Objective To evaluate the relation between intake of ultra-processed food and risk of inflammatory bowel disease (IBD). Design Prospective cohort study. Setting 21 low, middle, and high income countries across seven geographical regions (Europe and North America, South America, Africa, Middle East, south Asia, South East Asia, and China). Participants 116 087 adults aged 35-70 years with at least one cycle of follow-up and complete baseline food frequency questionnaire (FFQ) data (country specific validated FFQs were used to document baseline dietary intake). Participants were followed prospectively at least every three years. Main outcome measures The main outcome was development of IBD, including Crohn’s disease or ulcerative colitis. Associations between ultra-processed food intake and risk of IBD were assessed using Cox proportional hazard multivariable models. Results are presented as hazard ratios with 95% confidence intervals. Results Participants were enrolled in the study between 2003 and 2016. During the median follow-up of 9.7 years (interquartile range 8.9-11.2 years), 467 participants developed incident IBD (90 with Crohn’s disease and 377 with ulcerative colitis). After adjustment for potential confounding factors, higher intake of ultra-processed food was associated with a higher risk of incident IBD (hazard ratio 1.82, 95% confidence interval 1.22 to 2.72 for ≥5 servings/day and 1.67, 1.18 to 2.37 for 1-4 servings/day compared with <1 serving/day, P=0.006 for trend). Different subgroups of ultra-processed food, including soft drinks, refined sweetened foods, salty snacks, and processed meat, each were associated with higher hazard ratios for IBD. Results were consistent for Crohn’s disease and ulcerative colitis with low heterogeneity. Intakes of white meat, red meat, dairy, starch, and fruit, vegetables, and legumes were not associated with incident IBD. Conclusions Higher intake of ultra-processed food was positively associated with risk of IBD. Further studies are needed to identify the contributory factors within ultra-processed foods. Study registration ClinicalTrials.gov NCT03225586 .

The nuclear receptor retinoid X receptor (RXR) is a ligand-activated transcription factor. To create receptors for a new ligand, a structure-based approach was used to generate a library of Ϸ380,000 mutant RXR genes. To discover functional variants within the library, we used chemical complementation, a method of protein engineering that uses the power of genetic selection. Wild-type RXR has an EC50 of 500 nM for 9-cis retinoic acid (9cRA) and an EC50 of >10 M for the synthetic retinoid-like compound LG335 in yeast. T he human retinoid X receptor ␣ (RXR) is a ligand-activated transcription factor of the nuclear receptor superfamily. RXR plays an important role in morphogenesis and differentiation and serves as a dimerization partner for other nuclear receptors (1). Like most nuclear receptors, RXR has two structural domains, the DNA-binding domain (DBD) and the ligand-binding domain (LBD), which are connected by a flexible hinge region. The DBD contains two zinc modules, which bind a sequence of six bases (2). The LBD binds and activates transcription in response to multiple ligands including phytanic acid, docosahexaenoic acid and 9-cis retinoic acid (9cRA) (Fig. 5, which is published as supporting information on the PNAS web site) (3-6). RXR is a modular protein; the DBD and LBD function independently. Therefore, the LBD can be fused to other DBDs and retain function. A conformational change is induced in the LBD upon ligand-binding, which initiates recruitment of coactivators and the basal transcription machinery resulting in transcription of the target gene (7).Nuclear receptors have evolved to bind and activate transcription in response to a variety of small-molecule ligands. The known ligands for nuclear receptors are chemically diverse and include steroid and thyroid hormones, vitamin D, prostaglandins, fatty acids, leukotrienes, retinoids, antibiotics, and other xenobiotics. Evolutionarily closely related receptors (e.g., thyroid hormone receptor and retinoic acid receptor) bind different ligands, whereas some members of distant subfamilies (e.g., RXR and retinoic acid receptor) bind the same ligand (8). This diversity of ligand-receptor interactions demonstrates the versatility of the fold for ligandbinding and suggests that it should be possible to engineer LBDs with a large range of novel specificities.The crystal structure of RXR bound to 9cRA elucidates important hydrophobic and polar interactions in the LBD binding pocket (9). There are 20 hydrophobic and polar amino acids within 4.4 Å of the bound 9cRA (Fig. 6, which is published as supporting information on the PNAS web site). RXR is a good candidate for creating variants that bind different ligands through site-directed mutagenesis, because side-chain atoms, not main-chain atoms, contribute the majority of the ligand contacts (10-13). A library of RXR LBDs with all 20 amino acids at each of the 20 positions in the ligand-binding pocket screened against multiple compounds could potentially produce many new ligand-receptor pairs. However, the numb...

The cytochrome P450 (CYP) 4 family of enzymes contains several recently identified membersthat are referred to as “orphan P450s” because their endogenous substrates are unknown.Human CYP4V2 and CYP4F22 are two such orphan P450s that are strongly linked to ocular andskin disease, respectively. Genetic analyses have identified a wide spectrum of mutations in the CYP4V2gene from patients suffering from Bietti’s crystalline corneoretinal dystrophy, and mutations in theCYP4F22 gene have been linked to lamellar ichthyosis. The strong gene–disease associations provideunique opportunities for elucidating the substrate specificity of these orphan P450s and unraveling thebiochemical pathways that may be impacted in patients with CYP4V2 and CYP4F22 functional deficits.

BackgroundMolecular switch systems that activate gene expression by a small molecule are effective technologies that are widely used in applied biological research. Nuclear receptors are valuable candidates for these regulation systems due to their functional role as ligand activated transcription factors. Previously, our group engineered a variant of the retinoid × receptor to be responsive to the synthetic compound, LG335, but not responsive to its natural ligand, 9-cis-retinoic acid.ResultsThis work focuses on characterizing a molecular switch system that quantitatively controls transgene expression. This system is composed of an orthogonal ligand/nuclear receptor pair, LG335 and GRQCIMFI, along with an artificial promoter controlling expression of a target transgene. GRQCIMFI is composed of the fusion of the DNA binding domain of the yeast transcription factor, Gal4, and a retinoid × receptor variant. The variant consists of the following mutations: Q275C, I310M, and F313I in the ligand binding domain. When introduced into mammalian cell culture, the switch shows luciferase activity at concentrations as low as 100 nM of LG335 with a 6.3 ± 1.7-fold induction ratio. The developed one-component system activates transgene expression when introduced transiently or virally.ConclusionsWe have successfully shown that this system can induce tightly controlled transgene expression and can be used for transient transfections or retroviral transductions in mammalian cell culture. Further characterization is needed for gene therapy applications.