A dynamical stochastic model of yeast translation across the cell cycle

Translation is a central step in gene expression, however its quantitative and time-resolved regulation is poorly understood. We developed a discrete, stochastic model for protein translation in S. cerevisiae in a whole-transcriptome, single-cell context. A “base case” scenario representing an average cell highlights translation initiation rates as the main co-translational regulatory parameters. Codon usage bias emerges as a secondary regulatory mechanism through ribosome stalling. Demand for anticodons with low abundancy is shown to cause above-average ribosome dwelling times. Codon usage bias correlates strongly both with protein synthesis rates and elongation rates. Applying the model to a time-resolved transcriptome estimated by combining data from FISH and RNA-Seq experiments, it could be shown that increased total transcript abundance during the cell cycle decreases translation efficiency at single transcript level. Translation efficiency grouped by gene function shows highest values for ribosomal and glycolytic genes. Ribosomal proteins peak in S phase while glycolytic proteins rank highest in later cell cycle phases.Peer Reviewe

Marginality of bulk-edge correspondence for single-valley Hamiltonians

We study the correspondence between the non-trivial topological properties associated with the individual valleys of gapped bilayer graphene (BLG), as a prototypical multi-valley system, and the gapless modes at its edges and other interfaces. We find that the exact connection between the valley-specific Hall conductivity and the number of gapless edge modes does not hold in general, but is dependent on the boundary conditions, even in the absence of intervalley coupling. This non-universality is attributed to the absence of a well-defined topological invariant within a given valley of BLG; yet, a more general topological invariant may be defined in certain cases, which explains the distinction between the BLG-vacuum and BLG-BLG interfaces.Comment: 7 pages, 4 figure

Asie méridionale

Coste Nathanaël et Nicolas Ploumpidis, Bittersweet Waters / Eaux douces, eaux amères. Irrigation Practices and Modern Challenge in South India, Pondichéry, Institut français de Pondichéry (Publications hors série n° 5), DVD trilingue. Saint-Mézard Isabelle, Eastward Bound : India’s New Positioning in Asia, New Delhi, Manohar, French Research Institute in India, 2006, 500 p

Semi-spheroidal Quantum Harmonic Oscillator

A new single-particle shell model is derived by solving the Schr\"odinger equation for a semi-spheroidal potential well. Only the negative parity states of the $Z(z)$ component of the wave function are allowed, so that new magic numbers are obtained for oblate semi-spheroids, semi-sphere and prolate semi-spheroids. The semi-spherical magic numbers are identical with those obtained at the oblate spheroidal superdeformed shape: 2, 6, 14, 26, 44, 68, 100, 140, ... The superdeformed prolate magic numbers of the semi-spheroidal shape are identical with those obtained at the spherical shape of the spheroidal harmonic oscillator: 2, 8, 20, 40, 70, 112, 168 ...Comment: 4 pages, 3 figures, 1 tabl

New Approaches To Photometric Redshift Prediction Via Gaussian Process Regression In The Sloan Digital Sky Survey

Expanding upon the work of Way and Srivastava 2006 we demonstrate how the use of training sets of comparable size continue to make Gaussian process regression (GPR) a competitive approach to that of neural networks and other least-squares fitting methods. This is possible via new large size matrix inversion techniques developed for Gaussian processes (GPs) that do not require that the kernel matrix be sparse. This development, combined with a neural-network kernel function appears to give superior results for this problem. Our best fit results for the Sloan Digital Sky Survey (SDSS) Main Galaxy Sample using u,g,r,i,z filters gives an rms error of 0.0201 while our results for the same filters in the luminous red galaxy sample yield 0.0220. We also demonstrate that there appears to be a minimum number of training-set galaxies needed to obtain the optimal fit when using our GPR rank-reduction methods. We find that morphological information included with many photometric surveys appears, for the most part, to make the photometric redshift evaluation slightly worse rather than better. This would indicate that most morphological information simply adds noise from the GP point of view in the data used herein. In addition, we show that cross-match catalog results involving combinations of the Two Micron All Sky Survey, SDSS, and Galaxy Evolution Explorer have to be evaluated in the context of the resulting cross-match magnitude and redshift distribution. Otherwise one may be misled into overly optimistic conclusions.Comment: 32 pages, ApJ in Press, 2 new figures, 1 new table of comparison methods, updated discussion, references and typos to reflect version in Pres

Exposure to Melan-A/MART-126-35 tumor epitope specific CD8+T cells reveals immune escape by affecting the ubiquitin-proteasome system (UPS)

Efficient processing of target antigens by the ubiquitin-proteasome-system (UPS) is essential for treatment of cancers by T cell therapies. However, immune escape due to altered expression of IFN-γ-inducible components of the antigen presentation machinery and consequent inefficient processing of HLA- dependent tumor epitopes can be one important reason for failure of such therapies. Here, we show that short-term co-culture of Melan-A/MART-1 tumor antigen-expressing melanoma cells with Melan-A/MART-126-35-specific cytotoxic T lymphocytes (CTL) led to resistance against CTL-induced lysis because of impaired Melan-A/MART-126-35 epitope processing. Interestingly, deregulation of p97/VCP expression, which is an IFN-γ-independent component of the UPS and part of the ER-dependent protein degradation pathway (ERAD), was found to be essentially involved in the observed immune escape. In support, our data demonstrate that re-expression of p97/VCP in Melan-A/MART-126-35 CTL-resistant melanoma cells completely restored immune recognition by Melan-A/MART-126-35 CTL. In conclusion, our experiments show that impaired expression of IFN-γ-independent components of the UPS can exert rapid immune evasion of tumor cells and suggest that tumor antigens processed by distinct UPS degradation pathways should be simultaneously targeted in T cell therapies to restrict the likelihood of immune evasion due to impaired antigen processing

Monoclonal antibodies against human astrocytomas and their reactivity pattern

The establishment of hybridomas after fusion of X63-Ag8.653 mouse myeloma cells and splenocytes from mice hyperimmunized against human astrocytomas is presented. The animals were primed with 5 × 106 chemically modified uncultured or cultured glioma cells. Six weeks after the last immunization step an intrasplenal booster injection was administrated and 3 days later the spleen cells were prepared for fusion experiments. According to the specificity analysis of the generated antibodies 7 hybridoma products (MUC 7-22, MUC 8-22, MUC 10-22, MUC 11-22, MUC 14-22, MUC 15-22 and MUC 2-63) react with gliomas, neuroblastomas and melanomas as well as with embryonic and fetal cells but do not recognize non-neurogenic tumors. The selected monoclonal antibodies (McAbs) of IgG1 and IgG2a isotypes are not extensively characterized but these antibodies have been demonstrated to be reactive with a panel of glioma cell lines with varying patterns of antigen distribution. Using the McAbs described above and a series of cryosections of glioma biopsies and paraffin sections of the same material as well as glioma cultures established from these, variable antigenic profiles among glioma cell populations could be demonstrated. From these results it is evident that there is not only a distinct degree of antigenic heterogeneity among and within brain tumors, but also that the pattern of antigenic expression can change continuously. Some of the glioma associated antigens recognized by the selected antibodies persist after fixation with methanol/acetone and Karnovsky's fixative and probably are oncoembryonic/oncofetal antigen(s). The data suggest that the use of McAbs recognizing tumor associated oncofetal antigens in immunohistochemistry facilitates objective typing of intracranial malignancies and precise analysis of fine needle brain/tumor biopsies in a sensitive and reproducible manner