173 research outputs found
Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy
[EN] Viroids are small infectious, non-protein-coding circular RNAs that replicate independently and, in some cases, incite diseases in plants. They are classified into two families: Pospiviroidae, composed of species that have a central conserved region (CCR) and replicate in the cell nucleus, and Avsunviroidae, containing species that lack a CCR and whose multimeric replicative intermediates of either polarity generated in plastids self-cleave through hammerhead ribozymes. The compact, rod-like or branched, secondary structures of viroid RNAs have been predicted by RNA folding algorithms and further examined using different in vitro and in vivo experimental techniques. However, direct data about their native tertiary structure remain scarce. Here we have applied atomic force microscopy (AFM) to image at single-molecule resolution different variant RNAs of three representative viroids: potato spindle tuber viroid (PSTVd, family Pospiviroidae), peach latent mosaic viroid and eggplant latent viroid (PLMVd and ELVd, family Avsunviroidae). Our results provide a direct visualization of their native, three-dimensional conformations at 0 and 4 mM Mg2+ and highlight the role that some elements of tertiary structure play in their stabilization. The AFM images show that addition of 4 mM Mg2+ to the folding buffer results in a size contraction in PSTVd and ELVd, as well as in PLMVd when the kissing-loop interaction that stabilizes its 3D structure is preserved.This work was supported by the Spanish Ministerio de Economia y Competitividad (MINECO) grants BIO2016-79618-R (funded by EU under the FEDER programme) to C.B. and BFU2104-56812-P to R.F., as well as by the Comunidad de Madrid grant S2018/NMT-4349 to L.V. CIBERehd is funded by the Instituto de Salud Carlos III (ISCIII).Moreno, M.; VĂĄzquez, L.; LĂłpez Carrasco, A.; MartĂn-Gago, JA.; Flores Pedauye, R.; Briones, C. (2019). Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy. RNA Biology. 16(3):295-308. https://doi.org/10.1080/15476286.2019.1572436S295308163Diener, T. O. (2003). Discovering viroids â a personal perspective. Nature Reviews Microbiology, 1(1), 75-80. doi:10.1038/nrmicro736Flores, R., HernĂĄndez, C., Alba, A. E. M. de, Daròs, J.-A., & Serio, F. D. (2005). Viroids and Viroid-Host Interactions. Annual Review of Phytopathology, 43(1), 117-139. doi:10.1146/annurev.phyto.43.040204.140243Ding, B. (2009). The Biology of Viroid-Host Interactions. Annual Review of Phytopathology, 47(1), 105-131. doi:10.1146/annurev-phyto-080508-081927Zhang, Z., Qi, S., Tang, N., Zhang, X., Chen, S., Zhu, P., ⌠Wu, Q. (2014). 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Dissecting the secondary structure of the circular RNA of a nuclear viroid in vivo: A ÂŤnakedÂť rod-like conformation similar but not identical to that observed in vitro. RNA Biology, 14(8), 1046-1054. doi:10.1080/15476286.2016.1223005Wang, Y., Zirbel, C. L., Leontis, N. B., & Ding, B. (2018). RNA 3-dimensional structural motifs as a critical constraint of viroid RNA evolution. PLOS Pathogens, 14(2), e1006801. doi:10.1371/journal.ppat.1006801Zhong, X., Leontis, N., Qian, S., Itaya, A., Qi, Y., Boris-Lawrie, K., & Ding, B. (2006). Tertiary Structural and Functional Analyses of a Viroid RNA Motif by Isostericity Matrix and Mutagenesis Reveal Its Essential Role in Replication. Journal of Virology, 80(17), 8566-8581. doi:10.1128/jvi.00837-06Zhong, X., Tao, X., Stombaugh, J., Leontis, N., & Ding, B. (2007). Tertiary structure and function of an RNA motif required for plant vascular entry to initiate systemic trafficking. 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DELLA proteins regulate spore germination and reproductive development in <i>Physcomitrium patens</i>
Versatile Graphene-Based Platform for Robust Nanobiohybrid Interfaces
Technologically useful and robust graphene-based interfaces for devices
require the introduction of highly selective, stable, and covalently bonded
functionalities on the graphene surface, whilst essentially retaining the
electronic properties of the pristine layer. This work demonstrates that highly
controlled, ultrahigh vacuum covalent chemical functionalization of graphene
sheets with a thiol-terminated molecule provides a robust and tunable platform
for the development of hybrid nanostructures in different environments. We
employ this facile strategy to covalently couple two representative systems of
broad interest: metal nanoparticles, via S-metal bonds, and thiol-modified DNA
aptamers, via disulfide bridges. Both systems, which have been characterized by
a multi-technique approach, remain firmly anchored to the graphene surface even
after several washing cycles. Atomic force microscopy images demonstrate that
the conjugated aptamer retains the functionality required to recognize a target
protein. This methodology opens a new route to the integration of high-quality
graphene layers into diverse technological platforms, including plasmonics,
optoelectronics, or biosensing. With respect to the latter, the viability of a
thiol-functionalized chemical vapor deposition graphene-based solution-gated
field-effect transistor array was assessed
EvaluaciĂłn de la enseĂąanza a travĂŠs de la guĂa docente en la UPCT
[SPA]Este trabajo presenta una propuesta de metodologĂa para la evaluaciĂłn de guĂas docentes basada en un conjunto de tres
criterios principales (utilidad, coherencia e idoneidad), once subcriterios y una serie de indicadores cuyos valores se
obtienen a travĂŠs de cuestionarios dirigidos a centros, departamentos, estudiantes y profesorado. Los cuestionarios
parten del modelo de GuĂa Docente adoptado por la UPCT y contemplan todos los apartados de la misma. El mĂŠtodo
propuesto puede aplicarse tambiĂŠn para mejorar los programas de evaluaciĂłn del profesorado, pues aporta las
evidencias que se necesitan para valorar la labor de planificaciĂłn desarrollada por el mismo, la cual se plasma en la guĂa
docente. [ENG]This paper presents a methodological proposal for the evaluation of teaching guides based on three main criteria, i.e.
usefulness, consistency, and suitability, and eleven subcriteria. It is also based on different indicators obtained through
questionnaires aimed at Educational Centres, Departments, Students and Professors. These questionnnaires have been
prepared from the teaching guide model adopted by the Technical University of Cartagena (UPCT), and considering all
the sections included in that guide. The proposed methodology can be also used to improve the teaching staff evaluation
program, because of the inclusion of planning task carried out by the professor, an aspect considered in the teaching
guide.Campus Mare Nostrum, Universidad PolitĂŠcnica de Cartagena, Universidad de Murcia, RegiĂłn de Murcia
International lower limb collaborative (INTELLECT) study: a multicentre, international retrospective audit of lower extremity open fractures
Trauma remains a major cause of mortality and disability across the world1, with a higher burden in developing nations2. Open lower extremity injuries are devastating events from a physical3, mental health4, and socioeconomic5 standpoint. The potential sequelae, including risk of chronic infection and amputation, can lead to delayed recovery and major disability6. This international study aimed to describe global disparities, timely intervention, guideline-directed care, and economic aspects of open lower limb injuries
International Lower Limb Collaborative (INTELLECT) study: a multicentre, international retrospective audit of lower extremity open fractures
Salmonella Strains Isolated from GalĂĄpagos Iguanas Show Spatial Structuring of Serovar and Genomic Diversity
It is thought that dispersal limitation primarily structures host-associated bacterial populations because host distributions inherently limit transmission opportunities. However, enteric bacteria may disperse great distances during food-borne outbreaks. It is unclear if such rapid long-distance dispersal events happen regularly in natural systems or if these events represent an anthropogenic exception. We characterized Salmonella enterica isolates from the feces of free-living GalĂĄpagos land and marine iguanas from five sites on four islands using serotyping and genomic fingerprinting. Each site hosted unique and nearly exclusive serovar assemblages. Genomic fingerprint analysis offered a more complex model of S. enterica biogeography, with evidence of both unique strain pools and of spatial population structuring along a geographic gradient. These findings suggest that even relatively generalist enteric bacteria may be strongly dispersal limited in a natural system with strong barriers, such as oceanic divides. Yet, these differing results seen on two typing methods also suggests that genomic variation is less dispersal limited, allowing for different ecological processes to shape biogeographical patterns of the core and flexible portions of this bacterial species' genome
Global monitoring of soil animal communities using a common methodology.
Here we introduce the Soil BON Foodweb Team, a cross-continental collaborative network that aims to monitor soil animal communities and food webs using consistent methodology at a global scale. Soil animals support vital soil processes via soil structure modification, consumption of dead organic matter, and interactions with microbial and plant communities. Soil animal effects on ecosystem functions have been demonstrated by correlative analyses as well as in laboratory and field experiments, but these studies typically focus on selected animal groups or species at one or few sites with limited variation in environmental conditions. The lack of comprehensive harmonised large-scale soil animal community data including microfauna, mesofauna, and macrofauna, in conjunction with related soil functions, microbial communities, and vegetation, limits our understanding of biological interactions in soil systems and how these interactions affect ecosystem functioning. To provide such data, the Soil BON Foodweb Team invites researchers worldwide to use a common methodology to address six long-term goals: (1) to collect globally representative harmonised data on soil micro-, meso-, and macrofauna communities, (2) to describe key environmental drivers of soil animal communities and food webs, (3) to assess the efficiency of conservation approaches for the protection of soil animal communities, (4) to describe soil food webs and their association with soil functioning globally, (5) to establish a global research network for soil biodiversity monitoring and collaborative projects in related topics, (6) to reinforce local collaboration networks and expertise and support capacity building for soil animal research around the world. In this paper, we describe the vision of the global research network and the common sampling protocol to assess soil animal communities and advocate for the use of standard methodologies across observational and experimental soil animal studies. We will use this protocol to conduct soil animal assessments and reconstruct soil food webs at sites associated with the global soil biodiversity monitoring network, Soil BON, allowing us to assess linkages among soil biodiversity, vegetation, soil physico-chemical properties, climate, and ecosystem functions. In the present paper, we call for researchers especially from countries and ecoregions that remain underrepresented in the majority of soil biodiversity assessments to join us. Together we will be able to provide science-based evidence to support soil biodiversity conservation and functioning of terrestrial ecosystems
Genome Degradation in Brucella ovis Corresponds with Narrowing of Its Host Range and Tissue Tropism
Brucella ovis is a veterinary pathogen associated with epididymitis in sheep. Despite its genetic similarity to the zoonotic pathogens B. abortus, B. melitensis and B. suis, B. ovis does not cause zoonotic disease. Genomic analysis of the type strain ATCC25840 revealed a high percentage of pseudogenes and increased numbers of transposable elements compared to the zoonotic Brucella species, suggesting that genome degradation has occurred concomitant with narrowing of the host range of B. ovis. The absence of genomic island 2, encoding functions required for lipopolysaccharide biosynthesis, as well as inactivation of genes encoding urease, nutrient uptake and utilization, and outer membrane proteins may be factors contributing to the avirulence of B. ovis for humans. A 26.5 kb region of B. ovis ATCC25840 Chromosome II was absent from all the sequenced human pathogenic Brucella genomes, but was present in all of 17 B. ovis isolates tested and in three B. ceti isolates, suggesting that this DNA region may be of use for differentiating B. ovis from other Brucella spp. This is the first genomic analysis of a non-zoonotic Brucella species. The results suggest that inactivation of genes involved in nutrient acquisition and utilization, cell envelope structure and urease may have played a role in narrowing of the tissue tropism and host range of B. ovis
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