Examinando por Autor "Orellana, Ariel"
Mostrando 1 - 19 de 19
Resultados por página
Opciones de ordenación
Ítem A Rapid and Efficient Method for Purifying High Quality Total RNA from Peaches (Prunus persica) for Functional Genomics Analyses(Sociedad de Biología de Chile, 2005) Meissel, Lee; Fonseca, Beatriz; Gonzalez, Susana; Baeza-Yates, Ricardo; Cambiazo, Veronica; Campos, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Retamales, Julio; Silva, HermanPrunus persica has been proposed as a genomic model for deciduous trees and the Rosaceae family. Optimized protocols for RNA isolation are necessary to further advance studies in this model species such that functional genomics analyses may be performed. Here we present an optimized protocol to rapidly and efficiently purify high quality total RNA from peach fruits (Prunus persica). Isolating high-quality RNA from fruit tissue is often difficult due to large quantities of polysaccharides and polyphenolic compounds that accumulate in this tissue and co-purify with the RNA. Here we demonstrate that a modified version of the method used to isolate RNA from pine trees and the woody plant Cinnamomun tenuipilum is ideal for isolating high quality RNA from the fruits of Prunus persica. This RNA may be used for many functional genomic based experiments such as RT-PCR and the construction of large-insert cDNA libraries.Ítem Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality(BMC, 2009-09-10) Vizoso, Paula; Meisel, Lee A.; Tittarelli, Andrés; Latorre, Mariano; Saba, Juan; Caroca, Rodrigo; Maldonado, Jonathan; Cambiazo, Veronica; Campos-Vargas, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Silva, HermanBackground: Cold storage is used to inhibit peach fruit ripening during shipment to distant markets. However, this cold storage can negatively affect the quality of the fruit when it is ripened, resulting in disorders such as wooliness, browning or leathering. In order to understand the individual and combined biological effects that factors such as cold storage and ripening have on the fruit and fruit quality, we have taken a comparative EST transcript profiling approach to identify genes that are differentially expressed in response to these factors. Results: We sequenced 50,625 Expressed Sequence Tags (ESTs) from peach mesocarp (Prunus persica O'Henry variety) stored at four different postharvest conditions. A total of 10,830 Unigenes (4,169 contigs and 6,661 singletons) were formed by assembling these ESTs. Additionally, a collection of 614 full-length and 1,109 putative full-length cDNA clones within flanking loxP recombination sites was created. Conclusion: Statistically analyzing the EST population, we have identified genes that are differentially expressed during ripening, in response to cold storage or the combined effects of cold storage and ripening. Pair-wise comparisons revealed 197 contigs with at least one significant difference in transcript abundance between at least two conditions. Gene expression profile analyses revealed that the contigs may be classified into 13 different clusters of gene expression patterns. These clusters include groups of contigs that increase or decrease transcript abundance during ripening, in response to cold or ripening plus cold. These analyses have enabled us to statistically identify novel genes and gene clusters that are differentially expressed in response to post-harvest factors such as long-term cold storage, ripening or a combination of these two factors. These differentially expressed genes reveal the complex biological processes that are associated with these factors, as well as a large number of putative gene families that may participate differentially in these processes. In particular, these analyzes suggest that woolly fruits lack the increased boost of metabolic processes necessary for ripening. Additionally, these results suggest that the mitochondria and plastids play a major role in these processes. The EST sequences and full-length cDNA clones developed in this work, combined with the large population of differentially expressed genes may serve as useful tools and markers that will enable the scientific community to better define the molecular processes that affect fruit quality in response to post-harvest conditions and the organelles that participate in these processes. © 2009 Vizoso et al; licensee BioMed Central Ltd.Ítem Comparative study of two table grape varieties with contrasting texture during cold storage(MDPI AG, 2015-03) Ejsmentewicz, Troy; Balic, Iván; Sanhueza, Dayan; Barria, Romina; Meneses, Claudio; Orellana, Ariel; Prieto, Humberto; Defilippi, Bruno G.; Campos-Vargas, ReinaldoPostharvest softening of grape berries is one of the main problems affecting grape quality during export. Cell wall disassembly, especially of pectin polysaccharides, has been commonly related to fruit softening, but its influence has been poorly studied in grapes during postharvest life. In order to better understand this process, the Thompson seedless (TS) variety, which has significantly decreased berry texture after prolonged cold storage, was compared to NN107, a new table grape variety with higher berry firmness. Biochemical analysis revealed a greater amount of calcium in the cell wall of the NN107 variety and less reduction of uronic acids than TS during cold storage. In addition, the activity of polygalacturonase was higher in TS than NN107 berries; meanwhile pectin methylesterase activity was similar in both varieties. Polysaccharide analysis using carbohydrate gel electrophoresis (PACE) suggests a differential pectin metabolism during prolonged cold storage. Results revealed lower pectin fragments in TS after 60 days of cold storage and shelf life (SL) compared to 30 days of cold storage and 30 + SL, while NN107 maintained the same fragment profile across all time points evaluated. Our results suggest that these important differences in cell wall metabolism during cold storage could be related to the differential berry firmness observed between these contrasting table grape varieties. © 2015 by the authorsÍtem DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species(2023-12) Kobayashi, Sanae; E. Maldonado, Jonathan; Gaete, Alexis; Araya, Ingrid; Aguado‑Norese, Constanza; Cumplido, Nicolás; Espinoza, Alonso; Fernández, Edelmira; Gajardo, Felipe; González‑Ordenes, Felipe; Hauyon, Khantati; Maldonado, Piedad; Maldonado, Rodrigo; Pochet, Isabel; Riveros, Aníbal; Sandoval, Paula; Sepúlveda‑González, Ailynne; Stuardo, Camila; Tapia‑Reyes, Patricio; Thornton, Carolina; Undurraga, Soledad; Varas, Macarena; Valdivieso, Camilo; Earwig, School; Genome Consortium, Rodrigo A. Gutiérrez; Orellana, Ariel; Montecino, Martín; Maass, Alejandro; González, Mauricio; L. Allende, Miguel; Hodar, Christian; Irles, PaulaBackground: Despite representing the largest fraction of animal life, the number of insect species whose genome has been sequenced is barely in the hundreds. The order Dermaptera (the earwigs) suffers from a lack of genomic information despite its unique position as one of the basally derived insect groups and its importance in agroecosystems. As part of a national educational and outreach program in genomics, a plan was formulated to engage the participation of high school students in a genome sequencing project. Students from twelve schools across Chile were instructed to capture earwig specimens in their geographical area, to identify them and to provide material for genome sequencing to be carried out by themselves in their schools. Results: The school students collected specimens from two cosmopolitan earwig species: Euborellia annulipes (Fam. Anisolabididae) and Forficula auricularia (Fam. Forficulidae). Genomic DNA was extracted and, with the help of scientific teams that traveled to the schools, was sequenced using nanopore sequencers. The sequence data obtained for both species was assembled and annotated. We obtained genome sizes of 1.18 Gb (F. auricularia) and 0.94 Gb (E. annulipes) with the number of predicted protein coding genes being 31,800 and 40,000, respectively. Our analysis showed that we were able to capture a high percentage (≥ 93%) of conserved proteins indicating genomes that are useful for comparative and functional analysis. We were also able to characterize structural elements such as repetitive sequences and non-coding RNA genes. Finally, functional categories of genes that are overrepresented in each species suggest important differences in the process underlying the formation of germ cells, and modes of reproduction between them, features that are one of the distinguishing biological properties that characterize these two distant families of Dermaptera. Conclusions: This work represents an unprecedented instance where the scientific and lay community have come together to collaborate in a genome sequencing project. The versatility and accessibility of nanopore sequencers was key to the success of the initiative. We were able to obtain full genome sequences of two important and widely distributed species of insects which had not been analyzed at this level previously. The data made available by the project should illuminate future studies on the Dermaptera. © 2023, The Author(s).Ítem ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis(Nature Research, 2012) Ding, Zhaojun; Wang, Bangjun; Moreno, Ignacio; Duplá Ková, Nikoleta; Simon, Sibu; Carraro, Nicola; Reemmer, Jesica; Pě Nčí K, Aleš; Chen, Xu; Tejos, Ricardo; SkÅpa, Petr; Pollmann, Stephan; Mravec, Jozef; Petrá Š Ek, Jan; ZaÅimalova, Eva; Honys, David; Rolčí K, Jakub; Murphy, Angus; Orellana, Ariel; Geisler, Markus; Friml, JiříAuxin is a key coordinative signal required for many aspects of plant development and its levels are controlled by auxin metabolism and intercellular auxin transport. Here we find that a member of PIN auxin transporter family, PIN8 is expressed in male gametophyte of Arabidopsis thaliana and has a crucial role in pollen development and functionality. Ectopic expression in sporophytic tissues establishes a role of PIN8 in regulating auxin homoeostasis and metabolism. PIN8 co-localizes with PIN5 to the endoplasmic reticulum (ER) where it acts as an auxin transporter. Genetic analyses reveal an antagonistic action of PIN5 and PIN8 in the regulation of intracellular auxin homoeostasis and gametophyte as well as sporophyte development. Our results reveal a role of the auxin transport in male gametophyte development in which the distinct actions of ER-localized PIN transporters regulate cellular auxin homoeostasis and maintain the auxin levels optimal for pollen development and pollen tube growth. © 2012 Macmillan Publishers Limited. All rights reserved.Ítem Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes(BioMed Central Ltd, 2024-12) Morales, Pamela; Gajardo, Felipe; Valdivieso, Camilo; Valladares, Moisés A.; Di Genova, Alex; Orellana, Ariel; Gutiérrez, Rodrigo A.; González, Mauricio; Montecino, Martin; Maass, Alejandro; Méndez, Marco A.; Allende, Miguel L.Background: To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. Results: We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. Conclusions: The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape. © The Author(s) 2024.Ítem GoSAMTs are required for pectin methyl-esterification and mucilage release in seed coat epidermal cells(Frontiers Media S.A., 2023-01) Parra-Rojas, Juan Pablo; Sepúlveda-Orellana, Pablo; Sanhueza, Dayan; Salinas-Grenet, Hernán; Temple, Henry; Dupree, Paul; Saez-Aguayo, Susana; Orellana, ArielIntroduction: GoSAMTs play a role in the methylation of polysaccharides synthesized by the Golgi. Pectin homogalacturonan (HG) methyl-esterification is essential for the proper function of this polysaccharide in cell walls. In order to better understand the role of GoSAMTs in HG biosynthesis, we analyzed mucilage methyl-esterification in gosamt mutants. Methods: To determine the function of GoSAMT1 and GoSAMT2 in HG methyl-esterification we utilized epidermal cells of seed coats, as these structures produce mucilage, which is a pectic matrix. We evaluated differences in seed surface morphology and quantified mucilage release. We measured methanol release, and used antibodies and confocal microscopy to analyze HG methyl-esterification in mucilage. Results: We observed morphological differences on the seed surface and delayed, uneven mucilage release in gosamt1-1gosamt2-1 double mutants. We also found changes in the distal wall length indicating abnormal cell wall breakage in this double mutant. Using methanol release and immunolabeling, we confirmed that GoSAMT1 and GoSAMT2 are involved in HG methyl-esterification in mucilage. However, we did not find evidence of decreasing HG in the gosamt mutants. Confocal microscopy analyses detected different patterns in the adherent mucilage and a greater number of low-methyl-esterified domains near the seed coat surface, which correlates with a greater number of “egg-box” structures in this region. We also detected a shift in the partitioning between the Rhamnogalacturonan-I soluble and adherent layers of the double mutant, which correlated with increased amounts of arabinose and arabinogalactan-protein in the adherent mucilage. Discussion: The results show that the HG synthesized in gosamt mutant plants is less methyl esterified, resulting in more egg-box structures, which stiffen the cell walls in epidermal cells and change the rheological properties of the seed surface. The increased amounts of arabinose and arabinogalactan-protein in adherent mucilage, also suggests that compensation mechanisms were triggered in the gosamt mutants. Copyright © 2023 Parra-Rojas, Sepúlveda-Orellana, Sanhueza, Salinas-Grenet, Temple, Dupree, Saez-Aguayo and Orellana.Ítem PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis(Blackwell Publishing Ltd, 2016-07) Sibu, Simon; Skůpa, Petr; Viaene, Tom; Zwiewka, Marta; Tejos, Ricardo; Klíma, Petr; Čarná, Mária; Rolčík, Jakub; De Rycke, Riet; Moreno, Ignacio; Dobrev, Petre I.; Orellana, Ariel; Zažímalová, Eva; Friml, JiříSummary Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport.Ítem Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE)(BMC, 2010-01-18) Nilo, Ricardo; Saffie, Carlos; Lilley, Kathryn; Baeza-Yates, Ricardo; Cambiazo, Verónica; Campos-Vargas, Reinaldo; González, Mauricio; Meisel, Lee A.; Retamales, Julio; Silva, Herman; Orellana, ArielBackground: Peach fruit undergoes a rapid softening process that involves a number of metabolic changes. Storing fruit at low temperatures has been widely used to extend its postharvest life. However, this leads to undesired changes, such as mealiness and browning, which affect the quality of the fruit. In this study, a 2-D DIGE approach was designed to screen for differentially accumulated proteins in peach fruit during normal softening as well as under conditions that led to fruit chilling injury.Results: The analysis allowed us to identify 43 spots -representing about 18% of the total number analyzed- that show statistically significant changes. Thirty-nine of the proteins could be identified by mass spectrometry. Some of the proteins that changed during postharvest had been related to peach fruit ripening and cold stress in the past. However, we identified other proteins that had not been linked to these processes. A graphical display of the relationship between the differentially accumulated proteins was obtained using pairwise average-linkage cluster analysis and principal component analysis. Proteins such as endopolygalacturonase, catalase, NADP-dependent isocitrate dehydrogenase, pectin methylesterase and dehydrins were found to be very important for distinguishing between healthy and chill injured fruit. A categorization of the differentially accumulated proteins was performed using Gene Ontology annotation. The results showed that the 'response to stress', 'cellular homeostasis', 'metabolism of carbohydrates' and 'amino acid metabolism' biological processes were affected the most during the postharvest.Conclusions: Using a comparative proteomic approach with 2-D DIGE allowed us to identify proteins that showed stage-specific changes in their accumulation pattern. Several proteins that are related to response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism were detected as being differentially accumulated. Finally, a significant proportion of the proteins identified had not been associated with softening, cold storage or chilling injury-altered fruit before; thus, comparative proteomics has proven to be a valuable tool for understanding fruit softening and postharvest. © 2010 Nilo et al; licensee BioMed Central Ltd.Ítem SARS-CoV-2 infection in asymptomatic healthcare workers at a clinic in Chile(Public Library of Science, 2021-01) Olmos, Claudio; Campaña, Gonzalo; Monreal, Victor; Pidal, Paola; Sanchez, Nannet; Airola, Constanza; Sanhueza, Dayan; Tapia, Patricio; Muñoz, Ana María; Corvalan, Felipe; Meneses, Claudio; Orellana, Ariel; Montecino, Martin; Arriagada, Gloria; Bustos, Fernando JoseAsymptomatic SARS-CoV-2 infection of healthcare workers (HCWs) has been reported as a key player in the nosocomial spreading of COVID-19. Early detection of infected HCWs can prevent spreading of the virus in hospitals among HCWs and patients. We conducted a cross-sectional study to determine the asymptomatic infection of HCWs in a private clinic in the city of Santiago, Chile. Our study was conducted during a period of 5 weeks at the peak of transmission of SARS-CoV-2 in Chile. Nasopharyngeal samples were obtained from 413 HCWs and tested for the presence of SARS-CoV-2 using RT-qPCR. We found that a 3.14% of HCWs were positive for the presence of SARS-CoV-2 (14/413). Out of these, 7/14 were completely asymptomatic and did not develop symptoms within 3 weeks of testing. Sequencing of viral genomes showed the predominance of the GR clade; however, sequence comparison demonstrated numerous genetic differences among them suggesting community infection as the main focus of transmission among HCWs. Our study demonstrates that the protocols applied to protect HCWs and patients have been effective as no infection clusters due to asymptomatic carriers were found in the clinic. Together, these data suggest that infection with SARS-CoV-2 among HCWs of this health center is not nosocomial. © 2021 Olmos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Ítem The Arabidopsis Golgi-localized GDP-L-fucose transporter is required for plant development(NATURE PUBLISHING GROUP, 2016-07) Rautengarten, Carsten; Ebert, Berit; Liu, Lifeng; Stonebloom, Solomon; Smith-Moritz, Andreia M.; Pauly, Markus; Orellana, Ariel; Scheller, Henrik Vibe; Heazlewood, Joshua L.Nucleotide sugar transport across Golgi membranes is essential for the luminal biosynthesis of glycan structures. Here we identify GDP-fucose transporter 1 (GFT1), an Arabidopsis nucleotide sugar transporter that translocates GDP-L-fucose into the Golgi lumen. Using proteo-liposome-based transport assays, we show that GFT preferentially transports GDP-L-fucose over other nucleotide sugars in vitro, while GFT1-silenced plants are almost devoid of L-fucose in cell wall-derived xyloglucan and rhamnogalacturonan II. Furthermore, these lines display reduced L-fucose content in N-glycan structures accompanied by severe developmental growth defects. We conclude that GFT1 is the major nucleotide sugar transporter for import of GDP-L-fucose into the Golgi and is required for proper plant growth and development.Ítem The dynamic of the splicing of bZIP60 and the proteins encoded by the spliced and unspliced mRNAs reveals some unique features during the activation of UPR in Arabidopsis thaliana(Public Library of Science, 2015-04) Parra-Rojas, Juan; Moreno, Adrian; Mitina, Irina; Orellana, ArielThe unfolded protein response (UPR) is a signaling pathway that is activated when the workload of the endoplasmic reticulum (ER) is surpassed. IRE1 is a sensor involved in triggering the UPR and plays a key role in the unconventional splicing of an mRNA leading to the formation of a transcription factor that up-regulates the transcription of genes that play a role in restoring the homeostasis in the ER. In plants, bZIP60 is the substrate for IRE1; however, questions such as what is the dynamics of the splicing of bZIP60 and the fate of the proteins encoded by the spliced and unspliced forms of the mRNA, remain unanswered. In the present work, we analyzed the processing of bZIP60 by determining the levels of the spliced form mRNA in plants exposed to different conditions that trigger UPR. The results show that induction of ER stress increases the content of the spliced form of bZIP60 (bZIP60s) reaching a maximum, that depending on the stimuli, varied between 30 min or 2 hrs. In most cases, this was followed by a decrease in the content. In contrast to other eukaryotes, the splicing never occurred to full extent. The content of bZIP60s changed among different organs upon induction of the UPR suggesting that splicing is regulated differentially throughout the plant. In addition, we analyzed the distribution of a GFP-tagged version of bZIP60 when UPR was activated. A good correlation between splicing of bZIP60 and localization of the protein in the nucleus was observed. No fluorescence was observed under basal conditions, but interestingly, the fluorescence was recovered and found to co-localize with an ER marker upon treatment with an inhibitor of the proteasome. Our results indicate that the dynamics of bZIP60, both the mRNA and the protein, are highly dynamic processes which are tissue-specific and stimulus-dependent. © 2015 Parra-Rojas et al.Ítem The physiological role of the unfolded protein response in plants(Sociedad de Biología de Chile, 2011) Moreno, Adrian; Orellana, ArielUnfolded protein response (UPR) is a signaling mechanism activated by misfolded protein accumulation in the endoplasmic reticulum. It is a widespread process that has been described in organisms ranging from yeasts to mammals. In recent years, our understanding of UPR signaling pathway in plants has advanced. Two transcription factors from Arabidopsis thaliana have been reported to function as the sensor/ transducer of this response (AtbZIP60 and AtbZIP28). They seem to be involved in both heat and biotic stress. Furthermore, overexpression of one of them (AtbZIP60) produces plants with a higher tolerance for salt stress, suggesting that this transcription factor may play a role in abiotic stress. Furthermore, some data suggest that crosstalk between genes involved in abiotic stress and UPR may also exist in plants. On the other hand, UPR is related to programmed cell death (PCD) in plants given that that triggering UPR results in induction of PCD-related genes. This article reviews the latest progress in understanding UPR signaling in plants and analyzes its relationship to key processes in plant physiology.Ítem The Root Hair Specific SYP123 Regulates the Localization of Cell Wall Components and Contributes to Rizhobacterial Priming of Induced Systemic Resistance(FRONTIERS MEDIA SA, 2016-07) Rodriguez-Furlán, Cecilia; Salinas-Grenet, Hernán; Sandoval, Omar; Recabarren, Camilo; Arraño-Salinas, Paulina; Soto-Alvear, Sylvana; Orellana, Ariel; Blanco-Herrera, FranciscaRoot hairs are important for nutrient and water uptake and are also critically involved the interaction with soil inhabiting microbiota. Root hairs are tubular-shaped outgrowths that emerge from trichoblasts. This polarized elongation is maintained and regulated by a robust mechanism involving the endomembrane secretory and endocytic system. Members of the syntaxin family of SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) in plants (SYP), have been implicated in regulation of the fusion of vesicles with the target membranes in both exocytic and endocytic pathways. One member of this family. SYP123, is expressed specifically in the root hairs and accumulated in the growing tip region. This study shows evidence of the SYP123 role in polarized trafficking using knockout insertional mutant plants. We were able to observe defects in the deposition of cell wall proline rich protein PRP3 and cell wall polysaccharides. In a complementary strategy, similar results were obtained using a plant expressing a dominant negative soluble version of SYP123 (SP2 fragment) lacking the transmembrane domain. The evidence presented indicates that SYP123 is also regulating PRP3 protein distribution by recycling by endocytosis. We also present evidence that indicates that SYP123 is necessary for the response of roots to plant growth promoting rhizobacterium (PGPR) in order to trigger trigger induced systemic response (ISR). Plants with a defective SYP123 function were unable to mount a systemic acquired resistance in response to bacterial pathogen infection and ISR upon interaction with rhizobacteria. These results indicated that SYP123 was involved in the polarized localization of protein and polysaccharides in growing root hairs and that this activity also contributed to the establishment of effective plant defense responses. Root hairs represent very plastic structures were many biotic and abiotic factors can affect the number, anatomy and physiology of root hairs. Here, we presented evidence that indicates that interactions with soil PGPR could be closely regulated by signaling involving secretory and/or endocytic trafficking at the root hair tip as a quick way to response to changing environmental conditions.Ítem The UDP-glucose: Glycoprotein glucosyltransferase (UGGT), a key enzyme in ER quality control, plays a significant role in plant growth as well as biotic and abiotic stress in Arabidopsis thaliana(BioMed Central Ltd., 2015-06) Blanco-Herrera, Francisca; Moreno, Adrián A.; Tapia, Rodrigo; Reyes, Francisca; Araya, Macarena; D'Alessio, Cecilia; Parodi, Armando; Orellana, ArielBackground: UDP-glucose: glycoprotein glucosyltransferase (UGGT) is a key player in the quality control mechanism (ER-QC) that newly synthesized glycoproteins undergo in the ER. It has been shown that the UGGT Arabidopsis orthologue is involved in ER-QC; however, its role in plant physiology remains unclear. Results: Here, we show that two mutant alleles in the At1g71220 locus have none or reduced UGGT activity. In wild type plants, the AtUGGT transcript levels increased upon activation of the unfolded protein response (UPR). Interestingly, mutants in AtUGGT exhibited an endogenous up-regulation of genes that are UPR targets. In addition, mutants in AtUGGT showed a 30 % reduction in the incorporation of UDP-Glucose into the ER suggesting that this enzyme drives the uptake of this substrate for the CNX/CRT cycle. Plants deficient in UGGT exhibited a delayed growth rate of the primary root and rosette as well as an alteration in the number of leaves. These mutants are more sensitive to pathogen attack as well as heat, salt, and UPR-inducing stressors. Additionally, the plants showed impairment in the establishment of systemic acquired resistance (SAR). Conclusions: These results show that a lack of UGGT activity alters plant vegetative development and impairs the response to several abiotic and biotic stresses. Moreover, our results uncover an unexpected role of UGGT in the incorporation of UDP-Glucose into the ER lumen in Arabidopsis thaliana. © Blanco-Herrera et al.Ítem Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight(BIOMED CENTRAL, 2016-04) Muñoz-Espinoza, Claudia; Di Genova, Alex; Correa, José; Silva, Romina; Maass, Alejandro; González-Agüero, Mauricio; Orellana, Ariel; Hinrichsen, PatricioBackground Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.Ítem Using genomics to improve fruit quality(Sociedad de Biología de Chile, 2013) Meneses, Claudio; Orellana, ArielNew fruit varieties are needed to satisfy consumers, and the industry is facing new challenges in order to respond to these demands. The emergence of genomic tools is releasing information on polymorphisms that can be utilized to expedite breeding processes in species that are difficult to breed, given the long periods of time required to get new varieties. The present review describes the current stages of the ongoing efforts that are being taken to apply these technologies to obtain varieties with improved fruit quality in species of the family Rosaceae.Ítem Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants(BioMed Central Ltd., 2014-01) Di Genova, Alex; Almeida, Andrea M.; Muñoz-Espinoza, Claudia; Vizoso, Paula; Travisany, Dante; Moraga, Carol; Pinto, Manuel; Hinrichsen, Patricio; Orellana, Ariel; Maass, AlejandroBackground: Grapevine (Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both wine and spirits as well as table grape and raisins. Wine and table grape cultivars represent two divergent germplasm pools with different origins and domestication history, as well as differential characteristics for berry size, cluster architecture and berry chemical profile, among others. ‘Sultanina’ plays a pivotal role in modern table grape breeding providing the main source of seedlessness. This cultivar is also one of the most planted for fresh consumption and raisins production. Given its importance, we sequenced it and implemented a novel strategy for the de novo assembly of its highly heterozygous genome. Results: Our approach produced a draft genome of 466 Mb, recovering 82% of the genes present in the grapevine reference genome; in addition, we identified 240 novel genes. A large number of structural variants and SNPs were identified. Among them, 45 (21 SNPs and 24 INDELs) were experimentally confirmed in ‘Sultanina’ and six SNPs in other 23 table grape varieties. Transposable elements corresponded to ca. 80% of the repetitive sequences involved in structural variants and more than 2,000 genes were affected in their structure by these variants. Some of these genes are likely involved in embryo development, suggesting that they may contribute to seedlessness, a key trait for table grapes. Conclusions: This work produced the first structural variants and SNPs catalog for grapevine, constituting a novel and very powerful tool for genomic studies in this key fruit crop, particularly useful to support marker assisted breeding in table grapes.Ítem Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans(Nature Publishing Group, 2019-12) Vidal, Elena A.; Moyano, Tomás C.; Bustos, Bernabé I.; Pérez-Palma, Eduardo; Moraga, Carol; Riveras, Eleodoro; Montecinos, Alejandro; Azócar, Lorena; Soto, Daniela C.; Vidal, Mabel; Genova, Alex Di; Puschel, Klaus; Nürnberg, Peter; Buch, Stephan; Hampe, Jochen; Allende, Miguel L.; Cambiazo, Verónica; González, Mauricio; Hodar, , Christian; Montecino, Martín; Muñoz-Espinoza, Claudia; Orellana, Ariel; Reyes-Jara, Angélica; Travisany, Dante; Vizoso, Paula; Moraga, Mauricio; Eyheramendy, Susana; Maass, Alejandro; Ferrari, Giancarlo V. De; Miquel, Juan Francisco; Gutiérrez, Rodrigo A.Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 10 6 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations. © 2019, The Author(s).