Target highlights in CASP13: Experimental target structures through the eyes of their authors

The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.     

Accounting for residual heterogeneity in double-observer sightability models decreases bias in burro abundance estimates

Feral burros (Equus asinus) and horses (E. ferus caballus) inhabiting public land in the western United States are intended to be managed at population levels established to promote a thriving, natural ecological balance. Double-observer sightability (M_DS) models, which use detection records from multiple observers and sighting covariates, perform well for estimating feral horse abundances, but their effectiveness for use in burro populations is less understood. These M_DS models help minimize detection bias, yet bias can be further reduced with models that account for unmodeled variation, or residual heterogeneity, in detection probability. In populations containing radio-marked individuals, residual heterogeneity can be estimated with M_DS models by including a covariate that corresponds to the marked status of a group (M_H models). Another approach is to use information from detections missed by both observers to account for the characteristics that make groups more or less likely to be detected, or recaptured, by the second observer (M_R models). We used aerial survey data from 3 burro populations (Sinbad Herd Management Area, UT [2016–2018], Lake Pleasant Herd Management Area, AZ [2017], and Fort Irwin National Training Center, CA [2016–2017]) to develop M_DS models applicable for feral burros in the southwestern United States. Our objectives were to quantify precision and bias of standard M_DS surveys for feral burros and to examine which model type for incorporating residual heterogeneity (M_H or M_R) would result in the least-biased estimates of burro populations relative to the minimum number known alive (MNKA) within the Sinbad Herd Management Area. Standard M_DS model estimates achieved a mean coefficient of variation of 0.08, while underestimating MNKA by an average of 27.1%. Accounting for residual heterogeneity through recapture probability in M_R models resulted in estimates closer to MNKA than M_H models (9.5% vs. 16.5% less than MNKA). Our results indicate that M_DS models can achieve precise enough estimates to monitor feral burro populations, but they routinely produce negatively biased estimates. We encourage the use of radio-collars to reduce bias in future burro surveys by accounting for residual heterogeneity through M_R models.     

Label-free continuous enzyme assays with macrocycle-fluorescent dye complexes

We introduce a new economic, convenient and general assay principle based on the reversible interaction of water-soluble macrocycles and fluorescent dyes. We show that amino acid decarboxylase activity can be continuously monitored by measuring changes in fluorescence, which result from the competition of the enzymatic product and the dye for forming a complex with a cucurbituril or calixarene macrocycle. The new assay provides a complementary method to the use of antibodies, radioactive markers and labeled substrates.     

ICOS Mediates the Generation and Function of CD4+CD25+Foxp3+ Regulatory T Cells Conveying Respiratory Tolerance

Costimulatory molecules like ICOS are crucial in mediating T cell differentiation and function after allergen contact and thereby strongly affect the immunologic decision between tolerance or allergy development. In this study, we show in two independent approaches that interruption of the ICOS signaling pathway by application of a blocking anti-ICOSL mAb in wild-type (WT) mice and in ICOS(-/-) mice inhibited respiratory tolerance development leading to eosinophilic airway inflammation, mucus hypersecretion, and Th2 cytokine production in response to OVA sensitization. Respiratory Ag application almost doubled the number of CD4(+)Foxp3(+) regulatory T cells (Tregs) in the lung of WT mice with 77% of lung-derived Tregs expressing ICOS. In contrast, in ICOS(-/-) mice the number of CD4(+)CD25(+)Foxp3(+) Tregs did not increase after respiratory Ag application, and ICOS(-/-) Tregs produced significantly lower amounts of IL-10 than those of WT Tregs. Most importantly, in contrast to WT Tregs, ICOS(-/-) Tregs did not convey protection when transferred to "asthmatic" recipients demonstrating a strongly impaired Treg function in the absence of ICOS signaling. Our findings demonstrate a crucial role of ICOS for the generation and suppressive function of Tregs conveying respiratory tolerance and support the importance of ICOS as a target for primary prevention strategies.     

Synthesis of α-trifluoromethyl α-amino acids with aromatic, heteroaromatic and ferrocenyl subunits in the side chain

Summary. 5-Benzyloxy-4-trifluoromethyl-1,3-oxazoles, obtained from 5-fluoro-4-trifluoromethyloxazoles and benzyl alcohols, are capable for rearrangements. A 1,3 shift of a benzyl group is the key step of a new general route toward α-trifluoromethyl substituted aromatic and heteroaromatic amino acids, demonstrating that 5-fluoro-4-trifluoromethyl-1,3-oxazole is a synthetic Tfm-Gly equivalent. On reaction with benzpinacol partially fluorinated oxazoles are transformed into bis(trifluoromethyl) substituted 2,5-diamino adipic acid and N-benzoyl-2-benzhydryl-3,3,3-trifluoroalanine.     

Role of polyisoprenoids in tobacco resistance against biotic stresses

Infection with avirulent pathogens, tobacco mosaic virus (TMV) or Pseudomonas syringae pv. tabaci induced accumulation of polyisoprenoid alcohols, solanesol and a family of polyprenols [from polyprenol composed of 14 isoprene units (Pren-14) to -18, with Pren-16 dominating] in the leaves of resistant tobacco plants Nicotiana tabacum cv. Samsun NN. Upon TMV infection, solanesol content was increased seven- and eight-fold in the inoculated and upper leaves, respectively, while polyprenol content was increased 2.5- and 2-fold in the inoculated and upper leaves, respectively, on the seventh day post-infection. Accumulation of polyisoprenoid alcohols was also stimulated by exogenously applied hydrogen peroxide but not by exogenous salicylic acid (SA). On the contrary, neither inoculation of the leaves of susceptible tobacco plants nor wounding of tobacco leaves caused an increase in polyisoprenoid content. Taken together, these results indicate that polyisoprenoid alcohols might be involved in plant resistance against pathogens. A putative role of accumulated polyisoprenoids in plant response to pathogen attack is discussed. Similarly, the content of plastoquinone (PQ) was increased two-fold in TMV-inoculated and upper leaves of resistant plants. Accumulation of PQ was also stimulated by hydrogen peroxide, bacteria ( P.  syringae ) and SA. The role of PQ in antioxidant defense in cellular membranous compartments is discussed in the context of the enzymatic antioxidant machinery activated in tobacco leaves subjected to viral infection. Elevated activity of several antioxidant enzymes (ascorbate peroxidase, guaiacol peroxidase, glutathione reductase and superoxide dismutase, especially the CuZn superoxide dismutase isoform) and high, but transient elevation of catalase was found in inoculated leaves of resistant tobacco plants but not in susceptible plants.