Irene Lopez - Academia.edu (original) (raw)

Papers by Irene Lopez

Plant Journal, 2009

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are two classes of abundant 21–24 nucleoti... more MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are two classes of abundant 21–24 nucleotide small RNAs (smRNAs) that control gene expression in plants, mainly by guiding cleavage and degradation of target transcripts. Target identification based on predictive algorithms for base-paired complementarity requires further experimental validation and often fails to recognize miRNA::target pairs that escape from stringent complementarity rules. Here, we report on a microarray-based methodology to identify target mRNAs of miRNAs and siRNAs at a genomic scale. This strategy takes advantage of the RNA ligase-mediated amplification of 5′ cDNA ends (RLM-RACE) to isolate miRNA or siRNA cleavage products from biological samples. Cleaved transcripts are then subjected to T7 RNA polymerase-mediated amplification and microarray hybridizations. The use of suitable hybridization controls is what makes our strategy outperform previous analyses. We applied this method and identified more than 100 putative novel miRNA or siRNA target mRNAs that had not been previously predicted by computational or microarray-based methods. Our data expand the regulatory role of endogenous smRNAs to a wide range of cellular processes, with prevalence in the regulation of cellular solute homeostasis. The methodology described here is straightforward, avoids extensive computational analysis and allows simultaneous analyses of several biological replicates, thus reducing the biological variability inherent in genomic analysis. The application of this simple methodology offers a framework for systematic analysis of smRNA-guided cleaved transcriptomes in different plant tissues, genotypes or stress conditions, and should contribute to understanding of the physiological role of smRNAs in plants.

Nature, 2007

Jasmonates are essential phytohormones for plant development and survival. However, the molecular... more Jasmonates are essential phytohormones for plant development and survival. However, the molecular details of their signalling pathway remain largely unknown. The identification more than a decade ago of COI1 as an F-box protein suggested the existence of a repressor of jasmonate responses that is targeted by the SCF COI1 complex for proteasome degradation in response to jasmonate. Here we report the identification of JASMONATE-INSENSITIVE 3 (JAI3) and a family of related proteins named JAZ (jasmonate ZIM-domain), in Arabidopsis thaliana. Our results demonstrate that JAI3 and other JAZs are direct targets of the SCF COI1 E3 ubiquitin ligase and jasmonate treatment induces their proteasome degradation. Moreover, JAI3 negatively regulates the key transcriptional activator of jasmonate responses, MYC2. The JAZ family therefore represents the molecular link between the two previously known steps in the jasmonate pathway. Furthermore, we demonstrate the existence of a regulatory feed-back loop involving MYC2 and JAZ proteins, which provides a mechanistic explanation for the pulsed response to jasmonate and the subsequent desensitization of the cell.

Clinical Microbiology and Infection, 2002

Allogeneic transfusions of red blood cell (RBC) concentrates have been related to an increase in ... more Allogeneic transfusions of red blood cell (RBC) concentrates have been related to an increase in postoperative infections. Leukocytes present in RBC units might have deleterious effects on the receptor immune system, provoking a state of immunosuppression that favors the development of postoperative infections (TRIM effect). The bioactive substances released by leukocytes in a time-dependent form, accumulating in blood components during storage, might be responsible for the TRIM effect. Multiple observational studies with logistic regression have demonstrated a direct relationship between transfusion and infection. However, several factors related to surgical difficulty and patient illness severity might act as strong confounding variables on the relationship studied. Randomized controlled trials designed to establish a causal relationship between transfusion and infection have yielded contradictory results. While we await new studies, allogeneic transfusions should be considered as a possible risk factor for postoperative infection.

Clinical Nutrition, 2004

Background & aim: Despite severely reduced intakes, anorexia nervosa (AN) patients seem to mainta... more Background & aim: Despite severely reduced intakes, anorexia nervosa (AN) patients seem to maintain serum biochemical parameters within the safe limit. The aim of this study was to assess the evolution of some traditional serum biochemical indicators of nutritional status in a 1-year follow-up of patients with restricting-type AN.

Journal of Human Nutrition and Dietetics, 2007

Background Long-term studies on the evolution of serum biochemical indicators in anorexia nervos... more Background Long-term studies on the evolution of serum biochemical indicators in anorexia nervosa (AN) patients during treatment are lacking in the literature. Thus, a 1-year follow-up of serum biochemical parameters in a homogeneous group of AN patients was performed.Methods Fourteen restricting-type AN patients were studied on admission to hospital, after 1 month of inpatient treatment and after 6 and 12 months after admission.Results Red blood cell count (RBC) and haemoglobin, serum glucose, total protein and the enzyme activities aspartate aminotransferase (AST), alkaline phosphatase (AlP), lactate dehydrogenase (LDH) and creatine kinase (CK) were significantly lower in patients on admission than in the control group. Total protein, high-density lipoprotein cholesterol (HDL-c), AST, AlP and CK showed significant changes among time points (anova, P < 0.05). Significant correlations were found between the change in RBC, haemoglobin, haematocrit, and the change in weight and body mass index (r = 0.74–0.86; P < 0.01). High cholesterol and amylase activity were found at all time points. While AST, LDH and CK reached control values within 6 months of treatment, AlP was always lower.Conclusion Serum AlP, hypercholesterolaemia and RBC seem to need longer periods of treatment with further weight gain to fully normalize. Therefore, these parameters should be monitored in AN patients long-term follow-up.

European Journal of Nutrition, 2006

Background The benefits of probiotic therapy in immunocompromised subjects still need strong scie... more Background The benefits of probiotic therapy in immunocompromised subjects still need strong scientific evidences. Aim of the study To assess the effects of yogurt on certain immunological parameters in anorexia nervosa (AN) patients during refeeding. Methods A parallel 10-week nutritional intervention with yogurt was conducted on a group of patients with AN and on a group of healthy adolescents (HA). In total, 16 AN patients and 16 HA consumed 375 g/d of yogurt containing L. bulgaricus and S. thermophilus (groups AN-y and HA-y, respectively). The control groups for AN patients (n = 14) and healthy subjects (n = 19) consumed 400 ml/d of semi-skimmed milk (groups AN-c and HA-c, respectively). Blood lymphocyte subsets were assessed by flow cytometry and the in vitro production of IL-2, IFN-γ, IL-1, IL-6 and TNF-α by PHA-stimulated PBMC was measured by ELISA. Results A significant combined effect of time and nutritional intervention was found for the CD8+ subset and IFN-γ production, both in HA and AN patients. The CD8+ subset showed a significant increase after 10 weeks in HA-c and AN-c. As a consequence, the CD4+/CD8+ ratio was significantly lower in AN-c than in AN-y after treatment. A significant increase in IFN-γ production was found after yogurt intake in AN-y, while it decreased significantly in AN-c. Conclusion The findings suggest that the inclusion of yogurt in the refeeding therapy of AN patients may exert positive effects on the immunological markers related to the nutritional status of these patients, such as the CD4+/CD8+ ratio and the production of IFN-γ by lymphocytes.