Unusual Domain Research Articles

Unusual Domain Structure and Filamentary Superfluidity for 2D Hard-Core Bosons in Insulating Charge-Ordered Phase

We made use of a special algorithm for compute unified device architecture for NVIDIA graphics cards, a nonlinear conjugate-gradient method to minimize energy functional, and Monte-Carlo technique to directly observe the forming of the ground state configuration for the 2D hard-core bosons by lowering the temperature and its evolution with deviation away from half-filling. The novel technique allowed us to examine earlier implications and uncover novel features of the phase transitions, in particular, look upon the nucleation of the odd domain structure, emergence of filamentary superfluidity nucleated at the antiphase domain walls of the charge-ordered phase, and nucleation and evolution of different topological structures.

Multiferroic Domain Walls in Ferroelectric PbTiO3 with Oxygen Deficiency.

Atomically thin multiferroics with the coexistence and cross-coupling of ferroelectric and (anti)ferromagnetic order parameters are promising for novel magnetoelectric nanodevices. However, such ferroic order disappears at a critical thickness in nanoscale. Here, we show a potential path toward ultrathin multiferroics by engineering an unusual domain wall (DW)-oxygen vacancy interaction in nonmagnetic ferroelectric PbTiO3. We demonstrate from first-principles that oxygen vacancies formed at the DW unexpectedly bring about magnetism with a localized spin moment around the vacancy. This magnetism originates from the orbital symmetry breaking of the defect electronic state due to local crystal symmetry breaking at the DW. Moreover, the energetics of defects shows the self-organization feature of oxygen vacancies at the DW, resulting in a planar-arrayed concentration of magnetic oxygen vacancies, which consequently changes the deficient DWs into multiferroic atomic layers. This DW-vacancy engineering opens up a new possibility for novel ultrathin multiferroic.

Tailoring anisotropy and domain structure in amorphous TbCo thin films through combinatorial methods

We apply an in-plane external magnetic field during growth of amorphous TbCo thin films and examine the effects on the magnetic anisotropy and domain structure. A combinatorial approach is employed throughout the deposition and analysis to study a continuous range of compositions between 7–95 at.% Tb. Magnetometry measurements show that all samples have a strong out-of-plane anisotropy, much larger than any in-plane components, regardless of the presence of a growth field. However, magnetic force microscopy demonstrates that the growth field does indeed have a large effect on the magnetic domain structure, resulting in elongated domains aligned along the imprinting field direction. The results show that the anisotropy can be tuned in intricate ways in amorphous TbCo films giving rise to unusual domain structures. Furthermore the results reveal that a combinatorial approach is highly effective for mapping out these material properties.

Folding catastrophes due to viscosity in multiferroic domains: implications for room-temperature multiferroic switching

Unusual domains with curved walls and failure to satisfy the Landau–Lifshitz-Kittel Law are modeled as folding catastrophes (saddle-node bifurcations). This description of ballistic motion in a viscous medium is based upon early work by Dawber et al 2003 Appl. Phys. Lett. 82 436. It suggests that ferroelectric films can exhibit folds or vortex patterns but not both.

NMR assignments of the peptidyl-prolyl cis-trans isomerase domain of trigger factor from E. coli.

Trigger factor (TF) is a highly conserved multi-domain molecular chaperone in bacteria. It binds via its ribosome binding domain (RBD) to the ribosomal tunnel exit and facilitates co-translational folding of a broad range of protein substrates primarily through interactions with the substrate binding domain (SBD) adjacent to the RBD. Within the SBD, a peptidyl-prolyl cis-trans isomerase (PPIase) domain is inserted leading to an unusual domain insertion, which may provide stabilizing effect to the highly plastic SBD. Here we report the near complete NMR assignments of TF PPIase providing the basis for subsequent structural and folding in the context of the chaperone activity of TF.

Invention in the United States City System

This article draws on several empirical regularities underlying central place theory (CPT) to enhance understanding of the uneven distribution of invention in the U.S. city system, especially the immense array of specializations that comprise national technological advance. CPT depicts city systems as collections of places in which functions expand in number as city size increases. Small cities have few functions and large cities many. A long-term hierarchical system is successively inclusive if large cities have all of the functions of smaller cities and some additional ones. The functions investigated here are 399 patent classes distributed across 366 U.S. metropolitan areas in the period from 2000 to 2011. Evidence is strong that patent classes with large numbers of awards are widely spread across the city system. This leads to the average sizes of places active in generating patents in the robust classes to be significantly smaller compared with the average sizes of areas that generate patents in unusual classes. Small cities are tied to national technological advance through the generation of patents in the most active and ubiquitous inventive specialties. Inventors in large cities are more likely to invent in unusual domains. Bigger areas are significantly more diversified compared with smaller ones. The system is not, however, strictly successively inclusive. Whereas 88.3 percent of all patent class–area pairs are generated in at least 50 percent of equally sized and bigger areas, only 20.5 percent of pairs are 100 percent strictly hierarchical.

Identifying influenza-like illness presentation from unstructured general practice clinical narrative using a text classifier rule-based expert system versus a clinical expert

BackgroundWe designed and validated a rule-based expert system to identify influenza like illness (ILI) from routinely recorded general practice clinical narrative to aid a larger retrospective research study into the impact of the 2009 influenza pandemic in New Zealand.MethodsRules were assessed using pattern matching heuristics on routine clinical narrative. The system was trained using data from 623 clinical encounters and validated using a clinical expert as a gold standard against a mutually exclusive set of 901 records.ResultsWe calculated a 98.2 % specificity and 90.2 % sensitivity across an ILI incidence of 12.4 % measured against clinical expert classification. Peak problem list identification of ILI by clinical coding in any month was 9.2 % of all detected ILI presentations. Our system addressed an unusual problem domain for clinical narrative classification; using notational, unstructured, clinician entered information in a community care setting. It performed well compared with other approaches and domains. It has potential applications in real-time surveillance of disease, and in assisted problem list coding for clinicians.ConclusionsOur system identified ILI presentation with sufficient accuracy for use at a population level in the wider research study. The peak coding of 9.2 % illustrated the need for automated coding of unstructured narrative in our study.

Longitudinal domain wall formation in elongated assemblies of ferromagnetic nanoparticles.

Through evaporation of dense colloids of ferromagnetic ~13 nm ε-Co particles onto carbon substrates, anisotropic magnetic dipolar interactions can support formation of elongated particle structures with aggregate thicknesses of 100–400 nm and lengths of up to some hundred microns. Lorenz microscopy and electron holography reveal collective magnetic ordering in these structures. However, in contrast to continuous ferromagnetic thin films of comparable dimensions, domain walls appear preferentially as longitudinal, i.e., oriented parallel to the long axis of the nanoparticle assemblies. We explain this unusual domain structure as the result of dipolar interactions and shape anisotropy, in the absence of inter-particle exchange coupling.

Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes

Triphosphate tunnel metalloenzymes (TTMs) are present in all kingdoms of life and catalyze diverse enzymatic reactions such as mRNA capping, the cyclization of adenosine triphosphate, the hydrolysis of thiamine triphosphate, and the synthesis and breakdown of inorganic polyphosphates. TTMs have an unusual tunnel domain fold that harbors substrate- and metal co-factor binding sites. It is presently poorly understood how TTMs specifically sense different triphosphate-containing substrates and how catalysis occurs in the tunnel center. Here we describe substrate-bound structures of inorganic polyphosphatases from Arabidopsis and Escherichia coli, which reveal an unorthodox yet conserved mode of triphosphate and metal co-factor binding. We identify two metal binding sites in these enzymes, with one co-factor involved in substrate coordination and the other in catalysis. Structural comparisons with a substrate- and product-bound mammalian thiamine triphosphatase and with previously reported structures of mRNA capping enzymes, adenylate cyclases, and polyphosphate polymerases suggest that directionality of substrate binding defines TTM catalytic activity. Our work provides insight into the evolution and functional diversification of an ancient enzyme family.

Ménage a Trois to Form the Tricellular Junction

Tricellular junctions tightly seal epithelia at the corners of three cells. In this issue of Developmental Cell, Byri et al. (2015) show that Anakonda, a novel Drosophila transmembrane protein, contains an unusual tripartite extracellular domain organization, which explains the tripartite septum filling the tricellular junction, previously revealed by ultrastructure analysis.

Treasure Your Exceptions: Unusual Domains in Immune Receptors Reveal Host Virulence Targets

A mechanistic understanding of how plant pathogens modulate their hosts is critical for rationally engineered disease resistance in agricultural systems. Two new studies show that genomically paired plant immune receptors have incorporated decoy domains that structurally mimic pathogen virulence targets to monitor attempted host immunosuppression.

A noncanonical PWI domain in the N-terminal helicase-associated region of the spliceosomal Brr2 protein.

The spliceosomal RNA helicase Brr2 is required for the assembly of a catalytically active spliceosome on a messenger RNA precursor. Brr2 exhibits an unusual organization with tandem helicase units, each comprising dual RecA-like domains and a Sec63 homology unit, preceded by a more than 400-residue N-terminal helicase-associated region. Whereas recent crystal structures have provided insights into the molecular architecture and regulation of the Brr2 helicase region, little is known about the structural organization and function of its N-terminal part. Here, a near-atomic resolution crystal structure of a PWI-like domain that resides in the N-terminal region of Chaetomium thermophilum Brr2 is presented. CD spectroscopic studies suggested that this domain is conserved in the yeast and human Brr2 orthologues. Although canonical PWI domains act as low-specificity nucleic acid-binding domains, no significant affinity of the unusual PWI domain of Brr2 for a broad spectrum of DNAs and RNAs was detected in band-shift assays. Consistently, the C. thermophilum Brr2 PWI-like domain, in the conformation seen in the present crystal structure, lacks an expanded positively charged surface patch as observed in at least one canonical, nucleic acid-binding PWI domain. Instead, in a comprehensive yeast two-hybrid screen against human spliceosomal proteins, fragments of the N-terminal region of human Brr2 were found to interact with several other spliceosomal proteins. At least one of these interactions, with the Prp19 complex protein SPF27, depended on the presence of the PWI-like domain. The results suggest that the N-terminal region of Brr2 serves as a versatile protein-protein interaction platform in the spliceosome and that some interactions require or are reinforced by the PWI-like domain.

Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway.

A novel four-step pathway identified recently in mycobacteria channels trehalose to glycogen synthesis and is also likely involved in the biosynthesis of two other crucial polymers: intracellular methylglucose lipopolysaccharides and exposed capsular glucan. The structures of three of the intervening enzymes - GlgB, GlgE, and TreS - were recently reported, providing the first templates for rational drug design. Here we describe the structural characterization of the fourth enzyme of the pathway, mycobacterial maltokinase (Mak), uncovering a eukaryotic-like kinase (ELK) fold, similar to methylthioribose kinases and aminoglycoside phosphotransferases. The 1.15 Å structure of Mak in complex with a non-hydrolysable ATP analog reveals subtle structural rearrangements upon nucleotide binding in the cleft between the N- and the C-terminal lobes. Remarkably, this new family of ELKs has a novel N-terminal domain topologically resembling the cystatin family of protease inhibitors. By interfacing with and restraining the mobility of the phosphate-binding region of the N-terminal lobe, Mak's unusual N-terminal domain might regulate its phosphotransfer activity and represents the most likely anchoring point for TreS, the upstream enzyme in the pathway. By completing the gallery of atomic-detail models of an essential pathway, this structure opens new avenues for the rational design of alternative anti-tubercular compounds.

Concentric 360° domain wall nesting in magnetic tunnel junction films: a Lorentz TEM study

We describe the formation of an unusual concentric magnetic domain wall pattern in the free layer of a bottom pinned magnetic tunnel junction. Lorentz microscopy reveals that repeated switching of the free layer with a magnetic field applied perpendicular to the exchange bias direction can produce a series of concentric 360° domain wall loops, a phenomenon we refer to as domain wall nesting. We propose two necessary ingredients for the behaviour: (i) inhomogeneities in the grain-by-grain magnetic dispersion that break local symmetry to produce a preferential sense of magnetic rotation upon field switching; and (ii) structural defects that act to pin 360° domain walls. Further control of this behaviour may provide new functionality for future device applications.

Giant electrocaloric effect in ferroelectric nanotubes near room temperature.

Ferroelectric perovskite oxides possess large electrocaloric effect, but only at high temperature, which limits their potential as next generation solid state cooling devices. Here, we demonstrate from phase field simulations that a giant adiabatic temperature change exhibits near room temperature in the strained ferroelectric PbTiO3 nanotubes, which is several times in magnitude larger than that of PbTiO3 thin films. Such giant adiabatic temperature change is attributed to the extrinsic contribution of unusual domain transition, which involves a dedicated interplay among the electric field, strain, temperature and polarization. Careful selection of external strain allows one to harness the extrinsic contribution to obtain large adiabatic temperature change in ferroelectric nanotubes near room temperature. Our finding provides a novel insight into the electrocaloric response of ferroelectric nanostructures and leads to a new strategy to tailor and improve the electrocaloric properties of ferroelectric materials through domain engineering.

Diversity of Globins in Myxobacteria

Globins are heme proteins that are capable of reversible oxygen binding. All globins can be classified into three families: the M (myoglobin - like), S (sensor) and T (truncated) globins. M and S globins exhibit the canonical 3/3 α - helical fold, and T globins are characterized by a 2/2 α - he lical fold. Globins in the genomes of myxobacteria have not been characterized till date. Myxobacteria have very large genomes relative to other bacteria and have a unique life cycle that involves the aggregation of cells into fruiting bodies under starvat ion conditions. The diversity of globin like sequences in 14 sequenced genomes of myxobacteria is presented in this review. In myxobacterial globins some unusual domain architectures are identified that have not been characterized in bacteria so far; these are: i) a unique chimeric group I 2/2 HbN in the genome of Corallococcus coralloides DSM 2259; ii) M globin chimera harboring a central and a C - terminal globin domain in Sorangium cellulosum ‘so ce 56’ and Plesiocystis pacifica SIR - 1 respectively; iii) tw o tandem globin domains on the same M globin polypeptide in the genomes of Sorangium cellulosum .

NMR Characterization of an Unusual 37 kDa Epimerization Domain of Yersinabactin Synthetase

Nonribosomal Peptide Synthetases (NRPSs) are endogenous microbial supramolecular (1-4 MDa) assemblies that are responsible for the biosynthesis of important natural products, including antibiotics. Genetic reprogramming of NRPS machinery for the generation of novel-or perhaps “designer”-antibiotics (or other therapeutics) represents the apogee of NRPS research. Our model NRPS system is yersiniabactin synthetase (YS), which produces the virulence factor yersiniabactin. Heterocycles (e.g. thiazoline rings) in natural products, such as yersiniabactin, exhibit unique medicinal properties (antibiotic, anticancer, immunosuppressant). An unusual epimerization domain (EA) in YS catalyzes the stereoconversion of a chiral heterocyclic center. Interestingly, EA itself is embedded within the primary sequence of a so-called adenylation domain (A, recognizes and activates substrates). To understand the overall choreography of catalysis, we require structural models of each catalytic domain in its monomeric state, bound to its substrate(s), and in complex with other relevant domains. NRPS domains can be difficult to crystallize in the biologically relevant conformations and complexes, so we take advantage of NMR spectroscopy, which can offer structural, kinetic, thermodynamic, and dynamical data. However, conventional bimolecular NMR experiments will fail on domains such as EA (37 kDa) largely because of relaxation losses but also spectral crowding. This work discusses how nonuniform sampling allowed us to rescue sensitivity and collect preliminary data on a partially deuterated sample. We also exploit covariance NMR spectroscopy to ease the challenging backbone assignment procedure. Using such data we report ∼70% backbone assignment. We also present a chemical biology strategy that will allow us to synthesize otherwise challenging substrates, which will facilitate measurement of steady state kinetic parameters and inform our structural models.

Sequence Analysis and Evolutionary Studies of Reelin Proteins.

The reelin gene is conserved across many vertebrate species, including humans. The protein product of this gene plays several important roles in early brain development and regulation of neural network plasticity of a matured brain structure. With an extended structure of 3461 amino acid sequences, consisting of eight reelin repeats, the human reelin sequence stands out as an exceptional model for evolutionary studies. In this study, sequence analysis of the human reelin and its homologues and reelin sequences from 104 other species is described in detail. Interesting sequence conservation patterns of individual repeats have been highlighted. Sequence phylogeny of the reelin sequences indicates a pattern similar to the evolution of the species, thereby serving as a highly conserved family for evolutionary purposes. Multiple sequence alignment of different reelin domain repeats, derived from homologues, suggests specific functions for individual repeats and high sequence conservation across reelin repeats from different organisms, albeit with few unusual domain architectures. A three-dimensional structural model of the full-length human reelin is now available that provides clues on residues at the dimer interface.

Unusual domain movement in a multidomain protein in the presence of macromolecular crowders.

Domain movements play a fundamental and critical role in the specific biological function that multidomain proteins have evolved to perform. A significant amount of research has been carried out to investigate the effects of macromolecular crowding agents, mostly on single domain proteins, thereby furthering our appreciation for the crowding phenomenon. However similar studies on proteins having multiple domains are relatively scarce. Using the plasma protein human serum albumin (HSA) as the protein of interest, we have probed the influence of dextran based crowding agents (Dextran 6, Dextran 40, and Dextran 70) on the relative movements of domains I and II using FRET, with Trp-214 in domain II acting as the donor and acrylodan (Ac) covalently attached to Cys-34 of domain I as the acceptor. Amongst the higher molecular weight crowders, while both Dextran 70 and Dextran 40 induced a significant decrease in the distance between the aforesaid domains, however for the latter macromolecular crowder (Dextran 40), beyond 50 g L(-1), no change in domain separation was observed even up to concentrations of 175 g L(-1). On the other hand, contrary to our expectations, Dextran 6, having the highest packing density by virtue of it being the smallest crowding agent used, provided an asymmetric excluded volume which resulted in forced elongation of HSA along the Trp-Ac FRET axis. Additionally both chemical and thermal studies performed at varying concentrations of the chemical denaturant, urea, reveal unusual movements of the two domains, an aspect that can have important implications with regard to HSA being an avid transporter of fatty acids, with the binding of latter being known to invoke appreciable domain displacements. We hypothesise that we see a distinct crossover from entropy dominated depletion effects in the case of Dextran 6 to significant enthalpic contribution for Dextran 70 with Dextran 40 lying midway between these two crowders, having characteristics of both.

Rice terpene synthase 20 (OsTPS20) plays an important role in producing terpene volatiles in response to abiotic stresses.

This study examined the volatile terpenes produced by rice seedlings in response to oxidative stress induced by various abiotic factors. Solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) analyses revealed that when exposed to UV-B radiation, rice seedlings emitted a bouquet of monoterpene mixtures in a time-dependent manner. The mixtures comprised limonene, sabinene, myrcene, α-terpinene, β-ocimene, γ-terpinene, and α-terpinolene. Among them, (S)-limonene was the most abundant volatile, discriminated by chiral SPME-GC-MS. The volatile profiles collected from rice plants treated with both γ-irradiation and H2O2 were identical to those observed in the UV-B irradiated plants, thus indicating that the volatile mixtures were specifically produced in response to oxidative stress, particularly in the presence of H2O2. Using a reverse genetics approach, we isolated full-length rice terpene synthase 20 (OsTPS20, 599 amino acids, 69.39kDa), which was further characterized as an (S)-limonene synthase by removing the N-terminal signal peptide (63 amino acids) of the protein. The recombinant OsTPS20 protein catalyzed the conversion of geranyl diphosphate to (S)-limonene and other minor monoterpenes, essentially covering all of the volatile compounds detected from the plant. Moreover, qRT-PCR revealed that the transcript levels of OsTPS20 were significantly induced in response to oxidative stress, thereby suggesting that OsTPS20 plays a major role in producing terpene volatiles during abiotic stress. Detailed biochemical analyses and the unusual domain characteristics of OsTPS20 are also discussed in this report.