Publications by authors named "Jonathan Maldonado"

30 Publications

  • Page 1 of 1

Tomato Cultivars With Variable Tolerances to Water Deficit Differentially Modulate the Composition and Interaction Patterns of Their Rhizosphere Microbial Communities.

Front Plant Sci 2021 13;12:688533. Epub 2021 Jul 13.

Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.

Since drought is the leading environmental factor limiting crop productivity, and plants have a significant impact in defining the assembly of plant-specific microbial communities associated with roots, we aimed to determine the effect of thoroughly selected water deficit tolerant and susceptible cultivars on their rhizosphere microbiome and compared their response with plant-free soil microbial communities. We identified a total of 4,248 bacterial and 276 fungal different operational taxonomic units (OTUs) in soils by massive sequencing. We observed that tomato cultivars significantly affected the alpha and beta diversity of their bacterial rhizosphere communities but not their fungal communities compared with bulk soils (BSs), showing a plant effect exclusively on the bacterial soil community. Also, an increase in alpha diversity in response to water deficit of both bacteria and fungi was observed in the susceptible rhizosphere (SRz) but not in the tolerant rhizosphere (TRz) cultivar, implying a buffering effect of the tolerant cultivar on its rhizosphere microbial communities. Even though water deficit did not affect the microbial diversity of the tolerant cultivar, the interaction network analysis revealed that the TRz microbiota displayed the smallest and least complex soil network in response to water deficit with the least number of connected components, nodes, and edges. This reduction of the TRz network also correlated with a more efficient community, reflected in increased cooperation within kingdoms. Furthermore, we identified some specific bacteria and fungi in the TRz in response to water deficit, which, given that they belong to taxa with known beneficial characteristics for plants, could be contributing to the tolerant phenotype, highlighting the metabolic bidirectionality of the holobiont system. Future assays involving characterization of root exudates and exchange of rhizospheres between drought-tolerant and susceptible cultivars could determine the effect of specific metabolites on the microbiome community and may elucidate their functional contribution to the tolerance of plants to water deficit.
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http://dx.doi.org/10.3389/fpls.2021.688533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8313812PMC
July 2021

RNAseq reveals different transcriptomic responses to GA in early and midseason varieties before ripening initiation in sweet cherry fruits.

Sci Rep 2021 Jun 22;11(1):13075. Epub 2021 Jun 22.

Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, 7830490, Macul, Chile.

Gibberellin (GA) negatively affects color evolution and other ripening-related processes in non-climacteric fruits. The bioactive GA, gibberellic acid (GA), is commonly applied at the light green-to-straw yellow transition to increase firmness and delay ripening in sweet cherry (Prunus avium L.), though causing different effects depending on the variety. Recently, we reported that GA delayed the IAD parameter (a ripening index) in a mid-season variety, whereas GA did not delay IAD but reduced it at ripeness in an early-season variety. To further explore this contrasting behavior between varieties, we analyzed the transcriptomic responses to GA applied on two sweet cherry varieties with different maturity time phenotypes. At harvest, GA produced fruits with less color in both varieties. Similar to our previous report, GA delayed fruit color initiation and IAD only in the mid-season variety and reduced IAD at harvest only in the early-season variety. RNA-seq analysis of control- and GA-treated fruits revealed that ripening-related categories were overrepresented in the early-season variety, including 'photosynthesis' and 'auxin response'. GA also changed the expression of carotenoid and abscisic acid (ABA) biosynthetic genes in this variety. In contrast, overrepresented categories in the mid-season variety were mainly related to metabolic processes. In this variety, some PP2Cs putative genes were positively regulated by GA, which are negative regulators of ABA responses, and MYB44-like genes (putative repressors of PP2Cs expression) were downregulated. These results show that GA differentially modulates the transcriptome at the onset of ripening in a variety-dependent manner and suggest that GA impairs ripening through the modification of ripening associated gene expression only in the early-season variety; whereas in the mid-season variety, control of the ripening timing may occur through the PP2C gene expression regulation. This work contributes to the understanding of the role of GA in non-climacteric fruit ripening.
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http://dx.doi.org/10.1038/s41598-021-92080-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8219793PMC
June 2021

A comprehensive study of mobility functioning information in clinical notes: Entity hierarchy, corpus annotation, and sequence labeling.

Int J Med Inform 2021 03 24;147:104351. Epub 2020 Dec 24.

National Institutes of Health Clinical Center, Bethesda, MD‬, United States.

Background: Secondary use of Electronic Health Records (EHRs) has mostly focused on health conditions (diseases and drugs). Function is an important health indicator in addition to morbidity and mortality. Nevertheless, function has been overlooked in accessing patients' health status. The World Health Organization (WHO)'s International Classification of Functioning, Disability and Health (ICF) is considered the international standard for describing and coding function and health states. We pioneer the first comprehensive analysis and identification of functioning concepts in the Mobility domain of the ICF.

Results: Using physical therapy notes at the National Institutes of Health's Clinical Center, we induced a hierarchical order of mobility-related entities including 5 entities types, 3 relations, 8 attributes, and 33 attribute values. Two domain experts manually curated a gold standard corpus of 14,281 nested entity mentions from 400 clinical notes. Inter-annotator agreement (IAA) of exact matching averaged 92.3 % F1-score on mention text spans, and 96.6 % Cohen's kappa on attributes assignments. A high-performance Ensemble machine learning model for named entity recognition (NER) was trained and evaluated using the gold standard corpus. Average F1-score on exact entity matching of our Ensemble method (84.90 %) outperformed popular NER methods: Conditional Random Field (80.4 %), Recurrent Neural Network (81.82 %), and Bidirectional Encoder Representations from Transformers (82.33 %).

Conclusions: The results of this study show that mobility functioning information can be reliably captured from clinical notes once adequate resources are provided for sequence labeling methods. We expect that functioning concepts in other domains of the ICF can be identified in similar fashion.
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http://dx.doi.org/10.1016/j.ijmedinf.2020.104351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8104034PMC
March 2021

Single-stage Simultaneous Retrograde and Antegrade Endoscopic Treatment of Giant Prostatic and Bladder Urethral Calculi.

Urology 2020 Nov 25;145:299-300. Epub 2020 Jul 25.

Department of Urology, Loma Linda University Health, Loma Linda, CA.

Introduction: Calculi encountered in the lower urinary tract typically reside within the bladder, less often in the urethra. In this video, we present a minimally invasive endoscopic approach for removal of the largest total stone volume in the lower urinary tract reported in the literature to date.

Methods: A 25-year-old male (body mass index 61 kg/m) with neurogenic bladder presented with urosepsis and acute kidney injury secondary to obstructive uropathy. Computerized tomography (CT) of the abdomen and pelvis demonstrated bilateral severe hydroureteronephrosis, a 4.2-cm bladder stone, and 3 urethral stones, including a 7.7-cm prostatic urethral stone and 2 membranous urethral stones (Fig. 1). Urgent bilateral percutaneous nephrostomy tubes were placed. The patient elected for endoscopic management.

Results: The patient was placed in the supine lithotomy position. His buried penis and narrow urethra only accommodated a 16-French flexible cystoscope. Multiple stones were encountered in the membranous urethra. A 60-W SuperPulse Thulium Fiber laser at 2 J and 30 Hz was utilized to dust the urethral stones efficiently. Simultaneous ultrasound-guided percutaneous access into the bladder was obtained and ultrasonic lithotripsy via shockpulse was used to clear the bladder stone and prostatic stone from above. Total stone treatment time was 240 minutes. Suprapubic and urethral catheters were placed at the conclusion. Postoperative day 1 CT scan confirmed stone-free status and he was discharged postoperative day 2. Outpatient nephrostogram demonstrated patency of bilateral ureters and nephrostomy tubes were removed.

Conclusion: Higher morbidity procedures including open or laparoscopic approaches have been described for management of large lower urinary tract stones. In this video, we demonstrate a minimally invasive approach of combined simultaneous antegrade and retrograde lithotripsy to achieve a stone-free status in this morbidly obese and complicated patient.
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http://dx.doi.org/10.1016/j.urology.2020.07.022DOI Listing
November 2020

A de novo transcriptome analysis revealed that photomorphogenic genes are required for carotenoid synthesis in the dark-grown carrot taproot.

Mol Genet Genomics 2020 Nov 12;295(6):1379-1392. Epub 2020 Jul 12.

Facultad de Ciencias, Centro de Biología Molecular Vegetal, Universidad de Chile, Las Palmeras, 3425, Ñuñoa, Santiago, Chile.

Carotenoids are terpenoid pigments synthesized by all photosynthetic and some non-photosynthetic organisms. In plants, these lipophilic compounds are involved in photosynthesis, photoprotection, and phytohormone synthesis. In plants, carotenoid biosynthesis is induced by several environmental factors such as light including photoreceptors, such as phytochromes (PHYs) and negatively regulated by phytochrome interacting factors (PIFs). Daucus carota (carrot) is one of the few plant species that synthesize and accumulate carotenoids in the storage root that grows in darkness. Contrary to other plants, light inhibits secondary root growth and carotenoid accumulation suggesting the existence of new mechanisms repressed by light that regulate both processes. To identify genes induced by dark and repressed by light that regulate carotenoid synthesis and carrot root development, in this work an RNA-Seq analysis was performed from dark- and light-grown carrot roots. Using this high-throughput sequencing methodology, a de novo transcriptome model with 63,164 contigs was obtained, from which 18,488 were differentially expressed (DEG) between the two experimental conditions. Interestingly, light-regulated genes are preferably expressed in dark-grown roots. Enrichment analysis of GO terms with DEGs genes, validation of the transcriptome model and DEG analysis through qPCR allow us to hypothesize that genes involved in photomorphogenesis and light perception such as PHYA, PHYB, PIF3, PAR1, CRY2, FYH3, FAR1 and COP1 participate in the synthesis of carotenoids and carrot storage root development.
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http://dx.doi.org/10.1007/s00438-020-01707-4DOI Listing
November 2020

Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures.

Microorganisms 2020 Jun 24;8(6). Epub 2020 Jun 24.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7810000, Chile.

Autochthonous microorganisms are an important source of the distinctive metabolites that influence the chemical profile of wine. However, little is known about the diversity of fungal communities associated with grape musts, even though they are the source of local yeast strains with potential capacities to become starters during fermentation. By using internal transcribed spacer (ITS) amplicon sequencing, we identified the taxonomic structure of the yeast community in unfermented and fermented musts of a typical L. var. Sauvignon blanc from the Central Valley of Chile throughout two consecutive seasons of production. Unsurprisingly, represented the most abundant fungal genus in unfermented and fermented musts, mainly due to the contribution of (42.7%) and (80%). Unfermented musts were highly variable between seasons and showed higher values of fungal diversity than fermented musts. Since microbial physiological characterization is primarily achieved in culture, we isolated nine species belonging to six genera of fungi from the unfermented must samples. All isolates were characterized for their potential capacities to be used as new starters in wine. Remarkably, only could co-exist with a commercial strain under fermentative conditions, representing a feasible candidate strain for wine production.
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http://dx.doi.org/10.3390/microorganisms8060956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356840PMC
June 2020

Biochemical and Genomic Characterization of the Cypermethrin-Degrading and Biosurfactant-Producing Bacterial Strains Isolated from Marine Sediments of the Chilean Northern Patagonia.

Mar Drugs 2020 May 13;18(5). Epub 2020 May 13.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7810000, Chile.

Pesticides cause severe environmental damage to marine ecosystems. In the last ten years, cypermethrin has been extensively used as an antiparasitic pesticide in the salmon farming industry located in Northern Patagonia. The objective of this study was the biochemical and genomic characterization of cypermethrin-degrading and biosurfactant-producing bacterial strains isolated from cypermethrin-contaminated marine sediment samples collected in southern Chile (MS). Eleven strains were isolated by cypermethrin enrichment culture techniques and were identified by 16S rDNA gene sequencing analyses. The highest growth rate on cypermethrin was observed in four isolates (MS13, MS15a, MS16, and MS19) that also exhibited high levels of biosurfactant production. Genome sequence analyses of these isolates revealed the presence of genes encoding components of bacterial secondary metabolism, and the enzymes esterase, pyrethroid hydrolase, and laccase, which have been associated with different biodegradation pathways of cypermethrin. These novel cypermethrin-degrading and biosurfactant-producing bacterial isolates have a biotechnological potential for biodegradation of cypermethrin-contaminated marine sediments, and their genomes contribute to the understanding of microbial lifestyles in these extreme environments.
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http://dx.doi.org/10.3390/md18050252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281626PMC
May 2020

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment.

Sci Rep 2020 03 27;10(1):5560. Epub 2020 Mar 27.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.

The Atacama Desert is the most arid desert on Earth, focus of important research activities related to microbial biodiversity studies. In this context, metabolic characterization of arid soil bacteria is crucial to understand their survival strategies under extreme environmental stress. We investigated whether strain-specific features of two Microbacterium species were involved in the metabolic ability to tolerate/adapt to local variations within an extreme desert environment. Using an integrative systems biology approach we have carried out construction and comparison of genome-scale metabolic models (GEMs) of two Microbacterium sp., CGR1 and CGR2, previously isolated from physicochemically contrasting soil sites in the Atacama Desert. Despite CGR1 and CGR2 belong to different phylogenetic clades, metabolic pathways and attributes are highly conserved in both strains. However, comparison of the GEMs showed significant differences in the connectivity of specific metabolites related to pH tolerance and CO production. The latter is most likely required to handle acidic stress through decarboxylation reactions. We observed greater GEM connectivity within Microbacterium sp. CGR1 compared to CGR2, which is correlated with the capacity of CGR1 to tolerate a wider pH tolerance range. Both metabolic models predict the synthesis of pigment metabolites (β-carotene), observation validated by HPLC experiments. Our study provides a valuable resource to further investigate global metabolic adaptations of bacterial species to grow in soils with different abiotic factors within an extreme environment.
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http://dx.doi.org/10.1038/s41598-020-62130-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101325PMC
March 2020

Excision and Reconstruction for Urachal Adenocarcinoma: A Case Report With an Emphasis on Cosmesis.

Urology 2020 May 19;139:198-200. Epub 2020 Feb 19.

Department of Urology, Loma Linda University Health, Loma Linda, CA.

Objective: We report a urachal adenocarcinoma case managed surgically with two incisions and an emphasis on cosmesis while maintaining oncologic principles.

Introduction: Depending upon the cancer, excision of the urachal remnant and umbilectomy may require abdominal wall reconstruction and potentially could leave the patient with an altered anterior abdominal wall. Restoring function and cosmesis after surgery can be very important to oncologic quality of life. Therefore, we present a patient with urachal adenocarcinoma who underwent open partial cystectomy, urachal ligament excision with umbilectomy, and neo-umbilicoplasty via two incisions.

Conclusion: This case demonstrates the feasibility of performing an oncologically-sound operation for urachal adenocarcinoma while maintaining an emphasis on cosmesis.
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http://dx.doi.org/10.1016/j.urology.2020.02.011DOI Listing
May 2020

RNA-seq Analysis of Salt-Stressed Non Salt-Stressed Transcriptomes of Landrace R49.

Genes (Basel) 2019 12 16;10(12). Epub 2019 Dec 16.

Departamento de Producción Agrícola, Laboratorio de Genómica Funcional y Bioinformática, Universidad de Chile, Av. Santa Rosa 11315, Santiago 8820808, Chile.

Quinoa ( Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased with time. We report a strong transcriptional reprogramming of genes involved in biological processes like oxidation-reduction, response to stress and response to abscisic acid (ABA), and cell wall organization. Transcript analyses by real-time RT- qPCR supported the RNA-seq results and shed light on the contribution of roots and shoots to the overall transcriptional response. In addition, it revealed a time-dependent response in the expression of the analyzed DEGs, including a quick (within 1 h) response for some genes, suggesting a "stress-anticipatory preparedness" in this highly salt-tolerant genotype.
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http://dx.doi.org/10.3390/genes10121042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6947843PMC
December 2019

Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability.

Front Bioeng Biotechnol 2019 5;7:10. Epub 2019 Feb 5.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.

The Atacama Desert is a highly complex, extreme ecosystem which harbors microorganisms remarkable for their biotechnological potential. Here, a soil bacterial prospection was carried out in the high Altiplano region of the Atacama Desert (>3,800 m above sea level; m a.s.l.), where direct anthropogenic interference is minimal. We studied: (1) soil bacterial community composition using high-throughput sequencing of the 16S rRNA gene and (2) bacterial culturability, by using a soil extract medium (SEM) under a factorial design of three factors: temperature (15 and 30°C), nutrient content (high and low nutrient disposal) and oxygen availability (presence and absence). A total of 4,775 OTUs were identified and a total of 101 isolates were selected for 16S rRNA sequencing, 82 of them corresponded to unique or non-redundant sequences. To expand our view of the Altiplano landscape and to obtain a better representation of its microbiome, we complemented our Operational Taxonomic Units (OTUs) and isolate collection with data from other previous data from our group and obtained a merged set of OTUs and isolates that we used to perform our study. Taxonomic comparisons between culturable microbiota and metabarcoding data showed an overrepresentation of the phylum Firmicutes (44% of isolates vs. 2% of OTUs) and an underrepresentation of Proteobacteria (8% of isolates vs. 36% of OTUs). Within the Next Generation Sequencing (NGS) results, 33% of the OTUs were unknown up to genus, revealing an important proportion of putative new species in this environment. Biochemical characterization and analysis extracted from the literature indicated that an important number of our isolates had biotechnological potential. Also, by comparing our results with similar studies on other deserts, the Altiplano highland was most similar to a cold arid desert. In summary, our study contributes to expand the knowledge of soil bacterial communities in the Atacama Desert and complements the pipeline to isolate selective bacteria that could represent new potential biotechnological resources.
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http://dx.doi.org/10.3389/fbioe.2019.00010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371850PMC
February 2019

Transcriptome datasets from leaves and fruits of the sweet cherry cultivars 'Bing', 'Lapins' and 'Rainier'.

Data Brief 2019 Apr 22;23:103696. Epub 2019 Jan 22.

Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional, & Bioinformática, 820808 La Pintana, Santiago, Chile.

Sweet cherry fruits from different cultivars have different pre- and post-harvest qualities. Here we present the transcriptome profile datasets of leaves and mature fruits of three sweet cherry cultivars ('Bing', 'Lapin' and 'Rainier'). Using 454 GS-FLX technology (454 Life Sciences, Roche), transcriptomes of leaves and mature fruits were obtained from these cultivars. These transcriptome data sets are reported here.
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http://dx.doi.org/10.1016/j.dib.2019.01.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369327PMC
April 2019

Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils.

Sci Rep 2019 01 31;9(1):1042. Epub 2019 Jan 31.

FONDAP Center for Genome Regulation, Santiago, Chile.

The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native plant species of the Chilean Andean grasslands. We examined three soil compartments: the rhizosphere (bacteria firmly attached to the roots), the rhizosphere-surrounding soil (bacteria loosely attached to the roots) and the bulk soil (plant-free soil). The rhizosphere microbiome was in all cases the least diverse, exposing that the bulk soil was a more complex environment. Taxonomic analysis revealed an abrupt change between the rhizosphere and the rest of the non-rhizospheric soils. Thus, while rhizobacterial communities were enriched in Proteobacteria (mainly Alphaproteobacteria), Actinobacteria (mostly Blastocatellia) dominated in bulk soils. Finally, we detected certain taxonomic rhizosphere signatures, which could be attributed to a particular genotype. Overall, our results indicate that the thin layer of soil surrounding the roots constitute a distinctive soil environment. This study contributes to expand the knowledge about soil bacterial communities in the Chilean highlands and takes the first step to understand the processes that might lead to the rhizosphere differentiation in that area.
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http://dx.doi.org/10.1038/s41598-018-37776-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355873PMC
January 2019

Comparative Transcriptome Profiling in a Segregating Peach Population with Contrasting Juiciness Phenotypes.

J Agric Food Chem 2019 Feb 24;67(5):1598-1607. Epub 2019 Jan 24.

Laboratorio de Bioinformática y Expresión Génica , Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile , Av. El Líbano 5524 , Santiago , Chile.

Cold storage of fruit is one of the methods most commonly employed to extend the postharvest lifespan of peaches ( Prunus persica (L.) Batsch). However, fruit quality in this species is affected negatively by mealiness, a physiological disorder triggered by chilling injury after long periods of exposure to low temperatures during storage and manifested mainly as a lack of juiciness, which ultimately modifies the organoleptic properties of peach fruit. The aim of this study was to identify molecular components and metabolic processes underlying mealiness in susceptible and nonsusceptible segregants. Transcriptome and qRT-PCR profiling were applied to individuals with contrasting juiciness phenotypes in a segregating F population. Our results suggest that mealiness is a multiscale phenomenon, because juicy and mealy fruit display distinctive reprogramming processes affecting translational machinery and lipid, sugar, and oxidative metabolism. The candidate genes identified may be useful tools for further crop improvement.
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http://dx.doi.org/10.1021/acs.jafc.8b05177DOI Listing
February 2019

Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling.

PLoS One 2018 3;13(12):e0208032. Epub 2018 Dec 3.

Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, La Pintana, Santiago, Chile.

This study reports the construction of high density linkage maps of Japanese plum (Prunus salicina Lindl.) using single nucleotide polymorphism markers (SNPs), obtained with a GBS strategy. The mapping population (An x Au) was obtained by crossing cv. "Angeleno" (An) as maternal line and cv. "Aurora" (Au) as the pollen donor. A total of 49,826 SNPs were identified using the peach genome V2.1 as a reference. Then a stringent filtering was carried out, which revealed 1,441 high quality SNPs in 137 An x Au offspring, which were mapped in eight linkage groups. Finally, the consensus map was built using 732 SNPs which spanned 617 cM with an average of 0.96 cM between adjacent markers. The majority of the SNPs were distributed in the intragenic region in all the linkage groups. Considering all linkage groups together, 85.6% of the SNPs were located in intragenic regions and only 14.4% were located in intergenic regions. The genetic linkage analysis was able to co-localize two to three SNPs over 37 putative orthologous genes in eight linkage groups in the Japanese plum map. These results indicate a high level of synteny and collinearity between Japanese plum and peach genomes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208032PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277071PMC
May 2019

Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert.

Extremophiles 2018 Jul 23;22(4):665-673. Epub 2018 Apr 23.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.

As a consequence of the severe climatic change affecting our entire world, many lakes in the Andes Cordillera are likely to disappear within a few decades. One of these lakes is Lejía Lake, located in the central Atacama Desert. The objectives of this study were: (1) to characterize the bacterial community from Lejía Lake shore soil (LLS) using 16S rRNA sequencing and (2) to test a culture-based approach using a soil extract medium (SEM) to recover soil bacteria. This extreme ecosystem was dominated by three phyla: Bacteroidetes, Proteobacteria, and Firmicutes with 29.2, 28.2 and 28.1% of the relative abundance, respectively. Using SEM, we recovered 7.4% of the operational taxonomic units from LLS, all of which belonged to the same three dominant phyla from LLS (6.9% of Bacteroidetes, 77.6% of Proteobacteria, and 15.3% of Firmicutes). In addition, we used SEM to recover isolates from LLS and supplemented the culture medium with increasing salt concentrations to isolate microbial representatives of salt tolerance (Halomonas spp.). The results of this study complement the list of microbial taxa diversity from the Atacama Desert and assess a pipeline to isolate selective bacteria that could represent useful elements for biotechnological approaches.
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http://dx.doi.org/10.1007/s00792-018-1027-6DOI Listing
July 2018

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.

Sci Rep 2018 04 12;8(1):5875. Epub 2018 Apr 12.

Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.

Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.
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http://dx.doi.org/10.1038/s41598-018-23931-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5897386PMC
April 2018

RNA-seq analysis of the head-kidney transcriptome response to handling-stress in the red cusk-eel (Genypterus chilensis).

Comp Biochem Physiol Part D Genomics Proteomics 2017 12 20;24:111-117. Epub 2017 Sep 20.

Universidad Andres Bello, Departamento Ciencias Biológicas, Facultad Ciencias Biológicas, 8370146 Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), 4030000 Concepción, Chile; Universidad Andres Bello, Centro de Investigación Marina Quintay (CIMARQ), Facultad de Ecología y Recursos Naturales, 2340000 Valparaíso, Chile. Electronic address:

Stress is a primary contributing factor of fish disease and mortality in aquaculture. We have previously reported that the red cusk-eel (Genypterus chilensis), an important farmed marine fish, demonstrates a handling-stress response that results in increased juvenile mortality, which is mainly associated with skeletal muscle atrophy and liver steatosis. To better understand the systemic effects of stress on red cusk-eel immune-related gene expression, the present study assessed the transcriptomic head-kidney response to handling-stress. The RNA sequencing generated a total of 61,655,525 paired-end reads from control and stressed conditions. De novo assembly using the CLC Genomic Workbench produced 86,840 transcripts and created a reference transcriptome with a N50 of 1426bp. Reads mapped onto the assembled reference transcriptome resulted in the identification of 569 up-regulated and 513 down-regulated transcripts. Gene ontology enrichment analysis revealed a significant up-regulation of the biological processes, like response to stress, response to biotic stimulus, and immune response. Conversely, a significant down-regulation of biological processes is associated with metabolic processes. These results were validated by RT-qPCR analysis for nine candidate genes involved in the immune response. The present data demonstrated that short term stress promotes the immune innate response in the marine teleost G. chilensis. This study is an important step towards understanding the immune adaptive response to stress in non-model teleost species.
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http://dx.doi.org/10.1016/j.cbd.2017.09.002DOI Listing
December 2017

Renal Pelvic Pressure in Percutaneous Nephrolithotomy: The Effect of Multiple Tracts.

J Endourol 2017 10 14;31(10):1079-1083. Epub 2017 Sep 14.

Department of Urology, Loma Linda University Health , Loma Linda, California.

Introduction: During percutaneous nephrolithotomy (PCNL), elevated renal pelvic pressures (RPPs) may spread infection through pyelovenous backflow whereas decreased pressures can hinder observation and increase bleeding. The purpose of this study was to evaluate the effects of multiple access tracts and different sized endoscopic equipment on RPP in a porcine model.

Materials And Methods: RPP was measured in one- vs two-tract access, rigid vs flexible nephroscopy, and suction vs no suction. Twenty trials were performed for each condition. An independent samples Mann-Whitney U-test was used to compare parameters, with p < 0.05 considered significant.

Results: With one tract, rigid nephroscopy resulted in higher mean pressures (31.35 mm Hg) than flexible nephroscopy (11.1 mm Hg; p < 0.001). The RPP was higher with rigid nephroscopy in one tract (31.35 mm Hg) than when two tracts were present (9.35 mm Hg; p < 0.001). In contrast, there was no difference in pressure during the use of a flexible nephroscope in one (11.1 mm Hg) vs two tracts (10.7 mm Hg; p = 0.63). Use of suction with the rigid nephroscope resulted in significantly lower pressures with one (-1.3 mm Hg) than with two tracts (1.8 mm Hg; p = 0.004).

Conclusion: In PCNL, RPP is significantly affected by an additional tract during rigid nephroscopy and suctioning but not when using a flexible nephroscope. Understanding the effects of multiple tracts and equipment type on RPP may improve the safety of PCNL.
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http://dx.doi.org/10.1089/end.2017.0298DOI Listing
October 2017

Transcriptomic analysis of the hepatic response to stress in the red cusk-eel (Genypterus chilensis): Insights into lipid metabolism, oxidative stress and liver steatosis.

PLoS One 2017 27;12(4):e0176447. Epub 2017 Apr 27.

Universidad Andres Bello, Laboratorio de Biotecnología Molecular, Facultad Ciencias Biológicas, Santiago, Chile.

Teleosts exhibit a broad divergence in their adaptive response to stress, depending on the magnitude, duration, and frequency of stressors and the species receiving the stimulus. We have previously reported that the red cusk-eel (Genypterus chilensis), an important marine farmed fish, shows a physiological response to stress that results in increased skeletal muscle atrophy mediated by over-expression of components of the ubiquitin proteasome and autophagy-lysosomal systems. To better understand the systemic effects of stress on the red cusk-eel metabolism, the present study assessed the transcriptomic hepatic response to repetitive handling-stress. Using high-throughput RNA-seq, 259 up-regulated transcripts were found, mostly associated with angiogenesis, gluconeogenesis, and triacylglyceride catabolism. Conversely, 293 transcripts were down-regulated, associated to cholesterol biosynthesis, PPARα signaling, fatty acid biosynthesis, and glycolysis. This gene signature was concordant with hepatic metabolite levels and hepatic oxidative damage. Moreover, the increased plasmatic levels of AST (aspartate aminotransferase), ALT (alanine aminotransferase) and AP (alkaline phosphatase), as well as liver histology suggest stress-induced liver steatosis. This study offers an integrative molecular and biochemical analysis of the hepatic response to handling-stress, and reveals unknown aspects of lipid metabolism in a non-model teleost.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0176447PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5407771PMC
September 2017

Transcriptional Responses of Chilean Quinoa ( Willd.) Under Water Deficit Conditions Uncovers ABA-Independent Expression Patterns.

Front Plant Sci 2017 8;8:216. Epub 2017 Mar 8.

Laboratorio de Genómica Funcional & Bioinformática, Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile Santiago, Chile.

R49 genotype displayed best performance on selected physiological parameters and highest tolerance to drought.R49 drought over-represented transcripts has exhibited 19% of genes (306 contigs) that presented no homology to published databases.Expression pattern for canonical responses to drought such as ABA biosynthesis and other genes induced in response to drought were assessed by qPCR. Global freshwater shortage is one of the biggest challenges of our time, often associated to misuse, increased consumption demands and the effects of climate change, paralleled with the desertification of vast areas. (Willd.) represents a very promising species, due to both nutritional content and cultivation under water constraint. We characterized drought tolerance of three Chilean genotypes and selected Genotype R49 (Salares ecotype) based upon Relative Water Content (RWC), Electrolyte Leakage (EL) and maximum efficiency of photosystem II (F/F) after drought treatment, when compared to another two genotypes. Exploratory RNA-Seq of R49 was generated by Illumina paired-ends method comparing drought and control irrigation conditions. We obtained 104.8 million reads, with 54 million reads for control condition and 51 million reads for drought condition. Reads were assembled in 150,952 contigs, were 31,523 contigs have a reading frame of at least 300 nucleotides (100 aminoacids). BLAST2GO annotation showed a 15% of genes without homology to NCBI proteins, but increased to 19% (306 contigs) when focused into drought-induced genes. Expression pattern for canonical drought responses such as ABA biosynthesis and other genes induced were assessed by qPCR, suggesting novelty of R49 drought responses.
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http://dx.doi.org/10.3389/fpls.2017.00216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340777PMC
March 2017

High-Frequency Dusting Versus Conventional Holmium Laser Lithotripsy for Intrarenal and Ureteral Calculi.

J Endourol 2017 03 16;31(3):272-277. Epub 2017 Jan 16.

Department of Urology, Loma Linda University Health , Loma Linda, California.

Introduction: The efficiency of holmium laser lithotripsy for urolithiasis depends upon several factors, including laser pulse energy and frequency and stone composition and retropulsion. This study investigates the complex interplay between these factors and quantifies lithotripsy efficiency using different laser settings in a benchtop kidney and ureter model.

Materials And Methods: In vitro caliceal and ex vivo porcine ureteral models were constructed. Calcium oxalate monohydrate stones were fragmented using a 200-μm laser fiber. In the caliceal model, stone fragmentation and vaporization rates at settings of 0.6 J/5 Hz, 0.2 J/15 Hz, and 0.2 J/50 Hz were compared. In the ureteral model, fragmentation time, retropulsion rate, fragmentation rate, and fragmented stone weight were compared at settings of 0.6 J/5 Hz and 0.2 J/15 Hz. Retropulsive forces generated at 0.6 J/5 Hz, 0.2 J/15 Hz, and 0.2 J/50 Hz settings were compared. Analysis was performed using Student's t-test and one-way ANOVA.

Results: In the caliceal model, the 0.6 J/5 Hz setting fragmented and vaporized stones at a higher rate than the 0.2 J/15 Hz setting (0.072 vs. 0.049 mg/s; p < 0.001). However, when the 0.2 J energy setting was combined with the 50 Hz frequency, the fragmentation rate (0.069 mg/s) was similar to the fragmentation rate at 0.6 J/5 Hz (0.072 mg/s; p = 0.677). In the ureteral model, the 0.6 J/5 Hz setting produced higher fragmentation rates (0.089 vs. 0.049 mg/s; p < 0.001), but resulted in significantly lower fragmented stone weight overall (16.815 vs. 25.485 mg; p = 0.009) due to higher retropulsion rates (0.732 vs. 0.213 mm/s; p < 0.001). Retropulsive forces decreased significantly when pulse energy decreased from 0.6 to 0.2 J (0.907 vs. 0.223 N; p < 0.001). Frequency did not affect retropulsive force at 15 and 50 Hz settings (0.223 vs. 0.288 N; p = 0.509).

Conclusions: Laser lithotripsy of calcium oxalate monohydrate stones in the ureter should be performed using the low-energy, moderate-frequency dusting setting to minimize retropulsion and maximize efficiency. In the renal calix, the low-energy high-frequency setting performed similarly to the high-energy low-frequency setting.
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http://dx.doi.org/10.1089/end.2016.0547DOI Listing
March 2017

De novo transcriptome assembly of 'Angeleno' and 'Lamoon' Japanese plum cultivars (Prunus salicina).

Genom Data 2016 Sep 19;9:35-6. Epub 2016 Jun 19.

Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Macul, Santiago, Chile.

Japanese plum (Prunus salicina L.) is a fruit tree of the Rosaceae family, which is an economically important stone fruit around the world. Currently, Japanese plum breeding programs combine traditional breeding and plant physiology strategies with genetic and genomic analysis. In order to understand the flavonoid pathway regulation and to develop molecular markers associated to the fuit skin color (EST-SSRs), we performed a next generation sequencing based on Illumina Hiseq2000 platform. A total of 22.4 GB and 21 GB raw data were obtained from 'Lamoon' and 'Angeleno' respectively, corresponding to 85,404,726 raw reads to 'Lamoon' and 79,781,666 to 'Angeleno'. A total of 139,775,975 reads were filtered after removing low-quality reads and trimming the adapter sequences. De novo transcriptome assembly was performed using CLC Genome Workbench software and a total of 54,584 unique contigs were generated, with an N50 of 1343 base pair (bp) and a mean length of 829 bp. This work contributed with a specific Japanese plum skin transcriptome, providing two libraries of contrasting fruit skin color phenotype (yellow and red) and increasing substantially the GB of raw data available until now for this specie.
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http://dx.doi.org/10.1016/j.gdata.2016.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4925449PMC
September 2016

Genomic-Based Restriction Enzyme Selection for Specific Detection of Piscirickettsia salmonis by 16S rDNA PCR-RFLP.

Front Microbiol 2016 9;7:643. Epub 2016 May 9.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Fondap Center for Genoma RegulationSantiago, Chile; Laboratorio de Genómica Aplicada, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile.

The gram negative facultative bacterium P. salmonis is the etiological agent of Salmonid Rickettsial Septicaemia (SRS), a severe disease that causes important economic losses in the global salmon farmer industry. Despite efforts to control this disease, the high frequency of new epizootic events indicate that the vaccine and antibiotics treatments have limited effectiveness, therefore the preventive and diagnostic approaches must be improved. A comparison of several methodologies for SRS diagnostic indicate differences in their specificity and its capacity to detect other bacteria coexisting with P. salmonis in culture media (contamination) and fish samples (coinfection), aspects relevant for research, vaccine development and clinical diagnostic. By computer-simulation analyses, we identified a group of restriction enzymes that generate unique P. salmonis 16S rDNA band patterns, distinguishable from all other bacteria. From this information, we designed and developed a PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) assay, which was validated using 16S rDNA universal primers and restriction enzyme PmaCI for the amplification and digestion, respectively. Experimental validation was performed by comparing the restriction pattern of P. salmonis with the restriction patterns generated by bacteria that cohabit with P. salmonis (fish bacterial isolates and culture media contaminants). Our results indicate that the restriction enzyme selection pipeline was suitable to design a more specific, sensible, faster and cheaper assay than the currently used P. salmonis detection methodologies.
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http://dx.doi.org/10.3389/fmicb.2016.00643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860512PMC
May 2016

mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis).

BMC Genomics 2015 Dec 1;16:1024. Epub 2015 Dec 1.

Laboratorio de Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile.

Background: Fish reared under intensive conditions are repeatedly exposed to stress, which negatively impacts growth. Although most fish follow a conserved pattern of stress response, with increased concentrations of cortisol, each species presents specificities in the cell response and stress tolerance. Therefore, culturing new species requires a detailed knowledge of these specific responses. The red cusk-eel (Genypterus chilensis) is a new economically important marine species for the Chilean aquaculture industry. However, there is no information on the stress- and cortisol-induced mechanisms that decrease skeletal muscle growth in this teleost.

Results: Using Illumina RNA-seq technology, skeletal muscle sequence reads for G. chilensis were generated under control and handling stress conditions. Reads were mapped onto a reference transcriptome, resulting in the in silico identification of 785 up-regulated and 167 down-regulated transcripts. Gene ontology enrichment analysis revealed a significant up-regulation of catabolic genes associated with skeletal muscle atrophy. These results were validated by RT-qPCR analysis for ten candidates genes involved in ubiquitin-mediated proteolysis, autophagy and skeletal muscle growth. Additionally, using a primary culture of fish skeletal muscle cells, the effect of cortisol was evaluated in relation to red cusk-eel skeletal muscle atrophy.

Conclusions: The present data demonstrated that handling stress promotes skeletal muscle atrophy in the marine teleost G. chilensis through the expression of components of the ubiquitin-proteasome and autophagy-lysosome systems. Furthermore, cortisol was a powerful inductor of skeletal muscle atrophy in fish myotubes. This study is an important step towards understanding the atrophy system in non-model teleost species and provides novel insights on the cellular and molecular mechanisms that control skeletal muscle growth in early vertebrates.
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http://dx.doi.org/10.1186/s12864-015-2232-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667402PMC
December 2015

Complete genome sequence of Microbacterium sp. CGR1, bacterium tolerant to wide abiotic conditions isolated from the Atacama Desert.

J Biotechnol 2015 Dec 29;216:149-50. Epub 2015 Oct 29.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524 Santiago, Chile; Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada 2085 Santiago, Chile. Electronic address:

Microbacterium sp. CGR1 (RGM2230) is an isolate from the Atacama Desert that displays a wide pH, salinity and temperature tolerance. This strain exhibits riboflavin overproducer features and traits for developing an environmental arsenic biosensor. Here, we report the complete genome sequence of this strain, which represents the first genome of the genus Microbacterium sequenced and assembled in a single contig. The genome contains 3,634,864bp, 3299 protein-coding genes, 45 tRNAs, six copies of 5S-16S-23S rRNA and a high genome average GC-content of 68.04%.
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http://dx.doi.org/10.1016/j.jbiotec.2015.10.020DOI Listing
December 2015

Laser fiber cleaving techniques: effects on tip morphology and power output.

J Endourol 2015 Jan;29(1):84-9

Department of Urology, Loma Linda University Medical Center , Loma Linda, California.

Background And Purpose: Proper cleaving of reusable laser fibers is needed to maintain optimal functionality. This study quantifies the effect of different cleaving tools on power output of the holmium laser fiber and demonstrates morphologic changes using microscopy.

Materials And Methods: The uncleaved tips of new 272 μm reusable laser fibers were used to obtain baseline power transmission values at 3 W (0.6 J, 5 Hz). Power output for each of four cleaving techniques-11-blade scalpel, scribe pen cleaving tool, diamond cleaving wheel, and suture scissors-was measured in a single-blinded fashion. Dispersion of light from the fibers was compared with manufacturer specifications and rated as "ideal," "acceptable," or "unacceptable" by blinded reviewers. The fiber tips were also imaged using confocal and scanning electron microscopy. Independent samples Kruskal-Wallis test and chi square were used for statistical analysis (α<0.05).

Results: New uncleaved fiber tips transmitted 3.04 W of power and were used as a reference (100%). The scribe pen cleaving tool produced the next highest output (97.1%), followed by the scalpel (83.4%), diamond cleaving wheel (77.1%), and suture scissors (61.7%), a trend that was highly significant (P<0.001). On pairwise comparison, no difference in power output was seen between the uncleaved fiber tips and those cleaved with the scribe pen (P=1.0). The rating of the light dispersion patterns from the different cleaving methods followed the same trend as the power output results (P<0.001). Microscopy showed that the scribe pen produced small defects along the fiber cladding but maintained a smooth, flat core surface. The other cleaving techniques produced defects on both the core and cladding.

Conclusion: Cleaving techniques produce a significant effect on the initial power transmitted by reusable laser fibers. The scribe pen cleaving tool produced the most consistent and highest average power output.
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http://dx.doi.org/10.1089/end.2014.0175DOI Listing
January 2015

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.

Nat Genet 2013 May 24;45(5):487-94. Epub 2013 Mar 24.

Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA)-Centro di Ricerca per la Frutticoltura, Rome, Italy.

Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
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http://dx.doi.org/10.1038/ng.2586DOI Listing
May 2013

Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality.

BMC Genomics 2009 Sep 10;10:423. Epub 2009 Sep 10.

Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile.

Background: 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. 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.

Conclusion: 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.
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http://dx.doi.org/10.1186/1471-2164-10-423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748099PMC
September 2009

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

BMC Bioinformatics 2006 Nov 23;7:513. Epub 2006 Nov 23.

Millennium Nucleus in Plant Cell Biology and Plant Biotechnology Center, Andres Bello University, Santiago, Chile.

Background: Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task.

Results: In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access.

Conclusion: JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from http://genoma.unab.cl/juice_system/ or http://www.genomavegetal.cl/juice_system/.
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http://dx.doi.org/10.1186/1471-2105-7-513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1676024PMC
November 2006
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