pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5′/3′ arm variation including concomitant cleavage and polyuridylation patterns

Recent research hints at an underappreciated complexity in pre-miRNA processing and regulation. Global profiling of pre-miRNA and its potential to increase understanding of the pre-miRNA landscape is impeded by overlap with highly expressed classes of other non coding (nc) RNA. Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3′- and 5′-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Additionally, examination of nuclear-enriched flanking sequences of pre-miRNA, particularly those derived from polycistronic miRNA transcripts, provides insight into miRNA and miRNA-offset (moRNA) production, specifically identifying novel classes of RNA potentially functioning as moRNA precursors. Our findings point to particularly intricate regulation of the let-7 family in many ways reminiscent of DICER1-independent, pre-mir-451-like processing, introduce novel and unify known forms of pre-miRNA regulation and processing, and shed new light on overlooked products of miRNA processing pathways

Stripes Disorder and Correlation lengths in doped antiferromagnets

For stripes in doped antiferromagnets, we find that the ratio of spin and charge correlation lenghts, $\xi_{s}/\xi_{c}$, provide a sharp criterion for determining the dominant form of disorder in the system. If stripes disorder is controlled by topological defects then $\xi_{s}/\xi_{c}\lesssim 1$. In contast, if stripes correlations are disordered primarily by non-topological elastic deformations (i.e., a Bragg-Glass type of disorder) then $1<\xi _{s}/\xi_{c}\lesssim 4$ is expected. Therefore, the observation of $\xi _{s}/\xi_{c}\approx 4$ in $(LaNd)_{2-x}Sr_{x}CuO_{4}$ and $\xi_{s}/\xi _{c}\approx 3$ in $La_{2/3}Sr_{1/3}NiO_{4}$ invariably implies that the stripes are in a Bragg glass type state, and topological defects are much less relevant than commonly assumed. Expected spectral properties are discussed. Thus, we establish the basis for any theoretical analysis of the experimentally obsereved glassy state in these material.Comment: 4 pages, 2 figure

First principles study of local electronic and magnetic properties in pure and electron-doped Nd2_2CuO4_4

The local electronic structure of Nd2CuO4 is determined from ab-initio cluster calculations in the framework of density functional theory. Spin-polarized calculations with different multiplicities enable a detailed study of the charge and spin density distributions, using clusters that comprise up to 13 copper atoms in the CuO2plane. Electron doping is simulated by two different approaches and the resulting changes in the local charge distribution are studied in detail and compared to the corresponding changes in hole doped La2CuO4. The electric field gradient (EFG) at the copper nucleus is investigated in detail and good agreement is found with experimental values. In particular the drastic reduction of the main component of the EFG in the electron-doped material with respect to LaCuO4 is explained by a reduction of the occupancy of the 3d3z^2-r^2 atomic orbital. Furthermore, the chemical shieldings at the copper nucleus are determined and are compared to results obtained from NMR measurements. The magnetic hyperfine coupling constants are determined from the spin density distribution

Gaps and excitations in fullerides with partially filled bands : NMR study of Na2C60 and K4C60

We present an NMR study of Na2C60 and K4C60, two compounds that are related by electron-hole symmetry in the C60 triply degenerate conduction band. In both systems, it is known that NMR spin-lattice relaxation rate (1/T1) measurements detect a gap in the electronic structure, most likely related to singlet-triplet excitations of the Jahn-Teller distorted (JTD) C60^{2-} or C60^{4-}. However, the extended temperature range of the measurements presented here (10 K to 700 K) allows to reveal deviations with respect to this general trend, both at high and low temperatures. Above room temperature, 1/T1 deviates from the activated law that one would expect from the presence of the gap and saturates. In the same temperature range, a lowering of symmetry is detected in Na2C60 by the appearance of quadrupole effects on the 23Na spectra. In K4C60, modifications of the 13C spectra lineshapes also indicate a structural modification. We discuss this high temperature deviation in terms of a coupling between JTD and local symmetry. At low temperatures, 1/T$_1$T tends to a constant value for Na2C60, both for 13C and 23Na NMR. This indicates a residual metallic character, which emphasizes the proximity of metallic and insulting behaviors in alkali fullerides.Comment: 12 pages, 13 figure

Similarity of slow stripe fluctations between Sr-doped cuprates and oxygen-doped nickelates

Stripe fluctuations in La2NiO4.17 have been studied by 139La NMR using the field and temperature dependence of the linewidth and relaxation rates. In the formation process of the stripes the NMR line intensity is maximal below 230K, starts to diminish around 140K, disappears around 50K and recovers at 4K. These results are shown to be consistent with, but completely complementary to neutron measurements, and to be generic for oxygen doped nickelates and underdoped cuprates.Comment: 4 pages including 4 figure

First time determination of the microscopic structure of a stripe phase: Low temperature NMR in La2NiO4.17

The experimental observations of stripes in superconducting cuprates and insulating nickelates clearly show the modulation in charge and spin density. However, these have proven to be rather insensitive to the harmonic structure and (site or bond) ordering. Using 139La NMR in La2NiO4.17, we show that in the 1/3 hole doped nickelate below the freezing temperature the stripes are strongly solitonic and site ordered with Ni3+ ions carrying S=1/2 in the domain walls and Ni2+ ions with S=1 in the domains.Comment: 4 pages including 4 figure

Role of dynamic Jahn-Teller distortions in Na2C60 and Na2CsC60 studied by NMR

Through 13C NMR spin lattice relaxation (T1) measurements in cubic Na2C60, we detect a gap in its electronic excitations, similar to that observed in tetragonal A4C60. This establishes that Jahn-Teller distortions (JTD) and strong electronic correlations must be considered to understand the behaviour of even electron systems, regardless of the structure. Furthermore, in metallic Na2CsC60, a similar contribution to T1 is also detected for 13C and 133Cs NMR, implying the occurence of excitations typical of JT distorted C60^{2-} (or equivalently C60^{4-}). This supports the idea that dynamic JTD can induce attractive electronic interactions in odd electron systems.Comment: 3 figure

Nitrous oxide cycling in the Arabian Sea

Depth profiles of dissolved nitrous oxide (N2O) were measured in the central and western Arabian Sea during four cruises in May and July–August 1995 and May–July 1997 as part of the German contribution to the Arabian Sea Process Study of the Joint Global Ocean Flux Study. The vertical distribution of N2O in the water column on a transect along 65°E showed a characteristic double-peak structure, indicating production of N2O associated with steep oxygen gradients at the top and bottom of the oxygen minimum zone. We propose a general scheme consisting of four ocean compartments to explain the N2O cycling as a result of nitrification and denitrification processes in the water column of the Arabian Sea. We observed a seasonal N2O accumulation at 600–800 m near the shelf break in the western Arabian Sea. We propose that, in the western Arabian Sea, N2O might also be formed during bacterial oxidation of organic matter by the reduction of IO3 − to I−, indicating that the biogeochemical cycling of N2O in the Arabian Sea during the SW monsoon might be more complex than previously thought. A compilation of sources and sinks of N2O in the Arabian Sea suggested that the N2O budget is reasonably balanced

2,6-Di(pyrazol-1-yl)pyridine-4-carboxylate Esters with Alkyl Chain Substituents, and their Iron(II) Complexes

Two series of 4-(alkoxyphenyl) 2,6-bis{pyrazol-1-yl}pyridine-4-carboxyate (L3R) or alkyl 2,6-bis{pyrazol-1-yl}pyridine-4-carboxyate (L4R) esters have been synthesized and complexed to iron(II), where R = CnH2n+1 (n = 6, 12, 14, 16, 18); two other derivatives related to L3R are also reported. While the solid [Fe(L4R)2][BF4]2 compounds are isostructural by powder diffraction and show similar spin state behaviors, the [Fe(L3R)2][BF4]2 series shows more varied structures and magnetic properties. This was confirmed by solvated crystal structures of [Fe(L3R)2][BF4]2 with n = 6, 14, 16, which all adopt the P1̅ space group but show significantly different side-chain conformations and/or crystal packing. The solid complexes are mostly low spin at room temperature, with many exhibiting the onset of thermal spin crossover (SCO) upon warming. Heating the complexes with n ≥ 14 significantly above their SCO temperature transforms them irreversibly into a predominantly high spin state, which is accompanied by structure changes and loss of crystallinity by powder diffraction. These transformations do not coincide with lattice solvent loss and may reflect melting and refreezing of their alkyl chain conformations during the thermal cycle. Four of the complexes exhibit SCO in CD3CN solution with T1/2 = 273–277 K, which is apparently unaffected by their alkyl chain substituents

Modulating the Magnetic Properties of Copper(II)/Nitroxyl Heterospin Complexes by Suppression of the Jahn–Teller Distortion

A series of six-coordinate [Cu(L)L1][BF4]2 (L1 = 2,6-bis{1-oxyl-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-2-yl}pyridine) complexes are reported. Ferromagnetic coupling between the Cu and L1 ligand spins is enhanced by an L coligand with distal methyl substituents, which is attributed to a sterically induced suppression of its Jahn–Teller distortion