Carlos Oscar Sánchez Sorzano | CSIC (Consejo Superior de Investigaciones Científicas-Spanish National Research Council) (original) (raw)

Papers by Carlos Oscar Sánchez Sorzano

Research paper thumbnail of Elastic registration of biological images using vector-spline regularization

IEEE Transactions on Biomedical Engineering, 2005

We present an elastic registration algorithm for the alignment of biological images. Our method c... more We present an elastic registration algorithm for the alignment of biological images. Our method combines and extends some of the best techniques available in the context of medical imaging. We express the deformation field as a B-spline model, which allows us to deal with a rich variety of deformations. We solve the registration problem by minimizing a pixelwise mean-square distance measure between the target image and the warped source. The problem is further constrained by way of a vector-spline regularization which provides some control over two independent quantities that are intrinsic to the deformation: its divergence, and its curl. Our algorithm is also able to handle soft landmark constraints, which is particularly useful when parts of the images contain very little information or when its repartition is uneven. We provide an optimal analytical solution in the case when only landmarks and smoothness considerations are taken into account. We have applied our approach to perform the elastic registration of images such as electrophoretic gels and fly embryos. The validation of the results by experts has been favorable in all cases.

Research paper thumbnail of Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions

Journal of Structural Biology, 2005

Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transm... more Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transmission electron microscopy is still an open problem. In this article, we extend the applicability of the spectral signal-to-noise ratio (SSNR) to the evaluation of 3D volumes reconstructed with any reconstruction algorithm. The basis of the method is to measure the consistency between the data and a corresponding set of reprojections computed for the reconstructed 3D map. The idiosyncrasies of the reconstruction algorithm are taken explicitly into account by performing a noise-only reconstruction. This results in the definition of a 3D SSNR which provides an objective indicator of the quality of the 3D reconstruction. Furthermore, the information to build the SSNR can be used to produce a volumetric SSNR (VSSNR). Our method overcomes the need to divide the data set in two. It also provides a direct measure of the performance of the reconstruction algorithm itself; this latter information is typically not available with the standard resolution methods which are primarily focused on reproducibility alone.

Research paper thumbnail of Improved Bayesian image denoising based on wavelets with applications to electron microscopy

Pattern Recognition, 2006

In this work we discuss an improvement of the image-denoising wavelet-based method presented by B... more In this work we discuss an improvement of the image-denoising wavelet-based method presented by Bijaoui [Wavelets, Gaussian mixtures and Wiener filtering, Signal Process. 82 (2002) 709-712]. We show that the parameter estimation step can be replaced by a constrained nonlinear optimization. We propose three different methods to estimate the parameters. As in Bijaoui's original article, two of them deal with white noise. We show that the resulting algorithms improve the one originally proposed. Our third method extends the applicability of the denoising algorithm to colored noise. We test our algorithms with images simulating electron microscopy (EM) conditions as well as experimental EM images.

Research paper thumbnail of Immunogenic Profiling in Mice of a HIV/AIDS Vaccine Candidate (MVA-B) Expressing Four HIV1 Antigens and Potentiation by Specific Gene Deletions

PLOS One, 2010

Background: The immune parameters of HIV/AIDS vaccine candidates that might be relevant in protec... more Background: The immune parameters of HIV/AIDS vaccine candidates that might be relevant in protection against HIV-1 infection are still undefined. The highly attenuated poxvirus strain MVA is one of the most promising vectors to be use as HIV-1 vaccine. We have previously described a recombinant MVA expressing HIV-1 Env, Gag, Pol and Nef antigens from clade B (referred as MVA-B), that induced HIV-1-specific immune responses in different animal models and gene signatures in human dendritic cells (DCs) with immunoregulatory function.

Research paper thumbnail of Insertion of Vaccinia Virus C7L Host Range Gene into NYVAC-B Genome Potentiates Immune Responses against HIV1 Antigens

PLOS One, 2010

Background: The highly attenuated vaccinia virus strain NYVAC expressing HIV-1 components has bee... more Background: The highly attenuated vaccinia virus strain NYVAC expressing HIV-1 components has been evaluated as a vaccine candidate in preclinical and clinical trials with encouraging results. We have previously described that the presence of C7L in the NYVAC genome prevents the induction of apoptosis and renders the vector capable of replication in human and murine cell lines while maintaining an attenuated phenotype in mice.

Research paper thumbnail of A Candidate HIV/AIDS Vaccine (MVA-B) Lacking Vaccinia Virus Gene C6L Enhances Memory HIV1Specific T-Cell Responses

PLOS One, 2011

The vaccinia virus (VACV) C6 protein has sequence similarities with the poxvirus family Pox_A46, ... more The vaccinia virus (VACV) C6 protein has sequence similarities with the poxvirus family Pox_A46, involved in regulation of host immune responses, but its role is unknown. Here, we have characterized the C6 protein and its effects in virus replication, innate immune sensing and immunogenicity in vivo. C6 is a 18.2 kDa protein, which is expressed early during virus infection and localizes to the cytoplasm of infected cells. Deletion of the C6L gene from the poxvirus vector MVA-B expressing HIV-1 Env, Gag, Pol and Nef antigens from clade B (MVA-B DC6L) had no effect on virus growth kinetics; therefore C6 protein is not essential for virus replication. The innate immune signals elicited by MVA-B DC6L in human macrophages and monocyte-derived dendritic cells (moDCs) are characterized by the up-regulation of the expression of IFN-b and IFN-a/b-inducible genes. In a DNA prime/MVA boost immunization protocol in mice, flow cytometry analysis revealed that MVA-B DC6L enhanced the magnitude and polyfunctionality of the HIV-1-specific CD4 + and CD8 + T-cell memory immune responses, with most of the HIV-1 responses mediated by the CD8 + T-cell compartment with an effector phenotype. Significantly, while MVA-B induced preferentially Env-and Gag-specific CD8 + T-cell responses, MVA-B DC6L induced more Gag-Pol-Nef-specific CD8 + T-cell responses. Furthermore, MVA-B DC6L enhanced the levels of antibodies against Env in comparison with MVA-B. These findings revealed that C6 can be considered as an immunomodulator and that deleting C6L gene in MVA-B confers an immunological benefit by enhancing IFN-b-dependent responses and increasing the magnitude and quality of the T-cell memory immune responses to HIV-1 antigens. Our observations are relevant for the improvement of MVA vectors as HIV-1 vaccines.

Research paper thumbnail of Insertion of Vaccinia Virus C7L Host Range Gene into NYVAC-B Genome Potentiates Immune Responses against HIV1 Antigens

PLOS One, 2010

Background: The highly attenuated vaccinia virus strain NYVAC expressing HIV-1 components has bee... more Background: The highly attenuated vaccinia virus strain NYVAC expressing HIV-1 components has been evaluated as a vaccine candidate in preclinical and clinical trials with encouraging results. We have previously described that the presence of C7L in the NYVAC genome prevents the induction of apoptosis and renders the vector capable of replication in human and murine cell lines while maintaining an attenuated phenotype in mice.

Research paper thumbnail of High Quality Long-Term CD4+ and CD8+ Effector Memory Populations Stimulated by DNA-LACK/MVA-LACK Regimen in Leishmania major BALB/c Model of Infection

PLOS One, 2012

Heterologous vaccination based on priming with a plasmid DNA vector and boosting with an attenuat... more Heterologous vaccination based on priming with a plasmid DNA vector and boosting with an attenuated vaccinia virus MVA recombinant, with both vectors expressing the Leishmania infantum LACK antigen (DNA-LACK and MVA-LACK), has shown efficacy conferring protection in murine and canine models against cutaneus and visceral leishmaniasis, but the immune parameters of protection remain ill defined. Here we performed by flow cytometry an in depth analysis of the T cell populations induced in BALB/c mice during the vaccination protocol DNA-LACK/MVA-LACK, as well as after challenge with L. major parasites. In the adaptive response, there is a polyfunctional CD4 + and CD8 + T cell activation against LACK antigen. At the memory phase the heterologous vaccination induces high quality LACK-specific long-term CD4 + and CD8 + effector memory cells. After parasite challenge, there is a moderate boosting of LACK-specific CD4 + and CD8 + T cells. Anti-vector responses were largely CD8 + -mediated. The immune parameters induced against LACK and triggered by the combined vaccination DNA/MVA protocol, like polyfunctionality of CD4 + and CD8 + T cells with an effector phenotype, could be relevant in protection against leishmaniasis. Citation: Sánchez-Sampedro L, Gó mez CE, Mejías-Pérez E, S. Sorzano CO, Esteban M (2012) High Quality Long-Term CD4 + and CD8 + Effector Memory Populations Stimulated by DNA-LACK/MVA-LACK Regimen in Leishmania major BALB/c Model of Infection. PLoS ONE 7(6): e38859.

Research paper thumbnail of A Human Multi-Epitope Recombinant Vaccinia Virus as a Universal T Cell Vaccine Candidate against Influenza Virus

PLOS One, 2011

There is a need to develop a universal vaccine against influenza virus infection to avoid develop... more There is a need to develop a universal vaccine against influenza virus infection to avoid developing new formulations of a seasonal vaccine each year. Many of the vaccine strategies for a universal vaccine target strain-conserved influenza virus proteins, such as the matrix, polymerase, and nucleoproteins, rather than the surface hemagglutinin and neuraminidase proteins. In addition, non-disease-causing viral vectors are a popular choice as a delivery system for the influenza virus antigens. As a proof-of-concept, we have designed a novel influenza virus immunogen based on the NP backbone containing human T cell epitopes for M1, NS1, NP, PB1 and PA proteins (referred as NPmix) as well as a construct containing the conserved regions of influenza virus neuraminidase (N-terminal) and hemagglutinin (C-terminal) (referred as NA-HA). DNA vectors and vaccinia virus recombinants expressing NPmix (WR-NP) or both NPmix plus NA-HA (WR-flu) in the cytosol were tested in a heterologous DNA-prime/vaccinia virus-boost vaccine regimen in mice. We observed an increase in the number of influenza virus-specific IFNc-secreting splenocytes, composed of populations marked by CD4 + and CD8 + T cells producing IFNc or TNFa. Upon challenge with influenza virus, the vaccinated mice exhibited decreased viral load in the lungs and a delay in mortality. These findings suggest that DNA prime/poxvirus boost with human multi-epitope recombinant influenza virus proteins is a valid approach for a general T-cell vaccine to protect against influenza virus infection.

Research paper thumbnail of TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy

BMC Bioinformatics, 2007

Background: Transmission electron tomography is an increasingly common three-dimensional electron... more Background: Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomography fills the gap between high resolution structural methods (X-ray diffraction or nuclear magnetic resonance) and optical microscopy. We developed new software for transmission electron tomography, TomoJ. TomoJ is a plug-in for the now standard image analysis and processing software for optical microscopy, ImageJ.

Research paper thumbnail of Flexible image registration for the identification of best fitted protein models in 3DEM maps

Laura Fernández-de-Manuel 1 , María J. Ledesma-Carbayo 1* , Julián Atienza-Herrero 2 , ... Carlos... more Laura Fernández-de-Manuel 1 , María J. Ledesma-Carbayo 1* , Julián Atienza-Herrero 2 , ... Carlos OS Sorzano 2,3 , José-María Carazo 2 , Andrés Santos 1 ... 1 ETSI Telecomunicación, Universidad Politécnica de Madrid, Spain 2 Centro Nacional de ...

Research paper thumbnail of Optimization problems in electron microscopy of single particles

Annals of Operations Research, 2006

Electron Microscopy is a valuable tool for the elucidation of the three-dimensional structure of ... more Electron Microscopy is a valuable tool for the elucidation of the three-dimensional structure of macromolecular complexes. Knowledge about the macromolecular structure provides important information about its function and how it is carried out. This work addresses the issue of three-dimensional reconstruction of biological macromolecules from electron microscopy images. In particular, it focuses on a methodology known as “single-particles” and makes a thorough review of all those steps that can be expressed as an optimization problem. In spite of important advances in recent years, there are still unresolved challenges in the field that offer an excellent testbed for new and more powerful optimization techniques.

Research paper thumbnail of Command-line interfaces can be efficiently brought to graphics: COLIMATE (the COmmand LIne MATE

Software - Practice and Experience, 2002

Scientific computing has traditionally been done on workstations, most of the time running on UNI... more Scientific computing has traditionally been done on workstations, most of the time running on UNIX-like operating systems. These systems are often very robust, powerful and especially suited to heavy computation tasks; however, the usual user interface is based on a command line with all the information needed for the appropriate functioning of the algorithm. These command lines are seldom user-friendly but, on the other hand, they allow batch processes to be built. In this work, a model for command-line-driven packages is given, and at the same time the model includes objects that can be directly translated into a graphical user interface. A language (Colimate) implementing this model is shown to serve as a bridge between commandline-driven programs and more friendly user interfaces. Exploiting the specificness of the user interfaces addressed, powerful graphical interfaces can be built with a very simple syntax and small programming effort. Furthermore, the command-line program needs not to be modified, so in this way the possibility of making batches is not lost.

Research paper thumbnail of Marker-free image registration of electron tomography tilt-series

BMC Bioinformatics, 2009

Background: Tilt series are commonly used in electron tomography as a means of collecting three-d... more Background: Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3D reconstruction. Current alignment techniques usually employ gold particles or image derived markers to correctly align the images. When these markers are not present, correlation between adjacent views is used to align them. However, sequential pairwise correlation is prone to bias and the resulting alignment is not always optimal.

Research paper thumbnail of Grid Computing in 3DEM Image Processing Using Xmipp

Image processing in three-dimensional electron microscopy (3D-EM) is characterized by large amoun... more Image processing in three-dimensional electron microscopy (3D-EM) is characterized by large amounts of data, and voluminous computing requirements. Here, we report our first experience with grid computing in this area. We present an interface between grid computing middleware and our image processing package Xmipp. The efficacy of this approach was illustrated with an Xmipp application for estimation of the contrast transfer function. In addition, we report our experience with grid computing in the development of a novel image refinement algorithm based on maximum likelihood principles. Its extensive CPUrequirements might have seriously hampered the algorithm development, if not for the farreaching resources of grid computing. Our results suggest that electron microscopy image processing may be particularly well suited for grid computing.

Research paper thumbnail of Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization

Here we present a new image registration algorithm for the alignment of histological sections tha... more Here we present a new image registration algorithm for the alignment of histological sections that combines the ideas of B-spline based elastic registration and consistent image registration, to allow simultaneous registration of images in two directions (direct and inverse). In principle, deformations based on B-splines are not invertible. The consistency term overcomes this limitation and allows registration of two images in a completely symmetric way. This extension of the elastic registration method simplifies the search for the optimum deformation and allows registering with no information about landmarks or deformation regularization. This approach can also be used as the first step to solve the problem of group-wise registration.

Research paper thumbnail of Volumetric restrictions in single particle 3DEM reconstruction

Pattern Recognition, 2008

3D electron microscopy aims at the reconstruction of density volumes corresponding to the electro... more 3D electron microscopy aims at the reconstruction of density volumes corresponding to the electrostatic potential distribution of macromolecules. There are many factors limiting the resolution achievable when this technique is applied to biological macromolecules: microscope imperfections, molecule flexibility, lack of projections from certain directions, unknown angular distribution, noise, etc. In this communication we explore the quality gain in the reconstruction by including a priori knowledge such as particle symmetry, occupied volume, known surface relief, density nonnegativity and similarity to a known volume in order to improve the quality of the reconstruction. If the reconstruction is represented as a series expansion, such constraints can be expressed by set of equations that the expansion coefficients must satisfy. In this work, these equation sets are specified and combined in a novel way with the ART + blobs reconstruction algorithm. The effect of each one on the reconstruction of a realistic phantom is explored. Finally, the application of these restrictions to 3D reconstructions from experimental data are studied.

Research paper thumbnail of XMIPP: a new generation of an open-source image processing package for electron microscopy

Journal of Structural Biology, 2004

X-windows based microscopy image processing package (Xmipp) is a specialized suit of image proces... more X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. This public-domain software package was introduced to the electron microscopy field eight years ago, and since then it has changed drastically. New methodologies for the analysis of single-particle projection images have been added to classification, contrast transfer function correction, angular assignment, 3D reconstruction, reconstruction of crystals, etc. In addition, the package has been extended with functionalities for 2D crystal and electron tomography data. Furthermore, its current implementation in C++, with a highly modular design of well-documented data structures and functions, offers a convenient environment for the development of novel algorithms. In this paper, we present a general overview of a new generation of Xmipp that has been re-engineered to maximize flexibility and modularity, potentially facilitating its integration in future standardization efforts in the field. Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community.

Research paper thumbnail of Volumetric constraints in 3D tomography applied to electron microscopy

3D Electron Microscopy aims at the reconstruction of density volumes corresponding to the mass di... more 3D Electron Microscopy aims at the reconstruction of density volumes corresponding to the mass distribution of macromolecules imaged with an electron microscope. There are many factors limiting the resolution achievable when this technique is applied to biomolecules: microscope transfer function, molecule flexibility, lack of projections from certain directions, unknown angular distribution, image noise, etc. In this communication we propose the use of a priori information such as particle symmetry, occupied volume, known surface, density nonnegativity and similarity to a known volume in order to improve the quality of the reconstruction. When a series expansion of the reconstructed volume is done, all these constraints are expressed as a set of equations which the expansion coefficients must satisfy. In this work, this equation set is specified and the effect of each one on the reconstruction of a realistic phantom is explored.

Research paper thumbnail of Molecular image registration using mutual information and differential evolution optimization

In this work we propose a novel rigid image registration approach to determine the position of hi... more In this work we propose a novel rigid image registration approach to determine the position of high-resolution molecular structures in medium-resolution macromolecular complexes. Mutual Information similarity measure is used as an alternative to the cross-correlation coefficient commonly applied in this context. The optimum of the objective function is sought by means of differential evolution algorithm. This global optimization technique yields robust registration, exhibits fast convergence and is easy to use. In order to additionally improve its accuracy we combine it with a local gradient search strategy. The registration framework is tested both on simulated and experimental data sets forcing large rotations and translations. Results in terms of success rate and execution time, indicate the suitability of the proposed approach. * Corresponding author: mledesma@die.upm.es. Partial support is acknowledged to: the European Union (NoE EMIL 593569 and Marie Curie HPMT-CT-2001-420); the Spanish Health Ministry (Red Tematica IM3 G03/185) and Comunidad de Madrid (grant GR/SAL/0234).

Research paper thumbnail of Elastic registration of biological images using vector-spline regularization

IEEE Transactions on Biomedical Engineering, 2005

We present an elastic registration algorithm for the alignment of biological images. Our method c... more We present an elastic registration algorithm for the alignment of biological images. Our method combines and extends some of the best techniques available in the context of medical imaging. We express the deformation field as a B-spline model, which allows us to deal with a rich variety of deformations. We solve the registration problem by minimizing a pixelwise mean-square distance measure between the target image and the warped source. The problem is further constrained by way of a vector-spline regularization which provides some control over two independent quantities that are intrinsic to the deformation: its divergence, and its curl. Our algorithm is also able to handle soft landmark constraints, which is particularly useful when parts of the images contain very little information or when its repartition is uneven. We provide an optimal analytical solution in the case when only landmarks and smoothness considerations are taken into account. We have applied our approach to perform the elastic registration of images such as electrophoretic gels and fly embryos. The validation of the results by experts has been favorable in all cases.

Research paper thumbnail of Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions

Journal of Structural Biology, 2005

Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transm... more Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transmission electron microscopy is still an open problem. In this article, we extend the applicability of the spectral signal-to-noise ratio (SSNR) to the evaluation of 3D volumes reconstructed with any reconstruction algorithm. The basis of the method is to measure the consistency between the data and a corresponding set of reprojections computed for the reconstructed 3D map. The idiosyncrasies of the reconstruction algorithm are taken explicitly into account by performing a noise-only reconstruction. This results in the definition of a 3D SSNR which provides an objective indicator of the quality of the 3D reconstruction. Furthermore, the information to build the SSNR can be used to produce a volumetric SSNR (VSSNR). Our method overcomes the need to divide the data set in two. It also provides a direct measure of the performance of the reconstruction algorithm itself; this latter information is typically not available with the standard resolution methods which are primarily focused on reproducibility alone.

Research paper thumbnail of Improved Bayesian image denoising based on wavelets with applications to electron microscopy

Pattern Recognition, 2006

In this work we discuss an improvement of the image-denoising wavelet-based method presented by B... more In this work we discuss an improvement of the image-denoising wavelet-based method presented by Bijaoui [Wavelets, Gaussian mixtures and Wiener filtering, Signal Process. 82 (2002) 709-712]. We show that the parameter estimation step can be replaced by a constrained nonlinear optimization. We propose three different methods to estimate the parameters. As in Bijaoui's original article, two of them deal with white noise. We show that the resulting algorithms improve the one originally proposed. Our third method extends the applicability of the denoising algorithm to colored noise. We test our algorithms with images simulating electron microscopy (EM) conditions as well as experimental EM images.

Research paper thumbnail of Immunogenic Profiling in Mice of a HIV/AIDS Vaccine Candidate (MVA-B) Expressing Four HIV1 Antigens and Potentiation by Specific Gene Deletions

PLOS One, 2010

Background: The immune parameters of HIV/AIDS vaccine candidates that might be relevant in protec... more Background: The immune parameters of HIV/AIDS vaccine candidates that might be relevant in protection against HIV-1 infection are still undefined. The highly attenuated poxvirus strain MVA is one of the most promising vectors to be use as HIV-1 vaccine. We have previously described a recombinant MVA expressing HIV-1 Env, Gag, Pol and Nef antigens from clade B (referred as MVA-B), that induced HIV-1-specific immune responses in different animal models and gene signatures in human dendritic cells (DCs) with immunoregulatory function.

Research paper thumbnail of Insertion of Vaccinia Virus C7L Host Range Gene into NYVAC-B Genome Potentiates Immune Responses against HIV1 Antigens

PLOS One, 2010

Background: The highly attenuated vaccinia virus strain NYVAC expressing HIV-1 components has bee... more Background: The highly attenuated vaccinia virus strain NYVAC expressing HIV-1 components has been evaluated as a vaccine candidate in preclinical and clinical trials with encouraging results. We have previously described that the presence of C7L in the NYVAC genome prevents the induction of apoptosis and renders the vector capable of replication in human and murine cell lines while maintaining an attenuated phenotype in mice.

Research paper thumbnail of A Candidate HIV/AIDS Vaccine (MVA-B) Lacking Vaccinia Virus Gene C6L Enhances Memory HIV1Specific T-Cell Responses

PLOS One, 2011

The vaccinia virus (VACV) C6 protein has sequence similarities with the poxvirus family Pox_A46, ... more The vaccinia virus (VACV) C6 protein has sequence similarities with the poxvirus family Pox_A46, involved in regulation of host immune responses, but its role is unknown. Here, we have characterized the C6 protein and its effects in virus replication, innate immune sensing and immunogenicity in vivo. C6 is a 18.2 kDa protein, which is expressed early during virus infection and localizes to the cytoplasm of infected cells. Deletion of the C6L gene from the poxvirus vector MVA-B expressing HIV-1 Env, Gag, Pol and Nef antigens from clade B (MVA-B DC6L) had no effect on virus growth kinetics; therefore C6 protein is not essential for virus replication. The innate immune signals elicited by MVA-B DC6L in human macrophages and monocyte-derived dendritic cells (moDCs) are characterized by the up-regulation of the expression of IFN-b and IFN-a/b-inducible genes. In a DNA prime/MVA boost immunization protocol in mice, flow cytometry analysis revealed that MVA-B DC6L enhanced the magnitude and polyfunctionality of the HIV-1-specific CD4 + and CD8 + T-cell memory immune responses, with most of the HIV-1 responses mediated by the CD8 + T-cell compartment with an effector phenotype. Significantly, while MVA-B induced preferentially Env-and Gag-specific CD8 + T-cell responses, MVA-B DC6L induced more Gag-Pol-Nef-specific CD8 + T-cell responses. Furthermore, MVA-B DC6L enhanced the levels of antibodies against Env in comparison with MVA-B. These findings revealed that C6 can be considered as an immunomodulator and that deleting C6L gene in MVA-B confers an immunological benefit by enhancing IFN-b-dependent responses and increasing the magnitude and quality of the T-cell memory immune responses to HIV-1 antigens. Our observations are relevant for the improvement of MVA vectors as HIV-1 vaccines.

Research paper thumbnail of Insertion of Vaccinia Virus C7L Host Range Gene into NYVAC-B Genome Potentiates Immune Responses against HIV1 Antigens

PLOS One, 2010

Background: The highly attenuated vaccinia virus strain NYVAC expressing HIV-1 components has bee... more Background: The highly attenuated vaccinia virus strain NYVAC expressing HIV-1 components has been evaluated as a vaccine candidate in preclinical and clinical trials with encouraging results. We have previously described that the presence of C7L in the NYVAC genome prevents the induction of apoptosis and renders the vector capable of replication in human and murine cell lines while maintaining an attenuated phenotype in mice.

Research paper thumbnail of High Quality Long-Term CD4+ and CD8+ Effector Memory Populations Stimulated by DNA-LACK/MVA-LACK Regimen in Leishmania major BALB/c Model of Infection

PLOS One, 2012

Heterologous vaccination based on priming with a plasmid DNA vector and boosting with an attenuat... more Heterologous vaccination based on priming with a plasmid DNA vector and boosting with an attenuated vaccinia virus MVA recombinant, with both vectors expressing the Leishmania infantum LACK antigen (DNA-LACK and MVA-LACK), has shown efficacy conferring protection in murine and canine models against cutaneus and visceral leishmaniasis, but the immune parameters of protection remain ill defined. Here we performed by flow cytometry an in depth analysis of the T cell populations induced in BALB/c mice during the vaccination protocol DNA-LACK/MVA-LACK, as well as after challenge with L. major parasites. In the adaptive response, there is a polyfunctional CD4 + and CD8 + T cell activation against LACK antigen. At the memory phase the heterologous vaccination induces high quality LACK-specific long-term CD4 + and CD8 + effector memory cells. After parasite challenge, there is a moderate boosting of LACK-specific CD4 + and CD8 + T cells. Anti-vector responses were largely CD8 + -mediated. The immune parameters induced against LACK and triggered by the combined vaccination DNA/MVA protocol, like polyfunctionality of CD4 + and CD8 + T cells with an effector phenotype, could be relevant in protection against leishmaniasis. Citation: Sánchez-Sampedro L, Gó mez CE, Mejías-Pérez E, S. Sorzano CO, Esteban M (2012) High Quality Long-Term CD4 + and CD8 + Effector Memory Populations Stimulated by DNA-LACK/MVA-LACK Regimen in Leishmania major BALB/c Model of Infection. PLoS ONE 7(6): e38859.

Research paper thumbnail of A Human Multi-Epitope Recombinant Vaccinia Virus as a Universal T Cell Vaccine Candidate against Influenza Virus

PLOS One, 2011

There is a need to develop a universal vaccine against influenza virus infection to avoid develop... more There is a need to develop a universal vaccine against influenza virus infection to avoid developing new formulations of a seasonal vaccine each year. Many of the vaccine strategies for a universal vaccine target strain-conserved influenza virus proteins, such as the matrix, polymerase, and nucleoproteins, rather than the surface hemagglutinin and neuraminidase proteins. In addition, non-disease-causing viral vectors are a popular choice as a delivery system for the influenza virus antigens. As a proof-of-concept, we have designed a novel influenza virus immunogen based on the NP backbone containing human T cell epitopes for M1, NS1, NP, PB1 and PA proteins (referred as NPmix) as well as a construct containing the conserved regions of influenza virus neuraminidase (N-terminal) and hemagglutinin (C-terminal) (referred as NA-HA). DNA vectors and vaccinia virus recombinants expressing NPmix (WR-NP) or both NPmix plus NA-HA (WR-flu) in the cytosol were tested in a heterologous DNA-prime/vaccinia virus-boost vaccine regimen in mice. We observed an increase in the number of influenza virus-specific IFNc-secreting splenocytes, composed of populations marked by CD4 + and CD8 + T cells producing IFNc or TNFa. Upon challenge with influenza virus, the vaccinated mice exhibited decreased viral load in the lungs and a delay in mortality. These findings suggest that DNA prime/poxvirus boost with human multi-epitope recombinant influenza virus proteins is a valid approach for a general T-cell vaccine to protect against influenza virus infection.

Research paper thumbnail of TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy

BMC Bioinformatics, 2007

Background: Transmission electron tomography is an increasingly common three-dimensional electron... more Background: Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomography fills the gap between high resolution structural methods (X-ray diffraction or nuclear magnetic resonance) and optical microscopy. We developed new software for transmission electron tomography, TomoJ. TomoJ is a plug-in for the now standard image analysis and processing software for optical microscopy, ImageJ.

Research paper thumbnail of Flexible image registration for the identification of best fitted protein models in 3DEM maps

Laura Fernández-de-Manuel 1 , María J. Ledesma-Carbayo 1* , Julián Atienza-Herrero 2 , ... Carlos... more Laura Fernández-de-Manuel 1 , María J. Ledesma-Carbayo 1* , Julián Atienza-Herrero 2 , ... Carlos OS Sorzano 2,3 , José-María Carazo 2 , Andrés Santos 1 ... 1 ETSI Telecomunicación, Universidad Politécnica de Madrid, Spain 2 Centro Nacional de ...

Research paper thumbnail of Optimization problems in electron microscopy of single particles

Annals of Operations Research, 2006

Electron Microscopy is a valuable tool for the elucidation of the three-dimensional structure of ... more Electron Microscopy is a valuable tool for the elucidation of the three-dimensional structure of macromolecular complexes. Knowledge about the macromolecular structure provides important information about its function and how it is carried out. This work addresses the issue of three-dimensional reconstruction of biological macromolecules from electron microscopy images. In particular, it focuses on a methodology known as “single-particles” and makes a thorough review of all those steps that can be expressed as an optimization problem. In spite of important advances in recent years, there are still unresolved challenges in the field that offer an excellent testbed for new and more powerful optimization techniques.

Research paper thumbnail of Command-line interfaces can be efficiently brought to graphics: COLIMATE (the COmmand LIne MATE

Software - Practice and Experience, 2002

Scientific computing has traditionally been done on workstations, most of the time running on UNI... more Scientific computing has traditionally been done on workstations, most of the time running on UNIX-like operating systems. These systems are often very robust, powerful and especially suited to heavy computation tasks; however, the usual user interface is based on a command line with all the information needed for the appropriate functioning of the algorithm. These command lines are seldom user-friendly but, on the other hand, they allow batch processes to be built. In this work, a model for command-line-driven packages is given, and at the same time the model includes objects that can be directly translated into a graphical user interface. A language (Colimate) implementing this model is shown to serve as a bridge between commandline-driven programs and more friendly user interfaces. Exploiting the specificness of the user interfaces addressed, powerful graphical interfaces can be built with a very simple syntax and small programming effort. Furthermore, the command-line program needs not to be modified, so in this way the possibility of making batches is not lost.

Research paper thumbnail of Marker-free image registration of electron tomography tilt-series

BMC Bioinformatics, 2009

Background: Tilt series are commonly used in electron tomography as a means of collecting three-d... more Background: Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3D reconstruction. Current alignment techniques usually employ gold particles or image derived markers to correctly align the images. When these markers are not present, correlation between adjacent views is used to align them. However, sequential pairwise correlation is prone to bias and the resulting alignment is not always optimal.

Research paper thumbnail of Grid Computing in 3DEM Image Processing Using Xmipp

Image processing in three-dimensional electron microscopy (3D-EM) is characterized by large amoun... more Image processing in three-dimensional electron microscopy (3D-EM) is characterized by large amounts of data, and voluminous computing requirements. Here, we report our first experience with grid computing in this area. We present an interface between grid computing middleware and our image processing package Xmipp. The efficacy of this approach was illustrated with an Xmipp application for estimation of the contrast transfer function. In addition, we report our experience with grid computing in the development of a novel image refinement algorithm based on maximum likelihood principles. Its extensive CPUrequirements might have seriously hampered the algorithm development, if not for the farreaching resources of grid computing. Our results suggest that electron microscopy image processing may be particularly well suited for grid computing.

Research paper thumbnail of Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization

Here we present a new image registration algorithm for the alignment of histological sections tha... more Here we present a new image registration algorithm for the alignment of histological sections that combines the ideas of B-spline based elastic registration and consistent image registration, to allow simultaneous registration of images in two directions (direct and inverse). In principle, deformations based on B-splines are not invertible. The consistency term overcomes this limitation and allows registration of two images in a completely symmetric way. This extension of the elastic registration method simplifies the search for the optimum deformation and allows registering with no information about landmarks or deformation regularization. This approach can also be used as the first step to solve the problem of group-wise registration.

Research paper thumbnail of Volumetric restrictions in single particle 3DEM reconstruction

Pattern Recognition, 2008

3D electron microscopy aims at the reconstruction of density volumes corresponding to the electro... more 3D electron microscopy aims at the reconstruction of density volumes corresponding to the electrostatic potential distribution of macromolecules. There are many factors limiting the resolution achievable when this technique is applied to biological macromolecules: microscope imperfections, molecule flexibility, lack of projections from certain directions, unknown angular distribution, noise, etc. In this communication we explore the quality gain in the reconstruction by including a priori knowledge such as particle symmetry, occupied volume, known surface relief, density nonnegativity and similarity to a known volume in order to improve the quality of the reconstruction. If the reconstruction is represented as a series expansion, such constraints can be expressed by set of equations that the expansion coefficients must satisfy. In this work, these equation sets are specified and combined in a novel way with the ART + blobs reconstruction algorithm. The effect of each one on the reconstruction of a realistic phantom is explored. Finally, the application of these restrictions to 3D reconstructions from experimental data are studied.

Research paper thumbnail of XMIPP: a new generation of an open-source image processing package for electron microscopy

Journal of Structural Biology, 2004

X-windows based microscopy image processing package (Xmipp) is a specialized suit of image proces... more X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. This public-domain software package was introduced to the electron microscopy field eight years ago, and since then it has changed drastically. New methodologies for the analysis of single-particle projection images have been added to classification, contrast transfer function correction, angular assignment, 3D reconstruction, reconstruction of crystals, etc. In addition, the package has been extended with functionalities for 2D crystal and electron tomography data. Furthermore, its current implementation in C++, with a highly modular design of well-documented data structures and functions, offers a convenient environment for the development of novel algorithms. In this paper, we present a general overview of a new generation of Xmipp that has been re-engineered to maximize flexibility and modularity, potentially facilitating its integration in future standardization efforts in the field. Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community.

Research paper thumbnail of Volumetric constraints in 3D tomography applied to electron microscopy

3D Electron Microscopy aims at the reconstruction of density volumes corresponding to the mass di... more 3D Electron Microscopy aims at the reconstruction of density volumes corresponding to the mass distribution of macromolecules imaged with an electron microscope. There are many factors limiting the resolution achievable when this technique is applied to biomolecules: microscope transfer function, molecule flexibility, lack of projections from certain directions, unknown angular distribution, image noise, etc. In this communication we propose the use of a priori information such as particle symmetry, occupied volume, known surface, density nonnegativity and similarity to a known volume in order to improve the quality of the reconstruction. When a series expansion of the reconstructed volume is done, all these constraints are expressed as a set of equations which the expansion coefficients must satisfy. In this work, this equation set is specified and the effect of each one on the reconstruction of a realistic phantom is explored.

Research paper thumbnail of Molecular image registration using mutual information and differential evolution optimization

In this work we propose a novel rigid image registration approach to determine the position of hi... more In this work we propose a novel rigid image registration approach to determine the position of high-resolution molecular structures in medium-resolution macromolecular complexes. Mutual Information similarity measure is used as an alternative to the cross-correlation coefficient commonly applied in this context. The optimum of the objective function is sought by means of differential evolution algorithm. This global optimization technique yields robust registration, exhibits fast convergence and is easy to use. In order to additionally improve its accuracy we combine it with a local gradient search strategy. The registration framework is tested both on simulated and experimental data sets forcing large rotations and translations. Results in terms of success rate and execution time, indicate the suitability of the proposed approach. * Corresponding author: mledesma@die.upm.es. Partial support is acknowledged to: the European Union (NoE EMIL 593569 and Marie Curie HPMT-CT-2001-420); the Spanish Health Ministry (Red Tematica IM3 G03/185) and Comunidad de Madrid (grant GR/SAL/0234).