TCR repertoire profiling revealed antigen-driven CD8+ T cell clonal groups shared in synovial fluid of patients with spondyloarthritis.

Spondyloarthritis (SpA) comprises a number of inflammatory rheumatic diseases with overlapping clinical manifestations. Strong association with several HLA-I alleles and T cell infiltration into an inflamed joint suggest involvement of T cells in SpA pathogenesis. In this study, we performed high-throughput T cell repertoire profiling of synovial fluid (SF) and peripheral blood (PB) samples collected from a large cohort of SpA patients. We showed that synovial fluid is enriched with expanded T cell clones that are shared between patients with similar HLA genotypes and persist during recurrent synovitis. Using an algorithm for identification of TCRs involved in immune response we discovered several antigen-driven CD8+ clonal groups associated with risk HLA-B*27 or HLA-B*38 alleles. We further show that these clonal groups were enriched in SF and had higher frequency in PB of SpA patients vs healthy donors, implying their relevance to SpA pathogenesis. Several of the groups were shared among patients with different SpAs that suggests a common immunopathological mechanism of the diseases. In summary, our results provide evidence for the role of specific CD8+ T cell clones in pathogenesis of SpA.

Illuminating the dark conformational space of macrocycles using dominant rotors.

Three-dimensional conformation is the primary determinant of molecular properties. The thermal energy available at room temperature typically equilibrates the accessible conformational states. Here, we introduce a method for isolating unique and previously understudied conformations of macrocycles. The observation of unusual conformations of 16- to 22-membered rings has been made possible by controlling their interconversion using dominant rotors, which represent tunable atropisomeric constituents with relatively high rotational barriers. Density functional theory and in situ NMR measurements suggest that dominant rotor candidates for the amino-acid-based structures considered here should possess a rotational energy barrier of at least 25 kcal mol-1. Notable differences in the geometries of the macrocycle conformations were identified by NMR spectroscopy and X-ray crystallography. There is evidence that amino acid residues can be forced into rare turn motifs not observed in the corresponding linear counterparts and homodetic rings. These findings should unlock new avenues for studying the conformation-activity relationships of bioactive molecules.

Air Stable Iridium Catalysts for Direct Reductive Amination of Ketones.

Half-sandwich iridium complexes bearing bidentate urea-phosphorus ligands were found to catalyze the direct reductive amination of aromatic and aliphatic ketones under mild conditions at 0.5 mol % loading with high selectivity towards primary amines. One of the complexes was found to be active in both the Leuckart-Wallach (NH4 CO2 H) type reaction as well as in the hydrogenative (H2 /NH4 AcO) reductive amination. The protocol with ammonium formate does not require an inert atmosphere, dry solvents, as well as additives and in contrast to previous reports takes place in hexafluoroisopropanol (HFIP) instead of methanol. Applying NH4 CO2 D or D2 resulted in a high degree of deuterium incorporation into the primary amine α-position.

Solution processable metal-organic frameworks for mixed matrix membranes using porous liquids.

The combination of well-defined molecular cavities and chemical functionality makes crystalline porous solids attractive for a great number of technological applications, from catalysis to gas separation. However, in contrast to other widely applied synthetic solids such as polymers, the lack of processability of crystalline extended solids hampers their application. In this work, we demonstrate that metal-organic frameworks, a type of highly crystalline porous solid, can be made solution processable via outer surface functionalization using N-heterocyclic carbene ligands. Selective outer surface functionalization of relatively large nanoparticles (250 nm) of the well-known zeolitic imidazolate framework ZIF-67 allows for the stabilization of processable dispersions exhibiting permanent porosity. The resulting type III porous liquids can either be directly deployed as liquid adsorbents or be co-processed with state-of-the-art polymers to yield highly loaded mixed matrix membranes with excellent mechanical properties and an outstanding performance in the challenging separation of propylene from propane. We anticipate that this approach can be extended to other metal-organic frameworks and other applications.

Boramidine: A Versatile Structural Motif for the Design of Fluorescent Heterocycles.

Sodium cyanoborohydride-derived N-alkylnitriliumboranes were found to be versatile precursors for the synthesis of novel boron-containing heterocycles. The reaction between N-alkylnitriliumboranes and 2-aminopyridines, imidazoles, oxazoles, or isoxazoles leads to the incorporation of the [B-C] motif into a five-membered boramidine, which exists as a mixture of Z and E isomers. The resulting heterocycles are blue fluorescent in both the solid state and in solution with ca. 2700-8400 cm-1 Stokes shifts and quantum yields in the 65-74% range in water and in the 42-84% range in organic solvents. The combination of photophysical properties, structural tunability, stability, and solubility in various media is expected to find application in a range of disciplines.

Surface NKG2C Identifies Differentiated αßT-Cell Clones Expanded in Peripheral Blood.

T cells that express CD56 in peripheral blood of healthy humans represent a heterogeneous and poorly studied subset. In this work, we analyzed this subset for NKG2C expression. In both CD56+ and CD56- subsets most of the NKG2C+ T cells had a phenotype of highly differentiated CD8+ TEMRA cells. The CD56+NKG2C+ T cells also expressed a number of NK cell receptors, such as NKG2D, CD16, KIR2DL2/DL3, and maturation marker CD57 more often than the CD56-NKG2C+CD3+ cells. TCR ß-chain repertoire of the CD3+CD56+NKG2C+ cell fraction was limited by the prevalence of one or several clonotypes which can be found within the most abundant clonotypes in total or CD8+ T cell fraction TCRß repertoire. Thus, NKG2C expression in highly differentiated CD56+ T cells was associated with the most expanded αß T cell clones. NKG2C+ T cells produced almost no IFN-γ in response to stimulation with HCMV pp65-derived peptides. This may be partially due to the high content of CD45RA+CD57+ cells in the fraction. CD3+NKG2C+ cells showed signs of activation, and the frequency of this T-cell subset in HCMV-positive individuals was positively correlated with the frequency of NKG2C+ NK cells that may imply a coordinated in a certain extent development of the NKG2C+ T and NK cell subsets under HCMV infection.

Asymmetric Hydroboration of Heteroaryl Ketones by Aluminum Catalysis.

A series of methyl aluminum complexes bearing chiral biphenol-type ligands were found to be highly active catalysts in the asymmetric reduction of heterocyclic ketones (S/C = 100-500, ee up to 99%). The protocol is suitable for a wide range of substrates and has a high tolerance to functional groups. The formed 2-heterocyclic-alcohols are valuable building blocks in drug discovery or can be used as ligands in asymmetric catalysis. Isolation and comprehensive characterization of the reaction intermediates support a catalysis cycle proposed by DFT calculations.

Sustainable Manganese-Catalyzed Solvent-Free Synthesis of Pyrroles from 1,4-Diols and Primary Amines.

A general and selective metal-catalyzed conversion of biomass-derived primary diols and amines to the highly valuable 2,5-unsubstituted pyrroles has been developed. The reaction is catalyzed by a stable nonprecious manganese complex (1 mol %) in the absence of organic solvents whereby water and molecular hydrogen are the only side products. The manganese catalyst shows unprecedented selectivity, avoiding the formation of pyrrolidines, cyclic imides, and lactones.

Hydrogenation of CO2 -Derived Carbonates and Polycarbonates to Methanol and Diols by Metal-Ligand Cooperative Manganese Catalysis.

The first base-metal-catalysed hydrogenation of CO2 -derived carbonates to alcohols is presented. The reaction proceeds under mild conditions in the presence of a well-defined manganese complex with a loading as low as 0.25 mol %. The non-precious-metal homogenous catalytic system provides an indirect route for the conversion of CO2 into methanol with the co-production of value-added (vicinal) diols in yields of up to 99 %. Experimental and computational studies indicate a metal-ligand cooperative catalysis mechanism.

Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires.

The diversity of T-cell receptors recognizing foreign pathogens is generated through a highly stochastic recombination process, making the independent production of the same sequence rare. Yet unrelated individuals do share receptors, which together constitute a "public" repertoire of abundant clonotypes. The TCR repertoire is initially formed prenatally, when the enzyme inserting random nucleotides is downregulated, producing a limited diversity subset. By statistically analyzing deep sequencing T-cell repertoire data from twins, unrelated individuals of various ages, and cord blood, we show that T-cell clones generated before birth persist and maintain high abundances in adult organisms for decades, slowly decaying with age. Our results suggest that large, low-diversity public clones are created during pre-natal life, and survive over long periods, providing the basis of the public repertoire.

tcR: an R package for T cell receptor repertoire advanced data analysis.

BACKGROUND: The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing. RESULTS: Here we introduce tcR, a new R package, representing a platform for the advanced analysis of T cell receptor repertoires, which includes diversity measures, shared T cell receptor sequences identification, gene usage statistics computation and other widely used methods. The tool has proven its utility in recent research studies. CONCLUSIONS: tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. The stable version can be directly installed from The Comprehensive R Archive Network ( http://cran.r-project.org/mirrors.html ). The source code and development version are available at tcR GitHub ( http://imminfo.github.io/tcr/ ) along with the full documentation and typical usage examples.

[2+2+1] cycloadditions of bis(dialkylamino)acetylenes with SiI2(Idip): syntheses and reactivity studies of unprecedented 2,3,4,5-tetraamino-1 H-siloles.

A novel method for the synthesis of 1H-siloles is presented. It involves a [2+2+1] cycloaddition of the ynediamines R2N-C≡C-NR2 (R = Me, Et) with SiI2(Idip) (Idip = 1,3-bis(2,6-diisopropylphenyl)imidazolin-2-ylidene) to afford the orange-colored, highly water-sensitive 1,1-diiodo-2,3,4,5-tetraamino-1H-siloles SiI2{C4(NR2)4} (1-I: R = Me; 2-I R = Et). Treatment of 2-I with an excess of SiBr4 afforded after I/Br exchange the 1,1-dibromo-1H-silole SiBr2{C4(NEt2)4} (2-Br). The 1H-siloles 1-I, 2-I, and 2-Br were fully characterized and their molecular structures determined by single-crystal X-ray diffraction. The compounds feature a slightly twisted five-membered silacyclopenta-2,4-diene ring and a double/single C-C bond alternation in the diene fragment. Reaction of 2-I with the N-heterocyclic carbene IMe4 (IMe4 = 1,3,4,5-tetramethylimidazolin-2-ylidene) leads, after displacement of the iodide groups, to the unprecedented diiodide salt [Si(IMe4)2{C4(NEt2)4}](I)2 (3), containing a 1H-silole dication with a four-coordinate Si(IV) center. The crystal structure of 3 reveals similar bonding characteristics for the dicationic 1H-silole to those of the neutral 1H-siloles 1-I-2-Br. Two-electron reduction of 3 with C8K affords, after elimination of one IMe4 group, the thermolabile, carbene-stabilized 1-silacyclopentadien-1-ylidene Si{C4(NEt2)4}(IMe4) (4), which was characterized by elemental analysis and (1)H, (13)C{(1)H}, and (29)Si{(1)H} NMR spectroscopies.

Silicon-oxygen double bonds: a stable silanone with a trigonal-planar coordinated silicon center.

SiO in a complex: The first silanone that is stable at room temperature (3) is reported. The two-step synthesis involves carbonylation of the silylidyne complex 1 to give the chromiosilylene 2, followed by oxidation of 2 with N2 O. Silanone 3 features a polar, short SiO bond (1.526(3) Å) to a trigonal-planar-coordinated silicon center and reacts with water to give the dihydroxysilyl complex.

Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms.

The TCR repertoire is a mirror of the human immune system that reflects processes caused by infections, cancer, autoimmunity, and aging. Next generation sequencing (NGS) is becoming a powerful tool for deep TCR profiling; yet, questions abound regarding the methodological approaches for sample preparation and correct data interpretation. Accumulated PCR and sequencing errors along with library preparation bottlenecks and uneven PCR efficiencies lead to information loss, biased quantification, and generation of huge artificial TCR diversity. Here, we compare Illumina, 454, and Ion Torrent platforms for individual TCR profiling, evaluate the rate and character of errors, and propose advanced platform-specific algorithms to correct massive sequencing data. These developments are applicable to a wide variety of next generation sequencing applications. We demonstrate that advanced correction allows the removal of the majority of artificial TCR diversity with concomitant rescue of most of the sequencing information. Thus, this correction enhances the accuracy of clonotype identification and quantification as well as overall TCR diversity measurements.

Normalization of genomic DNA using duplex-specific nuclease.

An application of duplex-specific nuclease (DSN) normalization technology to whole-genome shotgun sequencing of genomes with a large proportion of repetitive DNA is described. The method uses a thermostable DSN from the Kamchatka crab that specifically hydrolyzes dsDNA. In model experiments on human genomic DNA, we demonstrated that DSN normalization of double-stranded DNA formed during C0t analysis is effective against abundant repetitive sequences with high sequence identity, while retaining highly divergent repeats and coding regions at base-line levels. Thus, DSN normalization applied to C0t analysis can be used to eliminate evolutionarily young repetitive elements from genomic DNA before sequencing, and should prove invaluable in studies of large eukaryotic genomes, such as those of higher plants.

A new set of markers for human identification based on 32 polymorphic Alu insertions.

A number of genetic systems for human genetic identification based on short tandem repeats or single nucleotide polymorphisms are widely used for crime detection, kinship studies and in analysis of victims of mass disasters. Here, we have developed a new set of 32 molecular genetic markers for human genetic identification based on polymorphic retroelement insertions. Allele frequencies were determined in a group of 90 unrelated individuals from four genetically distant populations of the Russian Federation. The mean match probability and probability of paternal exclusion, calculated based on population data, were 5.53 x 10(-14) and 99.784%, respectively. The developed system is cheap and easy to use as compared to all previously published methods. The application of fluorescence-based methods for allele discrimination allows to use the human genetic identification set in automatic and high-throughput formats.