Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs.

AIM: Heart disease is recognized as a consequence of dysregulation of cardiac gene regulatory networks. Previously, unappreciated components of such networks are the long non-coding RNAs (lncRNAs). Their roles in the heart remain to be elucidated. Thus, this study aimed to systematically characterize the cardiac long non-coding transcriptome post-myocardial infarction and to elucidate their potential roles in cardiac homoeostasis. METHODS AND RESULTS: We annotated the mouse transcriptome after myocardial infarction via RNA sequencing and ab initio transcript reconstruction, and integrated genome-wide approaches to associate specific lncRNAs with developmental processes and physiological parameters. Expression of specific lncRNAs strongly correlated with defined parameters of cardiac dimensions and function. Using chromatin maps to infer lncRNA function, we identified many with potential roles in cardiogenesis and pathological remodelling. The vast majority was associated with active cardiac-specific enhancers. Importantly, oligonucleotide-mediated knockdown implicated novel lncRNAs in controlling expression of key regulatory proteins involved in cardiogenesis. Finally, we identified hundreds of human orthologues and demonstrate that particular candidates were differentially modulated in human heart disease. CONCLUSION: These findings reveal hundreds of novel heart-specific lncRNAs with unique regulatory and functional characteristics relevant to maladaptive remodelling, cardiac function and possibly cardiac regeneration. This new class of molecules represents potential therapeutic targets for cardiac disease. Furthermore, their exquisite correlation with cardiac physiology renders them attractive candidate biomarkers to be used in the clinic.

Estudo semi-empírico de ácidos hidroxâmicos: ácido formoidroxâmico e derivados do aleloquímico dimboa

Open chain hydroxamic acid (Hx) can exist as Z and E diastereomers of two tautomers, hydroxamic acid and hydroximic acid. The conformational stability of the formohydroxamic acid isomers evaluated by PM3 compared better to ab initio results from the literature than AM1 results. Structural data of the cyclic Hx 2,4-dihydroxy-7-metoxy-2H-1,4-benzoxazin-3(4 H)-one (DIMBOA) obtained by both semiempirical methods compared well to ab initio results. pKa data from the literature for derivatives of the aldolic isomer of DIMBOA were compared to the stability of the anions resulting from the loss of protons of their phenol and hydroxamic acid groups, determined as the difference in heat of formation between anionic and neutral forms, calculated by AM1 and PM3 methods. Good correlations between theoretical and experimental data were obtained for both semiempirical methods.

Metodologia para obtenção de parâmetros de mecânica molecular aplicados a compostos de coordenação

A methodology is presented to obtain force field parameters to be used in molecular mechanics. The case of Ru(II) is investigated and the parameters obtained, specially its covalent radii, are employed to model Ru(II) coordination compound. The combined use of molecular mechanics with ab initio methods allowed us to predict the metal-ligand stretching force constant for Ru(II) coordination compounds.

Estudo QSPR sobre os coeficientes de partição: descritores mecânico-quânticos e análise multivariada

Quantum chemistry and multivariate analysis were used to estimate the partition coefficients between n-octanol and water for a serie of 188 compounds, with the values of the q 2 until 0.86 for crossvalidation test. The quantum-mechanical descriptors are obtained with ab initio calculation, using the solvation effects of the Polarizable Continuum Method. Two different Hartree-Fock bases were used, and two different ways for simulating solvent cavity formation. The results for each of the cases were analised, and each methodology proposed is indicated for particular case.

O uso de pseudopotenciais e modelos HF/MP2/DFT na previsão de freqüências vibracionais em complexos metálicos

Four different pseudopotentials and three methodologies were employed in the calculation of the geometry and the frequencies of metal complexes like [M(NH3)2X2] [X=halogen, M=Zn, Cd], and [Hg(NH3)2]Cl2. The vibrational assignments were carefully checked and compared to the theoretically calculated ones. Graphical procedures were employed to estimate family errors and their average behavior. The calculated results show the SBK-X basis set with the best results for the geometries and calculated frequencies, for individual species and statistical results. Its use is recommend, mainly if the neighborhood atoms are described with similar pseudopotentials. Excellent results were also obtained with the Hay and Wadt pseudopotential.

Análise estrutural de ciclodextrinas: um estudo comparativo entre métodos teóricos clássicos e quânticos

In the present work, we analyzed the accuracy of distinct theoretical methods to reproduce the solid state structures of cyclodextrins. The a, b and g-cyclodextrins (CD) were considered and also their hydrates with included water molecules: a-CD.2H2O, b-CD.10H2O and g-CD.12H2O. The geometries were fully optimized using Molecular Mechanics (MM2), semiempirical (AM1 and PM3) and ab initio (HF/3-21G) methods and quantitatively compared with experimental data from X ray diffraction. The results obtained from the classical MM2 method were in best agreement with the experiment. The semiempirical and ab initio structures were also in satisfactory accordance with the experimental data. In general, the PM3 method was found to be more suitable than the AM1 to describe the CD geometries, mainly when the intramolecular hydrogen bonds are considered.

Estrutura e propriedades de elipticinas

The ellipticines constitute a broad class of molecules with antitumor activity. In the present work we analyzed the structure and properties of a series of ellipticine derivatives in the gas phase and in solution using quantum mechanical and Monte Carlo methods. The results showed a good correlation between the solvation energies in water obtained with the continuum model and the Monte Carlo simulation. Molecular descriptors were considered in the development of QSAR models using the DNA association constant (log Kapp) as biological data. The results showed that the DNA binding is dominated by electronic parameters, with small contributions from the molecular volume and area.

NMR in Crystals and Powders of Topazes with Different Colours

The present work is a part of the large project with purpose to investigate microstructure and electronic structure of natural topazes using NMR method. To reach this task we determined the relative contents of fluorine and hydrogen in crystals blue, colorless, wine and wine irradiated topazes. Then we determined the electric field gradients in site of aluminium atoms by NMR method, calculated EFG using ab initio method, and measured relaxation time dependence on heating temperature for blue, colorless, Swiss blue and sky blue topazes. Nuclear magnetic resonance (NMR) is an effective method to investigate the local structure in the crystal. The NMR study of the single crystal gives detailed information especially about the local crystal structure. As a result of this work we have received practical data, which is possible to use in future for making personal dosimetry and for preparation of mullite, which is widely used in traditional and advanced ceramic materials.

Vibrational contribution to dipole polarizability and first hyperpolarizability of LiH

The role played by electron correlation and vibrational correction on the polarizability of the LiH molecule is demonstrated. We present results for the dipole moment, polarizability and first hyperpolarizability of the LiH molecule obtained through many-body perturbation-theory, coupled-cluster and quadratic configuration interaction methods. Our best result for the dipole polarizability, obtained using the QCISD(T) scheme, indicates that the vibrational contribution is appreciable, amounting to ca. 10% of the total polarizability. Regarding the first hyperpolarizability, the vibrational contribution is even more important and has opposite sign in comparison with the electronic contribution.

Cloração do anisol, tolueno e nitrobenzeno com ácido tricloroisocianúrico (ATCI): aspectos computacionais sobre a reatividade e regiosseletividade

We present in this educational article a theoretical analysis based on DFT/B3LYP 6-311++G (d,p) and ab initio MP2/6-311++G(d,p) computational calculation about the reactivity and the regioselectivity on the chlorination reaction of anisole, toluene and nitrobenzene, using trichloroisocyanuric acid (TICA) as donor of Cl+. The H.O.M.O. / L.U.M.O. energy and N.B.O. atomic charges of various aromatic systems were calculated in ab initio level. The energies of the reagents and intermediaries were calculated using D.F.T.. These results have been presented as a quantitative example for the S E A mechanism, in the undergraduate organic chemistry disciplines.

Estudo teórico de propriedades ópticas não-lineares de nanotubos de carbono de parede única quimicamente modificados

Structure and first hyperpolarizability for a series of armchair a(5,5) chemically modified carbon nanotubes (CNT) were calculated at semiempirical and density functional levels of theory. The 4,4´-substituted stilbenes were selected as chromophore with substituents at position 4´ set to X=NO2, H, Cl, OH and NH2. The calculated values for static first hyperpolarizability (β) were almost linearly dependent on the electronic effect of the group X, increasing from NO2 to NH2. At DFT level the effect of inserting the chromophore in the CNT surface was to enhance the β value up to 70% relative to the free 4,4´-substituted stilbene.

Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single-crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer.

Estudo da série iso-eletrônica do átomo de hélio pelo método hiperesférico

Neste trabalho estudamos o espectro da série iso-eletrônica do átomo de hélio utilizando o método hiperesférico adiabático. Este método permite o estudo dos níveis de energia de sistemas atômicos por meio de um conjunto de curvas de potencial, de forma semelhante à aproximação de Born-Oppenheimer para sistemas moleculares. As curvas de potencial são definidas com relação a uma única variável radial, independentemente do número de elétrons do sistema. Desta forma a análise e classificação dos níveis de energia é realizada de forma simples e intuitiva, o que não se observa em métodos como o variacional e Hartree-Fock. O objetivo desta pesquisa é o de descrever o comportamento do estado fundamental de sistemas heliônicos com a variação da carga nuclear. Além do método hiperesférico simplificar muito a análise dos resultados, é um processo ab-initio, cujos erros são limitados apenas pelos truncamentos do número de equações acopladas. Já na sua aproximação mais simples, onde todos os acoplamentos radiais são desprezados, o erro obtido para a energia do estado fundamental é inferior a 1% e com a introdução do acoplamento diagonal o erro cai para cerca de 0.3%. Resultados de grande precisão são obtidos com os acoplamentos não diagonais, atingindo precisões da ordem de 10-3 %.