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Biomedical subjects

J J Fernández

Publications and source records attributed to J J Fernández.

At least 19 recordsLinked to original sources
PubMed2006

CTF determination and correction in electron cryotomography.

Electron cryotomography (cryoET) has the potential to elucidate the structure of complex biological specimens at molecular resolution but technical and computational improvements are still needed. This work addresses the determination and correction of the contrast transfer function (CTF) of the electron microscope in cryoET. Our approach to CTF detection and defocus determination depends on strip-based periodogram averaging, extended throughout the tilt series to overcome the low contrast conditions found in cryoET. A method for CTF correction that deals with the defocus gradient in images of tilted specimens is also proposed. These approaches to CTF determination and correction have been applied here to several examples of cryoET of pleomorphic specimens and of single particles. CTF correction is essential for improving the resolution, particularly in those studies that combine cryoET with single particle averaging techniques.

Cryoelectron Microscopy↗
PubMed2004

Phan3D: design of biological phantoms in 3D electron microscopy.

Three-Dimensional Electron Microscopy (3DEM) has turned out to be a major player in structural proteomics. In 3DEM, tens of thousands of EM images from a macromolecule at different views are combined to derive its structure by means of a 3D reconstruction algorithm. However, for an optimal reconstruction, the most suitable algorithm has to be used and its parameters have to be tuned for the macromolecule under study and the experimental conditions found. The use of phantoms is central to objective comparison of reconstruction algorithms and optimization of their parameters. Phan3D is a tool intended to provide a fully visual and interactive environment that facilitates the design of phantoms resembling biological specimens in 3DEM. Phan3D has been developed as an alternative to the tedious, error-prone and old-fashioned phantom design that is based on hand-written text description files.

Computer Graphics↗
PubMed2004

Application of the exact exchange potential method for half metallic intermediate band alloy semiconductor.

In this paper we present an analysis of the convergence of the band structure properties, particularly the influence on the modification of the bandgap and bandwidth values in half metallic compounds by the use of the exact exchange formalism. This formalism for general solids has been implemented using a localized basis set of numerical functions to represent the exchange density. The implementation has been carried out using a code which uses a linear combination of confined numerical pseudoatomic functions to represent the Kohn-Sham orbitals. The application of this exact exchange scheme to a half-metallic semiconductor compound, in particular to Ga(4)P(3)Ti, a promising material in the field of high efficiency solar cells, confirms the existence of the isolated intermediate band in this compound.

Journal Article↗
PubMed2003

A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjustment.

In this work, a powerful parametric spectral estimation technique, 2D-auto regressive moving average modeling (ARMA), has been applied to contrast transfer function (CTF) detection in electron microscopy. Parametric techniques such as auto regressive (AR) and ARMA models allow a more exact determination of the CTF than traditional methods based only on the Fourier transform of the complete image or parts of it and performing some average (periodogram averaging). Previous works revealed that AR models can be used to improve CTF estimation and the detection of its zeros. ARMA models reduce the model order and the computing time, and more interestingly, achieve increased accuracy. ARMA models are generated from electron microscopy (EM) images, and then a stepwise search algorithm is used to fit all the parameters of a theoretical CTF model in the ARMA model previously calculated. Furthermore, this adjustment is truly two-dimensional, allowing astigmatic images to be properly treated. Finally, an individual CTF can be assigned to every point of the micrograph, by means of an interpolation at the functional level, provided that a CTF has been estimated in each one of a set of local areas. The user need only know a few a priori parameters of the experimental conditions of his micrographs, for turning this technique into an automatic and very powerful tool for CTF determination, prior to CTF correction in 3D-EM. The programs developed for the above tasks have been integrated into the X-Windows-based Microscopy Image Processing Package (Xmipp) software package, and are fully accessible at www.biocomp.cnb.uam.es.

Algorithms↗
PubMed2002

Okadaic acid, useful tool for studying cellular processes.

One of the most interesting groups of substances of marine origin, from structural and pharmacological points of view are polyether toxins, which generally present a great diversity in size and potent biological activities. The subject of this review is limited to okadaic acid (OA). It was the first example of a group of polyether toxins produced by marine microalgae, which is responsible for the natural phenomena known as Diarrhetic Shellfish Poisoning, DSP red tides. These toxins are accumulated in the digestive glands of the shellfish with a disastrous effect upon the shellfish industry in many parts of the world. Thus, it has been demonstrated that OA is a highly selective inhibitor of protein phosphatases type 1 (PP1) and 2A (PP2A), subsequently that it causes dramatic increases in phosphorylation of numerous proteins as well as being a potent tumour promoter. For that reason, OA is an extremely useful tool for studying the cellular processes that are regulated by reversible phosphorylation of proteins as signal transduction, cell division and memory.

Amino Acid Sequence↗
PubMed2001

Mono- and dinuclear five-coordinate cyclometalated palladium(II) compounds.

Reaction of cyclometalated halide-bridged Pd(II) complexes 1-4 with the tertiary triphosphine ligand (Ph2PCH2CH2)2PPh (triphos) yielded complexes [((Ph2PCH2CH2)2PPh-P,P,P)Pd(N(Cy)=(H)C)C6H2(C(H)=N(Cy))Pd((Ph2PCH2CH2)2PPh-P,P,P)][ClO4]2 5, [Pd(C6H4-N=NC6H5)((Ph2PCH2CH2)2PPh-P,P,P)][ClO4] 6, and [Pd(R-C6H3C(H)=NCy)((Ph2PCH2CH2)2PPh-P,P,P)][ClO4] (7; R = 4-CHO, 8; 3-CHO). Spectroscopic and analytic data suggest five-coordination on the palladium atom, which, for complexes 5, 6, and 7, was confirmed by X-ray crystallography. The geometry around palladium may be view as a distorted trigonal bipyramid, with the palladium, nitrogen, and terminal phosphorus atoms in the equatorial plane. Compound 5 is the first doubly cyclometalated palladium(II) compound with two pentacoordinated metal centers. The structure of 6 comprises two discrete cations with slightly different geometries, showing the importance of crystal packing forces in order to determine the coordination arrangement.

Journal Article↗
PubMed2001

Influence of amino acids on okadaic acid production.

Okadaic acid (OA) (1)) was the first example of a group of polyether toxins known to be produced by marine microalgae, which are responsible for the natural phenomena known as Diarrhetic Shellfish Poisoning (DSP) red tides. It is also a highly selective inhibitor of protein phosphatases type 1 (PP1) and 2A (PP2A), as well as being a potent tumour promoter. For these reasons, OA is an extremely useful tool for studying cellular processes and an important standard for polluted shellfish control. In this paper, we report on a double objective: to improve the production of toxins and verify the apparent participation of amino acids in the formation of these polyethers by monitoring their influence on the promotion of growth, total cell yield and increased in toxicity in Prorocentrum lima of the PL2V strain in batch cultures, in a modified K medium.

Amino Acids↗
PubMed2001

Isolation and structural determination of DTX-6, a new okadaic acid derivative.

Diarrhetic shellfish poisoning is an illness caused by toxins accumulated in shellfish and produced by dinoflagellates, mainly of the Dinophysis and Prorocentrum genera. This paper reports the isolation and spectroscopic structural elucidation of a new compound, DTX-6 (2), an ester derivative of okadaic acid (OA) (1), isolated from an artificial culture of strain PLV2 of Prorocentrum lima.

Animals↗
PubMed2000

Structural analysis of the bacteriophage T3 head-to-tail connector.

The connector protein of bacteriophage T3, p8, has been overexpressed in Escherichia coli. Purification of the oligomers built by several copies of p8 reveals a mixed population of dodecamers and tridecamers. The percentages of these two types of oligomers differ in every culture growth, indicating that assembly of this protein depends upon the conditions of the expression system. Those cultures that generated a majority of dodecamers allowed, after purification of the connectors, the two-dimensional crystallization of the dodecamers in a tetragonal arrangement, while the tridecamers did not form crystals. The processing and averaging of several images of frozen-hydrated crystals and their internal phase comparison shows that the crystals are arranged in a P42(1)2 space group, with cell unit dimensions of 165 x 165 A. The three-dimensional reconstruction generated with images of crystals ranging from 0 degrees to 60 degrees tilt reveals a wide domain surrounded by 12 protrusions and a narrow domain that serves to interact with the tail of the bacteriophage. A channel runs along the connector wide enough to allow the translocation of a double-stranded DNA molecule into the prohead. The general structure of the T3 connector is very similar to those obtained for other nonrelated bacteriophages and strongly suggests that the shape of this important viral structure is intimately related to its function.

Capsid↗
PubMed2000

Two-dimensional crystallization on lipid monolayers and three-dimensional structure of sticholysin II, a cytolysin from the sea anemone Stichodactyla helianthus.

Sticholysin II (Stn II), a potent cytolytic protein isolated from the sea anemone Stichodactyla helianthus, has been crystallized on lipid monolayers. With Fourier-based methods, a three-dimensional (3D) model of Stn II, up to a resolution of 15 A, has been determined. The two-sided plane group is p22(1)2, with dimensions a = 98 A, b = 196 A. The 3D model of Stn II displays a Y-shaped structure, slightly flattened, with a small curvature along its longest dimension (51 A). This protein, with a molecular mass of 19. 2 kDa, is one of the smallest structures reconstructed with this methodology. Two-dimensional (2D) crystals of Stn II on phosphatidylcholine monolayers present a unit cell with two tetrameric motifs, with the monomers in two different orientations: one with its longest dimension lying on the crystal plane and the other with this same axis leaning at an angle of approximately 60 degrees with the crystal plane.

Animals↗
PubMed1999

The three-dimensional structure of a DNA translocating machine at 10 A resolution.

BACKGROUND: Head-tail connectors are viral substructures that are very important in the viral morphogenetic cycle, having roles in the formation of the precursor capsid (prohead), DNA packaging, tail binding to the mature head and in the infection process. Structural information on the connector would, therefore, help us to understand how this structure is related to a multiplicity of functions. RESULTS: Recombinant bacteriophage phi29 connectors have been crystallized in two-dimensional aggregates. An average projection image and a three-dimensional map have been obtained at 8 A and 10 A resolution, respectively, from untilted and tilted images of vitrified specimens of the two-dimensional crystals. The average projection image reveals a central mass surrounding a channel with 12 appendages protruding from the central mass. The three-dimensional map reveals a wide domain surrounded by 12 appendages that interact with the prohead vertex, and a narrow domain that interacts with the bacteriophage tail. At the junction of the two domains, 12 smaller appendages are visualized. A channel runs along the axis of the connector structure and is sufficiently wide to allow a double-stranded DNA molecule to pass through. CONCLUSIONS: The propeller-like structure of the phi29 connector strengthens the notion of the connector rotating during DNA packaging. The groove formed by the two lanes of large and small appendages may act as a rail to prevent the liberation of the connector from the prohead vertex during rotation.

Bacillus Phages↗
PubMed1999

Growth inhibition by dehydrothyrsiferol - a non-Pgp modulator, derived from a marine red alga - in human breast cancer cell lines.

The novel marine terpenoid dehydrothyrsiferol (DHT) has been isolated from a Canarian red alga Laurencia viridis sp. nov (Ceramiales, Rhodomelaceae) (1). Its cytotoxicity against three human breast cancer cell lines, namely T47D, ZR-75-1, and Hs578T was examined and compared with the chemotherapeutic compound doxorubicin and the mitosis-inhibitor colchicine. Primary breast carcinomas exhibit MDR1 gene expression (3). As the investigated mammary cell lines did not exhibit rhodamine 123 efflux we proved in a P-glycoprotein (Pgp) overexpressing human epidermoid cancer cell line that the marine metabolite does not modulate Pgp mediated drug transport. Therefore, it could be used in Pgp expressing cancer cells without interference.

ATP Binding Cassette Transporter, Subfamily B↗
PubMed1998

Complexation of okadaic acid: a preliminary study.

A complexation study was carried out with okadaic acid (OA) and the univalent metal ions Li+, Na+ and K+, and the divalent metal ions Ca2+ and Mg2+. K+ binding was observed identical with a complex obtained from the natural source (OAC). The pharmacological trials demonstrated that this cation has a very important influence on the pharmacological activity of okadaic acid.

Calcium↗
PubMed1998

Evaluation of the cytotoxic activity of polyethers isolated from Laurencia.

In this paper, we report on the conformational analysis of several polyether triterpenes with a squalene carbon skeleton which exhibited significant cytotoxic activity using a Monte Carlo conformational search and spectroscopical data. These studies indicate that the conformation of the side chain C-14/C-19 and the arrangement and direction of this chain may be among the fundamental factors related to the activity of this type of metabolites.

Animals↗
PubMed1997

Inhibitory effects of okadaic acid on rat uterine contractile responses to different spasmogens.

In the present study, we examined the effects of okadaic acid, a selective inhibitor of type 1 and 2A protein phosphatases, on the mechanical responses evoked by oxytocin, K(+)- and Na(+)-modified solutions and ouabain in estrogen-primed rat myometrium. Oxytocin elicited a rapid, phasic contraction followed by rhythmic oscillations. The phasic response was partially resistant to the absence of external Ca2+. Okadaic acid (1 microM) and the L-type calcium channel blocker nifedipine (1 microM) abolished the oscillatory component and reduced the initial, phasic response to about 80% of the control response. High K+ (60 mM) solution, ouabain (1 mM), K(+)-free medium and low Na+ (25 mM) solution induced extracellular Ca(2+)-dependent biphasic responses composed by an early rapid (KCl, ouabain and K(+)-free solution) or slower developed (25 mM Na+ solution) phasic contraction followed by a sustained increase in tension. Okadaic acid and nifedipine, alone or in combination, abolished or decreased similarly the contractile response evoked by these stimulants. The okadaic acid- and nifedipine-insensitive responses to ouabain, K(+)-free and low Na+ solution were enhanced by increasing the extracellular concentration of Ca2+ in the medium and were inhibited in a dose-dependent manner by amiloride (0.05-0.5 mM). These data suggest that, in estrogen-primed rat uterus, dephosphorylating mechanisms by OA-sensitive protein phosphatases play an important role in regulating myometrial contractions elicited by Ca2+ entry through voltage-sensitive Ca2+ channels.

Animals↗
PubMed1997

[Bronchial atresia and bronchogenic cyst in an adult].

We present the case of an asymptomatic patient, with a right paracardiac mass discovered in a preoperative radiologic study. The bronchoscopy showed the intermedius bronchus atresia, finished in bottom of sack, with absence of middle and lower right lobes. With the chest computed tomographic scan, two lobulated contour mediastinal masses were seen. The patient was submitted to surgery, being the pathological findings consistent with bronchogenic cysts with atresia of the intermediarius bronchus. The patient evolved favourably after surgery.

Adult↗