Repeating Unit Research Articles

Enhancing deep learning predictive models with HAPPY (Hierarchically Abstracted rePeat unit of PolYmers) representation

We introduce HAPPY (Hierarchically ed rePeat unit of PolYmers), a string representation for polymers, designed to efficiently encapsulate essential polymer structure features for property prediction. HAPPY assigns single constituent elements to groups of sub-structures and employs grammatically complete and independent connectors between chemical linkages. Using a limited number of datapoints, we trained neural networks utilizing both HAPPY and conventional SMILES encoding of repeated unit structures and compared their performance in predicting five polymer properties: dielectric constant, glass transition temperature, thermal conductivity, solubility, and density. The results showed that the HAPPY-based network could achieve higher prediction R-squared score and two-fold faster training times. We further tested the robustness and versatility of HAPPY-based network with an augmented training dataset. Additionally, we present topo-HAPPY (Topological HAPPY), an extension that incorporates topological details of the constituent connectivity, leading to improved solubility and glass transition temperature prediction R-squared score.

Homochiral and Heterochiral Self-Sorting Assemblies of Antiaromatic Ni(II) Norcorrole Dimers.

Recently, π-π stacked antiaromatic π-systems have received considerable attention because theycan exhibit stacked-ring aromaticitydue tosubstantial intermolecular orbital interactions. Here, we report three antiaromatic norcorrole dimers that self-assemble to form supramolecular architectures through chiral self-sorting. A2,2'-linked norcorrole dimerwith 3,5-di-tert-butylphenyl groups forms aπ-stacked dimer both in solid and solution statesvia homochiral self-sorting. Its association constant in solution is(3.6 ± 1.7) × 105M-1at 20 °C. In the solid state,3,3'-linked norcorrole dimerswith 3,5-di-tert-butylphenyl and phenyl groups afford macrocyclic and helical supramolecular assemblies via heterochiral and homochiral self-sorting, respectively. Notably, the subtle modification in the substituent resulted in a complete change in the structure of the aggregates and the chiral self-sorting mode. The present findings demonstrate that structural manipulation in antiaromatic monomer units leads to the formation of various supramolecular assemblies on the basis of the attractive interactions between antiaromaticπ-systems.

Dual-Site Biomacromolecule Doped Poly(3, 4-Ethylenedioxythiophene) for Bosting Both Anticoagulant and Electrochemical Performances.

Poly(3, 4-ethylenedioxythiophene) (PEDOT) as a new generation of intelligent conductive polymers, is attracting much attention in the field of tissue engineering. However, its water dispersibility, conductivity, and biocompatibility are incompatible, which limit its further development. In this work, biocompatible electrode material of PEDOT doped with sodium sulfonated alginate (SS) which contains two functional groups of sulfonic acid and carboxylic acid per repeat unit of the macromolecule. The as dual-site doping strategy simultaneously boosts anticoagulant and electrochemical performances, for example, good hydrophilicity (water contact angle of 59.40°), well dispersibility (dispersion solution unstratified in 30 days), high conductivity (4.45 S m-1), and enhanced anticoagulant property (extended activated partial thrombin time value of 59.0 s), forming an adjustable PEDOT: biomacromolecule interface; this fills the technical gap of implantable bioelectronics in terms of coagulation and thrombosis risk. At the same time, the assembled all-in-one supercapacitor with anticoagulant properties is prepared by PEDOT: sodium sulfonated alginate as electrode material and sodium alginate hydrogel as electrolyte layer. The dual-site doping strategy provides a new opinion for the design and optimization of functional conductive polymers and its applications in implantable energy storage fields.

Vinyl and methyl-ester groups in the insoluble polymer drug patiromer identified and quantified by solid-state NMR

Patiromer (Veltassa®) is a crosslinked, insoluble co-polymer drug used as a nonabsorbent potassium binder, approved for treatment of hyperkalemia. Quantitative solid-state 13C nuclear magnetic resonance (NMR) analysis with comprehensive peak assignment, component quantification, and calculation of mole and weight fractions of monomer units was performed on three doses of patiromer. The workflow is documented in detail. Spectrally edited solid-state 13C NMR spectra of patiromer show =CHn peaks of matching intensity at 116 and 141 ppm, characteristic of -CH=CH2 vinyl groups. Similar spectral features can be observed in earlier studies but were previously ignored. In this study, the vinyl signals are well-resolved in a 2-s direct polarization (DP) spectrum without and with dipolar dephasing, which confirms that these sp2-hybridized carbons are bonded to hydrogen and partially mobile, consistent with vinyl side groups from incompletely reacted divinyl crosslinkers. The vinyl groups account for 1.6% of all carbon, 3% of the monomer units, and nearly 1/3 of the crosslinkers. Furthermore, an unexpected OCH3 moiety accounting for ∼1.2% of all carbons was identified by spectral editing; its chemical shift of 54 ppm is more consistent with a methyl ester than with a methyl ether. It can originate from incomplete hydrolysis of ∼6% of methyl-2-fluoroacrylate, the main monomer of patiromer. Characteristic cross peaks in two-dimensional 1H–13C heteronuclear correlation NMR confirm the presence of the vinyl and OCH3 groups. Trace amounts of xanthan gum are also detected. The quantitative 13C NMR spectrum of patiromer has been matched in a simulation using a model with five monomer units.

Determining glycosyltransferase functional order via lethality due to accumulated O-antigen intermediates, exemplified with Shigella flexneri O-antigen biosynthesis.

The O antigen (OAg) polysaccharide is one of the most diverse surface molecules of Gram-negative bacterial pathogens. The structural classification of OAg, based on serological typing and sequence analysis, is important in epidemiology and the surveillance of outbreaks of bacterial infections. Despite the diverse chemical structures of OAg repeating units (RUs), the genetic basis of RU assembly remains poorly understood and represents a major limitation in assigning gene functions in polysaccharide biosynthesis. Here, we describe a genetic approach to interrogate the functional order of glycosyltransferases (GTs). Using Shigella flexneri as a model, we established an initial glycosyltransferase (IT)-controlled system, which allows functional order allocation of the subsequent GT in a 2-fold manner as follows: (i) first, by reporting the growth defects caused by the sequestration of UndP through disruption of late GTs and (ii) second, by comparing the molecular sizes of stalled OAg intermediates when each putative GT is disrupted. Using this approach, we demonstrate that for RfbF and RfbG, the GT involved in the assembly of S. flexneri backbone OAg RU, RfbG, is responsible for both the committed step of OAg synthesis and the third transferase for the second L-Rha. We also show that RfbF functions as the last GT to complete the S. flexneri OAg RU backbone. We propose that this simple and effective genetic approach can be also extended to define the functional order of enzymatic synthesis of other diverse polysaccharides produced both by Gram-negative and Gram-positive bacteria.IMPORTANCEThe genetic basis of enzymatic assembly of structurally diverse O antigen (OAg) repeating units (RUs) in Gram-negative pathogens is poorly understood, representing a major limitation in our understanding of gene functions for the synthesis of bacterial polysaccharides. We present a simple genetic approach to confidently assign glycosyltransferase (GT) functions and the order in which they act during assembly of the OAg RU. We employed this approach to determine the functional order of GTs involved in Shigella flexneri OAg assembly. This approach can be generally applied in interrogating GT functions encoded by other bacterial polysaccharides to advance our understanding of diverse gene functions in the biosynthesis of polysaccharides, key knowledge in advancing biosynthetic polysaccharide production.

Bottlebrush Block Copolymers at the Interface of Immiscible Liquids: Adsorption and Lateral Packing.

Amphiphilic bottlebrush block copolymers (BBCPs), having a hydrophilic bottlebrush polymer (BP) linked covalently to a hydrophobic BP, were found to segregate to liquid-liquid interfaces to minimize the free energy of the system. The key parameter influencing the outcome of the experiments is the ratio between the degree of polymerization of the backbone (NBB) and that of the side-chain brushes (NSC). Specifically, a spherical, star-like configuration results when NBB < NSC, while a cylindrical, bottlebrush-like shape is preferred when NBB > NSC. Dynamic interfacial tension (γ) and fluorescence recovery after photobleaching (FRAP) measurements show that the BBCP configuration influences the areal density and in-plane diffusion at the fluid interface. The characteristic relaxation times associated with BBCP adsorption (τA) and reorganization (τR) were determined by fitting time-dependent interfacial tension measurements to a sum of two exponential relaxation functions. Both τA and τR initially increased with NBB up to 92 repeat units, due to the larger hydrodynamic radius in solution and slower in-plane diffusivity, attributed to a shorter cross-sectional diameter of the side-chains near the block junction. This trend reversed at NBB = 190, with shorter τA and τR attributed to increased segregation strength and exposure of the bare water/toluene interface due to tilting and/or wiggling of the backbone chains, respectively. The adsorption energy barrier decreased with higher NBB, due to a reduced BBCP packing density at the fluid interface. This study provides fundamental insights into macromolecular assembly at fluid interfaces, as it pertains to unique bottlebrush block architectures.

From Chemical Drawing to Electronic Properties of Semiconducting Polymers in Bulk: A Tool for Chemical Discovery.

A quantum chemistry (QC)/molecular dynamics (MD) scheme is developed to calculate electronic properties of semiconducting polymers in three steps: (i) constructing the polymer force field through a unified workflow, (ii) equilibrating polymer models, and (iii) calculating electronic structure properties (e.g., density of states and localization length) from the equilibrated models by QC approaches. Notably, as the second step of this scheme is generally the most time-consuming one, we introduce an alternative method to compute thermally averaged electronic properties in bulk, based on the simulation of a polymer chain in the solution of its repeat units, which is shown to reproduce the microstructure of polymer chains and their electrostatic effect (successfully tested for five benchmark polymers) 10 times faster than state-of-the-art methods. In fact, this scheme offers a consistent and speedy way of estimating electronic properties of polymers from their chemical drawings, thus ensuring the availability of a homogeneous set of simulations to derive structure-property relationships and material design principles. As an example, we show how the electrostatic effect of the polymer chain environment can disturb the localized electronic states at the band tails and how this effect is more significant in the case of diketopyrrolopyrrole polymers as compared to indacenodithiophene and dithiopheneindenofluorene ones.

Comprehensive genetic analysis of facioscapulohumeral muscular dystrophy by Nanopore long-read whole-genome sequencing

BackgroundFacioscapulohumeral muscular dystrophy (FSHD) is a high-prevalence autosomal dominant neuromuscular disease characterized by significant clinical and genetic heterogeneity. Genetic diagnosis of FSHD remains a challenge because it cannot be detected by standard sequencing methods and requires a complex diagnosis workflow.MethodsWe developed a comprehensive genetic FSHD detection method based on Oxford Nanopore Technologies (ONT) whole-genome sequencing. Using a case–control design, we applied this procedure to 29 samples and compared the results with those from optical genome mapping (OGM), bisulfite sequencing (BSS), and whole-exome sequencing (WES).ResultsUsing our ONT-based method, we identified 59 haplotypes (35 4qA and 24 4qB) among the 29 samples (including a mosaic sample), as well as the number of D4Z4 repeat units (RUs). The pathogenetic D4Z4 RU contraction identified by our ONT-based method showed 100% concordance with OGM results. The methylation levels of the most distal D4Z4 RU and the double homeobox 4 gene (DUX4) detected by ONT sequencing are highly consistent with the BSS results and showed excellent diagnostic efficiency. Additionally, our ONT-based method provided an independent methylation profile analysis of two permissive 4qA alleles, reflecting a more accurate scenario than traditional BSS. The ONT-based method detected 17 variations in three FSHD2-related genes from nine samples, showing 100% concordance with WES.ConclusionsOur ONT-based FSHD detection method is a comprehensive method for identifying pathogenetic D4Z4 RU contractions, methylation level alterations, allele-specific methylation of two 4qA haplotypes, and variations in FSHD2-related genes, which will all greatly improve genetic testing for FSHD.

Supramolecular Assemblies in Mn(II) and Zn(II) Metal–Organic Compounds Involving Phenanthroline and Benzoate: Experimental and Theoretical Studies

Two new Mn(II) and Zn(II) metal–organic compounds of 1,10-phenanthroline and methyl benzoates viz. [Mn(phen)2Cl2]2-ClBzH (1) and [Zn(4-MeBz)2(2-AmPy)2] (2) (where 4-MeBz = 4-methylbenzoate, 2-AmPy = 2-aminopyridine, phen = 1,10-phenanthroline, 2-ClBzH = 2-chlorobenzoic acid) were synthesized and characterized using elemental analysis, TGA, spectroscopic (FTIR, electronic) and single crystal X-ray diffraction techniques. The crystal structure analysis of the compounds revealed the presence of various non-covalent interactions, which provides stability to the crystal structures. The crystal structure analysis of compound 1 revealed the formation of a supramolecular dimer of 2-ClBzH enclathrate within the hexameric host cavity formed by the neighboring monomeric units. Compound 2 is a mononuclear compound of Zn(II) where flexible binding topologies of 4-CH3Bz are observed with the metal center. Moreover, various non-covalent interactions, such as lp(O)-π, lp(Cl)-π, C–H∙∙∙Cl, π-stacking interactions as well as N–H∙∙∙O, C–H∙∙∙O and C–H∙∙∙π hydrogen bonding interactions, are found to be involved in plateauing the molecular self-association of the compounds. The remarkable enclathration of the H-bonded 2-ClBzH dimer into a supramolecular cavity formed by two [Mn(phen)2Cl2] complexes were further studied theoretically using density functional theory (DFT) calculations, the non-covalent interaction (NCI) plot index and quantum theory of atoms in molecules (QTAIM) computational tools. Synergistic effects were also analyzed using molecular electrostatic potential (MEP) surface analysis.

Effect of polymer concentration and cross-linking density on the microstructure and properties of polyimide aerogels

AbstractPolyimide aerogels display excellent mechanical strength, high thermal stability, low thermal conductivity, and outstanding dielectric properties. Typically, the synthesis of polyimide aerogels involves the polycondensation of dianhydride and diamine into poly(amic acid) (PAA) oligomers, which are then cross-linked and chemically imidized into polyimide. The stoichiometry of dianhydride and diamine determines the number of repeat units and length of the PAA oligomers, which in turn determines the cross-linking density. Despite the critical role of polymer concentration and number of repeating units in determining the microstructure and properties of polyimide aerogels, few detailed studies exist on these two parameters. Here, we synthesized and characterized 16 polyimide aerogel formulations from the common monomers biphenyl-3,3′,4,4′-tetracarboxylic dianhydride (BPDA) and 4,4′-oxydianiline (ODA), with different repeat units (n = 5, 15, 30, 45) and total polymer concentrations (4, 7, 10, 13 wt%). An increased polymer concentration accelerated gelation and enhanced the mechanical performance of aerogels, but surprisingly, it also led to higher volumetric shrinkage during aging, solvent exchange, and supercritical drying (SCD). Specific surface areas (SSAs) reached a maximum at intermediate polymer concentrations. A shorter oligomer chain length, i.e., a higher cross-linking density, led to moderately higher SSAs (between 320 and 400 m2/g) and reduced shrinkage, resulting in lower densities for a given polymer concentration. The density dependence of the thermal conductivity exhibits a pronounced U-shaped curve with a minimum in thermal conductivity of 21–23 mW/(m·K) between 0.080 and 0.120 g/cm3, with somewhat lower values for more highly cross-linked aerogels. This systematic study of polyimide aerogels forms the basis for designing polyimide aerogels with tailored properties for targeted applications. Graphical Abstract

Polymorphism of spore germination receptor genes in Bacillus anthracis strains of major genetic lineages

Introduction. The genetic structure of the global population of Bacillus anthracis characterized by an unequal distribution of isolates of the main genetic lineages A, B and C, the reason for which is unknown. Determining the characteristics of genes encoding factors that determine the existence of this pathogen at the intra- and extra organismal stages of the life cycle, which can influence the prevalence of strains, is relevant. Aim — сharacterization of the genes and proteins of spore germination in strains of the anthrax pathogen of different genetic lineages. Materials and methods. Whole genome sequences of 46 B. anthracis strains and the CI strain of B. cereus biovar anthracis from the NCBI GenBank database studied. In silico analysis carried out using the programs “BLASTn”, “MEGA X”, “Tandem Repeat Finder”. Results. The number of SNPs, indels and pseudogenes in B. anthracis strains of line B was 2,7–25,6 times higher, in line C 2–23,5 times, and in the B. cereus biovar anthracis strain was 20–2841 times higher than in strains of line A. Significant substitutions in genes leading to changes in the amino acid composition of 10 germination receptor proteins were also significantly more common in B. anthracis strains of lines B, C and the B. cereus biovar anthracis strain. Undescribed VNTRs within the gerHA gene with repeat units of 78 and 117 bp identified, varying between and within isolates of different genetic lineages. Six germination receptor genes have been shown to have rare starting codons. Conclusion. A larger number of non-synonymous SNPs in the genes of spore germination receptors with changes in the amino acid composition of proteins in B. anthracis strains of the main genetic lines B, C and B. cereus biovar anthracis than in strains of line A suggests their limited adaptive capabilities and may be one of the explanations for the lower prevalence compared to line A. Differences in the gerHA and gerM genes make it possible to differentiate the major B and C genetic lineages from A.

Poly-3,4-dihydroxybenzylidenhydrazine, a different analogue of polydopamine

Abstract In this article, 3,4-dihydroybenzylidenehydrazine is synthesized for the first time, and its properties as a dopamine analogue for polymerization are investigated. Using an oxidative polymerization reaction, the reaction mechanism as well as the coating ability of the new polymer is determined and compared to that of polydopamine. The polymerization reactions were performed in a mixture of methanol–water with NaIO4 as an oxidation reagent. The polymer was used as a coating on both glass surfaces with a thickness of ∼5 nm as determined by AFM, as well as on TiO2 nanoparticles. For the latter, SEM/TEM and the pH-dependent variation of zeta potential were measured. As a free polymer, poly-3,4-dihydroxybenzylidenhydrazine was investigated by UV-Vis, ss-NMR, and FTIR, and a variety of monomeric units were found in the polymer matrix. The solubility in methanol or DMSO of the monomer and the slight solubility of the polymer allowed us to study the fluorescence and cyclic voltammetry properties for both the monomer and polymer.

A cerebellar ataxia patient harboring 229 pure GAA repeat units in FGF14 presenting with grip myotonia

AbstractSpinocerebellar ataxia 27 B (SCA27B) is caused by the expansion of GAA repeats in the intron of the fibroblast growth factor 14 (FGF14) on chromosome 13 and is inherited dominantly. An 80‐year‐old male visited the hospital complaining of ataxic gait and harboring 229 pure GAA repeat units in the FGF14. Almost all the clinical features were similar to that of SCA27B. However, the patient initially presented with episodic grip myotonia, which has not been previously reported.

Construction of an Elastin-like Polypeptide Gene in a High Copy Number Plasmid Using a Modified Method of Recursive Directional Ligation

Elastin-like polypeptides (ELPs) are popular biomaterials due to their reversible, temperature-dependent phase separation and their tunability, which is achievable by evolving procedures in recombinant technology. In particular, recursive direction ligation by plasmid reconstruction (PRe-RDL) is the predominant cloning technique used to generate ELPs of varying lengths. Pre-RDL provides precise control over the number of (VPGXG)n repeat units in an ELP due to the selection of type IIS restriction enzyme (REs) sites in the reconstructed pET expression plasmid, which is a low-to-medium copy number plasmid. While Pre-RDL can be used to seamlessly repeat essentially any gene sequence and overcome limitations of previous cloning practices, we modified the Pre-RDL technique, where a high copy number plasmid (pBluescript II SK(+)—using a new library of type IIS REs) was used instead of a pET plasmid. The modified technique successfully produced a diblock ELP gene of 240 pentapeptide repeats from 30 pentapeptide “monomers” composed of alanine, tyrosine, and leucine X residues. This study found that the large, GC-rich ELP gene compromised plasmid yields in pBluescript II SK(+) and favored higher plasmid yields in the pET19b expression plasmid. Additionally, the BL21 E. coli strain expression consistently provided a higher transformation efficiency and higher plasmid yield than the high cloning efficiency strain TOP10 E. coli. We hypothesize that the plasmid/high GC gene ratio may play a significant role in these observations, and not the total plasmid size or the total plasmid GC content. While expression of the final gene resulted in a diblock ELP with a phase separation temperature of 34.5 °C, future work will need to investigate RDL techniques in additional plasmids to understand the primary driving factors for improving yields of plasmids with large ELP-encoding genes.

Facile and rapid synthesis method of dielectric nanocomposite for simultaneous enhancement of electromagnetic wave absorbing/shielding characteristics

The present study involves the fabrication of poly[4-(2-thiophene)aniline] (PTA) nanocomposite for absorption-dependent shielding applications, demonstrating enhanced absorption and small reflection properties. The Microwave absorption characteristics of the fabricated polymer were studied at different loading ratios, resulting in a minimum reflection loss (RLmini) of − 44 dB for the 8 wt % loading ratio. The macromolecular architecture of the PTA material offers higher dielectric loss resulting from higher conduction and interfacial loss. Additionally, the shielding performance is also evaluated, and the sample containing 8 wt % filler demonstrates an impressive − 36.5 dB shielding efficacy. The performance of polymers is significantly impacted by their unit periodic order arrangement. Conducting polymers with linear structure and special π-orbitals angles possess unique characteristics in comparison to their branched and the random copolymer, making them highly sought after as efficient organic conductors, magnetic substances, electrochromic materials, and high dielectric agents. Monomer units contained two periodical cyclic structures and the creation of the inductive effects of heteroatoms elongates the conjugation and reduces the energy bandgap difference between the HOMO and LUMO levels, enabling smoother electron flow and enhancing absorption capacity. The findings indicate that PTA nanocomposite is a promising radar-absorbing coating material due to its superior absorption ability and outstanding shielding performance.

Heteroatom Substitution Strategy Modulates Thermodynamics Towards Chemically Recyclable Polyesters and Monomeric Unit Sequence by Temperature Switching.

In this paper, we proposed a heteroatom substitution strategy (HSS) in the δ-valerolactone (VL) system to modulate thermodynamics toward chemically recyclable polyesters. Three VL-based monomers containing different heteroatoms (M1 (N), M2 (S), and M3 (O)), instead of C-5 carbon, were designed and synthesized to verify our proposed HSS. All three monomers undergo organocatalytic living/controlled ROP and controllable depolymerization. Impressively, the resulting P(M1) achieved over 99 % monomer recovery under both mild solution depolymerization and high vacuum pyrolysis conditions without any side reactions, and the recycled monomers can be polymerized again forming new polymers. The systematic study of the relationship between heteroatom substitution and recyclability shows that introducing heteroatoms does change the thermodynamics of the monomers (ΔHp o, ΔSp o and Tc values), thereby adjusting the polymerizability and depolymerizability. DFT calculations found that the introduction of heteroatoms adjusts the ring strain by changing the angular strain of the monomers, and the order of their angular strain (M2>M1>M3) is consistent with the order of the experimentally obtained enthalpy change. Notably, the one-pot/one-step copolymerization of two of each of the three monomers enables the synthesis of sequence-controlled copolymers from gradient to random to block structures, by simply switching the copolymerization temperature.

Heteroatom Substitution Strategy Modulates Thermodynamics Towards Chemically Recyclable Polyesters and Monomeric Unit Sequence by Temperature Switching

AbstractIn this paper, we proposed a heteroatom substitution strategy (HSS) in the δ‐valerolactone (VL) system to modulate thermodynamics toward chemically recyclable polyesters. Three VL‐based monomers containing different heteroatoms (M1 (N), M2 (S), and M3 (O)), instead of C‐5 carbon, were designed and synthesized to verify our proposed HSS. All three monomers undergo organocatalytic living/controlled ROP and controllable depolymerization. Impressively, the resulting P(M1) achieved over 99 % monomer recovery under both mild solution depolymerization and high vacuum pyrolysis conditions without any side reactions, and the recycled monomers can be polymerized again forming new polymers. The systematic study of the relationship between heteroatom substitution and recyclability shows that introducing heteroatoms does change the thermodynamics of the monomers (ΔHpo, ΔSpo and Tc values), thereby adjusting the polymerizability and depolymerizability. DFT calculations found that the introduction of heteroatoms adjusts the ring strain by changing the angular strain of the monomers, and the order of their angular strain (M2&gt;M1&gt;M3) is consistent with the order of the experimentally obtained enthalpy change. Notably, the one‐pot/one‐step copolymerization of two of each of the three monomers enables the synthesis of sequence‐controlled copolymers from gradient to random to block structures, by simply switching the copolymerization temperature.

The Pentameric Ligand-Gated Ion Channel Family: A New Member of the Voltage Gated Ion Channel Superfamily?

In this report we present seven lines of bioinformatic evidence supporting the conclusion that the Pentameric Ligand-gated Ion Channel (pLIC) Family is a member of the Voltage-gated Ion Channel (VIC) Superfamily. In our approach, we used the Transporter Classification Database (TCDB) as a reference and applied a series of bioinformatic methods to search for similarities between the pLIC family and members of the VIC superfamily. These include: (1) sequence similarity, (2) compatibility of topology and hydropathy profiles, (3) shared domains, (4) conserved motifs, (5) similarity of Hidden Markov Model profiles between families, (6) common 3D structural folds, and (7) clustering analysis of all families. Furthermore, sequence and structural comparisons as well as the identification of a 3-TMS repeat unit in the VIC superfamily suggests that the sixth transmembrane segment evolved into a re-entrant loop. This evidence suggests that the voltage-sensor domain and the channel domain have a common origin. The classification of the pLIC family within the VIC superfamily sheds light onto the topological origins of this family and its evolution, which will facilitate experimental verification and further research into this superfamily by the scientific community.

Review of the pharmacokinetics of French maritime pine bark extract (Pycnogenol®) in humans.

The French maritime pine bark extract Pycnogenol® is a proprietary product from Pinus pinaster Aiton. It complies with the quality specifications in the United States Pharmacopeia monograph "Pine extract" in the section of dietary supplements. Pycnogenol® is standardized to contain 65-75% procyanidins which are a variety of biopolymers consisting of catechin and epicatechin monomeric units. The effects of Pycnogenol® have been researched in a multitude of human studies. The basis for any in vivo activity is the bioavailability of constituents and metabolites of the extract. General principles of compound absorption, distribution, metabolism and elimination as well as specific data from studies with Pycnogenol® are summarized and discussed in this review. Based on plasma concentration profiles it can be concluded that low molecular weight constituents of the extract, such as catechin, caffeic and ferulic acid, taxifolin are readily absorbed from the small intestine into systemic circulation. Procyanidin oligomers and polymers are subjected to gut microbial degradation in the large intestine yielding small bioavailable metabolites such as 5-(3',4'-dihydroxyphenyl)-γ-valerolactone. After intake of Pycnogenol®, constituents and metabolites have been also detected in blood cells, synovial fluid and saliva indicating a substantial distribution in compartments other than serum. In studies simultaneously investigating concentrations in different specimen, a preferential distribution of individual compounds has been observed, e.g., of ferulic acid and 5-(3',4'-dihydroxyphenyl)-γ-valerolactone into synovial fluid compared to serum. The main route of elimination of constituents and metabolites of the French pine bark extract is the renal excretion. The broad knowledge accumulated regarding the pharmacokinetics of compounds and metabolites of Pycnogenol® constitute a rational basis for effects characterized on a cellular level and observed in human clinical studies.

Structure of the type 38 Streptococcus pneumoniae capsular polysaccharide

Streptococcus pneumoniae is one of the globally important encapsulated human pathogens and more than 100 different serotypes have been identified. Despite very extensive genetic and immune-serological studies, the capsular polysaccharide repeating unit structure of several serotypes has not been determined yet, including the type 38 (type 38 in Danish nomenclature; type 71 in US nomenclature). Physicochemical data revealed that type 38 polysaccharide is composed of a pentasaccharide repeat unit →3)-[β-D-Galf(1→2)]-β-D-GalpA6(L-Ser)-(1→3)-α-D-GlcpNAc-(1→3)-α-D-Sugp-(1→4)-α-D-Galp(2OAc)-(1→. The polysaccharide is O-acetylated at position C2 of the α-Gal residue at approximately (68-87%) of the repeat units.