Dynamic Regulation of Alternative Splicing by Silencers that Modulate 5′ Splice Site Competition

SummaryAlternative splicing makes a major contribution to proteomic diversity in higher eukaryotes with ∼70% of genes encoding two or more isoforms. In most cases, the molecular mechanisms responsible for splice site choice remain poorly understood. Here, we used a randomization-selection approach in vitro to identify sequence elements that could silence a proximal strong 5′ splice site located downstream of a weakened 5′ splice site. We recovered two exonic and four intronic motifs that effectively silenced the proximal 5′ splice site both in vitro and in vivo. Surprisingly, silencing was only observed in the presence of the competing upstream 5′ splice site. Biochemical evidence strongly suggests that the silencing motifs function by altering the U1 snRNP/5′ splice site complex in a manner that impairs commitment to specific splice site pairing. The data indicate that perturbations of non-rate-limiting step(s) in splicing can lead to dramatic shifts in splice site choice

Free particle scattering off two oscillating disks

We investigate the two-dimensional classical dynamics of the scattering of point particles by two periodically oscillating disks. The dynamics exhibits regular and chaotic scattering properties, as a function of the initial conditions and parameter values of the system. The energy is not conserved since the particles can gain and loose energy from the collisions with the disks. We find that for incident particles whose velocity is on the order of the oscillating disk velocity, the energy of the exiting particles displays non-monotonic gaps of allowed energies, and the distribution of exiting particle velocities shows significant fluctuations in the low energy regime. We also considered the case when the initial velocity distribution is Gaussian, and found that for high energies the exit velocity distribution is Gaussian with the same mean and variance. When the initial particle velocities are in the irregular regime the exit velocity distribution is Gaussian but with a smaller mean and variance. The latter result can be understood as an example of stochastic cooling. In the intermediate regime the exit velocity distribution differs significantly from Gaussian. A comparison of the results presented in this paper to previous chaotic static scattering problems is also discussed.Comment: 9 doble sided pages 13 Postscript figures, REVTEX style. To appear in Phys. Rev.

Молитвенная практика в жизни студенческой молодежи Гомельского региона и Малопольского воеводства

Материалы XI Междунар. науч. конф. студентов, аспирантов и молодых ученых, Гомель, 17-18 мая 2018 г

A mechanistic model of tau amyloid aggregation based on direct observation of oligomers.

Protein aggregation plays a key role in neurodegenerative disease, giving rise to small oligomers that may become cytotoxic to cells. The fundamental microscopic reactions taking place during aggregation, and their rate constants, have been difficult to determine due to lack of suitable methods to identify and follow the low concentration of oligomers over time. Here we use single-molecule fluorescence to study the aggregation of the repeat domain of tau (K18), and two mutant forms linked with familial frontotemporal dementia, the deletion mutant ΔK280 and the point mutant P301L. Our kinetic analysis reveals that aggregation proceeds via monomeric assembly into small oligomers, and a subsequent slow structural conversion step before fibril formation. Using this approach, we have been able to quantitatively determine how these mutations alter the aggregation energy landscape.D.K. acknowledges funding from the Wellcome Trust (WT089703) and MRC. E.M. acknowledges funding from the Wellcome Trust (WT089703), DZNE and Max-Planck-Society. M.K. acknowledges fellowships from the Danish research council and the Lundbeck Foundation. N.S. and M.H.H acknowledge funding from the Augustus Newman foundation. G.A.G is funded by the Schiff Foundation. T.P.J.K acknowledges funding from the ERC, Augustus Newman Foundation and the BBSRC.This is the final version of the article. It first appeared from NPG via http://dx.doi.org/10.1038/ncomms802

Infrared spectroscopy of NGC 1068: Probing the obscured ionizing AGN continuum

The ISO-SWS 2.5-45 um infrared spectroscopic observations of the nucleus of the Seyfert 2 galaxy NGC 1068 (see companion paper) are combined with a compilation of UV to IR narrow emission line data to determine the spectral energy distribution (SED) of the obscured extreme-UV continuum that photoionizes the narrow line emitting gas in the active galactic nucleus. We search a large grid of gas cloud models and SEDs for the combination that best reproduces the observed line fluxes and NLR geometry. Our best fit model reproduces the observed line fluxes to better than a factor of 2 on average and is in general agreement with the observed NLR geometry. It has two gas components that are consistent with a clumpy distribution of dense outflowing gas in the center and a more extended distribution of less dense and more clumpy gas farther out that has no net outflow. The best fit SED has a deep trough at ~4 Ryd, which is consistent with an intrinsic Big Blue Bump that is partially absorbed by ~6x10^19 cm^-2 of neutral hydrogen interior to the NLR.Comment: 15 pp, 4 figures, ApJ accepte

Neutrino Mass Limit from Galaxy Cluster Number Density Evolution

Measurements of the evolution with redshift of the number density of massive galaxy clusters are used to constrain the energy density of massive neutrinos and so the sum of neutrino masses $\sum m_\nu$. We consider a spatially-flat cosmological model with cosmological constant, cold dark matter, baryonic matter, and massive neutrinos. Accounting for the uncertainties in the measurements of the relevant cosmological parameters we obtain a limit of $\sum m_\nu$ $<$ 2.4 eV (95 % C.L.).Comment: 6 pages, 2 figures and references added, accepted for publication in Phys. Rev.

The Case for Perspicuous Programming

This essay examines the nature of programs, classifies the traditional or enigmatic styles of programming, distinguishing template, prose and literate styles; notes the contrast between batch programs and interactive programs; and highlights the advantages of giving priority in developing interactive programs to the online documentation, and proposes that this documentation should be the principal target of development, with the executable program code being regarded of secondary and consequent

Tackling the Mouse‐on‐Mouse Problem in Cochlear Immunofluorescence: A Simple Double‐Blocking Protocol for Immunofluorescent Labeling of Murine Cochlear Sections with Primary Mouse Antibodies

The mouse is the most widely used animal model in hearing research. Immunohistochemistry and immunofluorescent staining of murine cochlear sections have, thus, remained a backbone of inner ear research. Since many primary antibodies are raised in mouse, the problem of "mouse-on-mouse" background arises due to the interaction between the anti-mouse secondary antibody and the native mouse immunoglobulins. Here, we describe the pattern of mouse-on-mouse background fluorescence in sections of the postnatal mouse cochlea. Furthermore, we describe a simple double-blocking immunofluorescence protocol to label mouse cochlear cryosections. The protocol contains a conventional blocking step with serum, and an additional blocking step with a commercially available anti-mouse IgG blocking reagent. This blocking technique virtually eliminates the "mouse-on-mouse" background in murine cochlear sections, while adding only a little time to the staining protocol. We provide detailed instructions and practical tips for tissue harvesting, processing, and immunofluorescence-labeling. Further protocol modifications are described, to shorten the duration of the protocol, based on the primary antibody incubation temperature. Finally, we demonstrate examples of immunofluorescence staining performed using different incubation times and various incubation temperatures with a commercially available mouse monoclonal primary antibody