Disruption of the Mammalian Ccr4-Not Complex Contributes to Transcription-Mediated Genome Instability.

The mammalian Ccr4-Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. It is involved in the control of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, and nuclear RNA surveillance; the Ccr4-Not complex also plays a central role in the regulation of mRNA decay. Growing evidence suggests that gene transcription has a vital role in shaping the landscape of genome replication and is also a potent source of replication stress and genome instability. Here, we have examined the effects of the inactivation of the Ccr4-Not complex, via the depletion of the scaffold subunit CNOT1, on DNA replication and genome integrity in mammalian cells. In CNOT1-depleted cells, the elevated expression of the general transcription factor TATA-box binding protein (TBP) leads to increased RNA synthesis, which, together with R-loop accumulation, results in replication fork slowing, DNA damage, and senescence. Furthermore, we have shown that the stability of TBP mRNA increases in the absence of CNOT1, which may explain its elevated protein expression in CNOT1-depleted cells. Finally, we have shown the activation of mitogen-activated protein kinase signalling as evidenced by ERK1/2 phosphorylation in the absence of CNOT1, which may be responsible for the observed cell cycle arrest at the border of G1/S.

Structural and binding characterization of the LacdiNAc-specific adhesin (LabA; HopD) exodomain from Helicobacter pylori.

Helicobacter pylori (H. pylori) uses several outer membrane proteins for adhering to its host's gastric mucosa, an important step in establishing and preserving colonization. Several adhesins (SabA, BabA, HopQ) have been characterized in terms of their three-dimensional structure. A recent addition to the growing list of outer membrane porins is LabA (LacdiNAc-binding adhesin), which is thought to bind specifically to GalNAcß1-4GlcNAc, occurring in the gastric mucosa. LabA47-496 protein expressed as His-tagged protein in the periplasm of E. coli and purified via subtractive IMAC after TEV cleavage and subsequent size exclusion chromatography, resulted in bipyramidal crystals with good diffraction properties. Here, we describe the 2.06 â€‹Å resolution structure of the exodomain of LabA from H. pylori strain J99 (PDB ID: 6GMM). Strikingly, despite the relatively low levels of sequence identity with the other three structurally characterized adhesins (20-49%), LabA shares an L-shaped fold with SabA and BabA. The 'head' region contains a 4 â€‹+ â€‹3 α-helix bundle, with a small insertion domain consisting of a short antiparallel beta sheet and an unstructured region, not resolved in the crystal structure. Sequence alignment of LabA from different strains shows a high level of conservation in the N- and C-termini, and identifies two main types based on the length of the insertion domain ('crown' region), the 'J99-type' (insertion ~31 â€‹amino acids), and the H. pylori '26695 type' (insertion ~46 â€‹amino acids). Analysis of ligand binding using Native Electrospray Ionization Mass Spectrometry (ESI-MS) together with solid phase-bound, ELISA-type assays could not confirm the originally described binding of GalNAcß1-4GlcNAc-containing oligosaccharides, in line with other recent reports, which also failed to confirm LacdiNAc binding.

Andreev Modes from Phase Winding in a Full-Shell Nanowire-Based Transmon.

We investigate transmon qubits made from semiconductor nanowires with a fully surrounding superconducting shell. In the regime of reentrant superconductivity associated with the destructive Little-Parks effect, numerous coherent transitions are observed in the first reentrant lobe, where the shell carries 2π winding of superconducting phase, and are absent in the zeroth lobe. As junction density was increased by gate voltage, qubit coherence was suppressed then lost in the first lobe. These observations and numerical simulations highlight the role of winding-induced Andreev states in the junction.

Mid-infrared interference coatings with excess optical loss below 10 ppm.

We present high-reflectivity substrate-transferred single-crystal GaAs/AlGaAs interference coatings at a center wavelength of 4.54 µm with record-low excess optical loss below 10 parts per million. These high-performance mirrors are realized via a novel microfabrication process that differs significantly from the production of amorphous multilayers generated via physical vapor deposition processes. This new process enables reduced scatter loss due to the low surface and interfacial roughness, while low background doping in epitaxial growth ensures strongly reduced absorption. We report on a suite of optical measurements, including cavity ring-down, transmittance spectroscopy, and direct absorption tests to reveal the optical losses for a set of prototype mirrors. In the course of these measurements, we observe a unique polarization-orientation-dependent loss mechanism which we attribute to elastic anisotropy of these strained epitaxial multilayers. A future increase in layer count and a corresponding reduction of transmittance will enable optical resonators with a finesse in excess of 100 000 in the mid-infrared spectral region, allowing for advances in high resolution spectroscopy, narrow-linewidth laser stabilization, and ultrasensitive measurements of various light-matter interactions.

Flux-induced topological superconductivity in full-shell nanowires.

Hybrid semiconductor-superconductor nanowires have emerged as a promising platform for realizing topological superconductivity (TSC). Here, we present a route to TSC using magnetic flux applied to a full superconducting shell surrounding a semiconducting nanowire core. Tunneling into the core reveals a hard induced gap near zero applied flux, corresponding to zero phase winding, and a gapped region with a discrete zero-energy state around one applied flux quantum, corresponding to 2π phase winding. Theoretical analysis indicates that the winding of the superconducting phase can induce a transition to a topological phase supporting Majorana zero modes. Measured Coulomb blockade peak spacing around one flux quantum shows a length dependence that is consistent with the existence of Majorana modes at the ends of the nanowire.

Near-infrared scanning cavity ringdown for optical loss characterization of supermirrors.

A cavity ringdown system for probing the spatial variation of optical loss across high-reflectivity mirrors is described. This system is employed to examine substrate-transferred crystalline supermirrors and to quantify the effect of manufacturing process imperfections. Excellent agreement is observed between the ringdown-generated spatial measurements and differential interference contrast microscopy images. A 2-mm diameter ringdown scan in the center of a crystalline supermirror reveals highly uniform coating properties with excess loss variations below 1 ppm.

Introduction of a C-terminal hexa-lysine tag increases thermal stability of the LacDiNac binding adhesin (LabA) exodomain from Helicobacter pylori.

Helicobacter pylori is a pathogenic microorganism infecting approximately 50% of the global population, and establishes life-long colonization despite the hostile stomach environment. H. pylori employs a wide range of outer membrane proteins (adhesins) for epithelial attachment, which specifically bind to glycans or non-carbohydrate structures expressed on the gastric epithelium. A recently described adhesin from H. pylori is LabA, named after its ability to bind to a disaccharide present in gastric mucus (LacdiNAc-specific adhesin). Here, we describe the recombinant expression of LabA from H. pylori strains J99 and 26695 in E. coli. High yields of recombinant LabA were obtained using periplasmic expression. We found that the addition of a C-terminal hexalysine (6K) tag enhanced the thermal stability of LabA without affecting its secondary structure, using differential scanning fluorimetry and circular dichroism spectroscopy. In contrast to our previous report for another H. pylori adhesin (BabA), the 6K tag did not enhance recombinant protein yield or solubility. Both versions of LabA, with or without the 6K tag, were expressed and isolated from the periplasmic space of Escherichia coli, with a surprisingly high yield of at least 40 mg/L for each independent preparation, following a two-step purification protocol. The proteins were analyzed with mass spectrometry (MS). Unlike its reported effect on stability of BabA, the 6K tag did not appear to protect the N-term of recombinant LabA from partial periplasmic degradation.

An Integrated Dyspepsia Module for First-year Pharmacy Students.

Objective. To design an integrated dyspepsia module for first year pharmacy students that combines clinical and professional practice with fundamental sciences in five different science subject areas. Methods. The approaches used in designing this module are described with emphasis on strategies adopted to integrate science and practice, and the new ways of working adopted by the design team. Students' views and experiences of the module and its integration were explored using questionnaires. Results. A high proportion of students reported positive views and experiences of the module, the integration and its impact (as self-reported) on their learning and practice. The assessment of student performance indicated learning and attainment was at an appropriate level for a first-year module. Both the student grades and research results indicate a positive student learning experience. Conclusion. The dyspepsia module provides a flexible and effective template for the integration of science and practice in theme-based modules, with students reporting positively about the integration, including their perception of its contribution to improving their learning and understanding. New and more collaborative ways of working are required when designing integrated modules.

[Improvement of Psychosomatic Rehabilitation after Prestationary Intervention]. / Verbesserung des Rehabilitationsergebnis durch prästationäre Intervention.

Aim of the study: Improvement of psychosomatic rehabilitation efforts with prestationary intervention. Method: The study is designed as a prospective and randomisized interventon study including 317 in patients. Result: Most of the patients were women (69.4 %), the mean age was 50.2 years. As measured with the BDI-II patients with prestationary intervention improved more than patients without intervention. The motivation has not been changed significantly in both treatment arms. Various independent cofactors like long duration of unemployment, disablement and patients who apply to pension were identified. Conclusion: Finally a prestationary telephon interview improves the results of psychosomatic rehabilitation measured with BDI.

Post-transcriptional Control of Tumor Cell Autonomous Metastatic Potential by CCR4-NOT Deadenylase CNOT7.

Accumulating evidence supports the role of an aberrant transcriptome as a driver of metastatic potential. Deadenylation is a general regulatory node for post-transcriptional control by microRNAs and other determinants of RNA stability. Previously, we demonstrated that the CCR4-NOT scaffold component Cnot2 is an inherited metastasis susceptibility gene. In this study, using orthotopic metastasis assays and genetically engineered mouse models, we show that one of the enzymatic subunits of the CCR4-NOT complex, Cnot7, is also a metastasis modifying gene. We demonstrate that higher expression of Cnot7 drives tumor cell autonomous metastatic potential, which requires its deadenylase activity. Furthermore, metastasis promotion by CNOT7 is dependent on interaction with CNOT1 and TOB1. CNOT7 ribonucleoprotein-immunoprecipitation (RIP) and integrated transcriptome wide analyses reveal that CNOT7-regulated transcripts are enriched for a tripartite 3'UTR motif bound by RNA-binding proteins known to complex with CNOT7, TOB1, and CNOT1. Collectively, our data support a model of CNOT7, TOB1, CNOT1, and RNA-binding proteins collectively exerting post-transcriptional control on a metastasis suppressive transcriptional program to drive tumor cell metastasis.

Structural basis of Lewis(b) antigen binding by the Helicobacter pylori adhesin BabA.

Helicobacter pylori is a leading cause of peptic ulceration and gastric cancer worldwide. To achieve colonization of the stomach, this Gram-negative bacterium adheres to Lewis(b) (Le(b)) antigens in the gastric mucosa using its outer membrane protein BabA. Structural information for BabA has been elusive, and thus, its molecular mechanism for recognizing Le(b) antigens remains unknown. We present the crystal structure of the extracellular domain of BabA, from H. pylori strain J99, in the absence and presence of Le(b) at 2.0- and 2.1-Å resolutions, respectively. BabA is a predominantly α-helical molecule with a markedly kinked tertiary structure containing a single, shallow Le(b) binding site at its tip within a ß-strand motif. No conformational change occurs in BabA upon binding of Le(b), which is characterized by low affinity under acidic [K D (dissociation constant) of ~227 µM] and neutral (K D of ~252 µM) conditions. Binding is mediated by a network of hydrogen bonds between Le(b) Fuc1, GlcNAc3, Fuc4, and Gal5 residues and a total of eight BabA amino acids (C189, G191, N194, N206, D233, S234, S244, and T246) through both carbonyl backbone and side-chain interactions. The structural model was validated through the generation of two BabA variants containing N206A and combined D233A/S244A substitutions, which result in a reduction and complete loss of binding affinity to Le(b), respectively. Knowledge of the molecular basis of Le(b) recognition by BabA provides a platform for the development of therapeutics targeted at inhibiting H. pylori adherence to the gastric mucosa.

A non-proteolytic role for ubiquitin in deadenylation of MHC-I mRNA by the RNA-binding E3-ligase MEX-3C.

The regulation of protein and mRNA turnover is essential for many cellular processes. We recently showed that ubiquitin--traditionally linked to protein degradation--directly regulates the degradation of mRNAs through the action of a newly identified family of RNA-binding E3 ubiquitin ligases. How ubiquitin regulates mRNA decay remains unclear. Here, we identify a new role for ubiquitin in regulating deadenylation, the initial and often rate-limiting step in mRNA degradation. MEX-3C, a canonical member of this family of RNA-binding ubiquitin ligases, associates with the cytoplasmic deadenylation complexes and ubiquitinates CNOT7(Caf1), the main catalytic subunit of the CCR4-NOT deadenylation machinery. We establish a new role for ubiquitin in regulating MHC-I mRNA deadenylation as ubiquitination of CNOT7 by MEX-3C regulates its deadenylation activity and is required for MHC-I mRNA degradation. Since neither proteasome nor lysosome inhibitors rescued MEX-3C-mediated MHC-I mRNA degradation, our findings suggest a new non-proteolytic function for ubiquitin in the regulation of mRNA decay.

Phosphonium Polymethacrylates for Short Interfering RNA Delivery: Effect of Polymer and RNA Structural Parameters on Polyplex Assembly and Gene Knockdown.

Synthetic polymers containing quaternary phosphonium salts are an emerging class of materials for the delivery of oligo/polynucleotides. In this work, cationic phosphonium salt-containing polymethacrylates and their corresponding ammonium analogues were synthesized by reversible addition-fragmentation chain transfer polymerization. Both the nature of the charged heteroatom (N vs P) and the length of the spacer separating the cationic units along the polymer backbone (oxyethylene vs trioxyethylene) were systematically varied. Polymers efficiently bound short interfering RNA (siRNA) at N(+)/P(-) or P(+)/P(-) ratios of 2 and above. At a 20:1 ratio, small polyplexes (Rh: 4-15 nm) suitable for cellular uptake were formed that displayed low cytotoxicity. While siRNA polyplexes from both ammonium and phosphonium polymers were efficiently internalized by green fluorescent protein (GFP)-expressing 3T3 cells, no knockdown of GFP expression was observed. However, 65% Survivin gene knockdown was observed when siRNA was replaced with novel, multimerized long interfering RNA in HeLa cells, demonstrating the importance of RNA macromolecular architecture on RNA-mediated gene silencing.

Discovery, synthesis and biochemical profiling of purine-2,6-dione derivatives as inhibitors of the human poly(A)-selective ribonuclease Caf1.

Eukaryotic mRNA contains a 3' poly(A) tail, which plays important roles in the regulation of mRNA stability and translation. Well-characterized enzymes involved in the shortening of the poly(A) tail include the multi-subunit Ccr4-Not deadenylase, which contains the Caf1 (Pop2) and Ccr4 catalytic components, and poly(A)-specific ribonuclease (PARN). Two Mg(2+) ions present in the active sites of these ribonucleases are required for RNA cleavage. Here, we report the discovery, synthesis and biochemical profiling of purine-2,6-dione derivatives as (sub)micromolar inhibitors of Caf1.

Comprehensive study on the light shielding potential of thermotropic layers for the development of new materials.

In recent years thermotropic overheating protection glazings have been the focus for both solar thermal collector technology and architecture. A thermotropic glazing changes its light transmittance from highly transparent to light diffusing upon reaching a certain threshold temperature autonomously and reversibly. In thermotropic systems with fixed domains (TSFD) the scattering domains are embedded in a polymer matrix, which exhibits a sudden change of the refractive index upon reaching a threshold temperature. The aim of the present study was to comprehensively investigate the light shielding characteristics and potential of TSFD materials by applying simulation of light scattering in particle-filled layers. In random walk simulations a variety of parameters were varied systematically, and the effect on the light transmission behavior of TSFD was studied. The calculation steps of the simulation process are shown in detail. The simulations demonstrate that there is great potential for the production of functional materials with high overheating protection efficiency.

The enzyme activities of Caf1 and Ccr4 are both required for deadenylation by the human Ccr4-Not nuclease module.

In eukaryotic cells, the shortening and removal of the poly(A) tail (deadenylation) of cytoplasmic mRNA is a key event in regulated mRNA degradation. A major enzyme involved in deadenylation is the Ccr4-Not deadenylase complex, which can be recruited to its target mRNA by RNA-binding proteins or the miRNA repression complex. In addition to six non-catalytic components, the complex contains two enzymatic subunits with ribonuclease activity: Ccr4 and Caf1 (Pop2). In vertebrates, each deadenylase subunit is encoded by two paralogues: Caf1, which can interact with the anti-proliferative protein BTG2, is encoded by CNOT7 and CNOT8, whereas Ccr4 is encoded by the highly similar genes CNOT6 and CNOT6L. Currently, it is unclear whether the catalytic subunits work co-operatively or whether the nuclease components have unique roles in deadenylation. We therefore developed a method to express and purify a minimal human BTG2-Caf1-Ccr4 nuclease sub-complex from bacterial cells. By using chemical inhibition and well-characterized inactivating amino acid substitutions, we demonstrate that the enzyme activities of Caf1 and Ccr4 are both required for deadenylation in vitro. These results indicate that Caf1 and Ccr4 cooperate in mRNA deadenylation and suggest that the enzyme activities of Caf1 and Ccr4 are regulated via allosteric interactions within the nuclease module.

Improved expression and purification of the Helicobacter pylori adhesin BabA through the incorporation of a hexa-lysine tag.

Helicobacter pylori is a pathogenic bacterium that has the remarkable ability to withstand the harsh conditions of the stomach for decades. This is achieved through unique evolutionary adaptations, which include binding Lewis(b) antigens found on the gastric epithelium using the outer membrane protein BabA. We show here the yield of a recombinant form of BabA, comprising its putative extracellular binding domain, can be significantly increased through the addition of a hexa-lysine tag to the C-terminus of the protein. BabA was expressed in the periplasmic space of Escherichia coli and purified using immobilised metal ion affinity and size exclusion chromatography - yielding approximately 1.8 mg of protein per litre of culture. The hexa-lysine tag does not inhibit the binding activity of BabA as the recombinant protein was found to possess affinity towards HSA-Lewis(b) glycoconjugates.

Simplification to abacavir/lamivudine + atazanavir maintains viral suppression and improves bone and renal biomarkers in ASSURE, a randomized, open label, non-inferiority trial.

OBJECTIVE: Simplification of antiretroviral therapy in patients with suppressed viremia may minimize long-term adverse effects. The study's primary objective was to determine whether abacavir/lamivudine + atazanavir (ABC/3TC+ATV) was virologically non-inferior to tenofovir/emtricitabine + atazanavir/ritonavir (TDF/FTC+ATV/r) over 24 weeks in a population of virologically suppressed, HIV-1 infected patients. DESIGN: This open-label, multicenter, non-inferiority study enrolled antiretroviral experienced, HIV-infected adults currently receiving a regimen of TDF/FTC+ATV/r for ≥ 6 months with no history of virologic failure and whose HIV-1 RNA had been ≤ 75 copies/mL on 2 consecutive measurements including screening. Patients were randomized 1 ∶ 2 to continue current treatment or simplify to ABC/3TC+ATV. METHODS: The primary endpoint was the proportion of patients with HIV-RNA<50 copies/mL at Week 24 by the Time to Loss of Virologic Response (TLOVR) algorithm. Secondary endpoints included alternative measures of efficacy, adverse events (AEs), and fasting lipids. Exploratory endpoints included inflammatory, coagulation, bone, and renal biomarkers. RESULTS: After 24 weeks, ABC/3TC+ATV (n = 199) was non-inferior to TDF/FTC+ATV/r (n = 97) by both the primary analysis (87% in both groups) and all secondary efficacy analyses. Rates of grade 2-4 AEs were similar between the two groups (40% vs 37%, respectively), but an excess of hyperbilirubinemia made the rate of grade 3-4 laboratory abnormalities higher in the TDF/FTC+ATV/r group (30%) compared with the ABC/3TC+ATV group (13%). Lipid levels were stable except for HDL cholesterol, which increased significantly in the ABC/3TC+ATV group. Bone and renal biomarkers improved significantly between baseline and Week 24 in patients taking ABC/3TC+ATV, and the difference between groups was significant at Week 24. No significant changes occurred in any inflammatory or coagulation biomarker within or between treatment groups. CONCLUSIONS: After 24 weeks, simplification to ABC/3TC+ATV from TDF/FTC+ATV/r maintained viral suppression was well-tolerated, and led to improvements in bone and renal biomarkers and HDL cholesterol. TRIAL REGISTRATION: ClinicalTrials.gov NCT01102972 GlaxoSmithKline Clinical Study Register #113734.

Parametric amplification of attosecond pulse trains at 11†nm.

We report the first experimental demonstration of the parametric amplification of attosecond pulse trains at around 11 nm. The helium amplifier is driven by intense laser pulses and seeded by high-order harmonics pulses generated in a neon gas jet. Our measurements suggest that amplification takes place only if the seed pulse-trains are perfectly synchronized in time with the driving laser field in the amplifier. Varying the delay, we estimate the durations of the individual extreme ultraviolet pulses within the train to be on the order of 0.2 fs. Our results demonstrate that strong-field parametric amplification can be a suitable tool to amplify weak attosecond pulses from non-destructive pump-probe experiments and it is an important step towards designing amplifiers for realization of energetic XUV pulses with sub-femtosecond duration using compact lasers fitting in university laboratories.

229Thorium-doped calcium fluoride for nuclear laser spectroscopy.

The (229)thorium isotope presents an extremely low-energy isomer state of the nucleus which is expected around 7.8 eV, in the vacuum ultraviolet (VUV) regime. This unique system may bridge between atomic and nuclear physics, enabling coherent manipulation and precision spectroscopy of nuclear quantum states using laser light. It has been proposed to implant (229)thorium into VUV transparent crystal matrices to facilitate laser spectroscopy and possibly realize a solid-state nuclear clock. In this work, we validate the feasibility of this approach by computer modelling of thorium doping into calcium fluoride single crystals. Using atomistic modelling and full electronic structure calculations, we find a persistent large band gap and no additional electronic levels emerging in the middle of the gap due to the presence of the dopant, which should allow direct optical interrogation of the nuclear transition.Based on the electronic structure, we estimate the thorium nuclear quantum levels within the solid-state environment. Precision laser spectroscopy of these levels will allow the study of a broad range of crystal field effects, transferring Mössbauer spectroscopy into the optical regime.