O6-Methylguanosine leads to position-dependent effects on ribosome speed and fidelity

Nucleic acids are under constant assault from endogenous and environmental agents that alter their physical and chemical properties. O6-methylation of guanosine (m(6)G) is particularly notable for its high mutagenicity, pairing with T, during DNA replication. Yet, while m(6)G accumulates in both DNA and RNA, little is known about its effects on RNA. Here, we investigate the effects of m(6)G on the decoding process, using a reconstituted bacterial translation system. m(6)G at the first and third position of the codon decreases the accuracy of tRNA selection. The ribosome readily incorporates near-cognate aminoacyl-tRNAs (aa-tRNAs) by forming m(6)G-uridine codon-anticodon pairs. Surprisingly, the introduction of m(6)G to the second position of the codon does not promote miscoding, but instead slows the observed rates of peptide-bond formation by \u3e1000-fold for cognate aa-tRNAs without altering the rates for near-cognate aa-tRNAs. These in vitro observations were recapitulated in eukaryotic extracts and HEK293 cells. Interestingly, the analogous modification N6-methyladenosine (m(6)A) at the second position has only a minimal effect on tRNA selection, suggesting that the effects on tRNA selection seen with m(6)G are due to altered geometry of the base pair. Given that the m6G:U base pair is predicted to be nearly indistinguishable from a Watson-Crick base pair, our data suggest that the decoding center of the ribosome is extremely sensitive to changes at the second position. Our data, apart from highlighting the deleterious effects that these adducts pose to cellular fitness, shed new insight into decoding and the process by which the ribosome recognizes codon-anticodon pairs

Ribosomes Left in the Dust: Diverse Strategies for Peptide-Mediated Translation Stalling

In two recent papers, Arenz et al. (2014a) and Bischoff et al. (2014) provide structural insights into drug-induced, peptide-mediated stalling of the ribosome

Prospects for the cavity-assisted laser cooling of molecules

Cooling of molecules via free-space dissipative scattering of photons is thought not to be practicable due to the inherently large number of Raman loss channels available to molecules and the prohibitive expense of building multiple repumping laser systems. The use of an optical cavity to enhance coherent Rayleigh scattering into a decaying cavity mode has been suggested as a potential method to mitigate Raman loss, thereby enabling the laser cooling of molecules to ultracold temperatures. We discuss the possibility of cavity-assisted laser cooling particles without closed transitions, identify conditions necessary to achieve efficient cooling, and suggest solutions given experimental constraints. Specifically, it is shown that cooperativities much greater than unity are required for cooling without loss, and that this could be achieved via the superradiant scattering associated with intracavity self-localization of the molecules. Particular emphasis is given to the polar hydroxyl radical (OH), cold samples of which are readily obtained from Stark deceleration.Comment: 18 pages, 10 figure

An international landmine telehealth symposium between Hawaii and Thailand using an Internet2 and multi-protocol videoconferencing bridge.

An international telehealth symposium was conducted between healthcare institutions in Hawaii and Thailand using a combination of Asynchronous Transfer Mode, and Internet2 connectivity. Military and civilian experts exchanged information on the acute and rehabilitative care of landmine victims in Southeast Asia. Videoconferencing can promote civil-military cooperation in healthcare fields that have multiple international stakeholders

An Active Role for the Ribosome in Determining the Fate of Oxidized mRNA

Chemical damage to RNA affects its functional properties and thus may pose a significant hurdle to the translational apparatus; however, the effects of damaged mRNA on the speed and accuracy of the decoding process and their interplay with quality-control processes are not known. Here, we systematically explore the effects of oxidative damage on the decoding process using a well-defined bacterial in vitro translation system. We find that the oxidative lesion 8-oxoguanosine (8-oxoG) reduces the rate of peptide-bond formation by more than three orders of magnitude independent of its position within the codon. Interestingly, 8-oxoG had little effect on the fidelity of the selection process, suggesting that the modification stalls the translational machinery. Consistent with these findings, 8-oxoG mRNAs were observed to accumulate and associate with polyribosomes in yeast strains in which no-go decay is compromised. Our data provide compelling evidence that mRNA-surveillance mechanisms have evolved to cope with damaged mRNA

3D Cosmic Shear: Cosmology from CFHTLenS

This paper presents the first application of 3D cosmic shear to a wide-field weak lensing survey. 3D cosmic shear is a technique that analyses weak lensing in three dimensions using a spherical harmonic approach, and does not bin data in the redshift direction. This is applied to CFHTLenS, a 154 square degree imaging survey with a median redshift of 0.7 and an effective number density of 11 galaxies per square arcminute usable for weak lensing. To account for survey masks we apply a 3D pseudo-Cl approach on weak lensing data, and to avoid uncertainties in the highly non-linear regime, we separately analyse radial wave numbers k<=1.5h/Mpc and k<=5.0h/Mpc, and angular wavenumbers l~400-5000. We show how one can recover 2D and tomographic power spectra from the full 3D cosmic shear power spectra and present a measurement of the 2D cosmic shear power spectrum, and measurements of a set of 2-bin and 6-bin cosmic shear tomographic power spectra; in doing so we find that using the 3D power in the calculation of such 2D and tomographic power spectra from data naturally accounts for a minimum scale in the matter power spectrum. We use 3D cosmic shear to constrain cosmologies with parameters OmegaM, OmegaB, sigma8, h, ns, w0, wa. For a non-evolving dark energy equation of state, and assuming a flat cosmology, lensing combined with WMAP7 results in h=0.78+/-0.12, OmegaM=0.252+/-0.079, sigma8=0.88+/-0.23 and w=-1.16+/-0.38 using only scales k<=1.5h/Mpc. We also present results of lensing combined with first year Planck results, where we find no tension with the results from this analysis, but we also find no significant improvement over the Planck results alone. We find evidence of a suppression of power compared to LCDM on small scales 1.5 < k < 5.0 h/Mpc in the lensing data, which is consistent with predictions of the effect of baryonic feedback on the matter power spectrum.Comment: Full journal article here http://mnras.oxfordjournals.org/content/442/2/1326.full.pdf+htm

Dissecting the molecular organization of the translocon-associated protein complex

In eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein (TRAP) complex is an integral component of the translocon, assisting the Sec61 protein-conducting channel by regulating signal sequence and transmembrane helix insertion in a substrate-dependent manner. Here we use cryo-electron tomography (CET) to study the structure of the native translocon in evolutionarily divergent organisms and disease-linked TRAP mutant fibroblasts from human patients. The structural differences detected by subtomogram analysis form a basis for dissecting the molecular organization of the TRAP complex. We assign positions to the four TRAP subunits within the complex, providing insights into their individual functions. The revealed molecular architecture of a central translocon component advances our understanding of membrane protein biogenesis and sheds light on the role of TRAP in human congenital disorders of glycosylation

Very weak lensing in the CFHTLS Wide: Cosmology from cosmic shear in the linear regime

We present an exploration of weak lensing by large-scale structure in the linear regime, using the third-year (T0003) CFHTLS Wide data release. Our results place tight constraints on the scaling of the amplitude of the matter power spectrum sigma_8 with the matter density Omega_m. Spanning 57 square degrees to i'_AB = 24.5 over three independent fields, the unprecedented contiguous area of this survey permits high signal-to-noise measurements of two-point shear statistics from 1 arcmin to 4 degrees. Understanding systematic errors in our analysis is vital in interpreting the results. We therefore demonstrate the percent-level accuracy of our method using STEP simulations, an E/B-mode decomposition of the data, and the star-galaxy cross correlation function. We also present a thorough analysis of the galaxy redshift distribution using redshift data from the CFHTLS T0003 Deep fields that probe the same spatial regions as the Wide fields. We find sigma_8(Omega_m/0.25)^0.64 = 0.785+-0.043 using the aperture-mass statistic for the full range of angular scales for an assumed flat cosmology, in excellent agreement with WMAP3 constraints. The largest physical scale probed by our analysis is 85 Mpc, assuming a mean redshift of lenses of 0.5 and a LCDM cosmology. This allows for the first time to constrain cosmology using only cosmic shear measurements in the linear regime. Using only angular scales theta> 85 arcmin, we find sigma_8(Omega_m/0.25)_lin^0.53 = 0.837+-0.084, which agree with the results from our full analysis. Combining our results with data from WMAP3, we find Omega_m=0.248+-0.019 and sigma_8 = 0.771+-0.029.Comment: 23 pages, 16 figures (A&A accepted

CFHTLenS: mapping the large-scale structure with gravitational lensing

We present a quantitative analysis of the largest contiguous maps of projected mass density obtained from gravitational lensing shear. We use data from the 154 deg^2 covered by the Canada–France–Hawaii Telescope Lensing Survey (CFHTLenS). Our study is the first attempt to quantitatively characterize the scientific value of lensing maps, which could serve in the future as a complementary approach to the study of the dark universe with gravitational lensing. We show that mass maps contain unique cosmological information beyond that of traditional two-point statistical analysis techniques. Using a series of numerical simulations, we first show how, reproducing the CFHTLenS observing conditions, gravitational lensing inversion provides a reliable estimate of the projected matter distribution of large-scale structure. We validate our analysis by quantifying the robustness of the maps with various statistical estimators. We then apply the same process to the CFHTLenS data. We find that the two-point correlation function of the projected mass is consistent with the cosmological analysis performed on the shear correlation function discussed in the CFHTLenS companion papers. The maps also lead to a significant measurement of the third-order moment of the projected mass, which is in agreement with analytic predictions, and to a marginal detection of the fourth-order moment. Tests for residual systematics are found to be consistent with zero for the statistical estimators we used. A new approach for the comparison of the reconstructed mass map to that predicted from the galaxy distribution reveals the existence of giant voids in the dark matter maps as large as 3° on the sky. Our analysis shows that lensing mass maps are not only consistent with the results obtained by the traditional shear approach, but they also appear promising for new techniques such as peak statistics and the morphological analysis of the projected dark matter distribution

Mix&Match: Towards Omitting Modelling Through In-Situ Alteration and Remixing of Model Repository Artifacts in Mixed Reality

The accessibility of tools to model artifacts is one of the core driving factors for the adoption of Personal Fabrication. Subsequently, model repositories like Thingiverse became important tools in (novice) makers' processes. They allow them to shorten or even omit the design process, offloading a majority of the effort to other parties. However, steps like measurement of surrounding constraints (e.g., clearance) which exist only inside the users' environment, can not be similarly outsourced. We propose Mix&Match a mixed-reality-based system which allows users to browse model repositories, preview the models in-situ, and adapt them to their environment in a simple and immediate fashion. Mix&Match aims to provide users with CSG operations which can be based on both virtual and real geometry. We present interaction patterns and scenarios for Mix&Match, arguing for the combination of mixed reality and model repositories. This enables almost modelling-free personal fabrication for both novices and expert makers.Comment: 12 pages, 15 figures, 1 table, To appear in the Proceedings of the ACM Conference on Human Factors in Computing Systems 2020 (CHI'20