Amyloid structures as biofilm matrix scaffolds

Recent insights into bacterial biofilm matrix structures have induced a paradigm shift toward the recognition of amyloid fibers as common building block structures that confer stability to the exopolysaccharide matrix. Here we describe the functional amyloid systems related to biofilm matrix formation in both Gram-negative and Gram-positive bacteria and recent knowledge regarding the interaction of amyloids with other biofilm matrix components such as extracellular DNA (eDNA) and the host immune system. In addition, we summarize the efforts to identify compounds that target amyloid fibers for therapeutic purposes and recent developments that take advantage of the amyloid structure to engineer amyloid fibers of bacterial biofilm matrices for biotechnological applications.This work, including the efforts of Jaione Valle, was funded by Ministerio de Economía y Competitividad (MINECO) (AGL2011-23954). This work, including the efforts of Íñigo Lasa, was funded by Ministerio de Economía y Competitividad (MINECO) (BIO2011-30503-C02-02 and BIO2014-53530-R)

SarA Is an Essential Positive Regulator of Staphylococcus epidermidis Biofilm Development

Staphylococcus epidermidis biofilm formation is associated with the production of the polysaccharide intercellular adhesin (PIA)--poly-N-acetylglucosamine polysaccharide (PNAG) by the products of the icaADBC operon. Recent evidence indicates that SarA, a central regulatory element that controls the production of Staphylococcus aureus virulence factors, is essential for the synthesis of PIA/PNAG and the ensuing biofilm development in this species. Based on the presence of a sarA homolog, we hypothesized that SarA could also be involved in the regulation of the biofilm formation process in S. epidermidis. To investigate this, we constructed nonpolar sarA deletions in two genetically unrelated S. epidermidis clinical strains, O-47 and CH845. The SarA mutants were completely defective in biofilm formation, both in the steady-state conditions of a microtiter dish assay and in the flow conditions of microfermentors. Reverse transcription-PCR experiments showed that the mutation in the sarA gene resulted in downregulation of the icaADBC operon transcription in an IcaR-independent manner. Purified SarA protein showed high-affinity binding to the icaA promoter region by electrophoretic mobility shift assays. Consequently, mutation in sarA provoked a significant decrease in the amount of PIA/PNAG on the cell surface. Furthermore, heterologous complementation of S. aureus sarA mutants with the sarA gene of S. epidermidis completely restored biofilm formation. In summary, SarA appeared to be a positive regulator of transcription of the ica locus, and in its absence, PIA/PNAG production and biofilm formation were diminished. Additionally, we present experimental evidence showing that SarA may be an important regulatory element that controls S. epidermidis virulence factors other than biofilm formation

Representación virtual interactiva del desaparecido convento del Carmen (Logroño) generada a partir de una maqueta de papel

[EN] The concept of mock-up, which share with the drawing the expressive synthesis for the analysis of the architectural form and evolution, is an invaluable asset for the preservation of the heritage. To mark the 175th anniversary of the Práxedes Mateo Sagasta’s secondary school of Logroño (Spain), an exhibition about the history of the institution was organized at the premises of La Rioja Library. The current school building became operational in 1900 and was built on the former site of a Carmelite convent. In fact, the convent rooms were the first location for the school, after the expropriations of religious communities during the mid-19th century. For the benefit of the aforementioned exhibition, it was considered interesting to generate a three-dimensional (3D) virtual reconstruction of the convent buildings to show how it would have looked. However, the lack of sufficient contemporary graphic information was a challenge, so it was decided that an efficient solution would be to generate the virtual reconstruction from a paper craft model, which had been created by the librarian of the secondary school as a result of his research on this matter. This text describes the 3D modelling of that cut-out element by means of monoscopic photogrammetry (perspective drawing) and the use of non-realistic rendering based on the appearance of the paper mock-up (and not trying to recreate the real image of the buildings) so as to provide a suggestive view of the convent and create interactive exhibition items. Moreover, the text deals with the long-term preservation and the improvement of the re-use of the 3D models. The former by resorting to institutional repositories —from which users can download the full detailed versions— and the latter employing versions able to be visualized in 3D warehouses (such as Sketchfab) and augmented reality (AR) applications.Highlights:A significant part of the architectural heritage is represented by mock-ups of different materials (paper, wood, metal and so on).Virtual modelling and augmented reality (AR) can be appropriate tools for materializing, recovering and disseminating scale models to the public.Techniques for geometric documentation and visual representation need to be adapted in order to tackle the peculiar features of these elements (size, materials, fragility, etc.).[ES] La maqueta, que comparte con el dibujo la síntesis expresiva para el análisis de la forma y evolución arquitectónica, resulta de un valor incalculable para la preservación del patrimonio. Con motivo del 175 aniversario del Instituto de Enseñanza Secundaria Práxedes Mateo Sagasta de Logroño (España) se organizó una exposición sobre su historia en la Biblioteca de La Rioja. El edificio que actualmente acoge el instituto fue inaugurado en el año 1900 y se construyó sobre el mismo terreno en el que, previamente, había estado un convento de Carmelitas. De hecho, la primera sede del instituto estuvo situada en las dependencias de este mismo convento, tras la desamortización de los edificios eclesiásticos que tuvo lugar a mediados del siglo XIX. Como parte de la muestra, se consideró interesante generar una reconstrucción virtual tridimensional (3D) de los edificios del convento con el fin de mostrar cómo debieron haber sido. La dificultad, sin embargo, residía en la escasez de fuentes gráficas de la época que permitieran conocer su forma y apariencia; por este motivo, se decidió utilizar como base para la recreación virtual una maqueta en papel que había sido realizada por el bibliotecario del instituto como resultado de sus investigaciones a lo largo de los años. El presente texto describe el proceso de modelado 3D a partir de esta maqueta de papel utilizando técnicas de fotogrametría monoscópica (dibujo perspectivo) y el empleo de renderizados no realistas basados en el aspecto de la maqueta de papel (y no en el que debieron tener los edificios) con el fin de generar vistas evocadoras del convento y crear contenidos útiles para la mencionada exposición. Asimismo, el texto trata la preservación a largo plazo de los modelos 3D y el incremento de su reutilización. En el primer caso, mediante el empleo de los repositorios institucionales —desde donde los usuarios pueden descargarse las versiones más detalladas— y, para el segundo fin, mediante la creación de versiones para su uso a través de almacenes de modelos 3D (como Sketchfab) y aplicaciones de realidad aumentada (RA).The authors wish to thank Mr. Alberto Abad Benito, director of the Práxedes Mateo Sagasta’s secondary school, for his enthusiasm and help in the development of this project. This article is dedicated to the memory of Mr. Fernando R. Blanco Martín, librarian of the Práxedes Mateo Sagasta’s secondary school for more than 25 years, who sadly died in 2019. We are grateful for both his tireless work in recovering information concerning the history of the city and the school, as well as the many pleasant conversations with him enjoyed by these authors. The participation of Jaione Korro in this research is supported by the Basque Government through a grant for doctoral studies of the call 2019-2020.Rodríguez-Miranda, A.; Valle Melón, JM.; Korro Bañuelos, J.; Elorriaga Aguirre, G. (2021). Interactive virtual representation of the disappeared convent of El Carmen (Logroño) generated from a paper craft model. Virtual Archaeology Review. 12(24):77-89. https://doi.org/10.4995/var.2021.14038OJS77891224Apollonio F. I. (2016). Classification schemes for visualization of uncertainty in digital hypothetical reconstructions. In S. Münster,M. Pfarr-Harfst, P. Kuroczyński & M. Ioannides (Eds.), 3D Research challenges in cultural heritage II. Lecture Notes in Computer Science, 10025, 173-197. Cham: Springer. http://dx.doi.org/10.1007/978-3-319-47647-6_9Azara, P., & Esparza, V. (2006). Maquetas en el mundo antiguo: entrevista a Pedro Azara. DC. Revista de crítica arquitectónica, 15-16, 55-62.Buriánek, J. (2011). Digital Langweil model of Prague. In K. Pavelka (Ed.). Proceedings of XXIII International CIPA Symposium. Prague, Czech Republic, September 12 - 16, 2011. Keynote speech, 19 pp.Chevrier, C., Jacquot, K., & Perrin, J. P. (2010). 3D Modelling of a town scale model. In Proceedings of the 3rd International Conference EuroMed 2010 (pp. 99-107). Lemessos, Cyprus.Chevrier, C. (2015). Semiautomatic Parametric Modelling of the Buildings on Town Scale Models. Journal on Computing and Cultural Heritage, 7, 20:1-20:20. https://doi.org/10.1145/2622609De la Torre, J. I. (2014). Del secreto de Estado a la didáctica militar. La fabricación y el coleccionismo de modelos y maquetas militares en España. In M. H. Herránez Martín, (Coord.), Modelos y maquetas: la vida a escala (pp. 59-87). Madrid: Ministerio de Educación, Cultura y Deporte (Spain).Demetrescu, E., Ferdani, D., Dell'Unto, N., Touatti, A.L., & Lindgren, S. (2016). Reconstructing the original splendour of the House of Caecilius Iucundus. A complete methodology for virtual archaeology aimed at digital exhibition. Scientific Research and Information Technology, 6(1), 51-66. http://dx.doi.org/10.2423/i22394303v6n1p51Favre-Brun, A. (2015). Architecture virtuelle et représentation de l'incertitude : analyse des solutions de visualisation de la representation 3D. In R. Vergnieux & C. Delevoie (Eds.), Actes du Colloque Virtual Retrospect 2013. Archéovision, 6, 91-96.Georgopoulos, A. (2019). CIPA slides on architectural photogrammetry: applying contemporary technologies from its early years. In E. Stylianidis (Ed.), CIPA - Heritage Documentation. 50 years: looking Backwards. The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, XLII-2/W14, 13-50. https://doi.org/10.5194/isprs-archives-XLII-2-W14-1-2019Granado, G., Barrera, J. A., & Aguilar-Camacho, J. (2016). La maqueta de Cádiz de 1779. Utilidad militar o metáfora del poder. Proyecto, Progreso, Arquitectura, 15, 16-28. http://dx.doi.org/10.12795/ppa.2016.i15.01Grellert, M. (2016). Rapid prototyping in the context of cultural heritage and museum displays. Buildings, cities, landscapes, illuminated models. In S. Münster, M. Pfarr-Harfst, P. Kuroczyński & M. Ioannides (Eds.), 3D Research challenges in cultural heritage II. Lecture Notes in Computer Science, 10025, 77-118. Cham: Springer. http://dx.doi.org/10.1007/978-3-319-47647-6_5Grellert, M., & Haas, F. (2016). Sharpness versus Uncertainty in 'Complete Models'. In S. Hoppe & S. Breitling (Eds.), Virtual Palaces, Part II. Lost Palaces and their Afterlife (pp. 119-148). https://doi.org/10.11588/arthistoricum.83.79Grussenmeyer, P., Hanke, K., Streilein, A. (2002) Architectural photogrammetry. In M. Kasser & Y. Egels (Eds.), Digital Photogrammetry (pp. 300-339). London: CRC Press.Guidi, G., Frischer, B., Simone, M.D., Cioci, A., Spinetti, A., Carosso, L., Micoli, L.L., Russo, M., & Grasso, T. (2005). Virtualizing ancient Rome: 3D acquisition and modeling of a large plaster-of-Paris model of imperial Rome. Electronic imaging, 5665, 119-133.Herrero, J. (2014). Modelos y maquetas en la historia. In M. H. Herránez Martín (Coord.), Modelos y maquetas: la vida a escala. Madrid: Ministerio de Educación, Cultura y Deporte (Spain), 7-24.Hervy, B., Billen, R., Laroche, F., Carré, C., Servieres, M., … & Kerouanton, J. (2012). A generalized approach for historical mock-up acquisition and data modelling: towards historically enriched 3D city models. Usage, Usability, and Utility of 3D City Models, 02009. https://doi.org/10.1051/3u3d/201202009Kersten, T. P., Keller, F., Saenger, J., & Schiewe, J. (2012). Automated Generation of an Historic 4D City Model of Hamburg and Its Visualisation with the GE Engine. In EuroMed 2012. Lecture Notes in Computer Science, 7616, 55-65. Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-34234-9_6Lecocq, F. (2004). Reconstitution virtuelle de Rome Antique. In R. Vergnieux & C. Delevoie (Eds.), Actes du Colloque Virtual Retrospect 2003. Archéovision, 1, 77-84.Lengyel, D., & Toulouse, C. (2016). Visualization of uncertainty in archaeological reconstructions. In S. Hoppe & S. Breitling (Eds.), Virtual Palaces, Part II. Lost Palaces and their Afterlife (pp. 103-117). Heidelberg: arthistoricum.net. https://doi.org/10.11588/arthistoricum.83.79Maiwald, F., Bruschke, J., Lehmann, C., & Niebling, F. (2019). A 4D information system for the exploration of multitemporal images and maps using photogrammetry, web technologies and VR/AR. Virtual Archaeology Review, 10(21), 1-13. https://doi.org/10.4995/var.2019.11867Moreno, M. (2014). Modelos y maquetas en el Museo Tiflológico. In M. H. Herránez Martín (Coord.), Modelos y maquetas: la vida a escala (pp. 205-211). Madrid: Ministerio de Educación, Cultura y Deporte (Spain).Noardo, F. (2018). Architectural heritage semantic 3D documentation in multi-scale standard maps. Journal of Cultural Heritage, 32, 156-165. https://doi.org/10.1016/j.culher.2018.02.009Quirós, F. (1994). Las colecciones militares de modelos de ciudades españolas, y el Real Gabinete Topográfico de Fernando VII. Una aproximación. Ería, 35, 203-224.Rizvic, S., Pletinckx, D., & Okanović, V. (2015). Enhancing museum exhibitions with interactive digital content. Sarajevo City Model Interactive. In XXV International Conference on Information, Communication and Automation Technologies (ICAT), Sarajevo, Bosnia and Herzegovina. https://doi.org/10.1109/ICAT.2015.7340510Rodríguez Hidalgo, J. M. (2010). De la reconstrucción tradicional a la virtual. Una visión desde la arqueología. Virtual Archaeology Review, 1(1), 163-167. https://doi.org/10.4995/var.2010.5140Rodríguez Miranda, Á., Korro Bañuelos, J., & Valle Melón, J. M. (2020). Archivo y difusión de contenidos 3D de elementos patrimoniales en repositorios institucionales y plataformas comerciales. Revista PH, 100, 78-80. https://doi.org/10.33349/2020.100.4641Rodríguez Miranda, Á., & Valle Melón, J. M. (2017). Recovering old stereoscopic negatives and producing digital 3D models of former appearances of historic buildings. The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, XLII-2/W3, 601-608. https://doi.org/10.5194/isprs-archives-XLII-2-W3-601-2017Rodríguez Miranda, Á., Valle Melón, J. M., & Lopetegi Galarraga, A. (2007). Ajuste radiométrico de texturas fotográficas en modelos virtuales y nubes de puntos de elementos patrimoniales. In 7ª Semana Geomática. Barcelona, Spain.Scopigno, R., Callieri, M., Dellepiane, M., Ponchio, F., & Potenziani, M. (2017). Delivering and using 3D models on the web: Are we ready?. Virtual Archaeology Review, 8(17), 1-9. http://dx.doi.org/10.4995/var.2017.6405Sedlácek, D., Buriánek, J., & Zára, J. (2013). 3D Reconstruction Data Set -The Langweil Model of Prague. International Journal of Heritage in the Digital Era, 2, 195-220. https://doi.org/10.1260/2047-4970.2.2.195Soycan, A., Soycan, M. (2019). Perspective correction of building facade images for architectural applications. Engineering Science and Technology, an International Journal, 22, 697-705. https://doi.org/10.1016/j.jestch.2018.12.012Spanò, A., Chiabrando, F., Dezzani, L., & Prencipe, A. (2016). Digital Segusio: from models generation to urban reconstruction. Virtual Archaeology Review, 7(15), 87-97. http://dx.doi.org/10.4995/var.2016.5874Statham, N. (2019). Scientific rigour of online platforms for 3D visualization of heritage. Virtual Archaeology Review, 10(20), 1-16. https://doi.org/10.4995/var.2019.9715Smutný, V., Prášek, P., Pajdla, T, & Palatka, P. (2007). 3D Reconstruction of Langweil's Model of Prague: Data Acquisition. EVA Berlin, 14, 102-107. https://doi.org/10.11588/arthistoricum.213.284Vela, F. (2014). La maqueta de arquitectura. La colección de la Escuela Técnica Superior de Arquitectura de Madrid. In M.H. Herránez Martín (Coord.), Modelos y maquetas: la vida a escala. Madrid: Ministerio de Educación, Cultura y Deporte (Spain), 25-41.Walmsley, A., & Kersten, T. P. (2019). Low-cost development of an interactive, immersive virtual reality experience of the historic city model Stade 1620. The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, XLII-2/W17, 405-411. https://doi.org/10.5194/isprs-archives-XLII-2-W17-405-2019Williamson, J. R., & Brill, M. H. (1990). Dimensional analysis through perspective. A reference manual. Dubuque (Iowa): American Society for Photogrammetry and Remote Sensing.Zhu, L., Ma, G., Mu, Y., & Shi, R. (2009) Reconstruction 3D-models of Old Beijing city by structured light scanning. In 22nd CIPA Symposium. Kyoto, Japan

Bacterial biofilm functionalization through Bap amyloid engineering

Biofilm engineering has emerged as a controllable way to fabricate living structures with programmable functionalities. The amyloidogenic proteins comprising the biofilms can be engineered to create self-assembling extracellular functionalized surfaces. In this regard, facultative amyloids, which play a dual role in biofilm formation by acting as adhesins in their native conformation and as matrix scaffolds when they polymerize into amyloid-like fibrillar structures, are interesting candidates. Here, we report the use of the facultative amyloid-like Bap protein of Staphylococcus aureus as a tool to decorate the extracellular biofilm matrix or the bacterial cell surface with a battery of functional domains or proteins. We demonstrate that the localization of the functional tags can be change by simply modulating the pH of the medium. Using Bap features, we build a tool for trapping and covalent immobilizing molecules at bacterial cell surface or at the biofilm matrix based on the SpyTag/SpyCatcher system. Finally, we show that the cell wall of several Gram-positive bacteria could be functionalized through the external addition of the recombinant engineered Bap-amyloid domain. Overall, this work shows a simple and modulable system for biofilm functionalization based on the facultative protein Bap. © 2022, The Author(s).This research was supported by grants from the Spanish Ministry of Science and Technology RTI2018-096011-B-I00 to J.V. and PID2020-113494RB-I00 to IL. L.M.-C. was supported by the predoctoral program of the Universidad Pública de Navarra