Ribosomal oxygenases are structurally conserved from prokaryotes to humans

2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components1,2 and in the hydroxylation of transcription factors3 and splicing factor proteins4. Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA5,6,7 and ribosomal proteins8 have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy9,10,11,12. The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans8 raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses arginine hydroxylation in the ribosomal protein L16; in humans, MYC-induced nuclear antigen (MINA53; also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone Nε-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases catalysing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate-oxidizing species reacts. This coordination flexibility has probably contributed to the evolution of the wide range of reactions catalysed by oxygenases

Heteropolymeric Triplex-Based Genomic Assay® to Detect Pathogens or Single-Nucleotide Polymorphisms in Human Genomic Samples

Human genomic samples are complex and are considered difficult to assay directly without denaturation or PCR amplification. We report the use of a base-specific heteropolymeric triplex, formed by native duplex genomic target and an oligonucleotide third strand probe, to assay for low copy pathogen genomes present in a sample also containing human genomic duplex DNA, or to assay human genomic duplex DNA for Single Nucleotide Polymorphisms (SNP), without PCR amplification. Wild-type and mutant probes are used to identify triplexes containing FVL G1691A, MTHFR C677T and CFTR mutations. The specific triplex structure forms rapidly at room temperature in solution and may be detected without a separation step. YOYO-1, a fluorescent bis-intercalator, promotes and signals the formation of the specific triplex. Genomic duplexes may be assayed homogeneously with single base pair resolution. The specific triple-stranded structures of the assay may approximate homologous recombination intermediates, which various models suggest may form in either the major or minor groove of the duplex. The bases of the stable duplex target are rendered specifically reactive to the bases of the probe because of the activity of intercalated YOYO-1, which is known to decondense duplex locally 1.3 fold. This may approximate the local decondensation effected by recombination proteins such as RecA in vivo. Our assay, while involving triplex formation, is sui generis, as it is not homopurine sequence-dependent, as are “canonical triplexes”. Rather, the base pair-specific heteropolymeric triplex of the assay is conformation-dependent. The highly sensitive diagnostic assay we present allows for the direct detection of base sequence in genomic duplex samples, including those containing human genomic duplex DNA, thereby bypassing the inherent problems and cost associated with conventional PCR based diagnostic assays

Approaching criticality via the zero dissipation limit in the abelian avalanche model

The discrete height abelian sandpile model was introduced by Bak, Tang & Wiesenfeld and Dhar as an example for the concept of self-organized criticality. When the model is modified to allow grains to disappear on each toppling, it is called bulk-dissipative. We provide a detailed study of a continuous height version of the abelian sandpile model, called the abelian avalanche model, which allows an arbitrarily small amount of dissipation to take place on every toppling. We prove that for non-zero dissipation, the infinite volume limit of the stationary measure of the abelian avalanche model exists and can be obtained via a weighted spanning tree measure. We show that in the whole non-zero dissipation regime, the model is not critical, i.e., spatial covariances of local observables decay exponentially. We then study the zero dissipation limit and prove that the self-organized critical model is recovered, both for the stationary measure and for the dynamics. We obtain rigorous bounds on toppling probabilities and introduce an exponent describing their scaling at criticality. We rigorously establish the mean-field value of this exponent for $d > 4$.Comment: 46 pages, substantially revised 4th version, title has been changed. The main new material is Section 6 on toppling probabilities and the toppling probability exponen

Olfactory function following open rhinoplasty: A 6-month follow-up study

<p>Abstract</p> <p>Background</p> <p>Patients undergoing any type of nasal surgery may experience degrees of postoperative olfactory dysfunction. We sought to investigate "when" the olfactory function recovers to its preoperative levels.</p> <p>Methods</p> <p>In this cohort design, 40 of 65 esthetic open rhinoplasty candidates with equal gender distribution, who met the inclusion criteria, were assessed for their olfactory function using the Smell Identification Test (SIT) with 40 familiar odors in sniffing bottles. All the patients were evaluated for the SIT scores preoperatively and postoperatively (at week 1, week 6, and month 6).</p> <p>Results</p> <p>At postoperative week one, 87.5% of the patients had anosmia, and the rest exhibited at least moderate levels of hyposmia. The anosmia, which was the dominant pattern at postoperative week 1, resolved and converted to various levels of hyposmia, so that no one at postoperative week 6 showed any such complain. At postoperative week six, 85% of the subjects experienced degrees of hyposmia, almost all being mild to moderate. At postoperative six month, the olfactory function had already reverted to the preoperative levels: no anosmia or moderate to severe hyposmia. A repeated ANOVA was indicative of significant differences in the olfactory function at the different time points. According to our post hoc Benfronney, the preoperative scores had a significant difference with those at postoperative week 1, week 6, but not with the ones at month 6.</p> <p>Conclusion</p> <p>Esthetic open rhinoplasty may be accompanied by some degrees of postoperative olfactory dysfunction. Patients need a time interval of 6 weeks to 6 months to fully recover their baseline olfactory function.</p

Elastic Properties of 4–6 nm-thick Glassy Carbon Thin Films

Glassy carbon is a disordered, nanoporous form of carbon with superior thermal and chemical stability in extreme environments. Freestanding glassy carbon specimens with 4–6 nm thickness and 0.5 nm average pore size were synthesized and fabricated from polyfurfuryl alcohol precursors. Elastic properties of the specimens were measured in situ inside a scanning electron microscope using a custom-built micro-electro-mechanical system. The Young’s modulus, fracture stress and strain values were measured to be about 62 GPa, 870 MPa and 1.3%, respectively; showing strong size effects compared to a modulus value of 30 GPa at the bulk scale. This size effect is explained on the basis of the increased significance of surface elastic properties at the nanometer length-scale

Heat transfer in solar absorber plates with micro-channels

Analytical, computational and experimental studies were carried out to investigate heat transfer and fluid flow in micro-channel absorber plates for compact (thin and light-weight) solar thermal collectors. The main objective of the work was to study different design and/or operating scenarios as well as study the significance of various micro-scaling effects. Analytical investigation showed that, under similar conditions, the proposed design yields a much higher fin efficiency, F and collector efficiency factor, F’ compared with the conventional solar collector design. An analytical model combining convective heat transfer in the collector fluid with axial conduction in the metal plate was developed. The predicted plate temperature profiles from the analytical model were in close agreement with the measured profiles. The model further showed that axial thermal conduction can significantly alter the plate temperature profile. Experiments were designed to represent real life operation of the proposed system. A CFD study, using the same design and operating parameters, produced results comparable with experiments. This numerical simulation also gave further insight into the heat transfer and fluid flow patterns in the micro-channel plate. The effect of channel cross section geometry was studied. The Nusselt number was observed to increase as the aspect ratio approached unity. Measured friction factors were similar in trend to the predictions for rectangular channels, although the overall rise in fluid temperature resulted in slightly lower friction factors. Thermal performance reduced slightly with increase in hydraulic diameter. The significance of various scaling effects was also investigated experimentally and numerically. Most of the typical scaling effects such as viscous dissipation and entrance effects were found to be insignificant however, conjugate heat transfer, surface boundary condition, surface finish and measurement uncertainties could be significant. The results showed a Reynolds number dependent Nusselt number which has been attributed to axial thermal conduction. It was also observed that only three walls were transferring heat; the walls of heat transfer had a uniform peripheral temperature while the heat flux varied peripherally. The closest simplified thermal boundary condition to represent heat transfer in these channels is the H1 with three (3) walls transferring heat. Increased surface roughness (obtained by using an etching technique to create the channels) was found to have a detrimental effect on heat transfer. The results showed that thermal improvement can be achieved by increasing the fluid velocity; however, pumping the thermal fluid above a pump power per plate area of 0.3 W/m2 resulted in marginal improvement. In practice, optimum microchannel geometry in plates should be sized based on fluid properties and operating conditions. The micro-channels should also have thin walls to minimise the effects of conjugate heat transfer. A Photovoltaic pump should be installed alongside the collector in order to provide pumping power required and minimise the overall fluid temperature rise. The results are beneficial for the design of micro-channel absorber plates for low heat flux operation up to 1000W/m2

Measurement of the branching fraction and CP content for the decay B(0) -> D(*+)D(*-)

This is the pre-print version of the Article. The official published version can be accessed from the links below. Copyright @ 2002 APS.We report a measurement of the branching fraction of the decay B0→D*+D*- and of the CP-odd component of its final state using the BABAR detector. With data corresponding to an integrated luminosity of 20.4  fb-1 collected at the Υ(4S) resonance during 1999–2000, we have reconstructed 38 candidate signal events in the mode B0→D*+D*- with an estimated background of 6.2±0.5 events. From these events, we determine the branching fraction to be B(B0→D*+D*-)=[8.3±1.6(stat)±1.2(syst)]×10-4. The measured CP-odd fraction of the final state is 0.22±0.18(stat)±0.03(syst).This work is supported by DOE and NSF (USA), NSERC (Canada), IHEP (China), CEA and CNRS-IN2P3 (France), BMBF (Germany), INFN (Italy), NFR (Norway), MIST (Russia), and PPARC (United Kingdom). Individuals have received support from the A.P. Sloan Foundation, Research Corporation, and Alexander von Humboldt Foundation

On some discrete boundary value problems in canonical domains

We study some discrete boundary value problems for discrete elliptic pseudo-differential equations in a half-space. These statements are related with a special periodic factorization of an elliptic symbol and a number of boundary conditions depends on an index of periodic factorizatio

Measurement of D-s(+) and D-s(*+) production in B meson decays and from continuum e(+)e(-) annihilation at √s=10.6 GeV

This is the pre-print version of the Article. The official published version can be accessed from the links below. Copyright @ 2002 APSNew measurements of Ds+ and Ds*+ meson production rates from B decays and from qq̅ continuum events near the Υ(4S) resonance are presented. Using 20.8 fb-1 of data on the Υ(4S) resonance and 2.6 fb-1 off-resonance, we find the inclusive branching fractions B(B⃗Ds+X)=(10.93±0.19±0.58±2.73)% and B(B⃗Ds*+X)=(7.9±0.8±0.7±2.0)%, where the first error is statistical, the second is systematic, and the third is due to the Ds+→φπ+ branching fraction uncertainty. The production cross sections σ(e+e-→Ds+X)×B(Ds+→φπ+)=7.55±0.20±0.34pb and σ(e+e-→Ds*±X)×B(Ds+→φπ+)=5.8±0.7±0.5pb are measured at center-of-mass energies about 40 MeV below the Υ(4S) mass. The branching fractions ΣB(B⃗Ds(*)+D(*))=(5.07±0.14±0.30±1.27)% and ΣB(B⃗Ds*+D(*))=(4.1±0.2±0.4±1.0)% are determined from the Ds(*)+ momentum spectra. The mass difference m(Ds+)-m(D+)=98.4±0.1±0.3MeV/c2 is also measured.This work was supported by DOE and NSF (USA), NSERC (Canada), IHEP (China), CEA and CNRS-IN2P3 (France), BMBF (Germany), INFN (Italy), NFR (Norway), MIST (Russia), and PPARC (United Kingdom). Individuals have received support from the Swiss NSF, A. P. Sloan Foundation, Research Corporation, and Alexander von Humboldt Foundation

Deletion of individual Ku subunits in mice causes an NHEJ-independent phenotype potentially by altering apurinic/apyrimidinic site repair

Ku70 and Ku80 form a heterodimer called Ku that forms a holoenzyme with DNA dependent-protein kinase catalytic subunit (DNA-PKCS) to repair DNA double strand breaks (DSBs) through the nonhomologous end joining (NHEJ) pathway. As expected mutating these genes in mice caused a similar DSB repair-defective phenotype. However, ku70-/- cells and ku80 -/- cells also appeared to have a defect in base excision repair (BER). BER corrects base lesions, apurinic/apyrimidinic (AP) sites and single stand breaks (SSBs) utilizing a variety of proteins including glycosylases, AP endonuclease 1 (APE1) and DNA Polymerase β (Pol β). In addition, deleting Ku70 was not equivalent to deleting Ku80 in cells and mice. Therefore, we hypothesized that free Ku70 (not bound to Ku80) and/or free Ku80 (not bound to Ku70) possessed activity that influenced BER. To further test this hypothesis we performed two general sets of experiments. The first set showed that deleting either Ku70 or Ku80 caused an NHEJ-independent defect. We found ku80-/- mice had a shorter life span than dna-pkcs-/- mice demonstrating a phenotype that was greater than deleting the holoenzyme. We also found Ku70-deletion induced a p53 response that reduced the level of small mutations in the brain suggesting defective BER. We further confirmed that Ku80-deletion impaired BER via a mechanism that was not epistatic to Pol β. The second set of experiments showed that free Ku70 and free Ku80 could influence BER. We observed that deletion of either Ku70 or Ku80, but not both, increased sensitivity of cells to CRT0044876 (CRT), an agent that interferes with APE1. In addition, free Ku70 and free Ku80 bound to AP sites and in the case of Ku70 inhibited APE1 activity. These observations support a novel role for free Ku70 and free Ku80 in altering BER. © 2014 Choi et al