Mammalian target of rapamycin complex 1: Signalling inputs,substrates and feedback mechanisms

The mammalian target of rapamycin (mTOR) signalling pathway is implicated in the pathogenesis of a number of cancers and inherited hamartoma syndromes which have led to mTOR inhibitors, such as rapamycin, being tested in clinical trials. Knowledge of the mTOR pathway is rapidly expanding. This review provides an update on the most recent additions to the mTOR pathway with particular emphasis on mTORC1 signalling. mTORC1 signalling is classically known for its role in regulating cell growth and proliferation through modulation of protein synthesis. Recent research has identified novel mTORC1 cell signalling mechanisms that modulate mitochondrial biogenesis, hypoxia signalling and cell cycle progression and uncovered novel mTORC1 targets; YY1, HIF and SGK1. It is unsurprising that regulation of mTORC1 is multifaceted with many positive and negative signalling inputs. We discuss the recent advances that have been made to determine the upstream mechanisms that control mTORC1 through hypoxia, energy sensing and nutrient signalling. Also discussed are current findings that have unravelled a series of novel mTORC1-associated proteins that directly control the activity of mTORC1 and include PRAS40, FKBP38, Rag GTPases and RalA.     

Double-strand break DNA repair genotype predictive of later mortality and cancer incidence in a cohort of non-smokers

We followed-up for mortality and cancer incidence 1088 healthy non-smokers from a population-based study, who were characterized for 22 variants in 16 genes involved in DNA repair pathways. Follow-up was 100% complete. The association between polymorphism and mortality or cancer incidence was analyzed using Cox Proportional Hazard regression models. Ninety-five subjects had died in a median follow-up time of 78 months (inter-quartile range 59-93 months). None of the genotypes was clearly associated with total mortality, except variants for two Double-Strand Break DNA repair genes, XRCC3 18067 C>T (rs#861539) and XRCC2 31479 G>A (rs#3218536). Adjusted hazard ratios were 2.25 (1.32-3.83) for the XRCC3 C/T genotype and 2.04 (1.00-4.13) for the T/T genotype (reference C/C), and 2.12 (1.14-3.97) for the XRCC2 G/A genotype (reference G/G). For total cancer mortality, the adjusted hazard ratios were 3.29 (1.23-7.82) for XRCC3 C/T, 2.84 (0.81-9.90) for XRCC3 T/T and 3.17 (1.21-8.30) for XRCC2 G/A. With combinations of three or more adverse alleles, the adjusted hazard ratio for all cause mortality was 17.29 (95% C.I. 8.13-36.74), and for all incident cancers the HR was 5.28 (95% C.I. 2.17-12.85). Observations from this prospective study suggest that polymorphisms of genes involved in the repair of DNA double-strand breaks significantly influence the risk of cancer and non-cancer disease, and can influence mortality.     

Preferences and Self‐efficacy for Diet Modification Among Primary Care Patients

Limited data exist about patient preferences and self‐efficacy for different diets. We explored the preferences and self‐efficacy of primary care patients for reducing fat, reducing carbohydrates, or reducing calories. We conducted a self‐administered survey study of 71 primary care patients (response rate of 52%). Of patients, 59%, 53%, and 60% had high self‐efficacy for reducing fat, reducing carbohydrates, and reducing calories from their diet, respectively. Preferences were comparable, with 76% highly willing to reduce fat, 76% highly willing to reduce carbohydrates, and 72% of patients highly willing to reduce calories/portions. Female sex and higher BMI were associated with high self‐efficacy for all three dietary changes. A significantly higher proportion of nonwhites than whites had high self‐efficacy for reducing fat and reducing carbohydrates (P < 0.05). Obese patients in our study have similarly high willingness and self‐efficacy and comparable preferences for adopting changes consistent with three popular diets.     

Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines

Background

Symptomatic infection by dengue virus (DENV) can range from dengue fever (DF) to dengue haemorrhagic fever (DHF), however, the determinants of DF or DHF progression are not completely understood. It is hypothesised that host innate immune response factors are involved in modulating the disease outcome and the expression levels of genes involved in this response could be used as early prognostic markers for disease severity.

Methodology/Principal Findings

mRNA expression levels of genes involved in DENV innate immune responses were measured using quantitative real time PCR (qPCR). Here, we present a novel application of the support vector machines (SVM) algorithm to analyze the expression pattern of 12 genes in peripheral blood mononuclear cells (PBMCs) of 28 dengue patients (13 DHF and 15 DF) during acute viral infection. The SVM model was trained using gene expression data of these genes and achieved the highest accuracy of ∼85% with leave-one-out cross-validation. Through selective removal of gene expression data from the SVM model, we have identified seven genes (MYD88, TLR7, TLR3, MDA5, IRF3, IFN-α and CLEC5A) that may be central in differentiating DF patients from DHF, with MYD88 and TLR7 observed to be the most important. Though the individual removal of expression data of five other genes had no impact on the overall accuracy, a significant combined role was observed when the SVM model of the two main genes (MYD88 and TLR7) was re-trained to include the five genes, increasing the overall accuracy to ∼96%.

Conclusions/Significance

Here, we present a novel use of the SVM algorithm to classify DF and DHF patients, as well as to elucidate the significance of the various genes involved. It was observed that seven genes are critical in classifying DF and DHF patients: TLR3, MDA5, IRF3, IFN-α, CLEC5A, and the two most important MYD88 and TLR7. While these preliminary results are promising, further experimental investigation is necessary to validate their specific roles in dengue disease.     

Elevated acetyl‐CoA by amino acid recycling fuels microalgal neutral lipid accumulation in exponential growth phase for biofuel production

Microalgal neutral lipids [mainly in the form of triacylglycerols (TAGs)], feasible substrates for biofuel, are typically accumulated during the stationary growth phase. To make microalgal biofuels economically competitive with fossil fuels, generating strains that trigger TAG accumulation from the exponential growth phase is a promising biological approach. The regulatory mechanisms to trigger TAG accumulation from the exponential growth phase (TAEP) are important to be uncovered for advancing economic feasibility. Through the inhibition of pyruvate dehydrogenase kinase by sodium dichloroacetate, acetyl‐CoA level increased, resulting in TAEP in microalga Dunaliella tertiolecta. We further reported refilling of acetyl‐CoA pool through branched‐chain amino acid catabolism contributed to an overall sixfold TAEP with marginal compromise (4%) on growth in a TAG‐rich D. tertiolecta mutant from targeted screening. Herein, a three‐step α loop‐integrated metabolic model is introduced to shed lights on the neutral lipid regulatory mechanism. This article provides novel approaches to compress lipid production phase and heightens lipid productivity and photosynthetic carbon capture via enhancing acetyl‐CoA level, which would optimize renewable microalgal biofuel to fulfil the demanding fuel market.     

Allosteric modulation of hormone release from thyroxine and corticosteroid-binding globulins

The release of hormones from thyroxine-binding globulin (TBG) and corticosteroid-binding globulin (CBG) is regulated by movement of the reactive center loop in and out of the β-sheet A of the molecule. To investigate how these changes are transmitted to the hormone-binding site, we developed a sensitive assay using a synthesized thyroxine fluorophore and solved the crystal structures of reactive loop cleaved TBG together with its complexes with thyroxine, the thyroxine fluorophores, furosemide, and mefenamic acid. Cleavage of the reactive loop results in its complete insertion into the β-sheet A and a substantial but incomplete decrease in binding affinity in both TBG and CBG. We show here that the direct interaction between residue Thr(342) of the reactive loop and Tyr(241) of the hormone binding site contributes to thyroxine binding and release following reactive loop insertion. However, a much larger effect occurs allosterically due to stretching of the connecting loop to the top of the D helix (hD), as confirmed in TBG with shortening of the loop by three residues, making it insensitive to the S-to-R transition. The transmission of the changes in the hD loop to the binding pocket is seen to involve coherent movements in the s2/3B loop linked to the hD loop by Lys(243), which is, in turn, linked to the s4/5B loop, flanking the thyroxine-binding site, by Arg(378). Overall, the coordinated movements of the reactive loop, hD, and the hormone binding site allow the allosteric regulation of hormone release, as with the modulation demonstrated here in response to changes in temperature.     

Mortality and oviposition of western cherry fruit fly (Diptera: Tephritidae) exposed to different insecticide baits for varying periods in the presence and absence of food

Spinosad bait is used to control western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), by killing flies before they oviposit. However, effects of different insecticide baits on management of reproductively mature flies are largely unknown. Objectives here were to determine mortality and oviposition of reproductively mature R. indifferens exposed to different insecticide baits for varying periods in the presence and absence of dried yeast extract and sucrose food. Spinosad bait (spinosad in a mix of protein, sugar, and other ingredients) was compared with acetamiprid, thiamethoxam, and imidacloprid in sucrose or Nu-Lure + sucrose bait. When flies were exposed to treatments and then offered cherries, Prunus avium (L.) L., for oviposition or when they were exposed to treatments and cherries simultaneously, both thiamethoxam bait and imidacloprid bait resulted in higher mortality and lower oviposition than spinosad bait and acetamiprid bait. Exposures to thiamethoxam bait and imidacloprid bait for six and 24 h were similarly effective, but 6-h exposures to spinosad bait and acetamiprid bait were less effective than 24-h exposures. There was little difference between sucrose and Nu-Lure + sucrose baits. When food was present, thiamethoxam bait and imidacloprid bait caused greater mortality and lower oviposition than spinosad bait and acetamiprid bait, but when food was absent, patterns were less consistent. Because of its ability to kill flies sooner after it is exposed to flies when food is present or absent, thiamethoxam or imidacloprid in sucrose or Nu-Lure bait may reduce infestations in cherries more than spinosad bait when mature R. indifferens are present in orchards.     

Isg15 controls p53 stability and functions

Degradation of p53 is a cornerstone in the control of its functions as a tumor suppressor. This process is attributed to ubiquitin-dependent modification of p53. In addition to polyubiquitination, we found that p53 is targeted for degradation through ISGylation. Isg15, a ubiquitin-like protein, covalently modifies p53 at 2 sites in the N and C terminus, and ISGylated p53 can be degraded by the 20S proteasome. ISGylation primarily targets a misfolded, dominant-negative p53, and Isg15 deletion in normal cells results in suppression of p53 activity and functions. We propose that Isg15-dependent degradation of p53 represents an alternative mechanism of controlling p53 protein levels, and, thus, it is an attractive pathway for drug discovery.