FaMYB123 interacts with FabHLH3 to regulate the late steps of anthocyanin and flavonol biosynthesis during ripening.

In this work, we identified and functionally characterized the strawberry (Fragaria × ananassa) R2R3 MYB transcription factor FaMYB123. As in most genes associated with organoleptic properties of ripe fruit, FaMYB123 expression is ripening-related, receptacle-specific, and antagonistically regulated by ABA and auxin. Knockdown of FaMYB123 expression by RNAi in ripe strawberry fruit receptacles downregulated the expression of enzymes involved in the late steps of anthocyanin/flavonoid biosynthesis. Transgenic fruits showed a parallel decrease in the contents of total anthocyanin and flavonoid, especially malonyl derivatives of pelargonidin and cyanidins. The decrease was concomitant with accumulation of proanthocyanin, propelargonidins, and other condensed tannins associated mainly with green receptacles. Potential coregulation between FaMYB123 and FaMYB10, which may act on different sets of genes for the enzymes involved in anthocyanin production, was explored. FaMYB123 and FabHLH3 were found to interact and to be involved in the transcriptional activation of FaMT1, a gene responsible for the malonylation of anthocyanin components during ripening. Taken together, these results demonstrate that FaMYB123 regulates the late steps of the flavonoid pathway in a specific manner. In this study, a new function for an R2R3 MYB transcription factor, regulating the expression of a gene that encodes a malonyltransferase, has been elucidated.This work was funded by the Spanish Ministerio de Ciencia e Innovacion (AGL2014-55784-C2-2-R and AGL2017-86531-C2-2-R). FJMR is supported by a ‘Margarita Salas’ post-doctoral fellowship (UCOR02MS) from the University of Cordoba (Requalification of the Spanish university system) from the Ministry of Universities financed by the European Union (NexGenerationEU). FJMH is supported by a ‘Juan de la Cierva-Incorporacion’ fellowship (IJC2020- 045526-I), funded by MCIN/AEI/10.13039/501100011033 and the European Union ‘NextGenerationEU’/PRTR. AR-F and SA are on the European Union’s Horizon 2020 Research and Innovation Program, Project PlantaSYST (SGA-CSA No. 739582 under FPA No. 664620). The authors thank Dr. Gema Garc ıa from the Microscopy Unit of UCAIB-IMIBIC for technical help with the microscope. Funding for open access charge: University of Cordoba/CBUA.S

Bacteria-inducing legume nodules involved in the improvement of plant growth, health and nutrition

Bacteria-inducing legume nodules are known as rhizobia and belong to the class Alphaproteobacteria and Betaproteobacteria. They promote the growth and nutrition of their respective legume hosts through atmospheric nitrogen fixation which takes place in the nodules induced in their roots or stems. In addition, rhizobia have other plant growth-promoting mechanisms, mainly solubilization of phosphate and production of indoleacetic acid, ACC deaminase and siderophores. Some of these mechanisms have been reported for strains of rhizobia which are also able to promote the growth of several nonlegumes, such as cereals, oilseeds and vegetables. Less studied are the mechanisms that have the rhizobia to promote the plant health; however, these bacteria are able to exert biocontrol of some phytopathogens and to induce the plant resistance. In this chapter, we revised the available data about the ability of the legume nodule-inducing bacteria for improving the plant growth, health and nutrition of both legumes and nonlegumes. These data showed that rhizobia meet all the requirements of sustainable agriculture to be used as bio-inoculants allowing the total or partial replacement of chemicals used for fertilization or protection of crops

Effect of the application of the ABA biosynthesis inhibitor NDGA on the expression of the strawberry ripening-related <i>NAC</i> genes determined by qRT-PCR.

<p>After treatment, relative expression values were calculated in relation to untreated control C_t, which was assigned an arbitrary value equal to the unity. Control: G-W fruit injected with H₂O; NDGA: G-W fruits injected with NDGA (100 μM). Both samples were harvested 8 days after beginning of treatment. Mean values ± SD of three independent experiments are shown. Student’s t-test determined statistical significance with respect to reference sample. (***) p-value < 0.001.</p

Developmental expression of the strawberry ripening-related <i>NAC</i> genes in fruit receptacles.

<p>qRT-PCR results were obtained using specific primers for <i>NAC</i> genes. Quantification is based on C_t values. Relative expression values were calculated in relation to G1 fruits receptacles C_t value in all cases, which was assigned an arbitrary value equal to unity. G1, green stage 1; G3, green stage 3; W, white stage; R, red stage; OR, overripe stage and SE, senescent stage. Data are a mean of three independent experiments. One-way ANOVA determined statistical significance. Letters indicate significant differences (p < 0.05, Scheffe post-hoc test).</p

Ligation Group (FvH) distribution of the curated collection of the strawberry <i>NAC</i> genes.

<p>The putative <i>NAC</i> genes were renamed from <i>FvNAC001</i> to <i>FvNAC112</i>, based on their placement into the Ligation Groups (FvH) or pseudo-chromosomes. The lengths of the drawings are proportional to the actual pseudo-chromosome lengths. FvH1 has a length of 24.25Mbp nucleotides and this can be used as a reference. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0196953#pone.0196953.s007" target="_blank">S7 Table</a> shows the correspondence between the current gene names provided in the <i>Fragaria</i> genome database and these newly assigned and ordered names, and the actual length in bases of all pseudo-chromosomes and contigs of the current V4.0.a1 of the genome.</p

Genome-wide analysis of the NAC transcription factor family and their expression during the development and ripening of the <i>Fragaria</i> × <i>ananassa</i> fruits

<div><p>NAC proteins are a family of transcription factors which have a variety of important regulatory roles in plants. They present a very well conserved group of NAC subdomains in the N-terminal region and a highly variable domain at the C-terminus. Currently, knowledge concerning NAC family in the strawberry plant remains very limited. In this work, we analyzed the NAC family of <i>Fragaria vesca</i>, and a total of 112 NAC proteins were identified after we curated the annotations from the version 4.0.a1 genome. They were placed into the ligation groups (pseudo-chromosomes) and described its physicochemical and genetic features. A microarray transcriptomic analysis showed six of them expressed during the development and ripening of the <i>Fragaria</i> x <i>ananassa</i> fruit. Their expression patterns were studied in fruit (receptacle and achenes) in different stages of development and in vegetative tissues. Also, the expression level under different hormonal treatments (auxins, ABA) and drought stress was investigated. In addition, they were clustered with other NAC transcription factor with known function related to growth and development, senescence, fruit ripening, stress response, and secondary cell wall and vascular development. Our results indicate that these six strawberry NAC proteins could play different important regulatory roles in the process of development and ripening of the fruit, providing the basis for further functional studies and the selection for NAC candidates suitable for biotechnological applications.</p></div

Developmental expression of the strawberry ripening-related <i>NAC</i> genes in fruit achenes determined by qRT-PCR.

<p>Relative expression values were calculated in relation to the fruit receptacle C_t at the G1 stage in all cases, which was assigned an arbitrary value equal to unity. G1 Rec: fruit receptacles at the G1 stage; SE Rec: fruit receptacles at the ripen stage; G1 Ach: achenes of G1 fruits; G3 Ach: achenes of G3 fruits; W Ach: achenes of white fruits; and R Ach: achenes of ripen strawberries. Data are a mean of three independent experiments. One-way ANOVA determined statistical significance. Letters indicate significant differences (p < 0.05, Scheffe post-hoc test).</p

Discovering HIV related information by means of association rules and machine learning

Acquired immunodeficiency syndrome (AIDS) is still one of the main health problems worldwide. It is therefore essential to keep making progress in improving the prognosis and quality of life of affected patients. One way to advance along this pathway is to uncover connections between other disorders associated with HIV/AIDS-so that they can be anticipated and possibly mitigated. We propose to achieve this by using Association Rules (ARs). They allow us to represent the dependencies between a number of diseases and other specific diseases. However, classical techniques systematically generate every AR meeting some minimal conditions on data frequency, hence generating a vast amount of uninteresting ARs, which need to be filtered out. The lack of manually annotated ARs has favored unsupervised filtering, even though they produce limited results. In this paper, we propose a semi-supervised system, able to identify relevant ARs among HIV-related diseases with a minimal amount of annotated training data. Our system has been able to extract a good number of relationships between HIV-related diseases that have been previously detected in the literature but are scattered and are often little known. Furthermore, a number of plausible new relationships have shown up which deserve further investigation by qualified medical experts

COVID-19 in hospitalized HIV-positive and HIV-negative patients : A matched study

CatedresObjectives: We compared the characteristics and clinical outcomes of hospitalized individuals with COVID-19 with [people with HIV (PWH)] and without (non-PWH) HIV co-infection in Spain during the first wave of the pandemic. Methods: This was a retrospective matched cohort study. People with HIV were identified by reviewing clinical records and laboratory registries of 10 922 patients in active-follow-up within the Spanish HIV Research Network (CoRIS) up to 30 June 2020. Each hospitalized PWH was matched with five non-PWH of the same age and sex randomly selected from COVID-19@Spain, a multicentre cohort of 4035 patients hospitalized with confirmed COVID-19. The main outcome was all-cause in-hospital mortality. Results: Forty-five PWH with PCR-confirmed COVID-19 were identified in CoRIS, 21 of whom were hospitalized. A total of 105 age/sex-matched controls were selected from the COVID-19@Spain cohort. The median age in both groups was 53 (Q1-Q3, 46-56) years, and 90.5% were men. In PWH, 19.1% were injecting drug users, 95.2% were on antiretroviral therapy, 94.4% had HIV-RNA < 50 copies/mL, and the median (Q1-Q3) CD4 count was 595 (349-798) cells/μL. No statistically significant differences were found between PWH and non-PWH in number of comorbidities, presenting signs and symptoms, laboratory parameters, radiology findings and severity scores on admission. Corticosteroids were administered to 33.3% and 27.4% of PWH and non-PWH, respectively (P = 0.580). Deaths during admission were documented in two (9.5%) PWH and 12 (11.4%) non-PWH (P = 0.800). Conclusions: Our findings suggest that well-controlled HIV infection does not modify the clinical presentation or worsen clinical outcomes of COVID-19 hospitalization