2 results
Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology
- Pablo Conesa, Yunior C. Fonseca, Jorge Jiménez de la Morena, Grigory Sharov, Jose Miguel de la Rosa-Trevín, Ana Cuervo, Alberto García Mena, Borja Rodríguez de Francisco, Daniel del Hoyo, David Herreros, Daniel Marchan, David Strelak, Estrella Fernández-Giménez, Erney Ramírez-Aportela, Federico Pedro de Isidro-Gómez, Irene Sánchez, James Krieger, José Luis Vilas, Laura del Cano, Marcos Gragera, Mikel Iceta, Marta Martínez, Patricia Losana, Roberto Melero, Roberto Marabini, José María Carazo, Carlos Oscar Sánchez Sorzano
-
- Journal:
- Biological Imaging / Volume 3 / 2023
- Published online by Cambridge University Press:
- 29 June 2023, e13
-
- Article
-
- You have access Access
- Open access
- HTML
- Export citation
-
Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.
Iron-modulated pseudocyst formation in Tritrichomonas foetus
- CÁSSIA CASTRO, RUBEM FIGUEIREDO SADOK MENNA-BARRETO, NILMA DE SOUZA FERNANDES, LEONARDO SABOIA-VAHIA, GEOVANE DIAS-LOPES, CONSTANÇA BRITTO, PATRICIA CUERVO, JOSÉ BATISTA DE JESUS
-
- Journal:
- Parasitology / Volume 143 / Issue 8 / July 2016
- Published online by Cambridge University Press:
- 13 April 2016, pp. 1034-1042
-
- Article
- Export citation
-
Iron is an essential element for the survival of trichomonads during host–parasite interaction. The availability of this metal modulates several metabolic pathways of the parasites and regulates the expression of virulence factors such as adhesins and proteolytic enzymes. In this study, we investigated the effect of iron depletion on the morphology and life cycle of Tritrichomonas foetus. Scanning and transmission electron microscopy analyses revealed that depletion of iron from the culture medium (named TYM-DIP inducer medium) induces morphological transformation of typical pear-shaped trophozoites into spherical and non-motile pseudocysts. Remarkably, inoculation of pseudocysts into an iron-rich medium (standard TYM medium), or addition of FeSO4 to a TYM-DIP inducer medium reverted the morphological transformation process and typical trophozoites were recovered. These results show that pseudocysts are viable forms of the parasite and highlight the role of iron as a modulator of the parasite phenotype. Although iron is required for the survival of T. foetus, iron depletion does not cause a cellular collapse of pseudocysts, but instead induces phenotypic alterations, probably in order to allow the parasite to survive conditions of nutritional stress. Together, these findings support previous studies that suggest pseudocysts are a resistance form in the life cycle of T. foetus and enable new approaches to understanding the multifactorial role of iron in the cell biology of this protozoan parasite.
![](/core/cambridge-core/public/images/lazy-loader.gif)