Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis

The E2F family of transcription factors has important roles in cell cycle progression. E2F4 is an E2F family member that has been proposed to be primarily a repressor of transcription, but the scope of its binding activity and functions in transcriptional regulation is not fully known. We used ChIP sequencing (ChIP-seq) to identify around 16 000 E2F4 binding sites which potentially regulate 7346 downstream target genes with wide-ranging functions in DNA repair, cell cycle regulation, apoptosis, and other processes. While half of all E2F4 binding sites (56%) occurred near transcription start sites (TSSs), ∼20% of sites occurred more than 20 kb away from any annotated TSS. These distal sites showed histone modifications suggesting that E2F4 may function as a long-range regulator, which we confirmed by functional experimental assays on a subset. Overexpression of E2F4 and its transcriptional cofactors of the retinoblastoma (Rb) family and its binding partner DP-1 revealed that E2F4 acts as an activator as well as a repressor. E2F4 binding sites also occurred near regulatory elements for miRNAs such as let-7a and mir-17, suggestive of regulation of miRNAs by E2F4. Taken together, our genome-wide analysis provided evidence of versatile roles of E2F4 and insights into its functions

Hypoglycemic effects of Berberis aristata and Tamarindus indica extracts in vitro

AbstractObjectiveThe objective of the present investigation was to evaluate the hypoglycemic potential of Berberis aristata and Tamarindus indica using various in vitro techniques.MethodsThe selected plant extracts were studied for their effects on glucose adsorption capacity, in vitro glucose diffusion, in vitro amylolysis kinetics and glucose transport across the yeast cells.ResultsIt was observed that both the plant extracts adsorbed glucose and the adsorption of glucose increased remarkably with an increase in glucose concentration. No significant (p⩽0.05) differences were observed between the adsorption capacities of B. aristata and T. indica. The results of amylolysis kinetic experimental model exhibited that the rate of glucose diffusion was increased with time from 30 to 180min and both the plant extracts demonstrated significant inhibitory effects on movement of glucose into external solution across dialysis membrane as compared to control. It was observed that the plant extracts also promoted glucose uptake by the yeast cells. Enhancement of glucose uptake was dependent on both the sample and glucose concentration. B. aristata extract exhibited significantly higher (p⩽0.05) activity than the extract of T. indica at all concentrations.ConclusionThe results of the study verified the hypoglycemic activity of the extracts of B. aristata and T. indica. However, the observed effects need to be confirmed using different in vivo models and clinical trials for their effective utilization as therapeutic agents

Cribado de la actividad hipoglucémica in vitro de Murraya koenigii y Catharanthus roseu

Objective: The study aimed to verify the hypoglycemic effect of Murraya koenigii (M. koenigii) and Catharanthus roseus (C. roseus) by using various in-vitro techniques. Method: The extracts were studied for their effects on glucose adsorption capacity, in-vitro glucose diffusion, in-vitro amylolysis kinetics and glucose transport across the yeast cells. Results: It was observed that the extracts of M. koenigii and C. roseus adsorbed glucose and the adsorption of glucose increased remarkably with an increase in glucose concentration. There were no significant (p≤0.05) differences between their adsorption capacities. In the amylolysis kinetic experimental model the rate of glucose diffusion was found to be increased with time from 30 to 180 min and both the plant extracts exhibited significant inhibitory effects on the movement of glucose into external solution across the dialysis membrane as compared to control. The extracts also promoted glucose uptake by the yeast cells and the enhancement of glucose uptake was dependent on both the sample and glucose concentration. The extract of M. koenigii exhibited significantly higher (p≤0.05) activity than the extract of C. roseus at all concentrations used in the study. Our report suggests the mechanism(s) for the hypoglycemic effect of M. koenigii and C. roseus. Conclusion: The said effect was observed to be mediated by inhibiting alpha amylase, inhibiting glucose diffusion by adsorbing glucose and by increasing glucose transport across the cell membranes as revealed by in-vitro model of yeast cells. However, these effects need to be affirmed by using different in vivo models and clinical trials.Objetivo: El estudio tuvo como objetivo verificar el efecto hipoglucémico de Murraya koenigii (M. koenigii) y Catharanthus roseus (C. roseus) mediante el uso de diversas técnicas in vitro. Método: Los extractos se estudiaron por sus efectos sobre la capacidad de adsorción de glucosa, la difusión de glucosa in vitro, la cinética de amilolisis in vitro y el transporte de glucosa a través de las células de levadura. Resultados: se observó que los extractos de M. koenigii y C. roseus adsorbieron glucosa y la adsorción de glucosa aumentó notablemente con un aumento en la concentración de glucosa. No hubo diferencias significativas (p≤0.05) entre sus capacidades de adsorción. En el modelo experimental cinético de amilolisis, se encontró que la velocidad de difusión de glucosa aumentaba con el tiempo de 30 a 180 min y ambos extractos de planta exhibían efectos inhibitorios significativos sobre el movimiento de la glucosa hacia la solución externa a través de la membrana de diálisis en comparación con el control. Los extractos también promovieron la absorción de glucosa por las células de levadura y la mejora de la captación de glucosa dependió tanto de la muestra como de la concentración de glucosa. El extracto de M. koenigii exhibió una actividad significativamente mayor (p≤0.05) que el extracto de C. roseus en todas las concentraciones utilizadas en el estudio. Nuestro informe sugiere el mecanismo (s) para el efecto hipoglucemiante de M. koenigii y C. roseus. Conclusión: Se observó que dicho efecto estaba mediado por la inhibición de la alfa amilasa, la inhibición de la difusión de glucosa por la adsorción de glucosa y el aumento del transporte de glucosa a través de las membranas celulares según lo revelado por el modelo in vitro de células de levadura. Sin embargo, estos efectos deben ser afirmados mediante el uso de diferentes modelos in vivo y ensayos clínicos

Evaluación de dimetilsulfóxido y Aloe vera como potenciadores de la penetración para la aplicación cutánea de lidocaína

Objective: The objective of the present work was to compare and verify efficacy of Aloe vera (1 to 3 %) with dimethyl sulfoxide (1 to 3 %) for its penetration enhancing property for topical delivery of lidocaine. Method: Carbopol 934 was used as gelling agent for preparation of lidocaine gel formulations containing or not dimetilsulfoxido or Aloe vera (1%, 2% and 3%). Gels were evaluated for physical appearance, rheological behavior, drug content, drug release and stability. Results: It was inferred from result that obtained gel formulation were good in appearance, homogeneity and consistency. In vitro drug release profiles showed that concentrations of Aloe vera gel increased in formulations, the drug release rate increased substantially. It was observed that F6 formulation which comprised of 3% Aloe vera as permeation enhancer exhibited 79.18 % of drug release. Similarly, for formulation F3 which comprised of 3% dimetilsulfoxido as permeation enhancer the drug release was found to be 84.52%. Use of Aloe vera may prove to be beneficial as compared to synthetic permeation enhancers. Conclusion: Based on results of the study it was concluded that the topical gel of lidocaine prepared along with Carbopol 934 by using Aloe vera as a natural penetration enhancer at a concentration of 3% can be used to enhance the penetration for lidocain across the skin.Objetivo: El objetivo del presente trabajo fue comparar y verificar la eficacia de Aloe vera (1 a 3%) con dimetilsulfoxido (1 a 3%) por su propiedad de mejora de la penetración para la administración tópica de lidocaína. Método: Carbopol 934 se usó como agente gelificante para la preparación de formulaciones de gel de lidocaína que contenían o no dimetilsulfoxido o Aloe vera (1%, 2% y 3%). Los geles se evaluaron por su aspecto físico, comportamiento reológico, contenido de fármaco, liberación de fármaco y estabilidad. Resultados: Se dedujo del resultado que la formulación del gel obtenido era adecuada en apariencia, homogeneidad y consistencia. Los perfiles de liberación de fármaco in vitro mostraron que conforme aumentaban el porcentaje de “Aloe vera” en las formulaciones, la tasa de liberación del fármaco se incrementaba sustancialmente. Se observó que la formulación F6 que contenía un 3% de Aloe vera como potenciador de la permeación exhibía un 79,18% de liberación de fármaco. De manera similar, para la formulación F3, que comprendía un 3% de DMSO como potenciador de la permeación, se encontró que la liberación del fármaco era del 84,52%. El uso de Aloe vera puede resultar beneficioso en comparación con los potenciadores de permeación sintéticos. Conclusión: Sobre la base de los resultados del estudio, se concluyó que el gel tópico de lidocaína preparado junto con Carbopol 934 mediante el uso de Aloe vera como un potenciador natural de la penetración a una concentración del 3%, se puede usar para mejorar la penetración de lidocaína en la piel

COMPARATIVE STANDARDIZATION OF MARKETED FORMULATIONS OF FERMENTED BIOMEDICINE – ARJUNARISTHA

Ayurvedic formulations have proved to be effective in the prevention and treatment of many life-threatening diseases. Asavas and Arishtas have been used as medicine for over 3000 years as appetizer and stimulant. In the present study 6 different marketed brands (Two having different batches) of Arjunarishta were thoroughly evaluated for their organoleptic characteristics and physicochemical parameters, to establish a routine procedure for standardization of these Ayurvedic formulations. The organoleptic tests performed include colour, odour and taste whereas the physicochemical parameters evaluated were pH, Refractive index, Specific gravity, Viscosity, density, surface tension, Water-soluble extractive, Alcohol-soluble extractive Acid value, Alcohol content, by distillation and  dichromate oxidation method, Total solid content, Total phenol content, In present communication, a TLC method was developed for the evaluation of Arjunarishta  by quantitative estimation of major compound gallic acid and ellagic acid

Glucosylceramide synthase upregulates MDR1 expression in the regulation of cancer drug resistance through cSrc and β-catenin signaling

<p>Abstract</p> <p>Background</p> <p>Drug resistance is the outcome of multiple-gene interactions in cancer cells under stress of anticancer agents. <it>MDR1 </it>overexpression is most commonly detected in drug-resistant cancers and accompanied with other gene alterations including enhanced glucosylceramide synthase (GCS). <it>MDR1 </it>encodes for P-glycoprotein that extrudes anticancer drugs. Polymorphisms of <it>MDR1 </it>disrupt the effects of P-glycoprotein antagonists and limit the success of drug resistance reversal in clinical trials. GCS converts ceramide to glucosylceramide, reducing the impact of ceramide-induced apoptosis and increasing glycosphingolipid (GSL) synthesis. Understanding the molecular mechanisms underlying <it>MDR1 </it>overexpression and how it interacts with GCS may find effective approaches to reverse drug resistance.</p> <p>Results</p> <p><it>MDR1 </it>and <it>GCS </it>were coincidently overexpressed in drug-resistant breast, ovary, cervical and colon cancer cells; silencing <it>GCS </it>using a novel mixed-backbone oligonucleotide (MBO-asGCS) sensitized these four drug-resistant cell lines to doxorubicin. This sensitization was correlated with the decreased <it>MDR1 </it>expression and the increased doxorubicin accumulation. Doxorubicin treatment induced GCS and <it>MDR1 </it>expression in tumors, but MBO-asGCS treatment eliminated "in-vivo" growth of drug-resistant tumor (NCI/ADR-RES). MBO-asGCS suppressed the expression of <it>MDR1 </it>with GCS and sensitized NCI/ADR-RES tumor to doxorubicin. The expression of P-glycoprotein and the function of its drug efflux of tumors were decreased by 4 and 8 times after MBO-asGCS treatment, even though this treatment did not have a significant effect on P-glycoprotein in normal small intestine. GCS transient transfection induced <it>MDR1 </it>overexpression and increased P-glycoprotein efflux in dose-dependent fashion in OVCAR-8 cancer cells. GSL profiling, silencing of globotriaosylceramide synthase and assessment of signaling pathway indicated that GCS transfection significantly increased globo series GSLs (globotriaosylceramide Gb3, globotetraosylceramide Gb4) on GSL-enriched microdomain (GEM), activated cSrc kinase, decreased β-catenin phosphorylation, and increased nuclear β-catenin. These consequently increased <it>MDR1 </it>promoter activation and its expression. Conversely, MBO-asGCS treatments decreased globo series GSLs (Gb3, Gb4), cSrc kinase and nuclear β-catenin, and suppressed <it>MDR-1 </it>expression in dose-dependent pattern.</p> <p>Conclusion</p> <p>This study demonstrates, for the first time, that GCS upregulates <it>MDR1 </it>expression modulating drug resistance of cancer. GSLs, in particular globo series GSLs mediate gene expression of <it>MDR1 </it>through cSrc and β-catenin signaling pathway.</p

Shape-based peak identification for ChIP-Seq

We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data analysis and provides a non-parametric approach that is robust to noise in experiments. Specifically, our method reduces the peak calling problem to the study of tree-based statistics derived from the data. We demonstrate the accuracy of our method on existing datasets, and we show that it can discover previously missed regions and can more clearly discriminate between multiple binding events. The software T-PIC (Tree shape Peak Identification for ChIP-Seq) is available at http://math.berkeley.edu/~vhower/tpic.htmlComment: 12 pages, 6 figure

Hypoglycemic effects of Lagenaria siceraria, Cynodon dactylon and Stevia rebaudiana extracts

Introduction: The aim of the current analysis was to judge the hypoglycemic action of the phyto-extracts of Lagenaria siceraria, Cynodon dactylon and Stevia rebaudiana using suitable in vitro approaches. Methods: The hypoglycemic activity of the phyto-material extracts was evaluated by employing various in-vitro methods namely glucose diffusion, amylolysis kinetics and glucose adsorption capacity. Results: The extracts of L. siceraria, C. dactylon and S. rebaudiana exhibited glucose dialysis retardation indices (GDRI) of 48.14%, 37.03% and 29.62%, respectively at 60 minutes which were reduced to 15.78%, 10.52% and 18.42%, respectively at 120 minutes. All the plant extracts used in the study adsorbed glucose and their adsorptions markedly enhanced with increase in sugar concentration. Conclusion: From the outcome of the assay it can be concluded that the extracts of L. siceraria, C. dactylon and S. rebaudiana have hypoglycemic activity as observed in various in-vitro assays. However, the beneficial actions require to be verified by adopting various in vivo techniques along with clinical trials for their efficient use as potential remedial moiety

Multi Agent System for Machine Learning Under Uncertainty in Cyber Physical Manufacturing System

Recent advancement in predictive machine learning has led to its application in various use cases in manufacturing. Most research focused on maximising predictive accuracy without addressing the uncertainty associated with it. While accuracy is important, focusing primarily on it poses an overfitting danger, exposing manufacturers to risk, ultimately hindering the adoption of these techniques. In this paper, we determine the sources of uncertainty in machine learning and establish the success criteria of a machine learning system to function well under uncertainty in a cyber-physical manufacturing system (CPMS) scenario. Then, we propose a multi-agent system architecture which leverages probabilistic machine learning as a means of achieving such criteria. We propose possible scenarios for which our architecture is useful and discuss future work. Experimentally, we implement Bayesian Neural Networks for multi-tasks classification on a public dataset for the real-time condition monitoring of a hydraulic system and demonstrate the usefulness of the system by evaluating the probability of a prediction being accurate given its uncertainty. We deploy these models using our proposed agent-based framework and integrate web visualisation to demonstrate its real-time feasibility