ATXN2-CAG42 sequesters PABPC1 into insolubility and induces FBXW8 in cerebellum of old ataxic knock-in mice

Spinocerebellar Ataxia Type 2 (SCA2) is caused by expansion of a polyglutamine encoding triplet repeat in the human ATXN2 gene beyond (CAG)31. This is thought to mediate toxic gain-of-function by protein aggregation and to affect RNA processing, resulting in degenerative processes affecting preferentially cerebellar neurons. As a faithful animal model, we generated a knock-in mouse replacing the single CAG of murine Atxn2 with CAG42, a frequent patient genotype. This expansion size was inherited stably. The mice showed phenotypes with reduced weight and later motor incoordination. Although brain Atxn2 mRNA became elevated, soluble ATXN2 protein levels diminished over time, which might explain partial loss-of-function effects. Deficits in soluble ATXN2 protein correlated with the appearance of insoluble ATXN2, a progressive feature in cerebellum possibly reflecting toxic gains-of-function. Since in vitro ATXN2 overexpression was known to reduce levels of its protein interactor PABPC1, we studied expansion effects on PABPC1. In cortex, PABPC1 transcript and soluble and insoluble protein levels were increased. In the more vulnerable cerebellum, the progressive insolubility of PABPC1 was accompanied by decreased soluble protein levels, with PABPC1 mRNA showing no compensatory increase. The sequestration of PABPC1 into insolubility by ATXN2 function gains was validated in human cell culture. To understand consequences on mRNA processing, transcriptome profiles at medium and old age in three different tissues were studied and demonstrated a selective induction of Fbxw8 in the old cerebellum. Fbxw8 is encoded next to the Atxn2 locus and was shown in vitro to decrease the level of expanded insoluble ATXN2 protein. In conclusion, our data support the concept that expanded ATXN2 undergoes progressive insolubility and affects PABPC1 by a toxic gain-of-function mechanism with tissuespecific effects, which may be partially alleviated by the induction of FBXW8

RHEBI Expression in Embryonic and Postnatal Mouse

Ras homolog enriched in brain (RHEB1) is a member within the superfamily of GTP-binding proteins encoded by the RAS oncogenes. RHEB1 is located at the crossroad of several important pathways including the insulin-signaling pathways and thus plays an important role in different physiological processes. To understand better the physiological relevance of RHEB1 protein, the expres- sion pattern of RHEB1 was analyzed in both embryonic (at E3.5–E16.5) and adult (1-month old) mice. RHEB1 immu- nostaining and X-gal staining were used for wild-type and Rheb1 gene trap mutant mice, respectively. These inde- pendent methods revealed similar RHEB1 expression pat- terns during both embryonic and postnatal developments. Ubiquitous uniform RHEB1/β-gal and/or RHEB1 expres- sion was seen in preimplantation embryos at E3.5 and post- implantation embryos up to E12.5. Between stages E13.5 and E16.5, RHEB1 expression levels became complex: In particular, strong expression was identified in neural tis- sues, including the neuroepithelial layer of the mesenceph- alon, telencephalon, and neural tube of CNS and dorsal root ganglia. In addition, strong expression was seen in certain peripheral tissues including heart, intestine, muscle, and urinary bladder. Postnatal mice have broad spatial RHEB1 expression in different regions of the cerebral cortex, sub- cortical regions (including hippocampus), olfactory bulb, medulla oblongata, and cerebellum (particularly in Purkinje cells). Significant RHEB1 expression was also viewed in internal organs including the heart, intestine, urinary blad- der, and muscle. Moreover, adult animals have complex tis- sue- and organ-specific RHEB1 expression patterns with different intensities observed throughout postnatal develop- ment. Its expression level is in general comparable in CNS and other organs of mouse. Thus, the expression pattern of RHEB1 suggests that it likely plays a ubiquitous role in the development of the early embryo with more tissue-specific roles in later development

RHEB1 Expression in Embryonic and Postnatal Mouse

Ras homolog enriched in brain (RHEB1) is a member within the superfamily of GTP-binding proteins encoded by the RAS oncogenes. RHEB1 is located at the crossroad of several important pathways including the insulin-signaling pathways and thus plays an important role in different physiological processes. To understand better the physiological relevance of RHEB1 protein, the expres-sion pattern of RHEB1 was analyzed in both embryonic (at E3.5–E16.5) and adult (1-month old) mice. RHEB1 immu-nostaining and X-gal staining were used for wild-type and Rheb1 gene trap mutant mice, respectively. These inde-pendent methods revealed similar RHEB1 expression pat-terns during both embryonic and postnatal developments. Ubiquitous uniform RHEB1/β-gal and/or RHEB1 expres-sion was seen in preimplantation embryos at E3.5 and post-implantation embryos up to E12.5. Between stages E13.5 and E16.5, RHEB1 expression levels became complex: In particular, strong expression was identified in neural tis-sues, including the neuroepithelial layer of the mesenceph-alon, telencephalon, and neural tube of CNS and dorsal root ganglia. In addition, strong expression was seen in certain peripheral tissues including heart, intestine, muscle, and urinary bladder. Postnatal mice have broad spatial RHEB1 expression in different regions of the cerebral cortex, sub-cortical regions (including hippocampus), olfactory bulb, medulla oblongata, and cerebellum (particularly in Purkinje cells). Significant RHEB1 expression was also viewed in internal organs including the heart, intestine, urinary blad-der, and muscle. Moreover, adult animals have complex tis-sue- and organ-specific RHEB1 expression patterns with different intensities observed throughout postnatal develop-ment. Its expression level is in general comparable in CNS and other organs of mouse. Thus, the expression pattern of RHEB1 suggests that it likely plays a ubiquitous role in the development of the early embryo with more tissue-specific roles in later development

Structural and mechanistic consequences of polypeptide binding by GroEL

The remarkable ability of the chaperonin GroEL to recognise a diverse range of non-native states of proteins constitutes one of the most fascinating molecular recognition events in protein chemistry. Recent structural studies have revealed a possible model for substrate binding by GroEL and a high-resolution image of the GroEL–GroES folding machinery has provided important new insights into our understanding of the mechanism of action of this chaperonin. Studies with a variety of model substrates reveal that the binding of substrate proteins to GroEL is not just a passive event, but can result in significant changes in the structure and stability of the bound polypeptide. The potential impact of this on the mechanism of chaperonin-assisted folding is not fully understood, but provides exciting scope for further experiment

Electron rescattering at metal nanotips induced by ultrashort laser pulses

We report on the first investigation of plateau and cut-off structures in photoelectron spectra from nano-scale metal tips interacting with few-cycle near-infrared laser pulses. These hallmarks of electron rescattering, well-known from atom-laser interaction in the strong-field regime, appear at remarkably low laser intensities with nominal Keldysh parameters of the order of $\gtrsim 10$. Quantum and quasi-classical simulations reveal that a large field enhancement near the tip and the increased backscattering probability at a solid-state target play a key role. Plateau electrons are by an order of magnitude more abundant than in comparable atomic spectra, reflecting the high density of target atoms at the surface. The position of the cut-off serves as an in-situ probe for the locally enhanced electric field at the tip apex

Calculating Energy and Its Spatial Distribution for a Subsurface Urban Heat Island Using a GIS-Approach

In urban areas, the human influence on the city-ecosystem often results in a Subsurface Urban Heat Island (SUHI), which can be used geothermally. Unfortunately, a model of a SUHI does not consider the geology and hydrogeology of the subsoil. These can vary significantly over short distances, and are of considerable importance for the energy balance. In this work, we calculated the energy and its density stored in the subsoil via a SUHI. For this so-called energy-SUHI (e-SUHI), we evaluated the geology and its physical parameters for the first 20 m below ground level in the German city of Nuremberg and linked them to measured underground temperatures in a GIS application. This approach revealed stored energy of 1.634 × 1010 MJ within the soil and water for the study area with an area of 163 km2 and a volume of 3.26 × 109 m3. It corresponds to an average energy density of 5.0 MJ/m3. The highest energy density of 16.5 MJ/m3 was found in the city center area and correlated well to increases in subsurface temperature. As expected, our model reacts sensitively to thickness changes in the geological layers and the unsaturated zone

Inheritance of gene density–related higher order chromatin arrangements in normal and tumor cell nuclei

A gene density–related difference in the radial arrangement of chromosome territories (CTs) was previously described for human lymphocyte nuclei with gene-poor CT #18 located toward the nuclear periphery and gene-dense CT #19 in the nuclear interior (Croft, J.A., J.M. Bridger, S. Boyle, P. Perry, P. Teague, and W.A. Bickmore. 1999. J. Cell Biol. 145:1119–1131). Here, we analyzed the radial distribution of chromosome 18 and 19 chromatin in six normal cell types and in eight tumor cell lines, some of them with imbalances and rearrangements of the two chromosomes. Our findings demonstrate that a significant difference in the radial distribution of #18 and #19 chromatin is a common feature of higher order chromatin architecture in both normal and malignant cell types. However, in seven of eight tumor cell lines, the difference was less pronounced compared with normal cell nuclei due to a higher fraction of nuclei showing an inverted CT position, i.e., a CT #18 located more internally than a CT #19. This observation emphasizes a partial loss of radial chromatin order in tumor cell nuclei

Characterization of the Si:Se+ Spin-Photon Interface

Silicon is the most-developed electronic and photonic technological platform and hosts some of the highest-performance spin and photonic qubits developed to date. A hybrid quantum technology harnessing an efficient spin-photon interface in silicon would unlock considerable potential by enabling ultralong-lived photonic memories, distributed quantum networks, microwave-to-optical photon converters, and spin-based quantum processors, all linked with integrated silicon photonics. However, the indirect band gap of silicon makes identification of efficient spin-photon interfaces nontrivial. Here we build upon the recent identification of chalcogen donors as a promising spin-photon interface in silicon. We determine that the spin-dependent optical degree of freedom has a transition dipole moment stronger than previously thought [here 1.96(8) D], and the spin T1 lifetime in low magnetic fields is longer than previously thought [here longer than 4.6(1.5) h]. We furthermore determine the optical excited-state lifetime [7.7(4) ns], and therefore the natural radiative efficiency [0.80(9)%], and by measuring the phonon sideband determine the zero-phonon emission fraction [16(1)%]. Taken together, these parameters indicate that an integrated quantum optoelectronic platform based on chalcogen-donor qubits in silicon is well within reach of current capabilities

Optimization of transcription factor binding map accuracy utilizing knockout-mouse models

Genome-wide assessment of protein-DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify \u27hyper ChIPable regions\u27 as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses, particularly when developing ChIP-assays with novel antibody reagents