Subsequent Substitutions Research Articles

Assessing the mechanisms of multi-drug resistant non-typhoidal Salmonella (NTS) serovars isolated from layer chicken farms in Nigeria.

In Nigeria, there have been reports of widespread multiple antimicrobial resistance (AMR) amongst Salmonella isolated from poultry. To mitigate the impact of mortality associated with Salmonella on their farms, farmers resort to the use of antimicrobials without sound diagnostic advice. We conducted this study to describe the AMR patterns, mechanisms and genetic similarities within some Salmonella serovars isolated from different layer farms. We determine the AMR profiles of two hundred Salmonella isolates, selected based on frequency, serovar, and geographical and sample type distribution. We also assessed the mechanisms of multi-drug resistance for specific genetic determinants by using PCR protocols and gene sequence analysis. Pulsed-field gel electrophoresis (PFGE) was conducted on seven selected serovars to determine their genetic relatedness. Of 200 isolates, 97 (48.5%) revealed various AMR profiles, with the multiple antibiotic resistance (MAR) index ranging from 0.07-0.5. Resistance to ciprofloxacin was common in all the multi-drug resistant isolates, while all the isolates were susceptible to cefotaxime, ceftazidime, and meropenem. Genotypic characterization showed the presence of resistance genes as well as mutations in the nucleotide genes with subsequent amino acid substitutions. Fifteen isolates (43%) of S. Kentucky were indistinguishable, but were isolated from four different states in Nigeria (Ogun, n = 9; Kaduna, n = 6; Plateau, n = 3, and: Bauchi, n = 2). PFGE revealed 40 pulsotype patterns (Kentucky, n = 12; Larochelle, n = 9; Virchow, n = 5; Saintpaul, n = 4; Poona, n = 3; Isangi, n = 2, and; Nigeria, n = 2). This study recorded strictly related but diversely distributed Salmonella serovars with high AMR rates in poultry. We recommend strict regulation on antimicrobial use and regular monitoring of AMR trends among bacteria isolated from animals and humans to inform public policy.

The importance of the first generic substitution: Evidence from Sweden

We analyze changes in the willingness to substitute from prescribed pharmaceuticals to more affordable generic equivalents in response to the first experience with a substitution. Using Swedish individual-level data of prescribed and dispensed pharmaceuticals, we employ a dynamic event study and an instrumental variable approach to show that an initial substitution reduces the probability of opposing subsequent substitutions by 39 percentage points. We recommend that policy-makers target patients with a history of opposed substitution and offer additional discounts to promote substitution as long-term savings outweigh one-time costs.

QoS-Aware Software-Defined Multicast in LEO Satellite Networks

The emerging low earth orbit (LEO) broadband constellations are capable of distributing videos via advanced multicasting techniques to multiplex bandwidth in both satellite access and backbone networks, thereby reducing huge amounts of traffics. Previous work on LEO-based multicast routing relied on IP multicast, which fails to employ global information to achieve the optimal bandwidth saving. In this article, we leverage the novel software-defined multicasting paradigm on LEO constellations to empower advanced video distribution with optimized multicast trees, thereby significantly outperforming conventional multicasting techniques. In the presence of quality-of-service (QoS) constraints, we propose weighted rectilinear Steiner minimal trees (WRSTs), which balance bandwidth saving and QoS requirements. Our multicast tree algorithm adopts the Voronoi diagram and Delaunay triangulation to obtain suitable candidate Steiner points, which are exploited by subsequent iterative edge substitutions for WRST construction. We also design QoS-aware multicast management schemes to deal with frequent member updates and potential failures in LEO constellations. We carry out thorough experiments to demonstrate the effectiveness and efficiency of the proposed routing tree construction algorithm and multicasting protocols when compared with traditional algorithms.

Inherently Chiral Cages via Hierarchical Desymmetrization.

A new type of cage inherent chirality was accessed by hierarchical desymmetrization of a D3h-symmetric prismlike cage motif. The dissymmetric C3v cage precursor C1 bearing two different phloroglucinol caps was first synthesized. The subsequent progressive substitutions on the three triazine arms by different nucleophiles furnished the desired C1-symmetric inherently chiral cages C3 and C4 with rich structural diversity. Resolution of the racemic cages was achieved by chiral chromatography, and the enantiopure cages were readily obtained on the gram scale. Convenient post-synthetic transformations of the chiral cages with retention of enantiomeric purity were also realized. The absolute configuration was determined by X-ray crystallography, and a chirality descriptor was provided to define the cage chirality. With the inherently chiral array of the electron-deficient triazine surfaces constituting three individual chiral V-shaped π cavities, regio- and enantioselective anion-π binding was probed for the first time with minimum interference of other interactions. As exemplified with chiral phosphate anions (CPAs), it was found that cage (-)-C3a preferably binds (S)-CPA- in the most electron-deficient cavity through synergistic anion-π interactions with considerable chiral selectivity.

Sulfonimidamides by Sequential Mechanochemical Chlorinations and Aminations of Sulfinamides.

Here, we report the first mechanochemical synthesis of sulfonimidamides. The one-pot, two-step method requires neither a solvent nor inert conditions. In a mixer mill, sulfinamides are rapidly converted to sulfonimidoyl chlorides by oxidative chlorination with N-chlorosuccinimide (NCS). Subsequent substitutions with amines provides a wide range of diversely substituted sulfonimidamides.

Structural features determining the vitamin K epoxide reduction activity in the VKOR family of membrane oxidoreductases.

Vitamin K epoxide reductases (VKORs) are a large family of integral membrane enzymes found from bacteria to humans. Human VKOR, specific target of warfarin, has both the epoxide and quinone reductase activity to maintain the vitamin K cycle. Bacterial VKOR homologs, however, are insensitive to warfarin inhibition and are quinone reductases incapable of epoxide reduction. What affords the epoxide reductase activity in human VKOR remains unknown. Here, we show that a representative bacterial VKOR homolog can be converted to an epoxide reductase that is also inhibitable by warfarin. To generate this new activity, we first substituted several regions surrounding the active site of bacterial VKOR by those from human VKOR based on comparison of their crystal structures. Subsequent systematic substitutions narrowed down to merely eight residues, with the addition of a membrane anchor domain, that are responsible for the epoxide reductase activity. Substitutions corresponding to N80 and Y139 in human VKOR provide strong hydrogen bonding interactions to facilitate the epoxide reduction. The rest of six substitutions increase the size and change the shape of the substrate-binding pocket, and the membrane anchor domain stabilizes this pocket while allowing certain flexibility for optimal binding of the epoxide substrate. Overall, our study reveals the structural features of the epoxide reductase activity carried out by a subset of VKOR family in the membrane environment.

Understanding the Fe-CO bond through the electronic structure of Fem+(CO)6-nLn, m = 2, 3,n = 0-3, L = Cl-, Br-, H2O or NH3.

Carbon monoxide (CO) exerts various protective effects on the body. Drugs known as CORMs (CO-releasing molecules) can continuously release small doses of CO into diseased tissues and cells. Transition metals interact strongly with the carbonyl group, and coordination compounds bearing carbonyl groups are a promising class of CORMs. This study investigates the octahedral coordination of Fe2+ and Fe3+ compounds with carbonyl groups (to give Fen+[CO]6) and subsequent substitutions with Cl-, Br-, NH3, and H2O, to understand how these ligands interfere in the M-CO bond. The geometry optimization calculations were performed with the methods BP86 and B3LYP and the atomic basis set def2-TZVP. The molecular orbitals and the properties derived from the electronic density based on QTAIM were analyzed. Coordination with ligands increased the influence of the metal atomic basin on the Fe-C bond, especially for the Fe2+ compounds, and the Cl- and Br- ligands led to lower local ionization energies at the Fe-C bonds. Trans effects were also observed in the QTAIM real functions: Fe-C bond distances were shorter when C was in trans position to a ligand.

Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins.

The rate of evolution differs between protein sites and changes with time. However, the link between these two phenomena remains poorly understood. Here, we design a phylogenetic approach for distinguishing pairs of amino acid sites that evolve concordantly, i.e., such that substitutions at one site trigger subsequent substitutions at the other; and also pairs of sites that evolve discordantly, so that substitutions at one site impede subsequent substitutions at the other. We distinguish groups of amino acid sites that undergo coordinated evolution and evolve discordantly from other such groups. In mitochondrion-encoded proteins of metazoans and fungi, we show that concordantly evolving sites are clustered in protein structures. By analysing the phylogenetic patterns of substitutions at concordantly and discordantly evolving site pairs, we find that concordant evolution has two distinct causes: epistatic interactions between amino acid substitutions and episodes of selection independently affecting substitutions at different sites. The rate of substitutions at concordantly evolving groups of protein sites changes in the course of evolution, indicating episodes of selection limited to some of the lineages. The phylogenetic positions of these changes are consistent between proteins, suggesting common selective forces underlying them.

Generalized enzymatic mechanism of catalysis by tetrameric l-asparaginases from mesophilic bacteria

The mechanism of catalysis by the l-glutaminase-asparaginase from Pseudomonas 7A (PGA) was investigated using structural, mass spectrometry, and kinetic data. We had previously proposed mechanism of hydrolysis of l-Asn by the type II l-asparaginase from E. coli (EcAII), but that work was limited to just one enzyme. Based on results presented in this report, we postulate that all homotetrameric l-asparaginases from mesophilic bacteria utilize a common ping-pong mechanism of catalysis consisting of two subsequent nucleophilic substitutions. Several new structures of non-covalent complexes of PGA with different substrates, as well as structures of covalent acyl-enzyme intermediates of PGA with canonical substrates (l-Asp and l-Glu) and an opportunistic ligand, a citrate anion, were determined. The results of kinetic experiments monitored by high-resolution LC/MS, when combined with new structural data, clearly show that the reaction catalyzed by l-glutaminase-asparaginases proceeds through formation of a covalent intermediate, as observed previously for EcAII. Additionally, by showing that the same mechanism applies to l-Asn and l-Gln, we postulate that it is common for all these structurally related enzymes.

The use of sentinel logs to assess host shifts in early beetle colonisers of deadwood under climate‐ and forestry‐induced tree species substitutions

Abstract Global change scenarios project drastic modifications in tree species range and an increase in exotic tree plantations. Subsequent tree species substitutions may alter habitat conditions for biodiversity. We measured substitutability between tree species for early deadwood colonisers, through a sentinel log approach, i.e. through the experimental exposure of paired down deadwood (DDW) pieces to native beetles in native stands. We compared two native/substitute tree species pairs: one conifer pair composed of a rapidly expanding exotic species (Douglas fir) and a declining native species (silver fir), and one deciduous pair composed of two native species, one expanding (sessile oak) and one retreating (beech) at the regional scale. The effects of expanding exotic and native trees on beetle communities were not in line with expectations. Species assemblages in Douglas fir DDW were indistinguishable from those in native silver fir DDW and did not contain fewer species. Assemblages were not more generalist on average in substitutes than in substituted trees: we did not note any decrease in species richness of functional groups to the detriment of specialist species. Moreover, species richness and abundance were higher in substitute oak than in native beech DDW, confirming that species from the regional pool were able to colonise oak, even though it is a minor tree species at the regional level. Large‐scale monitoring schemes including multi‐taxon, multi‐year and multiple native/substitute pairs would further our knowledge of the generic effects of tree species substitution on biodiversity and ecosystem functioning.

Vinyl Cation Stabilization by Silicon Enables a Formal Metal-Free α-Arylation of Alkyl Ketones.

The ability of silicon to stabilize vinyl cationic species leads to a redox arylation of alkynes whereby the stringent limitations of reactivity and regioselectivity of alkyl‐substituted alkynes are lifted. This allows the synthesis of a range of α‐silyl‐α′‐arylketones under mild conditions in good to excellent yields and with high functional group tolerance, whereby the silicon moiety in the final products can either be removed for a formal acetone monoarylation transform, or capitalized upon for subsequent electrophilic substitutions at either side of the carbonyl group.

Theoretical Explanation of Reaction Site Selectivity in the Addition of a Phenoxy Group to Perfluoropyridine.

Pentafluoropyridine, a potentially useful precursor in organofluorine methodology, undergoes selective substitution of a fluorine with a phenoxide at the site para to the nitrogen. Subsequent aryloxide substitutions can be accomplished at the ortho-positions with aryloxide groups containing various functional groups para to the phenoxide oxygen. During this phase of the reaction, "reverse reactions" involving substitutions of the original para substituent with a free fluoride or with another aryloxide moiety are observed with a frequency that depends on the functional group para to the oxygen on the aryloxide. Herein, we provide a theoretical explanation of these observations through use of density functional theory.

A novel algebraic solution to the perspective-three-line pose problem

In this work, we present a novel algebraic method to the perspective-three-line (P3L) problem for determining the position and attitude of a calibrated camera from features of three known reference lines. Unlike other methods, the proposed method uses an intermediate camera frame F and an intermediate world frame E, with sparse known line coordinates, facilitating formulations of the P3L problem. Additionally, the rotation matrix between the frame E and the frame F is parameterized by using its orthogonality, and then a closed-form solution for the P3L pose problem is obtained from subsequent substitutions. This algebraic method makes the processes more easily followed and significantly improves the performance. The experimental results show that the proposed method offers numerical stability, accuracy and efficiency comparable or better than that of state-of-the-art method.

Experimental and theoretical spectroscopic studies in relation to molecular structure investigation of para chloro, para fluoro and para nitro maleanilinic acids

In the present work novel para chloro, para fluoro and para nitro maleanilic acid derivatives were prepared and investigated using FT-IR, thermal analyses (TA) measurements (TGA/DTG and DTA) in comparison with mass spectral (MS) fragmentation at 70 eV. The crystallographic structures of studied compounds were investigated by X-ray diffraction (XRD). The vibrational frequencies and the corresponding normal modes were evaluated at the optimized geometry. Vibrational modes were analyzed using GAUSSVIEW software. Experimental FT-IR and Raman spectra of the three newly prepared derivatives, namely, (E) – oxo -4- ((4- nitro phenyl) amino)-4- oxobut-2-enoic acid (p-NMA), (E) -4- ((4- chloro phenyl)amino)-4- oxobut -2- enoic acid (p-ClMA), (E) -4- ((4- fluoro phenyl) amino)- 4- oxobut -2- enoic acid (p-FMA) were compared with the theoretically calculated one. FT-IR and the observed vibrational frequencies were assigned; thermal analysis and mass spectrum measurements of the maleanilic acid derivatives were recorded and discussed. The computational calculations were carried out by DFT - B3LYP method with 6-311++G(d,p) basis sets and the corresponding results were tabulated. The alternations of structures of p-FMA, p-ClMA and p-NMA due to the subsequent substitutions were investigated. This correlation between experimental and theoretical calculations provided a good confirmation of the proposed structures of the newly prepared compounds. The derivatives were found to be highly effective against Hepatocellular carcinoma cells > Breast carcinoma cells > colon carcinoma cells. It was recognized, that cancer cells over expression promotes tumorigenic functions; can be suppressed by p-NMA > p-FMA > p-ClMA inhibitors.

Stereoelectronic Flexibility of Ammonium-Functionalized Triazole-Derived Carbenes: Palladation and Catalytic Activities in Water

The postmodification approach allows convenient access to charge-tagged ammonium-functionalized bis(1,2,4-triazolin-5-ylidene)palladium(II) complexes even when the respective azolium salts are elusive. Bromo-functionalized 1,2,4-triazolium salts were first metalated to form the respective bromo-functionalized bis(NHC) complexes trans-[PdBr2(R-tazy-Br)2] (R = Ph, Cy, 1a,b). Subsequent postcoordinative nucleophilic substitutions converted the bromo into ammonium functions, leading to the water-soluble, charge-tagged complexes trans-[PdBr2(R-tazy-NEt3)2]Br2 (R = Ph, Cy, 2a,b). The catalytic activities of 2a,b in the aqueous Suzuki–Miyaura reaction were compared to those of their analogues 2c,d bearing more bulky mesityl and diisopropylphenyl substituents, and a detailed stereoelectronic profiling of the NHCs using %Vbur, HEP, and DFT calculations was conducted to rationalize their catalytic differences. Although all complexes are active, the more donating and less bulky complexes 2a,b performed significantly...

Asymmetric syntheses of (R)-4-halo-6,6a,7,8,9,10-hexahydro-5H-pyrazino[1,2-a][1,n]naphthyridines, important 5-HT2C agonist precursors

Asymmetric syntheses of N-protected (R)-4-halo-6,6a,7,8,9,10-hexahydro-5H-pyrazino[1,2-a][1,n]naphthyridines, advanced intermediates for the synthesis of highly potent and selective 5-HT2C agonists, are described. The key transformation involves ring opening of N-protected bicyclic sulfamidate (R)-hexahydro-3H-pyrazino[1,2-c][1,2,3]oxathiazine 1,1-dioxide with (4-halo-2-fluoropyridin-3-yl)lithiums or (3-bromo-5-fluoropyridin-4-yl)lithium. In situ hydrolyses of the resultant sulfamic acids and subsequent intramolecular nucleophilic aromatic substitutions (SNAr) produce the enantiopure tricycles. The two step procedure represents new methodology for the stereoselective syntheses of tetrahydronaphthyridines.

Pervasive contingency and entrenchment in a billion years of Hsp90 evolution

Interactions among mutations within a protein have the potential to make molecular evolution contingent and irreversible, but the extent to which epistasis actually shaped historical evolutionary trajectories is unclear. To address this question, we experimentally measured how the fitness effects of historical sequence substitutions changed during the billion-year evolutionary history of the heat shock protein 90 (Hsp90) ATPase domain beginning from a deep eukaryotic ancestor to modern Saccharomyces cerevisiae We found a pervasive influence of epistasis. Of 98 derived amino acid states that evolved along this lineage, about half compromise fitness when introduced into the reconstructed ancestral Hsp90. And the vast majority of ancestral states reduce fitness when introduced into the extant S. cerevisiae Hsp90. Overall, more than 75% of historical substitutions were contingent on permissive substitutions that rendered the derived state nondeleterious, became entrenched by subsequent restrictive substitutions that made the ancestral state deleterious, or both. This epistasis was primarily caused by specific interactions among sites rather than a general effect on the protein's tolerance to mutation. Our results show that epistasis continually opened and closed windows of mutational opportunity over evolutionary timescales, producing histories and biological states that reflect the transient internal constraints imposed by the protein's fleeting sequence states.

Electronic and vibrational spectroscopic (FT-IR and FT-Raman) investigation using ab initio (HF) and DFT (B3LYP and B3PW91) and HOMO/LUMO/MEP analysis on the structure of l-serine methyl ester hydrogen chloride

The vibrational spectroscopy (Fourier Transform Raman and Infrared spectra) of l-serine methyl ester hydrogen chloride (LHCL) have been recorded and the observed vibrational frequencies are assigned and tabulated. The Gaussian hybrid computational calculations were determined by HF and DFT (B3LYP and B3PW91) methods with 6–31++G(d,p) and 6–311++G(d,p) as basis sets. The mulliken and natural charge in the functional group has the maximum magnitude of 0.305 and 0.498 among the hydrogen atoms present in the compound and here, the entire hydrogen atoms exhibit a net positive charge. The change of structure of amino acid due to the addition of subsequent substitutions of methyl, ethyl, carboxylic and hydroxyl chain is investigated. It plays a vital role in the production of different pharmaceutical and cosmetics industries.13C NMR and 1H NMR were calculated by using the gauge independent atomic orbital (GIAO) method with the B3LYP methods and the 6-311 + G(d,p) basis set and nuclear magnetic resonance chemical shifts related to TMS were compared. A study on the optoelectronics properties: absorption wavelengths, excitation energy, oscillator strength, dipole moment and FMO were executed by the HF and DFT methods. UV–Visible spectrum of the present compound is recorded in the region is 200–400 nm and the electronic properties HOMO and LUMO energies are deliberated by TD-DFT method. The polarizability, anisotropy, dipole moment and first order hyperpolarizability of the molecule have been discussed.

An efficient solution to the perspective-three-point pose problem

In this paper, we present a new algebraic method to solve the perspective-three-point (P3P) problem, which directly computes the rotation and position of a camera in the world frame without the intermediate derivation of the points in the camera frame. Unlike other online methods, the proposed method uses an “object” coordinate frame, in which the known 3D coordinates are sparse, facilitating formulations of the P3P problem. Additionally, two auxiliary variables are introduced to parameterize the rotation and position matrix, and then a closed-form solution for the camera pose is obtained from subsequent substitutions. This algebraic approach makes the processes more easily followed and significantly improves the performance. Experimental results demonstrated that our method offers accuracy and precision comparable to the existing state-of-the art methods but it has better computational efficiency.

Mutagenic Effects of Ribavirin on Hepatitis E Virus-Viral Extinction versus Selection of Fitness-Enhancing Mutations.

Hepatitis E virus (HEV), an important agent of viral hepatitis worldwide, can cause severe courses of infection in pregnant women and immunosuppressed patients. To date, HEV infections can only be treated with ribavirin (RBV). Major drawbacks of this therapy are that RBV is not approved for administration to pregnant women and that the virus can acquire mutations, which render the intra-host population less sensitive or even resistant to RBV. One of the proposed modes of action of RBV is a direct mutagenic effect on viral genomes, inducing mismatches and subsequent nucleotide substitutions. These transition events can drive the already error-prone viral replication beyond an error threshold, causing viral population extinction. In contrast, the expanded heterogeneous viral population can facilitate selection of mutant viruses with enhanced replication fitness. Emergence of these mutant viruses can lead to therapeutic failure. Consequently, the onset of RBV treatment in chronically HEV-infected individuals can result in two divergent outcomes: viral extinction versus selection of fitness-enhanced viruses. Following an overview of RNA viruses treated with RBV in clinics and a summary of the different antiviral modes of action of this drug, we focus on the mutagenic effect of RBV on HEV intrahost populations, and how HEV is able to overcome lethal mutagenesis.