Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (\u3ci\u3eGlycine max\u3c/i\u3e) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode

Background: Ubiquitination is a major post-translational protein modification that regulates essentially all cellular and physiological pathways in eukaryotes. The ubiquitination process typically involves three distinct classes of enzymes, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3). To date, a comprehensive identification and analysis of core components comprising of the whole soybean (Glycine max) ubiquitin system (UBS) has not been reported. Results: We performed a systematic, genome-wide analysis of genes that encode core members of the soybean UBS in this study. A total of 1431 genes were identified with high confidence to encode putative soybean UBS components, including 4 genes encoding E1s, 71 genes that encode the E2s, and 1356 genes encoding the E3-related components. Among the E3-encoding genes, 760 encode RING-type E3s, 124 encode U-box domain-containing E3s, and 472 encode F-box proteins. To find out whether the identified soybean UBS genes encode active enzymes, a set of genes were randomly selected and the enzymatic activities of their recombinant proteins were tested. Thioester assays indicated proteins encoded by the soybean E1 gene GmUBA1 and the majority of selected E2 genes are active E1 or E2 enzymes, respectively. Meanwhile, most of the purified RING and U-box domain-containing proteins displayed E3 activity in the in vitro ubiquitination assay. In addition, 1034 of the identified soybean UBS genes were found to express in at least one of 14 soybean tissues examined and the transcript level of 338 soybean USB genes were significantly changed after abiotic or biotic (Fusarium oxysporum and Rhizobium strains) stress treatment. Finally, the expression level of a large number of the identified soybean UBS-related genes was found significantly altered after soybean cyst nematode (SCN) treatment, suggesting the soybean UBS potentially plays an important role in soybean immunity against SCN. Conclusions: Our findings indicate the presence of a large and diverse number of core UBS proteins in the soybean genome, which suggests that target-specific modification by ubiquitin is a complex and important part of cellular and physiological regulation in soybean. We also revealed certain members of the soybean UBS may be involved in immunity against soybean cyst nematode (SCN). This study sets up an essential foundation for further functional characterization of the soybean UBS in various physiological processes, such as host immunity against SCN

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Next-Generation Reduction Sensitive Lipid Conjugates of Tenofovir: Antiviral Activity and Mechanism of Release

The pharmacokinetic properties of tenofovir (TFV) and other charged nucleoside analogues are dramatically improved upon conjugation to a lipid prodrug. We previously prepared reduction-sensitive lipid conjugates of TFV that demonstrate superior antiviral activity compared to other lipid conjugates including the clinically approved formulation, tenofovir disoproxil fumarate (TDF). In continuation of that work, we have synthesized next-generation conjugates with reduced cytotoxicity that retain potent antiviral activity against HIV-1 and HBV with a therapeutic index >100000 for our most potent conjugate. We also show that disulfide reduction is not responsible for prodrug cleavage unless 3-<i>exo</i>-<i>tet</i> intramolecular cyclization can occur, suggesting that enzymatic hydrolysis is predominantly responsible for activity of our prodrugs in vitro

Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (\u3ci\u3eGlycine max\u3c/i\u3e) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode

Background: Ubiquitination is a major post-translational protein modification that regulates essentially all cellular and physiological pathways in eukaryotes. The ubiquitination process typically involves three distinct classes of enzymes, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3). To date, a comprehensive identification and analysis of core components comprising of the whole soybean (Glycine max) ubiquitin system (UBS) has not been reported. Results: We performed a systematic, genome-wide analysis of genes that encode core members of the soybean UBS in this study. A total of 1431 genes were identified with high confidence to encode putative soybean UBS components, including 4 genes encoding E1s, 71 genes that encode the E2s, and 1356 genes encoding the E3-related components. Among the E3-encoding genes, 760 encode RING-type E3s, 124 encode U-box domain-containing E3s, and 472 encode F-box proteins. To find out whether the identified soybean UBS genes encode active enzymes, a set of genes were randomly selected and the enzymatic activities of their recombinant proteins were tested. Thioester assays indicated proteins encoded by the soybean E1 gene GmUBA1 and the majority of selected E2 genes are active E1 or E2 enzymes, respectively. Meanwhile, most of the purified RING and U-box domain-containing proteins displayed E3 activity in the in vitro ubiquitination assay. In addition, 1034 of the identified soybean UBS genes were found to express in at least one of 14 soybean tissues examined and the transcript level of 338 soybean USB genes were significantly changed after abiotic or biotic (Fusarium oxysporum and Rhizobium strains) stress treatment. Finally, the expression level of a large number of the identified soybean UBS-related genes was found significantly altered after soybean cyst nematode (SCN) treatment, suggesting the soybean UBS potentially plays an important role in soybean immunity against SCN. Conclusions: Our findings indicate the presence of a large and diverse number of core UBS proteins in the soybean genome, which suggests that target-specific modification by ubiquitin is a complex and important part of cellular and physiological regulation in soybean. We also revealed certain members of the soybean UBS may be involved in immunity against soybean cyst nematode (SCN). This study sets up an essential foundation for further functional characterization of the soybean UBS in various physiological processes, such as host immunity against SCN

Size Controlled Mechanochemical Synthesis Of Zrsi2

Mechanochemical metathesis reactions were utilized to synthesize nanocrystalline ZrSi2 ranging from 9–30 nm in size. Size was controlled through dilution with CaCl2. A linear relationship was found between diluent concentration and crystallite size. Unlike typical self-propagating metathesis reactions, this reaction did not self-propagate, requiring the input of mechanical energy. © The Royal Society of Chemistry

Reduction Sensitive Lipid Conjugates of Tenofovir: Synthesis, Stability, and Antiviral Activity

The therapeutic value of numerous small molecules hinges on their ability to permeate the plasma membrane. This is particularly true for tenofovir (TFV), adefovir, and other antiviral nucleosides that demonstrate potent antiviral activity but poor bioavailability. Using TFV as a model substrate, we hybridized two disparate prodrug strategies to afford novel reduction-sensitive lipid conjugates of TFV that exhibit subnanomolar activity toward HIV-1 and are stable in human plasma for more than 24 h with a therapeutic index approaching 30000. These compounds significantly rival the clinically approved formulation of TFV and revitalize the potential of disulfide-bearing prodrugs which have seen limited in vitro and in vivo success since their debut over 20 years ago. We further demonstrate the utility of these conjugates as a tool to indirectly probe the enzymatic hydrolysis of phosphonomonoesters that may further advance the development of other prodrug strategies for nucleosides, peptides, and beyond

Mechanochemically Enhanced Synthesis Of Isomorphously Substituted Kaolinites

A mechanochemical method for the rapid, bulk synthesis of kaolinite has been developed. Metal hydroxides and silicic acid are mechanically ground and hydrothermally treated for as little as a day at 250 °C to produce X-ray pure crystalline materials. This approach has been expanded to allow the synthesis of kaolinites with a portion of the aluminum sites isomorphously substituted with other trivalent metals. The synthetic parameters, such as length of mechanical and hydrothermal treatment, were studied. Products were analyzed by powder X-ray diffraction, attenuated total reflectance infrared spectrometry, scanning electron microscopy, and transmission electron microscopy. The samples exhibited strong order along the c axis and less order along the a and b axes. Trivalent transition and rare earth metals were used to replace aluminum in the structure. These metals included Cr, La, Ce, Pr, Nd, Eu, Gd, Ho, and Er. Cerium (III) substituted kaolinite was successfully synthesized utilizing air-free conditions. This approach allows bulk quantities of substituted kaolinites to be prepared in a relatively short amount of time and offers a new route to synthesize pure and substituted kaolinites that may have novel catalytic properties. © 2011 Elsevier B.V

Low-Temperature (210 °C) Deposition Of Crystalline Germanium Via In Situ Disproportionation Of Gei 2

A new approach is reported for depositing crystalline germanium films. The deposition occurs at low temperatures (210-260 °C) via in situ disproportionation of GeI 2 and is thereby useful for depositing Ge onto a wide range of surfaces. Deposition onto glass and polymer substrates is demonstrated. The rate of deposition onto glass is found to be 25 ng min -1. New synthetic routes to GeI 2, GeI 4, and Cu 3Ge are also reported. These are valuable precursors for the synthesis of germanium nanostructures and organo-germanium compounds. © 2012 Elsevier Ltd. All rights reserved

Heterogeneous Metal-Free Hydrogenation Over Defect-Laden Hexagonal Boron Nitride

Catalytic hydrogenation is an important process used for the production of everything from foods to fuels. Current heterogeneous implementations of this process utilize metals as the active species. Until recently, catalytic heterogeneous hydrogenation over a metal-free solid was unknown; implementation of such a system would eliminate the health, environmental, and economic concerns associated with metal-based catalysts. Here, we report good hydrogenation rates and yields for a metal-free heterogeneous hydrogenation catalyst as well as its unique hydrogenation mechanism. Catalytic hydrogenation of olefins was achieved over defect-laden h-BN (dh-BN) in a reactor designed to maximize the defects in h-BN sheets. Good yields (\u3e90%) and turnover frequencies (6 × 10−5−4 × 10−3) were obtained for the hydrogenation of propene, cyclohexene, 1,1-diphenylethene, (E)- and (Z)-1,2-diphenylethene, octadecene, and benzylideneacetophenone. Temperature-programmed desorption of ethene over processed h-BN indicates the formation of a highly defective structure. Solid-state NMR (SSNMR) measurements of dh-BN with high and low propene surface coverages show four different binding modes. The introduction of defects into h-BN creates regions of electronic deficiency and excess. Density functional theory calculations show that both the alkene and hydrogen-bond order are reduced over four specific defects: boron substitution for nitrogen (BN), vacancies (VB and VN), and Stone−Wales defects. SSNMR and binding-energy calculations show that VN are most likely the catalytically active sites. This work shows that catalytic sites can be introduced into a material previously thought to be catalytically inactive through the production of defects

Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (Glycine max) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode

Abstract Background Ubiquitination is a major post-translational protein modification that regulates essentially all cellular and physiological pathways in eukaryotes. The ubiquitination process typically involves three distinct classes of enzymes, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3). To date, a comprehensive identification and analysis of core components comprising of the whole soybean (Glycine max) ubiquitin system (UBS) has not been reported. Results We performed a systematic, genome-wide analysis of genes that encode core members of the soybean UBS in this study. A total of 1431 genes were identified with high confidence to encode putative soybean UBS components, including 4 genes encoding E1s, 71 genes that encode the E2s, and 1356 genes encoding the E3-related components. Among the E3-encoding genes, 760 encode RING-type E3s, 124 encode U-box domain-containing E3s, and 472 encode F-box proteins. To find out whether the identified soybean UBS genes encode active enzymes, a set of genes were randomly selected and the enzymatic activities of their recombinant proteins were tested. Thioester assays indicated proteins encoded by the soybean E1 gene GmUBA1 and the majority of selected E2 genes are active E1 or E2 enzymes, respectively. Meanwhile, most of the purified RING and U-box domain-containing proteins displayed E3 activity in the in vitro ubiquitination assay. In addition, 1034 of the identified soybean UBS genes were found to express in at least one of 14 soybean tissues examined and the transcript level of 338 soybean USB genes were significantly changed after abiotic or biotic (Fusarium oxysporum and Rhizobium strains) stress treatment. Finally, the expression level of a large number of the identified soybean UBS-related genes was found significantly altered after soybean cyst nematode (SCN) treatment, suggesting the soybean UBS potentially plays an important role in soybean immunity against SCN. Conclusions Our findings indicate the presence of a large and diverse number of core UBS proteins in the soybean genome, which suggests that target-specific modification by ubiquitin is a complex and important part of cellular and physiological regulation in soybean. We also revealed certain members of the soybean UBS may be involved in immunity against soybean cyst nematode (SCN). This study sets up an essential foundation for further functional characterization of the soybean UBS in various physiological processes, such as host immunity against SCN