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Human recombination-activating gene (RAG) deficiency can manifest with distinct clinical and immunological phenotypes. By applying a multiomics approach to a large group of RAG -mutated patients, we aimed at characterizing the immunopathology associated with each phenotype. Although defective T and B cell development is common to all phenotypes, patients with hypomorphic RAG variants can generate T and B cells with signatures of immune dysregulation and produce autoantibodies to a broad range of self-antigens, including type I interferons. T helper 2 (T H 2) cell skewing and a prominent inflammatory signature characterize Omenn syndrome, whereas more hypomorphic forms of RAG deficiency are associated with a type 1 immune profile both in blood and tissues. We used cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) analysis to define the cell lineage-specific contribution to the immunopathology of the distinct RAG phenotypes. These insights may help improve the diagnosis and clinical management of the various forms of the disease.

Background: Heterozygous immunoproteasome subunit beta-type 10 (PSMB10) mutations can cause severe combined immunodeficiency (SCID) and Omenn syndrome (OS). Hematopoietic stem cell transplantation in these patients is associated with severe complications and poor immune reconstitution, often resulting in death., Objective: To perform immunological and molecular characterization of an infant with a PSMB10 heterozygous variant., Methods: A heterozygous variant in PSMB10 (p.G201R) was identified in the index but not her parents. Detailed immunophenotyping and functional studies, including flow cytometry, immunoblotting, and T-cell development in artificial thymic organoids (ATO), were performed., Results: The patient presented with severe B-, NK-, as well as T-cell lymphopenia, with a progressive increase in memory CD4+ and loss of CD8+ T-cells, diminished Vbeta family diversity, and abnormal IL-7 signaling. Immunoproteasome protein expression (PSMB10 and 9) was markedly reduced in the patient's cells, including PBMCs, EBV-transformed B cells, and fibroblasts, the mutation likely acting in a dominant negative fashion. Patient CD34+ cells showed a normal early T-cell development but slightly impaired generation of CD3+TCRαβ+ cells in ATO, and human thymus single cell RNA sequencing demonstrated that PSMB10 is expressed in different subsets of cortical and medullary thymic epithelial cells. Collectively, these data indicate that PSMB10 mutations affect positive selection of CD8 T-cells, generation of a diverse T-cell repertoire, and negative selection of autoreactive T-cells., Conclusion: The PSMB10 G201R variant is associated with reduced immunoproteasome expression levels that appear to play vital roles in hematopoietic and extra-hematopoietic immune system development and function. PSMB10-associated thymoproteasome dysfunction leads to impaired thymopoiesis and the development of SCID and OS, suggesting possible benefit from thymus implantation., (Copyright © 2024. Published by Elsevier Inc.)

We report in this article the cytotoxicity of Streptomyces sp. SS1-1 against the human lung cancer A549 cell line, its draft genome sequence and a total of 20 predicted secondary metabolite biosynthetic gene clusters. Streptomyces sp. SS1-1 was an endophytic bacterial strain isolated from the plant Catharanthus roseus in Ho Chi Minh City, Vietnam. When cultured in the PY medium, this strain shows a cytotoxic effect on the A549 cell line. The draft genome of Streptomyces sp. SS1-1 has four contigs of total 7,815,656 bp and the GC content of this genome is 72.2%. AntiSMASH analysis reveals 20 putative biosynthetic gene clusters for the largest contig. The genome sequencing of Streptomyces sp. SS1-1 is essential for the molecular identification of gene cluster(s) responsible for secondary metabolite(s) with cytotoxic activity., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 The Author(s).)

We report here the biosynthesis of daidzein in Streptomyces sp. SS52, its genome sequence and the analysis of its genome for finding putative genes involved in daidzein biosynthesis. The Streptomyces sp. SS52 strain was isolated from the plant Phyllanthus urinaria in Tra Vinh province, Vietnam. This endophytic strain is capable of producing the isoflavone daidzein in the culture medium. Streptomyces sp. SS52 possesses a linear genome of 8,184,045 bp and the GC content of this genome is 72.5%. The preliminary genome analysis identified homologs of genes involved in the de novo biosynthesis of daidzein in the genome of Streptomyces sp. SS52. The genome sequencing of Streptomyces sp. SS52 was essential for the study of the biosynthesis of daidzein in Streptomyces bacteria., (© 2019 The Author(s).)

Microbubbles in combination with ultrasound provide a new and promising way to deliver drugs into living cells. It is believed that the stable vibration or the collapse of the bubbles under ultrasound are the two main mechanisms that induce the formation of pores in the cell membranes, through which drugs may get inside the cell cytoplasm. The bubble collapse hypothesis is not only intuitive since released shock waves can easily penetrate and create pores in the membrane, but it is also confirmed by both experiment and theory. In contrast, the molecular mechanism of stable vibration is not well-understood because of experimental difficulties resulting from the fragility of bubbles and the lack of molecular dynamics simulation studies. To obtain a better understanding of this mechanism, we developed a lipid-coated bubble model that we applied to simulate the stable cavitation of the bubble in the presence of a lipid bilayer. We show that the wall shear stress generated by the bubble vibration does not induce the membrane pore formation. Instead, the bubble fuses with the membrane and subsequent cavitation pulls lipid molecules out of the membrane, creating pores. This could help one to choose the best combination of the bubble shell materials, the ultrasound frequency, and intensity, so that the opening and closing of pores will be optimized.

The enantiomers of a variety of N-alkyl-, N-aralkyl-, and N-cyclopropylalkyl-9β-hydroxy-5-(3-hydroxyphenyl)morphans were synthesized employing cyanogen bromide and K 2 CO 3 to improve the original N-demethylation procedure. Their binding affinity to the μ-, δ-, and κ-opioid receptors (ORs) was determined and functional (GTP γ 35 S) assays were carried out on those with reasonable affinity. The 1R,5R,9S-enantiomers (1R,5R,9S)-(-)-5-(3-hydroxyphenyl)-2-(4-nitrophenethyl)-2-azabicyclo[3.3.1]nonan-9-ol (1R,5R,9S-16), (1R,5R,9S)-(-) 2-cinnamyl-5-(3-hydroxyphenyl)-2-azabicyclo[3.3.1]nonan-9-ol (1R,5R,9S-20), and (1R,5R,9S)-(-)-5-(3-hydroxyphenyl)-2-(4-(trifluoromethyl)phenethyl)-2-azabicyclo[3.3.1]nonan-9-ol (1R,5R,9S-15), had high affinity for the μ-opioid receptor (e.g., 1R,5R,9S-16: Ki=0.073, 0.74, and 1.99nM, respectively). The 1R,5R,9S-16 and 1R,5R,9S-15 were full, high efficacy μ-agonists (EC 50 =0.74 and 18.5nM, respectively) and the former was found to be a partial agonist at δ-OR and an antagonist at κ-OR, while the latter was a partial agonist at δ-OR and κ-OR in the GTP γ 35 S assay. The enantiomer of 1R,5R,9S-16, (+)-1S,5S,9R-16 was unusual, it had good affinity for the μ-OR (Ki=26.5nM) and was an efficacious μ-antagonist (Ke=29.1nM). Molecular dynamics simulations of the μ-OR were carried out with the 1R,5R,9S-16 μ-agonist and the previously synthesized (1R,5R,9S)-(-)-5-(9-hydroxy-5-(3-hydroxyphenyl-2-phenylethyl)-2-azabicyclo[3.3.1]nonane (1R,5R,9S-(-)-NIH 11289) to provide a structural basis for the observed high affinities and efficacies. The critical roles of both the 9β-OH and the p-nitro group are elucidated, with the latter forming direct, persistent hydrogen bonds with residues deep in the binding cavity, and the former interacting with specific residues via highly structured water bridges., (Published by Elsevier Ltd.)

Formation of intracellular plaques and small oligomeric species of amyloid β (Aβ) peptides inside neurons is a hallmark of Alzheimer's disease. The most abundant Aβ species in the brain are Aβ1-40 and Aβ1-42, which are composed, respectively, of 40 and 42 residues. Aβ1-42 differs from Aβ1-40 only in two residues, Ile41 and Ala42, yet it shows remarkably faster aggregation and greater neurotoxicity than Aβ1-40. Thus, it is crucial to understand the relative contributions of Ile41 and Ala42 to these distinct behaviors. To achieve this, secondary structures of the Aβ1-41 monomer, which contribute to aggregation propensity, were studied by all-atom molecular dynamics simulation in an implicit solvent and compared to those of Aβ1-40 and Aβ1-42. We find that the secondary structure populations of Aβ1-41 are much closer to those of Aβ1-40 than to those of Aβ1-42, suggesting that Aβ1-41 and Aβ1-40 are likely to have similar aggregation properties. This prediction was confirmed through a thioflavin-T aggregation assay. Thus, our finding indicates that the hydrophobic residue at position 42 is the major contributor to the increased fibril formation rates and consequently neurotoxicity of Aβ peptides.

Self-assembled functional peptide biomaterials are emerging with a wide range of envisioned applications in the field of nanotechnology. Currently, methods and tools have been developed to control and manipulate as well as to explore new properties of self-assembled structures. However, considerably fewer studies are being devoted to developing efficient methods to degrade or recycle such extremely stable biomaterials. With this in mind, here we suggest a theoretical framework, inspired by the recent developed mid-infrared free-electron laser pulse technology, to dissociate peptide nanotubes. Adopting a diphenylalanine channel as a prototypical example, we find that the primary step in the dissociation process occurs due to the strong resonance between the carboxylate bond vibrations of the diphenylalanine peptides and the tuned laser frequencies. The effects of laser irradiation are determined by a balance between tube formation and dissociation. Our work shows a proof of concept and should provide a motivation for future experimental developments with the final aim to open a new and efficient way to cleave or to recycle bio-inspired materials.

Recent experiments have shown that the Taiwan mutation (D7H) slows the fibril formation of amyloid peptides Aβ40 and Aβ42. Motivated by this finding, we have studied the influence of D7H mutation on structures of Aβ peptide monomers using the replica exchange molecular dynamics simulations with OPLS force field and implicit water model. Our study reveals that the mechanism behind modulation of aggregation rates is associated with decrease of β-content and dynamics of the salt bridge D23-K28. Estimating the bending free energy of this salt bridge, we have found that, in agreement with the experiments, the fibril formation rate of both peptides Aβ40 and Aβ42 is reduced about two times by mutation.

Carbonyl-ene reactions of 2,3-diketoesters catalyzed by [Cu{(S,S)-tBu-box}](SbF6)2 [box=bis(oxazoline)] generate chiral α-functionalized α-hydroxy-β-ketoesters in up to 94% yield and 97% ee. The 2,3-diketoesters are conveniently accessed from the corresponding α-diazo-β-ketoester, and a catalyst loading as low as 1.0 mol% can be achieved., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The synthesis of α-carbonylimines by rhodium(II)-catalyzed reactions of α-diazoesters and organic azides has been developed and applied in hetero-Diels-Alder reactions to form highly functionalized tetrahydropyrimidines and in a one-pot, multicomponent transformation between aryldiazoacetates, p-anisyl azide, and an enonediazoacetate to produce β-lactams in high yields and diastereoselectivities.

Regio- and diastereoselective Lewis acid catalyzed cycloaddition reactions between imines and donor-acceptor cyclopropenes generated from silyl-protected enoldiazoacetates provide direct access to stable cyclopropane-fused tetrahydroquinolines and, with cyclopropane ring opening under mild conditions, to 1H-benzazipine derivatives.