Nuclear RNA Surveillance in \u3cem\u3eSaccharomyces cerevisiae\u3c/em\u3e: Trf4p-dependent Polyadenylation of Nascent Hypomethylated tRNA and an Aberrant Form of 5S rRNA

1-Methyladenosine modification at position 58 of tRNA is catalyzed by a two-subunit methyltransferase composed of Trm6p and Trm61p in Saccharomyces cerevisiae. Initiator tRNA (tRNAiMet) lacking m1A58 (hypomethylated) is rendered unstable through the cooperative function of the poly(A) polymerases, Trf4p/Trf5p, and the nuclear exosome. We provide evidence that a catalytically active Trf4p poly(A) polymerase is required for polyadenylation of hypomethylated tRNAiMet in vivo. DNA sequence analysis of tRNAiMet cDNAs and Northern hybridizations of poly(A)+ RNA provide evidence that nascent pre-tRNAiMet transcripts are targeted for polyadenylation and degradation. We determined that a mutant U6 snRNA and an aberrant form of 5S rRNA are stabilized in the absence of Trf4p, supporting that Trf4p facilitated RNA surveillance is a global process that stretches beyond hypomethylated tRNAiMet. We conclude that an array of RNA polymerase III transcripts are targeted for Trf4p/ Trf5p-dependent polyadenylation and turnover to eliminate mutant and variant forms of normally stable RNAs

RNA Unwinding by the Trf4/Air2/Mtr4 Polyadenylation (TRAMP) Complex

Many RNA-processing events in the cell nucleus involve the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex, which contains the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for processing by the nuclear exosome. In addition, TRAMP functions as an exosome cofactor during RNA degradation, and it has been speculated that this role involves disruption of RNA secondary structure. However, it is unknown whether TRAMP displays RNA unwinding activity. It is also not clear how unwinding would be coordinated with polyadenylation and the function of the RNA helicase Mtr4p in modulating poly(A) addition. Here, we show that TRAMP robustly unwinds RNA duplexes. The unwinding activity of Mtr4p is significantly stimulated by Trf4p/Air2p, but the stimulation of Mtr4p does not depend on ongoing polyadenylation. Nonetheless, polyadenylation enables TRAMP to unwind RNA substrates that it otherwise cannot separate. Moreover, TRAMP displays optimal unwinding activity on substrates with a minimal Mtr4p binding site comprised of adenylates. Our results suggest a model for coordination between unwinding and polyadenylation activities by TRAMP that reveals remarkable synergy between helicase and poly(A) polymerase

Degradation of Hypomodified tRNA\u3csub\u3ei\u3c/sub\u3e\u3csup\u3eMet\u3c/sup\u3e in vivo Involves RNA-dependent ATPase Activity of the DExH Helicase Mtr4p

Effective turnover of many incorrectly processed RNAs in yeast, including hypomodified tRNAi Met, requires the TRAMP complex, which appends a short poly(A) tail to RNA designated for decay. The poly(A) tail stimulates degradation by the exosome. The TRAMP complex contains the poly(A) polymerase Trf4p, the RNA-binding protein Air2p, and the DExH RNA helicase Mtr4p. The role of Mtr4p in RNA degradation processes involving the TRAMP complex has been unclear. Here we show through a genetic analysis that MTR4 is required for degradation but not for polyadenylation of hypomodified tRNAi Met. A suppressor of the trm6-504 mutation in the tRNA m1A58 methyltransferase (Trm6p/Trm61p), which causes a reduced level of tRNAi Met, was mapped to MTR4. This mtr4-20 mutation changed a single amino acid in the conserved helicase motif VI of Mtr4p. The mutation stabilizes hypomodified tRNAi Met in vivo but has no effect on TRAMP complex stability or polyadenylation activity in vivo or in vitro. We further show that purified recombinant Mtr4p displays RNA-dependent ATPase activity and unwinds RNA duplexes with a 3′-to-5′ polarity in an ATP-dependent fashion. Unwinding and RNA-stimulated ATPase activities are strongly reduced in the recombinant mutant Mtr4-20p, suggesting that these activities of Mtr4p are critical for degradation of polyadenylated hypomodified tRNAi Met

Unique continuation and extensions of Killing vectors at boundaries for stationary vacuum space-times

Generalizing Riemannian theorems of Anderson-Herzlich and Biquard, we show that two $(n+1)$-dimensional stationary vacuum space-times (possibly with cosmological constant $\Lambda \in \R$) that coincide up to order one along a timelike hypersurface \mycal T are isometric in a neighbourhood of \mycal T. We further prove that KIDS of $\partial M$ extend to Killing vectors near $\partial M$. In the AdS type setting, we show unique continuation near conformal infinity if the metrics have the same conformal infinity and the same undetermined term. Extension near $\partial M$ of conformal Killing vectors of conformal infinity which leave the undetermined Fefferman-Graham term invariant is also established

Rex1p Deficiency Leads to Accumulation of Precursor Initiator tRNA\u3csup\u3eMet\u3c/sup\u3e and Polyadenylation of Substrate RNAs in \u3cem\u3eSaccharomyces cerevisiae\u3c/em\u3e

A synthetic genetic array was used to identify lethal and slow-growth phenotypes produced when a mutation in TRM6, which encodes a tRNA modification enzyme subunit, was combined with the deletion of any non-essential gene in Saccharomyces cerevisiae. We found that deletion of the REX1 gene resulted in a slow-growth phenotype in the trm6-504 strain. Previously, REX1 was shown to be involved in processing the 3′ ends of 5S rRNA and the dimeric tRNAArg-tRNAAsp. In this study, we have discovered a requirement for Rex1p in processing the 3′ end of tRNAiMet precursors and show that precursor tRNAiMet accumulates in a trm6-504 rex1Δ strain. Loss of Rex1p results in polyadenylation of its substrates, including tRNAiMet, suggesting that defects in 3′ end processing can activate the nuclear surveillance pathway. Finally, purified Rex1p displays Mg2+-dependent ribonuclease activity in vitro, and the enzyme is inactivated by mutation of two highly conserved amino acids

Unique continuation results for Ricci curvature and applications

Unique continuation results are proved for metrics with prescribed Ricci curvature in the setting of bounded metrics on compact manifolds with boundary, and in the setting of complete, conformally compact metrics. Related to this issue, an isometry extension property is proved: continuous groups of isometries at conformal infinity extend into the bulk of any complete conformally compact Einstein metric. Relations of this property with the invariance of the Gauss-Codazzi constraint equations under deformations are also discussed.Comment: 32 pages, supercedes math.DG/0501067; final published versio

A learning approach to the detection of gravitational wave transients

We investigate the class of quadratic detectors (i.e., the statistic is a bilinear function of the data) for the detection of poorly modeled gravitational transients of short duration. We point out that all such detection methods are equivalent to passing the signal through a filter bank and linearly combine the output energy. Existing methods for the choice of the filter bank and of the weight parameters rely essentially on the two following ideas: (i) the use of the likelihood function based on a (possibly non-informative) statistical model of the signal and the noise, (ii) the use of Monte-Carlo simulations for the tuning of parametric filters to get the best detection probability keeping fixed the false alarm rate. We propose a third approach according to which the filter bank is "learned" from a set of training data. By-products of this viewpoint are that, contrarily to previous methods, (i) there is no requirement of an explicit description of the probability density function of the data when the signal is present and (ii) the filters we use are non-parametric. The learning procedure may be described as a two step process: first, estimate the mean and covariance of the signal with the training data; second, find the filters which maximize a contrast criterion referred to as deflection between the "noise only" and "signal+noise" hypothesis. The deflection is homogeneous to the signal-to-noise ratio and it uses the quantities estimated at the first step. We apply this original method to the problem of the detection of supernovae core collapses. We use the catalog of waveforms provided recently by Dimmelmeier et al. to train our algorithm. We expect such detector to have better performances on this particular problem provided that the reference signals are reliable.Comment: 22 pages, 4 figure

No increase in radiation-induced chromosome aberration complexity detected by m-FISH after culture in the presence of 5’-bromodeoxyuridine

The thymidine analogue, 5’-bromodeoxyuridine (BrdU), is a known mutagen that is routinely introduced into culture media for subsequent Harlequin stain analysis and determination of cell cycle status. Previously, we examined the induction of chromosome aberrations in human peripheral blood lymphocytes (PBL) known to be in their 1st cell division following exposure to a low dose (0.5 Gy, average one -particle per cell) of high-LET α-particles. We found complex chromosome aberrations to be characteristic of exposure to high-LET radiation and suggested the features of complex exchange to reflect qualitatively the spatial deposition of this densely ionising radiation. To exclude the possibility that BrdU addition post-irradiation influenced the complexity of chromosomal damage observed by m-FISH, the effect of increasing BrdU concentration on aberration complexity was investigated. Comparisons between BrdU concentration (0, 10, and 40 M) and between sham- and α-particle irradiated PBL, were made both independently and in combination to enable discrimination between BrdU and high-LET radiation effects. Aberration type, size, complexity and completeness were assessed by m-FISH, and the relative progression through cell division was evaluated. We found no evidence of any qualitative difference in the complexity of damage as visualized by m-FISH but did observe an increase in the frequency of complex exchanges with increasing BrdU concentration indicative of altered cell cycle kinetics. The parameters measured here are consistent with findings from previous in vitro and in vivo work, indicating that each complex aberration visualised by m-FISH is characteristic of the structure of the high-LET α-particle track and the geometry of cell irradiated

Evidence for the band broadening across the ferromagnetic transition in Cr1/3_{1/3}NbSe2_2

The electronic structure of Cr$_{1/3}$NbSe$_2$ is studied via optical spectroscopy. We observe two low-energy interband transitions in the paramagnetic phase, which split into four peaks as the compound enters the ferromagnetic state. The band structure calculation indicates the four peaks are interband transitions to the spin up Cr e$_g$ states. We show that the peak splitting below the Curie temperature is \emph{not} due to the exchange splitting of spin up and down bands, but directly reflects a band broadening effect in Cr-derived states upon the spontaneous ferromagnetic ordering.Comment: 6 pages, 5 figures, to be published in Phys. Rev.