Structure-preserving Gaussian denoising of FIB-SEM volumes

FIB-SEM (Focused Ion Beam-Scanning Electron Microscopy) is an imaging technique that allows 3D ultrastructural analysis of cells and tissues at the nanoscale. The acquired FIB-SEM data are highly noisy, which makes denoising an essential step prior to volume interpretation. Gaussian filtering is a standard method in the field because it is fast and straightforward. However, it tends to blur the biological features due to its linear nature that ignores the rapid changes of the structures throughout the volume. To address this issue, we have developed a new approach to structure-preserving noise reduction for FIB-SEM. It has abilities to locally adapt the filtering to the biological structures while taking advantage of the simplicity of Gaussian filtering. It uses the Optical Flow (OF) to estimate the variations of the structural features across the volume, so that they are compensated before the subsequent filtering with a Gaussian function. As demonstrated qualitatively and objectively with datasets from different samples and acquired under different conditions, our denoising approach outperforms the standard Gaussian filtering and is competitive with state-of-the-art methods in terms of noise reduction and preservation of the sharpness of the structures.

Fungal Patterns Induce Cytokine Expression through Fluxes of Metabolic Intermediates That Support Glycolysis and Oxidative Phosphorylation

Cytokine expression is fine-tuned by metabolic intermediates, which makes research on immunometabolism suitable to yield drugs with a wider prospect of application than the biological therapies that block proinflammatory cytokines. Switch from oxidative phosphorylation (OXPHOS) to glycolysis has been considered a characteristic feature of activated immune cells. However, some stimuli might enhance both routes concomitantly. The connection between the tricarboxylic acid cycle and cytokine expression was scrutinized in human monocyte-derived dendritic cells stimulated with the fungal surrogate zymosan. Results showed that nucleocytosolic citrate and ATP-citrate lyase activity drove IL1B, IL10, and IL23A expression by yielding acetyl-CoA and oxaloacetate, with the latter one supporting glycolysis and OXPHOS by maintaining cytosolic NAD⁺ and mitochondrial NADH levels through mitochondrial shuttles. Succinate dehydrogenase showed a subunit-specific ability to modulate IL23A and IL10 expression. Succinate dehydrogenase A subunit activity supported cytokine expression through the control of the 2-oxoglutarate/succinate ratio, whereas C and D subunits underpinned cytokine expression by conveying electron flux from complex II to complex III of the electron transport chain. Fatty acids may also fuel the tricarboxylic acid cycle and influence cytokine expression. Overall, these results show that fungal patterns support cytokine expression through a strong boost of glycolysis and OXPHOS supported by the use of pyruvate, citrate, and succinate, along with the compartmentalized NAD(H) redox state maintained by mitochondrial shuttles.

Optical flow driven interpolation for isotropic FIB-SEM reconstructions

BACKGROUND AND OBJECTIVE

Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) allows three-dimensional ultrastructural analysis of cells and tissues at the nanoscale. The technique iteratively removes a section of the sample with a FIB and takes an SEM image from the exposed surface. The section thickness is usually higher than the image pixel size to reduce acquisition time, thus resulting in anisotropic resolution. In this work, we explore novel interpolation methods along the sectioning direction to produce isotropic resolution and facilitate proper interpretation of the FIB-SEM 3D volumes.

METHODS

Classical interpolation methods are usually applied in this context under the assumption that the changes through successive images are relatively smooth. However, the actual 3D arrangement of the structures in the sample may cause significant changes in the biological features between consecutive images of the FIB-SEM stacks. We have developed a novel interpolation strategy that accounts for this variation by using the Optical Flow (OF) to estimate it. As an intermediate stage, OF-compensated images are produced by aligning the spatial regions of the biological structures. Interpolated images are then generated from these OF-compensated images. The final isotropic stack is assembled by interleaving the interpolated images with the original images of the anisotropic stack.

RESULTS

OF-driven and classical interpolation methods were compared using an objective assessment based on Pearson Correlation Coefficient (PCC) and a qualitative evaluation based on visual results, using public datasets and representative anisotropy conditions. The objective assessment demonstrated that the OF-driven interpolation always yields higher PCC values, with interpolated images closer to the ground truth. The qualitative evaluation corroborated those results and confirmed that classical interpolation may blur areas with substantial changes between consecutive images whereas OF-driven interpolation provides sharpness.

CONCLUSIONS

We have developed an OF-driven interpolation approach to generating FIB-SEM stacks with isotropic resolution from experimental anisotropic data. It adapts to the rapid variation of the biological structures observed through the images of the FIB-SEM stack. Our approach outperforms classical interpolation and manages to produce sharp interpolated views in cases where there are significant changes between consecutive experimental images.

TomoEED: fast edge-enhancing denoising of tomographic volumes

Summary

TomoEED is an optimized software tool for fast feature-preserving noise filtering of large 3D tomographic volumes on CPUs and GPUs. The tool is based on the anisotropic nonlinear diffusion method. It has been developed with special emphasis in the reduction of the computational demands by using different strategies, from the algorithmic to the high performance computing perspectives. TomoEED manages to filter large volumes in a matter of minutes in standard computers.

Availability and implementation

TomoEED has been developed in C. It is available for Linux platforms at http://www.cnb.csic.es/%7ejjfernandez/tomoeed.

Supplementary information

Supplementary data are available at Bioinformatics online.

Delocalization and heat transport in multidimensional trapped ion systems

We study the connection between heat transport properties of systems coupled to different thermal baths in two separate regions and their underlying nonequilibrium dynamics. We consider classical systems of interacting particles that may exhibit a certain degree of delocalization and whose effective dimensionality can be modified through the controlled variation of a global trapping potential. We focus on Coulomb crystals of trapped ions, which offer a versatile playground to shed light on the role that spatial constraints play on heat transport. We use a three-dimensional model to simulate the trapped ion system and show in a numerically rigorous manner to what extent heat transport properties could be feasibly tuned across the structural phase transitions among the linear, planar zigzag, and helical configurations. By solving the classical Langevin equations of motion, we analyze the steady state spatial distributions of the particles, the temperature profiles, and total heat flux through the various structural phase transitions that the system may experience. The results evidence a clear correlation between the degree of delocalization of the internal ions and the emergence of a nonzero gradient in the temperature profiles. The signatures of the phase transitions in the total heat flux as well as the optimal spatial configuration for heat transport are shown.

Preliminary analysis of Diffusion Coefficient Measurements in ternary mIXtures 4 (DCMIX4) experiment on board the International Space Station

In the frame of the Diffusion Coefficient Measurements in ternary mIXtures 4 (DCMIX4) project the thermodiffusion experiments were conducted on the International Space Station (ISS) in the Selectable Optical Diagnostics Instrument (SODI) which is on orbit since 2009. We describe the results of the preliminary analysis of images downloaded during the execution of DCMIX4 in order to check the quality of the running experiments and, if needed, adjust the experiment parameters for the following runs. The quick analysis of raw data showed that they are meaningful and will allow to obtain the transport coefficients of examined ternary and binary mixtures.

Spiralyde A, an Antikinetoplastid Dolabellane from the Brown Alga Dictyota spiralis

Bioassay-guided fractionation of the antikinetoplastid extract of the brown alga Dictyota spiralis has led to the isolation of spiralyde A (1), a new dolabellane aldehyde, along with other five known related diterpenes (2⁻6). Their structures were determined by HRESIMS, 1D and 2D NMR spectroscopy, and comparison with data reported in the literature. The antiparasitic activity of all compounds was evaluated. Spiralyde A (1) and the known compound 3,4-epoxy-7,18-dolabelladiene (2) were the most active compounds against Leishmania amazonensis and Trypanosoma cruzi. Spiralyde A (1) was the most potent compound, comparable to benznidazole, the reference drug for trypanocidal activity.

The toxic benthic dinoflagellate Prorocentrum maculosum Faust is a synonym of Prorocentrum hoffmannianum Faust

Three strains of the toxic benthic dinoflagellate Prorocentrum hoffmannianum were isolated in the Canary Islands (north-east Atlantic Ocean, Spain). The identity of the strains was determined by phylogenetic analyses of partial LSU rDNA (D1-D2 regions) but their morphology based on SEM images corresponded to P. maculosum. Their toxin profiles were analyzed by liquid chromatography and high resolution mass spectrometry analysis (LC-HRMS) on cell extracts and culture media. Okadaic acid and three analogs were detected in all strains. Rather, in culture media the detected compounds were variable among strains, two of them being okadaic acid analogs not found on cell extracts. As a result, the taxonomy of the species was revised and P. maculosum is proposed as a junior synonym of P. hoffmannianum whose description is emended.

Marine Longilenes, Oxasqualenoids with Ser-Thr Protein Phosphatase 2A Inhibition Activity

The red seaweed Laurencia viridis is a rich source of oxygenated secondary metabolites that were derived from squalene. We report here the structures of three novel compounds, (+)-longilene peroxide (1), longilene (2), and (+)-prelongilene (3) that were isolated from this alga, in addition to other substances, 4 and 5, resulting from their acid-mediated degradation. The effect of compounds 1 and 3 against Ser-Thr protein phosphatase type 2A (PP2A) was evaluated, showing that (+)-longilene peroxide (1) inhibited PP2A (IC₅₀ 11.3 μM). In order to explain the interaction between PP2A and compounds 1 and 3, molecular docking simulations onto the PP2A enzyme-binding region were used.

Endoplasmic Reticulum Stress Sensor IRE1α Enhances IL-23 Expression by Human Dendritic Cells

Human monocyte-derived dendritic cells (DCs) exposed to pathogen-associated molecular patterns (PAMPs) undergo bioenergetic changes that influence the immune response. We found that stimulation with PAMPs enhanced glycolysis in DCs, whereas oxidative phosphorylation remained unaltered. Glucose starvation and the hexokinase inhibitor 2-deoxy-d-glucose (2-DG) modulated cytokine expression in stimulated DCs. Strikingly, IL23A was markedly induced upon 2-DG treatment, but not during glucose deprivation. Since 2-DG can also rapidly inhibit protein N-glycosylation, we postulated that this compound could induce IL-23 in DCs via activation of the endoplasmic reticulum (ER) stress response. Indeed, stimulation of DCs with PAMPs in the presence of 2-DG robustly activated inositol-requiring protein 1α (IRE1α) signaling and to a lesser extent the PERK arm of the unfolded protein response. Additional ER stressors such as tunicamycin and thapsigargin also promoted IL-23 expression by PAMP-stimulated DCs. Pharmacological, biochemical, and genetic analyses using conditional knockout mice revealed that IL-23 induction in ER stressed DCs stimulated with PAMPs was IRE1α/X-box binding protein 1-dependent upon zymosan stimulation. Interestingly, we further evidenced PERK-mediated and CAAT/enhancer-binding protein β-dependent trans-activation of IL23A upon lipopolysaccharide treatment. Our findings uncover that the ER stress response can potently modulate cytokine expression in PAMP-stimulated human DCs.

Heteroleptic mononuclear compounds of ruthenium(ii): synthesis, structural analyses, in vitro antitumor activity and in vivo toxicity on zebrafish embryos

The limitations of platinum complexes in cancer treatment have motivated the extensive investigation into other metal complexes such as ruthenium. We herein present the synthesis and characterization of a new family of ruthenium compounds 1a-5a with the general formula [Ru(bipy)₂L][CF₃SO₃]₂ (bipy = 2,2'-bipyridine; L = bidentate ligand: N,N; N,P; P,P; P,As) which have been characterized by elemental analysis, ES-MS, ¹H and ³¹P-{¹H} NMR, FTIR and conductivity measurements. The molecular structures of four Ru(ii) complexes were determined by single crystal X-ray diffraction. All compounds displayed moderate cytotoxic activity in vitro against human A2780 ovarian, MCF7 breast and HCT116 colorectal tumor cells. Compound 5a was the most cytotoxic compound against A2780 and MCF7 tumor cells with an IC₅₀ of 4.75 ± 2.82 μM and 20.02 ± 1.46 μM, respectively. The compounds showed no cytotoxic effect on normal human primary fibroblasts but rather considerable selectivity for A2780, MCF7 and HCT116 tumor cells. All compounds induce apoptosis and autophagy in A2780 ovarian carcinoma cells and some nuclear DNA fragmentation. All compounds interact with CT-DNA with intrinsic binding constants in the order 1a > 4a > 2a > 3a > 5a. The observed hyperchromic effect may be due to the electrostatic interaction between positively charged cations and the negatively charged phosphate backbone at the periphery of the double helix-CT-DNA. Interestingly, compound 1a shows a concentration dependent DNA double strand cleavage. In addition in vivo toxicity has been evaluated on zebrafish embryos unveiling the differential toxicity between the compounds, with LC₅₀ ranging from 8.67 mg L^-1 for compound 1a to 170.30 mg L^-1 for compound 2a.

Gene expression profiles in the cerebellum of transgenic mice over expressing the human FMR1 gene with CGG repeats in the normal range

Modifications in the GABA pathway are considered to be responsible for motor alterations in animal models for fragile X-associated tremor ataxia syndrome. We analyzed the expression profile in the cerebellum in a transgenic mouse model that over expresses the human FMR1 gene with CGG repeats in the normal range. We used the "GeneChip Mouse Gene 1.0 ST Array" from Affymetrix analyzing 28,853 well-described and -characterized genes. Based on data from the comparative analysis of the expression profile, we detected a significant gradient with a P value <0.1 and changes in expression equal to or greater than 1.5 times compared to the control mouse genes. There were significant changes in the expression of 104 genes, among which 72% had decreased and 28% had increased expression. With the exception of GabarapL2, no changes in expression of genes from the GABA pathway were observed, which may explain the absence of an altered motor phenotype in these mice. These results further support the view that toxic effects in fragile X-associated tremor ataxia syndrome are due to expansion of CGG repeats rather than increased mRNA levels, since in the transgenic mice the FMR1 mRNA levels were increased 20-100 times compared with those of control littermates.

New polyether triterpenoids from Laurencia viridis and their biological evaluation

The red seaweed Laurencia viridis is a rich source of secondary metabolites derived from squalene. New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines.

Studies on polyethers produced by red algae

Two novel squalene-derived triterpenes, spirodehydrovenustatriol (3) and 14-keto-dehydrothyrsiferol (4) were isolated from the red alga Laurencia viridis, together with two new and unusual C(17) terpenoids, adejen A (5) and B (6). These truncated structures possess structural similarities with other known squalene metabolites and their biogenetic origin has been proposed on the basis of an oxidative process of the squalene skeleton. All the structures were elucidated by extensive use of 2D NMR spectroscopic methods.

Vectorization with SIMD extensions speeds up reconstruction in electron tomography

Electron tomography allows structural studies of cellular structures at molecular detail. Large 3D reconstructions are needed to meet the resolution requirements. The processing time to compute these large volumes may be considerable and so, high performance computing techniques have been used traditionally. This work presents a vector approach to tomographic reconstruction that relies on the exploitation of the SIMD extensions available in modern processors in combination to other single processor optimization techniques. This approach succeeds in producing full resolution tomograms with an important reduction in processing time, as evaluated with the most common reconstruction algorithms, namely WBP and SIRT. The main advantage stems from the fact that this approach is to be run on standard computers without the need of specialized hardware, which facilitates the development, use and management of programs. Future trends in processor design open excellent opportunities for vector processing with processor's SIMD extensions in the field of 3D electron microscopy.

Exploiting desktop supercomputing for three-dimensional electron microscopy reconstructions using ART with blobs

Three-dimensional electron microscopy allows direct visualization of biological macromolecules close to their native state. The high impact of this technique in the structural biology field is highly correlated with the development of new image processing algorithms. In order to achieve subnanometer resolution, the size and number of images involved in a three-dimensional reconstruction increase and so do computer requirements. New chips integrating multiple processors are hitting the market at a reduced cost. This high-integration, low-cost trend has just begun and is expected to bring real supercomputers to our laboratory desktops in the coming years. This paper proposes a parallel implementation of a computation-intensive algorithm for three-dimensional reconstruction, ART, that takes advantage of the computational power in modern multicore platforms. ART is a sophisticated iterative reconstruction algorithm that has turned out to be well suited for the conditions found in three-dimensional electron microscopy. In view of the performance obtained in this work, these modern platforms are expected to play an important role to face the future challenges in three-dimensional electron microscopy.

Sharpening high resolution information in single particle electron cryomicroscopy

Advances in single particle electron cryomicroscopy have made possible to elucidate routinely the structure of biological specimens at subnanometer resolution. At this resolution, secondary structure elements are discernable by their signature. However, identification and interpretation of high resolution structural features are hindered by the contrast loss caused by experimental and computational factors. This contrast loss is traditionally modeled by a Gaussian decay of structure factors with a temperature factor, or B-factor. Standard restoration procedures usually sharpen the experimental maps either by applying a Gaussian function with an inverse ad hoc B-factor, or according to the amplitude decay of a reference structure. EM-BFACTOR is a program that has been designed to widely facilitate the use of the novel method for objective B-factor determination and contrast restoration introduced by Rosenthal and Henderson [Rosenthal, P.B., Henderson, R., 2003. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721-745]. The program has been developed to interact with the most common packages for single particle electron cryomicroscopy. This sharpening method has been further investigated via EM-BFACTOR, concluding that it helps to unravel the high resolution molecular features concealed in experimental density maps, thereby making them better suited for interpretation. Therefore, the method may facilitate the analysis of experimental data in high resolution single particle electron cryomicroscopy.

EGEETomo: a user-friendly, fault-tolerant and grid-enabled application for 3D reconstruction in electron tomography

Electron tomography is the leading technique to elucidate the structure of complex biological specimens. Due to the resolution needs, huge reconstructions are required. Grid computing has the potential to face the significant computational demands involved. However, there are a number of key issues, such as stability or difficult user-grid interaction, that currently preclude fully exploitation of its potential. EGEETomo is a user-friendly application that facilitates the interaction with the grid for the non-specialized user and automates job submission and supervision. In addition, EGEETomo is supplied with an automated fault recovery mechanism, which is key to make all the work transparent to the user. EGEETomo significantly accelerates tomographic reconstruction by exploiting the computational resources in the EGEE grid with minimal user intervention.

AVAILABILITY

http://www.ace.ual.es/~jrbcast/EGEETomo.tar.gz

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.

[Study of effectiveness of craving control with topiramate in patients with substance dependence disorders]

INTRODUCTION

Effectiveness and tolerability of topiramate at 3 and 6 months was assessed in patients requesting dehabituation programs.

METHODS

Observational, prospective, national and multicenter study of 6 months, in patients on treatment with topiramate, who fulfilled criteria for dependence of opiates according to ICD-10 participating in therapeutic programs of dehabituation, without concomitant psychiatric illnesses and any responsible relative. Main measures of effectiveness were retention rates, alcohol consumption and other illicit drugs by urine tests (opiates, cannabis, cocaine) and treatment needs by EuropASI scale. Other parameters were HAM-D, DAS-SV and SF-36.

RESULTS

Patients with consumption by urine tests decreased from 94.1 % (n = 64) at baseline to 39.6 % (n = 19) after 6 months of treatment, as was seen by means of the mean score in EuropASI scale, for all substances except methadone. No consumption was accompanied by a low rate of relapse of 33.3 % at 6 months. Twenty one patients had adverse reactions (28 %). The most frequent adverse reactions were somnolence (n = 9; 12 %), paraesthesia (n = 5; 6.7 %) and depression (n = 4; 5.3 %).

CONCLUSIONS

In real clinical practice, topiramate showed a good response with a relevant decrease of percent of patients with abuse or consumption, and a satisfactory tolerability profile for the treatment of patients with dependence on heroine, cocaine, and other opiates, showing better outcomes than those obtained in previous trials.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Inhibitory effects of a novel marine terpenoid on sensitive and multidrug resistant KB cell lines

Mechanisms of growth inhibition by the novel marine compound dehydrothyrsiferol (DHT) were investigated in a sensitive and an MDR+ human epidermoid cancer cell line. DHT was found to circumvent multidrug resistance mediated by P-glycoprotein. Cell cycle analysis revealed an accumulation in S-phase. The anchorage independent clonogenic growth in soft agar was not significantly reduced at IC50 concentrations. Reduced cell growth caused by induction of apoptotic or necrotic cell death could not be verified. Therefore, cell proliferation during an incubation period of five days was measured and found to be significantly reduced. We conclude that growth inhibition by dehydrothyrsiferol in KB cancer cells is not mediated by apoptosis but by growth retardation; the reasons for this are worth being investigated in detail.

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.

[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.

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.

Analysis of structural variability within two-dimensional biological crystals by a combination of patch averaging techniques and self organizing maps

We study in this work the use of self organizing maps to analyze the structural variability that can be found along two-dimensional crystals of biological macromolecules. Small areas of the crystals, termed "patches" by previous researchers, are used to obtain local average images that are then used as the input of a Self Organizing Map. This procedure allows for a fast and accurate image classification. Multivariate Statistical Analysis is then used on the resulting code vectors producing a very condensed data representation. This methodology is applied to previously studied crystals of bacteriophage phi 29 p10 connector, finding a crystalline heterogeneity probably associated to multilayers in some areas of the crystal.

Proposal for a new distributed database of macromolecular and subcellular structures from different areas of microscopy

In this work we address the problem of information access that arises in the field of three-dimensional structure determination, by means of image processing, from data obtained by various types of microscopy. A prototype of a distributed database containing three-dimensional structural information is presented. In this database the volume information is linked, if possible, to other sources of catalogued information such as sequence data, atomic coordinates, and bibliographies. The solution we propose is sufficiently general to be applicable to data in other fields of biomedical science.

Inhibitory and contractile effects of okadaic acid on rat uterine muscle

The effects of okadaic acid and its interactions with various agents known to increase, by different mechanisms, the intracellular levels of cyclic AMP and/or cyclic GMP were investigated in isolated strips of rat myometrium. Okadaic acid showed inhibitory effects at concentrations between 10(-7) M and 3 x 10(-6) M. At higher concentrations, a biphasic, contractile and then relaxant response was observed. The results obtained suggest that, in rat uterine smooth muscle, the inhibitory effects of okadaic acid are not entirely mediated by the activation of cyclic AMP- and/or cyclic GMP-dependent pathways. The data also point to the existence of a clear interaction between okadaic acid and methylxanthines, although further studies are needed to clarify the mechanisms involved in this interaction.

[Soy and corn flour precooked with microwaves and its use in the preparation of arepas]

Unhusked corn and soy grits were used as raw material, with a particle size ranging between 10 and 20 mesh (ASTM). The results obtained in this study reveal that microwave heating is effective in destroying the antinutritional factors present in soybeans. The trypsin inhibitor activity, in effect, was reduced to a 76% inactivation. The hemagglutinating titer was labile to the heating process, showing values of +8 to +3 for the full-fat soy flour and precooked soy flour, respectively. The quality of soy protein was measured by the protein efficiency ratio (PER) showing values of 2.63 for the precooked soy flour, and 2.46 to 2.21 for the precooked corn:soy blends (70:30 and 50:50). These uncooked blends present values of 1.17 and 1.04. The enriched corn:soy flour had a PER value of 1.60, in comparison to casein (PER = 2.90). The microwave heating improved the digestibility of the soy flour and blends. There were no significant differences (P less than or equal to 0.05) in relation to the functionality of the precooked flour and mixtures. The results obtained revealed that the applied process markedly improve the functional properties and nutritional value of the enriched flour, and of the "arepas" prepared from them.

Paracoccidioidal infection in the wife of a patient with paracoccidioidomycosis

Three agar immunoprecipitin techniques (double immunodiffusion, immunoelectrophoresis and immunoelectroosmophoresis-immunodiffusion) made with paracoccidioidin and serum of a paracoccidioidomycosis patient's wife, permitted us to observe a specific band in 6 successive samples of blood taken from the wife over a period of 21 months. The case represents an example of a subclinical paracoccidioidomycosis infection that is usually diagnosed in its disseminated, progressive form. Three possible sources of infection are discussed. But an interhuman contagion appears to be the most feasible.