Synthetic biology approach to reconstituting the ubiquitylation cascade in bacteria

Covalent modification of proteins with ubiquitin (Ub) is widely implicated in the control of protein function and fate. Over 100 deubiquitylating enzymes rapidly reverse this modification, posing challenges to the biochemical and biophysical characterization of ubiquitylated proteins. We circumvented this limitation with a synthetic biology approach of reconstructing the entire eukaryotic Ub cascade in bacteria. Co‐expression of affinity‐tagged substrates and Ub with E1, E2 and E3 enzymes allows efficient purification of ubiquitylated proteins in milligram quantity. Contrary to in‐vitro assays that lead to spurious modification of several lysine residues of Rpn10 (regulatory proteasomal non‐ATPase subunit), the reconstituted system faithfully recapitulates its monoubiquitylation on lysine 84 that is observed in vivo. Mass spectrometry revealed the ubiquitylation sites on the Mind bomb E3 ligase and the Ub receptors Rpn10 and Vps9. Förster resonance energy transfer (FRET) analyses of ubiquitylated Vps9 purified from bacteria revealed that although ubiquitylation occurs on the Vps9‐GEF domain, it does not affect the guanine nucleotide exchanging factor (GEF) activity in vitro. Finally, we demonstrated that ubiquitylated Vps9 assumes a closed structure, which blocks additional Ub binding. Characterization of several ubiquitylated proteins demonstrated the integrity, specificity and fidelity of the system, and revealed new biological findings.     

Natural levels of colour polymorphism reduce performance of visual predators searching for camouflaged prey

Polymorphism, the coexistence of two or more variants within a population, has served as a classic model system to address questions about the evolution and maintenance of intraspecific variation. It has been hypothesized that a natural level of colour polymorphism may impair the search efficiency of visually orientated predators. To test this polymorphism protects hypothesis, we asked human participants to search for images of natural black, striped or grey Tetrix subulata grasshopper colour morphs presented against photographs of their natural habitat on computer screens. Fewer grasshoppers were detected when morphs were presented in mixed than in uniform sequences. All three morphs benefited to comparable degrees, in terms of reduced detection, from being presented in polymorphic sequences. Our findings demonstrate that natural levels of polymorphic variation can impede the efficiency of visually orientated predators and increase survival of prey. This protective effect supports the limited attention hypothesis, explains why predators develop ‘search images’, may account for the spread and establishment of novel colour variants, and contributes to maintenance of polymorphisms. © 2014 The Authors. Biological Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 546–555.     

Cytoplasmic incompatibility and multiple symbiont infection in the ash whitefly parasitoid, Encarsia inaron

Terrestrial arthropods are commonly infected with maternally inherited symbionts that cause reproductive incompatibilities between hosts with differing infection status. Such symbionts can have major effects on the efficacy of a biological control program if releases are comprised of mixtures of differentially infected individuals. In this study, the ash whitefly parasitoid, Encarsia inaron (Hymenoptera: Aphelinidae) from Arizona was surveyed for the presence of heritable bacterial symbionts; experiments were also performed to test for two phenotypes known to be caused by Encarsia symbionts—cytoplasmic incompatibility and changes in oviposition behavior and host use. E. inaron has successfully reduced ash whitefly to non-pest status in all three locations it has been released (California, Arizona, and North Carolina) and is also notable as one of the only Encarsia species that is not autoparasitic, with both male and female wasps developing as primary parasitoids of whiteflies. We show that E. inaron is infected with both Wolbachia and Cardinium. While there was no effect of the symbionts on oviposition behavior or host use, crosses between doubly infected male wasps and uninfected females resulted in a severe reduction in the number of female offspring; male offspring production was unaffected. This study thus serves as a further warning that ascribing a phenotype to a symbiont with confidence depends on eliminating the possibility of a mixed infection, and establishes E. inaron as a useful model for dissecting Wolbachia–Cardinium interactions.     

Bacterial population and innate immunity-related genes in rat gastrointestinal tract are altered by vitamin A-deficient diet

Vitamin A and its derivatives have been shown to regulate the growth and differentiation of gastrointestinal epithelial cells; in addition, vitamin A deficiency has been convincingly shown to be associated with increased susceptibility to infection. The gastrointestinal mucosal barrier, which is a component of the innate immune system, is considered the first line of defense, as it provides a barrier between the external environment and the internal milieu. A disturbance in the integrity of the intestinal epithelium is one of the main factors involved in increased incidence of infections during vitamin A deficiency. In this study, the effects of vitamin A deficiency on microbial ecology and the expression of genes related to the intestinal mucosa's innate immunity were examined in a rat model. Using the 16s rDNA method, we demonstrate that a vitamin A-deficient (VAD) diet increases the total amount of bacteria in the gastrointestinal tract and alters the intestinal microflora. Results show a decrease in the relative proportion of Lactobacillus spp. and the simultaneous appearance of Escherichia coli strains. Lack of vitamin A significantly changed mucin (MUC) dynamics, as reflected by the enlarged goblet-cell "cup" area relative to controls; decreased MUC2 mRNA expression in the jejunum, ileum and colon of VAD rats and increased MUC3 mRNA expression in the ileum and colon of these rats. In addition, vitamin A deficiency down-regulated defensin 6 mRNA expression while up-regulating toll-like receptors 2 and 5 mRNA expressions. The current study indicates that vitamin A deficiency interferes with the integrity of the gastrointestinal mucosal barrier.     

LINKING BIG: THE CONTINUING PROMISE OF EVOLUTIONARY SYNTHESIS

Synthetic science promises an unparalleled ability to find new meaning in old data, extant results, or previously unconnected methods and concepts, but pursuing synthesis can be a difficult and risky endeavor. Our experience as biologists, informaticians, and educators at the National Evolutionary Synthesis Center has affirmed that synthesis can yield major insights, but also revealed that technological hurdles, prevailing academic culture, and general confusion about the nature of synthesis can hamper its progress. By presenting our view of what synthesis is, why it will continue to drive progress in evolutionary biology, and how to remove barriers to its progress, we provide a map to a future in which all scientists can engage productively in synthetic research.     

An IDH1-vitamin C crosstalk drives human erythroid development by inhibiting pro-oxidant mitochondrial metabolism

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Stimulus-dependent Maximum Entropy Models of Neural Population Codes

Neural populations encode information about their stimulus in a collective fashion, by joint activity patterns of spiking and silence. A full account of this mapping from stimulus to neural activity is given by the conditional probability distribution over neural codewords given the sensory input. For large populations, direct sampling of these distributions is impossible, and so we must rely on constructing appropriate models. We show here that in a population of 100 retinal ganglion cells in the salamander retina responding to temporal white-noise stimuli, dependencies between cells play an important encoding role. We introduce the stimulus-dependent maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear model of a single neuron, to a pairwise-coupled neural population. We find that the SDME model gives a more accurate account of single cell responses and in particular significantly outperforms uncoupled models in reproducing the distributions of population codewords emitted in response to a stimulus. We show how the SDME model, in conjunction with static maximum entropy models of population vocabulary, can be used to estimate information-theoretic quantities like average surprise and information transmission in a neural population.     

Red white and blue – bright light effects in a diurnal rodent model for seasonal affective disorder

Despite the common use of bright light exposure for treatment of seasonal affective disorder (SAD), the underlying biology of the therapeutic effect is not clear. Moreover, there is a debate regarding the most efficacious wavelength of light for treatment. Whereas according to the traditional approach full-spectrum light is used, recent studies suggest that the critical wavelengths are within the range of blue light (460 and 484 nm). Our previous work shows that when diurnal rodents are maintained under short photoperiod they develop depression- and anxiety-like behavioral phenotype that is ameliorated by treatment with wide-spectrum bright light exposure (2500 lux at the cage, 5000 K). Our current study compares the effect of bright wide-spectrum (3,000 lux, wavelength 420- 780 nm, 5487 K), blue (1,300 lux, wavelength 420-530 nm) and red light (1,300 lux, wavelength range 600-780 nm) exposure in the fat sand rat (Psammomys Obesus) model of SAD. We report results of experiments with six groups of sand rats that were kept under various photoperiods and light treatments, and subjected to behavioral tests related to emotions: forced swim test, elevated plus maze and social interactions. Exposure to either intense wide-spectrum white light or to blue light equally ameliorated depression-like behavior whereas red light had no effect. Bright wide-spectrum white light treatment had no effect on animals maintained under neutral photoperiod, meaning that light exposure was only effective in the pathological-like state. The resemblance between the effects of bright white light and blue light suggests that intrinsically photosensitive retinal ganglion cells (ipRGCs) are involved in the underlying biology of SAD and light therapy.