Unusual Poly Research Articles

Gilthead seabream mucus glycosylation is complex, differs between epithelial sites and carries unusual poly N-acetylhexosamine motifs

Gilthead seabream (Sparus aurata) is a marine finfish of economic importance in aquaculture. Despite its adaptability to varying culture conditions, gilthead seabream culture can be affected by viral, bacterial or parasitic diseases. The main route of entry of pathogens is through mucosal surfaces. Teleost external and internal surfaces are covered by mucus, mainly comprised of highly glycosylated proteins called mucins. The mucin glycans regulate pathogen growth, adhesion, virulence and inter and intra species communication. Here, we characterized the gilthead seabream mucus glycosylation, compared it to previously described species and investigated associations with microbiota. 214 glycans were identified. The majority of the glycans were found at more than one epithelial surface, but 27, 22 and 89 O-glycan structures were unique to skin, gill and intestinal sample groups, respectively. Six O-glycan core types were observed. The majority of the seabream skin and gill O-glycans were neutral with unusual poly HexNAc motifs. In contrast, seabream intestinal O-glycans were highly acidic and not of the ‘poly HexNAc’ type observed in skin and gill. Furthermore, gilthead seabream gill mucosa had less oligomannose and more complex N-glycans compared to skin and intestine. The concentration and diversity of bacteria was similar in skin, gill and intestine, but the bacterial species differed between epithelia and co-varied with glycan epitopes. The presence of a complex mucus glycosylation with plenty of glycan epitopes for bacterial foraging, suggest that the skin mucosal defense in seabream includes an abundant resident microbiota. This large library of structures provides a platform for further studies, for example aiming to identifying glycans to use for diagnostic purposes, to study host-microbe interactions or disease intervention therapies.

Probing the Nano-Assembly Leading to Periodic Gratings in Poly(p-dioxanone).

This study used scanning electron microscopy via 3D dissection coupled with synchrotron radiation with microfocal beams of both small-angle X-ray scattering and wide-angle X-ray diffraction to analyze the periodic crystal aggregates of unusual poly(p-dioxanone) (PPDO) dendritic cactus-arm-like ring bands upon crystallization with a diluent poly(vinyl alcohol) (PVA) that is capable of hydrogen bonding interactions with PPDO. Three-dimensional microscopy interior dissection clearly expounds that the banded periodic architectures are packed by alternately normal-oriented flat-on crystals underneath the valley, periodically interfaced/branched with horizontal-oriented edge-on fibrils underneath the ridge. The oblique angles between the valley's flat-on crystals with the branches are ca. 25-45° (depending on gradient inclines and bending), which is also proved by the azimuthal angle in microbeam X-ray diffraction. The grating-like strut-rib assembly in the PPDO cactus-arm-like ring bands is further proved by novel iridescence tests.

Evidence of an Unusual Poly(A) RNA Signature Detected by High-Throughput Chemical Mapping.

Homopolymeric adenosine RNA plays numerous roles in both cells and noncellular genetic material. We report herein an unusual poly(A) signature in chemical mapping data generated by the Eterna Massive Open Laboratory. Poly(A) sequences of length seven or more show unexpected results in the selective 2'-hydroxyl acylation read out by primer extension (SHAPE) and dimethyl sulfate (DMS) chemical probing. This unusual signature first appears in poly(A) sequences of length seven and grows to its maximum strength at length ∼10. In a long poly(A) sequence, the substitution of a single A by any other nucleotide disrupts the signature, but only for the 6 or so nucleotides on the 5' side of the substitution.

A novel polythreading Ag(I) coordination polymer with blue photoluminescence

One new compound, [Ag(p-bix)]3[Ag(Hbtc)2]·2H2O (H3btc=1,2,4-benzenetricarboxylate, p-bix=1,4-bis(imidazol-1-ylmethyl)-benzene), has been synthesized under hydrothermal conditions and characterized by elemental analysis, IR, PXRD, luminescent analysis, and single-crystal X-ray diffraction. X-ray structural analysis revealed that 0-D unit [Ag(Hbtc)2]3− and two kinds of 1-D linear chain [Ag(p-bix)]∞+, can be found within the crystal structure. The combination of 0-D [Ag(Hbtc)2]3− unit and 1-D undulated chain [Ag1(p1-bix)]∞+ through weak Ag–O bond gave rise to 2-D anionic supramolecular doublelayer. Then the grids of the 2-D layer are threaded by 1-D linear cationic chain [Ag2(p2-bix)]∞+ to generate entangled 3-D architecture with unusual poly(pseudo-rotaxane)-type arrangements. Luminescent properties of the title complex were also studied in this paper.

Plasmodium falciparum spliceosomal RNAs: 3′ and 5′ end processing

The major spliceosomal small nuclear ribonucleoproteins (snRNPs) consist of snRNA (U1, U2, U4 or U5) and several proteins which can be unique or common to each snRNP particle. The common proteins are known as Sm proteins; they are crucial for RNP assembly and nuclear import of spliceosomal RNPs. This paper reports detecting the interaction between Plasmodium falciparum snRNAs and Sm proteins, and the usual 5′ trimethylated caps on the snRNAs, by immunoprecipitation with specific antibodies. Furthermore, an unusual poly(A) tail was detected on these non-coding RNAs.

Fractal aggregates of the Pt nanoparticles synthesized by the polyol process and poly(N-vinyl-2-pyrrolidone) reduction

Small-angle X-ray scattering was used to characterize the size and aggregation behavior of the Pt nanoparticles synthesized by the polyol process and the unusual poly(N-vinyl-2-pyrrolidone) (PVP) reduction. With formaldehyde (HCHO) as the reduction agent, the Pt nanoparticles synthesized in aqueous solutions with a high PVP/PtCl4 weight ratio were characterized by short rods with a 70% polydispersity in rod length. The size and size distribution of the rod-like Pt nanoparticles (3 nm in rod length and 2 nm in rod diameter) are consistent with the corresponding transmission electron microscopy image. With a comparable PVP/PtCl4 weight ratio in the aqueous solution containing HCHO, the high number density of reduced Pt nanoparticles led to a fractal-like aggregation with a fractal dimension of 2.1 and a correlation length of ~30 nm. We also demonstrated that Pt nanoparticles can be synthesized by PVP reduction at 323 K without HCHO. The particle size and the clustering behavior of the Pt nanoparticles reduced by PVP are closely related to the PVP concentration in the solution. Both the Pt nanoparticles synthesized in the commonly used polyol process and the unusual PVP reduction form fractal-like clusters via the PVP–metal nanoparticle association when the number density of the Pt nanoparticles in the solutions is high.

Polythreading of Infinite 1D Chains into Different Structural Motifs: Two Poly(pseudo-rotaxane) Architectures Constructed by Concomitant Coordinative and Hydrogen Bonds

Two new compounds, [Co(4,4‘-bipy)(H2O)4]·(H2bptc)·2H2O (1) and [Ni(4,4‘-bipy)(H2O)4]·0.5(btc)·H2O (2) (4,4‘-bipy = 4,4‘-bipyridine, H4bptc = 3,3‘,4,4‘-biphenyltetracarboxylate acid, H4btc = 1,2,4,5-benzenetetracarboxylate acid), have been synthesized under hydrothermal conditions and characterized by elemental analysis, IR, TG analysis, and single-crystal X-ray diffraction. X-ray structural analysis revealed that two different structural motifs (1D covalent zigzag chain and 1D hydrogen-bonded ladder for 1 and 1D linear chain and 2D hydrogen-bonded sheet for 2) can be found within their crystal structures, and most intriguingly, they coexist in such a way that 1D covalently bonded chains of composition [M(4,4‘-bipy)(H2O)4]2+ (M = Co or Ni) thread into the hydrogen-bonded 1D ladders or 2D sheets formed by uncoordinated carboxylate anions and lattice water molecules, giving rise to overall entangled architectures with unusual poly(pseudo-rotaxane)-type arrangements. Thermal stability of the two compounds was also studied in this paper.

Symplekin and xGLD-2 Are Required for CPEB-Mediated Cytoplasmic Polyadenylation

Cytoplasmic polyadenylation-induced mRNA translation is a hallmark of early animal development. In Xenopus oocytes, where the molecular mechanism has been defined, the core factors that control this process include CPEB, an RNA binding protein whose association with the CPE specifies which mRNAs undergo polyadenylation; CPSF, a multifactor complex that interacts with the near-ubiquitous polyadenylation hexanucleotide AAUAAA; and maskin, a CPEB and eIF4E binding protein whose regulation of initiation is governed by poly(A) tail length. Here, we define two new factors that are essential for polyadenylation. The first is symplekin, a CPEB and CPSF binding protein that serves as a scaffold upon which regulatory factors are assembled. The second is xGLD-2, an unusual poly(A) polymerase that is anchored to CPEB and CPSF even before polyadenylation begins. The identification of these factors has broad implications for biological process that employ polyadenylation-regulated translation, such as gametogenesis, cell cycle progression, and synaptic plasticity.

Unusual Poly(phenylacetyloxy)-Substituted 1,1′: 4′,1″-Terphenyl Derivatives from Fruiting Bodies of the BasidiomyceteThelephora ganbajun

Five new poly(phenylacetyloxy)-substituted 1,1′: 4′,1″-terphenyl derivatives, ganbajunins A – E (2 – 6) were isolated from the fruiting bodies of the Basidiomycete Thelephora ganbajun Zang. Their structures were established by spectroscopic (including 2D-NMR) and chemical means.

A nodule-specific gene family from Alnus glutinosa encodes glycine- and histidine-rich proteins expressed in the early stages of actinorhizal nodule development.

Two cDNAs representing different members (agNt84 and ag164) of a gene family encoding glycine- and histidine-rich proteins have been isolated from cDNA libraries from Alnus glutinosa root nodules. Expression of the corresponding genes could only be detected in nodules. With in situ hybridization, the expression in nodules was found to occur in young, infected cells of the prefixation zone (zone 2). The encoded proteins contain putative signal peptides for targeting to the endomembrane system, sharing sequence similarity with signal peptides from plant glycine-rich proteins, among them nodulin 24, a nodule-specific protein from soybean. This similarity suggests that, analogous to nodulin-24, proteins encoded by agNt84/ag164 may be located at the interface between the host plant membrane and the matrix surrounding the endosymbiont. The 3' untranslated regions of the cDNAs contain unusual poly(AT)n stretches that may play a role in the regulation of RNA stability. The protein encoded by agNt84 cDNA was expressed in Escherichia coli as a fusion with maltose-binding protein, and was shown to have the ability to bind to a nickel-chelating resin, indicating that it may function as a metal-binding protein.

Production of shorter mRNA for protein phosphatase 2Aβ by alternative poly(A) addition

Two types of cDNA clones of protein phosphatase 2Aβ, PP-2AβL and PP-2AβS, were isolated from a rat testis cDNA library. PP-2AβL was 1.8 kb in length and corresponded to the 2.0 kb mRNA that is the major species expressed in somatic tissues. PP-2AβS was 1.3 kb in length and corresponded to the 1.4 kb mRNA that is the major species expressed in germ cells of the testis. Nucleotide sequencing of these two clones revealed that their open reading frames were identical. The only difference between these two cDNAs was at the 3′ non-coding region due to alternative poly(A) addition: the 1.8 kb cDNA had a consensus poly(A) addition signal, AATAAA, but the 1.3 kb cDNA had an unusual poly(A) addition signal, probably with the sequence AATATA. These data suggest that in germ cells there may be some mechanism that utilizes the specific poly(A) addition signal.

Cloned cytochrome P-450 cDNA. Nucleotide sequence and homology to multiple phenobarbital-induced mRNA species.

Phenobarbital (PB) treatment of rats of various strains leads to the accumulation of liver mRNAs which encode two or three immunochemically related but electrophoretically separable cytochrome P-450 polypeptides. These mRNAs hybridize efficiently to a single cloned cDNA derived from mRNA of PB-treated rats and, therefore, must have extensive sequence homology. The nucleotide sequence of this cloned cDNA was determined and shown to encode the COOH-terminal 211 amino acids of one of the major cytochrome P-450 isozymes induced in rat liver by PB. Together with the recently reported sequence data of Fujii-Kuriyama et al. (Fujii-Kuriyama, Y., Mizukami, Y., Kawajiri, K., Sagawa, K., and Muramatsu, M. (1982) Proc. Natl. Acad. Sci. U. S. A. 79, 2793-2797) for cloned rat cytochrome P-450 cDNA, our data suggest that differences between two closely related P-450 isozymes are restricted to the COOH-terminal half of the polypeptides, with highly divergent regions flanking a tridecapeptide which has been previously shown to be highly conserved in two dissimilar forms of rabbit liver cytochrome P-450. The significance of other interesting features of the cDNA sequence such as a second long (409 residues) open frame, an unusual poly(A) addition signal, and the absence of long hydrophobic stretches in the encoded polypeptide is discussed.

Copper(I) and silver(I) ions in unusual poly donor-atom environments; X-ray crystal and molecular structures of [M{( R)( S)-1,2-(5-Me-thiophene-2-CHz.dbnd;N) 2-cyclohexane} 2](O 3SCF 3), M = Cu I or Ag I

Coordination properties of 0.t’ and Cu’ with ligand systems containing N and S donor atoms as potential coordinating sites continue to be of interest as models for the redox active sites in the ‘blue’ proteins [ 1] . The conformation and rigidity of the carbon skeleton connecting the hetero-atoms, as well as the types and number of hetero-atoms in the model ligand systems, are important with respect to both the number of metal atoms which can be bonded and the ultimate configuration at the metal centres. Recently we have shown that the quadridentate N-donor ligands (R)(S)-1 ,2-(6-R-py-2-CH=N)Z-cyclohexane (R = H or Me), in which the inner two N-donor sites are connected by the (R)(S)-1,2cyclohexanediyl ring, act as di-bidentate ligands binding two Cur or Ag’ atoms (see Fig. 1) [2]. The application of INEPT “N and ro9Ag NMR spectroscopy revealed that the structural features found for the silver(I) complex [Ag,{(R@)-1,2(py-2-CH=N)z-cyclohexane),l(03SCF3)2 in the solid, with characteristic alternating two short and two long Ag-N distances around the distorted tetrahedral silver centres [2], are retained in solution [3] . Attempts to form mononuclear Cu’ or Ag’ complexes with these N4donor ligands, using ‘A Curor Agr-to-ligand ratios were unsuccessful. Interpretation of these results requires more information concerning the influence of the donor sites on the coordination properties of these types of potentially quadridentate ligands. For this purpose we have now investigated the bonding features of the N2S, ligand system (R)(S)-1,2-(5-R-thiophene-