenyl[4.4]-triphenylparacyclophane.

A new octaphenyl[4.4]triphenylparacyclophanediene was readily synthesized in six steps from p-xylene via the installment of bromine atoms, replacement with a vinyl group, carbonylative coupling, intermolecular followed by intramolecular double Grubbs olefin metathesis, Knoevenagel condensation, and Diels-Alder cycloaddition. The belt-shaped structure and trans-stereochemistry of the alkene moieties of the octaphenyl[4.4]triphenylparacyclophane and a synthetic intermediate, 2,21-dioxo-11,30-diene[3.4.3.4]paracyclophane, were determined by X-ray crystallography. The synthetic methodology leading to octaphenyl[4.4]triphenylparacyclophane is applicable for the synthesis of substituted triphenylparacyclophanes and possibly their corresponding bis-hexabenzocoronenylparacyclophanes via a Scholl-Mullen oxidative aryl-aryl coupling reaction.

Computational Studies of Intrinsically Disordered Proteins.

Frequently elusive to experimental characterizations, intrinsically disordered proteins (IDPs) can be probed using molecular dynamics to provide detailed insight into their complex structure, dynamics, and function. However, previous computational studies were often found to disagree with experiment due to either force field biases or insufficient sampling. In this study, nine unstructured short peptides and the HIV-1 Rev protein were simulated and extended to microseconds to assess these limitations in IDP simulations. In short peptide simulations, a tested IDP-specific force field ff14IDPSFF outperforms its generic counterpart ff14SB as agreement of simulated NMR observables with experiment improves, though its advantages are not clear-cut in apo Rev simulations. It is worth noting that sampling is probably still not sufficient in the ff14SB simulations of apo Rev even if 10 ms have been collected. This indicates that enhanced sampling techniques would greatly benefit IDP simulations. Finally, detailed structural analyses of apo Rev conformations demonstrate different secondary structural preferences between ff14SB (helical) and ff14IDPSFF (random coil). A natural next step is to ask a more quantitative question: whether ff14SB is too ordered or ff14IDPSFF is too disordered in simulations of more complex IDPs such as Rev. This requires further quantitative analyses both experimentally and computationally.

Targeting substrate-site in Jak2 kinase prevents emergence of genetic resistance.

Emergence of genetic resistance against kinase inhibitors poses a great challenge for durable therapeutic response. Here, we report a novel mechanism of JAK2 kinase inhibition by fedratinib (TG101348) that prevents emergence of genetic resistance. Using in vitro drug screening, we identified 211 amino-acid substitutions conferring resistance to ruxolitinib (INCB018424) and cross-resistance to the JAK2 inhibitors AZD1480, CYT-387 and lestaurtinib. In contrast, these resistant variants were fully sensitive to fedratinib. Structural modeling, coupled with mutagenesis and biochemical studies, revealed dual binding sites for fedratinib. In vitro binding assays using purified proteins showed strong affinity for the substrate-binding site (Kd = 20 nM) while affinity for the ATP site was poor (Kd = ~8 µM). Our studies demonstrate that mutations affecting the substrate-binding pocket encode a catalytically incompetent kinase, thereby preventing emergence of resistant variants. Most importantly, our data suggest that in order to develop resistance-free kinase inhibitors, the next-generation drug design should target the substrate-binding site.

Biodegradable nanogels for oral delivery of interferon for norovirus infection.

Norwalk virus (NV) replicon-harboring cells have provided an excellent tool to the development of antivirals. Previously we demonstrated that the expression levels of replicon RNA and proteins were significantly reduced in the presence of various interferons (IFNs) including IFN-α and IFN-γ in a dose-dependent manner in the NV replicon-harboring cells, and suggested that IFNs could be therapeutic options for norovirus infection. It was also demonstrated that innate immunity including IFNs is crucial in the replication and pathogenicity of murine norovirus (MNV) in vitro (RAW267.4 cells) and in vivo. IFNs have a short half-life in vitro and in vivo due to low stability. Thus it is important to have a good delivery system to improve the stability of IFNs. Nanogels are nanosized networks of chemically cross-linked polymers that swell in physiologic solutions and provide improved stability and bioavailability to drugs. We have synthesized nanogels based on cross-linked polyethyleneimine (PEI)-polyethylenglycol (PEG). The PEI/PEG nanogels were further acetylated (AcNg) to reduce cellular penetration and cytotoxicity. The IFN-AcNg complex was prepared by incubating two components together at 4 °C and lyophilization. The IFN activity of IFN-AcNg was evaluated in the NV- and HCV-replicon-harboring cells and against MNV-1 in RAW267.4 cells in comparison to IFN without AcNg. The AcNg improved the stability of IFN stored at 4 °C, and was well tolerated in the cells. Furthermore, the activity of IFN was significantly higher when combined with AcNg in the replicon-harboring cells and against MNV-1 in RAW267.4 cells. We concluded that AcNg may be pursued further as a vehicle for oral delivery of IFNs in norovirus infection.