Genome wide chromatin occupancy of mrhl RNA and its role in gene regulation in mouse spermatogonial cells

Mrhl RNA is a nuclear lncRNA encoded in the mouse genome and negatively regulates Wnt signaling in spermatogonial cells through p68/Ddx5 RNA helicase. Mrhl RNA is present in the chromatin fraction of mouse spermatogonial Gc1-Spg cells and genome wide chromatin occupancy of mrhl RNA by ChOP (Chromatin oligo affinity precipitation) technique identified 1370 statistically significant genomic loci. Among these, genes at 37 genomic loci also showed altered expression pattern upon mrhl RNA down regulation which are referred to as GRPAM (Genes Regulated by Physical Association of Mrhl RNA). p68 interacted with mrhl RNA in chromatin at these GRPAM loci. p68 silencing drastically reduced mrhl RNA occupancy at 27 GRPAM loci and also perturbed the expression of GRPAM suggesting a role for p68 mediated mrhl RNA occupancy in regulating GRPAM expression. Wnt3a ligand treatment of Gc1-Spg cells down regulated mrhl RNA expression and also perturbed expression of these 27 GRPAM genes that included genes regulating Wnt signaling pathway and spermatogenesis, one of them being Sox8, a developmentally important transcription factor. We also identified interacting proteins of mrhl RNA associated chromatin fraction which included Pc4, a chromatin organizer protein and hnRNP A/B and hnRNP A2/B1 which have been shown to be associated with lincRNA-Cox2 function in gene regulation. Our findings in the Gc1-Spg cell line also correlate with the results from analysis of mouse testicular tissue which further highlights the in vivo physiological significance of mrhl RNA in the context of gene regulation during mammalian spermatogenesis.

Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions

Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate-aromatic interactions including CH-pi and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to beta-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.

The contribution of grain boundary sliding in tensile deformation of an ultrafine-grained aluminum alloy having high strength and high ductility

An as-cast Al-7 % Si alloy was processed by high-pressure torsion (HPT) for up to 10 turns at temperatures of 298 or 445 K. The HPT-processed samples had ultrafine-grained structures and they were tested in tension at room temperature at various strain rates in the range from 1.0 x 10(-4) to 1.0 x 10(-2) s(-1). The contributions of grain boundary sliding (GBS) to the total strain were measured directly using atomic force microscopy. Samples simultaneously showing both high strength and high ductility contained the highest fractions of high-angle grain boundaries (HAGB) and exhibited the highest contributions from GBS, whereas samples showing high strength but low ductility gave negligible values for the sliding contributions. It is concluded that high strength and high ductility require both an ultrafine grain size and a high fraction of HAGB.

Experimental studies on the influence of intermediate principal stress and inclination on the mechanical behaviour of angular sands

A comprehensive experimental study has been made on angular sand to investigate various aspects of mechanical behavior. A hollow cylinder torsion testing apparatus is used in this program to apply a range of stress conditions on this angular quartzitic fine sand under monotonic drained shear. The effect of the magnitude and inclination of the principal stresses on an element of sand is studied through these experiments. This magnitude and inclination of the principal stresses are presented as an ``ensemble measure of fabric in sands''. This ensemble measure of fabric in the sands evolves through the shearing process, and reaches the final state, which indeed has a unique fabric. The sand shows significant variation in strength with changing inclination of the principal stresses. The locus of the final stress state in principal stress space is also mapped from these series of experiments. Additional aspects of non-coaxiality, a benchmarking exercise with a few constitutive models is presented here. This experimental approach albeit indirect shows that a unique state which is dependent on the fabric, density and confining stress exists. This suite of experiments provides a well-controlled data set for a clear understanding on the mechanical behavior of sands.

Bayesian parameter identification in dynamic state space models using modified measurement equations

When Markov chain Monte Carlo (MCMC) samplers are used in problems of system parameter identification, one would face computational difficulties in dealing with large amount of measurement data and (or) low levels of measurement noise. Such exigencies are likely to occur in problems of parameter identification in dynamical systems when amount of vibratory measurement data and number of parameters to be identified could be large. In such cases, the posterior probability density function of the system parameters tends to have regions of narrow supports and a finite length MCMC chain is unlikely to cover pertinent regions. The present study proposes strategies based on modification of measurement equations and subsequent corrections, to alleviate this difficulty. This involves artificial enhancement of measurement noise, assimilation of transformed packets of measurements, and a global iteration strategy to improve the choice of prior models. Illustrative examples cover laboratory studies on a time variant dynamical system and a bending-torsion coupled, geometrically non-linear building frame under earthquake support motions. (C) 2015 Elsevier Ltd. All rights reserved.

Structural characterization of folded and extended conformations in peptides containing gamma amino acids with proteinogenic side chains: crystal structures of gamma(n), (alpha gamma)(n) and gamma gamma delta gamma sequences

The crystal structures of nine peptides containing gamma(4)Val and gamma(4)Leu are described. The short sequences Boc-gamma(4)(R)Val](2)-OMe 1, Boc-gamma(4)(R)Val](3)-NHMe 2 and Boc-gamma(4)(S)Val-gamma(4)(R)Val-OMe 3 adopt extended apolar, sheet like structures. The tetrapeptide Boc-gamma(4)(R)Val](4)-OMe 4 adopts an extended conformation, in contrast to the folded C-14 helical structure determined previously for Boc-gamma(4)(R)Leu](4)-OMe. The hybrid alpha gamma sequence Boc-Ala-gamma(4)(R)Leu](2)-OMe 5 adopts an S-shaped structure devoid of intramolecular hydrogen bonds, with both alpha residues adopting local helical conformations. In sharp contrast, the tetrapeptides Boc-Aib-gamma(4)(S)Leu](2)-OMe 6 and Boc-Leu-gamma(4)(R)Leu](2)-OMe 7 adopt folded structures stabilized by two successive C-12 hydrogen bonds. gamma(4)Val residues have also been incorporated into the strand segments of a crystalline octapeptide, Boc-Leu-gamma(4)(R)Val-Val-(D)Pro-Gly-Leu-gamma(4)(R)Val-Val-OMe 8. The gamma gamma delta gamma tetrapeptide containing gamma(4)Val and delta(5)Leu residues adopts an extended sheet like structure. The hydrogen bonding pattern at gamma residues corresponds to an apolar sheet, while a polar sheet is observed at the lone delta residue. The transition between folded and extended structures at gamma residues involves a change of the torsion angle from the gauche to the trans conformation about the C-beta-C-alpha bond.

Generation of Temperature Dependent Transversely Isotropic Properties for Zigzag and Armchair Single-Walled Carbon Nanotubes

Finite element analysis has been carried out to obtain temperature dependent transversely isotropic properties of the single-walled carbon nanotubes (SWCNTs). Finite element models of SWCNTs are generated by specifying the C-C bond rigidities. The five independent transversely isotropic properties for different chiralities are evaluated using the stress fields of thick-walled cylinders and the elastic deformations of SWCNTs subjected to pure extension, internal pressure and pure torsion loads. Empirical relations are provided for the five independent elastic constants useful to armchair and zigzag SWCNTs.

Influence of mode of deformation on microstructural heterogeneities in Ni subjected to large strain deformation

In the present work, the effect of deformation mode (uniaxial compression, rolling and torsion) on the microstructural heterogeneities in a commercial purity Ni is reported. For a given equivalent von Mises strain, samples subjected to torsion have shown higher fraction of high-angle boundaries, kernel average misorientation and recrystallization nuclei when compared to uniaxially compressed and rolled samples. This is attributed to the differences in the slip system activity under different modes of deformation.

Efficient coupled polynomial interpolation scheme for out-of-plane free vibration analysis of curved beams

The performance of two curved beam finite element models based on coupled polynomial displacement fields is investigated for out-of-plane vibration of arches. These two-noded beam models employ curvilinear strain definitions and have three degrees of freedom per node namely, out-of-plane translation (v), out-of-plane bending rotation (theta(z)) and torsion rotation (theta(s)). The coupled polynomial interpolation fields are derived independently for Timoshenko and Euler-Bernoulli beam elements using the force-moment equilibrium equations. Numerical performance of these elements for constrained and unconstrained arches is compared with the conventional curved beam models which are based on independent polynomial fields. The formulation is shown to be free from any spurious constraints in the limit of `flexureless torsion' and `torsionless flexure' and hence devoid of flexure and torsion locking. The resulting stiffness and consistent mass matrices generated from the coupled displacement models show excellent convergence of natural frequencies in locking regimes. The accuracy of the shear flexibility added to the elements is also demonstrated. The coupled polynomial models are shown to perform consistently over a wide range of flexure-to-shear (EI/GA) and flexure-to-torsion (EI/GJ) stiffness ratios and are inherently devoid of flexure, torsion and shear locking phenomena. (C) 2015 Elsevier B.V. All rights reserved.

Optimal input cross-power spectra in shake table testing of asymmetric structures

The study considers earthquake shake table testing of bending-torsion coupled structures under multi-component stationary random earthquake excitations. An experimental procedure to arrive at the optimal excitation cross-power spectral density (psd) functions which maximize/minimize the steady state variance of a chosen response variable is proposed. These optimal functions are shown to be derivable in terms of a set of system frequency response functions which could be measured experimentally without necessitating an idealized mathematical model to be postulated for the structure under study. The relationship between these optimized cross-psd functions to the most favourable/least favourable angle of incidence of seismic waves on the structure is noted. The optimal functions are also shown to be system dependent, mathematically the sharpest, and correspond to neither fully correlated motions nor independent motions. The proposed experimental procedure is demonstrated through shake table studies on two laboratory scale building frame models.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel -sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac(12)c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac(12)c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C-,C--dialkylated residue Ac(12)c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel -sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac(12)c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel -sheet in crystals, twisted or helical -sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted -sheet assembly in crystals. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel -sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac(12)c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac(12)c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C-,C--dialkylated residue Ac(12)c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel -sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac(12)c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel -sheet in crystals, twisted or helical -sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted -sheet assembly in crystals. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd.