999 resultados para molecular hybridization
Resumo:
Selection of zebu (Bos indicus) beef and dairy cattle in Brazil and the validation process of genetic markers for growth, carcass and meat quality traits and also for milk production, fat and protein milk content are discussed as concerned to the concepts and details of their use as auxiliary tools in selection processes. It is highlighted, also, the importance of right selection of ova donor cows for production of embryos to be transferred.
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Background: The thin-spined porcupine, also known as the bristle-spined rat, Chaetomys subspinosus (Olfers, 1818), the only member of its genus, figures among Brazilian endangered species. In addition to being threatened, it is poorly known, and even its taxonomic status at the family level has long been controversial. The genus Chaetomys was originally regarded as a porcupine in the family Erethizontidae, but some authors classified it as a spiny-rat in the family Echimyidae. Although the dispute seems to be settled in favor of the erethizontid advocates, further discussion of its affinities should be based on a phylogenetic framework. In the present study, we used nucleotide-sequence data from the complete mitochondrial cytochrome b gene and karyotypic information to address this issue. Our molecular analyses included one individual of Chaetomys subspinosus from the state of Bahia in northeastern Brazil, and other hystricognaths. Results: All topologies recovered in our molecular phylogenetic analyses strongly supported Chaetomys subspinosus as a sister clade of the erethizontids. Cytogenetically, Chaetomys subspinosus showed 2n = 52 and FN = 76. Although the sexual pair could not be identified, we assumed that the X chromosome is biarmed. The karyotype included 13 large to medium metacentric and submetacentric chromosome pairs, one small subtelocentric pair, and 12 small acrocentric pairs. The subtelocentric pair 14 had a terminal secondary constriction in the short arm, corresponding to the nucleolar organizer region (Ag-NOR), similar to the erethizontid Sphiggurus villosus, 2n = 42 and FN = 76, and different from the echimyids, in which the secondary constriction is interstitial. Conclusion: Both molecular phylogenies and karyotypical evidence indicated that Chaetomys is closely related to the Erethizontidae rather than to the Echimyidae, although in a basal position relative to the rest of the Erethizontidae. The high levels of molecular and morphological divergence suggest that Chaetomys belongs to an early radiation of the Erethizontidae that may have occurred in the Early Miocene, and should be assigned to its own subfamily, the Chaetomyinae.
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Background: Bovine anaplasmosis, caused by the rickettsial tick-borne pathogen Anaplasma marginale (Rickettsiales: Anaplasmataceae), is vectored by Rhipicephalus (Boophilus) microplus in many tropical and subtropical regions of the world. A. marginale undergoes a complex developmental cycle in ticks which results in infection of salivary glands from where the pathogen is transmitted to cattle. In previous studies, we reported modification of gene expression in Dermacentor variabilis and cultured Ixodes scapularis tick cells in response to infection with A. marginale. In these studies, we extended these findings by use of a functional genomics approach to identify genes differentially expressed in R. microplus male salivary glands in response to A. marginale infection. Additionally, a R. microplus-derived cell line, BME26, was used for the first time to also study tick cell gene expression in response to A. marginale infection. Results: Suppression subtractive hybridization libraries were constructed from infected and uninfected ticks and used to identify genes differentially expressed in male R. microplus salivary glands infected with A. marginale. A total of 279 ESTs were identified as candidate differentially expressed genes. Of these, five genes encoding for putative histamine-binding protein (22Hbp), von Willebrand factor (94Will), flagelliform silk protein (100Silk), Kunitz-like protease inhibitor precursor (108Kunz) and proline-rich protein BstNI subfamily 3 precursor (7BstNI3) were confirmed by real-time RT-PCR to be down-regulated in tick salivary glands infected with A. marginale. The impact of selected tick genes on A. marginale infections in tick salivary glands and BME26 cells was characterized by RNA interference. Silencing of the gene encoding for putative flagelliform silk protein (100Silk) resulted in reduced A. marginale infection in both tick salivary glands and cultured BME26 cells, while silencing of the gene encoding for subolesin (4D8) significantly reduced infection only in cultured BME26 cells. The knockdown of the gene encoding for putative metallothionein (93 Meth), significantly up-regulated in infected cultured BME26 cells, resulted in higher A. marginale infection levels in tick cells. Conclusions: Characterization of differential gene expression in salivary glands of R. microplus in response to A. marginale infection expands our understanding of the molecular mechanisms at the tick-pathogen interface. Functional studies suggested that differentially expressed genes encoding for subolesin, putative von Willebrand factor and flagelliform silk protein could play a role in A. marginale infection and multiplication in ticks. These tick genes found to be functionally relevant for tick-pathogen interactions will likely be candidates for development of vaccines designed for control of both ticks and tick-borne pathogens.
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In this perspectives article, we reflect upon the existence of chirality in atmospheric aerosol particles. We then show that organic particles collected at a field site in the central Amazon Basin under pristine background conditions during the wet and dry seasons consist of chiral secondary organic material. We show how the chiral response from the aerosol particles can be imaged directly without the need for sample dissolution, solvent extraction, or sample preconcentration. By comparing the chiral-response images with optical images, we show that chiral responses always originate from particles on the filter, but not all aerosol particles produce chiral signals. The intensity of the chiral signal produced by the size resolved particles strongly indicates the presence of chiral secondary organic material in the particle. Finally, we discuss the implications of our findings on chiral atmospheric aerosol particles in terms of climate-related properties and source apportionment.
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The dynamic polarizability and optical absorption spectrum of liquid water in the 6-15 eV energy range are investigated by a sequential molecular dynamics (MD)/quantum mechanical approach. The MD simulations are based on a polarizable model for liquid water. Calculation of electronic properties relies on time-dependent density functional and equation-of-motion coupled-cluster theories. Results for the dynamic polarizability, Cauchy moments, S(-2), S(-4), S(-6), and dielectric properties of liquid water are reported. The theoretical predictions for the optical absorption spectrum of liquid water are in good agreement with experimental information.
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The electronic properties of liquid ammonia are investigated by a sequential molecular dynamics/quantum mechanics approach. Quantum mechanics calculations for the liquid phase are based on a reparametrized hybrid exchange-correlation functional that reproduces the electronic properties of ammonia clusters [(NH(3))(n); n=1-5]. For these small clusters, electron binding energies based on Green's function or electron propagator theory, coupled cluster with single, double, and perturbative triple excitations, and density functional theory (DFT) are compared. Reparametrized DFT results for the dipole moment, electron binding energies, and electronic density of states of liquid ammonia are reported. The calculated average dipole moment of liquid ammonia (2.05 +/- 0.09 D) corresponds to an increase of 27% compared to the gas phase value and it is 0.23 D above a prediction based on a polarizable model of liquid ammonia [Deng , J. Chem. Phys. 100, 7590 (1994)]. Our estimate for the ionization potential of liquid ammonia is 9.74 +/- 0.73 eV, which is approximately 1.0 eV below the gas phase value for the isolated molecule. The theoretical vertical electron affinity of liquid ammonia is predicted as 0.16 +/- 0.22 eV, in good agreement with the experimental result for the location of the bottom of the conduction band (-V(0)=0.2 eV). Vertical ionization potentials and electron affinities correlate with the total dipole moment of ammonia aggregates. (c) 2008 American Institute of Physics.
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We model interface formation by metal deposition on the conjugated polymer poly-para-phenylene vinylene, studying direct aluminum and layered aluminum-calcium structures Al/PPV and Al/Ca/PPV. To do that we use classical molecular dynamics simulations, checked by ab initio density-functional theory calculations, for selected relevant configurations. We find that Al not only migrates easily into the film, with a strong charge transfer to the neighboring chains, but also promotes rearrangement of the polymer in the interfacial region to the hexagonal structure. On the other hand, our results indicate that a thin Ca layer is sufficient to protect the film and maintain a well-defined metal/polymer interface, and that also a thin Al capping layer may protect the whole from environmental degradation.
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We have performed ab initio molecular dynamics simulations to generate an atomic structure model of amorphous hafnium oxide (a-HfO(2)) via a melt-and-quench scheme. This structure is analyzed via bond-angle and partial pair distribution functions. These results give a Hf-O average nearest-neighbor distance of 2.2 angstrom, which should be compared to the bulk value, which ranges from 1.96 to 2.54 angstrom. We have also investigated the neutral O vacancy and a substitutional Si impurity for various sites, as well as the amorphous phase of Hf(1-x)Si(x)O(2) for x=0.25, 0375, and 0.5.
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The adsorption of atomic and molecular hydrogen on armchair and zigzag boron carbonitride nanotubes is investigated within the ab initio density functional theory. The adsorption of atomic H on the BC(2)N nanotubes presents properties which are promising for nanoelectronic applications. Depending on the adsorption site for the H, the Fermi energy moves toward the bottom of the conduction band or toward the top of the valence band, leading the system to exhibit donor or acceptor characteristics, respectively. The H(2) molecules are physisorbed on the BC(2)N surface for both chiralities. The binding energies for the H(2) molecules are slightly dependent on the adsorption site, and they are near to the range to work as a hydrogen storage medium.
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The ground states of a few electrons confined in two vertically coupled quantum rings in the presence of an external magnetic field are studied systematically within the current spin-density functional theory. Electron-electron interactions combined with inter-ring tunneling affect the electronic structure and the persistent current. For small values of the external magnetic field, we recover the zero magnetic field molecular quantum ring ground state configurations. Increasing the magnetic field many angular momentum, spin, and isospin transitions are predicted to occur in the ground state. We show that these transitions follow certain rules, which are governed by the parity of the number of electrons, the single-particle picture, Hund's rules, and many-body effects. (C) 2009 American Institute of Physics. [doi:10.1063/1.3223360]
Molecular determinants of improved cathepsin B inhibition by new cystatins obtained by DNA shuffling
Resumo:
Background: Cystatins are inhibitors of cysteine proteases. The majority are only weak inhibitors of human cathepsin B, which has been associated with cancer, Alzheimer's disease and arthritis. Results: Starting from the sequences of oryzacystatin-1 and canecystatin-1, a shuffling library was designed and a hybrid clone obtained, which presented higher inhibitory activity towards cathepsin B. This clone presented two unanticipated point mutations as well as an N-terminal deletion. Reversing each point mutation independently or both simultaneously abolishes the inhibitory activity towards cathepsin B. Homology modeling together with experimental studies of the reverse mutants revealed the likely molecular determinants of the improved inhibitory activity to be related to decreased protein stability. Conclusion: A combination of experimental approaches including gene shuffling, enzyme assays and reverse mutation allied to molecular modeling has shed light upon the unexpected inhibitory properties of certain cystatin mutants against Cathepsin B. We conclude that mutations disrupting the hydrophobic core of phytocystatins increase the flexibility of the N-terminus, leading to an increase in inhibitory activity. Such mutations need not affect the inhibitory site directly but may be observed distant from it and manifest their effects via an uncoupling of its three components as a result of increased protein flexibility.
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The title 2:1 complex of 3-nitrophenol (MNP) and 4,4'-bipyridyl N, N'-dioxide (DPNO), 2C(6)H(5)NO(3)center dot C(10)H(8)N(2)O(2) or 2MNP center dot DPNO, crystallizes as a centrosymmetric three-component adduct with a dihedral angle of 59.40 (8)degrees between the planes of the benzene rings of MNP and DPNO (the DPNO moiety lies across a crystallographic inversion centre located at the mid-point of the C-C bond linking its aromatic rings). The complex owes its formation to O-H center dot center dot center dot O hydrogen bonds [O center dot center dot center dot O = 2.605 (3) angstrom]. Molecules are linked by intermolecular C-H center dot center dot center dot O and C-H center dot center dot center dot N interactions forming R(2)(1) (6) and R(2)(2) (10) rings, and R(6)(6) (34) and R(4)(4) (26) macro-rings, all of which are aligned along the [(1) over bar 01] direction, and R(2)(2) (10) and R(2)(1) (7) rings aligned along the [010] direction. The combination of chains of rings along the [(1) over bar 01] and [010] directions generates the three-dimensional structure. A total of 27 systems containing the DNPO molecule and forming molecular complexes of an organic nature were analysed and compared with the structural characteristics of the dioxide reported here. The N-O distance [1.325 (2) angstrom] depends not only on the interactions involving the O atom at the N-O group, but also on the structural ordering and additional three-dimensional interactions in the crystal structure. A density functional theory (DFT) optimized structure at the B3LYP/6-311G(d,p) level is compared with the molecular structure in the solid state.
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Schistosomes are unable to synthesize purines de novo and depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds to Schistosoma mansoni PNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are used to propose a structural explanation for the selective binding of adenosine to some LMW PNPs but not to others. The results indicate that transition-state analogues based on adenosine or other 6-amino nucleosides should not be discounted as potential starting points for alternative inhibitors.
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This paper describes a new and simple method to determine the molecular weight of proteins in dilute solution, with an error smaller than similar to 10%, by using the experimental data of a single small-angle X-ray scattering (SAXS) curve measured on a relative scale. This procedure does not require the measurement of SAXS intensity on an absolute scale and does not involve a comparison with another SAXS curve determined from a known standard protein. The proposed procedure can be applied to monodisperse systems of proteins in dilute solution, either in monomeric or multimeric state, and it has been successfully tested on SAXS data experimentally determined for proteins with known molecular weights. It is shown here that the molecular weights determined by this procedure deviate from the known values by less than 10% in each case and the average error for the test set of 21 proteins was 5.3%. Importantly, this method allows for an unambiguous determination of the multimeric state of proteins with known molecular weights.
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The crystalline structure of transition-metals (TM) has been widely known for several decades, however, our knowledge on the atomic structure of TM clusters is still far from satisfactory, which compromises an atomistic understanding of the reactivity of TM clusters. For example, almost all density functional theory (DFT) calculations for TM clusters have been based on local (local density approximation-LDA) and semilocal (generalized gradient approximation-GGA) exchange-correlation functionals, however, it is well known that plain DFT fails to correct the self-interaction error, which affects the properties of several systems. To improve our basic understanding of the atomic and electronic properties of TM clusters, we report a DFT study within two nonlocal functionals, namely, the hybrid HSE (Heyd, Scuseria, and Ernzerhof) and GGA + U functionals, of the structural and electronic properties of the Co(13), Rh(13), and Hf(13) clusters. For Co(13) and Rh(13), we found that improved exchange-correlation functionals decrease the stability of open structures such as the hexagonal bilayer (HBL) and double simple-cubic (DSC) compared with the compact icosahedron (ICO) structure, however, DFT-GGA, DFT-GGA + U, and DFT-HSE yield very similar results for Hf(13). Thus, our results suggest that the DSC structure obtained by several plain DFT calculations for Rh(13) can be improved by the use of improved functionals. Using the sd hybridization analysis, we found that a strong hybridization favors compact structures, and hence, a correct description of the sd hybridization is crucial for the relative energy stability. For example, the sd hybridization decreases for HBL and DSC and increases for ICO in the case of Co(13) and Rh(13), while for Hf(13), the sd hybridization decreases for all configurations, and hence, it does not affect the relative stability among open and compact configurations.