An mRNA-specific tRNAi carrier eIF2A plays a pivotal role in cell proliferation under stress conditions: Stress-resistant translation of c-Src mRNA is mediated by eIF2A

c-Src, a non-receptor protein tyrosine kinase, activates NF-��B and STAT3, which in turn triggers the transcription of anti-apoptosis- and cell cycle-related genes. c-Src protein regulates cell proliferation, cell motility and programmed cell death. And the elevated level of activated c-Src protein is related with solid tumor generation. Translation of c-Src mRNA is directed by an IRES element which mediates persistent translation under stress conditions when translation of most mRNAs is inhibited by a phosphorylation of the alpha subunit of eIF2 carrying the initiator tRNA (tRNAi) to 40S ribosomal subunit under normal conditions. The molecular basis of the stress-resistant translation of c-Src mRNA remained to be elucidated. Here, we report that eIF2A, an alternative tRNAi carrier, is responsible for the stress-resistant translation of c-Src mRNA. eIF2A facilitates tRNAi loading onto the 40S ribosomal subunit in a c-Src mRNAdependent manner. And a direct interaction between eIF2A and a stem-loop structure (SL I) in the c-Src IRES is required for the c-Src IRES-dependent translation under stress conditions but not under normal conditions. Finally, we showed that the eIF2Adependent translation of c-Src mRNA plays a pivotal role in cell proliferation under stress conditions. ? The Author(s) 2016.115sciescopu

Distribution and Redistribution of HIV-1 Nucleocapsid Protein in Immature, Mature, and Integrase-Inhibited Virions: a Role for Integrase in Maturation

During virion maturation, HIV-1 capsid protein assembles into a conical core containing the viral ribonucleoprotein (vRNP) complex, thought to be composed mainly of the viral RNA and nucleocapsid protein (NC). After infection, the viral RNA is reverse transcribed into double-stranded DNA, which is then incorporated into host chromosomes by integrase (IN) catalysis. Certain IN mutations (class II) and antiviral drugs (allosteric IN inhibitors [ALLINIs]) adversely affect maturation, resulting in virions that contain “eccentric condensates,” electron-dense aggregates located outside seemingly empty capsids. Here we demonstrate that in addition to this mislocalization of electron density, a class II IN mutation and ALLINIs each increase the fraction of virions with malformed capsids (from ∼12% to ∼53%). Eccentric condensates have a high NC content, as demonstrated by “tomo-bubblegram” imaging, a novel labeling technique that exploits the susceptibility of NC to radiation damage. Tomo-bubblegrams also localized NC inside wild-type cores and lining the spherical Gag shell in immature virions. We conclude that eccentric condensates represent nonpackaged vRNPs and that either genetic or pharmacological inhibition of IN can impair vRNP incorporation into mature cores. Supplying IN in trans as part of a Vpr-IN fusion protein partially restored the formation of conical cores with internal electron density and the infectivity of a class II IN deletion mutant virus. Moreover, the ability of ALLINIs to induce eccentric condensate formation required both IN and viral RNA. Based on these observations, we propose a role for IN in initiating core morphogenesis and vRNP incorporation into the mature core during HIV-1 maturation

The bent conformation of poly(A)-binding protein induced by RNA-binding is required for its translational activation function

A recent study revealed that poly(A)-binding protein (PABP) bound to poly(A) RNA exhibits a sharply bent configuration at the linker region between RNA-recognition motif 2 (RRM2) and RRM3, whereas free PABP exhibits a highly flexible linear configuration. However, the physiological role of the bent structure of mRNA-bound PABP remains unknown. We investigated a role of the bent structure of PABP by constructing a PABP variant that fails to form the poly(A)-dependent bent structure but maintains its poly (A)-binding activity. We found that the bent structure of PABP/poly(A) complex is required for PABP's efficient interaction with eIF4G and eIF4G/eIF4E complex. Moreover, the mutant PABP had compromised translation activation function and failed to augment the formation of 80S translation initiation complex in an in vitro translation system. These results suggest that the bent conformation of PABP, which is induced by the interaction with 30 poly(A) tail, mediates poly(A)-dependent translation by facilitating the interaction with eIF4G and the eIF4G/eIF4E complex. The preferential binding of the eIF4G/eIF4E complex to the bent PABP/poly(A) complex seems to be a mechanism discriminating the mRNA-bound PABPs participating in translation from the idling mRNA-unbound PABPs.111Ysciescopu

In vitro volatile organic compound profiling using GCGC-TOFMS to differentiate bacteria associated with lung infections: A proof-of-concept study

© 2016 IOP Publishing Ltd. Chronic pulmonary infections are the principal cause of morbidity and mortality in individuals with cystic fibrosis (CF). Due to the polymicrobial nature of these infections, the identification of the particular bacterial species responsible is an essential step in diagnosis and treatment. Current diagnostic procedures are time-consuming, and can also be expensive, invasive and unpleasant in the absence of spontaneously expectorated sputum. The development of a rapid, non-invasive methodology capable of diagnosing and monitoring early bacterial infection is desired. Future visions of real-time, in situ diagnosis via exhaled breath testing rely on the differentiation of bacteria based on their volatile metabolites. The objective of this proof-of-concept study was to investigate whether a range of CF-associated bacterial species (i.e. Pseudomonas aeruginosa, Burkholderia cenocepacia, Haemophilus influenzae, Stenotrophomonas maltophilia, Streptococcus pneumoniae and Streptococcus milleri) could be differentiated based on their in vitro volatile metabolomic profiles. Headspace samples were collected using solid phase microextraction (SPME), analyzed using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GCGC-TOFMS) and evaluated using principal component analysis (PCA) in order to assess the multivariate structure of the data. Although it was not possible to effectively differentiate all six bacteria using this method, the results revealed that the presence of a particular pattern of VOCs (rather than a single VOC biomarker) is necessary for bacterial species identification. The particular pattern of VOCs was found to be dependent upon the bacterial growth phase (e.g. logarithmic versus stationary) and sample storage conditions (e.g. short-term versus long-term storage at -18 °C). Future studies of CF-associated bacteria and exhaled breath condensate will benefit from the approaches presented in this study and further facilitate the production of diagnostic tools for the early detection of bacterial lung infections

Impairing autophagy in retinal pigment epithelium leads to inflammasome activation and enhanced macrophage-mediated angiogenesis

Age-related decreases in autophagy contribute to the progression of age-related macular degeneration (AMD). We have now studied the interaction between autophagy impaired in retinal pigment epithelium (RPE) and the responses of macrophages. We find that dying RPE cells can activate the macrophage inflammasome and promote angiogenesis. In vitro, inhibiting rotenone-induced autophagy in RPE cells elicits caspase-3 mediated cell death. Co-culture of damaged RPE with macrophages leads to the secretion of IL-1β, IL-6 and nitrite oxide. Exogenous IL-6 protects the dysfunctional RPE but IL-1β causes enhanced cell death. Furthermore, IL-1β toxicity is more pronounced in dysfunctional RPE cells showing reduced IRAK3 gene expression. Co-culture of macrophages with damaged RPE also elicits elevated levels of pro-angiogenic proteins that promote ex vivo choroidal vessel sprouting. In vivo, impaired autophagy in the eye promotes photoreceptor and RPE degeneration and recruitment of inflammasome-activated macrophages. The degenerative tissue environment drives an enhanced pro-angiogenic response, demonstrated by increased size of laser-induced choroidal neovascularization (CNV) lesions. The contribution of macrophages was confirmed by depletion of CCR2 + monocytes, which attenuates CNV in the presence of RPE degeneration. Our results suggest that the interplay between perturbed RPE homeostasis and activated macrophages influences key features of AMD development

Use of clinical guidelines in cardiology practice in Sudan

Rationale, aims, and objective: The aim of this study was to explore the views of prescribers in cardiology in Sudan about the use of guidelines in clinical practice and the extent to which guidelines whether national or international can be adopted in clinical practice in Sudan. Methods: Interviews were conducted with the consultants in 2 of the main cardiac hospitals in Sudan. This was followed by a survey amongst the doctors in the hospitals to examine the views of a larger population of prescribers about the matter investigated. Results: Twelve consultants were interviewed, and 47 prescribers (60%) replied to the questionnaire that followed. Most doctors relied on foreign guidelines to prescribe for their patients. The doctors acknowledged the limitation of using foreign guidelines in Sudan. A number of doctors were not in favour of following any guidelines, as they perceived that the practice in Sudan does not allow implementation of guidelines. Conclusion: The prescribers in Sudan had to rely on guidelines made in foreign countries if they want to get the benefit of evidence‐based medicine to their patients, but they had to find a way to adapt these guidelines to their patients and to the health care system they are working within. However, it is not known if this adaptation of foreign guidelines is providing the benefits intended or is risking evidence‐based medicine

Effective action of three-dimensional extended supersymmetric matter on gauge superfield background

We study the low-energy effective actions for gauge superfields induced by quantum N=2 and N=4 supersymmetric matter fields in three-dimensional Minkowski space. Analyzing the superconformal invariants in the N=2 superspace we propose a general form of the N=2 gauge invariant and superconformal effective action. The leading terms in this action are fixed by the symmetry up to the coefficients while the higher order terms with respect to the Maxwell field strength are found up to one arbitrary function of quasi-primary N=2 superfields constructed from the superfield strength and its covariant spinor derivatives. Then we find this function and the coefficients by direct quantum computations in the N=2 superspace. The effective action of N=4 gauge multiplet is obtained by generalizing the N=2 effective action.Comment: 1+27 pages; v2: minor corrections, references adde

Water seepage beneath dams on soluble evaporite deposits: a laboratory and field study (Caspe Dam, Spain)

The paper presents analytical methods and results for assessing the variation in the concentration of sulphate (and other ions) over space and time in groundwater flowing through a soluble evaporite terrain beneath a dam. The influence of effective porosity, groundwater flow velocity and the specific rate of dissolution (K′) are considered. The theoretical analysis was tested in a scale model simulating a dam constructed on heavily karstified bedrock. A simple and useful method for assessing how much material is lost through dissolution and how the rate of dissolution changes over time is considered in the context of the Caspe Dam, Spain

Anomaly Cancelation in Field Theory and F-theory on a Circle

We study the manifestation of local gauge anomalies of four- and six-dimensional field theories in the lower-dimensional Kaluza-Klein theory obtained after circle compactification. We identify a convenient set of transformations acting on the whole tower of massless and massive states and investigate their action on the low-energy effective theories in the Coulomb branch. The maps employ higher-dimensional large gauge transformations and precisely yield the anomaly cancelation conditions when acting on the one-loop induced Chern-Simons terms in the three- and five-dimensional effective theory. The arising symmetries are argued to play a key role in the study of the M-theory to F-theory limit on Calabi-Yau manifolds. For example, using the fact that all fully resolved F-theory geometries inducing multiple Abelian gauge groups or non-Abelian groups admit a certain set of symmetries, we are able to generally show the cancelation of pure Abelian or pure non-Abelian anomalies in these models.Comment: 48 pages, 2 figures; v2: typos corrected, comments on circle fluxes adde

F-Theorem without Supersymmetry

The conjectured F-theorem for three-dimensional field theories states that the finite part of the free energy on S^3 decreases along RG trajectories and is stationary at the fixed points. In previous work various successful tests of this proposal were carried out for theories with {\cal N}=2 supersymmetry. In this paper we perform more general tests that do not rely on supersymmetry. We study perturbatively the RG flows produced by weakly relevant operators and show that the free energy decreases monotonically. We also consider large N field theories perturbed by relevant double trace operators, free massive field theories, and some Chern-Simons gauge theories. In all cases the free energy in the IR is smaller than in the UV, consistent with the F-theorem. We discuss other odd-dimensional Euclidean theories on S^d and provide evidence that (-1)^{(d-1)/2} \log |Z| decreases along RG flow; in the particular case d=1 this is the well-known g-theorem.Comment: 34 pages, 2 figures; v2 refs added, minor improvements; v3 refs added, improved section 4.3; v4 minor improvement