Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

BACKGROUND: High throughput parallel sequencing, RNA-Seq, has recently emerged as an appealing alternative to microarray in identifying differentially expressed genes (DEG) between biological groups. However, there still exists considerable discrepancy on gene expression measurements and DEG results between the two platforms. The objective of this study was to compare parallel paired-end RNA-Seq and microarray data generated on 5-azadeoxy-cytidine (5-Aza) treated HT-29 colon cancer cells with an additional simulation study. METHODS: We first performed general correlation analysis comparing gene expression profiles on both platforms. An Errors-In-Variables (EIV) regression model was subsequently applied to assess proportional and fixed biases between the two technologies. Then several existing algorithms, designed for DEG identification in RNA-Seq and microarray data, were applied to compare the cross-platform overlaps with respect to DEG lists, which were further validated using qRT-PCR assays on selected genes. Functional analyses were subsequently conducted using Ingenuity Pathway Analysis (IPA). RESULTS: Pearson and Spearman correlation coefficients between the RNA-Seq and microarray data each exceeded 0.80, with 66%~68% overlap of genes on both platforms. The EIV regression model indicated the existence of both fixed and proportional biases between the two platforms. The DESeq and baySeq algorithms (RNA-Seq) and the SAM and eBayes algorithms (microarray) achieved the highest cross-platform overlap rate in DEG results from both experimental and simulated datasets. DESeq method exhibited a better control on the false discovery rate than baySeq on the simulated dataset although it performed slightly inferior to baySeq in the sensitivity test. RNA-Seq and qRT-PCR, but not microarray data, confirmed the expected reversal of SPARC gene suppression after treating HT-29 cells with 5-Aza. Thirty-three IPA canonical pathways were identified by both microarray and RNA-Seq data, 152 pathways by RNA-Seq data only, and none by microarray data only. CONCLUSIONS: These results suggest that RNA-Seq has advantages over microarray in identification of DEGs with the most consistent results generated from DESeq and SAM methods. The EIV regression model reveals both fixed and proportional biases between RNA-Seq and microarray. This may explain in part the lower cross-platform overlap in DEG lists compared to those in detectable genes

Influencia de la inyección alternante de aire en el color y el “alambrado” de aceitunas negras naturales Arauco c.v., en comparación con el método tradicional argentino

Ripe black olives cv. Arauco were processed under different conditions to evaluate the effects of alternating air injection (AI) on the color of olives and on spoilage known as “alambrado”, using a system based on the one patented by the “Instituto de la Grasa” (Sevilla, Spain), as compared with the traditional Argentine processing method, which consists of drying the olives in natural air (“extendido”) for 24 hours at 7, 14 and 21 days of fermentation. Four types of fermentation were used: brine at 2% NaCl plus AI; brine at 2% NaCl plus three “extendidos”; brine at 9% NaCl plus three “extendidos”; and brine at 9% NaCl plus AI and one “extendido”. As previously observed in other varieties by other authors, we noticed that lower pH values were achieved in 2% NaCl fermentations vs. 9% NaCl fermentations. AI prevented the “alambrado” whereas brine at 2% NaCl reduced this spoilage as compared with brine at 9% NaCl. The darkest color of olives was obtained with three “extendidos”, but 83% of brightness reduction was achieved with only one “extendido”. The “extendido” process decreased the texture. We conclude that the combination of AI and “extendido” can add benefits to natural black olives of the Arauco variety.Se elaboraron aceitunas negras maduras variedad Arauco en distintas condiciones para evaluar la inyección alternante de aire (IA) con un sistema basado en el patentado por el Instituto de la Grasa, en comparación con la elaboración tradicional argentina donde se realiza exposición al aire en seco (“extendido”) de los frutos durante 24 h, en tres momentos de la fermentación (después de 7, 14 y 21 días). Se hicieron cuatro tipos de fermentaciones: en salmuera al 2% con IA; en salmuera al 2% y 9% con tres “extendidos” y salmuera 9% con IA y un “extendido”. Se alcanzaron los valores mas bajos de pH en fermentaciones con el 2% de NaCl versus las de 9%. La IA evita el defecto de “alambrado” y lo reduce la concentración de 2% versus la de 9%. El color más oscuro se obtiene aplicando el “extendido” en tres oportunidades, pero con una aplicación se alcanza el 83% de la reducción de luminosidad alcanzada por las tres aplicaciones. La textura se ve disminuida por el proceso de “extendido”. La combinación de la IA y el “extendido” reducen el defecto de “alambrado” y oscurecen las aceitunas negras al natural de la variedad Arauco

The HubBLe Trial: haemorrhoidal artery ligation (HAL) versus rubber band ligation (RBL) for symptomatic second- and third-degree haemorrhoids: a multicentre randomised controlled trial and health-economic evaluation.

BACKGROUND: Optimal surgical intervention for low-grade haemorrhoids is unknown. Rubber band ligation (RBL) is probably the most common intervention. Haemorrhoidal artery ligation (HAL) is a novel alternative that may be more efficacious. OBJECTIVE: The comparison of HAL with RBL for the treatment of grade II/III haemorrhoids. DESIGN: A multicentre, parallel-group randomised controlled trial. PERSPECTIVE: UK NHS and Personal Social Services. SETTING: 17 NHS Trusts. PARTICIPANTS: Patients aged ≥ 18 years presenting with grade II/III (second- and third-degree) haemorrhoids, including those who have undergone previous RBL. INTERVENTIONS: HAL with Doppler probe compared with RBL. OUTCOMES: Primary outcome - recurrence at 1 year post procedure; secondary outcomes - recurrence at 6 weeks; haemorrhoid severity score; European Quality of Life-5 Dimensions, 5-level version (EQ-5D-5L); Vaizey incontinence score; pain assessment; complications; and cost-effectiveness. RESULTS: A total of 370 participants entered the trial. At 1 year post procedure, 30% of the HAL group had evidence of recurrence compared with 49% after RBL [adjusted odds ratio (OR) = 2.23, 95% confidence interval (CI) 1.42 to 3.51; p = 0.0005]. The main reason for the difference was the number of extra procedures required to achieve improvement/cure. If a single HAL is compared with multiple RBLs then only 37.5% recurred in the RBL arm (adjusted OR 1.35, 95% CI 0.85 to 2.15; p = 0.20). Persistence of significant symptoms at 6 weeks was lower in both arms than at 1 year (9% HAL and 29% RBL), suggesting significant deterioration in both groups over the year. Symptom score, EQ-5D-5L and Vaizey score improved in both groups compared with baseline, but there was no difference between interventions. Pain was less severe and of shorter duration in the RBL group; most of the HAL group who had pain had mild to moderate pain, resolving by 3 weeks. Complications were low frequency and not significantly different between groups. It appeared that HAL was not cost-effective compared with RBL. In the base-case analysis, the difference in mean total costs was £1027 higher for HAL. Quality-adjusted life-years (QALYs) were higher for HAL; however, the difference was very small (0.01) resulting in an incremental cost-effectiveness ratio of £104,427 per additional QALY. CONCLUSIONS: At 1 year, although HAL resulted in fewer recurrences, recurrence was similar to repeat RBL. Symptom scores, complications, EQ-5D-5L and continence score were no different, and patients had more pain in the early postoperative period after HAL. HAL is more expensive and unlikely to be cost-effective in terms of incremental cost per QALY. LIMITATIONS: Blinding of participants and site staff was not possible. FUTURE WORK: The incidence of recurrence may continue to increase with time. Further follow-up would add to the evidence regarding long-term clinical effectiveness and cost-effectiveness. The polysymptomatic nature of haemorrhoidal disease requires a validated scoring system, and the data from this trial will allow further assessment of validity of such a system. These data add to the literature regarding treatment of grade II/III haemorrhoids. The results dovetail with results from the eTHoS study [Watson AJM, Hudson J, Wood J, Kilonzo M, Brown SR, McDonald A, et al. Comparison of stapled haemorrhoidopexy with traditional excisional surgery for haemorrhoidal disease (eTHoS): a pragmatic, multicentre, randomised controlled trial. Lancet 2016, in press.] comparing stapled haemorrhoidectomy with excisional haemorrhoidectomy. Combined results will allow expansion of analysis, allowing surgeons to tailor their treatment options to individual patients. TRIAL REGISTRATION: Current Controlled Trials ISRCTN41394716. FUNDING: This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 20, No. 88. See the NIHR Journals Library website for further project information

Efecto de las altas presiones hidrostáticas sobre la calidad y vida útil de duraznos mínimamente procesados : aspectos bioquímicos, fisicoquímicos, higiénico-sanitarios, nutricionales y sensoriales

Consumers demand fresh-cut fruits, free from additives and with fresh appearance. However, the alteration caused by the processing to the tissues limits their shelf life. The aim of this work was to study the effect of High Pressure Processing (HPP) on the preservation of minimally processed peaches. Cubes/cylinders of peaches were processed by combining a dipping pre-treatment in organic acids solution, with vacuum-packing and HPP at room temperature. HPP conditions were optimized, with the combination 600MPa-5min being able to cause the greater enzyme inactivation with a minimum alteration of the color and texture. Besides, it was studied the relevance of selecting varieties with low polyphenoloxidase activity as raw material, to control the enzymatic browning. Moreover, some biochemical processes (e.g. the expression and activity of enzymes) were still active in the pressurized peaches and, although HPP modified some characteristics of the living tissues, the pressurized products keep the appearance, texture and flavor of the fresh fruit. Finally, it was determined that the optimal storage temperature was 4°C, which allows a suitable preservation of the final product for 42 days without any microbial and sensorial deterioration. Interestingly, it was found that at 20°C the product can be maintained with suitable commercial quality.Fil: Denoya, Gabriela Inés. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaLos consumidores demandan frutas mínimamente procesadas libres de aditivos y con apariencia fresca. Sin embargo, el daño provocado por el procesamiento a los tejidos acorta su vida útil. El presente trabajo se realizó con la finalidad de estudiar el efecto de las Altas Presiones Hidrostáticas (APH) para preservar duraznos mínimamente procesados. Cubos/cilindros de durazno fueron procesados combinando inmersión en solución de ácidos orgánicos, envasado al vacío y tratamiento por APH a temperatura ambiente. Se optimizaron las condiciones del tratamiento, determinándose que con 600MPa-5min se lograba la mayor inactivación de enzimas, con la mínima alteración de la textura y el color. También se estudió la importancia de seleccionar como materia prima variedades con baja actividad de la polifenoloxidasa, para controlar el pardeamiento enzimático del producto. Se encontró que en los duraznos presurizados se mantienen activos ciertos procesos bioquímicos (expresión y actividad de enzimas) y aunque se modifican algunas características de los tejidos vivos, el producto final mantiene la apariencia, textura y flavor de la fruta fresca. Finalmente, se determinó que la temperatura óptima de conservación es de 4°C, pudiendo mantenerse el producto sin deterioro microbiológico ni sensorial por 42 días. Notablemente, a 20°C el producto podría ser conservado con calidad comercial adecuada

Enzyme activities in aged conidia of N. crassa

Enzyme activities in aged conidia of N. crass

The effects of canning on B-vitamin retention in a model cat diet with an emphasis on thiamine

Master of ScienceDepartment of Grain Science and IndustryGreg AldrichWater soluble B-vitamins play an integral role in normal metabolic function in cats. For example, thiamine deficiency results in anorexia, neurological impairment, and, in severe cases, death in a few weeks’ time. However, little research has addressed how these vitamins are affected during cat food canning. Thiamine is the most susceptible to degradation during this process, with less known about how it affects the other B-vitamins. Therefore, our objectives were to determine the effects of modifying processing parameters on thiamine and other water-soluble B-vitamins in a model canned cat food. In a series of five experiments, various processing parameters were adjusted: including cook (retort) time, batter moisture and temperature, pH, protein source, and the addition of sulfites. Pressure (172368.93 Pa) and temperature (121 ̊C) within the retort remained the same for all treatments. As retort time increased, thiamine concentration decreased (P ≤ 0.05). No loss of B-vitamin concentration was noted for thiamine, riboflavin, cobalamin, and pantothenic acid as batter moisture increased. Likewise, as batter temperature increased, concentration of riboflavin, niacin, pyridoxine, folic acid, and pantothenic acid remained constant (P ˃ 0.10). When different types of thiamine were included for supplementation, thiamine mononitrate tended to have a greater retention of the vitamin than thiamine hydrochloride (P = 0.12). The protein sources selected for the experiment included chicken as a control, beef liver, chicken liver, pork liver, salmon, tuna, and whitefish. The salmon, tuna, and whitefish were grouped together for analysis. Beef liver, chicken liver, and pork liver were grouped together for analysis. The vitamin retention of each group was compared. When compared to chicken or liver, thiamine retention was greatest in diets containing fish (P≤ 0.05). In addition, riboflavin, niacin, and cobalamin retentions were greatest (P≤ 0.05) in diets containing liver. The addition of sulfites came from dehydrated potatoes added to thediets in exchange for rice. Thiamine tended to decrease in those diets with sulfite containing dehydrated potatoes (P= 0.07) compared to diets containing rice. Pyridoxine and pantothenic acid retention decreased in diets containing dehydrated potatoes (P≤ 0.05) compared to diets containing rice. The largest negative impact on thiamine retention was time in the retort; cobalamin, folic acid, and riboflavin were also negatively affected. Including sulfite-containing potatoes in the diet tended to decrease thiamine, pyridoxine, and pantothenic acid. It was expected that diets containing chicken would retain more thiamine than those formulated with fish and liver. However, diets containing fish retained more thiamine, pyridoxine, and pantothenic acid. Therefore, it appears that processing and diet composition can affect the B-vitamin content of canned cat foods and must be accounted for when producing commercial products

Las criptomonedas y su naturaleza jurídica en el derecho comparado y Argentina

Como objetivos tuvimos: 1° Realizar una breve reseña sobre lo que es el dinero, para luego poder explicar lo que significa Bitcoin, analizando la naturaleza jurídica del mismo en el derecho comparado. 2° Establecer la naturaleza jurídica dentro del derecho argentino, en función de la normativa vigente que resulta aplicable. 3° Elaboración posibles lineamientos jurídicos que repercutan en un tratamiento legal acorde a la utilización de la tecnología Bitcoin; para lo cual se realizó búsqueda y relevamiento de información a nivel mundial, lectura de bibliográfica nacional y extranjera aplicable y el análisis de un leading case sobre la materia - ocurrido en los Estados Unidos - el cual sirve de referencia legal para el presente trabajo.- Este trabajo es presentado en forma sucinta dada la brevedad que impone el reglamento. A los conceptos anteriores, dinero y bitcoin, se le suma una somera explicación de esta tecnología revolucionaria que importa un nuevo tren de desarrollo a nivel regional y mundial. Los principales resultados obtenidos son: la naturaleza jurídica del Bitcoin en diversos países, ya sea tratado como un commoditie, medio de pago voluntario, un valor negociable, permuta e incluso como un bien inmaterial susceptible de valor. Respecto de Argentina, sabemos que actualmente es considerado como bien inmaterial susceptible de valor. En las conclusiones llegamos a determinar la naturaleza jurídica acorde a la practicidad que la tecnología brinda, fijando posibles lineamientos para un futuro tratamiento legal del Bitcoin al estilo japonés, y de esa forma considerarlo como un medio de pago voluntario.-Fil: Denoya Rolla, Pablo Daniel. Argentina. Universidad Nacional del Noroeste

Comparison of different analytical methods to evaluate the heat shock protein (HSP) response in fruits. Application to tomatoes subjected to stress treatments

Heat shock proteins (HSP) are synthesized in living tissues exposed to transient increase in temperature and play a central role in the protective response against heat and other stresses. In fruits, this response to heat treatment provides resistance to a physiological alteration known as chilling injury. Despite the physiological importance of this group of proteins, publications comparing different methodological alternatives for their analysis are rather scarce. In the present paper, we conducted a comparative study using different electrophoretic and immunological techniques to evaluate the HSP response in fruits. Proteins were extracted from tomato fruit exposed to an HSP-inducing temperature (38º C) for different times (0, 3, 20, and 27 hours). Different alternatives of analysis (SDS-PAGE, SDS-PAGE followed by IEF, western blot, and dot blot) were performed, and their potential application discussed. The study was complemented with a practical application, in which tomatoes were subjected to heat and anaerobic treatments and then stored in a chill-inducing temperature. This application evidences the relevance of knowing the level of proteins attained by stress treatments which correlates with the acquired tolerance.Fil: Polenta, Gustavo Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Tecnología de Alimentos; Argentina. Universidad de Morón. Facultad de Agronomía y Ciencias Agroalimentarias; Argentina.Fil: Guidi, Silvina Mabel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Tecnología de Alimentos; Argentina. Universidad de Morón. Facultad de Agronomía y Ciencias Agroalimentarias; Argentina.Fil: Ambrosi, Vanina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Tecnología de Alimentos; Argentina. Universidad de Morón. Facultad de Agronomía y Ciencias Agroalimentarias; Argentina.Fil: Denoya, Gabriela Inés. Instituto Nacional de Tecnología Agropecuaria (INTA).Instituto de Investigación Tecnología de Alimentos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina

Comparison of the Contents of Bioactive Compounds and Quality Parameters in Selected Mango Cultivars

Mango cultivars Tommy Atkins, Zill, Peach, Sabre, Rosa and Phiva were analyzed for their quality parameters (fruit weight, flesh color chroma, L, h0, total soluble solid [TSS]/titratable acidity [TA], firmness), bioactive compounds (total phenols, carotenoids, ascorbic acid, antioxidant activity) and polyphenol oxidase (PPO) activity. Cv. Sabre showed highest total phenolic content (76.43 mg gallic acid/100 g FW), carotenoids (9.90 mg/100 g of FW), ascorbic acid content (69.71 mg/100 g of FW) and antioxidant activity (1.2 mg of gallic acid/g of FW), whereas cv. Peach mango contained lower bioactive compounds. Multivariate principal component analysis analysis showed higher concentration of bioactive compounds in cv. Sabre mango, whereas cv. Tommy Atkins was firm and heavier. Cv. Rosa and Phiva were moderately rich in bioactive compounds and lower in fruit weight and firmness, whereas cv. Peach was higher in TSS/ TA. The PPO activity was higher in cvs. Rosa and Zill.Instituto de Tecnología de AlimentosFil: Sellamuthu, Periyar Selvam. Tshwane University of Technology. Department of Crop Science. Postharvest Technology Group; SudáfricaFil: Denoya, Gabriela Inés. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Tecnología de Alimento. Laboratorio de Compuestos Proteicos; ArgentinaFil: Sivakumar, Dharini. Tshwane University of Technology. Department of Crop Science. Postharvest Technology Group; SudáfricaFil: Polenta, Gustavo Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Tecnología de Alimento. Laboratorio de Compuestos Proteicos; ArgentinaFil: Soundy, Puffy. Tshwane University of Technology. Department of Crop Science. Postharvest Technology Group; Sudáfric

Use of brillant blue dye on canned cherries

Introduction: The toxicity of erythrosine as well as other photochemical and biochemical degradation products thereof has been addressed in several studies. However, it is often employed in the preparation of canned cherries, since its use is allowed by regulatory agencies such as the FDA. Therefore, it would be important to find less risky replacement dyes for their use in food. Methodology: canned cherries were produced by a slow confit process, reaching at least 55° Brix, and were then subjected to commercial pasteurization. Results: Brilliant Blue dyed cherries met the required standard and had a suitable degree of acceptance in the tested population, with the expected parameters being attained in all trials. In addition, the stability test proved that blue dyed cherries remained unchanged, while Erb dyed product suffered an important discoloration. Conclusion: cherries colored by blue brilliant can be elaborated without problemEEA MendozaFil: Maldonado, Mariela. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Zanonc, Marianela Universidad Católica de Cuyo. Facultad de Don Bosco de Enología y Ciencias de la Alimentación; ArgentinaFil: Polenta, Gustavo Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Tecnología de Alimento; ArgentinaFil: Denoya, Gabriela Inés. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Tecnología de Alimento; ArgentinaFil: Sanow, Luis Claudio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Tecnología de Alimento; Argentin