Gene expression: degrade to derepress

Chromatin immunoprecipitation and sequencing (ChIP‐seq) provides a static snap‐shot of DNA‐associated proteins which fails to reflect the dynamics of the DNA‐bound proteome. Now, Catic and co‐workers combine ubiquitin ChIP‐seq and proteasome inhibitors to map sites of DNA‐associated protein degradation on a genome‐wide scale. They identify an ubiquitin ligase which targets a transcriptional repressor for destruction by the proteasome, thus activating transcription of specific genes. These findings reveal that the ubiquitin proteasome system actively regulates transcription

Using Biomechanical Optimization to Interpret Dancers\u27 Pose Selection for a Partnered Spin

Swing dancing is a high tempo, athletic form of dancing. In performing their physically rigorous jumps, lifts, and spins, dancers often talk about using the laws of physics. However, they do not have mathematical evidence to support these claims. Our goal was to determine whether expert swing dancers physically optimize their pose for a partnered spin. In a partnered spin, two dancers connect hands and spin around a single vertical axis. A biomechanical model built in Mathematica allowed comparisons of mathematically produced optimal poses to live dancers with the use of a motion capture system. We hypothesized that expert swing dancers would achieve a higher fraction of their optimal acceleration than beginners. We were unable to determine a statistically significant difference between the posses of expert and beginner dancers. However, the optimal pose predicted by the model was intuitively reasonable

What Would the Nautilus Say? Unleashing Creativity in Mathematics!

While the nautilus shell is often represented in popular culture as an example of a golden spiral, according to many mathematicians it is not. In this paper we examine multiple arguments for and against considering the nautilus as a “golden” spiral and offer a semi-structured task that is accessible to middle school students and beyond to begin their own investigation. Our hope is that asking, what would the nautilus say, can serve as a starting point for children and adults alike to push against the walls we so often draw around mathematical questions and begin to see where their creativity takes them as they venture outside of the maths box

Keeping the proportions of protein complex components in check

How do cells maintain relative proportions of protein complex components? Advances in quantitative, genome-wide measurements have begun to shed light onto the roles of protein synthesis and degradation in establishing the precise proportions in living cells: on the one hand, ribosome profiling studies indicate that proteins are already produced in the correct relative proportions. On the other hand, proteomic studies found that many complexes contain subunits that are made in excess and subsequently degraded. Here, we discuss these seemingly contradictory findings, emerging principles, and remaining open questions. We conclude that establishing precise protein levels involves both coordinated synthesis and post-translational fine-tuning via protein degradation

Quantitative proteomics reveals dynamic interaction of c-Jun N-terminal kinase (JNK) with RNA transport granule proteins splicing factor proline- and glutamine-rich (Sfpq) and non-POU domain-containing octamer-binding protein (Nono) during neuronal differentiation

The c-Jun N-terminal kinase (JNK) is an important mediator of physiological and pathophysiological processes in the central nervous system. Importantly, JNK is not only involved in neuronal cell death but also plays a significant role in neuronal differentiation and regeneration. For example, nerve growth factor (NGF) induces JNK-dependent neuronal differentiation in several model systems. The mechanism how JNK mediates neuronal differentiation is not well understood. Here, we employ a proteomic strategy to better characterize the function of JNK during neuronal differentiation. We use SILAC-based quantitative proteomics to identify proteins that interact with JNK in PC12 cells in an NGF-dependent manner. Intriguingly, we find that JNK interacts with neuronal transport granule proteins such as Sfpq and Nono upon NGF treatment. We validate the specificity of these interactions by showing that they are disrupted by a specific peptide inhibitor that blocks the interaction of JNK with its substrates. Immunoprecipitation and western blotting experiments confirm the interaction of JNK1 with Sfpq/Nono and demonstrate that it is RNA dependent. Confocal microscopy and subcellular fractionation indicates that JNK1 associates with neuronal granule proteins in the cytosol of PC12 cells, primary cortical neurons and P19-neuronal cells. Finally, siRNA experiments confirm that Sfpq is necessary for neuronal outgrowth in PC12 cells and that it is most likely acting in the same pathway as JNK. In summary, our data indicate that the interaction of JNK1 with transport granule proteins in the cytosol of differentiating neurons plays an important role during neuronal development

Electronic bulk and domain wall properties in B-site doped hexagonal ErMnO3_3

Acceptor and donor doping is a standard for tailoring semiconductors. More recently, doping was adapted to optimize the behavior at ferroelectric domain walls. In contrast to more than a century of research on semiconductors, the impact of chemical substitutions on the local electronic response at domain walls is largely unexplored. Here, the hexagonal manganite ErMnO$_3$ is donor doped with Ti$^{4+}$. Density functional theory calculations show that Ti$^{4+}$ goes to the B-site, replacing Mn$^{3+}$. Scanning probe microscopy measurements confirm the robustness of the ferroelectric domain template. The electronic transport at both macro- and nanoscopic length scales is characterized. The measurements demonstrate the intrinsic nature of emergent domain wall currents and point towards Poole-Frenkel conductance as the dominant transport mechanism. Aside from the new insight into the electronic properties of hexagonal manganites, B-site doping adds an additional degree of freedom for tuning the domain wall functionality

Extensive allele-specific translational regulation in hybrid mice

Translational regulation is mediated through the interaction between diffusible trans-factors and cis-elements residing within mRNA transcripts. In contrast to extensively studied transcriptional regulation, cis-regulation on translation remains underexplored. Using deep sequencing-based transcriptome and polysome profiling, we globally profiled allele-specific translational efficiency for the first time in an F1 hybrid mouse. Out of 7,156 genes with reliable quantification of both alleles, we found 1,008 (14.1%) exhibiting significant allelic divergence in translational efficiency. Systematic analysis of sequence features of the genes with biased allelic translation revealed that local RNA secondary structure surrounding the start codon and proximal out-of-frame upstream AUGs could affect translational efficiency. Finally, we observed that the cis-effect was quantitatively comparable between transcriptional and translational regulation. Such effects in the two regulatory processes were more frequently compensatory, suggesting that the regulation at the two levels could be coordinated in maintaining robustness of protein expression

Intrinsic and extrinsic conduction contributions at nominally neutral domain walls in hexagonal manganites

Conductive and electrostatic atomic force microscopy (cAFM and EFM) are used to investigate the electric conduction at nominally neutral domain walls in hexagonal manganites. The EFM measurements reveal a propensity of mobile charge carriers to accumulate at the nominally neutral domain walls in ErMnO3, which is corroborated by cAFM scans showing locally enhanced d.c. conductance. Our findings are explained based on established segregation enthalpy profiles for oxygen vacancies and interstitials, providing a microscopic model for previous, seemingly disconnected observations ranging from insulating to conducting domain wall behavior. In addition, we observe variations in conductance between different nominally neutral walls that we attribute to deviations from the ideal charge-neutral structure within the bulk, leading to a superposition of extrinsic and intrinsic contributions. Our study clarifies the complex transport properties at nominally neutral domain walls in hexagonal manganites and establishes new possibilities for tuning their electronic response based on oxidation conditions, opening the door for domain-wall based sensor technology.Comment: 5 pages, 3 figure

Maf links Neuregulin1 signaling to cholesterol synthesis in myelinating Schwann cells

Cholesterol is a major constituent of myelin membranes, which insulate axons and allow saltatory conduction. Therefore, Schwann cells, the myelinating glia of the peripheral nervous system, need to produce large amounts of cholesterol. Here, we define a crucial role of the transcription factor Maf in myelination and cholesterol biosynthesis and show that Maf acts downstream from Neuregulin1 (Nrg1). Maf expression is induced when Schwann cells begin myelination. Genetic ablation of Maf resulted in hypomyelination that resembled mice with defective Nrg1 signaling. Importantly, loss of Maf or Nrg1 signaling resulted in a down-regulation of the cholesterol synthesis program, and Maf directly binds to enhancers of cholesterol synthesis genes. Furthermore, we identified the molecular mechanisms by which Nrg1 signaling regulates Maf levels. Transcription of Maf depends on calmodulin-dependent kinases downstream from Nrg1, whereas Nrg1-MAPK signaling stabilizes Maf protein. Our results delineate a novel signaling cascade regulating cholesterol synthesis in myelinating Schwann cells