Asymmetric Chain Research Articles

Gene Cloning, Expression, and Characterization of a Cyclic Nucleotide Phosphodiesterase from Arthrobacter sp. CGMCC 3584

Based on thermal asymmetric interlaced polymerase chain reaction, the arpde gene encoding a cyclic nucleotide-specific phosphodiesterase was cloned from Arthrobacter sp. CGMCC 3584 for the first time. The 930-bp region encoded a 309-amino-acid protein with a molecular weight of 33.6 kDa. The recombinant ArPDE was able to hydrolyze 3',5'-cAMP, 3',5'-cGMP, and 2',3'-cAMP. The K m values of ArPDE for 3',5'-cAMP and 3',5'-cGMP were 6.82 and 12.82 mM, respectively. ArPDE was thermostable and displayed optimal activity at 45 °C and pH 7.5. The enzyme did not require any metal cofactors, although its activity was stimulated by 2 mM Co(2+) and inhibited by Zn(2+). Nucleotides, reducing agents, and sulfhydryl reagents had different inhibitory effects on the activity of ArPDE. NaF, the actual compound used to improve the industrial yield of cAMP, exhibited 62 % inhibitions at concentrations of 10 mM.

Modeling and self-assembly behavior of PEG–PLA–PEG triblock copolymers in aqueous solution

A series of poly(ethylene glycol)-polylactide-poly(ethylene glycol) (PEG-PLA-PEG) triblock copolymers with symmetric or asymmetric chain structures were synthesized by combination of ring-opening polymerization and copper-catalyzed click chemistry. The resulting copolymers were used to prepare self-assembled aggregates by dialysis. Various architectures such as nanotubes, polymersomes and spherical micelles were observed from transmission electron microscopy (TEM), cryo-TEM and atomic force microscopy (AFM) measurements. The formation of diverse aggregates is explained by modeling from the angle of both geometry and thermodynamics. From the angle of geometry, a "blob" model based on the Daoud-Cotton model for star polymers is proposed to describe the aggregate structures and structural changes with copolymer composition and molar mass. In fact, the copolymer chains extend in aqueous medium to form single layer polymersomes to minimize the system's free energy if one of the two PEG blocks is short enough. The curvature of polymersomes is dependent on the chain structure of copolymers, especially on the length of PLA blocks. A constant branch number of aggregates (f) is thus required to preserve the morphology of polymersomes. Meanwhile, the aggregation number (N(agg)) determined from the thermodynamics of self-assembly is roughly proportional to the total length of polymer chains. Comparing f to N(agg), the aggregates take the form of polymersomes if N(agg) ≈ f, and change to nanotubes if N(agg) > f to conform to the limits from both curvature and aggregation number. The length of nanotubes is mainly determined by the difference between N(agg) and f. However, the hollow structure becomes unstable when both PEG segments are too long, and the aggregates eventually collapse to yield spherical micelles. Therefore, this work gives new insights into the self-assembly behavior of PEG-PLA-PEG triblock copolymers in aqueous solution which present great interest for biomedical and pharmaceutical applications.

RRP41L, a Putative Core Subunit of the Exosome, Plays an Important Role in Seed Germination and Early Seedling Growth in Arabidopsis

In prokaryotic and eukaryotic cells, the 3'-5'-exonucleolytic decay and processing of RNAs are essential for RNA metabolism. However, the understanding of the mechanism of 3'-5'-exonucleolytic decay in plants is very limited. Here, we report the characterization of an Arabidopsis (Arabidopsis thaliana) transfer DNA insertional mutant that shows severe growth defects in early seedling growth, including delayed germination and cotyledon expansion, thinner yellow/pale-green leaves, and a slower growth rate. High-efficiency thermal asymmetric interlaced polymerase chain reaction analysis showed that the insertional locus was in the sixth exon of AT4G27490, encoding a predicted 3'-5'-exonuclease, that contained a conserved RNase phosphorolytic domain with high similarity to RRP41, designated RRP41L. Interestingly, we detected highly accumulated messenger RNAs (mRNAs) that encode seed storage protein and abscisic acid (ABA) biosynthesis and signaling pathway-related protein during the early growth stage in rrp41l mutants. The mRNA decay kinetics analysis for seed storage proteins, 9-cis-epoxycarotenoid dioxygenases, and ABA INSENSITIVEs revealed that RRP41L catalyzed the decay of these mRNAs in the cytoplasm. Consistent with these results, the rrp41l mutant was more sensitive to ABA in germination and root growth than wild-type plants, whereas overexpression lines of RRP41L were more resistant to ABA in germination and root growth than wild-type plants. RRP41L was localized to both the cytoplasm and nucleus, and RRP41L was preferentially expressed in seedlings. Altogether, our results showed that RRP41L plays an important role in seed germination and early seedling growth by mediating specific cytoplasmic mRNA decay in Arabidopsis.

Agrobacterium tumefaciens-Mediated Transformation for Investigating Pathogenicity Genes of the Phytopathogenic Fungus Colletotrichum sansevieriae

Agrobacterium tumefaciens-mediated transformation (AtMT) has become a common technique for DNA transformation of yeast and filamentous fungi. In this study, we first established a protocol of AtMT for the phytopathogenic fungus Colletotrichum sansevieriae. Binary T-DNA vector containing the hygromycin B phosphotransferase gene controlled by the Aspergillus nidulans gpdA promoter and the trpC terminator was constructed with pCAMBIA0380 and used with three different strains LBA4404, GV3101, and GV2260 of A. tumefaciens. Transformants were most effectively obtained when GV2260 and C. sansevieriae Sa-1-2 were co-cultivated; there were about 320 transformants per 10(6) spores. When 1,048 transformants were inoculated on Sansevieria trifasciata, three transformants were found to have completely lost their pathogenicity and two transformants displayed reduced pathogenicity. All of the five transformants had a single copy of T-DNA in their genomes. The three pathogenicity-deficient transformants were subjected to thermal asymmetric interlaced polymerase chain reaction and the reaction allowed us to amplify the sequences flanking the left and/or right borders. The flanking sequences of the two transformants, M154 and M875, showed no homology to any sequences in databases, but the sequences of M678 contained motifs of alpha-1,3-glucan synthase, suggesting that the gene might contribute to the pathogenicity of C. sansevieriae. This study describes a useful method for investigating pathogenicity genes in C. sansevieriae.

Asymmetric-Lanczos-Chain-Driven Implementation of Electronic Resonance Convergent Coupled-Cluster Linear Response Theory.

We present an implementation of the damped coupled-cluster linear response function based on an asymmetric Lanczos chain algorithm for the hierarchy of coupled-cluster approximations CCS (coupled-cluster singles), CC2 (coupled-cluster singles and approximate doubles), and CCSD (coupled-cluster singles and doubles). Triple corrections to the excitation energies can be included via the CCSDR(3) (coupled-cluster singles and doubles with noniterative-triples-corrected excitation energies) approximation. The performance and some of the potentialities of the approach are investigated in calculations of the visible/ultraviolet absorption spectrum and the dispersion of the real polarizability in near-resonant regions of pyrimidine, the near-edge absorption fine structure (NEXAFS) of ammonia, and the direct determination of the C6 dipole-dipole dispersion coefficient of the benzene dimer.

T-DNA integration patterns in transgenic maize lines mediated by Agrobacterium tumefaciens

To explore transfer deoxyribonucleic acid (T-DNA) integration patterns in the maize genome, we improved the protocol of thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR), and amplified the flanking sequences around T-DNA integration sites from 70 independent transgenic maize lines mediated by Agrobacterium tumefaciens . Out of 64 specific amplified fragments, 32 and 9 are homologous to the sequences of the maize genome and the expression plasmid, respectively. For 26 of them, a filler sequence was found flanking the cleavage sites. These results demonstrate that cleavage occurs not only during the T-DNA borders but also inside or outside the borders. The border sequences and some inside sequences can be deleted, and filler sequences can be inserted. Illegitimate recombination is a major pattern of T-DNA integration, while some hot spots and preference are present on maize chromosomes. Key words : Agrobacterium tumefaciens, maize, thermal asymmetric interlaced PCR, transfer DNA,transgenics.

Enhancement effect of asymmetry on the thermal conductivity of double-stranded chain systems

Using nonequilibrium molecular dynamics simulations, we study the thermal conductivity of asymmetric double chains. We couple two different single chains through interchain coupling to build three kinds of asymmetric double-stranded chain system: intrachain interaction, external potential, and mass asymmetric double chains. It is reported that asymmetry is helpful in improving the thermal conductivity of the system. We first propose double-heat flux channels to explain the influence of asymmetric structures on the thermal conductivity. The phonon spectral behaviour and finite size effect are also included.

The Adsorption and Self-Assembly of Mixtures of Alkylbenzene Sulfonate Isomers and the Role of Divalent Electrolyte

In this paper, the role of the different structural isomers of the anionic surfactant sodium para-dodecyl benzene sulfonate, LAS, on surface adsorption and solution self-assembly has been studied. Using a combination of neutron reflectivity, NR, and small angle neutron scattering, SANS, the effect of mixing an isomer with a short symmetric hydrocarbon chain with one which has an asymmetric hydrocarbon chain on both the equilibrium surface adsorption behavior and the solution microstructure of the mixtures, both in the presence and absence of a divalent cation (Ca(2+)), has been investigated. In the absence of electrolyte, the LAS isomer mixtures form small charged globular micelles throughout the composition range studied. The micelle aggregation number increases with the increase in the asymmetric isomer content, reflecting an increase in the packing efficiency within the micelle. The addition of calcium ions promotes the formation of planar aggregates, as multilamellar vesicles, but only when the symmetric LAS isomer is the major component of the mixture. At a surfactant concentration just above the critical micelle concentration, CMC, and in the absence of electrolyte, the variation in the surface composition is close to the solution composition. Regular solution theory, RST, calculations show that this variation is also close to what is expected for ideal mixing. The addition of Ca(2+) ions induces a different surface behavior, resulting in the formation of multilayer structures at the interface throughout the entire composition range.

Self-consistent mean-field model for palmitoyloleoylphosphatidylcholine-palmitoyl sphingomyelin-cholesterol lipid bilayers.

The connection between membrane inhomogeneity and the structural basis of lipid rafts has sparked interest in the lateral organization of model lipid bilayers of two and three components. In an effort to investigate anisotropic lipid distribution in mixed bilayers, a self-consistent mean-field theoretical model is applied to palmitoyloleoylphosphatidylcholine (POPC)--palmitoyl sphingomyelin (PSM)--cholesterol mixtures. The compositional dependence of lateral organization in these mixtures is mapped onto a ternary plot. The model utilizes molecular dynamics simulations to estimate interaction parameters and to construct chain conformation libraries. We find that at some concentration ratios the bilayers separate spatially into regions of higher and lower chain order coinciding with areas enriched with PSM and POPC, respectively. To examine the effect of the asymmetric chain structure of POPC on bilayer lateral inhomogeneity, we consider POPC-lipid interactions with and without angular dependence. Results are compared with experimental data and with results from a similar model for mixtures of dioleoylphosphatidylcholine, steroyl sphingomyelin, and cholesterol.

Analysis of T-DNA Flanking Sequences and Event-Specific Detection of Transgenic Alfalfa with Gene Encoding Betaine Aldehyde Dehydrogenase

The gene encoding betaine aldehyde dehydrogenase (BADH) has been transformed into alfalfa ( Medicago sativa L.) and resulted in 42 transgenic plants with improved salt tolerance. However, these transgenic lines were derived from the same transformant vector, which were unable to distinguish them from each other using common methods. For differentiating these transformants at molecular level, thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) was performed to separate the T-DNA flanking sequences for identifying transgenic plants in event-specific detection. A total of 6 sequences flanking either the left or the right borders of the T-DNA were obtained. The left border sequence of T-DNA was completely deleted from the vector and not integrated into the genome of alfalfa in the transgenic plant B196. Although the left border flanking sequence in the transgenic plant B127 was reserved, it was filled with a DNA sequence of unknown origin. The forward and backward primers for PCR were designed based on the characteristics of the flanking sequences originating from the vector sequence and the alfalfa genomic sequence adjacent to the integrated vector sequence, respectively. According to the result of PCR amplification in the 42 BADH-transgenic lines, plants B106, B125, B127, B138, B157, B158, B289, B295, and B305 presented the same amplification banding pattern. Plants B196, B203, B220, and B223 exhibited the same banding pattern, which was different from that amplified from other plants. These results indicated that the plants with identical amplification banding patterns may come from the same transformation event.

Supply Chain Competition with Multiple Manufacturers and Retailers

We study competition in a supply chain where multiple manufacturers compete in quantities to supply a set of products to multiple risk-averse retailers who compete in quantities to satisfy the uncertain consumer demand. For the symmetric supply chain, we give closed-form expressions for the unique equilibrium. We find that, provided there is a sufficiently large number of manufacturers and retailers, the supply chain efficiency (the ratio of the aggregate utility in the decentralized and centralized chains) can be raised to 1 by inducing the right degree of retailer differentiation. Also, risk aversion results in triple marginalization: retailers require a strictly positive margin to distribute even when they are perfectly competitive, because otherwise they are unwilling to undertake the risk associated with the uncertainty in demand. For the asymmetric supply chain, we show how numerical optimization can be used to compute the equilibria, and we find that the supply chain efficiency may drop sharply with the asymmetry of either manufacturers or retailers. We also find that the introduction of asymmetric product assortment reduces the degree of competition among retailers and thus has an effect similar to that of reducing the number of retailers. We show that, unlike in the symmetric chain, the asymmetric chain efficiency depends on product differentiation and risk aversion because of the interaction between these features and the asymmetry of manufacturers and retailers.

The main transition enthalpy of the gel-to-liquid crystal phases for a series of asymmetric chain length d-erythro (2S, 3R) sphingomyelins

A series of d-erythro (2S, 3R) sphingomyelins (SMs) whose acyl chain was 16, 18, 20, 22, and 24 carbons long was synthesized by the acylation of d-erythro-sphingosyl-phosphorylcholine of 18 carbons long. All the SMs were found to exist as asymmetric chain-length lipids. DSC heating scans of the respective SM dispersions showed two transitions that were reversible and reproducible upon reheating. However, the enthalpy change (ΔHM) of the main gel-to-liquid crystal phase transition exhibited a slight decrease with an increase in the effective chain length (N), which contrasted with the generally accepted phenomenon for lipid-water systems. The behavior of ΔHMvs. N curve was discussed from the viewpoint of the effect of a mismatched chain-length segment in the acyl chain on the chain–chain van der Waals interaction energy that accounts for 2/3 of ΔHM, on the basis of a partial interdigitation for the chain packing arrangement of asymmetric chain length lipids.

Block Copolymer Nanocomposites Based on Multiwall Carbon Nanotubes: Effect of the Functionalization of Multiwall Carbon Nanotubes on the Morphology of the Block Copolymer

AbstractFilms based on a commercial block copolymer and multiwall carbon nanotubes (MWCNTs) were prepared by solution casting. The block copolymer has a star asymmetric chain architecture, with polystyrene chains of different lengths and a polybutadiene core. The block copolymer has a lamellar morphology. The MWCNT were grafted with polystyrene chains under atom transfer radical polymerization (ATRP) conditions. The nanocomposites were characterized by transmission electron microscopy (TEM) and simultaneous small angle X‐ray scattering (SAXS)/strain–stress tests. The morphology of the nanocomposites is influenced by the polystyrene chain grafted from the MWCNT. In the case of the nanocomposite based on pristine MWCNT, most of the nanotubes intersect the lamellar domains of the block copolymer. With the increase of the molecular weight and the grafting chain density of the polystyrene anchored to the MWCNT, a favorable interaction between the polystyrene microdomain phases in the block copolymer and the MWCNT is observed. In the case where the MWCNT grafted with the relative highest molecular weight (20 kg·mol−1) and polystyrene grafted content (> 90 wt%), the MWCNT locally templates the lamellar morphology of the block copolymer. The effect on the block copolymer is analyzed based on the orientation of the morphology under an external deformation.

Cloning and characterization of a novel stress-responsive WRKY transcription factor gene (MusaWRKY71) from Musa spp. cv. Karibale Monthan (ABB group) using transformed banana cells

WRKY transcription factor proteins play significant roles in plant stress responses. Here, we report the cloning and characterization of a novel WRKY gene, MusaWRKY71 isolated from an edible banana cultivar Musa spp. Karibale Monthan (ABB group). MusaWRKY71, initially identified using in silico approaches from an abiotic stress-related EST library, was later extended towards the 3' end using rapid amplification of cDNA ends technique. The 1299-bp long cDNA of MusaWRKY71 encodes a protein with 280 amino acids and contains a characteristic WRKY domain in the C-terminal half. Although MusaWRKY71 shares good similarity with other monocot WRKY proteins the substantial size difference makes it a unique member of the WRKY family in higher plants. The 918-bp long 5' proximal region determined using thermal asymmetric interlaced-polymerase chain reaction has many putative cis-acting elements and transcription factor binding motifs. Subcellular localization assay of MusaWRKY71 performed using a GFP-fusion platform confirmed its nuclear targeting in transformed banana suspension cells. Importantly, MusaWRKY71 expression in banana plantlets was up-regulated manifold by cold, dehydration, salt, ABA, H2O2, ethylene, salicylic acid and methyl jasmonate treatment indicating its involvement in response to a variety of stress conditions in banana. Further, transient overexpression of MusaWRKY71 in transformed banana cells led to the induction of several genes, homologues of which have been proven to be involved in diverse stress responses in other important plants. The present study is the first report on characterization of a banana stress-related transcription factor using transformed banana cells.

Construction of a Tn5-Tagged Mutant Library of Xanthomonas oryzae pv. oryzicola as An Invaluable Resource for Functional Genomics

To genome-widely mine pathogenesis-related genes of Xanthomonas oryzae pv. oryzicola (Xoc), which is the casual agent of bacterial leaf streak resulting in significant yield loss and poor quality in rice, a Tn5 transposon-mediated mutation library was generated. Twenty-five thousand transformants were produced by using Tn5 transposome, appropriately corresponding to 5 × ORF coverage of the genome, and inoculated into rice and tobacco, individually and respectively, for screening candidate virulence genes. Southern blot and thermal asymmetric interlaced polymerase chain reaction analysis of Tn5 insertion sites of randomly selected mutants suggested a random mode of transposition and a saturation library. Characterization of extracellular polysaccharides, extracellular protease activity, and pigment production of individual mutants in the growth media revealed that 11 mutants enhanced in growth, 12 reduced extracellular polysaccharide production, 12 lost extracellular protease activity completely or partially, and 21 were pigment deficient. In planta pathogenicity assays revealed 253 mutants reduced virulence in rice, but kept triggering hypersensitive response in tobacco; 49 lost the ability to elicit HR in tobacco and pathogenicity in rice; and 3 still induced hypersensitive response in tobacco, but lost pathogenicity in rice. The achieved mutant library of Xoc is of high-quality and nearly saturated and candidate virulence mutants provided a strong basis for functional genomics of Xoc.

Isolation and functional characterization of a waterlogging-induced promoter from maize

Using thermal asymmetric interlaced polymerase chain reaction (TAIL PCR), promoter sequences of 1,444bp (HM241145) and 1,249bp (HM241146) from the Zea mays zinc finger (zmzf) protein gene were isolated from the maize inbred lines Mo17 and Hz32, respectively. Sequence analysis demonstrated that the Mo17 zmzf promoter contained multiple cis-regulatory elements responding to anaerobic conditions. These included two GC-motifs, five anaerobic response elements (AREs), one GT-motif, and four G-boxes. Sequence alignment revealed that there was a 195bp DNA deletion (-258 to -452bp) in the Hz32 zmzf promoter compared with the Mo17 promoter. The deleted fragment contained three AREs. According to quantitative real time PCR analysis, the expression of the uidA gene driven by the Mo17 zmzf promoter increased after day 1 waterlogging treatment, peaked after day 2 and decreased at days 4-8. Staining for β-glucuronidase (GUS) was observed in the roots of Mo17 zmzf transgenic lines under waterlogged conditions, but not in the leaves. GUS expression was not observed in the roots and leaves of Hz32 zmzf transgenic lines, even under submerged conditions, indicating that the Hz32 zmzf promoter was non-functional because of the deletion of three AREs. We propose that the Mo17 zmzf promoter was inducible by waterlogging, highly active, and root-specific, and might be useful for the genetic engineering of waterlogging tolerance.

Magnetic frustration induced quantum phase transitions in the [formula omitted] vertically asymmetric diamond chain

By means of the second derivative of the ground-state energy for a finite-size system method, the quantum phase transitions (QPTs) for the frustrated vertically asymmetric diamond chain (VADC) are investigated. Our results display the plentiful frustration induced quantum phases in the model. Meanwhile, using the transfer matrix renormalization group technique (TMRG), we calculate the fidelity susceptibility and magnetic susceptibility of the VADC model in the thermodynamic limit to give a further understanding of the QPTs.

Exploring relational asymmetry in supply chains: the retailer's perspective

PurposeThe purpose of this paper is to explore the phenomenon of asymmetric supply chain relationships and investigate how firms manage these relationships.Design/methodology/approachUsing grounded theory methodology, qualitative data was accumulated from experienced supply chain managers. Depth interviews were utilized in order to gain a deeper understanding of asymmetric supply chain relationships.FindingsPrior research has conceptualized asymmetry as a lack of dyadic balance in a core relationship attribute and has focused on causal effects of asymmetry in relationships. However, this study finds asymmetry is a more complex issue and that there are three distinguishable types of relationship asymmetry.Research limitations/implicationsThe types of asymmetry that emerged in this exploratory research potentially have different impacts on supply chain relationships. Therefore, the strong negative connotation associated with existing asymmetry literature may well be because the type of asymmetry that primarily triggers negative relationship impacts were being investigated. However, this paper suggests that some types of asymmetry have positive relational outcomes.Practical implicationsThis exploratory paper provides managers with additional insight into a common type of supply chain relationship and suggests that asymmetric relationships should be segmented in order to more effectively manage transaction costs.Originality/valueThe notion that asymmetry is a simple, unidimensional construct is now called into question. According to the findings of this paper, asymmetry is a complex issue and managers employ different strategies to address the potential supply chain relationship performance implications with each type of asymmetry.

Asymmetric exclusion model with impurities

An integrable asymmetric exclusion process with impurities is formulated. The model displays the full spectrum of the stochastic asymmetric XXZ chain plus new levels. We derive the Bethe equations and calculate the spectral gap for the totally asymmetric diffusion at half filling. While the standard asymmetric exclusion process without impurities belongs to the KPZ universality class with an exponent 3/2, our model has a scaling exponent 5/3.

On the construction of a pseudo-Hermitian quantum system with a pre-determined metric in the Hilbert space

A class of pseudo-Hermitian quantum system with an explicit form of the positive-definite metric in the Hilbert space is presented. The general method involves a realization of the basic canonical commutation relations defining the quantum system in terms of operators that are Hermitian with respect to a pre-determined positive-definite metric in the Hilbert space. Appropriate combinations of these operators result in a large number of pseudo-Hermitian quantum systems admitting entirely real spectra and unitary time evolution. The examples considered include simple harmonic oscillators with complex angular frequencies, Stark (Zeeman) effect with non-Hermitian interaction, non-Hermitian general quadratic form of N boson (fermion) operators, symmetric and asymmetric XXZ spin chain in the complex magnetic field, non-Hermitian Haldane–Shastry spin chain and Lipkin–Meshkov–Glick model.