Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2

The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry. The Spike protein of SARS-CoV-2 is cleaved into two segments, the S1 (residues (res.) 1–685) and the S2 (res. 686–1273) domains by furin protease. Nrp1 predominantly binds to the C-terminal RRAR amino acid motif (res. 682–685) of the S1 domain. In this study, we firstly modeled the association of an Nrp1 protein (consisting of domains a2-b1-b2) with the Spike protein. Next, we studied the separation of S2 from the S1 domain, with and without Nrp1 bound, by utilizing molecular dynamics pulling simulations. During the separation, Nrp1 stabilizes the S1 C-terminal region (res. 640–685) and thereby assists the detachment of S2 N-terminal region (res. 686–700). Without Nrp1 bound, S1 tends to become stretched, whereas the bound Nrp1 stimulates an earlier separation of S2 from the S1 domain. The liberated S2 domain is known to mediate the fusion of virus and host membranes; thus, Nrp1 likely increases virus infectivity by facilitating the S1 and S2 separation. We further analyzed the possible topological structure of the SARS-CoV-2 Spike protein when bound with Nrp1 and angiotensin-converting enzyme 2 (ACE2). Understanding of such an Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future Nrp1-ACE2 targeted combination therapy.     

Characteristics of synaptic connections between rodent primary somatosensory and motor cortices

The reciprocal connections between primary motor (M1) and primary somatosensory cortices (S1) are hypothesized to play a crucial role in the ability to update motor plans in response to changes in the sensory periphery. These interactions provide M1 with information about the sensory environment that in turn signals S1 with anticipatory knowledge of ongoing motor plans. In order to examine the synaptic basis of sensorimotor feedforward (S1–M1) and feedback (M1–S1) connections directly, we utilized whole-cell recordings in slices that preserve these reciprocal sensorimotor connections. Our findings indicate that these regions are connected via direct monosynaptic connections in both directions. Larger magnitude responses were observed in the feedforward direction (S1–M1), while the feedback (M1–S1) responses occurred at shorter latencies. The morphology as well as the intrinsic firing properties of the neurons in these pathways indicates that both excitatory and inhibitory neurons are targeted. Differences in synaptic physiology suggest that there exist specializations within the sensorimotor pathway that may allow for the rapid updating of sensory–motor processing within the cortex in response to changes in the sensory periphery.     

Design and synthesis of the BODIPY–BSA complex for biological applications

A quinoxaline‐functionalized styryl–BODIPY derivative (S1) was synthesized by microwave‐assisted Knoevenagel condensation. It exhibited fluorescence enhancement upon micro‐encapsulation into the hydrophobic cavity of bovine serum albumin (BSA). The S1–BSA complex was characterized systematically using ultraviolet (UV)–visible absorption, fluorescence emission, kinetics, circular dichroism and time‐resolved lifetime measurements. The binding nature of BSA towards S1 was strong, and was found to be stable over a period of days. The studies showed that the S1–BSA complex could be used as a new biomaterial for fluorescence‐based high‐throughput assay for kinase enzymes.     

Immunogenicity of an S1D epitope from porcine epidemic diarrhea virus and cholera toxin B subunit fusion protein transiently expressed in infiltrated Nicotiana benthamiana leaves

Porcine epidemic diarrhea virus (PEDV) belongs to the Coronaviridae family and causes acute enteritis in pigs. A fragment of the large spike glycoprotein, termed the S1D epitope (aa 636–789), alone and fused with cholera toxin B subunit, were independently cloned into plant expression vectors, yielding plasmids pMYV717 and pMYV719, respectively. Plant expression vectors were transformed into Agrobacterium tumefaciens and subsequently infiltrated into Nicotiana benthamiana leaves. The highest expression level of S1D was found at 2?days post infiltration (dpi), reached 0.04?% of total soluble protein, and rapidly decreased thereafter. The expression and assembly of CTB–S1D fusion protein were confirmed by Western blot and G_M1-ELISA. The highest expression level of CTB–S1D fusion protein was 0.07?% of TSP at 4 dpi, with a rapid decrease thereafter. In the presence of p19 protein from tomato bushy stunt virus, the S1D and CTB–S1D protein levels peaked at 6 dpi and were fourfold to sevenfold higher than in the absence of p19, respectively. After oral administration of transiently expressed CTB–S1D fusion protein, or with bacterial cholera toxin or rice callus expressing mutant cholera toxin 61F, mice exhibited significantly greater serum IgG and sIgA levels against bacterial CTB and S1D antigen, peaking at week 6. Transiently expressed CTB–S1D fusion protein will be administered orally to pigs to assess the immune response against PEDV.     

Cyclic cystine knot and its strong implication on the structure and dynamics of cyclotides

The archetypal Viola odorata cyclotide cycloviolacin-O1 and its seven analogs, created by partial or total reduction of the three native S–S linkages belonging to the “cyclic cystine knot” (CCK) motif are studied for their structural and dynamical diversities using molecular dynamics simulations. The results indicate interesting interplay between the constraints imposed by the S–S bonds on the dynamical modes and the corresponding structure of the model peptide. Principal component analysis brings out the variation in the extent of dynamical freedom along the peptide backbone for each model. The motions are characterized by low amplitude diffusive modes in the peptides retaining most of the native S–S linkages in contrast to the large amplitude discrete jumps where at least two or all of the three S–S linkages are reduced. Simulation results further indicate that the disulfide bond between Cys1–18 is formed at a much faster pace compared with its two other peers Cys5–20 and Cys10–25 as found in the native peptide. This gives insight as to why the S–S linkages appear in the native peptide in a particular combination. Model therapeutics and drug delivery engines can potentially utilize this information to customize the engineered S–S bonds and gauge its impact on the dynamic flexibility of a model macrocyclic peptide.     

Rationalizing Electrocatalysis of Li–S Chemistry by Mediator Design: Progress and Prospects

The lithium–sulfur (Li–S) battery is regarded as a next‐generation energy storage system due to its conspicuous merits in high theoretical capacity (1672 mAh g^?1), overwhelming energy density (2600 Wh kg^?1), and the cost‐effectiveness of sulfur. However, the practical application of Li–S batteries is still handicapped by a multitude of key challenges, mainly pertaining to fatal lithium polysulfide (LiPS) shuttling and sluggish sulfur redox kinetics. In this respect, rationalizing electrocatalytic processes in Li–S chemistry to synergize the entrapment and conversion of LiPSs is of paramount significance. This review summarizes recent progress and well‐developed strategies of the mediator design toward promoted Li–S chemistry. The current advances, existing challenges, and future directions are accordingly highlighted, aiming at providing in‐depth understanding of the sulfur reaction mechanism and guiding the rational mediator design to realize high‐energy and long‐life Li–S batteries.     

SOT1, a pentatricopeptide repeat protein with a small MutS‐related domain,is required for correct processing of plastid 23S–4.5S rRNA precursors in Arabidopsis thaliana

Ribosomal RNA processing is essential for plastid ribosome biogenesis, but is still poorly understood in higher plants. Here, we show that SUPPRESSOR OF THYLAKOID FORMATION1 (SOT1), a plastid‐localized pentatricopeptide repeat (PPR) protein with a small MutS‐related domain, is required for maturation of the 23S–4.5S rRNA dicistron. Loss of SOT1 function leads to slower chloroplast development, suppression of leaf variegation, and abnormal 23S and 4.5S processing. Predictions based on the PPR motif sequences identified the 5′ end of the 23S–4.5S rRNA dicistronic precursor as a putative SOT1 binding site. This was confirmed by electrophoretic mobility shift assay, and by loss of the abundant small RNA ‘footprint’ associated with this site in sot1 mutants. We found that more than half of the 23S–4.5S rRNA dicistrons in sot1 mutants contain eroded and/or unprocessed 5′ and 3′ ends, and that the endonucleolytic cleavage product normally released from the 5′ end of the precursor is absent in a sot1 null mutant. We postulate that SOT1 binding protects the 5′ extremity of the 23S–4.5S rRNA dicistron from exonucleolytic attack, and favours formation of the RNA structure that allows endonucleolytic processing of its 5′ and 3′ ends.     

Stereoselective Degradation of alpha‐Cypermethrin and Its Enantiomers in Rat Liver Microsomes

Alpha‐cypermethrin (α‐CP), [(RS)‐a‐cyano‐3‐phenoxy benzyl (1RS)‐cis‐3‐(2, 2‐dichlorovinyl)‐2, 2‐dimethylcyclopropanecarboxylate], comprises a diastereoisomer pair of cypermethrin, which are (+)‐(1R‐cis‐αS)–CP (insecticidal) and (?)‐(1S‐cis‐αR)–CP (inactive). In this experiment, the stereoselective degradation of α‐CP was investigated in rat liver microsomes by high‐performance liquid chromatography (HPLC) with a cellulose‐tris‐ (3, 5‐dimethylphenylcarbamate)‐based chiral stationary phase. The results revealed that the degradation of (?)‐(1S‐cis‐αR)‐CP was much faster than (+)‐(1R‐cis‐αS)‐CP both in enantiomer monomers and rac‐α‐CP. As for the enzyme kinetic parameters, there were some variances between rac‐α‐CP and the enantiomer monomers. In rac‐α‐CP, the V_max and CL_int of (+)‐(1R‐cis‐αS)–CP (5105.22 ± 326.26 nM/min/mg protein and 189.64 mL/min/mg protein) were about one‐half of those of (?)‐(1S‐cis‐αR)–CP (9308.57 ± 772.24 nM/min/mg protein and 352.19 mL/min/mg protein), while the K_m of the two α‐CP enantiomers were similar. However, in the enantiomer monomers of α‐CP, the V_max and K_m of (+)‐(1R‐cis‐αS) ‐CP were 2‐fold and 5‐fold of (?)‐(1S‐cis‐αR)‐CP, respectively, which showed a significant difference with rac‐α‐CP. The CL_int of (+)‐(1R‐cis‐αS)–CP (140.97 mL/min/mg protein) was still about one‐half of (?)‐(1S‐cis‐αR)–CP (325.72 mL/min/mg protein) in enantiomer monomers. The interaction of enantiomers of α‐CP in rat liver microsomes was researched and the results showed that there were different interactions between the IC₅₀ of (?)‐ to (+)‐(1R‐cis‐αS)‐CP and (+)‐ to (?)‐(1S‐cis‐αR)‐CP(IC_50(?)/(+) / IC_50(+)/(?) = 0.61). Chirality 28:58–64, 2016. © 2015 Wiley Periodicals, Inc.     

Synthesis of 4-(2-substituted hydrazinyl)benzenesulfonamides and their carbonic anhydrase inhibitory effects

In this study, 4-(2-substituted hydrazinyl)benzenesulfonamides were synthesized by microwave irradiation and their chemical structures were confirmed by ¹H NMR, ¹³CNMR, and HRMS. Ketones used were: Acetophenone (S1), 4-methylacetophenone (S2), 4-chloroacetophenone (S3), 4-fluoroacetophenone (S4), 4-bromoacetophenone (S5), 4-methoxyacetophenone (S6), 4-nitroacetophenone (S7), 2-acetylthiophene (S8), 2-acetylfuran (S9), 1-indanone (S10), 2-indanone (S11). The compounds S9, S10 and S11 were reported for the first time, while S1–S8 was synthesized by different method than literature reported using microwave irradiation method instead of conventional heating in this study. The inhibitory effects of 4-(2-substituted hydrazinyl)benzenesulfonamide derivatives (S1–S11) against hCA I and II were studied. Cytosolic hCA I and II isoenzymes were potently inhibited by new synthesized sulphonamide derivatives with K_is in the range of 1.79?±?0.22–2.73?±?0.08?nM against hCA I and in the range of 1.72?±?0.58–11.64?±?5.21?nM against hCA II, respectively.     

Variations in essential and non-essential element composition and yield of silage corn fertilized with sulfur

Abstract

The effect of sulfur fertilization on the silage yield and essential and non-essential element composition of silage corn was investigated at the Experimental Field of Research and Experiment Station of the Ankara University during the years 2002 and 2003. The experimental design was a randomized complete block with five replications. Sulfur was applied at 1000 (S₁) and 1500 (S₂) kg ha^?1 as gypsum. Element concentration of the plants was measured by polarized energy dispersive X-ray fluorescence (PEDXRF). Sulfur fertilization increased S concentrations and improved silage corn yield for both years. Applied S reduced P and Mo concentrations, increased Fe and Mn concentrations, and had no significant effect on the K, Ca, Mg, Zn and Cl concentrations of silage corn. Non-essential element composition of silage corn was also influenced by S fertilization. Applied S significantly increased Sr and Pb, reduced Si, Ba and U, while had no effect on Na, Ti, Ni, Br and Rb concentrations of silage corn. In the current work, essential and non-essential element concentrations of silage corn in 2002 and 2003 years under our experimental conditions were as follows; 1.58–1.89 S, 1.07–1.046 P, 14.3–15.9 K, 8.35–9.20 Ca, 3.34–4.28 Mg, 0.26–0.53 Na, 1.36–2.46 Cl, 38.4–42.1 Si as g kg^?1, and 2.06–3.13 Mo, 140–144 Fe, 6.08–17.69 Zn, 104–116 Mn, 9.37–12.2 Cu, 23.9–22.6 Ti, 2.10–2.31 Ni, 6.54–6.71 Br, 7.04–8.74 Rb, 94.8–118.8 Sr, 24.0–31.51 Ba, 1.20–2.22 Pb and 3.17–4.07 U as mg kg^?1.     

Highly luminescent S,N co‐doped carbon quantum dots‐sensitized chemiluminescence on luminol–H2O2 system for the determination of ranitidine

S,N co‐doped carbon quantum dots (N,S‐CQDs) with super high quantum yield (79%) were prepared by the hydrothermal method and characterized by transmission electron microscopy, photoluminescence, UV–Vis spectroscopy and Fourier transformed infrared spectroscopy. N,S‐CQDs can enhance the chemiluminescence intensity of a luminol–H₂O₂ system. The possible mechanism of the luminol–H₂O₂–(N,S‐CQDs) was illustrated by using chemiluminescence, photoluminescence and ultraviolet analysis. Ranitidine can quench the chemiluminescence intensity of a luminol–H₂O₂–N,S‐CQDs system. So, a novel flow‐injection chemiluminescence method was designed to determine ranitidine within a linear range of 0.5–50 μg ml^?1 and a detection limit of 0.12 μg ml^?1. The method shows promising application prospects.     

The Raman Spectroscopy,XRD, SEM,and AFM Study of Arabinogalactan Sulfates Obtained Using Sulfamic Acid

The structure of sodium salts of arabinogalactan (AG) sulfates obtained by sulfating AG of larch wood with a sulfamic acid–urea mixture in 1,4-dioxane was studied by the methods of Raman spectroscopy, X-ray diffraction (XRD) phase analysis, scanning electron microscopy (SEM), and atomic force microscopy (AFM). The introduction of sulfate groups into the structure of arabinogalactan was confirmed by the appearance in the Raman spectra of new absorption bands related to the deformation vibrations δ (SO₃) at 420 cm^–1 and δ (О=S=O) at 588 cm^–1, stretching vibrations ν (C–O–S) at 822 cm^–1, symmetrical stretching vibrations ν_s (O=S=O) at 1076 cm^–1, and asymmetric stretching vibrations of ν_as (O=S=O) at 1269 cm^–1. According to the XRD data, the amorphization of arabinogalactan structure occurs during the sulfation process. The SEM method revealed a significant difference in the morphology of the sulfated and starting arabinogalactan. The starting AG consists of particles of predominantly globular shape with a size of 10 to 90 μm; arabinogalactan sulfates, of particles of various shapes with sizes of 1–8 μm. According to the AFM, the surface of sulfated arabinogalactan film consists of rather homogeneous spherical particles about 70 nm in size. The root-mean-square value of the surface roughness is 33 nm. The surface of sulfated AG film does not contain impurities.     

Studies on the role of amino acid residues 31 through 46 of ribosomal protein S4 in the mechanism of 30 S ribosome assembly.

We have described previously the isolation of a large fragment of 30 S ribosomal protein S4 (Changchien &; Craven, 1976). This S4-fragment is produced by the digestion of the S4–16S RNA complex with trypsin and it retains a full capacity to associate specifically with 16S RNA. It was also demonstrated that the S4-fragment has approximately 46 amino acid residues missing from the N-terminus and an intact C-terminus (also shown by Newberry et al., 1977). Preliminary experiments with this S4-fragment indicated that it could not fully replace the intact protein S4 in the process of 30 S ribosome assembly in vitro.We have also recently reported (Changchien et al., 1978) the preparation of a new fragment of protein S4 which has only 30 amino acid residues cleaved from the N-terminus. This was achieved by the use of the reagent 2-nitro-5-thiocyanobenzoic acid which selectively modifies the cysteine residue at position 31 followed by a cleavage of the adjacent peptide bond.We have now fully characterized the capacity of these two fragments, S4-fragment (47–203) and S4-fragment(31–203), to participate in the 30 S ribosome assembly process in vitro. Using 2-dimensional polyacrylamide gel electrophoresis, we find that when S4-fragment(47–203) is a component of the in vitro assembly reaction, proteins S1, S2, S10, S18 and S21 fail to become incorporated into the final particle. In contrast, S4-fragment(31–203) appears to participate in the reconstitution reaction without impairment allowing the complete incorporation of all 20 proteins of the 30 S subunit. The resultant particle, containing the S4-fragment (31–203), is fully active in the binding of poly(U), but is completely inactive for non-enzymatic poly(U)-directed binding of Phe-tRNA (Changchien et al., 1978). These results suggest that residues 1 through 30 of protein S4 are not involved in the assembly of the 30 S ribosome, but are required for the proper construction of the tRNA binding site. In addition residues 31 through 46 must be somehow critically important for the assembly of proteins S1, S2, S10, S18 and S21. We present evidence to show that the absence of residues 31 through 46 of protein S4 prevents a conformational change in the structure of 16 S RNA which normally accompanies the RI to RI transition and that this results in the inability of these proteins to participate in the assembly process.     

A dopamine D3 receptor agonist, 7-OH-DPAT,causes vomiting in the dog

R(+)7-hydroxy-N,N-di-n-propyl-2-aminotetralin (R(+)-7-OH-DPAT), a selective dopamine D₃ receptor agonist, (0.03–0.3 mg/Kg, S.c.) dose-relatedly caused emesis, whereas S (−)-7-OH-DPAT at even 1 mg/kg did not induce emesis in dogs. Apomorphine (0.03-0.3 mg/kg, s.c.) or quinpirole (0.03–0.1 mg/Kg, S.c.) also caused emesis in a dose-dependent manner. The potency of R(+)-7-OH-DPAT in inducing emesis was the same as that of apomorpine and quipirole. On the other hand, SKF-38393 (1 and 3 mg/Kg, S.c.), a selective d₁ receptor agonist, failed to induce emesis in dogs. The emesis induced by R(+)-7-OH-DPAT (0.3 mg/Kg, S.c.) was inhibited by S(−)-eticlopride (0.01–0.1 mg/Kg, S.c.), a potent D₂ and D₃ receptor antagonist but not by SCH-23390 (1 mg/Kg, S.c.), a selective d₁ receptor antagonist or clozapine (1 mg/Kg, S.c.), a D₄ receptor antagonist. These results indicate that dopamine D₃ receptors play an important role in the genesis of emesis in dogs.     

Frogspawn‐Coral‐Like Hollow Sodium Sulfide Nanostructured Cathode for High‐Rate Performance Sodium–Sulfur Batteries

Room‐temperature (RT) sodium–sulfur (Na–S) batteries are attractive cost‐effective platforms as the next‐generation energy storage systems by using all earth‐abundant resources as electrode materials. However, the slow kinetics of Na–S chemistry makes it hard to achieve high‐rate performance. Herein, a facile and scalable approach has been developed to synthesize hollow sodium sulfide (Na₂S) nanospheres embedded in a highly hierarchical and spongy conductive carbon matrix, forming an intriguing architecture similar to the morphology of frogspawn coral, which has shown great potential as a cathode for high‐rate performance RT Na–S batteries. The shortened Na‐ion diffusion pathway benefits from the hollow structures together with the fast electron transfer from the carbon matrix contributes to high electrochemical reactivity, leading to superior electrochemical performance at various current rates. At high current densities of 1.4 and 2.1 A g^?1, high initial discharge capacities of 980 and 790 mAh g^?1_sulfur can be achieved, respectively, with reversible capacities stabilized at 600 and 400 mAh g^?1_sulfur after 100 cycles. As a proof of concept, a Na‐metal‐free Na–S battery is demonstrated by pairing the hollow Na₂S cathode with tin‐based anode. This work provides guidance on rational materials design towards the success of RT high‐rate Na–S batteries.     

Inhibition of Protein Synthesis by Antiviral Protein from Yucca recurvifolia Leaves

We analyzed 18S and 26S rRNA partial base sequences [positions 1451–1618 (168 bases) of 18S rRNA and positions 1611–1835 (225 bases) and 493–622 (130 bases) of 26S rRNA] of a total of three strains of Pichia jadinii and Candida utilis. The three strains had identical base sequences with the type strain of P. jadinii (IFO 0987) in the 18S rRNA partial base sequencings. In the 26S rRNA partial base sequencings, there were partial base sequences similar to each other (1–0 base difference and 87–95 percent similarities). The sequence data obtained are discussed taxonomically and phylogenetically, especially in connection with Williopsis saturnus, the type species of the genus Williopsis ZENDER.     

The Phylogeny of Species of the Genus Saccharomycopsis Schiönning (Saccharomycetaceae) Based on the Partial Sequences of 18S and 26S Ribosomal RNAs

Eight strains of Saccharomycopsis species were examined for their partial base sequences of 18S and 26S rRNAs. The base sequences on the fingerprint segment showed three kinds of ACUAU, UCUAU, and AUAU. In the partial base sequences (positions 1451–1618, 168 bases) of 18S rRNA, all the strains of Saccharomycopsis species examined had 1–0 base difference except for the strains of Saccharomycopsis fibuligera (base differences, 5–4). In the partial base sequences on the positions 1611–1835 region (225 bases) of 26S rRNA, however, S’copsis vini had 15–11 base differences. The other species had 7–2 base differences. In the partial base sequences on the positions 493–622 region (130 bases) of 26S rRNA, the calculated percent similarities were 62–77. Discussion was made phylogenetically and taxonomically, especially on the separation of S’copsis fibuligera (≡ Endomyces fibuliger) from the genus Saccharomycopsis.     

Modulators of the Sphingosine 1-phosphate receptor 1

The Sphingosine 1-phosphate receptor (S1P-R) signaling system has proven to be of biological and medical importance in autoimmune settings. S1P₁-R is a validated drug target for multiple sclerosis (MS) for which FTY720 (Fingolimod), a S1P_1,3–5-R pan-agonist, was recently approved as the first orally active drug for the treatment of relapsing-remitting MS. Transient bradycardia and long half-life are the FTY720 critical pitfalls. This review provides the latest advances on next-generation S1P₁-R modulators from 2012 up to date, with an overview of the chemical structures, structure–activity relationships, and relevant biological and clinical properties.     

Studies on Menthol Derivatives

(–)-Menthyl carbinol (1-(R)-methyl-3-(R)-hydroxymethyl-4-(S)-isopropylcyclohexane) (4) was prepared stereospecifically in good yield by treatment of formaldehyde with the Grignard reagent from (–)-menthyl chloride (2), which was prepared from (–)-menthol-(1-(R)-methyl-3-(R)-hydroxy-4-(S)-isopropylcyclohexane) (1) by chlorination using the Lucas reagent (HCl+ZnCl₂). The configuration of 4 was assigned by the chemical method.