The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate

BACKGROUND: The mitochondrial genomes of flowering plants vary greatly in size, gene content, gene order, mutation rate and level of RNA editing. However, the narrow phylogenetic breadth of available genomic data has limited our ability to reconstruct these traits in the ancestral flowering plant and, therefore, to infer subsequent patterns of evolution across angiosperms. RESULTS: We sequenced the mitochondrial genome of Liriodendron tulipifera, the first from outside the monocots or eudicots. This 553,721 bp mitochondrial genome has evolved remarkably slowly in virtually all respects, with an extraordinarily low genome-wide silent substitution rate, retention of genes frequently lost in other angiosperm lineages, and conservation of ancestral gene clusters. The mitochondrial protein genes in Liriodendron are the most heavily edited of any angiosperm characterized to date. Most of these sites are also edited in various other lineages, which allowed us to polarize losses of editing sites in other parts of the angiosperm phylogeny. Finally, we added comprehensive gene sequence data for two other magnoliids, Magnolia stellata and the more distantly related Calycanthus floridus, to measure rates of sequence evolution in Liriodendron with greater accuracy. The Magnolia genome has evolved at an even lower rate, revealing a roughly 5,000-fold range of synonymous-site divergence among angiosperms whose mitochondrial gene space has been comprehensively sequenced. CONCLUSIONS: Using Liriodendron as a guide, we estimate that the ancestral flowering plant mitochondrial genome contained 41 protein genes, 14 tRNA genes of mitochondrial origin, as many as 7 tRNA genes of chloroplast origin, >700 sites of RNA editing, and some 14 colinear gene clusters. Many of these gene clusters, genes and RNA editing sites have been variously lost in different lineages over the course of the ensuing ∽200 million years of angiosperm evolution

An analysis of double exposure lithography options

The current optical photolithography technology is approaching the physical barrier to the minimum achievable feature size. To produce smaller devices, new resolution enhancement technologies must be developed. Double exposure lithography has shown promise as potential pathway that is attractive because it is much cheaper than double patterning lithography and it can be deployed on existing imaging tools. However, this technology is not possible without the development of new materials with nonlinear response to exposure dose. The performance of existing materials such as reversible contrast enhancement layers (rCELs) and theoretical materials such as intermediate state two-photon (ISTP) and optical threshold layer (OTL) materials in double exposure applications was investigated through computer simulation. All three materials yielded process windows in double exposure mode. OTL materials showed the largest process window (DOF 0.137 µm, EL 5.06 %). ISTP materials had the next largest process window (DOF 0.124 µm, EL 3.22 %) followed by the rCEL (0.105 µm, 0.58 %). This study is an analysis of the feasibility of using the materials in double exposure mode

Infrared spectroscopy of ionized corannulene in the gas phase

The gas-phase infrared spectra of radical cationic and protonated corannulene were recorded by infrared multiple-photon dissociation (IRMPD) spectroscopy using the IR free electron laser for infrared experiments. Electrospray ionization was used to generate protonated corannulene and an IRMPD spectrum was recorded in a Fourier-transform ion cyclotron resonance mass spectrometer monitoring H-loss as a function of IR frequency. The radical cation was produced by 193-nm UV photoionization of the vapor of corannulene in a 3D quadrupole trap and IR irradiation produces H, H2, and C2Hx losses. Summing the spectral response of the three fragmentation channels yields the IRMPD spectrum of the radical cation. The spectra were analyzed with the aid of quantum-chemical calculations carried out at various levels of theory. The good agreement of theoretical and experimental spectra for protonated corannulene indicates that protonation occurs on one of the peripheral C-atoms, forming an sp3 hybridized carbon. The spectrum of the radical cation was examined taking into account distortions of the C5v geometry induced by the Jahn-Teller effect as a consequence of the degenerate 2E1 ground electronic state. As indicated by the calculations, the five equivalent Cs minima are separated by marginal barriers, giving rise to a dynamically distorted system. Although in general the character of the various computed vibrational bands appears to be in order, only a qualitative match to the experimental spectrum is found. Along with a general redshift of the calculated frequencies, the IR intensities of modes in the 1000-1250 cm−1 region show the largest discrepancy with the harmonic predictions. In addition to CH "in-plane" bending vibrations, these modes also exhibit substantial deformation of the pentagonal inner ring, which may relate directly to the vibronic interaction in the radical cation

A novel piggyback strategy for mRNA delivery exploiting adenovirus entry biology

Molecular therapies exploiting mRNA vectors embody enormous potential, as evidenced by the utility of this technology for the context of the COVID-19 pandemic. Nonetheless, broad implementation of these promising strategies has been restricted by the limited repertoires of delivery vehicles capable of mRNA transport. On this basis, we explored a strategy based on exploiting the well characterized entry biology of adenovirus. To this end, we studied an adenovirus-polylysine (AdpL) that embodied piggyback transport of the mRNA on the capsid exterior of adenovirus. We hypothesized that the efficient steps of Ad binding, receptor-mediated entry, and capsid-mediated endosome escape could provide an effective pathway for transport of mRNA to the cellular cytosol for transgene expression. Our studies confirmed that AdpL could mediate effective gene transfer of mRNA vectors in vitro and in vivo. Facets of this method may offer key utilities to actualize the promise of mRNA-based therapeutics

Frictional behavior of oceanic transform faults and its influence on earthquake characteristics

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 117 (2012): B04315, doi:10.1029/2011JB009025.We use a three-dimensional strike-slip fault model in the framework of rate and state-dependent friction to investigate earthquake behavior and scaling relations on oceanic transform faults (OTFs). Gabbro friction data under hydrothermal conditions are mapped onto OTFs using temperatures from (1) a half-space cooling model, and (2) a thermal model that incorporates a visco-plastic rheology, non-Newtonian viscous flow and the effects of shear heating and hydrothermal circulation. Without introducing small-scale frictional heterogeneities on the fault, our model predicts that an OTF segment can transition between seismic and aseismic slip over many earthquake cycles, consistent with the multimode hypothesis for OTF ruptures. The average seismic coupling coefficient χ is strongly dependent on the ratio of seismogenic zone width W to earthquake nucleation size h*; χ increases by four orders of magnitude as W/h* increases from ∼1 to 2. Specifically, the average χ = 0.15 ± 0.05 derived from global OTF earthquake catalogs can be reached at W/h* ≈ 1.2–1.7. Further, in all simulations the area of the largest earthquake rupture is less than the total seismogenic area and we predict a deficiency of large earthquakes on long transforms, which is also consistent with observations. To match these observations over this narrow range of W/h* requires an increase in the characteristic slip distance dc as the seismogenic zone becomes wider and normal stress is higher on long transforms. Earthquake magnitude and distribution on the Gofar and Romanche transforms are better predicted by simulations using the visco-plastic model than the half-space cooling model.This work was supported by NSF-EAR award 1015221, NSF-OCE award 1061203, and a J. Lamar Worzel Assistant Scientist Fund to Y. Liu at WHOI.2012-10-2

Comparison of three Ni-Hard I alloys

This report documents the results of an investigation which was undertaken to reveal the similarities and differences in the mechanical properties and microstructural characteristics of three Ni-Hard I alloys. One alloy (B1) is ASTM A532 class IA Ni-Hard containing 4.2 wt. pct. Ni. The second alloy (B2) is similar to B1 but higher in Cr, Si, and Mo. The third alloy (T1) also falls in the same ASTM specification, but it contains 3.3 wt. pct. Ni. The alloys were evaluated in both as-cast and stress-relieved conditions except for B2, which was evaluated in the stress-relieved condition only. While the matrix of the high Ni alloys is composed of austenite and martensite in both conditions, the matrix of the low Ni alloy consists of a considerable amount of bainite, in addition to the martensite and the retained austenite in as cast condition, and primarily bainite, with some retained austenite, in the stress relieved condition. It was found that the stress relieving treatment does not change the tensile strength of the high Ni alloy. Both the as cast and stress relieved high Ni alloys had a tensile strength of about 350 MPa. On the other hand, the tensile strength of the low Ni alloy increased from 340 MPa to 452 MPa with the stress relieving treatment. There was no significant difference in the wear resistance of these alloys in both as-cast and stressrelieved conditions