Cell Type-Specific Induction of Inflammation-Associated Genes in Crohn’s Disease and Colorectal Cancer

Based on the rapid increase in incidence of inflammatory bowel disease (IBD), the identification of susceptibility genes and cell populations contributing to this condition is essential. Previous studies suggested multiple genes associated with the susceptibility of IBD; however, due to the analysis of whole-tissue samples, the contribution of individual cell populations remains widely unresolved. Single-cell RNA sequencing (scRNA-seq) provides the opportunity to identify underlying cellular populations. We determined the enrichment of Crohn’s disease (CD)-induced genes in a publicly available Crohn’s disease scRNA-seq dataset and detected the strongest induction of these genes in innate lymphoid cells (ILC1), highly activated T cells and dendritic cells, pericytes and activated fibroblasts, as well as epithelial cells. Notably, these genes were highly enriched in IBD-associated neoplasia, as well as sporadic colorectal cancer (CRC). Indeed, the same six cell populations displayed an upregulation of CD-induced genes in a CRC scRNA-seq dataset. Finally, after integrating and harmonizing the CD and CRC scRNA-seq data, we demonstrated that these six cell types display a gradual increase in gene expression levels from a healthy state to an inflammatory and tumorous state. Together, we identified cell populations that specifically upregulate CD-induced genes in CD and CRC patients and could, therefore, contribute to inflammation-associated tumor development.     

The ATP-binding site of protein kinase CK2 holds a positive electrostatic area and conserved water molecules

CK2 is a highly pleiotropic Ser/Thr protein kinase that is able to promote cell survival and enhance the tumour phenotype under specific circumstances. We have determined the crystal structure of three new complexes with tetrabromobenzimidazole derivatives that display K(i) values between 0.15 and 0.30 microM. A comparative analysis of these data with those of four other inhibitors of the same family revealed the presence of some highly conserved water molecules in the ATP-binding site. These waters reside near Lys68, in an area with a positive electrostatic potential that is able to attract and orient negatively charged ligands. The presence of this positive region and two unique bulky residues that are typical of CK2, Ile66 and Ile174, play a critical role in determining the ligand orientation and binding selectivity.     

Determination of polyphenolic content and antioxidant activity of kudingcha made from Ilex kudingcha C.J. Tseng

The total polyphenol content and the antioxidant activity of kudingcha made from Ilex kudingcha C.J. Tseng were determined by Folin–Ciocalteu reagent, and DPPH, FRAP, and TEAC methods, respectively. The crude extract (CE) of kudingcha and its four fractions of chloroform (CfF), ethyl acetate (EaF), n-butanol (nBF), and water (WtF) were prepared and subjected to antioxidant evaluation and analysis by high performance liquid chromatography. The extracts of kudingcha contained large amounts of caffeoylquinic acid (CQA) derivatives, including 3-CQA, 5-CQA, 3,4-diCQA, 3,5-diCQA, and 4,5-diCQA, and showed potent antioxidant activity. The antioxidant activities of CE and its fractions decreased in the order of EaF > nBF > CE > WtF > CfF, according to the DPPH assay and FRAP assay, which were the same, with the exception of the rank order of CfF and WtF, as the TEAC assay. Furthermore, a satisfactory correlation between total polyphenol content and antioxidant activity was observed.     

Evaluation of the effect of probiotic cultures added to commercial yogurt over a known population of Listeria monocytogenes and Escherichia coli O157:H7

The effect of probiotic cultures over Listeria monocytogenes and Escherichia coli O157:H7 during yogurt storage was evaluated. Two different yogurt brands, one with additional probiotic cultures (Lactobacillus casei and L. acidophilus) were inoculated with known populations (106 UFC/g) of either L. monocytogenes or E. coli O157:H7 in three different times and stored for 32 days at 5 degrees C. Every four days the count of lactic bacteria, the added pathogens and pH was evaluated, according to the methodology described in the Bacteriological Analytical Manual. The pH and lactic bacteria population were constant during the testing period. Yogurt with additional probiotic cultures reduced the population of L. monocytogenes in 8 days, the population of E. coli O157:H7 in 16; yogurt with no additional probiotics took 20 days to reduce L. monocytogenes to non-detectable levels and even after 28 days of storage, E. coli O157:H7 was cultured. In this work, the beneficial effects of additional probiotic cultures in yogurt is confirmed again.     

New N,O-containing ligands for the biomimetic copper-catalyzed polymerization of 2,6-dimethylphenol

Poly(2,6-dimethyl-1,4-phenylene ether) (PPE), which is widely used in high-performance engineering plastics, is obtained by the copper-catalyzed oxidative coupling of 2,6-dimethylphenol. The oxidative polymerizations have been carried out in acetonitrile with structurally related [copper-(N,O-containing ligand)] complexes as the catalyst precursor compounds, which appeared to be of great interest for a better understanding of the factors influencing the catalytic activities. Steric effects (influence of a methyl group close to the metal center; ligands 4–7) or electronic effects (imino versus amino group; ligands 4, 5, 8 and 6, 7, 9, respectively) on the polymerization rates have been demonstrated. The use of mono- or dinucleating ligands has strengthened the proposed mechanism of the reaction involving dinuclear active species.     

Alteration of the Route to Menaquinone towards Isochorismate-Derived Metabolites

Chorismate and isochorismate constitute branch-point intermediates in the biosynthesis of many aromatic metabolites in microorganisms and plants. To obtain unnatural compounds, we modified the route to menaquinone in Escherichia coli. We propose a model for the binding of isochorismate to the active site of MenD ((1R,2S, 5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxycyclohex-3-ene-1-carboxylate (SEPHCHC) synthase) that explains the outcome of the native reaction with α-ketoglutarate. We have rationally designed variants of MenD for the conversion of several isochorismate analogues. The double-variant Asn117Arg–Leu478Thr preferentially converts (5S,6S)-5,6-dihydroxycyclohexa-1,3-diene-1-carboxylate (2,3-trans-CHD), the hydrolysis product of isochorismate, with a >70-fold higher ratio than that for the wild type. The single-variant Arg107Ile uses (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate (2,3-trans-CHA) as substrate with >6-fold conversion compared to wild-type MenD. The novel compounds have been made accessible in vivo (up to 5.3 g L⁻¹). Unexpectedly, as the identified residues such as Arg107 are highly conserved (>94 %), some of the designed variations can be found in wild-type SEPHCHC synthases from other bacteria (Arg107Lys, 0.3 %). This raises the question for the possible natural occurrence of as yet unexplored branches of the shikimate pathway.     

Synthesis of Long-Chain β-Lactones and Their Antibacterial Activities against Pathogenic Mycobacteria

In the quest for new antibacterial agents, a series of novel long- and medium-chain mono- and disubstituted β-lactones was developed. Their activity against three pathogenic mycobacteria—M. abscessus, M. marinum, and M. tuberculosis—was assessed by the resazurin microtiter assay (REMA). Among the 16 β-lactones synthesized, only 3-hexadecyloxetan-2-one (VM005) exhibited promising activity against M. abscessus, whereas most of the β-lactones showed interesting activities against M. marinum, similar to that of the classical antibiotic, isoniazid. Regarding M. tuberculosis, six compounds were found to be active against this mycobacterium, with β-lactone VM008 [trans-(Z)-3-(hexadec-7-en-1-yl)-4-propyloxetan-2-one] being the best growth inhibitor. The promising antibacterial activities of the best compounds in this series suggest that these molecules may serve as leads for the development of much more efficient antimycobacterial agents.     

Influence of α′‐/α‐crystal polymorphism on properties of poly(l‐lactic acid)

Poly(l ‐lactic acid) (PLLA) is a biodegradable and biocompatible thermoplastic polyester produced from renewable sources, widely used for biomedical devices, in food packaging and in agriculture. It is a semicrystalline polymer, and as such its properties are strongly affected by the developed semicrystalline morphology. As a function of the crystallization temperature, PLLA can form different crystal modifications, namely α′‐crystals below about 120 °C and α‐crystals at higher temperatures. The α′ modification is therefore of special importance as it may be the preferred polymorph developing at processing‐relevant conditions. It is a metastable modification which typically transforms into the more stable α‐crystals on annealing at elevated temperature. The structure, kinetics of formation and thermodynamics of α′‐ and α‐crystals of PLLA are reviewed in this contribution, together with the effect of α′‐/α‐crystal polymorphism on the properties of PLLA. © 2018 Society of Chemical Industry     

lordif: An R Package for Detecting Differential Item Functioning Using Iterative Hybrid Ordinal Logistic Regression/Item Response Theory and Monte Carlo Simulations

Logistic regression provides a flexible framework for detecting various types of differential item functioning (DIF). Previous efforts extended the framework by using item response theory (IRT) based trait scores, and by employing an iterative process using group-specific item parameters to account for DIF in the trait scores, analogous to purification approaches used in other DIF detection frameworks. The current investigation advances the technique by developing a computational platform integrating both statistical and IRT procedures into a single program. Furthermore, a Monte Carlo simulation approach was incorporated to derive empirical criteria for various DIF statistics and effect size measures. For purposes of illustration, the procedure was applied to data from a questionnaire of anxiety symptoms for detecting DIF associated with age from the Patient-Reported Outcomes Measurement Information System.