Transcriptomic analysis of tomato carpel development reveals alterations in ethylene and gibberellin synthesis during pat3/pat4 parthenocarpic fruit set

<p>Abstract</p> <p>Background</p> <p>Tomato fruit set is a key process that has a great economic impact on crop production. We employed the Affymetrix GeneChip Tomato Genome Array to compare the transcriptome of a non-parthenocarpic line, UC82, with that of the parthenocarpic line RP75/59 (<it>pat3/pat4 </it>mutant). We analyzed the transcriptome under normal conditions as well as with forced parthenocarpic development in RP75/59, emasculating the flowers 2 days before anthesis. This analysis helps to understand the fruit set in tomato.</p> <p>Results</p> <p>Differentially expressed genes were extracted with maSigPro, which is designed for the analysis of single and multiseries time course microarray experiments. 2842 genes showed changes throughout normal carpel development and fruit set. Most of them showed a change of expression at or after anthesis. The main differences between lines were concentrated at the anthesis stage. We found 758 genes differentially expressed in parthenocarpic fruit set. Among these genes we detected cell cycle-related genes that were still activated at anthesis in the parthenocarpic line, which shows the lack of arrest in the parthenocarpic line at anthesis. Key genes for the synthesis of gibberellins and ethylene, which were up-regulated in the parthenocarpic line were also detected.</p> <p>Conclusion</p> <p>Comparisons between array experiments determined that anthesis was the most different stage and the key point at which most of the genes were modulated. In the parthenocarpic line, anthesis seemed to be a short transitional stage to fruit set. In this line, the high GAs contends leads to the development of a parthenocarpic fruit, and ethylene may mimic pollination signals, inducing auxin synthesis in the ovary and the development of a jelly fruit.</p

The pURI family of expression vectors: A versatile set of ligation independent cloning plasmids for producing recombinant His-fusion proteins

A family of restriction enzyme- and ligation-independent cloning vectors has been developed for producing recombinant His-tagged fusion proteins in Escherichia coli. These are based on pURI2 and pURI3 expression vectors which have been previously used for the successful production of recombinant proteins at the milligram scale. The newly designed vectors combines two different promoters (lppp-5 and T7 RNA polymerase Ø10), two different endoprotease recognition sites for the His6-tag removal (enterokinase and tobacco etch virus), different antibiotic selectable markers (ampicillin and erythromycin resistance), and different placements of the His 6-tag (N- and C-terminus). A single gene can be cloned and further expressed in the eight pURI vectors by using six nucleotide primers, avoiding the restriction enzyme and ligation steps. A unique NotI site was introduced to facilitate the selection of the recombinant plasmid. As a case study, the new vectors have been used to clone the gene coding for the phenolic acid decarboxylase from Lactobacillus plantarum. Interestingly, the obtained results revealed markedly different production levels of the target protein, emphasizing the relevance of the cloning strategy on soluble protein production yield. Efficient purification and tag removal steps showed that the affinity tag and the protease cleavage sites functioned properly. The novel family of pURI vectors designed for parallel cloning is a useful and versatile tool for the production and purification of a protein of interest. © 2010 Elsevier Inc. All rights reserved.This work was supported by grants RM2008-00002 (Instituto Nacional de Investigación Agraria y Alimentaría), AGL2008-01052, Consolider INGENIO 2010 CSD2007-00063 FUN-C-FOOD (Comisión Interministerial de Ciencia y Tecnología), and S-0505/AGR/000153 and S2009/AGR-1469 (ALIBIRD) (Comunidad de Madrid). J.M.M. thanks the Ministerio de Ciencia e Innovación for a research grant (BFU2007-67404/BMC) and “Factoría de Cristalización” Consolider-Ingenio 2010 in support of his research. The technical assistance of M.V. Santamaría is greatly appreciated. J.A. Curiel is a recipient of a predoctoral fellowship from the MEC.Peer Reviewe

EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration

This article is available from: http://www.biomedcentral.com/1471-2105/9/5[Background] Expressed sequence tag (EST) collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector regions, eliminate redundancy and sequencing errors, and provide biologically relevant information. In order to provide a suitable way of performing the different steps in the analysis of the ESTs, flexible computation pipelines adapted to the local needs of specific EST projects have to be developed. Furthermore, EST collections must be stored in highly structured relational databases available to researchers through user-friendly interfaces which allow efficient and complex data mining, thus offering maximum capabilities for their full exploitation.[Results] We have created EST2uni, an integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections. The pipeline uses standard EST analysis tools and the software has a modular design to facilitate the addition of new analytical methods and their configuration. Currently implemented analyses include functional and structural annotation, SNP and microsatellite discovery, integration of previously known genetic marker data and gene expression results, and assistance in cDNA microarray design. It can be run in parallel in a PC cluster in order to reduce the time necessary for the analysis. It also creates a web site linked to the database, showing collection statistics, with complex query capabilities and tools for data mining and retrieval.[Conclusion] The software package presented here provides an efficient and complete bioinformatics tool for the management of EST collections which is very easy to adapt to the local needs of different EST projects. The code is freely available under the GPL license and can be obtained at http:// bioinf.comav.upv.es/est2uni. This site also provides detailed instructions for installation and configuration of the software package. The code is under active development to incorporate new analyses, methods, and algorithms as they are released by the bioinformatics community.Partially funded by "Conselleria de Agricultura, Pesca y Alimentacion de la Comunidad Valenciana" and Spanish "Ministerio de Ciencia y Tecnologia" (research grants GEN2001-4885-C05 and GEN2003-20237-C06).Peer reviewe

Ni-Co Alloy and Multisegmented Ni/Co Nanowire Arrays Modulated in Composition: Structural Characterization and Magnetic Properties

Design of novel multisegmented magnetic nanowires can pave the way for the next generation of data storage media and logical devices, magnonic crystals, or in magneto-plasmonics, among other energy conversion, recovery, and storage technological applications. In this work, we present a detailed study on the synthesis, morphology, structural, and magnetic properties of Ni, Co, and Ni-Co alloy and multisegmented Ni/Co nanowire

Bases genéticas, moleculares y bioquímicas del envejecimiento auditivo ¿Qué nos enseñan los modelos experimentales

Age-related hearing loss (ARHL) affects one in three people older than 65 years and is the most prevalent sensorineural deficit. This type of hearing loss precedes and accelerates the onset of cognitive impairment and is associated with an increased risk for neurodegenerative diseases such as dementia and Alzheimer disease. The onset and progression of ARHL is influenced by genetic factors, which are still poorly understood, and environmental factors, which in particular include exposure to excessive noise and ototoxic substances. At present, no effective drug treatments are available for ARHL prevention or treatment, and therefore research in this field is a priority. In the research field, animal models offer a crucial tool for i) identifying new genes associated with ARHL, ii) understanding the cellular and molecular basis of auditory ageing and iii) defining new therapeutic targets and evaluating candidate treatments.La presbiacusia afecta a una de cada tres personas mayores de 65 años y constituye el déficit neurosensorial más prevalente. Antecede a la aparición de la fragilidad cognitiva, la acelera y se asocia con un mayor riesgo de padecer enfermedades neurodegenerativas como la demencia o el Alzheimer. La aparición y evolución de la presbiacusia están influidas por factores genéticos, todavía poco conocidos, y ambientales, entre los que destacan la exposición a ruido excesivo o a sustancias ototóxicas. En la actualidad no disponemos de tratamientos farmacológicos eficaces para prevenir o tratar la presbiacusia, por lo que la investigación en este campo es prioritaria. En este contexto, los modelos animales son una herramienta esencial para: a) identificar nuevos genes de presbiacusia, b) comprender las bases celulares y moleculares del envejecimiento auditivo, y c) definir nuevas dianas terapéuticas y evaluar posibles tratamientos

The impact of COVID-19 on home, social, and productivity integration of people with chronic traumatic brain injury or stroke living in the community

Compare community integration of people with stroke or traumatic brain injury (TBI) living in the community before and during the coronavirus severe acute respiratory syndrome coronavirus 2 disease (COVID-19) when stratifying by injury: participants with stroke (G1) and with TBI (G2); by functional independence in activities of daily living: independent (G3) and dependent (G4); by age: participants younger than 54 (G5) and older than 54 (G6); and by gender: female (G7) and male (G8) participants. Prospective observational cohort study In-person follow-up visits (before COVID-19 outbreak) to a rehabilitation hospital in Spain and on-line during COVID-19. Community dwelling adults (≥18 years) with chronic stroke or TBI. Community integration questionnaire (CIQ) the total-CIQ as well as the subscale domains (ie, home-CIQ, social-CIQ, productivity CIQ) were compared before and during COVID-19 using the Wilcoxon ranked test or paired t test when appropriate reporting Cohen effect sizes (d). The functional independence measure was used to assess functional independence in activities of daily living. Two hundred four participants, 51.4% with stroke and 48.6% with TBI assessed on-line between June 2020 and April 2021 were compared to their own in-person assessments performed before COVID-19. When analyzing total-CIQ, G1 (d = −0.231), G2 (d = −0.240), G3 (d = −0.285), G5 (d = −0.276), G6 (d = −0.199), G7 (d = −0.245), and G8 (d = −0.210) significantly decreased their scores during COVID-19, meanwhile G4 was the only group with no significant differences before and during COVID-19. In productivity-CIQ, G1 (d = −0.197), G4 (d = −0.215), G6 (d = −0.300), and G8 (d = −0.210) significantly increased their scores, meanwhile no significant differences were observed in G2, G3, G5, and G7. In social-CIQ, all groups significantly decreased their scores: G1 (d = −0.348), G2 (d = −0.372), G3 (d = −0.437), G4 (d = −0.253), G5 (d = −0.394), G6 (d = −0.319), G7 (d = −0.355), and G8 (d = −0.365). In home-CIQ only G6 (d = −0.229) significantly decreased, no significant differences were observed in any of the other groups. The largest effect sizes were observed in total-CIQ for G3, in productivity-CIQ for G6, in social-CIQ for G3 and in home-CIQ for G6 (medium effect sizes). Stratifying participants by injury, functionality, age or gender allowed identifying specific CIQ subtotals where remote support may be provided addressing them

The Impact of Body Mass Index on Functional Rehabilitation Outcomes of Working-age Inpatients with Stroke

BACKGROUND: Stroke is the most relevant cause of acquired persistent disability in adulthood. The relationship between patient’s weight during rehabilitation and stroke functional outcome is controversial, previous research reported positive, negative and no effects, with scarce studies specifically addressing working-age patients.AIM: To evaluate the association between Body Mass Index (BMI) and the functional progress of adult (\u3c65 \u3eyears) patients with stroke admitted to a rehabilitation hospital.DESIGN: Retrospective observational cohort study.SETTING: Inpatient rehabilitation center.POPULATION: 178 stroke patients (ischemic or hemorrhagic).METHODS: Point-biserial and Spearman’s correlations, multivariate linear regressions and analysis of covariance were used to describe differences in functional outcomes after adjusting for age, sex, severity, dysphagia, depression and BMI category. Functional Independence Measure (FIM), FIM gain, efficiency and effectiveness were assessed.RESULTS: Participants were separated in 3 BMI categories: normal weight (47%), overweight (33%) and obese (20%). There were no significant differences between BMI categories in any functional outcome (total FIM (TFIM), cognitive (CFIM), motor (MFIM)) at discharge, admission, gain, efficiency or effectiveness. In regression models BMI (as continuous variable) was not significant predictor of TFIM at discharge after adjusting for age, sex, severity, dysphagia, depression and ataxia (R2=0.4813), significant predictors were TFIM at admission (β = 0.528) and NIHSS (β=-0.208). MFIM efficiency did not significantly differ by BMI subgroups, neither did CFIM efficiency. Length of stay (LOS) and TFIM effectiveness were associated for normal (r=0.33) and overweight (r=0.43), but not for obese. LOS and TFIM efficiency were strongly negatively associated only for obese (r=-0.50).CONCLUSIONS: FIM outcomes were not associated to BMI, nevertheless each BMI category when individually considered (normal weight, overweight or obese) was characterized by different associations involving FIM outcomes and clinical factors. CLINICAL REHABILITATION IMPACT: In sub-acute post-stroke working-age patients undergoing rehabilitation, BMI was not associated to FIM outcomes (no obesity paradox was reported in this sample). Distinctive significant associations emerged within each BMI category, (supporting their characterization) such as length of stay and TFIM effectiveness were associated for normal weight and overweight, but not for obese. Length of stay and TFIM efficiency were strongly negatively associated only for obese

Carbon-encapsulated iron nanoparticles as reusable adsorbents for micropollutants removal from water

Adsorption represents the most plausible technology for micropollutants removal from water nowadays. Nevertheless, the regeneration of the saturated carbon materials is still an important challenge, being these solids in practice commonly disposed. This work aims at overcoming this issue by using innovative carbonencapsulated iron nanoparticles (CE-nFe). This material was synthesized by a low-cost and green method viz. hydrothermal carbonization (HTC), using olive mill wastewater as carbonaceous source. The solid was fully characterized by different techniques (magnetic properties, elemental analyses, N2-sorption isotherms, pHPZC, ICP, XRD and TEM). It showed a clear core-shell structure of around 40 nm in diameter. The core was mainly formed by zero-valent iron and the shell by graphitized carbon. Accordingly, it showed an essentially mesoporous structure, with a specific surface area of 169 m2 g−1 , and a clear hydrophobic character (pHPZC = 10). Its adsorption performance was investigated using three relevant micropollutants (diclofenac (DCF), sulfamethoxazole (SMX) and metronidazole (MNZ)). A very fast removal of the micropollutants was achieved (30 min at the most, with rate constants in the range of 0.11–0.41 g mg−1 min−1 ). The adsorption isotherms revealed the vertical packing of the adsorbate molecules onto the adsorbent active centers, being the data successfully described by the GAB model. The saturated adsorbents were effectively regenerated by heterogeneous Fenton oxidation, taking advantage of the iron core of CE-nFe and the opened mesoporous carbon shell. The regeneration efficiency increased with increasing the operating temperature (25–75 ◦C) and contact time (1–4 h), as well as the H2O2 dose up to 6 g L-1. The micropollutant nature affected the adsorbent regeneration yield in the order: SMX > DCF > MNZ, consistent with their reactivity towards Fenton oxidationThis research has been supported by the Spanish MINECO through the project CTM-2016-76454-R and by the CM through the project P2018/EMT-4341. M. Munoz and J. Nieto-Sandoval thank the Spanish MINECO for the Ramón y Cajal postdoctoral contract (RYC-2016-20648) and the FPI predoctoral grant (BES-2017-081346), respectivel

Facile, fast and green synthesis of a highly porous calcium-syringate bioMOF with intriguing triple bioactivity

A facile, fast and green strategy based on ethanol is utilized to prepare a new bioMOF, namely, CaSyr-1, with particular characteristics of full biocompatibility given by using just calcium and syringic acid, the latter being a phenolic natural product found in fruits and vegetables, permanent porosity with an outstanding surface area >1000 m2 g−1, and a micropore diameter of 1.4 nm close to mesopore values. Collectively, these data establish CaSyr-1 as one of the most porous bioMOFs reported to date, with high molecular adsorption capacity. The CaSyr-1 adsorptive behavior is revised here through the reversible adsorption of CO2 and the encapsulation of bioactive ingredients in the structure. Remarkably, CaSyr-1 enables the development of triple therapeutic entities, involving bioactive Ca2+, syringic acid and an impregnated drug

Differences in the clinical management of women and men after detection of a solitary pulmonary nodule in clinical practice

Objectives To explore differences in the clinical management of men and women in the 5 years after detecting a solitary pulmonary nodule (SPN) by chest radiograph or CT in routine clinical practice. Methods We followed up 545 men and 347 women with an SPN detected by chest radiograph or CT in a retrospective cohort of 25,422 individuals undergoing routine thoracic imaging in 2010–2011.We compared the frequency of each management strategy (no further test, immediate intervention or follow up) according to sex by means of chi-squared.We estimated the relative risk of women versus men of having been followed up instead of an immediate intervention using multivariate logistic regression. We compared by sex the time between detection of the nodule and lung cancer diagnosis, the time between diagnosis and death by means of Mann-Whitney U test and the cumulative effective dose of radiation in each management strategy by means of t test. Results Women were more likely than men to have follow-up rather than immediate intervention (aRR = 1.8, CI 1.3–2.7, p = 0.002), particularly in those who underwent CT (aRR = 4.2, CI 1.9–9.3, p < 0.001). The median time between SPN detection and lung cancer diagnosis was higher in women (4.2 months, interquartile range (IQR) 5.1) than in men (1.5 months, IQR 16.2). The mean cumulative effective dose was 21.3 mSv, 19.4 mSv in men and 23.9mv in women (p = 0.023). Conclusions Our results could reflect decisions based on a greater suspicion of lung cancer in men. The incidental detection of SPNs is increasing, and it is necessary to establish clear strategies aimed to reduce variability in their management according to patient’s sex