Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.

Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.

Multifractal Intermittency in Granular Flow through Bottlenecks.

We experimentally analyze the intermittent nature of granular silo flow when the discharge is controlled by an extracting belt at the bottom. We discover the existence of four different scenarios. For low extraction rates, the system is characterized by an on-off intermittency. When the extraction rate is increased the structure functions of the grains velocity increments, calculated for different lag times, reveal the emergence of multifractal intermittency. Finally, for very high extraction rates that approach the purely gravitational discharge, we observe that the dynamics become dependent on the outlet size. For large orifices the behavior is monofractal, whereas for small ones, the fluctuations of the velocity increments deviate from Gaussianity even for very large time lags.

Rpb1 foot mutations demonstrate a major role of Rpb4 in mRNA stability during stress situations in yeast.

The RPB1 mutants in the foot region of RNA polymerase II affect the assembly of the complex by altering the correct association of both the Rpb6 and the Rpb4/7 dimer. Assembly defects alter both transcriptional activity as well as the amount of enzyme associated with genes. Here, we show that the global transcriptional analysis of foot mutants reveals the activation of an environmental stress response (ESR), which occurs at a permissive temperature under optimal growth conditions. Our data indicate that the ESR that occurs in foot mutants depends mostly on a global post-transcriptional regulation mechanism which, in turn, depends on Rpb4-mRNA imprinting. Under optimal growth conditions, we propose that Rpb4 serves as a key to globally modulate mRNA stability as well as to coordinate transcription and decay. Overall, our results imply that post-transcriptional regulation plays a major role in controlling the ESR at both the transcription and mRNA decay levels.

Lung histopathological findings in fatal pandemic influenza A (H1N1).

OBJECTIVE: To describe the lung pathological changes in influenza A (H1N1) viral pneumonia. We studied morphological changes, nitro-oxidative stress and the presence of viral proteins in lung tissue. METHODS AND PATIENTS: Light microscopy was used to examine lung tissue from 6 fatal cases of pandemic influenza A (H1N1) viral pneumonia. Fluorescence for oxidized dihydroethydium, nitrotyrosine, inducible NO synthase (NOS2) and human influenza A nucleoprotein (NP) (for analysis under confocal microscopy) was also studied in lung tissue specimens. RESULTS: Age ranged from 15 to 50 years. Three patients were women, and 5 had preexisting medical conditions. Diffuse alveolar damage (DAD) was present in 5 cases (as evidenced by hyaline membrane formation, alveolo-capillary wall thickening and PMN infiltrates), and interstitial fibrosis in one case. In the fluorescence studies there were signs of oxygen radical generation, increased NOS2 protein and protein nitration in lung tissue samples, regardless of the duration of ICU admission. Viral NP was found in lung tissue samples from three patients. Type I pneumocytes and macrophages harbored viral NP, as evidenced by confocal immunofluorescence microscopy. CONCLUSIONS: Lung tissue from patients with pandemic influenza A (H1N1) viral pneumonia shows histological findings consistent with DAD. Prolonged nitro-oxidative stress is present despite antiviral treatment. Viral proteins may remain in lung tissue for prolonged periods of time, lodged in macrophages and type I pneumocytes.

Pattern formation and interface pinch-off in rotating Hele-Shaw flows: a phase-field approach.

Viscous fingering dynamics driven by centrifugal forcing is studied for arbitrary viscosity contrast. Theoretical methods, including exact solutions, and numerics based on a phase-field approach are used. Both confirm that pinch-off singularities in patterns originated from the centrifugally driven instability may occur spontaneously and be inherent to the two-dimensional Hele-Shaw dynamics. They are systematically more frequent for lower viscosity contrasts consistently with experimental evidence. The analytical insights provide an interpretation of this fact in terms of the asymptotic matching of the different regions of the fingering patterns. The phase-field numerical scheme is shown to be particularly adequate to elucidate the existence of finite-time singularities through the dependence of the singularity time on the interface thickness, in particular for varying viscosity contrast.

Experiments of periodic forcing of Saffman-Taylor fingers.

We report on an experimental study of long normal Saffman-Taylor fingers subject to periodic forcing. The sides of the finger develop a low amplitude, long wavelength instability. We discuss the finger response in stationary and nonstationary situations, as well as the dynamics towards the stationary states. The response frequency of the instability increases with forcing frequency at low forcing frequencies, while, remarkably, it becomes independent of forcing frequency at large forcing frequencies. This implies a process of wavelength selection. These observations are in good agreement with previous numerical results reported in [Ledesma-Aguilar, Phys. Rev. E 71, 016312 (2005)]. We also study the average value of the finger width, and its fluctuations, as a function of forcing frequency. The average finger width is always smaller than the width of the steady-state finger. Fluctuations have a nonmonotonic behavior with a maximum at a particular frequency.

Instabilities in the oscillatory flow of a complex fluid.

The dynamics of a fluid in a vertical tube, subjected to an oscillatory pressure gradient, is studied experimentally for both a Newtonian and a viscoelastic shear-thinning fluid. Particle image velocimetry is used to determine the two-dimensional velocity fields in the vertical plane of the tube axis, in a range of driving amplitudes from 0.8 to 2.5 mm and of driving frequencies from 2.0 to 11.5 Hz. The Newtonian fluid exhibits a laminar flow regime, independent of the axial position, in the whole range of drivings. For the complex fluid, instead, the parallel shear flow regime exhibited at low amplitudes [Torralba, Phys. Rev. E 72, 016308 (2005)] becomes unstable at higher drivings against the formation of symmetric vortices, equally spaced along the tube. At even higher drivings the vortex structure itself becomes unstable, and complex nonsymmetric structures develop. Given that inertial effects remain negligible even at the hardest drivings (Re < 10(-1)), it is the complex rheology of the fluid that is responsible for the instabilities observed. The system studied represents an interesting example of the development of shear-induced instabilities in nonlinear complex fluids in purely parallel shear flow.

Saccharomyces cerevisiae signature genes for predicting nitrogen deficiency during alcoholic fermentation.

Genome-wide analysis of the wine yeast strain Saccharomyces cerevisiae PYCC4072 identified 36 genes highly expressed under conditions of low or absent nitrogen in comparison with a nitrogen-replete condition. Reverse transcription-PCR analysis for four of these transcripts with this strain and its validation with another wine yeast strain underlines the usefulness of these signature genes for predicting nitrogen deficiency and therefore the diagnosis of wine stuck/sluggish fermentations.

Transcriptional response of Saccharomyces cerevisiae to different nitrogen concentrations during alcoholic fermentation.

Gene expression profiles of a wine strain of Saccharomyces cerevisiae PYCC4072 were monitored during alcoholic fermentations with three different nitrogen supplies: (i) control fermentation (with enough nitrogen to complete sugar fermentation), (ii) nitrogen-limiting fermentation, and (iii) the addition of nitrogen to the nitrogen-limiting fermentation (refed fermentation). Approximately 70% of the yeast transcriptome was altered in at least one of the fermentation stages studied, revealing the continuous adjustment of yeast cells to stressful conditions. Nitrogen concentration had a decisive effect on gene expression during fermentation. The largest changes in transcription profiles were observed when the early time points of the N-limiting and control fermentations were compared. Despite the high levels of glucose present in the media, the early responses of yeast cells to low nitrogen were characterized by the induction of genes involved in oxidative glucose metabolism, including a significant number of mitochondrial associated genes resembling the yeast cell response to glucose starvation. As the N-limiting fermentation progressed, a general downregulation of genes associated with catabolism was observed. Surprisingly, genes encoding ribosomal proteins and involved in ribosome biogenesis showed a slight increase during N starvation; besides, genes that comprise the RiBi regulon behaved distinctively under the different experimental conditions. Here, for the first time, the global response of nitrogen-depleted cells to nitrogen addition under enological conditions is described. An important gene expression reprogramming occurred after nitrogen addition; this reprogramming affected genes involved in glycolysis, thiamine metabolism, and energy pathways, which enabled the yeast strain to overcome the previous nitrogen starvation stress and restart alcoholic fermentation.

Pressure-dependent scaling scenarios in experiments of spontaneous imbibition.

The scaling properties of the rough liquid-air interface formed in the spontaneous imbibition of a viscous liquid by a model porous medium are found to be very sensitive to the magnitude of the pressure difference applied at the liquid inlet. Interface fluctuations change from obeying intrinsic anomalous scaling at large negative pressure differences, to being super-rough with the same dynamic exponent z approximately =3 at less negative pressure differences, to finally obeying ordinary Family-Vicsek scaling with z approximately =2 at large positive pressure differences. This rich scenario reflects the relative importance on different length scales of capillary and permeability disorder, and the role of surface tension and viscous pressure in damping interface fluctuations.

Relevance of dynamic wetting in viscous fingering patterns.

We demonstrate that wetting effects at moving contact lines have a strong impact in viscous fingering patterns. Experiments in a rotating Hele-Shaw (HS) cell, dry or prewetted, show consistent morphological differences. When the wetting fluid invades a dry region, contact angle dynamics yield a kinetic contribution to the interface pressure drop that scales with capillary number as Ca(2/3) but is significantly larger than the Park-Homsy kinetic correction. Numerical results are in very good agreement with experiments and show that standard HS equations work best for prewetted cells.

[The utility of interictal SPECT in temporal lobe epilepsy]. / ¿Es útil la SPECT interictal en la epilepsia del lóbulo temporal?

INTRODUCTION: Interictal brain single photon emission computed tomography (SPECT) is used in the presurgical evaluation of patients with complex partial epilepsy. The aim of the present study was to compare interictal SPECT, MRI and video-electroencephalography (EEG) for seizure focus localization in patients with temporal lobe epilepsy, one year after temporal lobectomy, in order to determine the utility of interictal brain SPECT. PATIENTS AND METHODS: Thirty four consecutive patients with refractory temporal epilepsy were evaluated with video-EEG, MRI and interictal SPECT for seizure focus localization before surgery. Seizure focus was confirmed with the clinical follow-up one year after temporal lobectomy in all patients. MRI and SPECT analysis was performed visually. RESULTS: 31/34 patients were seizure free one year after surgery and the remaining 3 patients remain with seizures occasionally. Video-EEG results coincided with postsurgical seizure focus localization in 31 (91%) patients. MRI localized seizure focus correctly in 30 (88%) patients and was normal in 3 cases. Interictal brain SPECT was normal in 10 patients and showed temporal hypoperfusion consistent with postsurgical seizure focus in 23 (68%) patients. In all patients with abnormalities in the interictal SPECT, seizure focus was identified with video-EEG or MRI. CONCLUSIONS: When MRI and video-EEG localize seizure focus in the same temporal lobe, interictal brain SPECT does not offer any additional information for surgical decision making.

Fluctuations in Saffman-Taylor fingers with quenched disorder.

We make an experimental characterization of the effect that static disorder has on the shape of a normal Saffman-Taylor finger. We find that static noise induces a small amplitude and long wavelength instability on the sides of the finger. Fluctuations on the finger sides have a dominant wavelength, indicating that the system acts as a selective amplifier of static noise. The dominant wavelength does not seem to be very sensitive to the intensity of static noise present in the system. On the other hand, at a given flow rate, rms fluctuations of the finger width, decrease with decreasing intensity of static noise. This might explain why the sides of the fingers are flat for typical Saffman-Taylor experiments. Comparison with previous numerical studies of the effect that temporal noise has on the Saffman-Taylor finger, leads to conclude that the effect of temporal noise and static noise are similar. The behavior of fluctuations of the finger width found in our experiments, is qualitatively similar to one recently reported, in the sense that, the magnitude of the width fluctuations decays as a power law of the capillary number, at low flow rates, and increases with capillary number for larger flow rates.

[Ovarian and para-aortic recurrence from cervix cancer detected by PET/CT]. / Recurrencia ovárica y paraaórtica de un carcinoma de cuello uterino detectada mediante PET/TC.

We present the case of a 34-year-old woman diagnosed of an adenosquamous carcinoma of the uterine cervix, stage IIB of the FIGO classification (International Federation of Gynecology and Obstetrics), treated with quimiotherapy, radiotheraphy and brachytheraphy with posterior hysterectomy. A recurrence of the disease was suspected due to the progressive rise of CEA levels. A PET/CT revealed abnormal foci in both ovaries, that had been transposed to avoid lesions due to radiation, and in a left para-aortic adenopathy. The diagnosis of recurrence in these sites was confirmed by biopsy. PET with FDG (F18-fluorodeoxyglucose) is useful in the staging of primary tumour and in the detection of recurrence in uterine cervical carcinoma, with better sensitivity and specificity than CT and MRI. PET/CT improves anatomic resolution and helps to resolve the origin of unclear foci like in the case presented in which ovaries were not in their normal situation due to transposition.

Anomalous roughening of viscous fluid fronts in spontaneous imbibition.

We report experiments on spontaneous imbibition of a viscous fluid by a model porous medium in the absence of gravity. The average position of the interface satisfies Washburn's law. Scaling of the interface fluctuations suggests a dynamic exponent z approximately 3, indicative of global dynamics driven by capillary forces. The complete set of exponents clearly shows that interfaces are not self-affine, exhibiting distinct local and global scaling, both for time (beta = 0.64 +/- 0.02, beta(*) = 0.33 +/- 0.03) and space (alpha = 1.94 +/- 0.20, alpha(loc) = 0.94 +/- 0.10). These values are compatible with an intrinsic anomalous scaling scenario.

Measurements of the bulk and interfacial velocity profiles in oscillating Newtonian and Maxwellian fluids.

We present the dynamic velocity profiles of a Newtonian fluid (glycerol) and a viscoelastic Maxwell fluid (CPyCl-NaSal in water) driven by an oscillating pressure gradient in a vertical cylindrical pipe. The frequency range explored has been chosen to include the first three resonance peaks of the dynamic permeability of the viscoelastic-fluid--pipe system. Three different optical measurement techniques have been employed. Laser Doppler anemometry has been used to measure the magnitude of the velocity at the center of the liquid column. Particle image velocimetry and optical deflectometry are used to determine the velocity profiles at the bulk of the liquid column and at the liquid-air interface respectively. The velocity measurements in the bulk are in good agreement with the theoretical predictions of a linear theory. The results, however, show dramatic differences in the dynamic behavior of Newtonian and viscoelastic fluids, and demonstrate the importance of resonance phenomena in viscoelastic fluid flows, biofluids in particular, in confined geometries.

CYGD: the Comprehensive Yeast Genome Database.

The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.

[Psoas abscess as cause of lumbar spine pain detected by scintigraphy with gallium in a patient with suspicion of spondylodiscitis]. / Absceso del psoas como causa de dolor lumbar detectado mediante gammagrafía con galio en un paciente con sospecha de espondilodiscitis.

A 56 year old man with fever and lumbar pain who underwent an abdominal CT scan that showed lumbar arthrosic changes, although it was not possible to rule out infectious disease in L5/S1. Bone scintigraphy was requested. It showed heterogeneous hyperuptake that did not make it possible to exclude a spondylodiscitis in this site. Scintigraphy with 67Ga-citrate excluded infectious diseases in the lumbar spine column. However, a pathological uptake was observed in the left iliac fossa suggestive of psoas abscess, which was confirmed by ultrasonography, isolating streptococcus viridans.