Determinants of the temperature adaptation of mRNA degradation

The rate of chemical reactions increases proportionally with temperature, but the interplay of biochemical reactions permits deviations from this relation and adaptation. The degradation of individual mRNAs in yeast increased to varying degrees with temperature. We examined how these variations are influenced by the translation and codon composition of mRNAs. We developed a method that revealed the existence of a neutral half-life above which mRNAs are stabilized by translation but below which they are destabilized. The proportion of these two mRNA subpopulations remained relatively constant under different conditions, even with slow cell growth due to nutrient limitation, but heat shock reduced the proportion of translationally stabilized mRNAs. At the same time, the degradation of these mRNAs was partially temperature-compensated through Upf1, the mediator of nonsense-mediated decay. Compensation was also promoted by some asparagine and serine codons, whereas tyrosine codons promote temperature sensitization. These codons play an important role in the degradation of mRNAs encoding key cell membrane and cell wall proteins, which promote cell integrity

Medical record: systematic centralization versus secure on demand aggregation

<p>Abstract</p> <p>Background</p> <p>As patients often see the data of their medical histories scattered among various medical records hosted in several health-care establishments, the purpose of our multidisciplinary study was to define a pragmatic and secure on-demand based system able to gather this information, with no risk of breaching confidentiality, and to relay it to a medical professional who asked for the information via a specific search engine.</p> <p>Methods</p> <p>Scattered data are often heterogeneous, which makes the task of gathering information very hard. Two methods can be compared: trying to solve the problem by standardizing and centralizing all the information about every patient in a single Medical Record system or trying to use the data "as is" and find a way to obtain the most complete and the most accurate information. Given the failure of the first approach, due to the lack of standardization or privacy and security problems, for example, we propose an alternative that relies on the current state of affairs: an on-demand system, using a specific search engine that is able to retrieve information from the different medical records of a single patient.</p> <p>Results</p> <p>We describe the function of Medical Record Search Engines (MRSE), which are able to retrieve all the available information regarding a patient who has been hospitalized in different hospitals and to provide this information to health professionals upon request. MRSEs use pseudonymized patient identities and thus never have access to the patient's identity. However, though the system would be easy to implement as it by-passes many of the difficulties associated with a centralized architecture, the health professional would have to validate the information, i.e. read all of the information and create his own synthesis and possibly reject extra data, which could be a drawback. We thus propose various feasible improvements, based on the implementation of several tools in our on-demand based system.</p> <p>Conclusions</p> <p>A system that gathers all of the currently available information regarding a patient on the request of health-care professionals could be of great interest. This low-cost pragmatic alternative to centralized medical records could be developed quickly and easily. It could also be designed to include extra features and should thus be considered by health authorities.</p

Partial cricotracheal resection for paediatric subglottic stenosis: update of the Lausanne experience with 129 cases.

OBJECTIVES: Partial cricotracheal resection (PCTR) is widely accepted for treating severe paediatric laryngotracheal stenosis (LTS). However, it remains limited to a few experienced centres. Here we report an update of the Lausanne experience in paediatric PCTR performed or supervised by a senior surgeon (Philippe Monnier). METHODS: An ongoing database of 129 paediatric patients who underwent PCTR for benign LTS between March 1978 and July 2012 at our hospital was retrospectively reviewed. Demographic characteristics and information on preoperative status, stenosis and surgery were collected. Primary outcomes were measured as overall and operation-specific decannulation rates (ODR and OSDR, respectively), and secondary outcomes as morbidity, mortality and postoperative functional results. RESULTS: A total of 129 paediatric patients [79 males and 50 females; mean age, 4.1 years (1 month-16 years, median age of 2 years old)] underwent PCTR during the study period. ODR and OSDR were 90 and 81%, respectively. The decannulation rates were significantly superior for single-stage PCTR compared with double-stage PCTR in both ODR and OSDR. Eight patients died postoperatively for reasons unrelated to surgery. Partial anastomotic dehiscence was seen in 13 patients, 9 of whom were successfully treated by revision surgery. Respiratory, voice and swallowing functions were near normal or only minimally impaired in 86, 65 and 81% of patients, respectively. CONCLUSIONS: PCTR is effective and feasible with good ODR and OSDR for highgrade / severe LTS. Glottic involvement and the presence of comorbidities were negative predictive factors of decannulation. Early detection and reintervention of postoperative incipient dehiscence contribute to avoiding the progress to late restenosis; however, voice improvement remains a challenge

Global regulatory architecture of human, mouse and rat tissue transcriptomes

Background Predicting molecular responses in human by extrapolating results from model organisms requires a precise understanding of the architecture and regulation of biological mechanisms across species. Results Here, we present a large-scale comparative analysis of organ and tissue transcriptomes involving the three mammalian species human, mouse and rat. To this end, we created a unique, highly standardized compendium of tissue expression. Representative tissue specific datasets were aggregated from more than 33,900 Affymetrix expression microarrays. For each organism, we created two expression datasets covering over 55 distinct tissue types with curated data from two independent microarray platforms. Principal component analysis (PCA) revealed that the tissue-specific architecture of transcriptomes is highly conserved between human, mouse and rat. Moreover, tissues with related biological function clustered tightly together, even if the underlying data originated from different labs and experimental settings. Overall, the expression variance caused by tissue type was approximately 10 times higher than the variance caused by perturbations or diseases, except for a subset of cancers and chemicals. Pairs of gene orthologs exhibited higher expression correlation between mouse and rat than with human. Finally, we show evidence that tissue expression profiles, if combined with sequence similarity, can improve the correct assignment of functionally related homologs across species. Conclusion The results demonstrate that tissue-specific regulation is the main determinant of transcriptome composition and is highly conserved across mammalian species

Dectin-1 binding to annexins on apoptotic cells induces peripheral immune tolerance via NADPH oxidase-2

Summary Uptake of apoptotic cells (ACs) by dendritic cells (DCs) and induction of a tolerogenic DC phenotype is an important mechanism for establishing peripheral tolerance to self-antigens. The receptors involved and underlying signaling pathways are not fully understood. Here, we identify Dectin-1 as a crucial tolerogenic receptor binding with nanomolar affinity to the core domain of several annexins (annexin A1, A5, and A13) exposed on ACs. Annexins bind to Dectin-1 on a site distinct from the interaction site of pathogen-derived β-glucans. Subsequent tolerogenic signaling induces selective phosphorylation of spleen tyrosine kinase (SYK), causing activation of NADPH oxidase-2 and moderate production of reactive oxygen species. Thus, mice deficient for Dectin-1 develop autoimmune pathologies (autoantibodies and splenomegaly) and generate stronger immune responses (cytotoxic T cells) against ACs. Our data describe an important immunological checkpoint system and provide a link between immunosuppressive signals of ACs and maintenance of peripheral immune tolerance

Bmi1 loss produces an increase in astroglial cells and a decrease in neural stem cell population and proliferation

The polycomb transcriptional repressor Bmi1 promotes cell cycle progression, controls cell senescence, and is implicated in brain development. Loss of Bmi1 leads to a decreased brain size and causes progressive ataxia and epilepsy. Recently, Bmi1 was shown to control neural stem cell (NSC) renewal. However, the effect of Bmi1 loss on neural cell fate in vivo and the question whether the action of Bmi1 was intrinsic to the NSCs remained to be investigated. Here, we show that Bmi1 is expressed in the germinal zone in vivo and in NSCs as well as in progenitors proliferating in vitro, but not in differentiated cells. Loss of Bmi1 led to a decrease in proliferation in zones known to contain progenitors: the newborn cortex and the newborn and adult subventricular zone. This decrease was accentuated in vitro, where we observed a drastic reduction in NSC proliferation and renewal because of NSC-intrinsic effects of Bmi1 as shown by the means of RNA interference. Bmi1(-/-) mice also presented more astrocytes at birth, and a generalized gliosis at postnatal day 30. At both stages, colocalization of bromodeoxyuridine and GFAP demonstrated that Bmi1 loss did not prevent astrocyte precursor proliferation. Supporting these observations, Bmi1(-/-) neurospheres generate preferentially astrocytes probably attributable to a different responsiveness to environmental factors. Bmi1 is therefore necessary for NSC renewal in a cell-intrinsic mode, whereas the altered cell pattern of the Bmi1(-/-) brain shows that in vivo astrocyte precursors can proliferate in the absence of Bmi1

Continuum and line modeling of disks around young stars II. Line diagnostics for GASPS from the DENT grid

Aims. We want to understand the chemistry and physics of disks on the basis of a large unbiased and statistically relevant grid of disk models. One of the main goals is to explore the diagnostic power of various gas emission lines and line ratios for deriving main disk parameters such as the gas mass. Methods. We explore the results of the DENT grid (Disk Evolution with Neat Theory) that consists of 300 000 disk models with 11 free parameters. Through a statistical analysis, we search for correlations and trends in an effort to find tools for disk diagnostic. Results. All calculated quantities like species masses, temperatures, continuum and line fluxes differ by several orders of magnitude across the entire parameter space. The broad distribution of these quantities as a function of input parameters shows the limitation of using a prototype T Tauri or Herbig Ae/Be disk model. The statistical analysis of the DENT grid shows that CO gas is rarely the dominant carbon reservoir in disks. Models with large inner radii (10 times the dust condensation radius) and/or shallow surface density gradients lack massive gas phase water reservoirs. Also, 60% of the disks have gas temperatures averaged over the oxygen mass in the range between 15 and 70 K; the average gas temperatures for CO and O differ by less than a factor two. Studying the observational diagnostics, the [CII] 158 \mum fine structure line flux is very sensitive to the stellar UV flux and presence of a UV excess and it traces the outer disk radius (Rout). In the submm, the CO low J rotational lines also trace Rout. Low [OI] 63/145 line ratios (< a few) can be explained with cool atomic O gas in the uppermost surface layers leading to self-absorption in the 63 \mum line; this occurs mostly for massive non-flaring, settled disk models without UV excess. ... abbreviatedComment: 15 pages, 25 figures, accepted for publication in A&

First light of the VLT planet finder SPHERE. I. Detection and characterization of the sub-stellar companion GJ 758 B

GJ758 B is a brown dwarf companion to a nearby (15.76 pc) solar-type, metal-rich (M/H = +0.2 dex) main-sequence star (G9V) that was discovered with Subaru/HiCIAO in 2009. From previous studies, it has drawn attention as being the coldest (~600K) companion ever directly imaged around a neighboring star. We present new high-contrast data obtained during the commissioning of the SPHERE instrument at the VLT. The data was obtained in Y-, J-, H-, and Ks-bands with the dual-band imaging (DBI) mode of IRDIS, providing a broad coverage of the full near-infrared (near-IR) range at higher contrast and better spectral sampling than previously reported. In this new set of high-quality data, we report the re-detection of the companion, as well as the first detection of a new candidate closer-in to the star. We use the new 8 photometric points for an extended comparison of GJ758 B with empirical objects and 4 families of atmospheric models. From comparison to empirical object, we estimate a T8 spectral type, but none of the comparison object can accurately represent the observed near-IR fluxes of GJ758 B. From comparison to atmospheric models, we attribute a Teff = 600K $\pm$ 100K, but we find that no atmospheric model can adequately fit all the fluxes of GJ758 B. The photometry of the new candidate companion is broadly consistent with L-type objects, but a second epoch with improved photometry is necessary to clarify its status. The new astrometry of GJ758 B shows a significant proper motion since the last epoch. We use this result to improve the determination of the orbital characteristics using two fitting approaches, Least-Square Monte Carlo and Markov Chain Monte Carlo. Finally, we analyze the sensitivity of our data to additional closer-in companions and reject the possibility of other massive brown dwarf companions down to 4-5 AU. [abridged]Comment: 20 pages, 15 figures. Accepted for publication in A&

First light of the VLT planet finder SPHERE. II. The physical properties and the architecture of the young systems PZ Tel and HD 1160 revisited

[Abridged] Context. The young systems PZ Tel and HD 1160, hosting known low-mass companions, were observed during the commissioning of the new planet finder SPHERE with several imaging and spectroscopic modes. Aims. We aim to refine the physical properties and architecture of both systems. Methods. We use SPHERE commissioning data and REM observations, as well as literature and unpublished data from VLT/SINFONI, VLT/NaCo, Gemini/NICI, and Keck/NIRC2. Results. We derive new photometry and confirm the nearly daily photometric variability of PZ Tel A. Using literature data spanning 38 yr, we show that the star also exhibits a long-term variability trend. The 0.63-3.8 mic SED of PZ Tel B allows us to revise its properties: spectral type M7+/-1, Teff=2700+/-100 K, log(g)<4.5 dex, log(L/L_Sun)=-2.51+/-0.10 dex, and mass 38-72 MJ. The 1-3.8 mic SED of HD 1160 B suggests a massive brown dwarf or a low-mass star with spectral type M5.5-7.0, Teff=3000+/-100 K, [M/H]=-0.5-0.0 dex, log(L/L_Sun)=-2.81+/-0.10 dex, and mass 39-168 MJ. We confirm the deceleration and high eccentricity (e>0.66) of PZ Tel B. For e<0.9, the inclination, longitude of the ascending node, and time of periastron passage are well constrained. The system is seen close to an edge-on geometry. We reject other brown dwarf candidates outside 0.25" for both systems, and massive giant planets (>4 MJ) outside 0.5" for the PZ Tel system. We also show that K1-K2 color can be used with YJH low-resolution spectra to identify young L-type companions, provided high photometric accuracy (<0.05 mag) is achieved. Conclusions. SPHERE opens new horizons in the study of young brown dwarfs and giant exoplanets thanks to high-contrast imaging capabilities at optical and near-infrared wavelengths, as well as high signal-to-noise spectroscopy in the near-infrared from low (R~30-50) to medium resolutions (R~350).Comment: 25 pages, 23 figures, accepted for publication in A&A on Oct. 13th, 2015; version including language editing. Typo on co-author name on astroph page corrected, manuscript unchange