RESUMEN
Single Particle analysis (SPA) aims to determine the three-dimensional structure of proteins and macromolecular complexes. The current state of the art has allowed us to achieve near-atomic and even atomic resolutions. To obtain high-resolution structures, a set of well-defined image processing steps is required. A critical one is the estimation of the Contrast Transfer Function (CTF), which considers the sample defocus and aberrations of the microscope. Defocus is usually globally estimated; in this case, it is the same for all the particles in each micrograph. But proteins are ice-embedded at different heights, suggesting that defocus should be measured in a local (per particle) manner. There are four state-of-the-art programs to estimate local defocus (Gctf, Relion, CryoSPARC, and Xmipp). In this work, we have compared the results of these software packages to check whether the resolution improves. We have used the Scipion framework and developed a specific program to analyze local defocus. The results produced by different programs do not show a clear consensus using the current test datasets in this study.
Asunto(s)
Procesamiento de Imagen Asistido por Computador , Imagen Individual de Molécula , Microscopía por Crioelectrón/métodos , Procesamiento de Imagen Asistido por Computador/métodos , Sustancias Macromoleculares , Programas Informáticos , AlgoritmosRESUMEN
Single particle analysis (SPA) in cryo-electron microscopy (cryo-EM) is highly used to obtain the near-atomic structure of biological macromolecules. The current methods allow users to produce high-resolution maps from many samples. However, there are still challenging cases that require extra processing to obtain high resolution. This is the case when the macromolecule of the sample is composed of different components and we want to focus just on one of them. For example, if the macromolecule is composed of several flexible subunits and we are interested in a specific one, if it is embedded in a viral capsid environment, or if it has additional components to stabilize it, such as nanodiscs. The signal from these components, which in principle we are not interested in, can be removed from the particles using a projection subtraction method. Currently, there are two projection subtraction methods used in practice and both have some limitations. In fact, after evaluating their results, we consider that the problem is still open to new solutions, as they do not fully remove the signal of the components that are not of interest. Our aim is to develop a new and more precise projection subtraction method, improving the performance of state-of-the-art methods. We tested our algorithm with data from public databases and an in-house data set. In this work, we show that the performance of our algorithm improves the results obtained by others, including the localization of small ligands, such as drugs, whose binding location is unknown a priori.
Asunto(s)
Algoritmos , Imagen Individual de Molécula , Microscopía por Crioelectrón/métodos , Sustancias Macromoleculares/químicaRESUMEN
Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline. The Scipion framework, originally developed for SPA (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project. The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.
Asunto(s)
Tomografía con Microscopio Electrónico , Programas Informáticos , Algoritmos , Microscopía por Crioelectrón/métodos , Procesamiento de Imagen Asistido por Computador/métodos , Reproducibilidad de los ResultadosRESUMEN
The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded.
Asunto(s)
Procesamiento de Imagen Asistido por Computador , Microscopía por Crioelectrón/métodos , Microscopía ElectrónicaRESUMEN
Electron cryomicroscopy (cryo-EM) has emerged as a powerful structural biology instrument to solve near-atomic three-dimensional structures. Despite the fast growth in the number of density maps generated from cryo-EM data, comparison tools among these reconstructions are still lacking. Current proposals to compare cryo-EM data derived volumes perform map subtraction based on adjustment of each volume grey level to the same scale. We present here a more sophisticated way of adjusting the volumes before comparing, which implies adjustment of grey level scale and spectrum energy, but keeping phases intact inside a mask and imposing the results to be strictly positive. The adjustment that we propose leaves the volumes in the same numeric frame, allowing to perform operations among the adjusted volumes in a more reliable way. This adjustment can be a preliminary step for several applications such as comparison through subtraction, map sharpening, or combination of volumes through a consensus that selects the best resolved parts of each input map. Our development might also be used as a sharpening method using an atomic model as a reference. We illustrate the applicability of this algorithm with the reconstructions derived of several experimental examples. This algorithm is implemented in Xmipp software package and its applications are user-friendly accessible through the cryo-EM image processing framework Scipion.
Asunto(s)
Algoritmos , Microscopía por Crioelectrón/métodos , Procesamiento de Imagen Asistido por Computador/métodos , Imagenología Tridimensional/métodos , Sustancias Macromoleculares/ultraestructura , Cápside/química , Cápside/ultraestructura , Virus de la Hepatitis B/ultraestructura , Sustancias Macromoleculares/química , Modelos Moleculares , Conformación Molecular , Conformación Proteica , Reproducibilidad de los Resultados , Glicoproteína de la Espiga del Coronavirus/química , Glicoproteína de la Espiga del Coronavirus/ultraestructuraRESUMEN
The presence of preferred orientations in single particle analysis (SPA) by cryo-Electron Microscopy (cryoEM) is currently one of the hurdles preventing many structural analyses from yielding high-resolution structures. Although the existence of preferred orientations is mostly related to the grid preparation, in this technical note, we show that some image processing algorithms used for angular assignment and three-dimensional (3D) reconstruction are more robust than others to these detrimental conditions. We exemplify this argument with three different data sets in which the presence of preferred orientations hindered achieving a 3D reconstruction without artifacts or, even worse, a 3D reconstruction could never be achieved.
Asunto(s)
Microscopía por Crioelectrón/métodos , Imagen Individual de Molécula/métodos , Algoritmos , Artefactos , Procesamiento de Imagen Asistido por Computador/métodos , Imagenología Tridimensional/métodosRESUMEN
Advances in cryo-electron microscopy (cryo-EM) have made it possible to obtain structures of large biological macromolecules at near-atomic resolution. This "resolution revolution" has encouraged the use and development of modeling tools able to produce high-quality atomic models from cryo-EM density maps. Unfortunately, many practical problems appear when combining different packages in the same processing workflow, which make difficult the use of these tools by non-experts and, therefore, reduce their utility. We present here a major extension of the image processing framework Scipion that provides inter-package integration in the model building area and full tracking of the complete workflow, from image processing to structure validation.
Asunto(s)
Procesamiento de Imagen Asistido por Computador , Programas Informáticos , Microscopía por Crioelectrón , Flujo de TrabajoRESUMEN
A novel method to quantitate vitamin D and its main metabolites (vitamin D3, vitamin D2, and their 25-hydroxy metabolites) in breast milk by supercritical fluid chromatography has been developed and fully validated. A small volume of sample (1 mL) is subjected to ethanolic protein precipitation and liquid-liquid extraction. Final extracts are derivatized with 4-phenyl-1,2,4-triazoline-3,5-dione and vitamin D derivatives analyzed by supercritical fluid chromatography hyphenated to tandem mass spectrometry with atmospheric pressure chemical ionization. Multiple reaction monitoring is used for quantitation. Separation conditions were optimized using a gradient of methanol-water-ammonium formate into carbon dioxide. Make-up solvent was methanol containing ammonium formate. The quantitation limit reached levels as low as 50 pmol/L, with intra- and inter-day relative standard deviations lower than 15% and 20% for all analytes. Accuracy was evaluated by spiking experiments and was well within acceptability ratios (± 15%). The method was then applied to a subset of commercially available human milk samples. The newly developed method provides opportunities to determine the nutritional status of mother-infant dyads from a non-invasive measure, or for interventional or observational studies building knowledge on the composition of human milk. Graphical abstract.
Asunto(s)
Cromatografía con Fluido Supercrítico/métodos , Leche Humana/metabolismo , Espectrometría de Masas en Tándem/métodos , Vitamina D/metabolismo , Calibración , Femenino , Humanos , Recién Nacido , Límite de Detección , Estándares de Referencia , Vitamina D/normasRESUMEN
The introduction of Direct Electron Detector (DED) videos in the Electron Microscope field has boosted Single Particle Analysis to a point in which it is currently considered to be a key technique in Structural Biology. In this article we introduce an approach to estimate the DED camera gain at each pixel from the movies themselves. This gain is needed to have the set of recorded frames into a coherent gray level range, homogeneous over the whole image. The algorithm does not need any other input than the DED movie itself, being capable of providing an estimate of the camera gain image, helping to identify dead pixels and cases of incorrectly calibrated cameras. We propose the algorithm to be used either to validate the experimentally acquired gain image (for instance, to follow its possible change over time) or to verify that there is no residual gain image after experimentally correcting for the camera gain. We show results for a number of DED camera models currently in use (DE, Falcon II, Falcon 3, and K2).
Asunto(s)
Microscopía Electrónica/métodos , Algoritmos , Microscopía por Crioelectrón , Procesamiento de Imagen Asistido por Computador , FotograbarRESUMEN
The availability of reproducible broth microdilution (BMD) methods including inter log2 antibiotic dilutions for measuring Staphylococcus aureus (SA) vancomycin minimum inhibitory concentrations (MICs) within the susceptible range is needed to elucidate the impact of vancomycin MICs on clinical outcomes of invasive SA infections. Here, we report on the development of a very precise BMD method that incorporates the following incremental antibiotic concentrations: 0.50, 0.62, 0.75, 0.87, 1.0, 1.25, 1.40, 1.50, 1.60, 1.75, and 2.0 µg/mL. The intra- and inter-assay coefficients of variation of this method were around 20%. The mean of the differences in MIC values for all isolates obtained across two independent runs performed at one center was 0.04 µg/mL [95% confidence interval (CI), 0.011-0.07 µg/mL] and that for ten isolates measured at two different centers was 0.04 µg/mL (95% CI, 0-13 µg/mL). Vancomycin MIC values differed by less than 0.1 µg/mL between runs for most isolates. Storage of isolates at -20 °C for up to 3 months had no impact on the vancomycin MIC values. The mean vancomycin MIC values obtained by the Etest using a standard inoculum (0.5 McFarland) were significantly higher (p ≤ 0.001) than those measured by BMD and the MIC values measured by the two methods correlated poorly (Rho, 0.319; p = 0.148). Nevertheless, the mean MIC values measured by the Etest using lower inocula (107 or 106 CFU/mL) and those measured by BMD were comparable and correlated significantly (p = 0.004 for 107 CFU/mL and p = 0.029 for 106 CFU/mL).
Asunto(s)
Antibacterianos/farmacología , Pruebas de Sensibilidad Microbiana/métodos , Staphylococcus aureus/efectos de los fármacos , Vancomicina/farmacología , Relación Dosis-Respuesta a Droga , Reproducibilidad de los ResultadosRESUMEN
In this study, we assessed the association between single-nucleotide polymorphisms (SNPs) in seven candidate genes involved in orchestrating the immune response against cytomegalovirus (CMV) and the 12-month incidence of CMV infection in 315 CMV-seropositive kidney transplant (KT) recipients. Patients were managed either by antiviral prophylaxis or preemptive therapy. CMV infection occurred in 140 patients (44.4%), including 13 episodes of disease. After adjusting for various clinical covariates, patients harboring T-allele genotypes of interleukin-28B (IL28B) (rs12979860) SNP had lower incidence of CMV infection (adjusted hazard ratio [aHR]: 0.66; 95% confidence interval [CI]: 0.46-0.96; p-value = 0.029). In the analysis restricted to patients not receiving prophylaxis, carriers of the TT genotype of toll-like receptor 9 (TLR9) (rs5743836) SNP had lower incidence of infection (aHR: 0.61; 95% CI: 0.38-0.96; p-value = 0.035), whereas the GG genotype of dendritic cell-specific ICAM 3-grabbing nonintegrin (DC-SIGN) (rs735240) SNP exerted the opposite effect (aHR: 1.86; 95% CI: 1.18-2.94; p-value = 0.008). An independent association was found between the number of unfavorable SNP genotypes carried by the patient and the incidence of CMV infection. In conclusion, specific SNPs in IL28B, TLR9 and DC-SIGN genes may play a role in modulating the susceptibility to CMV infection in CMV-seropositive KT recipients.
Asunto(s)
Infecciones por Citomegalovirus/genética , Inmunidad Innata/genética , Fallo Renal Crónico/cirugía , Trasplante de Riñón , Polimorfismo de Nucleótido Simple , Adulto , Anciano , Alelos , Moléculas de Adhesión Celular/genética , Infecciones por Citomegalovirus/sangre , Femenino , Genotipo , Humanos , Incidencia , Interferones , Interleucinas/genética , Fallo Renal Crónico/sangre , Fallo Renal Crónico/genética , Lectinas Tipo C/genética , Masculino , Persona de Mediana Edad , Oportunidad Relativa , Modelos de Riesgos Proporcionales , Estudios Prospectivos , Receptores de Superficie Celular/genética , Receptores de TrasplantesRESUMEN
BACKGROUND: The functional profile of cytomegalovirus (CMV)-specific CD8(+) T cells that associate with protection from and control of CMV DNAemia in allogeneic stem cell transplant (allo-SCT) recipients remains incompletely characterized. METHODS: We enumerated pp65 and immediate early (IE)-1-specific CD8(+) T cells expressing interferon-gamma, tumor necrosis factor-alpha, and CD107a, by flow cytometry in 94 patients at days +30 and +60 after allo-SCT. RESULTS: Fifty of 94 patients had CMV DNAemia within the first 100 days after transplant. CMV-specific CD8(+) T-cell responses (of any functional type) were more likely to be detected in patients who did not display CMV DNAemia than in those who did (P = 0.04). Qualitatively, no major differences in the functional signature of CMV-specific CD8(+) T cells were noted between patients who had or did not have CMV DNAemia. Patients displaying levels of polyfunctional CD8(+) T cells at day +30 >0.30 cell/µL had a lower risk of CMV DNAemia (positive predictive value 76%, and negative predictive value 43%). CONCLUSION: The presence of polyfunctional CD8(+) T cells (either expressing CD107a or not) was associated with lower levels of CMV replication, and higher frequency of self-resolved episodes. The data reported further clarify the role of polyfunctional CD8(+) T cells in control of CMV DNAemia in allo-SCT recipients.
Asunto(s)
Linfocitos T CD8-positivos/inmunología , Infecciones por Citomegalovirus/inmunología , Citomegalovirus/inmunología , ADN Viral/sangre , Fosfoproteínas/metabolismo , Trasplante de Células Madre/efectos adversos , Proteínas de la Matriz Viral/metabolismo , Adolescente , Adulto , Anciano , Linfocitos T CD8-positivos/metabolismo , Estudios de Cohortes , Citomegalovirus/genética , Citomegalovirus/metabolismo , Infecciones por Citomegalovirus/virología , Femenino , Humanos , Interferón gamma/inmunología , Interferón gamma/metabolismo , Masculino , Persona de Mediana Edad , Fosfoproteínas/inmunología , Trasplante Homólogo/efectos adversos , Factor de Necrosis Tumoral alfa/inmunología , Factor de Necrosis Tumoral alfa/metabolismo , Proteínas de la Matriz Viral/inmunología , Adulto JovenRESUMEN
BACKGROUND: This study aimed to characterize the dynamics of acquisition of cytomegalovirus (CMV)-specific cell-mediated immunity (CMI) in CMV donor positive/recipient negative solid organ transplant (SOT) patients receiving long-term antiviral prophylaxis, and to determine whether development of CMI confers protection against CMV disease. METHODS: A prospective multicenter study was conducted in Spain from September 2009 to September 2012. Whole blood specimens were prospectively collected at 30, 90, 120, 200, and 365 days after SOT, and CMI was determined by enumeration of CMV pp65 and IE-1-specific CD69(+) /interferon-γ-producing CD8(+) and CD4(+) T cells by flow cytometry for intracellular cytokine staining. As part of a simultaneous clinical trial, patients received either early prophylaxis (in the first 3 days after transplantation) in the first period of the study or delayed prophylaxis (initiated at day 14) during the second period of the study. The impact of the dynamics of acquisition of CMV-specific CMI on the incidence of CMV disease was evaluated by Kaplan-Meier survival analysis. RESULTS: A total of 95 SOT recipients were recruited. CMV infection and disease occurred in 38 (40%) and 26 (27.4%) patients, respectively. The proportion of patients achieving any detectable CMV-specific CMI response at each of the different monitoring points was higher in liver transplant recipients, as compared to kidney or heart transplant recipients. The presence of any detectable response at day 120 or 200 was protective against the development of CMV disease (positive predictive values 92% and 93%, respectively). CONCLUSIONS: The rate of acquisition of CMV-specific CMI in SOT recipients undergoing antiviral prophylaxis differed significantly between different SOT populations. Patients developing any detectable CMI response were protected against the occurrence of CMV disease.
Asunto(s)
Antivirales/uso terapéutico , Infecciones por Citomegalovirus/prevención & control , Citomegalovirus/inmunología , Ganciclovir/análogos & derivados , Inmunidad Celular , Trasplante de Órganos , Complicaciones Posoperatorias/prevención & control , Adulto , Anciano , Infecciones por Citomegalovirus/etiología , Infecciones por Citomegalovirus/inmunología , Infecciones por Citomegalovirus/virología , Femenino , Estudios de Seguimiento , Ganciclovir/uso terapéutico , Humanos , Estimación de Kaplan-Meier , Masculino , Persona de Mediana Edad , Cuidados Posoperatorios/métodos , Complicaciones Posoperatorias/inmunología , Complicaciones Posoperatorias/virología , Estudios Prospectivos , Resultado del Tratamiento , ValganciclovirRESUMEN
We present the theoretical description of the image formation with the in-line germanium Bragg Magnifier Microscope (BMM) and the first successful phase retrieval of X-ray holograms recorded with this imaging system. The conditions under which the BMM acts as a linear shift invariant system are theoretically explained and supported by the experiment. Such an approach simplifies the mathematical treatment of the image formation and reconstruction as complicated propagation of the wavefront onto inclined planes can be avoided. Quantitative phase retrieval is demonstrated using a test sample and a proof of concept phase imaging of a spider leg is also presented.
RESUMEN
OBJECTIVE: Letermovir (LMV) is used for prophylaxis of cytomegalovirus (CMV) reactivation and end-organ disease in adult CMV-seropositive allogeneic hematopoietic stem cell transplant recipients (allo-HSCT). In turn, sirolimus (SLM) which displays in vitro anti-CMV activity, is frequently employed for prophylaxis of Graft vs. Host disease in allo-HSCT. Here, we aimed at assessing whether LMV and SLM used in combination may act synergistically in vitro on inhibiting CMV replication. METHODS: The antiviral activity of LMV and SLM alone or in combination was evaluated by a checkerboard assay, using ARPE-19 cells infected with CMV strain BADrUL131-Y. LMV and SLM were used at concentrations ranging from 24 nM to 0.38 nM and 16 nM to 0.06 nM, respectively. RESULTS: The mean EC50 for LMV and SLM was 2.44 nM (95% CI, 1.66-3.60) and 1.40 nM (95% CI, 0.41-4.74), respective. LMV and SLM interaction yielded mainly additive effects over the range of concentrations tested. CONCLUSIONS: The additive nature of the combination of LMV and SLM against CMV may have relevant clinical implications in management of CMV infection in allo-HSCT recipients undergoing prophylaxis with LMV.
Asunto(s)
Infecciones por Citomegalovirus , Trasplante de Células Madre Hematopoyéticas , Adulto , Humanos , Citomegalovirus , Sirolimus/farmacología , Sirolimus/uso terapéutico , Infecciones por Citomegalovirus/tratamiento farmacológico , Infecciones por Citomegalovirus/prevención & control , Antivirales/farmacología , Antivirales/uso terapéuticoRESUMEN
INTRODUCTION: A randomised trial implementing Enhanced Recovery After Surgery (ERAS) for high complexity advanced ovarian cancer (AOC) surgery (PROFAST) demonstrated a reduction of median length of stay and hospital readmissions when compared to patients managed conventionally. One secondary objective was to determine if an ERAS pathway in the perioperative management of advanced ovarian cancer patients led to cost savings. MATERIAL AND METHODS: Secondary objective of a prospective randomised trial of patients with suspected or diagnosed advanced ovarian cancer allocated to conventional or ERAS perioperative management, carried out at a referral centre from June 2014 to March 2018. Treatment was determined by a computer-generated random allocation system. METHODS: Gross counting was employed to estimate the cost of hospitalisation in wards, intensive care unit (ICU) and surgical care, while micro-costing was used to obtain image and laboratory test costs. Mean costs between trial arms were considered. Sensitivity analyses were performed. RESULTS: Ninety-nine patients (n = 50 ERAS group, n = 49 Conventional group) were included. Mean costs per patient were 10,719 in the ERAS group and 11,028 in the conventional group, leading to an average saving of 309 per patient. These results were based on 96 patients, excluding 3 extreme outliers mainly related with very high ICU costs. Savings, which were significant for hospital ward costs (-33% total; 759 per patient in first hospitalisation, and 914 per partient/day of readmission) were found as robust in the sensitivity analysis. CONCLUSIONS: Implementation of an ERAS pathway leads to cost savings when compared to conventional management after AOC surgery.
Asunto(s)
Recuperación Mejorada Después de la Cirugía , Neoplasias Ováricas , Femenino , Humanos , Carcinoma Epitelial de Ovario , Costos de Hospital , Tiempo de Internación , Neoplasias Ováricas/cirugía , Complicaciones Posoperatorias , Estudios Prospectivos , Ensayos Clínicos Controlados Aleatorios como AsuntoRESUMEN
Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands of macromolecules that are assumed to be structurally identical are combined into a single 3D map representing the Coulomb potential of the macromolecule under study. This article discusses possible caveats along the image-processing path and how to avoid them to obtain a reliable 3D structure. Some of these problems are very well known in the community. These may be referred to as sample-related (such as specimen denaturation at interfaces or non-uniform projection geometry leading to underrepresented projection directions). The rest are related to the algorithms used. While some have been discussed in depth in the literature, such as the use of an incorrect initial volume, others have received much less attention. However, they are fundamental in any data-analysis approach. Chiefly among them, instabilities in estimating many of the key parameters that are required for a correct 3D reconstruction that occur all along the processing workflow are referred to, which may significantly affect the reliability of the whole process. In the field, the term overfitting has been coined to refer to some particular kinds of artifacts. It is argued that overfitting is a statistical bias in key parameter-estimation steps in the 3D reconstruction process, including intrinsic algorithmic bias. It is also shown that common tools (Fourier shell correlation) and strategies (gold standard) that are normally used to detect or prevent overfitting do not fully protect against it. Alternatively, it is proposed that detecting the bias that leads to overfitting is much easier when addressed at the level of parameter estimation, rather than detecting it once the particle images have been combined into a 3D map. Comparing the results from multiple algorithms (or at least, independent executions of the same algorithm) can detect parameter bias. These multiple executions could then be averaged to give a lower variance estimate of the underlying parameters.
Asunto(s)
Imagenología Tridimensional , Sesgo , Consenso , Microscopía por Crioelectrón/métodos , Imagenología Tridimensional/métodos , Reproducibilidad de los ResultadosRESUMEN
Cryo-electron microscopy has become one of the most important tools in biological research to reveal the structural information of macromolecules at near-atomic resolution. In single-particle analysis, the vitrified sample is imaged by an electron beam and the detectors at the end of the microscope column produce movies of that sample. These movies contain thousands of images of identical particles in random orientations. The data need to go through an image processing workflow with multiple steps to obtain the final 3D reconstructed volume. The goal of the image processing workflow is to identify the acquisition parameters to be able to reconstruct the specimen under study. Scipion provides all the tools to create this workflow using several image processing packages in an integrative framework, also allowing the traceability of the results. In this article the whole image processing workflow in Scipion is presented and discussed with data coming from a real test case, giving all the details necessary to go from the movies obtained by the microscope to a high resolution final 3D reconstruction. Also, the power of using consensus tools that allow combining methods, and confirming results along every step of the workflow, improving the accuracy of the obtained results, is discussed.
Asunto(s)
Procesamiento de Imagen Asistido por Computador , Imagen Individual de Molécula , Microscopía por Crioelectrón , Sustancias Macromoleculares , Flujo de TrabajoRESUMEN
Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software.
RESUMEN
Several strategies have been developed to decrease the concentration limits of detection (LODs) in capillary electrophoresis (CE). Nowadays, chromatographic-based preconcentration using a microcartridge integrated in the separation capillary for in-line solid-phase extraction capillary electrophoresis (SPE-CE) is one of the best alternatives for high throughput and reproducible sample clean-up and analyte preconcentration. This review covers different designs (geometrical configurations, with frits or fritless, capillary types, compatibility with commercial instrumentation, etc.) and materials (sorbents, supports, affinity ligands, etc.) applied for almost 30 years to prepare in-line SPE-CE microcartridges (i.e. analyte concentrators), with emphasis on the conventional unidirectional configuration in capillary format. Advantages, disadvantages and future perspectives are analyzed in detail to provide the reader a wide overview about the great potential of this technique to enhance sensitivity and address trace analysis.