Alternative splicing generates protein diversity and allows for post-transcriptional gene regulation. Estimates suggest that 10% of the genes in Caenorhabditis elegans undergo alternative splicing. ...We constructed a splicing-sensitive microarray to detect alternative splicing for 352 cassette exons and tested for changes in alternative splicing of these genes during development. We found that the microarray data predicted that 62/352 (approximately 18%) of the alternative splicing events studied show a strong change in the relative levels of the spliced isoforms (>4-fold) during development. Confirmation of the microarray data by RT-PCR was obtained for 70% of randomly selected genes tested. Among the genes with the most developmentally regulated alternatively splicing was the hnRNP F/H splicing factor homolog, W02D3.11 - now named hrpf-1. For the cassette exon of hrpf-1, the inclusion isoform comprises 65% of hrpf-1 steady state messages in embryos but only 0.1% in the first larval stage. This dramatic change in the alternative splicing of an alternative splicing factor suggests a complex cascade of splicing regulation during development. We analyzed splicing in embryos from a strain with a mutation in the splicing factor sym-2, another hnRNP F/H homolog. We found that approximately half of the genes with large alternative splicing changes between the embryo and L1 stages are regulated by sym-2 in embryos. An analysis of the role of nonsense-mediated decay in regulating steady-state alternative mRNA isoforms was performed. We found that 8% of the 352 events studied have alternative isoforms whose relative steady-state levels in embryos change more than 4-fold in a nonsense-mediated decay mutant, including hrpf-1. Strikingly, 53% of these alternative splicing events that are affected by NMD in our experiment are not obvious substrates for NMD based on the presence of premature termination codons. This suggests that the targeting of splicing factors by NMD may have downstream effects on alternative splicing regulation.
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For the development of redox responsive MRI probes based on the Mn
III
/Mn
II
couple, stable complexation of both reduced and oxidized forms of the metal ion and appropriate tuning of the redox ...potential in the biologically relevant range are key elements. The water soluble fluorinated Mn-porphyrin derivative Mn-
3
satisfies both requirements. In aqueous solutions, it can reversibly switch between Mn
III
/Mn
II
oxidation states. In the presence of ascorbic acid or β-mercaptoethanol, the Mn
III
form undergoes reduction, which is slowly but fully reversed in the presence of air oxygen. A UV-Vis kinetic study of Mn
III
/Mn
II
reduction under oxygen-free conditions yielded second-order rate constants,
k
2
, of 46.1 M
−1
s
−1
and 13.8 M
−1
s
−1
for the reaction with ascorbic acid and β-mercaptoethanol, respectively. This could correspond, in the absence of oxygen, to a half-life of a few minutes in blood plasma and a few seconds in circulating immune cells where ascorbic acid reaches 20-40 μM and a few mM concentrations, respectively. In contrast to expectations based on the redox potential, reduction with glutathione or cysteine does not occur. It is prevented by the coordination of the glutathione carboxylate group(s) to Mn
III
in the axial position, as was evidenced by NMR data. Therefore, Mn
III
-
3
acts as an ascorbate specific turn-on MRI probe, which in turn can be re-oxidized by oxygen. The relaxivity increase from the oxidized to the reduced form is considerably improved at medium frequencies (up to 80 MHz) with respect to the previously studied Mn-TPPS
4
analogues; at 20 MHz, it amounts to 150%. No
in vitro
cytotoxicity is detectable for Mn-
3
in the typical MRI concentration range. Finally,
19
F NMR resonances of Mn
III
-
3
are relatively sharp which could open further opportunities to exploit such complexes as paramagnetic
19
F NMR probes.
A water-soluble fluorinated Mn
III/II
porphyrin responds reversibly to ascorbate redox state as a turn-on MRI probe.
Alternative splicing coupled to nonsense-mediated decay (AS-NMD) is a mechanism for post-transcriptional regulation of gene expression. We analyzed the global effects of mutations in seven genes of ...the C. elegans NMD pathway on AS isoform ratios. We find that mutations in two NMD factors, smg-6 and smg-7, have weaker global effects relative to mutations in other smg genes. We did an in-depth analysis of 12 pre-mRNA splicing factor genes that are subject to AS-NMD. For four of these, changes in the ratio of alternatively spliced isoforms during development are caused by developmentally regulated inhibition of NMD, and not by changes in alternative splicing. Using sucrose gradient analysis of mRNAs undergoing translation, we find several examples of NMD-dependent enrichment of premature termination codon (PTC) isoforms in the monosome fraction. In contrast, we present evidence of two genes for which the PTC-containing isoforms are found in polysomes and have a translational profile similar to non-PTC-containing transcripts from the same gene. We propose that NMD of certain alternatively spliced isoforms is regulated, and that some stabilized NMD targets may be translated.
Regulation of alternative splicing is controlled by pre-mRNA sequences (cis-elements) and trans-acting protein factors that bind them. The combinatorial interactions of multiple protein factors with ...the cis-elements surrounding a given alternative splicing event lead to an integrated splicing decision. The mechanism of multifactorial splicing regulation is poorly understood. Using a splicing-sensitive DNA microarray, we assayed 352 Caenorhabditis elegans alternative cassette exons for changes in embryonic splicing patterns between wild-type and 12 different strains carrying mutations in a splicing factor. We identified many alternative splicing events that are regulated by multiple splicing factors. Many splicing factors have the ability to behave as splicing repressors for some alternative cassette exons and as splicing activators for others. Unexpectedly, we found that the ability of a given alternative splicing factor to behave as an enhancer or repressor of a specific splicing event can change during development. Our observations that splicing factors can change their effects on a substrate during development support a model in which combinatorial effects of multiple factors, both constitutive and developmentally regulated ones, contribute to the overall splicing decision.
We discuss a procedure to build new sequences of magnetised, equilibrium tori around Kerr black holes which combines two approaches previously considered in the literature. For simplicity we have ...assumed that the test-fluid approximation holds, and hence we neglected the self-gravity of the fluid. The models were built assuming a particular form of the angular momentum distribution from which the location and morphology of equipotential surfaces can be computed. This ansatz includes, in particular, the constant angular momentum case originally employed in the construction of thick tori – or Polish doughnuts – and it has already been used to build equilibrium sequences of purely hydrodynamical models. We discuss the properties of the new models and their dependence on the initial parameters. These new sequences can be used as initial data for magnetohydrodynamical evolutions in general relativity.
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Testing the true nature of black holes-the no-hair hypothesis-will become increasingly more precise in the next few years as new observational data is collected in both the gravitational-wave channel ...and the electromagnetic channel. In this paper we consider numerically generated spacetimes of Kerr black holes with synchronized scalar hair and build stationary models of magnetized thick disks (or tori) around them. Our approach assumes that the disks are not self-gravitating, they obey a polytropic equation of state, the distribution of their specific angular momentum is constant, and they are marginally stable, i.e., the disks completely fill their Roche lobe. Moreover, contrary to existing approaches in the literature, our models are thermodynamically relativist, as the specific enthalpy of the fluid can adopt values significantly larger than unity. We study the dependence of the morphology and properties of the accretion tori on the type of black hole considered, from purely Kerr black holes with varying degrees of spin parameter, namely from a Schwarzschild black hole to a nearly extremal Kerr case, to Kerr black holes with scalar hair with different Arnowitt-Deser-Misner mass and horizon angular velocity. Comparisons between the disk properties for both types of black holes are presented. The sequences of magnetized, equilibrium disks around Kerr black holes with scalar hair discussed in this study are morphologically and thermodynamically different than their Kerr black hole counterparts, namely their vertical size is larger, the high-density central region is more extended, and the fluid is more relativistic. Therefore, we expect significant differences to appear when these sequences are used as initial data for numerical relativity codes to investigate their dynamical (nonlinear) stability and used in tandem with ray-tracing codes to obtain synthetic images of black holes (i.e., shadows) in astrophysically relevant situations where the light source is provided by an emitting accretion disk.
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In the last few years, we have observed an exponential increasing of the information systems, and parking information is one more example of them. The needs of obtaining reliable and updated ...information of parking slots availability are very important in the goal of traffic reduction. Also parking slot prediction is a new topic that has already started to be applied. San Francisco in America and Santander in Spain are examples of such projects carried out to obtain this kind of information.The aim of this thesis is the study and evaluation of methodologies for parking slot prediction and the integration in a web application, where all kind of users will be able to know the current parking status and also future status according to parking model predictions. The source of the data is ancillary in this work but it needs to be understood anyway to understand the parking behaviour. Actually, there are many modelling techniques used for this purpose such as time series analysis, decision trees, neural networks and clustering. In this work, the author explains the best techniques at this work, analyzes the result and points out the advantages and disadvantages of each one. The model will learn the periodic and seasonal patterns of the parking status behaviour, and with this knowledge it can predict future status values given a date.The data used comes from the Smart Park Ontinyent and it is about parking occupancy status together with timestamps and it is stored in a database. After data acquisition, data analysis and pre-processing was needed for model implementations.The first test done was with the boosting ensemble classifier, employed over a set of decision trees, created with C5.0 algorithm from a set of training samples, to assign a prediction value to each object. In addition to the predictions, this work has got measurements error that indicates the reliability of the outcome predictions being correct. The second test was done using the function fitting seasonal exponential smoothing tbats model. Finally as the last test, it has been tried a model that is actually a combination of the previous two models, just to see the result of this combination. The results were quite good for all of them, having error averages of 6.2, 6.6 and 5.4 in vacancies predictions for the three models respectively. This means from a parking of 47 places a 10% average error in parking slot predictions. This result could be even better with longer data available.In order to make this kind of information visible and reachable from everyone having a device with internet connection, a web application was made for this purpose. Beside the data displaying, this application also offers different functions to improve the task of searching for parking. The new functions, apart from parking prediction, were:- Park distances from user location. It provides all the distances to user current location to the different parks in the city.- Geocoding. The service for matching a literal description or an address to a concrete location.- Geolocation. The service for positioning the user.- Parking list panel. This is not a service neither a function, is just a better visualization and better handling of the information.
We present stationary solutions of geometrically thick discs (or tori) endowed with a self-consistent toroidal magnetic field distribution surrounding a nonrotating black hole in an analytical, ...static, spherically-symmetric f(R)-gravity background. These f(R)-gravity models introduce a Yukawa-like modification to the Newtonian potential, encoded in a single parameter δ which controls the strength of the modified potential and whose specific values affect the disc configurations when compared to the general relativistic case. Our models span different magnetic field strengths, from purely hydrodynamical discs to highly magnetized tori. The characteristics of the solutions are identified by analyzing the central density, mass, geometrical size, angular size, and the black hole metric deviations from the Schwarzschild space-time. In the general relativistic limit (δ=0) our models reproduce previous results for a Schwarzschild black hole. For small values of the δ parameter, corresponding to ∼10% deviations from general relativity, we find variations of ∼2% in the event horizon size, a ∼5% shift in the location of the inner edge and center of the disc, while the outer edge increases by ∼10%. Our analysis for |δ|>0.1, however, reveals notable changes in the black hole space-time solution which have a major impact in the morphological and thermodynamical properties of the discs. The comparison with general relativity is further investigated by computing the size of the photon ring produced by a source located at infinity. This allows us to place constraints on the parameters of the f(R)-gravity model based on the Event Horizon Telescope observations of the size of the light ring in M87 and SgrA*.
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Alternative splicing is regulated by cis sequences in the pre-mRNA that serve as binding sites for trans-acting alternative splicing factors. In a previous study, we used bioinformatics and molecular ...biology to identify and confirm that the intronic hexamer sequence UCUAUC is a nematode alternative splicing regulatory element. In this study, we used RNA affinity chromatography to identify trans factors that bind to this sequence. HRP-2, the Caenorhabditis elegans homolog of human heterogeneous nuclear ribonucleoproteins Q and R, binds to UCUAUC in the context of unc-52 intronic regulatory sequences as well as to RNAs containing tandem repeats of this sequence. The three Us in the hexamer are the most important determinants of this binding specificity. We demonstrate, using RNA interference, that HRP-2 regulates the alternative splicing of two genes, unc-52 and lin-10, both of which have cassette exons flanked by an intronic UCUAUC motif. We propose that HRP-2 is a protein responsible for regulating alternative splicing through binding interactions with the UCUAUC sequence.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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