Hop stunt viroid infection induces heterochromatin reorganization.

Viroids are pathogenic noncoding RNAs that completely rely on their host molecular machinery to accomplish their life cycle. Several interactions between viroids and their host molecular machinery have been identified, including interference with epigenetic mechanisms such as DNA methylation. Despite this, whether viroids influence changes in other epigenetic marks such as histone modifications remained unknown. Epigenetic regulation is particularly important during pathogenesis processes because it might be a key regulator of the dynamism of the defense response. Here we have analyzed the changes taking place in Cucumis sativus (cucumber) facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2, with a tendency to decrease the levels of repressive epigenetic marks through infection progression. These epigenetic changes are connected to the transcriptional regulation of their expected targets, genes, and transposable elements. Indeed, several genes related to the defense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, providing further information about the complexity of the multiple layers of interactions between pathogens/viroids and hosts/plants.

Integrative time-scale and multi-omics analysis of host responses to viroid infection.

Viroids are circular RNAs of minimal complexity compelled to subvert plant-regulatory networks to accomplish their infectious process. Studies focused on the response to viroid-infection have mostly addressed specific regulatory levels and considered specifics infection-times. Thus, much remains to be done to understand the temporal evolution and complex nature of viroid-host interactions. Here we present an integrative analysis of the temporal evolution of the genome-wide alterations in cucumber plants infected with hop stunt viroid (HSVd) by integrating differential host transcriptome, sRNAnome and methylome. Our results support that HSVd promotes the redesign of the cucumber regulatory-pathways predominantly affecting specific regulatory layers at different infection-phases. The initial response was characterised by a reconfiguration of the host-transcriptome by differential exon-usage, followed by a progressive transcriptional downregulation modulated by epigenetic changes. Regarding endogenous small RNAs, the alterations were limited and mainly occurred at the late stage. Significant host-alterations were predominantly related to the downregulation of transcripts involved in plant-defence mechanisms, the restriction of pathogen-movement and the systemic spreading of defence signals. We expect that these data constituting the first comprehensive temporal-map of the plant-regulatory alterations associated with HSVd infection could contribute to elucidate the molecular basis of the yet poorly known host-response to viroid-induced pathogenesis.

SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity.

The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides. Host-derived sncRNAs, including microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), and small nucleolar RNA-derived small RNAs (sdRNAs) exhibited significant differential expression in infected patients compared to controls. Importantly, miRNA expression was predominantly down-regulated in response to SARS-CoV-2 infection, especially in patients with severe symptoms. Furthermore, we identified specific tsRNAs derived from Glu- and Gly-tRNAs as major altered elements upon infection, with 5' tRNA halves being the most abundant species and suggesting their potential as biomarkers for viral presence and disease severity prediction. Additionally, down-regulation of C/D-box sdRNAs and altered expression of tinyRNAs (tyRNAs) were observed in infected patients. These findings provide valuable insights into the host sncRNA response to SARS-CoV-2 infection and may contribute to the development of further diagnostic and therapeutic strategies in the clinic.

Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network.

Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of response of melon to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress combinations, most interactions were negative, suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling pieces of evidence that the response to combined stresses cannot be easily predicted from the study individual stresses.

A new approach to define optimized range of medium composition for enhancement of hairy root production in fed-batch process.

This work proposes a new methodology to identify the best medium concentrations for fed-batch production of hairy root using Datura innoxia as a model. Firstly, the role of each component on the growth rate is investigated separately. Then, an experimental design allows refining the optimization studying the interactions between the major species. The result analysis let to define concentration range optimized for fed-batch process. The work novelties lie in two aspects. Firstly, concentrations have been kept constant during each run. Thus, biomass uptakes do not affect the optimization and the growth rate is maintained constant during the exponential phase. Secondly, the effects of salts are generally studied. In this work, the influences of each ion are investigated in order to avoid bias due to the counter-ion effects. Compared to the classical B(5) medium, the optimized medium shows a significant improvement leading to more than 80% increase of final biomass production.

Indicadores de calidad intrahospitalaria / Indicators of intrahospital quality

Fundamento: la infección intrahospitalaria es uno de los problemas de salud mundial, y es un indicador de calidad del hospital. Objetivo: valorar los indicadores del programa de infección intrahospitalaria en el Hospital Universitario Martín Chang Puga de Nuevitas desde el año 2007 al primer semestre de 2008. Método: se realizó un estudió descriptivo y transversal, de los ciento treinta y seis casos de infección hospitalaria en el año 2007 y se compararon con los doscientos cincuenta y nueve casos de infección hospitalaria del año 1997, para apreciar los cambios en los indicadores. Coincidió la muestra con el universo en ambos años. Se realizó un registro con los indicadores de infección de todos los pacientes reportados, el cual constituyó la fuente primaria de obtención de los datos. Resultados: la mayor tasa de infección fue del servicio de nefrología con 4,6 por ciento. De la localización de las infecciones, las heridas quirúrgicas, las respiratorias, y las cardiovasculares, para un 18,3 por ciento respectivamente. Se utilizaron antibióticos como: la cefazolina, y la ciprofloxacina. De mayor resistencias, la penicilina y la eritromicina con el 10,1 por ciento, las cefazolinas 14,2 por ciento y la ampicilina con el 21,1 por ciento. Los gérmenes más aislados fueron los staphylococcus epidérmides con el 23,9 por ciento, y los aureus con 21,7 por ciento. Conclusiones: la tasa global de infección de 2007 fue inferior al año 1997. El servicio Nefrología fue el de más incidencia con una tasa muy superior al resto de los servicios. De los gérmenes más aislados, resultaron los staphylococcus epidérmides y los aureus, y los antibióticos más utilizados fueron ciprofloxacina y la cefazolina.

Background: intrahospital infection is one of the worldwide health problems, and it is a hospital’s quality indicator. Objective: to value the indicators of intrahospital infection program in the University Hospital Martin Chang Puga of Nuevitas from 2007 to the first semester of 2008. Method: a descriptive and cross-sectional study of one-hundred thirty-six cases of hospital infection in the year 2007 was carried out which were compared with two-hundred fifty-nine cases of the year 1997, to appreciate the changes in the indicators. The sample coincided with the universe in both years. A recording was carried out with infection indicators of all the reported patients, which constituted data primary source. Results: the biggest infection rate was in the nephrology service with 4,6 percent. Of the localization of infections, surgical wounds, breathing, and cardiovascular ones, to a 18,3 percent respectively. Antibiotics that were used: cefazolin and ciprofloxacin. The ones of greater resistance, penicillin and erythromycin with 10,1 percent, cefazolin 14,2 percent and ampicillin with 21,1 percent. The most isolated germs were the staphylococcus epidérmides with 23,9 percent, and the aureus ones with 21,7 percent. Conclusions: the infection global rate of 2007 was inferior to the year 1997. The Nephrology service had the highest incidence with a very superior rate to the remainder services. Of the most isolated germs, were the staphylococcus epidérmides and the aureus, and regarding antibiotics the most used were ciprofloxacin and cefazolin.