DEGRONOPEDIA:a web server for proteome-wide inspection of degrons

E3 ubiquitin ligases recognize substrates through their short linear motifs termed degrons. While degron-signaling has been a subject of extensive study, resources for its systematic screening are limited. To bridge this gap, we developed DEGRONOPEDIA, a web server that searches for degrons and maps them to nearby residues that can undergo ubiquitination and disordered regions, which may act as protein unfolding seeds. Along with an evolutionary assessment of degron conservation, the server also reports on post-translational modifications and mutations that may modulate degron availability. Acknowledging the prevalence of degrons at protein termini, DEGRONOPEDIA incorporates machine learning to assess N-/C-terminal stability, supplemented by simulations of proteolysis to identify degrons in newly formed termini. An experimental validation of a predicted C-terminal destabilizing motif, coupled with the confirmation of a post-proteolytic degron in another case, exemplifies its practical application. DEGRONOPEDIA can be freely accessed at degronopedia.com

DEGRONOPEDIA:a web server for proteome-wide inspection of degrons

E3 ubiquitin ligases recognize substrates through their short linear motifs termed degrons. While degron-signaling has been a subject of extensive study, resources for its systematic screening are limited. To bridge this gap, we developed DEGRONOPEDIA, a web server that searches for degrons and maps them to nearby residues that can undergo ubiquitination and disordered regions, which may act as protein unfolding seeds. Along with an evolutionary assessment of degron conservation, the server also reports on post-translational modifications and mutations that may modulate degron availability. Acknowledging the prevalence of degrons at protein termini, DEGRONOPEDIA incorporates machine learning to assess N-/C-terminal stability, supplemented by simulations of proteolysis to identify degrons in newly formed termini. An experimental validation of a predicted C-terminal destabilizing motif, coupled with the confirmation of a post-proteolytic degron in another case, exemplifies its practical application. DEGRONOPEDIA can be freely accessed at degronopedia.com

Structure effects in Ne-20+Pb-208 quasi-elastic scattering

Preliminary results of an analysis of experiments devoted to a study of the sensitivity of the 20Ne + 208Pb quasi-elastic angular distributions at two near-barrier energies and the previously measured corresponding barrier distribution to the value of the nuclear quadrupole deformation length of 20Ne are reported

Lorentz Invariance Violation induced time delays in GRBs in different cosmological models

Lorentz Invariance Violation (LIV) manifesting itself by energy dependent modification of standard relativistic dispersion relation has recently attracted a considerable attention. Ellis et al. previously investigated the energy dependent time offsets in different energy bands on a sample of gamma ray bursts and, assuming standard cosmological model, they found a weak indication for redshift dependence of time delays suggestive of LIV. Going beyond the $\Lambda$CDM cosmology we extend this analysis considering also four alternative models of dark energy (quintessence with constant and variable equation of state, Chaplygin gas and brane-world cosmology). It turns out that the effect noticed by Ellis et al. is also present in those models and is the strongest for quintessence with variable equation of state.Comment: 14 pages, 1 figur

Are the weak channels really weak?

The transfer probabilities for 20Ne + 90Zr and 20Ne + 92Zr at energies near the Coulomb barrier were measured. This quantity turned out to be very similar for both Zr isotopes and does not explain the observed differences in the barrier height distributions for these systems

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Background: The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues. Results: Randomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Graphia was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development. Conclusion: Expression profiles obtained from public RNA-seq datasets - despite being generated by different laboratories using different methodologies - can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species

Badania przetwórstwa stopowego biodegradowalnych poliestrów alifatyczno-aromatycznych na wyroby włókniste

Research is described in the article concerning the melt processing of biodegradable aliphatic-aromatic copolyesters into fibrous products. Copolyesters containing 57 - 60% of a tri-component aliphatic portion (copolymers of butylene glycol and adypic-, succinic-, glutaric acid and terephtalic acid) prepared on a large laboratory scale were used in fibres and nonwoven from molten polymers. Fibres were made in a two-step process comprising spinning and drawing. Nonwovens were formed by the spunbond method. Main properties are given of the polymers and fibres, and the nonwoven made thereof. It was found that the aliphatic-aromatic copolyesters prepared reveal good spinability. Thermal properties: Tg g < 0 °C oraz niską T m ~115 °C włókna z alifatyczno-aromatycznych kopoliestrówmogą być stosowane w ograniczonym zakresie, przede wszystkim na wyroby jednorazowego użytku. Ze względów ekonomicznych bardziej wskazany jest przerób tych polimerów na gotowe wyroby włókiennicze, np. włókniny spun bonded