Opposite Orientation Research Articles

Intra- and intermolecular N–H•••O=C hydrogen bonds in 1-acyl urea compounds: Synthesis, X-ray structure, conformational and Hirshfeld surface analyses of 1-(2,3-dichlorophenyl)-3-pivaloylurea

Reaction of freshly prepared pivaloyl isothiocyanate with 2,3-dichloroaniline afforded the 1-(2,3-dichlorophenyl)-3-pivaloylthiourea intermediate (2) which was efficiently converted into the title urea (3) by grinding with wet silica supported potassium permanganate under solvent-free conditions in an excellent yield and purity. The structure was confirmed by the spectroscopic, elemental analysis and single crystal X-ray diffraction data. In the most stable conformation, the two C=O groups adopt a mutually opposite orientation. Intramolecular N–H•••O=C hydrogen bond occurs between the carbonyl (C=O) and urea (–NH) groups forming a six membered pseudo-ring that stabilize the most stable form. The bonding nature of this interaction has been scrutinized by using Natural Bond Orbital (NBO) population analysis, demonstrating the occurrence of a strong hyperconjugative remote interaction between the donor lone pairs located on the carbonyl oxygen and the N–H group. To visualize the intermolecular interactions in the crystal of the title compound, a Hirshfeld surface (HS) analysis was also carried out demonstrating that hydrogen-bonding and van der Waals interactions were the dominant interactions in the crystal packing. The urea groups form centrosymmetric dimers connected by intermolecular N–H•••O=C hydrogen bonds in a R22(8) motif. The 2,3-dichloro substitution has important effects on the packing stability, mostly via H•••Cl contacts, with H•••Cl/Cl•••H contributions of 26.1% of the intermolecular interactions.

Water Orientation at the Calcite-Water Interface.

Mineral-water interfaces play an important role in many natural as well as technological fields. Fundamental properties of these interfaces are governed by the presence of the interfacial water and its specific structure at the surface. Calcite is particularly interesting as a dominant rock-forming mineral in the earth’s crust. Here, we combine atomic force microscopy, sum-frequency generation spectroscopy, and molecular dynamics simulations to determine the position and orientation of the water molecules in the hydration layers of the calcite surface with high resolution. While atomic force microscopy provides detailed information about the position of the water molecules at the interface, sum-frequency generation spectroscopy can deduce the orientation of the water molecules. Comparison of the calcite-water interface to the interfaces of magnesite-water, magnesite-ethanol, and calcite-ethanol reveals a comprehensive picture with opposite water orientations in the first and second layer of the interface, which is corroborated by the molecular dynamics simulations.

Watermelon crinkle leaf-associated virus 1 and watermelon crinkle leaf-associated virus 2 have a bipartite genome with molecular signatures typical of the members of the genus Coguvirus (family Phenuiviridae).

Watermelon crinkle leaf-associated virus 1 and watermelon crinkle leaf-associated virus 2 (WCLaV-1 and WCLaV-2), two unclassified members of the order Bunyavirales, are phylogenetically related to members of the genus Coguvirus (family Phenuiviridae). The genome of both viruses was reported previously to be composed of three RNA segments. However, the terminal sequences of two genomic RNA segments, namely those encoding the putative movement protein (MP) and the nucleocapsid (NP) protein, remained undetermined. High-throughput sequencing of total RNA and small RNA preparations, combined with reverse transcription PCR amplification followed by sequencing, revealed that the WCLaV-1 and WCLaV-2 possess a bipartite genome consisting of a negative-sense RNA1, encoding the RNA-dependent RNA polymerase, and an ambisense RNA2, encoding the putative movement (MP) and nucleocapsid (NP) proteins. The two open reading frames of RNA2 are in opposite orientations and are separated by a long AU-rich intergenic region (IR) that may assume a hairpin conformation. RNA1 and RNA2 of both viruses share almost identical 5' and 3' termini, which are complementary to each other up to 20 nt. This genome organization is typical of members of the genus Coguvirus, with which WCLaV-1 and WCLaV-2 also share similar terminal 5' and 3' sequences of RNA1 and RNA2. These molecular features, together with phylogenetic reconstructions support the classification of WCLaV-1 and WCLaV2 as members of two new species in the genus Coguvirus.

Modulation of laccase catalysed oxidations at the surface of magnetic nanoparticles

We explored the coupling of laccases to magnetic nanoparticles (MNPs) with different surface chemical coating. Two laccase variants offering two opposite and precise orientations of the substrate oxidation site were immobilised onto core-shell MNPs presenting either aliphatic aldehyde, aromatic aldehyde or azide functional groups at the particles surface. Oxidation capabilities of the six-resulting laccase-MNP hybrids were compared on ABTS and coniferyl alcohol. Herein, we show that the original interfaces created differ substantially in their reactivities with an amplitude from 1 to > 4 folds depending on the nature of the substrate. Taking enzyme orientation into account in the design of surface modification represents a way to introduce selectivity in laccase catalysed reactions.

The structures of E. coli NfsA bound to the antibiotic nitrofurantoin; to 1,4-benzoquinone and to FMN.

NfsA is a dimeric flavoprotein that catalyses the reduction in nitroaromatics and quinones by NADPH. This reduction is required for the activity of nitrofuran antibiotics. The crystal structure of free Escherichia coli NfsA and several homologues have been determined previously, but there is no structure of the enzyme with ligands. We present here crystal structures of oxidised E. coli NfsA in the presence of several ligands, including the antibiotic nitrofurantoin. Nitrofurantoin binds with the furan ring, rather than the nitro group that is reduced, near the N5 of the FMN. Molecular dynamics simulations show that this orientation is only favourable in the oxidised enzyme, while potentiometry suggests that little semiquinone is formed in the free protein. This suggests that the reduction occurs by direct hydride transfer from FMNH− to nitrofurantoin bound in the reverse orientation to that in the crystal structure. We present a model of nitrofurantoin bound to reduced NfsA in a viable hydride transfer orientation. The substrate 1,4-benzoquinone and the product hydroquinone are positioned close to the FMN N5 in the respective crystal structures with NfsA, suitable for reaction, but are mobile within the active site. The structure with a second FMN, bound as a ligand, shows that a mobile loop in the free protein forms a phosphate-binding pocket. NfsA is specific for NADPH and a similar conformational change, forming a phosphate-binding pocket, is likely to also occur with the natural cofactor.

Investigating reverse butterfly fractures: An experimental approach and application of fractography

Butterfly fractures are expected to form with the transverse portion on the tension side and the wedge portion on the compression side of a bent bone, however wedges have also been observed in the reverse orientation and are reported to be frequent in concentrated 4-point bending. To investigate how these fractures form, concentrated 4-point bending experiments were performed on nine human femora and documented using high-speed video. Videos showed the wedge portion formed as fracture initiated in tension, branched obliquely, then curved to terminate on the tension face. The transverse portion formed as a crack traveled between the curved fracture branch and the compression face. Fractography was also applied to evaluate fracture surfaces. At least one fractography feature was present in all femora and 32/35 bone fragments examined. Fracture propagation sequences interpreted using fractography matched those observed on video, demonstrating the utility of this method for evaluating complex fracture patterns.

Exact 1/N expansion of Wilson loop correlators in mathcal{N} = 4 Super-Yang-Mills theory

Supersymmetric circular Wilson loops in mathcal{N} = 4 Super-Yang-Mills theory are discussed starting from their Gaussian matrix model representations. Previous results on the generating functions of Wilson loops are reviewed and extended to the more general case of two different loop contours, which is needed to discuss coincident loops with opposite orientations. A combinatorial formula representing the connected correlators of multiply wound Wilson loops in terms of the matrix model solution is derived. Two new results are obtained on the expectation value of the circular Wilson loop, the expansion of which into a series in 1/N and to all orders in the ’t Hooft coupling λ was derived by Drukker and Gross about twenty years ago. The connected correlators of two multiply wound Wilson loops with arbitrary winding numbers are calculated as a series in 1/N. The coefficient functions are derived not only as power series in λ, but also to all orders in λ by expressing them in terms of the coefficients of the Drukker and Gross series. This provides an efficient way to calculate the 1/N series, which can probably be generalized to higher-point correlators.

The Virgin Land megaproject and the Land reform as the global experiment of steppe self-restoration in North Eurasia

Among all agrarian-social megaprojects realized in the steppe zone, the Virgin Land [Tselina] (1954-1963) and the Land reform of the 1990s exerted the most considerable influence on the state and properties of current agro-landscapes. It was the projects of opposite orientation which every on its stage set the highest in history pace of the landscape dynamics in the steppe zone. The consistent impact of these megaprojects, one of which practically annihilated steppes, and the other created terms to realize steppe restoration potential, allows considering them in totality as the united experiment of the global scale for revealing and evaluation of steppe self-restoration. Thanks to this experiment in the steppes of Eurasia, new dynamic space – after virgin land was formed. Using new data, including field studies and discovered novel factors, we estimated the Virgin land campaign’s consequences and the Land reform. A further fundamental generalization of these megaprojects’ effects, landscape, and scientific heritage required developing an adaptation of steppe land use was conducted as a response to climatic and other current challenges.

Large-Scale Computational Discovery of Binding Motifs in tRNA Fragments.

Accumulating evidence has suggested that tRNA-derived fragments (tRFs) could be loaded to Argonaute proteins and function as regulatory small RNAs. However, their mode of action remains largely unknown, and investigations of their binding mechanisms have been limited, revealing little more than microRNA-like seed regions in a handful of tRFs and a few targets. Here, we identified such regions of potential interaction on a larger scale, using in vivo formed hybrids of guides and targets in crosslinked chimeric reads in two orientations. We considered “forward pairs” (with guides located on the 5′ ends and targets on the 3′ ends of hybrids) and “reverse pairs” (opposite orientation) and compared them as independent sets of biological constructs. We observed intriguing differences between the two chimera orientations, including the paucity of tRNA halves and abundance of polyT-containing targets in forward pairs. We found a total of 197 quality-ranked motifs supported by ∼120,000 tRF–mRNA chimeras, with 103 interacting motifs common in forward and reverse pairs. By analyzing T→C conversions in human and mouse PAR-CLIP datasets, we detected Argonaute crosslinking sites in tRFs, conserved across species. We proposed a novel model connecting the formation of asymmetric pairs in two sets to the potential binding mechanisms of tRFs, involving the identified interaction motifs and crosslinking sites to Argonaute proteins. Our results suggest the way forward for further experimental elucidation of tRF-binding mechanisms.

Regulation of closely juxtaposed proto-oncogene c-fms and HMGXB3 gene expression by mRNA 3' end polymorphism in breast cancer cells.

Sense-antisense mRNA pairs generated by convergent transcription is a way of gene regulation. c-fms gene is closely juxtaposed to the HMGXB3 gene in the opposite orientation, in chromosome 5. The intergenic region (IR) between c-fms and HMGXB3 genes is 162 bp. We found that a small portion (∼4.18%) of HMGXB3 mRNA is transcribed further downstream, including the end of the c-fms gene generating antisense mRNA against c-fms mRNA. Similarly, a small portion (∼1.1%) of c-fms mRNA is transcribed further downstream, including the end of the HMGXB3 gene generating antisense mRNA against the HMGXB3 mRNA. Insertion of the strong poly(A) signal sequence in the IR results in decreased c-fms and HMGXB3 antisense mRNAs, resulting in up-regulation of both c-fms and HMGXB3 mRNA expression. miR-324-5p targets HMGXB3 mRNA 3′ UTR, and as a result, regulates c-fms mRNA expression. HuR stabilizes c-fms mRNA, and as a result, down-regulates HMGXB3 mRNA expression. UALCAN analysis indicates that the expression pattern between c-fms and HMGXB3 proteins are opposite in vivo in breast cancer tissues. Together, our results indicate that the mRNA encoded by the HMGXB3 gene can influence the expression of adjacent c-fms mRNA, or vice versa.

Acoustic topological interface states of one dimensional metamaterial propagating through a T-shaped junction

We design a supermolecular structure composed of two identical scatterers with opposite orientations in air. By adjusting the interval between them and rotating them, topological phase transitions occur. The combination of rotational and translational operations provides us with wide scope of interface states and multiple-choice to achieve interface states. Therefore, the interface states must exist at the interface between two sublattices with different topological phases. We investigate the subwavelength interface states propagating through a T-shaped junction theoretically, which consists of three one-dimensional waveguides. The results have promising prospects in developing acoustic double-channel transmission devices based on interface states.

Reverse orientation in the ultrasound-assisted [3 + 2]-cycloaddition reaction of nitrile imines with 3-formylchromone-Meldrum's acid adducts.

The [3 + 2]-cycloaddition reaction of nitrile imines with 2,2-dimethyl-5-[(4-oxo-4H-chromen-3-yl)methylene]-1,3-dioxane-4,6-dione tends to form the reverse-orientation products under ultrasound irradiation in EtOH in the presence of Et3N. Evidence for the structure of product 5b was obtained from single-crystal X-ray analysis.

To Reverse Item Orientation or Not to Reverse Item Orientation, That Is the Question.

To investigate the effect of using negatively oriented items, we wrote semantic reversals of the items in the Rosenberg Self Esteem Scale, UCLA Loneliness Scale, and the General Belongingness Scale and used them to create four experimental conditions. Participants (N = 2,019) were recruited through Amazon's Mechanical Turk. Data were assessed for dimensionality, item functioning, instrument properties, and associations with other variables. Regarding dimensionality, although a two-factor model (positively vs. negatively oriented factors) exhibits better fit than a unidimensional model across all conditions, bifactor indices were used to argue that a unidimensional interpretation of the data can be employed. With respect to item functioning, factor loadings were found to be nearly invariant across conditions, but thresholds were not. Concerning instrument properties, inclusion of negatively oriented items results in lower mean scores and higher score variances. Instruments with both positively and negatively oriented items demonstrated lower reliability estimates than those with only one orientation. For associations with other variables, path coefficients in a model where loneliness mediates the effects of belongingness on life satisfaction and self-esteem were found to vary across conditions. Findings suggest that negatively oriented items have minor impact on instrument quality, but influence measurement model and path coefficients.

Electric-Field Control of a Single-Atom Polar Bond.

We expose the polar covalent bond between a single Au atom terminating the apex of an atomic force microscope tip and a C atom of graphene on SiC(0001) to an external electric field. For one field orientation, the Au─C bond is strong enough to sustain the mechanical load of partially detached graphene, while for the opposite orientation, the bond breaks easily. Calculations based on density-functional theory and nonequilibrium Green's function methods support the experimental observations by unveiling bond forces that reflect the polar character of the bond. Field-induced charge transfer between the atomic orbitals modifies the polarity of the different electronegative reaction partners and the Au─C bond strength.

Bounds for the extremal eigenvalues of gain Laplacian matrices

A complex unit gain graph (T-gain graph), Φ=(G,φ) is a graph where the function φ assigns a unit complex number to each orientation of an edge of G, and its inverse is assigned to the opposite orientation. A T-gain graph Φ is balanced if the product of the edge gains of each cycle (with a fixed orientation) is 1. Signed graphs are special cases of T-gain graphs.The adjacency matrix of Φ, denoted by A(Φ) is defined canonically. The gain Laplacian for Φ is defined as L(Φ)=D(Φ)−A(Φ), where D(Φ) is the diagonal matrix with diagonal entries are the degrees of the vertices of G. The minimum number of vertices (resp., edges) to be deleted from Φ in order to get a balanced gain graph is the frustration number (resp, frustration index). We show that frustration number and frustration index are bounded below by the smallest eigenvalue of L(Φ). We provide several lower and upper bounds for extremal eigenvalues of L(Φ) in terms of different graph parameters such as the number of edges, vertex degrees, and average 2-degrees. The signed graphs are particular cases of the T-gain graphs, all the bounds established in this paper hold for signed graphs. Most of the bounds established here are new for signed graphs. Finally, we perform comparative analysis for all the obtained bounds in the paper with the state-of-the-art bounds available in the literature for randomly generated Erdős-Reýni graphs.Some of the major highlights of our paper are the gain-dependent bounds, limit convergence of the bounds to the extremal eigenvalues, and optimal extremal bounds obtained by posing optimization problems to achieve the best possible bounds.

Conformal generation of an exotic rotationally invariant harmonic oscillator

An exotic rotationally invariant harmonic oscillator (ERIHO) is constructed by applying a non-unitary isotropic conformal bridge transformation (CBT) to a free planar particle. It is described by the isotropic harmonic oscillator Hamiltonian supplemented by a Zeeman type term with a real coupling constant $g$. The model reveals the Euclidean ($|g|<1$) and Minkowskian ($|g|>1$) phases separated by the phases $g=+1$ and $g=-1$ of the Landau problem in the symmetric gauge with opposite orientation of the magnetic field. A hidden symmetry emerges in the system at rational values of $g$. Its generators, together with the Hamiltonian and angular momentum produce non-linearly deformed $\mathfrak{u}(2)$ and $\mathfrak{gl}(2,{\mathbb R})$ algebras in the cases of $0<|g|<1$ and $\infty>|g|>1$, which transmute one into another under the inversion $g\rightarrow -1/g$. Similarly, the true, $\mathfrak{u}(2)$, and extended conformal, $\mathfrak{gl}(2,{\mathbb R})$, symmetries of the isotropic Euclidean oscillator ($g=0$) interchange their roles in the isotropic Minkowskian oscillator ($|g|=\infty$), while two copies of the $\mathfrak{gl}(2,{\mathbb R})$ algebra of analogous symmetries mutually transmute in Landau phases. We show that the ERIHO system is transformed by a peculiar unitary transformation into the anisotropic harmonic oscillator generated, in turn, by anisotropic CBT. The relationship between the ERIHO and the subcritical phases of the harmonically extended Landau problem, as well as with a plane isotropic harmonic oscillator in a uniformly rotating reference frame, is established.

Differential use of complementarity-determining regions by synthetic nanobodies identifies multiple epitopes on receptor binding domain of SARS-CoV2

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, enters host cells through the receptor angiotensin-converting enzyme 2 (ACE2). Identification of numerous variant strains of SARS-CoV-2 have demanded unprecedented attention in developing rapid diagnostics, effective therapies, and safe vaccines to bring the current pandemic under control. Rapid progress is underway in the characterization of fundamental aspects of the structure and mechanisms of viral adsorption to cells, entry, and replication as well as in studies of the immune response to the virus. Here we report binding studies and crystal structures of the spike protein receptor binding domain (RBD) in complex with two individual synthetic nanobodies (sybodies) (Sb16 and Sb45). These bind the RBD at the previously identified ACE2 interface, positioning their complementarity determining region (CDR)2 and CDR3 in diametrically opposite orientations with large buried surface area. We also solved a structure of the RBD simultaneously bound by two sybodies, Sb45 and Sb68. In this structure, Sb45 binds at the ACE2 interface and Sb68 interacts at a second site. Comparison of structures of Sb16 both free and bound to RBD reveals a large movement of its CDR2 loop. Structural insights gained from these synthetic nanobody complexes will be helpful in designing new vaccines and expand the possibilities of using high affinity antibodies or linked bifunctional antibodies for therapy.

The spin-polarized electronic and magnetic properties of zinc selenide heavy doped with chromium

Atthe first stage, the structureof theZnSe crystal doped with chromium atoms (ZnCrSe)has been found by optimization procedure. At the second stage, the electronic properties of this material have been evaluated within the two approaches. The exchange-correlation functionals used here are based on the generalized gradient approximation (GGA) and the hybrid functional PBE0. The GGA approach provides the metallic state for electrons with the spin up, and for opposite spin orientation the material ZnCrSe bahaves as semiconductor, with the band gap of 2.48 eV. The hybrid functional approach also gives a gapless state for a spin up electron states, and for a spin down it provides the forbidden gap value of 2.39 eV. The magnetic moment of the unit cell, found with the two functionals, is the same and equals to 4 Bμ(Bohr magnetons). So, the calculations with the two exchange-correlation functionals provide the prediction of half-metallic properties of the ZnCrSe material, which is an interesting candidate for spintronic applications.

Transcriptome analysis of early stages of sorghum grain mold disease reveals defense regulators and metabolic pathways associated with resistance

BackgroundSorghum grain mold is the most important disease of the crop. The disease results from simultaneous infection of the grain by multiple fungal species. Host responses to these fungi and the underlying molecular and cellular processes are poorly understood. To understand the genetic, molecular and biochemical components of grain mold resistance, transcriptome profiles of the developing grain of resistant and susceptible sorghum genotypes were studied.ResultsThe developing kernels of grain mold resistant RTx2911 and susceptible RTx430 sorghum genotypes were inoculated with a mixture of fungal pathogens mimicking the species complexity of the disease under natural infestation. Global transcriptome changes corresponding to multiple molecular and cellular processes, and biological functions including defense, secondary metabolism, and flavonoid biosynthesis were observed with differential regulation in the two genotypes. Genes encoding pattern recognition receptors (PRRs), regulators of growth and defense homeostasis, antimicrobial peptides, pathogenesis-related proteins, zein seed storage proteins, and phytoalexins showed increased expression correlating with resistance. Notably, SbLYK5 gene encoding an orthologue of chitin PRR, defensin genes SbDFN7.1 and SbDFN7.2 exhibited higher expression in the resistant genotype. The SbDFN7.1 and SbDFN7.2 genes are tightly linked and transcribed in opposite orientation with a likely common bidirectional promoter. Interestingly, increased expression of JAZ and other transcriptional repressors were observed that suggested the tight regulation of plant defense and growth. The data suggest a pathogen inducible defense system in the developing grain of sorghum that involves the chitin PRR, MAPKs, key transcription factors, downstream components regulating immune gene expression and accumulation of defense molecules. We propose a model through which the biosynthesis of 3-deoxyanthocynidin phytoalexins, defensins, PR proteins, other antimicrobial peptides, and defense suppressing proteins are regulated by a pathogen inducible defense system in the developing grain.ConclusionsThe transcriptome data from a rarely studied tissue shed light into genetic, molecular, and biochemical components of disease resistance and suggested that the developing grain shares conserved immune response mechanisms but also components uniquely enriched in the grain. Resistance was associated with increased expression of genes encoding regulatory factors, novel grain specific antimicrobial peptides including defensins and storage proteins that are potential targets for crop improvement.

Genomic Structure of the Porcine CYP19 Locus and Expression of the CYP19A3 Paralog.

Proper, tissue-specific regulation of CYP19, the gene encoding aromatase, the key enzyme of estrogen synthesis, is essential for reproductive processes. Here, we analyzed transcriptional regulation of the porcine CYP19 in female and male gonads and brain by 5’RACE and RT-PCR and comprehensively mapped the pig CYP19 locus by in silico analysis. Our data revealed that the complete locus, including three paralogous copies, CYP19A1, CYP19A2 and CYP19A3, spans approximately 330 kb of the porcine chromosome 1. The locus also harbors the first exon of the Gliomedin gene (GLDN) in reverse orientation. Only transcripts of the CYP19A3 paralog were substantially expressed in gonads and hypothalamus. We identified CYP19A3-associated untranslated exons approximately 160 kb and 50 kb distal from the first codon. The 5´ untranslated regions of transcripts were derived from either a proximal or from one of these distal untranslated exons. Transcripts including only untranslated exons could be amplified from testis, thus suggesting long non-coding transcripts. The data revealed an additional layer of complexity in the regulation of the porcine CYP19 locus. Tissue-specific expression is not only achieved by tissue- and stage-specific expression of the three different CYP19 paralogs, but also by directing the expression of CYP19A3 from different, proximal and distal promoter regions.