In-depth chemical understanding of complex biological processes hinges upon the ability to systematically perturb individual systems. However, current approaches to study impacts of biologically ...relevant reactive small molecules involve bathing of the entire cell or isolated organelle with excess amounts, leading to off-target effects. The resultant lack of biochemical specificity has plagued our understanding of how biological electrophiles mediate signal transduction or regulate responses that confer defense mechanisms to cellular electrophilic stress. Here we introduce a target-specific electrophile delivery platform that will ultimately pave the way to interrogate effects of reactive electrophiles on specific target proteins in cells. The new methodology is demonstrated by photoinducible targeted delivery of 4-hydroxynonenal (HNE) to the proteins Keap1 and PTEN. Covalent conjugation of the HNE-precursor to HaloTag fused to the target proteins enables directed HNE delivery upon photoactivation. The strategy provides proof of concept of selective delivery of reactive electrophiles to individual electrophile-responsive proteins in mammalian cells. It opens a new avenue enabling more precise determination of the pathophysiological consequences of HNE-induced chemical modifications on specific target proteins in cells.
This Protocol Extension describes the adaptation of an existing Protocol detailing the use of targetable reactive electrophiles and oxidants, an on-demand redox targeting toolset in cultured cells. ...The adaptation described here is for use of reactive electrophiles and oxidants technologies in live zebrafish embryos (Z-REX). Zebrafish embryos expressing a Halo-tagged protein of interest (POI)-either ubiquitously or tissue specifically-are treated with a HaloTag-specific small-molecule probe housing a photocaged reactive electrophile (either natural electrophiles or synthetic electrophilic drug-like fragments). The reactive electrophile is then photouncaged at a user-defined time, enabling proximity-assisted electrophile-modification of the POI. Functional and phenotypic ramifications of POI-specific modification can then be monitored, by coupling to standard downstream assays, such as click chemistry-based POI-labeling and target-occupancy quantification; immunofluorescence or live imaging; RNA-sequencing and real-time quantitative polymerase chain reaction analyses of downstream-transcript modulations. Transient expression of requisite Halo-POI in zebrafish embryos is achieved by messenger RNA injection. Procedures associated with generation of transgenic zebrafish expressing a tissue-specific Halo-POI are also described. The Z-REX experiments can be completed in <1 week using standard techniques. To successfully execute Z-REX, researchers should have basic skills in fish husbandry, imaging and pathway analysis. Experience with protein or proteome manipulation is useful. This Protocol Extension is aimed at helping chemical biologists study precision redox events in a model organism and fish biologists perform redox chemical biology.
ABSTRACT
Predicting the environmental responses of leaf photosynthesis is central to many models of changes in the future global carbon cycle and terrestrial biosphere. The steady‐state biochemical ...model of C3 photosynthesis of Farquhar et al. (Planta 149, 78–90, 1980) provides a basis for these larger scale predictions; but a weakness in the application of the model as currently parameterized is the inability to accurately predict carbon assimilation at the range of temperatures over which significant photosynthesis occurs in the natural environment. The temperature functions used in this model have been based on in vitro measurements made over a limited temperature range and require several assumptions of in vivo conditions. Since photosynthetic rates are often Rubisco‐limited (ribulose, 1‐5 bisphosphate carboxylase/oxygenase) under natural steady‐state conditions, inaccuracies in the functions predicting Rubisco kinetic properties at different temperatures may cause significant error. In this study, transgenic tobacco containing only 10% normal levels of Rubisco were used to measure Rubisco‐limited photosynthesis over a large range of CO2 concentrations. From the responses of the rate of CO2 assimilation at a wide range of temperatures, and CO2 and O2 concentrations, the temperature functions of Rubisco kinetic properties were estimated in vivo. These differed substantially from previously published functions. These new functions were then used to predict photosynthesis in lemon and found to faithfully mimic the observed pattern of temperature response. There was also a close correspondence with published C3 photosynthesis temperature responses. The results represent an improved ability to model leaf photosynthesis over a wide range of temperatures (10–40 °C) necessary for predicting carbon uptake by terrestrial C3 systems.
Borrowing some quotes from Harper Lee's novel “To Kill A Mockingbird” to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that ...function in live organisms and use reactive biotin species for this purpose. We then consider ways to add new dimensions to these experimental regimens, principally by releasing less reactive (i. e., more selective) (preter)natural electrophiles. Although electrophile release methods may have lower resolution and label fewer proteins than biotinylation methods, their ability to probe simultaneously protein function and locale raises new and interesting possibilities for the field.
What Stirs Beneath. Understanding protein–specific interactomes, or localization, is crucial for decoding protein function. New biotinylation methods can do just that even in live organisms. However, these methods have some limitations as they are intrinsically unable to directly probe function. Here new methods that can investigate locale–specific reactivity, are discussed, opening routes to locale–specific perturbation of function.
The nuclear factor erythroid 2‐related factor 2 (Nrf2) signaling axis is a target of covalent drugs and bioactive native electrophiles. However, much of our understanding of Nrf2 regulation has been ...focused at the protein level. Here we report a post‐transcriptional modality to directly regulate Nrf2‐mRNA. Our initial studies focused on the effects of the key mRNA‐binding protein (mRBP) HuR on global transcriptomic changes incurred upon oxidant or electrophile stimulation. These RNA‐sequencing data and subsequent mechanistic analyses led us to discover a novel role of HuR in regulating Nrf2 activity, and in the process, we further identified the related mRBP AUF1 as an additional novel Nrf2 regulator. Both mRBPs regulate Nrf2 activity by direct interaction with the Nrf2 transcript. Our data showed that HuR enhances Nrf2‐mRNA maturation and promotes its nuclear export, whereas AUF1 stabilizes Nrf2‐mRNA. Both mRBPs target the 3'‐UTR of Nrf2‐mRNA. Using a Nrf2 activity‐reporter zebrafish strain, we document that this post‐transcriptional control of Nrf2 activity is conserved at the whole‐vertebrate level.—Poganik, J. R., Long, M. J. C., Disare, M. T., Liu, X., Chang, S.‐H., Hla, T., Aye, Y. Post‐transcriptional regulation of Nrf2‐mRNA by the mRNA‐binding proteins HuR and AUF1. FASEB J. 33, 14636‐14652 (2019). www.fasebj.org
Short-range experiments testing the gravitational inverse-square law at the submillimeter scale offer uniquely sensitive probes of Lorentz invariance. A combined analysis of results from the ...short-range gravity experiments HUST-2015, HUST-2011, IU-2012, and IU-2002 permits the first independent measurements of the 14 nonrelativistic coefficients for Lorentz violation in the pure-gravity sector at the level of 10^{-9} m^{2}, improving by an order of magnitude the sensitivity to numerous types of Lorentz violation involving quadratic curvature derivatives and curvature couplings.
Annulus fibrosus (AF) defects from annular tears, herniation, and discectomy procedures are associated with painful conditions and accelerated intervertebral disc (IVD) degeneration. Currently, no ...effective treatments exist to repair AF damage, restore IVD biomechanics and promote tissue regeneration. An injectable fibrin-genipin adhesive hydrogel (Fib-Gen) was evaluated for its performance repairing large AF defects in a bovine caudal IVD model using ex vivo organ culture and biomechanical testing of motion segments, and for its in vivo longevity and biocompatibility in a rat model by subcutaneous implantation. Fib-Gen sealed AF defects, prevented IVD height loss, and remained well-integrated with native AF tissue following approximately 14,000 cycles of compression in 6-day organ culture experiments. Fib-Gen repair also retained high viability of native AF cells near the repair site, reduced nitric oxide released to the media, and showed evidence of AF cell migration into the gel. Biomechanically, Fib-Gen fully restored compressive stiffness to intact levels validating organ culture findings. However, only partial restoration of tensile and torsional stiffness was obtained, suggesting opportunities to enhance this formulation. Subcutaneous implantation results, when compared with the literature, suggested Fib-Gen exhibited similar biocompatibility behaviour to fibrin alone but degraded much more slowly. We conclude that injectable Fib-Gen successfully sealed large AF defects, promoted functional restoration with improved motion segment biomechanics, and served as a biocompatible adhesive biomaterial that had greatly enhanced in vivo longevity compared to fibrin. Fib-Gen offers promise for AF repairs that may prevent painful conditions and accelerated degeneration of the IVD, and warrants further material development and evaluation.
The introduction of adjuvant systemic treatment for patients with high-risk melanomas necessitates accurate staging of disease. However, inconsistencies in outcomes exist between disease stages as ...defined by the American Joint Committee on Cancer (8th edition). We aimed to develop a tool to predict patient-specific outcomes in people with melanoma rather than grouping patients according to disease stage.
Patients older than 13 years with confirmed primary melanoma who underwent sentinel lymph node biopsy (SLNB) between Oct 29, 1997, and Nov 11, 2013, at four European melanoma centres (based in Berlin, Germany; Amsterdam and Rotterdam, the Netherlands; and Warsaw, Poland) were included in the development cohort. Potential predictors of recurrence-free and melanoma-specific survival assessed were sex, age, presence of ulceration, primary tumour location, histological subtype, Breslow thickness, sentinel node status, number of sentinel nodes removed, maximum diameter of the largest sentinel node metastasis, and Dewar classification. A prognostic model and nomogram were developed to predict 5-year recurrence-free survival on a continuous scale in patients with stage pT1b or higher melanomas. This model was also calibrated to predict melanoma-specific survival. Model performance was assessed by discrimination (area under the time-dependent receiver operating characteristics curve AUC) and calibration. External validation was done in a cohort of patients with primary melanomas who underwent SLNB between Jan 30, 1997, and Dec 12, 2013, at the Melanoma Institute Australia (Sydney, NSW, Australia).
The development cohort consisted of 4071 patients, of whom 2075 (51%) were female and 1996 (49%) were male. 889 (22%) had sentinel node-positive disease and 3182 (78%) had sentinel node-negative disease. The validation cohort comprised 4822 patients, of whom 1965 (41%) were female and 2857 (59%) were male. 891 (18%) had sentinel node-positive disease and 3931 (82%) had sentinel node-negative disease. Median follow-up was 4·8 years (IQR 2·3–7·8) in the development cohort and 5·0 years (2·2–8·9) in the validation cohort. In the development cohort, 5-year recurrence-free survival was 73·5% (95% CI 72·0–75·1) and 5-year melanoma-specific survival was 86·5% (85·3–87·8). In the validation cohort, the corresponding estimates were 66·1% (64·6–67·7) and 83·3% (82·0–84·6), respectively. The final model contained six prognostic factors: sentinel node status, Breslow thickness, presence of ulceration, age at SLNB, primary tumour location, and maximum diameter of the largest sentinel node metastasis. In the development cohort, for the model's prediction of recurrence-free survival, the AUC was 0·80 (95% CI 0·78–0·81); for prediction of melanoma-specific survival, the AUC was 0·81 (0·79–0·84). External validation showed good calibration for both outcomes, with AUCs of 0·73 (0·71–0·75) and 0·76 (0·74–0·78), respectively.
Our prediction model and nomogram accurately predicted patient-specific risk probabilities for 5-year recurrence-free and melanoma-specific survival. These tools could have important implications for clinical decision making when considering adjuvant treatments in patients with high-risk melanomas.
Erasmus Medical Centre Cancer Institute.
We announce the discovery of a new satellite of the Milky Way in the constellation of Bootes at a distance of 660 kpc. It was found in a systematic search for stellar overdensities in the north ...Galactic cap using Sloan Digital Sky Survey Data Release 5. The color-magnitude diagram shows a well-defined turnoff, red giant branch, and extended horizontal branch. Its absolute magnitude is M sub(v) 6 -5.8 mag, which makes it one of the faintest galaxies known. The half-light radius is 6220 pc. The isodensity contours are elongated and have an irregular shape, suggesting that Boo may be a disrupted dwarf spheroidal galaxy.
Precision measurements of the inverse-square law via experiments on short-range gravity provide sensitive tests of Lorentz symmetry. A combined analysis of data from experiments at the Huazhong ...University of Science and Technology and Indiana University sets simultaneous limits on all 22 coefficients for Lorentz violation correcting the Newton force law as the inverse sixth power of distance. Results are consistent with no effect at the level of 10^{-12} m^{4}.
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