Canonical Structure Research Articles

Effect of annealing in the formation of well-crystallized and textured SrFe12O19 films grown by RF magnetron sputtering

We have studied the influence of the annealing treatment on the crystalline growth of SrFe12O19 previously deposited on Si (100) substrates using radio frequency (RF) magnetron sputtering. For this goal, two grown films, with and without ex situ heating step, have been analyzed and compared to determine the differences in their structural, compositional, and magnetic properties. The results obtained by the different analysis techniques, in particular Mössbauer spectroscopy together with EXAFS and XANES data, suggest that the as-grown film is composed of nanocrystalline maghemite nanoparticles and amorphous strontium oxide. Specifically, Mössbauer spectroscopy results pointed out the presence of Fe3+ cations occupying octahedral and tetrahedral sites with hyperfine magnetic fields 49.3 T and 44.2 T, respectively, characteristic of a spinel-related structure. A strontium hexaferrite canonical structure with a c-axis orientation in the sample plane was found for the annealed film.Graphical abstract

Evolutionary Diversity of Dus2 Enzymes Reveals Novel Structural and Functional Features among Members of the RNA Dihydrouridine Synthases Family.

Dihydrouridine (D) is an abundant modified base found in the tRNAs of most living organisms and was recently detected in eukaryotic mRNAs. This base confers significant conformational plasticity to RNA molecules. The dihydrouridine biosynthetic reaction is catalyzed by a large family of flavoenzymes, the dihydrouridine synthases (Dus). So far, only bacterial Dus enzymes and their complexes with tRNAs have been structurally characterized. Understanding the structure-function relationships of eukaryotic Dus proteins has been hampered by the paucity of structural data. Here, we combined extensive phylogenetic analysis with high-precision 3D molecular modeling of more than 30 Dus2 enzymes selected along the tree of life to determine the evolutionary molecular basis of D biosynthesis by these enzymes. Dus2 is the eukaryotic enzyme responsible for the synthesis of D20 in tRNAs and is involved in some human cancers and in the detoxification of β-amyloid peptides in Alzheimer's disease. In addition to the domains forming the canonical structure of all Dus, i.e., the catalytic TIM-barrel domain and the helical domain, both participating in RNA recognition in the bacterial Dus, a majority of Dus2 proteins harbor extensions at both ends. While these are mainly unstructured extensions on the N-terminal side, the C-terminal side extensions can adopt well-defined structures such as helices and beta-sheets or even form additional domains such as zinc finger domains. 3D models of Dus2/tRNA complexes were also generated. This study suggests that eukaryotic Dus2 proteins may have an advantage in tRNA recognition over their bacterial counterparts due to their modularity.

A Canonical Complex Structure and the Bosonic Signature Operator for Scalar Fields in Globally Hyperbolic Spacetimes

The bosonic signature operator is defined for Klein–Gordon fields and massless scalar fields on globally hyperbolic Lorentzian manifolds of infinite lifetime. The construction is based on an analysis of families of solutions of the Klein–Gordon equation with a varying mass parameter. It makes use of the so-called bosonic mass oscillation property which states that integrating over the mass parameter generates decay of the field at infinity. We derive a canonical decomposition of the solution space of the Klein–Gordon equation into two subspaces, independent of observers or the choice of coordinates. This decomposition endows the solution space with a canonical complex structure. It also gives rise to a distinguished quasi-free state. Taking a suitable limit where the mass tends to zero, we obtain corresponding results for massless fields. Our constructions and results are illustrated in the examples of Minkowski space and ultrastatic spacetimes.

Show me your ID: NLR immune receptors with integrated domains in plants.

Nucleotide-binding and leucine-rich repeat receptors (NLRs) are intracellular plant immune receptors that recognize pathogen effectors secreted into the plant cell. Canonical NLRs typically contain three conserved domains including a central nucleotide binding (NB-ARC) domain, C-terminal leucine-rich repeats (LRRs) and an N-terminal domain. A subfamily of plant NLRs contain additional noncanonical domain(s) that have potentially evolved from the integration of the effector targets in the canonical NLR structure. These NLRs with extra domains are thus referred to as NLRs with integrated domains (NLR-IDs). Here, we first summarize our current understanding of NLR-ID activation upon effector binding, focusing on the NLR pairs Pik-1/Pik-2, RGA4/RGA5, and RRS1/RPS4. We speculate on their potential oligomerization into resistosomes as it was recently shown for certain canonical plant NLRs. Furthermore, we discuss how our growing understanding of the mode of action of NLR-ID continuously informs engineering approaches to design new resistance specificities in the context of rapidly evolving pathogens.

Spectral analysis of matrices resulting from isogeometric immersed methods and trimmed geometries

Dealing with complex and trimmed geometries is one of the current challenges in isogeometric analysis. Coupling the isogeometric paradigm with the framework of immersed boundary methods is an attractive practical strategy. In this paper, we consider general variable-coefficient Poisson problems and propose a new formulation of an immersed Galerkin discretization based on tensor-product cardinal B-splines. The weakly imposed boundary conditions do not require any tuning of user-defined penalty or stabilization parameters, and the system matrices are symmetric for symmetric problems. We analyze the spectral behavior of such matrices and prove that they enjoy an asymptotic spectral distribution when the matrix size tends to infinity. We provide an explicit description of this asymptotic distribution which turns out to have a canonical structure incorporating the coefficients of the differential operator and the discretization technique. In the spirit of the isogeometric paradigm, trimmed (single-patch) geometry maps can be treated by means of the same immersed approach. Therefore, we are able to describe spectral properties of matrices in the context of trimmed geometries as well. The theoretical findings are complemented with a selection of numerical experiments.

Characterization of the complete chloroplast genome of Hevea pauciflora (Euphorbiaceae), an important wild relative of the rubber tree

Hevea pauciflora belongs to the Euphorbiaceae family, an important wild relative of the rubber tree. This study sequenced, assembled, and annotated the complete chloroplast genome of H. pauciflora. The complete chloroplast genome is 161,123 bp with a canonical quadripartite structure containing a large single-copy (LSC) region (89,109 bp), a small single-copy (SSC) region (18,376 bp), and two inverted repeat regions (IRa and IRb) (26,819 bp, each). A total of 134 genes were annotated, including 86 protein-coding genes, four pseudogenes, 36 tRNA genes, and eight rRNA genes. The 134 genes include four major groups: ‘self-replication’, ‘photosynthesis’, ‘unknown function’, and ‘others’. A phylogenetic analysis clustered H. pauciflora, H. brasiliensis, H. camargoana, and H. benthamiana into one clade, consistent with traditional taxonomy. This study provides useful data for further studies of Hevea genus and the phylogenetic relationships of Euphorbiaceae species.

2D F(R) gravity and AdS2/CFT1correspondence

We studied the canonical structure of 2D F(R) gravity. Its equivalence with Jackiw-Teitelboim gravity is demonstrated when no matter is present. Then, due to AdS2/CFT1 correspondence, such F(R) gravity is equivalent to the Sachdev-Ye-Kitaev models. The singular limit of F(R) gravity is also studied. It is shown that in such a limit AdS2/CFT1 correspondence is not realized.

Fully zwitterionic diaminobenzoquinonediimines promoted by cyanoaromatic N-substituents

2,5-Diamino-1,4-benzoquinonediimine (DABQDI) derivatives possessing two electron-withdrawing aromatic N-substituents can potentially exhibit a zwitterionic ground state in lieu of the expected canonical structure. It was previously shown that the use of nitroaromatics electron-withdrawing groups (EWG) could yield the quantitative formation of zwitterionic tautomer of DABQDI in polar solvents, while a mixture of canonical and zwitterionic forms was present in low polarity solvents. In this work, we report that the replacement of nitro-containing EWG by weaker nitrile ones prevents the formation of canonical species in apolar solvents for the benefit of the zwitterionic tautomer. This counterintuitive observation is rationalized with theoretical calculations, which points out that the fully zwitterionic electronic structure of the nitrile-containing DABQDI arises from the absence of possible intramolecular hydrogen bonding between the cyanoaromatic N-substituent and the N–H proton of the bridge in the canonical form.

Comparative analysis of mitochondrial genomes among the family Peltoperlidae (Plecoptera: Systellognatha) and phylogenetic implications

Nowadays, the position of Peltoperlidae in Systellognatha has been resolved based on morphological analyses. However, there are different opinions based on molecular data. To date, only three peltoperlid mitogenomes are available, and more sampling is needed to obtain precise phylogenetic relationships. In this study, we obtained the complete mitogenomes of Cryptoperla kawasawai (15,832 bp) and Peltoperlopsis sagittata (15,756 bp). Our results show that gene content, gene order, DmTTF binding site, nucleotide composition, codon usage, ribonucleic acid (RNA) structure, and structural elements in the control region are highly conserved in peltoperlids. Heatmap analysis of codon usage shows that the AT-rich codons UUA, AUU, UUU, and AUA were commonly used codons in the Peltoperlidae. Evolutionary rate analyses of protein-coding genes reveal that different genes have been subject to different rates of molecular evolution correlated with the GC content. All tRNA genes in peltoperlid mitogenomes have a canonical cloverleaf secondary structure except for trnS1, whose dihydrouridine arm simply forms a loop. The control region of the family has several distinct structural characteristics and has the potential to serve as effective phylogenetic markers. Phylogenetic analyses support the monophyly of Perloidea, but the monophyly of Pteronarcyoidea is still not supported. The Peltoperlidae is placed as the earliest branch within the Systellognatha, and the estimated phylogenetic relationship is: Peltoperlidae + {(Styloperlidae + Pteronarcyidae) + [Perlidae + (Chloroperlidae + Perlodidae)]}. Our results provide new insight into the phylogeny of this group.

Design of Wideband Base Station Antenna by Involving Fragment-Type Structures on Dipole Arms

Base station antenna usually requires dual-polarization operation with satisfactory input return loss, adequate dual-polarization isolation, stable gain, and half-power beamwidth (HPBW) in a wide bandwidth covering the entire or part of the mobile communication bands. Such comprehensive requirements provoke great challenges in antenna design. A novel design scheme is proposed by involving fragment-type structures (FTSs) in antenna and seeking for the optimal FTS by multiobjective optimization searching. The technique is demonstrated by improving crossed dipoles for operation in band ranging from 1.7 to 3.8 GHz. Part of the dipole arms can be gridded into cells and reconfigured by using FTS elements. For automatic optimization searching, a binary coding scheme for both the FTS distributions and canonical dipole structure dimensions is proposed. Simulation and measurement show that the optimal crossed dipole antenna may acquire a wide operation bandwidth of 76.3%, with the return loss higher than 15 dB, isolation higher than 30 dB, HPBW of 65° ± 5°, and gain of 9 dBi ± 0.65 dBi for ±45° polarizations.

Systematic Synthesis of a Class of Smooth Parameter Projection Operators for Stable Adaptive Systems

Abstract In this letter, a systematic synthesis of a new class of smooth parameter projection operators is presented. To elaborate such an approach, the adaptive control problem for a nth-order, single-input, linearly parametrizable, nonlinear system in the controllable canonical structure is considered. The stability of the closed-loop adaptive system, with the augmentation of such a class of smooth projection operators, is analyzed by a Lyapunov-like analysis. With this systematic construction, two novel smooth projection operators are devised as examples. A simulation study is performed to validate the proposed strategy and compare its performance against a non-smooth, parameter projection solution.

The canonical wall structure and intrinsic mirror symmetry

As announced in Gross and Siebert (in Algebraic geometry: Salt Lake City 2015, Proceedings of Symposia in Pure Mathematics, vol 97, no 2. AMS, Providence, pp 199–230, 2018) in 2016, we construct and prove consistency of the canonical wall structure. This construction starts with a log Calabi–Yau pair (X, D) and produces a wall structure, as defined in Gross et al. (Mem. Amer. Math. Soc. 278(1376), 1376, 1–103, 2022). Roughly put, the canonical wall structure is a data structure which encodes an algebro-geometric analogue of counts of Maslov index zero disks. These enumerative invariants are defined in terms of the punctured invariants of Abramovich et al. (Punctured Gromov–Witten invariants, 2020. arXiv:2009.07720v2 [math.AG]). There are then two main theorems of the paper. First, we prove consistency of the canonical wall structure, so that, using the setup of Gross et al. (Mem. Amer. Math. Soc. 278(1376), 1376, 1–103, 2022), the canonical wall structure gives rise to a mirror family. Second, we prove that this mirror family coincides with the intrinsic mirror constructed in Gross and Siebert (Intrinsic mirror symmetry, 2019. arXiv:1909.07649v2 [math.AG]). While the setup of this paper is narrower than that of Gross and Siebert (Intrinsic mirror symmetry, 2019. arXiv:1909.07649v2 [math.AG]), it gives a more detailed description of the mirror.

On a family of vertex operator superalgebras

This paper is to study vertex operator superalgebras which are strongly generated by their weight-2 and weight-32 homogeneous subspaces. Among the main results, it is proved that if such a vertex operator superalgebra V is simple, then V(2) has a canonical commutative associative algebra structure equipped with a non-degenerate symmetric associative bilinear form and V(32) is naturally a V(2)-module equipped with a V(2)-valued symmetric bilinear form and a non-degenerate (C-valued) symmetric bilinear form, satisfying a set of conditions. On the other hand, assume that A is any commutative associative algebra equipped with a non-degenerate symmetric associative bilinear form and assume that U is an A-module equipped with a symmetric A-valued bilinear form and a non-degenerate (C-valued) symmetric bilinear form, satisfying the corresponding conditions. Then we construct a Lie superalgebra L(A,U) and a simple vertex operator superalgebra LL(A,U)(ℓ,0) for every nonzero number ℓ such that LL(A,U)(ℓ,0)(2)=A and LL(A,U)(ℓ,0)(32)=U.

Physical Optics Scattering by A PEC Missile in Uniform Rectilinear Motion

Electromagnetic scattering by a perfect electric conductor (PEC) missile in uniform rectilinear motion is formulated and computed in X-band under the physical optics (PO) approximation. The missile dimensions are picked as 80 [cm] in length and 6.6 [cm] in radius as adapted from the well-known Soviet M-13 missile. We adopt a canonical structure simulated by a cylindrical body, an ellipsoid nose, and four planar tail fins. The surface of the missile is meshed using triangular facets. First, the formulation and computations are carried out for a stationary missile in MATLABTM and compared to simulations by the commercial full-wave simulator CSTTM. Good agreements that reveal the validity of PO formulation are observed. Finally, PO formulation and numerical results for a missile in uniform rectilinear motion are provided and discussed. These simulations are based on the principle of superposition of the formulas developed recently for scattering by a moving PEC flat plate.

Early diagnostic indicators of childhood apraxia of speech in young children with 7q11.23 duplication syndrome: preliminary findings

ABSTRACT Limited evidence for early indicators of childhood apraxia of speech (CAS) precludes reliable diagnosis before 36 months, although a few prior studies have identified several potential early indicators. We examined these possible early indicators in 10 toddlers aged 14–24 months at risk for CAS due to a genetic condition: 7q11.23 duplication syndrome (Dup7). Phon Vocalisation analyses were conducted on phonetic transcriptions of each child’s vocalisations during an audio-video recorded 30-minute play session with a caregiver and/or a trained research assistant. The resulting data were compared to data previously collected by Overby from similar-aged toddlers developing typically (TD), later diagnosed with CAS (LCAS), or later diagnosed with another speech sound disorder (LSSD). The Dup7 group did not differ significantly from the LCAS group on any measure. In contrast, the Dup7 group evidenced significant delays relative to the LSSD group on canonical babble frequency, volubility, consonant place diversity, and consonant manner diversity and relative to the TD group not only on these measures but also on canonical babble ratio, consonant diversity, and vocalisation structure diversity. Toddlers with Dup7 also demonstrated expressive vocabulary delay as measured by both number of word types orally produced during the play sessions and primary caregivers’ responses on a standardised parent-report measure of early expressive vocabulary. Examining babble, phonetic, and phonotactic characteristics from the productions of young children may allow for earlier identification of CAS and a better understanding of the nature of CAS.

Making space for freshwater biodiversity in low‐income fishing economies

AbstractGlobally, freshwater biodiversity and the food system that it underpins are under enormous threat. Historically damaged by overfishing, environmental deterioration (e.g., pollution, damming, water extraction and watershed modification) is now destroying canonical ecosystem structure. Under pressure to secure the food supply and create jobs, local politicians are reluctant to enforce rules that would reduce fishing pressure and threaten the already vulnerable economies of many fishing communities. Aquaculture can directly address food supply but has in the past been troubled with its own negative environmental footprint. New technology is available to solve these problems. Modern aquaculture, as a commercial alternative to capture fishing can take advantage of existing infrastructure to grow more food, but more importantly, create new and better jobs in places where few alternatives exist, making economic and local political space for policies that operate for both food production and the protection of aquatic biodiversity. This opinion seeks to revise the current vision of aquaculture as a competitor and threat to inland fisheries, arguing rather that the way to approach the biodiversity crisis in freshwater is to create economic alternatives to fishing and environmental abuse so that poor people can afford to care about nature.

Understanding the role of non‐Watson‐Crick base pairs in DNA–protein recognition: Structural and energetic aspects using crystallographic database analysis and quantum chemical calculation

Specific recognition of DNA base sequences by proteins is vital for life-cycles of all organisms. In a large number of crystal structures of protein-DNA complexes, DNA conformation significantly deviates from the canonical B-DNA structure. A key question is whether such alternate conformations exist prior to protein binding and one is selected for complexation or the structure observed is induced by protein binding. Non-canonical base pairs, such as Hoogsteen base pairs, are often observed in crystal structures of protein-DNA complexes. We decided to explore whether the occurrence of such non-canonical base pairs in protein-DNA complexes is induced by the protein or is selected from pre-existing conformations. Detailed quantum chemical calculations with dispersion-corrected density functional theory (DFT-D) indicated that most of the non-canonical base pairs with DNA bases are stable even in the absence of the interacting amino acids. However, the G:G Hoogsteen base pair, which also appears in the telomere structure, appears to be unstable in the absence of other stabilizing agents, such as positively charged amino acids. Thus, the stability of many of the non-canonical base pair containing duplexes may be close to the canonical B-DNA structure and hence energetically accessible in the ground state; suggesting that the selection from pre-existing conformations may be an important mechanism for observed non-canonical base pairs in protein-DNA complexes.

Distributions, First Integrals and Legendrian Foliations

We study germs of holomorphic distributions with “separated variables”. In codimension one, a well know example of this kind of distribution is given by $$\begin{aligned} dz=(y_1dx_1-x_1dy_1)+\dots +(y_mdx_m-x_mdy_m), \end{aligned}$$which defines the canonical contact structure on \({\mathbb {C}}{\mathbb {P}}^{2m+1}\). Another example is the Darboux distribution $$\begin{aligned} dz=x_1dy_1+\dots +x_mdy_m, \end{aligned}$$which gives the normal local form of any contact structure. Given a germ \({\mathcal {D}}\) of holomorphic distribution with separated variables in \(({\mathbb {C}}^n,0)\), we show that there exists , for some \(\kappa \in {\mathbb {Z}}_{\ge 0}\) related to the Taylor coefficients of \({\mathcal {D}}\), a holomorphic submersion $$\begin{aligned} H_{{\mathcal {D}}}:({\mathbb {C}}^n,0)\rightarrow ({\mathbb {C}}^{\kappa },0) \end{aligned}$$such that \({\mathcal {D}}\) is completely non-integrable on each level of \(H_{{\mathcal {D}}}\). Furthermore, we show that there exists a holomorphic vector field Z tangent to \({\mathcal {D}}\), such that each level of \(H_{{\mathcal {D}}}\) contains a leaf of Z that is somewhere dense in the level. In particular, the field of meromorphic first integrals of Z and that of \({\mathcal {D}}\) are the same. Between several other results, we show that the canonical contact structure on \({\mathbb {C}}{\mathbb {P}}^{2m+1}\) supports a Legendrian holomorphic foliation whose generic leaves are dense in \({\mathbb {C}}{\mathbb {P}}^{2m+1}\). So we obtain examples of injectively immersed Legendrian holomorphic open manifolds that are everywhere dense.

Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors.

The NusG protein family is structurally and functionally conserved in all domains of life. Its members directly bind RNA polymerases and regulate transcription processivity and termination. RfaH, a divergent sub-family in its evolutionary history, is known for displaying distinct features than those in NusG proteins, which allows them to regulate the expression of virulence factors in enterobacteria in a DNA sequence-dependent manner. A striking feature is its structural interconversion between an active fold, which is the canonical NusG three-dimensional structure, and an autoinhibited fold, which is distinctively novel. How this novel fold is encoded within RfaH sequence to encode a metamorphic protein remains elusive. In this work, we used publicly available genomic RfaH protein sequences to construct a complete multiple sequence alignment, which was further augmented with metagenomic sequences and curated by predicting their secondary structure propensities using JPred. Coevolving pairs of residues were calculated from these sequences using plmDCA and GREMLIN, which allowed us to detect the enrichment of key metamorphic contacts after sequence filtering. Finally, we combined our coevolutionary predictions with molecular dynamics to demonstrate that these interactions are sufficient to predict the structures of both native folds, where coevolutionary-derived non-native contacts may play a key role in achieving the compact RfaH novel fold. All in all, emergent coevolutionary signals found within RfaH sequences encode the autoinhibited and active folds of this protein, shedding light on the key interactions responsible for the action of this metamorphic protein.

Caulobacter lipid A is conditionally dispensable in the absence of fur and in the presence of anionic sphingolipids.

SUMMARYLipid A, the membrane-anchored portion of lipopolysaccharide (LPS), is an essential component of the outer membrane (OM) of nearly all Gram-negative bacteria. Here we identify regulatory and structural factors that together render lipid A nonessential in Caulobacter crescentus. Mutations in the ferric uptake regulator fur allow Caulobacter to survive in the absence of either LpxC, which catalyzes an early step of lipid A synthesis, or CtpA, a tyrosine phosphatase homolog we find is needed for wild-type lipid A structure and abundance. Alterations in Fur-regulated processes, rather than iron status per se, underlie the ability to survive when lipid A synthesis is blocked. Fitness of lipid A-deficient Caulobacter requires an anionic sphingolipid, ceramide phosphoglycerate (CPG), which also mediates sensitivity to the antibiotic colistin. Our results demonstrate that, in an altered regulatory landscape, anionic sphingolipids can support the integrity of a lipid A-deficient OM.