Type I interferon as a biomarker in autoimmunity and viral infection: a leukocyte subset-specific analysis unveils hidden diagnostic options

Abstract

Interferon alpha and its surrogates, including IP-10 and SIGLEC1, paralleled changes of disease activity in systemic lupus erythematosus (SLE). However, the whole blood interferon signature (WBIFNS)—the current standard for type I IFN assessment in SLE—does not correlate with SLE disease activity in individual patients over time. The underlying causes for this apparent contradiction have not been convincingly demonstrated. Using a multicenter dataset of gene expression data from leukocyte subsets in SLE, we identify distinctive subset-specific contributions to the WBIFNS. In a subsequent analysis, the effects of type I interferon on cellular blood composition in patients with SLE and hepatitis B were also studied over time. We found that type I interferon mediates significant alterations in whole blood composition, including a neutropenia and relative lymphocytosis. Given different effects of type 1 interferon on different leukocyte subsets, these shifts confound measurement of a type 1 interferon signature in whole blood. To minimize and overcome these limitations of the WBIFNS, we suggest to measure IFN-induced transcripts or proteins in a specific leukocyte subset to improve clinical impact of interferon biomarkers.

Key messages

• Myeloid cells contribute more to the WBIFNS in SLE than their lymphocytic counterpart.

• Very similar leukocyte subsets reveal distinctive IFN signatures.

• IFN alpha mixes up composition of blood and leads to a preferential neutropenia, yielding relative lymphocytosis.

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Identification and characterization of a biosynthetic gene cluster for tryptophan dimers in deep sea-derived Streptomyces sp. SCSIO 03032

Abstract

Tryptophan dimers (TDs) are an important class of natural products with diverse bioactivities and share conserved biosynthetic pathways. We report the identification of a partial gene cluster (spm) responsible for the biosynthesis of a class of unusual TDs with non-planar skeletons including spiroindimicins (SPMs), indimicins (IDMs), and lynamicins (LNMs) from the deep-sea derived Streptomyces sp. SCSIO 03032. Bioinformatics analysis, targeted gene disruptions, and heterologous expression studies confirmed the involvement of the spm gene cluster in the biosynthesis of SPM/IDM/LNMs, and revealed the indispensable roles for the halogenase/reductase pair SpmHF, the amino acid oxidase SpmO, and the chromopyrrolic acid (CPA) synthase SpmD, as well as the positive regulator SpmR and the putative transporter SpmA. However, the spm gene cluster was unable to confer a heterologous host the ability to produce SPM/IDM/LNMs. In addition, the P450 enzyme SpmP and the monooxygenase SpmX2 were found to be non-relevant to the biosynthesis of SPM/IDM/LNMs. Sequence alignment and structure modeling suggested the lack of key conserved amino acid residues in the substrate-binding pocket of SpmP. Furthermore, feeding experiments in the non-producing ΔspmO mutant revealed several biosynthetic precursors en route to SPMs, indicating that key enzymes responsible for the biosynthesis of SPMs should be encoded by genes outside of the identified spm gene cluster. Finally, the biosynthetic pathways of SPM/IDM/LNMs are proposed to lay a basis for further insights into their intriguing biosynthetic machinery.

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Over-the-counter medications containing diphenhydramine and doxylamine used by older adults to improve sleep, a Letter

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Effects of Pt content on the crystallinity and optical properties of Ag/Pt nanoboxes: from solid to single and polycrystalline mesoporous nanostructures

Abstract

Synthetic methods to obtain hollow-like systems based on galvanic reaction are of wide importance due to the simplicity and efficiency of the method, yet due to fast and spontaneous reduction, the reaction for platinum-based structures is usually not well controlled. Systematic studies over the evolution of the galvanization process are still important in order to determine key feature on the structural transformation. On this paper, electron microscopy techniques were used to correlate the crystallinity of Ag/Pt nanoboxes of 78 nm in size with low and high-index facets surfaces from Ag nanocubes template. It was observed that 1.6 μmol addition of platinum precursor is enough to produce Ag/Pt nanoboxes. However, the crystallinity of the walls was tune from single crystal to polycrystalline by increasing the amount of platinum. More importantly, electron tomography reconstructions allow us to identify the concavities sides on the polycrystalline double-layer porous sample. Platinum content and nanostructure has been also associated to the optical properties were an extinction of the absorption band is observed after the solid template has been fully transformed to a nanobox. The final Ag/Pt porous/hollow nanoboxes with concave sides were tested on a model reaction for the reduction of 4-ntp to 4-amp.

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Triangular CdS nanostructure: effect of Mn doping on photoluminescence, electron spin resonance, and magneto-optical properties

Abstract

In this paper, we report synthesis and study of magneto-optic Faraday effect for dilute magnetic semiconductor nanostructure. The colloidal CdS nanocrystals were prepared via hot injection method and successfully doped with Mn²⁺ cations. The synthesized nanoparticles were characterized by using UV–Vis spectroscopy, X-ray diffraction, photoluminescence spectroscopy, transmission electron microscopy, and electron spin resonance spectroscopy. Systematic studies on effect of Mn²⁺ doping on photoluminescence, electron spin resonance, and magneto-optical properties are carried out. UV–Vis spectral analysis confirms blue shift in bandgap of CdS nanoparticles due to quantum confinement effect. The X-ray diffraction study confirms hexagonal wurtzite phase formation of CdS nanoparticles without any impurity phases. TEM analysis confirms uniform particle size, having particle size distribution around 5 nm. As-synthesized undoped CdS shows triangular-shaped nanocrystals with hexagonal structure; however, triangular shape of CdS nanoparticles is not conserved after Mn²⁺ doping. The photoluminescence characteristic spectra of Mn²⁺-doped CdS nanocrystals showed emission band at 660 nm and its intensity was found to increase with increasing Mn²⁺ concentration. Electron spin resonance signal, with six-line hyperfine structure splitting, confirmed doping of Mn²⁺ ions in CdS lattice. Magneto-optic measurements showed linear variation of Faraday rotation with respect to applied magnetic field, indicating paramagnetic behavior of Mn-doped CdS. The highest Verdet constant 24.81 deg/T cm was observed for 2% Mn-doped CdS nanocrystals, which further decreases with increasing Mn²⁺ concentration.

Graphical abstract

Illustration of Magneto-optic Faraday effect using dilute magnetic semiconductors (TEM image of triangular CdS nanoparticles)

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Proteomic Analysis Revealed the Fruiting-Body Protein Profile of Auricularia polytricha

Abstract

Auricularia polytricha is one of the most widely cultivated edible mushrooms in China. Many advances have been made to A. polytricha, but there is still no proteomic information of this species. Our current understanding was based upon the translated information of its transcriptome or other relative species. This study presented the proteomic information of fruiting-body proteins by shotgun liquid chromatography and tandem mass spectrometry (LC–MS/MS), which identified 15,508 peptides corresponding to 1850 high-confidence proteins. Of these, 1383 were annotated across the GO subcategories with 829 (44.81%) involved in biological process, 908 (49.08%) in molecular function, and 406 (21.95%) in cellular components. Among these high-confidence proteins, 132 proteins were annotated as carbohydrate-active enzymes, of which 51 were secreted enzymes. Moreover, a number of commercially important enzymes were detected, functioning as auxiliary activity (AA) family 5 glyoxal oxidase, AA5 galactose oxidase, glycoside hydrolase (GH) family 20 hexosaminidase, and GH47 alpha-mannosidase. To the best of our knowledge, this is the first study to characterize A. polytricha proteome, and also fills the gap of our knowledge on the under-developed mushroom species.

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Characterization of Inducible ccdB Gene as a Counterselectable Marker in Escherichia coli Recombineering

Abstract

Recombineering is a homologous-based DNA cloning and modification technique. Recombineering-mediated chromosomal gene knock-in usually involves a selectable/counterselectable cassette. Though a variety of selectable/counterselectable cassettes were developed; however, a specifically designed gene deletion strain or minimal medium is often required. Herein, we describe a novel selectable/counterselectable cassette P_lac-ccdB-aacC1 in which aacC1 (gentamicin resistance gene) is used as the selectable marker for the homologous arm-flanked cassette knock-in, while the IPTG inducible ccdB gene is used as the counterselectable marker for chromosomal gene knock-in. The counterselection is achieved via supplementing 1 mM IPTG in the LB agar medium. An oligonucleotide designed to evade the mismatch repair system was utilized to engineer an Escherichia coli DH10B-derived gyrA462 strain that was used to as the host for the plasmid harboring the P_lac-ccdB-aacC1 cassette. By using the P_lac-ccdB-aacC1 cassette, a linear–linear homologous recombination (LLHR) system was generated by knocking a 6.2 kb araC-P_BAD-redγ-recET-recA DNA fragment into the E. coli DH10B chromosome. The functional of the LLHR recombineering system was characterized by cloning of the target DNA from PCR product as well as from the genomic DNA mixture. The P_lac-ccdB-aacC1 cassette will be a useful tool in E. coli recombineering.

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