Biochemistry and Pharmacology - Research Publications

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    ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions.
    Kazemi, M ; Sorzano, COS ; Carazo, JM ; des Georges, A ; Abrishami, V ; Vargas, J (Elsevier, 2021)
    Cryo-electron microscopy using single particle analysis requires the computational averaging of thousands of projection images captured from identical macromolecules. However, macromolecules usually present some degree of flexibility showing different conformations. Computational approaches are then required to classify heterogeneous single particle images into homogeneous sets corresponding to different structural states. Nonetheless, sometimes the attainable resolution of reconstructions obtained from these smaller homogeneous sets is compromised because of reduced number of particles or lack of images at certain macromolecular orientations. In these situations, the current solution to improve map resolution is returning to the electron microscope and collect more data. In this work, we present a fast approach to partially overcome this limitation for heterogeneous data sets. Our method is based on deforming and then moving particles between different conformations using an optical flow approach. Particles are then merged into a unique conformation obtaining reconstructions with improved resolution, contrast and signal-to-noise ratio. We present experimental results that show clear improvements in the quality of obtained 3D maps, however, there are also limits to this approach, i.e., the method is restricted to small deformations and cannot determine local patterns of flexibility of small elements, such as secondary structures, which we discuss in the manuscript.
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    Analysis of capnogram using linear predictive coding (LPC) to differentiate asthmatic conditions
    Kazemi, M ; Malarvili, MB (OMICS International, 2011)
    In this paper, an analysis of capnogram to differentiate asthmatic and non-asthmatic patients is presented by using linear predictive coding (LPC) technique. In the previous studies, manual study on capnogram signal has been conducted by several researchers. All previous researches show significant correlation between the capnogram and asthmatic patient. However all of them are just manual study conducted through the conventional time domain method. In this preliminary, a number of 8 LPC coefficients (α1- α8) for both asthmatic (CAP) and non-asthmatic patients’ capnogram (CNP) are extracted. Usefulness and performance of these coefficients to differentiate the asthmatic conditions by means of receiver operating characteristic (ROC) curve analysis are shown. Our preliminary results show that α3, α4, α5, and α6 can be used to distinguish the asthmatic conditions.
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    Scipion web tools: Easy to use cryo-EM image processing over the web
    Conesa Mingo, P ; Gutierrez, J ; Quintana, A ; de la Rosa Trevin, JM ; Zaldivar-Peraza, A ; Cuenca Alba, J ; Kazemi, M ; Vargas, J ; del Cano, L ; Segura, J ; Sorzano, COS ; Maria Carazo, J (WILEY, 2018-01-01)
    Macromolecular structural determination by Electron Microscopy under cryogenic conditions is revolutionizing the field of structural biology, interesting a large community of potential users. Still, the path from raw images to density maps is complex, and sophisticated image processing suites are required in this process, often demanding the installation and understanding of different software packages. Here, we present Scipion Web Tools, a web-based set of tools/workflows derived from the Scipion image processing framework, specially tailored to nonexpert users in need of very precise answers at several key stages of the structural elucidation process.
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    Assessment on methods used to detect asthmatic and non-asthmatic conditions using capnogram signal
    Kazemi, M ; Imarah, NI ; Malarvili, MB (Penerbit UTM Press, 2013)
    In this paper, a review on methods for detecting asthmatic conditions using capnogram is presented. This includes an investigation on capnography as a new approach for monitoring asthma and related researches. Manual analysis of capnogram is time-consuming and led to erroneous due to human factor such as tiredness and lack of expertise. Therefore, in this preliminary study, a new method based on signal processing approach is developed to automatically detect asthmatic patients. This developed algorithm is expected to cluster different states of asthmatic conditions by using the RBF (Radial Basis Function) network, instantaneously. In the future, this developed algorithm is expected to help health-care professional involved in respiratory care as it would be possible to monitor severity of asthma automatically and instantaneously.
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    A survey of the use of iterative reconstruction algorithms in electron microscopy
    Sorzano, COS ; Vargas, J ; Otón, J ; de la Rosa-Trevín, JM ; Vilas, JL ; Kazemi, M ; Melero, R ; Del Ca no, L ; Cuenca, J ; Conesa, P ; Gomez-Blanco, J ; Marabini, R ; Carazo, JM (Hindawi, 2017)
    One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).
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    An Asymmetric Opening of HIV-1 Envelope Mediates Antibody-Dependent Cellular Cytotoxicity
    Alsahafi, N ; Bakouche, N ; Kazemi, M ; Richard, J ; Ding, S ; Bhattacharyya, S ; Das, D ; Anand, SP ; Prevost, J ; Tolbert, WD ; Lu, H ; Medjahed, H ; Gendron-Lepage, G ; Delgado, GGO ; Kirk, S ; Melillo, B ; Mothes, W ; Sodroski, J ; Smith, AB ; Kaufmann, DE ; Wu, X ; Pazgier, M ; Rouiller, I ; Finzi, A ; Munro, JB (CELL PRESS, 2019-04-10)
    The HIV-1 envelope glycoprotein (Env) (gp120-gp41)3 is the target for neutralizing antibodies and antibody-dependent cellular cytotoxicity (ADCC). HIV-1 Env is flexible, sampling different conformational states. Before engaging CD4, Env adopts a closed conformation (State 1) that is largely antibody resistant. CD4 binding induces an intermediate state (State 2), followed by an open conformation (State 3) that is susceptible to engagement by antibodies that recognize otherwise occluded epitopes. We investigate conformational changes in Env that induce ADCC in the presence of a small-molecule CD4-mimetic compound (CD4mc). We uncover an asymmetric Env conformation (State 2A) recognized by antibodies targeting the conserved gp120 inner domain and mediating ADCC. Sera from HIV+ individuals contain these antibodies, which can stabilize Env State 2A in combination with CD4mc. Additionally, triggering State 2A on HIV-infected primary CD4+ T cells exposes epitopes that induce ADCC. Strategies that induce this Env conformation may represent approaches to fight HIV-1 infection.
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    New prognostic index to detect the severity of asthma automatically using signal processing techniques of capnogram
    Kazemi, M ; Teo, AH (Najafabad Branch, Islamic Azad University (IAUN), 2016)
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    ENRICH: a fast method to improve the quality of flexible macromolecular reconstructions
    Kazemi, M ; Sorzano, COS ; Des Georges, A ; Carazo, JM ; Vargas, J (Cold Spring Harbor Laboratory, 2018)
    Cryo-electron microscopy using single particle analysis requires the computational averaging of thousands of projection images captured from identical macromolecules. However, macromolecules usually present some degree of flexibility showing different conformations. Computational approaches are then required to classify heterogeneous single particle images into homogeneous sets corresponding to different structural states. Nonetheless, sometimes the attainable resolution of reconstructions obtained from these smaller homogeneous sets is compromised because of reduced number of particles or lack of images at certain macromolecular orientations. In these situations, the current solution to improve map resolution is returning to the electron microscope and collect more data. In this work, we present a fast approach to partially overcome this limitation for heterogeneous data sets. Our method is based on deforming and then moving particles between different conformations using an optical flow approach. Particles are then merged into a unique conformation obtaining reconstructions with improved resolution, contrast and signal-to-noise ratio, then, partially circumventing many issues that impact obtaining high quality reconstructions from small data sets. We present experimental results that show clear improvements in the quality of obtained 3D maps, however, there are also limits to this approach, which we discuss in the manuscript.
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    Improving 3D reconstructions of macromolecular conformations
    Kazemi, M ; Sorzano, COS ; Des Georges, A ; Carazo, J-M ; Vargas, J (International Union of Crystallography (IUCr), 2018-07-20)