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Sample records for total rna extracted

  1. Extraction of total RNA in the developing chicken forebrain

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    Sayed Rasoul Zaker

    2014-01-01

    Full Text Available Background: Gene expression of Gama-Aminobutyric acid (GABA A receptor subunits may change during development. Procedures in molecular biology are required to understand the gene expression profile GABA A R in chicken. The outcome of the results depends on good-quality high-molecular-weight RNA. Several procedures can be used to isolate RNA from the brain of chicken; however, most of them are time-consuming and require disruption of cells or freeze and thaw in the presence of RNase inhibitors. The aim of this experiment was isolation of RNA from chicken embryonic brain tissues using appropriate RNA extraction kit. Materials and Methods: Fertilized eggs from Ross breed (Gallus gallus were incubated at 38°C and 60% relative humidity in a forced-draft incubator and were turned every 3 h. After 3, 7, 14 and 20 days of incubation, eggs were cooled on ice to induce deep anesthesia. Then whole brains were dissected out. As brains could not be excised in a reproducible way from earlier embryos (embryonic days 4 and 6, whole heads were collected. Chicken embryos between day 7 to 20 and 1 day after birth were decapitated, and their brains removed. Samples were immediately inserted into lysis buffer and stored at −70°C. Total RNA was isolated and a contaminating genomic deoxyribonucleic acid (DNA was digested. RNA quality was checked using gel electrophoresis. Results: We obtained 52 mg/ml to 745 mg/ml with A260/280 1.7-2.2. Only high-quality RNA, with no signs of degradation, was used for further experiments. Conclusion: In conclusion, protocol was found to be suitable for the isolation of total RNA from embryonic chicken cells.

  2. Comparative evaluation of total RNA extraction methods in Theobroma cacao using shoot apical meristems.

    Science.gov (United States)

    Silva, D V; Branco, S M J; Holanda, I S A; Royaert, S; Motamayor, J C; Marelli, J P; Corrêa, R X

    2016-03-04

    Theobroma cacao is a species of great economic importance with its beans used for chocolate production. The tree has been a target of various molecular studies. It contains many polyphenols, which complicate the extraction of nucleic acids with the extraction protocols requiring a large amount of plant material. These issues, therefore, necessitate the optimization of the protocols. The aim of the present study was to evaluate different methods for extraction of total RNA from shoot apical meristems of T. cacao 'CCN 51' and to assess the influence of storage conditions for the meristems on the extraction. The study also aimed to identify the most efficient protocol for RNA extraction using a small amount of plant material. Four different protocols were evaluated for RNA extraction using one shoot apical meristem per sample. Among these protocols, one that was more efficient was then tested to extract RNA using four different numbers of shoot apical meristems, subjected to three different storage conditions. The best protocol was tested for cDNA amplification using reverse transcription-polymerase chain reaction; the cDNA quality was determined to be satisfactory for molecular analyses. The study revealed that with the best RNA extraction protocol, one shoot apical meristem was sufficient for extraction of high-quality total RNA. The results obtained might enable advances in genetic analyses and molecular studies using reduced amount of plant material.

  3. Establishment of the total RNA extraction system for lily bulbs with ...

    African Journals Online (AJOL)

    USER

    2011-12-07

    Dec 7, 2011 ... The brightness of. CTAB was higher than that of SDS, which indicated that only improved CTAB method can extract biologically active. RNA from lily bulbs. DISCUSSION. The presence of RNase, which can be classified into endogenous and exogenous, is the major cause for the failure of RNA extraction.

  4. COMPARISON OF TWO TOTAL RNA EXTRACTION PROTOCOLS FROM CHO-K1 CELLS FOR RT-PCR: CUT-OFF COST FOR RESEARCHERS

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    Vasila Packeer Mohamed

    2014-05-01

    Full Text Available ABSTRACT: Various methods have been described to extract RNA from adherent mammalian cells. RNA isolation in conjunction with reverse transcription polymerase chain reaction (RT-PCR is a valuable tool used to study gene expression profiling. This approach is now being used in mammalian cell bioprocessing to help understand and improve the system. The objective of this study was to compare and determine the most suitable RNA extraction method for CHO-K1 cells in a setting where a relatively large amount of samples was involved. Total RNA was extracted using Total RNA purification kit (without DNase treatment; Norgen, Canada and RNeasy mini kit (with DNase treatment; Qiagen, USA respectively. The extracted RNA was then reverse transcribed, and the cDNA was subjected to PCR-amplifying 18S. Yield from RNeasy kit was significantly higher (0.316 ± 0.033 µg/µl; p=0.004 than Total RNA purification kit (0.177 ± 0.0243 µg/µl. However, RNA purity for both methods was close to 2.0 and there was no significant difference between the methods. Total RNA purification kit is less expensive than RNeasy kit. Since there is no DNase treatment step in the former, extraction time for RNA is shorter. When the extracted RNA was subjected to RT-PCR, both methods were able to show detection of 18S at 219 bp.   Therefore, this study demonstrates that both protocols are suitable for RNA extraction for CHO-K1 cells. RNeasy mini kit (Qiagen is recommended if higher yields is the primary concern and Total RNA Purification kit (Norgen is recommended if time and cost are concerned. ABSTRAK: Pelbagai kaedah telah digunakan untuk mengekstrak RNA daripada sel mamalia lekat.  Pemencilan RNA dengan menggunakan reaksi rantai polimerase transkripsi berbalik (RT-PCR merupakan kaedah penting yang digunakan dalam mengkaji pernyataan gen berprofil.  Pendekatan ini kini digunakan dalam pemprosesan bio sel mamalia untuk memahami dan menambah baik sistem.  Tujuan kajian dijalankan

  5. Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies.

    Science.gov (United States)

    Schneider, Dominik; Wemheuer, Franziska; Pfeiffer, Birgit; Wemheuer, Bernd

    2017-01-01

    Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has been increased in the last few years, the vast majority of marine diversity is rather unexplored. Moreover, most studies focused on the entire bacterial community and thus disregarded active microbial community players. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and for the generation of cDNA from the isolated RNA which can be used as a universal template in various marker gene studies.

  6. Extraction of total nucleic acid based on silica-coated magnetic particles for RT-qPCR detection of plant RNA virus/viroid.

    Science.gov (United States)

    Sun, Ning; Deng, Congliang; Zhao, Xiaoli; Zhou, Qi; Ge, Guanglu; Liu, Yi; Yan, Wenlong; Xia, Qiang

    2014-02-01

    In this study, a nucleic acid extraction method based on silica-coated magnetic particles (SMPs) and RT-qPCR assay was developed to detect Arabis mosaic virus (ArMV), Lily symptomless virus (LSV), Hop stunt viroid (HSVd) and grape yellow speckle viroid 1 (GYSVd-1). The amplification sequences of RT-qPCR were reversely transcribed in vitro as RNA standard templates. The standard curves covered six or seven orders of magnitude with a detection limit of 100 copies per each assay. Extraction efficiency of the SMPs method was evaluated by recovering spiked ssRNAs from plant samples and compared to two commercial kits (TRIzol and RNeasy Plant mini kit). Results showed that the recovery rate of SMPs method was comparable to the commercial kits when spiked ssRNAs were extracted from lily leaves, whereas it was two or three times higher than commercial kits when spiked ssRNAs were extracted from grapevine leaves. SMPs method was also used to extract viral nucleic acid from15 ArMV-positive lily leaf samples and 15 LSV-positive lily leaf samples. SMPs method did not show statistically significant difference from other methods on detecting ArMV, but LSV. The SMPs method has the same level of virus load as the TRIzol, and its mean virus load of was 0.5log10 lower than the RNeasy Plant mini kit. Nucleic acid was extracted from 19 grapevine-leaf samples with SMPs and the two commercial kits and subsequently screened for HSVd and GYSVd-1 by RT-qPCR. Regardless of HSVd or GYSVd-1, SMPs method outperforms other methods on both positive rate and the viroid load. In conclusion, SMPs method was able to efficiently extract the nucleic acid of RNA viruses or viroids, especially grapevine viroids, from lily-leaf or grapevine-leaf samples for RT-qPCR detection. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Isolation of Microarray-Grade Total RNA, MicroRNA, and DNA from a Single PAXgene Blood RNA Tube

    DEFF Research Database (Denmark)

    Kruhøffer, Mogens; Andersen, Lars Dyrskjøt; Voss, Thorsten

    2007-01-01

    We have developed a procedure for isolation of microRNA and genomic DNA in addition to total RNA from whole blood stabilized in PAXgene Blood RNA tubes. The procedure is based on automatic extraction on a BioRobot MDx and includes isolation of DNA from a fraction of the stabilized blood...... and recovery of small RNA species that are otherwise lost. The procedure presented here is suitable for large-scale experiments and is amenable to further automation. Procured total RNA and DNA was tested using Affymetrix Expression and single-nucleotide polymorphism GeneChips, respectively, and isolated micro......RNA was tested using spotted locked nucleic acid-based microarrays. We conclude that the yield and quality of total RNA, microRNA, and DNA from a single PAXgene blood RNA tube is sufficient for downstream microarray analysis....

  8. Preparation of Total RNA from Fission Yeast.

    Science.gov (United States)

    Bähler, Jürg; Wise, Jo Ann

    2017-04-03

    Treatment with hot phenol breaks open fission yeast cells and begins to strip away bound proteins from RNA. Deproteinization is completed by multiple extractions with chloroform/isoamyl alcohol and separation of the aqueous and organic phases using MaXtract gel, an inert material that acts as a physical barrier between the phases. The final step is concentration of the RNA by ethanol precipitation. The protocol can be used to prepare RNA from several cultures grown in parallel, but it is important not to process too many samples at once because delays can be detrimental to RNA quality. A reasonable number of samples to process at once would be three to four for microarray or RNA sequencing analyses and six for preliminary investigations of mutants implicated in RNA metabolism. © 2017 Cold Spring Harbor Laboratory Press.

  9. Extraction of low molecular weight RNA from Citrus trifolita tissues ...

    African Journals Online (AJOL)

    We employed a simple and quick method involving trizol for total RNA extraction from citrus tissues, then generation of LMW RNA using 4M LiCl, which have been successfully utilized in studies in our laboratory. Compared with traditional methods, this method is less expensive and produced high RNA yields while avoiding ...

  10. Human Milk MicroRNA and Total RNA Differ Depending on Milk Fractionation.

    Science.gov (United States)

    Alsaweed, Mohammed; Hepworth, Anna R; Lefèvre, Christophe; Hartmann, Peter E; Geddes, Donna T; Hassiotou, Foteini

    2015-10-01

    MicroRNA have been recently discovered in human milk signifying potentially important functions for both the lactating breast and the infant. Whilst human milk microRNA have started to be explored, little data exist on the evaluation of sample processing, and analysis to ensure that a full spectrum of microRNA can be obtained. Human milk comprises three main fractions: cells, skim milk, and lipids. Typically, the skim milk fraction has been measured in isolation despite evidence that the lipid fraction may contain more microRNA. This study aimed to standardize isolation of microRNA and total RNA from all three fractions of human milk to determine the most appropriate sampling and analysis procedure for future studies. Three different methods from eight commercially available kits were tested for their efficacy in extracting total RNA and microRNA from the lipid, skim, and cell fractions of human milk. Each fraction yielded different concentrations of RNA and microRNA, with the highest quantities found in the cell and lipid fractions, and the lowest in skim milk. The column-based phenol-free method was the most efficient extraction method for all three milk fractions. Two microRNAs were expressed and validated in the three milk fractions by qPCR using the three recommended extraction kits for each fraction. High expression levels were identified in the skim and lipid milk factions for these microRNAs. These results suggest that careful consideration of both the human milk sample preparation and extraction protocols should be made prior to embarking upon research in this area. © 2015 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.

  11. Parallel RNA extraction using magnetic beads and a droplet array.

    Science.gov (United States)

    Shi, Xu; Chen, Chun-Hong; Gao, Weimin; Chao, Shih-Hui; Meldrum, Deirdre R

    2015-02-21

    Nucleic acid extraction is a necessary step for most genomic/transcriptomic analyses, but it often requires complicated mechanisms to be integrated into a lab-on-a-chip device. Here, we present a simple, effective configuration for rapidly obtaining purified RNA from low concentration cell medium. This Total RNA Extraction Droplet Array (TREDA) utilizes an array of surface-adhering droplets to facilitate the transportation of magnetic purification beads seamlessly through individual buffer solutions without solid structures. The fabrication of TREDA chips is rapid and does not require a microfabrication facility or expertise. The process takes less than 5 minutes. When purifying mRNA from bulk marine diatom samples, its repeatability and extraction efficiency are comparable to conventional tube-based operations. We demonstrate that TREDA can extract the total mRNA of about 10 marine diatom cells, indicating that the sensitivity of TREDA approaches single-digit cell numbers.

  12. Comparison of RNA extraction methods in Thai aromatic coconut water

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    Nopporn Jaroonchon

    2015-10-01

    Full Text Available Many researches have reported that nucleic acid in coconut water is in free form and at very low yields which makes it difficult to process in molecular studies. Our research attempted to compare two extraction methods to obtain a higher yield of total RNA in aromatic coconut water and monitor its change at various fruit stages. The first method used ethanol and sodium acetate as reagents; the second method used lithium chloride. We found that extraction using only lithium chloride gave a higher total RNA yield than the method using ethanol to precipitate nucleic acid. In addition, the total RNA from both methods could be used in amplification of betaine aldehyde dehydrogenase2 (Badh2 genes, which is involved in coconut aroma biosynthesis, and could be used to perform further study as we expected. From the molecular study, the nucleic acid found in coconut water increased with fruit age.

  13. TruSeq Stranded mRNA and Total RNA Sample Preparation Kits

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    Total RNA-Seq enabled by ribosomal RNA (rRNA) reduction is compatible with formalin-fixed paraffin embedded (FFPE) samples, which contain potentially critical biological information. The family of TruSeq Stranded Total RNA sample preparation kits provides a unique combination of unmatched data quality for both mRNA and whole-transcriptome analyses, robust interrogation of both standard and low-quality samples and workflows compatible with a wide range of study designs.

  14. A Simple and Efficient RNA Extraction Method from Deep-Sea Hydrothermal Vent Chimney Structures.

    Science.gov (United States)

    Muto, Hisashi; Takaki, Yoshihiro; Hirai, Miho; Mino, Sayaka; Sawayama, Shigeki; Takai, Ken; Nakagawa, Satoshi

    2017-12-27

    RNA-based microbiological analyses, e.g., transcriptome and reverse transcription-quantitative PCR, require a relatively large amount of high quality RNA. RNA-based analyses on microbial communities in deep-sea hydrothermal environments often encounter methodological difficulties with RNA extraction due to the presence of unique minerals in and the low biomass of samples. In the present study, we assessed RNA extraction methods for deep-sea vent chimneys that had complex mineral compositions. Mineral-RNA adsorption experiments were conducted using mock chimney minerals and Escherichia coli total RNA solution, and showed that detectable RNA significantly decreased possibly due to adsorption onto minerals. This decrease in RNA was prevented by the addition of sodium tripolyphosphate (STPP), deoxynucleotide triphosphates (dNTPs), salmon sperm DNA, and NaOH. The addition of STPP was also effective for RNA extraction from the mixture of E. coli cells and mock chimney minerals when TRIzol reagent and the RNeasy column were used, but not when the RNeasy PowerSoil total RNA kit was used. A combination of STPP, TRIzol reagent, the RNeasy column, and sonication resulted in the highest RNA yield from a natural chimney. This indirect extraction procedure is simple, rapid, inexpensive, and may be used for large-scale RNA extraction.

  15. High-quality total RNA isolation from melon (Cucumis melo L. fruits rich in polysaccharides

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    Gabrielle Silveira de Campos

    2017-08-01

    Full Text Available Melon, a member of the family Cucurbitaceae, is the fourth most important fruit in the world market and, on a volume basis, is Brazil’s main fresh fruit export. Many molecular techniques used to understand the maturation of these fruits require high concentrations of highly purified RNA. However, melons are rich in polyphenolic compounds and polysaccharides, which interfere with RNA extraction. This study aimed to determine the most appropriate method for total RNA extraction from melon fruits. Six extraction buffers were tested: T1 guanidine thiocyanate/phenol/chloroform; T2 sodium azide/?-mercaptoethanol; T3 phenol/guanidine thiocyanate; T4 CTAB/PVP/?-mercaptoethanol; T5 SDS/sodium perchlorate/PVP/?-mercaptoethanol, and T6 sarkosyl/PVP/guanidine thiocyanate, using the AxyPrepTM Multisource Total RNA Miniprep Kit. The best method for extracting RNA from both mature and green fruit was based on the SDS/PVP/?-mercaptoethanol buffer, because it rapidly generated a high quality and quantity of material. In general, higher amounts of RNA were obtained from green than mature fruits, probably due to the lower concentration of polysaccharides and water. The purified material can be used as a template in molecular techniques, such as microarrays, RT-PCR, and in the construction of cDNA and RNA-seq data.

  16. Optimization of RNA Extraction from Rat Pancreatic Tissue

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    Sanaz Dastgheib

    2014-05-01

    Full Text Available Background: Optimized RNA extraction from tissues and cell lines consists of four main stages regardless of the method of extraction: 1 homogenizing, 2 effective denaturation of proteins from RNA, 3 inactivation of ribonuclease, and 4 removal of any DNA, protein, and carbohydrate contamination. Isolation of undamaged intact RNA is challenging when the related tissue contains high levels of RNase. Various technical difficulties occur during extraction of RNA from pancreatic tissue due to spontaneous autolysis. Since standard routine protocols yield unacceptable results in pancrease, we have designed a simple method for RNA extraction by comparing different protocols. Methods: We obtained 20-30 mg pancreatic tissues in less than 2 min from 30 rats. Several methods were performed to extract RNA from pancreatic tissue and evaluate its integrity. All methods were performed three times to obtain reproducible results. Results: Immersing pancreatic tissue in RNA-later for 24 h at -80ºC yielded high quality RNA by using the TriPure reagent which was comparable to the commercial RNeasy Micro Kit. The quality of RNA was evaluated by spectrophotometer, electrophoresis and RT-PCR. We separated intact 28S and 18S ribosomal RNA (rRNA when our procedure was compared with the RNeasy Micro Kit. Finally, full length of the actin gene was amplified by RT-PCR. Conclusion: We designed a simple, fast, cost-effective method for complete RNA extraction from the least amount of quantitatively intact pancreatic tissue

  17. Isolation of high-quality total RNA from leaves of Myrciaria dubia "CAMU CAMU".

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    Gómez, Juan Carlos Castro; Reátegui, Alina Del Carmen Egoavil; Flores, Julián Torres; Saavedra, Roberson Ramírez; Ruiz, Marianela Cobos; Correa, Sixto Alfredo Imán

    2013-01-01

    Myrciaria dubia is a main source of vitamin C for people in the Amazon region. Molecular studies of M. dubia require high-quality total RNA from different tissues. So far, no protocols have been reported for total RNA isolation from leaves of this species. The objective of this research was to develop protocols for extracting high-quality total RNA from leaves of M. dubia. Total RNA was purified following two modified protocols developed for leaves of other species (by Zeng and Yang, and by Reid et al.) and one modified protocol developed for fruits of the studied species (by Silva). Quantity and quality of purified total RNA were assessed by spectrophotometric and electrophoretic analysis. Additionally, quality of total RNA was evaluated with reverse-transcription polymerase chain reaction (RT-PCR). With these three modified protocols we were able to isolate high-quality RNA (A260nm/A280nm >1.9 and A260nm/A230nm >2.0). Highest yield was produced with the Zeng and Yang modified protocol (384±46µg ARN/g fresh weight). Furthermore, electrophoretic analysis showed the integrity of isolated RNA and the absence of DNA. Another proof of the high quality of our purified RNA was the successful cDNA synthesis and amplification of a segment of the M. dubia actin 1 gene. We report three modified protocols for isolation total RNA from leaves of M. dubia. The modified protocols are easy, rapid, low in cost, and effective for high-quality and quantity total RNA isolation suitable for cDNA synthesis and polymerase chain reaction.

  18. Comparison of methods for miRNA extraction from plasma and quantitative recovery of RNA from plasma and cerebrospinal fluid

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    Melissa A McAlexander

    2013-05-01

    Full Text Available Interest in extracellular RNA has intensified as evidence accumulates that these molecules may be useful as indicators of a wide variety of biological conditions. To establish specific extracellular RNA molecules as clinically relevant biomarkers, reproducible recovery from biological samples and reliable measurements of the isolated RNA are paramount. Towards these ends, careful and rigorous comparisons of technical procedures are needed at all steps from sample handling to RNA isolation to RNA measurement protocols. In the investigations described in this methods paper, RT-qPCR was used to examine the apparent recovery of specific endogenous miRNAs and a spiked-in synthetic RNA from blood plasma samples. RNA was isolated using several widely used RNA isolation kits, with or without the addition of glycogen as a carrier. Kits examined included total RNA isolation systems that have been commercially available for several years and commonly adapted for extraction of biofluid RNA, as well as more recently introduced biofluids-specific RNA methods. Our conclusions include the following: some RNA isolation methods appear to be superior to others for the recovery of RNA from biological fluids; addition of a carrier molecule seems to be beneficial for some but not all isolation methods; and partially or fully quantitative recovery of RNA is observed from increasing volumes of plasma and cerebrospinal fluid.

  19. Extraction of low molecular weight RNA from Citrus trifolita tissues ...

    African Journals Online (AJOL)

    Jane

    2010-12-20

    Dec 20, 2010 ... many biological and metabolic processes, including tissue ... water before getting LMW RNA. ... 1 cm) were collected from five-year-old trifoliate orange (C. ... using 700 µl 75% ethanol and total RNA was precipitated by.

  20. Graphene Oxide Conjugated Magnetic Beads for RNA Extraction.

    Science.gov (United States)

    Pham, Xuan-Hung; Baek, Ahruem; Kim, Tae Han; Lee, Sang Hun; Rho, Won-Yeop; Chung, Woo-Jae; Kim, Dong-Eun; Jun, Bong-Hyun

    2017-08-04

    A magnetic material that consists of silica-coated magnetic beads conjugated with graphene oxide (GO) was successfully prepared for facile ribonucleic acid (RNA) extraction. When the GO-modified magnetic beads were applied to separate the RNA from the lysed cell, the cellular RNAs were readily adsorbed to and readily desorbed from the surface of the GO-modified magnetic beads by urea. The amount of RNA extracted by the GO-modified magnetic beads was ≈170 % as much as those of the control extracted by a conventional phenol-based chaotropic solution. These results demonstrate that the facile method of RNA separation by using GO-modified magnetic beads as an adsorbent is an efficient and simple way to purify intact cellular RNAs and/or microRNA from cell lysates. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Comparison of RNA extraction methods from biofilm samples of Staphylococcus epidermidis

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    França Angela

    2011-12-01

    Full Text Available Abstract Background Microbial biofilms are communities of bacteria adhered to a surface and surrounded by an extracellular polymeric matrix. Biofilms have been associated with increased antibiotic resistance and tolerance to the immune system. Staphylococcus epidermidis is the major bacterial species found in biofilm-related infections on indwelling medical devices. Obtaining high quality mRNA from biofilms is crucial to validate the transcriptional measurements associated with the switching to the biofilm mode of growth. Therefore, we selected three commercially available RNA extraction kits with distinct characteristics, including those using silica membrane or organic extraction methods, and enzymatic or mechanical cell lysis, and evaluated the RNA quality obtained from two distinct S. epidermidis bacterial biofilms. Results RNA extracted using the different kits was evaluated for quantity, purity, integrity, and functionally. All kits were able to extract intact and functional total RNA from the biofilms generated from each S. epidermidis strain. The results demonstrated that the kit based on mechanical lysis and organic extraction (FastRNA® Pro Blue was the only one that was able to isolate pure and large quantities of RNA. Normalized expression of the icaA virulence gene showed that RNA extracted with PureLink™ had a significant lower concentration of icaA mRNA transcripts than the other kits tested. Conclusions When working with complex samples, such as biofilms, that contain a high content extracellular polysaccharide and proteins, special care should be taken when selecting the appropriate RNA extraction system, in order to obtain accurate, reproducible, and biologically significant results. Among the RNA extraction kits tested, FastRNA® Pro Blue was the best option for both S. epidermidis biofilms used.

  2. Extraction of mRNA from coagulated horse blood and analysis of inflammation-related cytokine responses to coagulation

    DEFF Research Database (Denmark)

    Bovbjerg, Kirsten Katrine Lindegaard; Heegaard, Peter M. H.; Skovgaard, Kerstin

    2010-01-01

    the peripheral blood mononuclear cells present in the blood clot, homogenizing the clot by rotating knife homogenization (GentleMACS, Miltenyi Biotec) in the presence of QIAzol extraction buffer (Qiagen). The RNA extracted yielded high concentrations of total RNA (50-265 ng/μl) and quality measures (RIN=8...

  3. Response Surface Optimized Extraction of Total Triterpene Acids ...

    African Journals Online (AJOL)

    Purpose: To optimize extraction of total triterpene acids from loquat leaf and evaluate their in vitro antioxidant activities. Methods: The independent variables were ethanol concentration, extraction time, and solvent ratio, while the dependent variable was content of total triterpene acids. Composite design and response ...

  4. Total lipid profile with aqueous fruit extract of Solanum macrocarpum ...

    African Journals Online (AJOL)

    Abstract. Studies were undertaken to investigate the effects of the aqueous fruit extract of Solanum macrocarpum Linn. on the total lipid profile: total cholesterol, triglycerides, high density lipoprotein-cholesterol (HDL-C) and low density lipoprotein-cholesterol (LDL-C) on hypercholesterolaemic rats. Total serum cholesterol ...

  5. Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study

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    Lui Wing-bong

    2006-02-01

    Full Text Available Abstract Background We have previously developed a test for the diagnosis and prognostic assessment of the severe acute respiratory syndrome (SARS based on the detection of the SARS-coronavirus RNA in serum by real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR. In this study, we evaluated the feasibility of automating the serum RNA extraction procedure in order to increase the throughput of the assay. Methods An automated nucleic acid extraction platform using the MagNA Pure LC instrument (Roche Diagnostics was evaluated. We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The modified protocol was compared with a column-based extraction kit (QIAamp viral RNA mini kit, Qiagen for quantitative performance, analytical sensitivity and precision. Results The newly developed automated protocol was shown to be free from carry-over contamination and have comparable performance with other standard protocols and kits designed for the MagNA Pure LC instrument. However, the automated method was found to be less sensitive, less precise and led to consistently lower serum SARS-coronavirus concentrations when compared with the column-based extraction method. Conclusion As the diagnostic efficiency and prognostic value of the serum SARS-CoV RNA RT-PCR test is critically associated with the analytical sensitivity and quantitative performance contributed both by the RNA extraction and RT-PCR components of the test, we recommend the use of the column-based manual RNA extraction method.

  6. Microwave-assisted extraction and antihyperlipidemic effect of total ...

    African Journals Online (AJOL)

    The process of microwave-assisted extraction (MAE) of total flavonoids from corn silk and the hypolipidemia in animal models were studied. Influence of solvent concentration, microwave power, extraction time and dose of solvent were investigated and then, the orthogonal experiments were performed. Animal models of ...

  7. Total Phenol amd Flavonoid contents of Crude Extract and Fractions ...

    African Journals Online (AJOL)

    Phenolic compounds are numerous in plants and are essential part of human diet. Picralima nitida has been extensively used in African folk medicine especially in West Africa. The present study evaluated the total phenolic and flavonoid contents of the extract and fractions of Picralima nitida. The methanol extracts of P.

  8. ANTIOXIDANT ACTIVITY, TOTAL PHENOLIC AND FLAVONOID CONTENT OF MORINDA CITRIFOLIA FRUIT EXTRACTS FROM VARIOUS EXTRACTION PROCESSES

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    PRAVEEN K. RAMAMOORTHY

    2007-04-01

    Full Text Available Soxhlet, Ultrasonic extract of Morinda citrifolia L. fruit and four extracts from high pressure extraction at 10 MPa using ethanol, ethyl acetate as solvent and dried by vacuum oven and spray dryer were analyzed for their antioxidant activity by peroxide value method and diphenylpicrylhydrazyl radical scavenging method. The five extracts along with the reference samples, butylated hydroxyl toluene and tannic acid were further analyzed to determine their total phenolic content by Folin-Ciocalteau method and total flavonoid content by Dowd method. The M. citrifolia extract by high pressure extraction with ethyl acetate as solvent and spray dried was found to exhibit highest antioxidant activity and total flavonoid content. High total phenolic content was determined in the high pressure extract using ethyl acetate as solvent and vacuum dried. It was interesting to note that ultrasonic extract exhibited significant antioxidant activity, total phenolic and flavonoid content. High pressure extracted M. citrifolia in ethanol was found to express lesser values comparatively. The significant difference in activity among the high pressure extracts was found to be due to the polarity of the solvents used for extraction as M. citrifolia fruit contains relatively larger quantity of non-polar antioxidant compounds. It was also found that the drying methods had significant impact on the antioxidant activity, total phenolic and flavonoid content of the extracts.

  9. Molecular Techniques for Dicistrovirus Detection without RNA Extraction or Purification

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    Jailson F. B. Querido

    2013-01-01

    Full Text Available Dicistroviridae is a new family of small, nonenveloped, and +ssRNA viruses pathogenic to both beneficial arthropods and insect pests as well. Triatoma virus (TrV, a dicistrovirus, is a pathogen of Triatoma infestans (Hemiptera: Reduviidae, one of the main vectors of Chagas disease. In this work, we report a single-step method to identify TrV, a dicistrovirus, isolated from fecal samples of triatomines. The identification method proved to be quite sensitive, even without the extraction and purification of RNA virus.

  10. Extraction and determination of total flavonoids in jujube by alcohol extraction

    Science.gov (United States)

    Ji, Y. B.; Ru, X.; Yu, M.; Wang, S. W.; Lu, L.; Qiao, A. N.; Guo, A. Z.

    2017-12-01

    Jujube is a ripe fruit of Rhamnaceae. Its main active component is flavonoids, so the extraction and determination of total flavonoids in jujube will help to develop and utilize the medicinal value of jujube. In this study, the total flavonoids were extracted from jujube by alcohol extraction method. Through single factor investigation and orthogonal test, it was found that the total flavonoids content in jujube was the highest under the condition of 70°C, material ratio of 1:40, and extraction of 30 min by 70% ethanol. The content of total flavonoids in the extract of jujube was 1.57% at the wavelength of 510 nm by UV and rutin as the standard. The method was evaluated by methodological study, and it was determined that this method could be used as the detection of total flavonoids in jujube extraction.

  11. RNA extraction from decaying wood for (meta)transcriptomic analyses.

    Science.gov (United States)

    Adamo, Martino; Voyron, Samuele; Girlanda, Mariangela; Marmeisse, Roland

    2017-10-01

    Wood decomposition is a key step of the terrestrial carbon cycle and is of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating in wood decay, we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds. This protocol was implemented on 22 wood samples representing as many tree species from 11 plant families in the Angiosperms and Gymnosperms. RNA was successfully extracted from all samples and converted into cDNAs from which were amplified both fungal and bacterial protein coding genes, including genes encoding hydrolytic enzymes participating in lignocellulose hydrolysis. This protocol applicable to a wide range of decomposing wood types represents a first step towards a metatranscriptomic analysis of wood degradation under natural conditions.

  12. Isolation of high-quality total RNA from rumen anaerobic bacteria and fungi, and subsequent detection of glycoside hydrolases.

    Science.gov (United States)

    Wang, Pan; Qi, Meng; Barboza, Perry; Leigh, Mary Beth; Ungerfeld, Emilio; Selinger, L Brent; McAllister, Tim A; Forster, Robert J

    2011-07-01

    The rumen is one of the most powerful fibrolytic fermentation systems known. Gene expression analyses, such as reverse transcription PCR (RT-PCR), microarrays, and metatranscriptomics, are techniques that could significantly expand our understanding of this ecosystem. The ability to isolate and stabilize representative RNA samples is critical to obtaining reliable results with these procedures. In this study, we successfully isolated high-quality total RNA from the solid phase of ruminal contents by using an improved RNA extraction method. This method is based on liquid nitrogen grinding of whole ruminal solids without microbial detachment and acid guanidinium - phenol - chloroform extraction combined with column purification. Yields of total RNA were as high as 150 µg per g of fresh ruminal content. The typical large subunit/small subunit rRNA ratio ranged from 1.8 to 2.0 with an RNA integrity number (Agilent Technologies) greater than 8.5. By eliminating the detachment step, the resulting RNA was more representative of the complete ecosystem. Our improved method removed a major barrier limiting analysis of rumen microbial function from a gene expression perspective. The polyA-tailed eukaryotic mRNAs obtained have successfully been applied to next-generation sequencing, and metatranscriptomic analysis of the solid fraction of rumen contents revealed abundant sequences related to rumen fungi.

  13. Phytochemical screening, total phenolic, total flavonoids contents and antioxidant activity of cinchona ledgeriana leaves ethanol extract

    Science.gov (United States)

    Sundowo, Andini; Artanti, Nina; Hanafi, M.; Minarti, Primahana, Gian

    2017-11-01

    C ledgeriana is a medicinal plant that contains alkaloids, especially on the barks for commercial production of quinine as antimalarial. The main alkaloids in this plant are cinchonine, cinchonidine, quinine and quinidine. Besides for antiamalarial this plant is also commonly used to treat whooping cough, influenza and dysentery. Compare to other medicinal plants, nowadays only very few studies were conducted in Cinchona species. Our current study aims to determine the content of phytochemical, total phenol and total flavonoids from C. ledgeriana leaves 70% ethanol extract. The extraction was performed by maceration method using 70% ethanol solvent and then fractionated into hexane, ethylacetate and butanol. Phytochemical screening was performed to determine the content of alkaloids, flavonoids, terpenoids, tannins and saponins. Total phenol and flavonoid contents of the extract were determined by Folin-Ciocalteu and alumunium chloride colorimetric methods using gallic acid and quercetin as standards. The antioxidant activity was determined by using 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity. The results of phytochemical screening showed that the 70% ethanol extract of C. ledgeriana leaves contained alkaloids, flavonoids, terpenoids, tannins and saponins. The total phenol and total flavonoids analysis showed that ethyl acetate fraction had the highest total phenol (40.23%) and total flavonoids (65.34%).

  14. rich extract on total polyphenols and antioxidant activity obtained

    African Journals Online (AJOL)

    Z. Ghouila

    USTHB, Organic Functional Analysis Laboratory, 16111 Bab Ezzouar, Algiers, ... Keywords: Ahmeur Bouamer, extraction, grape seeds, total polyphenols, ... These compounds are known as good natural antioxidant agents arising from natural ... surface between solid and liquid phases; this is mainly due to the dispersion of ...

  15. Comparison of RNA Extraction Methods for Molecular Analysis of Oral Cytology

    Directory of Open Access Journals (Sweden)

    Mônica Ghislaine Oliveira Alves

    2016-01-01

    Full Text Available Objective of work: The aim of this study was to compare three methods of RNA extraction for molecular analysis of oral cytology to establish the best technique, considering its concentration and purity for molecular tests of oral lesions such as real-time reverse transcriptase reaction. Material and methods: The sample included exfoliative cytology from the oral cavity mucosa of patients with no visible clinical changes, using Orcellex Rovers Brush®. The extraction of total RNA was performed using the following three techniques: 30 samples were extracted by Trizol® technique, 30 by the DirectzolTM RNA Miniprep system and 30 by the RNeasy mini Kit. The absorbance was measured by spectrophotometer to estimate the purity. The estimated RNA concentration was obtained by multiplying the value of A260 (ng/mL by 40. Statistical analysis of the obtained data was performed using GraphPad Prism 5.03 software with Student t, analysis of variance and Bonferroni tests, considering p ≤0.05. Results: Trizol® group revealed higher average concentration, followed by Direct-zolTM and Rneasy group. It was observed that the RNA Direct-zolTM group had the highest purity, followed by RNeasy and Trizol® groups, allowing for the two ratios. Conclusion: Considering all aspects, concentration, purity and time spent in the procedures, the Direct-zolTM group showed the best results.

  16. PIG-B: a homemade monophasic cocktail for the extraction of RNA.

    Science.gov (United States)

    Weber, K; Bolander, M E; Sarkar, G

    1998-02-01

    An inexpensive monophasic reagent has been developed for the extraction of total RNA from cells or tissues. The main ingredients of the reagent are Phenol, Isoamyl alcohol, Guanidinium isothiocyanate, and Beta-mercaptoethanol (PIG-B). The quality and yield of RNA obtained by this reagent is at par with that obtained by TRIzol, an expensive but widely used monophasic reagent available commercially. The complete composition and method of preparation of PIG-B is provided to aid preparation of the reagent in the laboratory.

  17. Sample preservation, transport and processing strategies for honeybee RNA extraction: Influence on RNA yield, quality, target quantification and data normalization.

    Science.gov (United States)

    Forsgren, Eva; Locke, Barbara; Semberg, Emilia; Laugen, Ane T; Miranda, Joachim R de

    2017-08-01

    Viral infections in managed honey bees are numerous, and most of them are caused by viruses with an RNA genome. Since RNA degrades rapidly, appropriate sample management and RNA extraction methods are imperative to get high quality RNA for downstream assays. This study evaluated the effect of various sampling-transport scenarios (combinations of temperature, RNA stabilizers, and duration) of transport on six RNA quality parameters; yield, purity, integrity, cDNA synthesis efficiency, target detection and quantification. The use of water and extraction buffer were also compared for a primary bee tissue homogenate prior to RNA extraction. The strategy least affected by time was preservation of samples at -80°C. All other regimens turned out to be poor alternatives unless the samples were frozen or processed within 24h. Chemical stabilizers have the greatest impact on RNA quality and adding an extra homogenization step (a QIAshredder™ homogenizer) to the extraction protocol significantly improves the RNA yield and chemical purity. This study confirms that RIN values (RNA Integrity Number), should be used cautiously with bee RNA. Using water for the primary homogenate has no negative effect on RNA quality as long as this step is no longer than 15min. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. ncRNA-class Web Tool: Non-coding RNA feature extraction and pre-miRNA classification web tool

    KAUST Repository

    Kleftogiannis, Dimitrios A.; Theofilatos, Konstantinos A.; Papadimitriou, Stergios; Tsakalidis, Athanasios K.; Likothanassis, Spiridon D.; Mavroudi, Seferina P.

    2012-01-01

    Until recently, it was commonly accepted that most genetic information is transacted by proteins. Recent evidence suggests that the majority of the genomes of mammals and other complex organisms are in fact transcribed into non-coding RNAs (ncRNAs), many of which are alternatively spliced and/or processed into smaller products. Non coding RNA genes analysis requires the calculation of several sequential, thermodynamical and structural features. Many independent tools have already been developed for the efficient calculation of such features but to the best of our knowledge there does not exist any integrative approach for this task. The most significant amount of existing work is related to the miRNA class of non-coding RNAs. MicroRNAs (miRNAs) are small non-coding RNAs that play a significant role in gene regulation and their prediction is a challenging bioinformatics problem. Non-coding RNA feature extraction and pre-miRNA classification Web Tool (ncRNA-class Web Tool) is a publicly available web tool ( http://150.140.142.24:82/Default.aspx ) which provides a user friendly and efficient environment for the effective calculation of a set of 58 sequential, thermodynamical and structural features of non-coding RNAs, plus a tool for the accurate prediction of miRNAs. © 2012 IFIP International Federation for Information Processing.

  19. An Improved Quick Method for the Isolation of Total RNA from Cotton ...

    African Journals Online (AJOL)

    David PANG

    2011-11-02

    Nov 2, 2011 ... in liquid nitrogen in a mortar and pestle and stored until. RNA isolation. ... our laboratory for microarray analysis, cDNA pyro- sequencing studies and construction ..... Economic and rapid method for extracting cotton genomic ...

  20. Isolated total RNA and protein are preserved after thawing for more than twenty-four hours

    Science.gov (United States)

    de Oliveira, Ivone Braga; Ramos, Débora Rothstein; Lopes, Karen Lucasechi; de Souza, Regiane Machado; Heimann, Joel Claudio; Furukawa, Luzia Naôko Shinohara

    2012-01-01

    OBJECTIVE: The preservation of biological samples at a low temperature is important for later biochemical and/or histological analyses. However, the molecular viability of thawed samples has not been studied sufficiently in depth. The present study was undertaken to evaluate the viability of intact tissues, tissue homogenates, and isolated total RNA after defrosting for more than twenty-four hours. METHODS: The molecular viability of the thawed samples (n = 82) was assessed using the A260/A280 ratio, the RNA concentration, the RNA integrity, the level of intact mRNA determined by reverse transcriptase polymerase chain reaction, the protein level determined by Western blotting, and an examination of the histological structure. RESULTS: The integrity of the total RNA was not preserved in the thawed intact tissue, but the RNA integrity and level of mRNA were perfectly preserved in isolated defrosted samples of total RNA. Additionally, the level of β-actin protein was preserved in both thawed intact tissue and homogenates. CONCLUSION: Isolated total RNA does not undergo degradation due to thawing for at least 24 hours, and it is recommended to isolate the total RNA as soon as possible after tissue collection. Moreover, the protein level is preserved in defrosted tissues. PMID:22473407

  1. Extractions of High Quality RNA from the Seeds of Jerusalem Artichoke and Other Plant Species with High Levels of Starch and Lipid.

    Science.gov (United States)

    Mornkham, Tanupat; Wangsomnuk, Preeya Puangsomlee; Fu, Yong-Bi; Wangsomnuk, Pinich; Jogloy, Sanun; Patanothai, Aran

    2013-04-29

    Jerusalem artichoke (Helianthus tuberosus L.) is an important tuber crop. However, Jerusalem artichoke seeds contain high levels of starch and lipid, making the extraction of high-quality RNA extremely difficult and the gene expression analysis challenging. This study was aimed to improve existing methods for extracting total RNA from Jerusalem artichoke dry seeds and to assess the applicability of the improved method in other plant species. Five RNA extraction methods were evaluated on Jerusalem artichoke seeds and two were modified. One modified method with the significant improvement was applied to assay seeds of diverse Jerusalem artichoke accessions, sunflower, rice, maize, peanut and marigold. The effectiveness of the improved method to extract total RNA from seeds was assessed using qPCR analysis of four selected genes. The improved method of Ma and Yang (2011) yielded a maximum RNA solubility and removed most interfering substances. The improved protocol generated 29 to 41 µg RNA/30 mg fresh weight. An A260/A280 ratio of 1.79 to 2.22 showed their RNA purity. Extracted RNA was effective for downstream applications such as first-stranded cDNA synthesis, cDNA cloning and qPCR. The improved method was also effective to extract total RNA from seeds of sunflower, rice, maize and peanut that are rich in polyphenols, lipids and polysaccharides.

  2. Extractions of High Quality RNA from the Seeds of Jerusalem Artichoke and Other Plant Species with High Levels of Starch and Lipid

    Directory of Open Access Journals (Sweden)

    Tanupat Mornkham

    2013-04-01

    Full Text Available Jerusalem artichoke (Helianthus tuberosus L. is an important tuber crop. However, Jerusalem artichoke seeds contain high levels of starch and lipid, making the extraction of high-quality RNA extremely difficult and the gene expression analysis challenging. This study was aimed to improve existing methods for extracting total RNA from Jerusalem artichoke dry seeds and to assess the applicability of the improved method in other plant species. Five RNA extraction methods were evaluated on Jerusalem artichoke seeds and two were modified. One modified method with the significant improvement was applied to assay seeds of diverse Jerusalem artichoke accessions, sunflower, rice, maize, peanut and marigold. The effectiveness of the improved method to extract total RNA from seeds was assessed using qPCR analysis of four selected genes. The improved method of Ma and Yang (2011 yielded a maximum RNA solubility and removed most interfering substances. The improved protocol generated 29 to 41 µg RNA/30 mg fresh weight. An A260/A280 ratio of 1.79 to 2.22 showed their RNA purity. Extracted RNA was effective for downstream applications such as first-stranded cDNA synthesis, cDNA cloning and qPCR. The improved method was also effective to extract total RNA from seeds of sunflower, rice, maize and peanut that are rich in polyphenols, lipids and polysaccharides.

  3. Antioxidant Activities of Total Pigment Extract from Blackberries

    Directory of Open Access Journals (Sweden)

    Jiechao Liu

    2005-01-01

    Full Text Available Total pigment has been extracted from blackberries and its antioxidant activity against lipid peroxidation and scavenging capacities towards superoxide anion radicals, hydroxyl radicals and nitrite in different in vitro systems have been investigated. The total pigment extract from blackberries (TPEB exhibited strong antioxidant activity against lipid peroxidation in a linoleic acid model system and scavenging capacities towards superoxide anion radicals, generated by a pyrogallol autoxidation system or by an illuminating riboflavin system, hydroxyl radicals generated by Fenton reaction, and nitrite. Furthermore, the antioxidant activities were correlated with the concentrations of the TPEB. In the test concentration range, the maximum inhibition percentage against linoleic acid peroxidation was 98.32 % after one week’s incubation, and the maximum scavenging percentages for the free radicals and nitrite inhibition in the above reactive systems reached 90.48, 96.48, 93.58 and 98.94 %, respectively. The TPEB is a natural, edible colorant with excellent antioxidant activities and health benefits and it seems to be applicable in both healthy food and medicine.

  4. Soil DNA extraction procedure influences protist 18S rRNA gene community profiling outcome

    DEFF Research Database (Denmark)

    Santos, Susana S.; Nunes, Ines Marques; Nielsen, Tue K.

    2017-01-01

    Advances in sequencing technologies allow deeper studies of the soil protist diversity and function. However, little attention has been given to the impact of the chosen soil DNA extraction procedure to the overall results. We examined the effect of three acknowledged DNA recovery methods, two...... manual methods (ISOm-11063, GnS-GII) and one commercial kit (MoBio), on soil protist community structures obtained from different sites with different land uses. Results from 18S rRNA gene amplicon sequencing suggest that DNA extraction method significantly affect the replicate homogeneity, the total...... number of operational taxonomic units (OTUs) recovered and the overall taxonomic structure and diversity of soil protist communities. However, DNA extraction effects did not overwhelm the natural variation among samples, as the community data still strongly grouped by geographical location...

  5. Antioxidant activity, total phenolic, and total flavonoid of extracts from stems of Jasminum nervosum Lour

    Directory of Open Access Journals (Sweden)

    Wei, Xiangyong

    2011-06-01

    Full Text Available Guangxi traditional Chinese Medical University Universidad de Medicina Tradicional China de Guangxi This study evaluated the antioxidant activities of the extracts of Jasminum nervosum Lour. stems along with the effects of different extract solvents on total phenolics (TP, total flavonoids (TF, and antioxidant potential. The antioxidant activity of the extracts was assessed using the following methods: DPPH, ABTS+ both free radicals scavenging assays, and reducing assays. TP and TF were detected by spectrophotometric and HPLC methods. In former methods, the highest amount of TP content was ethy lacetate extract (EAE, expressed as gallic acid equivalents. The greatest TF content was in the n-butanol extract (BE, expressed as lutin equivalents. No significant difference was observed in the TP/TF content between these two extracts. The antioxidant activity and TP/TF content of three extracts seemed to follow the same trend. This implied that there is a good correlation between antioxidant activities and TP/TF content. But in HPLC methods, EAE contained the highest content of lutin and gallic acid, which decreased in the same order of EAE > BE > PE, the rank order of TP/TF content of EAE and BE were different according to antioxidant ability. The overall results showed that the EAE and BE were richer in phenolics and flavonoids than petroleum ether extract (PE, and may represent a good source of antioxidants.Este estudio evaluó las actividades antioxidantes de extractos de tallos de Jasminum nervosum Lour., y el efecto de diferentes disolventes de extracción en los fenoles totales (TP y flavonoides totales (TF, y su potencial antioxidante. La actividad antioxidante de los extractos fue evaluada usando los siguientes métodos: DPPH, ABTS+ y ensayos reductores. TP y TF fueron detectados por métodos espectroscópicos y por HPLC. Con el primer método, el contenido más alto de TP se obtuvo en el extracto con acetato de etilo (EAE, expresado como

  6. Fire severity effects on ash extractable Total Phosphorous

    Science.gov (United States)

    Pereira, Paulo; Úbeda, Xavier; Martin, Deborah

    2010-05-01

    Phosphorous (P) is a crucial element to plant nutrition and limits vegetal production. The amounts of P in soil are lower and great part of this nutrient is absorbed or precipitated. It is well known that fire has important implications on P cycle, that can be lost throughout volatilization, evacuated with the smoke, but also more available to transport after organic matter mineralization imposed by the fire. The release of P depends on ash pH and their chemical and physical characteristics. Fire temperatures impose different severities, according to the specie affected and contact time. Fire severity is often evaluated by ash colour and this is a low-cost and excellent methodology to assess the fire effects on ecosystems. The aim of this work is study the ash properties physical and chemical properties on ash extractable Total Phosphorous (TP), collected in three wildfires, occured in Portugal, (named, (1) Quinta do Conde, (2) Quinta da Areia and (3) Casal do Sapo) composed mainly by Quercus suber and Pinus pinaster trees. The ash colour was assessed using the Munsell color chart. From all three plots we analyzed a total of 102 ash samples and we identified 5 different ash colours, ordered in an increasing order of severity, Very Dark Brown, Black, Dark Grey, Very Dark Grey and Light Grey. In order to observe significant differences between extractable TP and ash colours, we applied an ANOVA One Way test, and considered the differences significant at a p<0.05. The results showed that significant differences in the extractable TP among the different ash colours. Hence, to identify specific differences between each ash colour, we applied a post-hoc Fisher LSD test, significant at a p<0.05. The results obtained showed significant differences between the extractable TP from Very dark Brown and Black ash, produced at lower severities, in relation to Dark Grey, Very Dark Grey and Light Grey ash, generated at higher severities. The means of the first group were higher

  7. Extraction of low molecular weight RNA from Citrus trifolita tissues ...

    African Journals Online (AJOL)

    Jane

    2010-12-20

    Dec 20, 2010 ... A critical prerequisite in miRNA studies is acquisition of high quality LMW RNA. LMW RNA is ..... air-dried for a few minutes and then exposed to BIOMAX X-ray film for 48 h using an .... Approaches to microRNA discovery. Nat.

  8. Evaluation of RNA extraction methods in rice and their application in expression analysis of resistance genes against Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Parisa Azizi

    2017-01-01

    Full Text Available Extraction of RNA of high quality and integrity is essential for gene expression studies and all downstream RNA-based techniques. The leaves of 16 merit Malaysian rice varieties were used to isolate total RNA using five different methods. The quantity, quality and integrity of extracted RNA were confirmed using three different means. The ratios of A260/280 ranged from 2.12 to 2.20. Electrophoresis (1.5% agarose gel was performed, illustrating intact and sharp bands representing the 28S, 18S, 5.8S and 5S ribosomal subunits of RNA, presenting intact RNA. RNA quality was verified using semi-quantitative polymerase chain reaction (sqPCR. The objective of this study was to identify different genes involved in the resistance of rice plants using high-quality RNA extracted 31 h after inoculation of Magnaporthe oryzae pathotype P7.2. The expression levels of eight blast resistance genes, Pikh, Pib, Pita, Pi21, Pi9, Os11gRGA8, OsWRKY22 and OsWRKY45, were evaluated by real-time PCR (RT-PCR. Real-time PCR was performed to identify candidate genes using RNA extracted by the TRIzol method, which showed the highest score compared with other methods in terms of RNA quantity, purity and integrity. In addition, the results of real-time PCR confirmed that the up-regulation of seven blast resistance genes may confer stronger resistance for the MR 276 variety against M. oryzae pathotype P7.2.

  9. Next Generation Sequencing Analysis of Human Platelet PolyA+ mRNAs and rRNA-Depleted Total RNA

    Science.gov (United States)

    Kissopoulou, Antheia; Jonasson, Jon; Lindahl, Tomas L.; Osman, Abdimajid

    2013-01-01

    Background Platelets are small anucleate cells circulating in the blood vessels where they play a key role in hemostasis and thrombosis. Here, we compared platelet RNA-Seq results obtained from polyA+ mRNA and rRNA-depleted total RNA. Materials and Methods We used purified, CD45 depleted, human blood platelets collected by apheresis from three male and one female healthy blood donors. The Illumina HiSeq 2000 platform was employed to sequence cDNA converted either from oligo(dT) isolated polyA+ RNA or from rRNA-depleted total RNA. The reads were aligned to the GRCh37 reference assembly with the TopHat/Cufflinks alignment package using Ensembl annotations. A de novo assembly of the platelet transcriptome using the Trinity software package and RSEM was also performed. The bioinformatic tools HTSeq and DESeq from Bioconductor were employed for further statistical analyses of read counts. Results Consistent with previous findings our data suggests that mitochondrially expressed genes comprise a substantial fraction of the platelet transcriptome. We also identified high transcript levels for protein coding genes related to the cytoskeleton function, chemokine signaling, cell adhesion, aggregation, as well as receptor interaction between cells. Certain transcripts were particularly abundant in platelets compared with other cell and tissue types represented by RNA-Seq data from the Illumina Human Body Map 2.0 project. Irrespective of the different library preparation and sequencing protocols, there was good agreement between samples from the 4 individuals. Eighteen differentially expressed genes were identified in the two sexes at 10% false discovery rate using DESeq. Conclusion The present data suggests that platelets may have a unique transcriptome profile characterized by a relative over-expression of mitochondrially encoded genes and also of genomic transcripts related to the cytoskeleton function, chemokine signaling and surface components compared with other cell and

  10. Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer

    Science.gov (United States)

    2017-09-01

    AWARD NUMBER: W81XWH-14-1-0080 TITLE: Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer . PRINCIPAL INVESTIGATOR...TITLE AND SUBTITLE Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer . 5a. CONTRACT NUMBER 5b. GRANT NUMBER GRANT11489...institutional, NIH-funded study of genetic and epigenetic alterations of pre-invasive DCIS that did or did not progress to invasive breast cancer , with an

  11. Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

    Science.gov (United States)

    Bruskiewich, Richard; Burris, Jason N.; Carrigan, Charlotte T.; Chase, Mark W.; Clarke, Neil D.; Covshoff, Sarah; dePamphilis, Claude W.; Edger, Patrick P.; Goh, Falicia; Graham, Sean; Greiner, Stephan; Hibberd, Julian M.; Jordon-Thaden, Ingrid; Kutchan, Toni M.; Leebens-Mack, James; Melkonian, Michael; Miles, Nicholas; Myburg, Henrietta; Patterson, Jordan; Pires, J. Chris; Ralph, Paula; Rolf, Megan; Sage, Rowan F.; Soltis, Douglas; Soltis, Pamela; Stevenson, Dennis; Stewart, C. Neal; Surek, Barbara; Thomsen, Christina J. M.; Villarreal, Juan Carlos; Wu, Xiaolei; Zhang, Yong; Deyholos, Michael K.; Wong, Gane Ka-Shu

    2012-01-01

    Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ≥1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers. PMID:23185583

  12. Urinary extracellular vesicles for RNA extraction: optimization of a protocol devoid of prokaryote contamination.

    Science.gov (United States)

    Tataruch-Weinert, Dorota; Musante, Luca; Kretz, Oliver; Holthofer, Harry

    2016-01-01

    Urinary extracellular vesicles (UEVs) represent an ideal platform for biomarker discovery. They carry different types of RNA species, and reported profile discrepancies related to the presence/absence of 18s and 28s rRNA remain controversial. Moreover, sufficient urinary RNA yields and respective quality RNA profiles are still to be fully established. UEVs were enriched by hydrostatic filtration dialysis, and RNA content was extracted using 7 different commercially available techniques. RNA quantity was assessed using spectrophotometry and fluorometry, whilst RNA quality was determined by capillary electrophoresis. The presence of prokaryotic transcriptome was stressed when cellular RNA, as a control, was spiked into the UEVs samples before RNA extraction. The presence of bacteria in hydrostatic filtration dialysis above 1,000 kDa molecular weight cut-off and in crude urine was confirmed with growth media plates. The efficiency in removing urinary bacteria was evaluated by differential centrifugation, filtration (0.22 µm filters) and chemical pretreatment (water purification tablet). For volumes of urine >200 ml, the chemical treatment provides ease of handling without affecting vesicle integrity, protein and RNA profiles. This protocol was selected to enrich RNA with 7 methods, and its respective quality and quantity were assessed. The results were given as follows: (a) Fluorometry gave more repeatability and reproducibility than spectrophotometry to assess the RNA yields, (b) UEVs were enriched with small RNA, (c) Ribosomal RNA peaks were not observed for any RNA extraction method used and (d) RNA yield was higher for column-based method designed for urinary exosome, whilst the highest relative microRNA presence was obtained using TRIzol method. Our results show that the presence of bacteria can lead to misidentification in the electrophoresis peaks. Fluorometry is more reliable than spectrophotometry. RNA isolation method must be selected in conjunction with

  13. RNA preservation agents and nucleic acid extraction method bias perceived bacterial community composition.

    Directory of Open Access Journals (Sweden)

    Ann McCarthy

    Full Text Available Bias is a pervasive problem when characterizing microbial communities. An important source is the difference in lysis efficiencies of different populations, which vary depending on the extraction protocol used. To avoid such biases impacting comparisons between gene and transcript abundances in the environment, the use of one protocol that simultaneously extracts both types of nucleic acids from microbial community samples has gained popularity. However, knowledge regarding tradeoffs to combined nucleic acid extraction protocols is limited, particularly regarding yield and biases in the observed community composition. Here, we evaluated a commercially available protocol for simultaneous extraction of DNA and RNA, which we adapted for freshwater microbial community samples that were collected on filters. DNA and RNA yields were comparable to other commonly used, but independent DNA and RNA extraction protocols. RNA protection agents benefited RNA quality, but decreased DNA yields significantly. Choice of extraction protocol influenced the perceived bacterial community composition, with strong method-dependent biases observed for specific phyla such as the Verrucomicrobia. The combined DNA/RNA extraction protocol detected significantly higher levels of Verrucomicrobia than the other protocols, and those higher numbers were confirmed by microscopic analysis. Use of RNA protection agents as well as independent sequencing runs caused a significant shift in community composition as well, albeit smaller than the shift caused by using different extraction protocols. Despite methodological biases, sample origin was the strongest determinant of community composition. However, when the abundance of specific phylogenetic groups is of interest, researchers need to be aware of the biases their methods introduce. This is particularly relevant if different methods are used for DNA and RNA extraction, in addition to using RNA protection agents only for RNA

  14. Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA.

    Directory of Open Access Journals (Sweden)

    Antheia Kissopoulou

    Full Text Available BACKGROUND: Platelets are small anucleate cells circulating in the blood vessels where they play a key role in hemostasis and thrombosis. Here, we compared platelet RNA-Seq results obtained from polyA+ mRNA and rRNA-depleted total RNA. MATERIALS AND METHODS: We used purified, CD45 depleted, human blood platelets collected by apheresis from three male and one female healthy blood donors. The Illumina HiSeq 2000 platform was employed to sequence cDNA converted either from oligo(dT isolated polyA+ RNA or from rRNA-depleted total RNA. The reads were aligned to the GRCh37 reference assembly with the TopHat/Cufflinks alignment package using Ensembl annotations. A de novo assembly of the platelet transcriptome using the Trinity software package and RSEM was also performed. The bioinformatic tools HTSeq and DESeq from Bioconductor were employed for further statistical analyses of read counts. RESULTS: Consistent with previous findings our data suggests that mitochondrially expressed genes comprise a substantial fraction of the platelet transcriptome. We also identified high transcript levels for protein coding genes related to the cytoskeleton function, chemokine signaling, cell adhesion, aggregation, as well as receptor interaction between cells. Certain transcripts were particularly abundant in platelets compared with other cell and tissue types represented by RNA-Seq data from the Illumina Human Body Map 2.0 project. Irrespective of the different library preparation and sequencing protocols, there was good agreement between samples from the 4 individuals. Eighteen differentially expressed genes were identified in the two sexes at 10% false discovery rate using DESeq. CONCLUSION: The present data suggests that platelets may have a unique transcriptome profile characterized by a relative over-expression of mitochondrially encoded genes and also of genomic transcripts related to the cytoskeleton function, chemokine signaling and surface components

  15. Evidence for an RNA polymerization activity in axolotl and Xenopus egg extracts.

    Directory of Open Access Journals (Sweden)

    Hélène Pelczar

    2010-12-01

    Full Text Available We have previously reported a post-transcriptional RNA amplification observed in vivo following injection of in vitro synthesized transcripts into axolotl oocytes, unfertilized (UFE or fertilized eggs. To further characterize this phenomenon, low speed extracts (LSE from axolotl and Xenopus UFE were prepared and tested in an RNA polymerization assay. The major conclusions are: i the amphibian extracts catalyze the incorporation of radioactive ribonucleotide in RNase but not DNase sensitive products showing that these products correspond to RNA; ii the phenomenon is resistant to α-amanitin, an inhibitor of RNA polymerases II and III and to cordycepin (3'dAMP, but sensitive to cordycepin 5'-triphosphate, an RNA elongation inhibitor, which supports the existence of an RNA polymerase activity different from polymerases II and III; the detection of radiolabelled RNA comigrating at the same length as the exogenous transcript added to the extracts allowed us to show that iii the RNA polymerization is not a 3' end labelling and that iv the radiolabelled RNA is single rather than double stranded. In vitro cell-free systems derived from amphibian UFE therefore validate our previous in vivo results hypothesizing the existence of an evolutionary conserved enzymatic activity with the properties of an RNA dependent RNA polymerase (RdRp.

  16. Radiation-induced alternative transcripts as detected in total and polysome-bound mRNA.

    Science.gov (United States)

    Wahba, Amy; Ryan, Michael C; Shankavaram, Uma T; Camphausen, Kevin; Tofilon, Philip J

    2018-01-02

    Alternative splicing is a critical event in the posttranscriptional regulation of gene expression. To investigate whether this process influences radiation-induced gene expression we defined the effects of ionizing radiation on the generation of alternative transcripts in total cellular mRNA (the transcriptome) and polysome-bound mRNA (the translatome) of the human glioblastoma stem-like cell line NSC11. For these studies, RNA-Seq profiles from control and irradiated cells were compared using the program SpliceSeq to identify transcripts and splice variations induced by radiation. As compared to the transcriptome (total RNA) of untreated cells, the radiation-induced transcriptome contained 92 splice events suggesting that radiation induced alternative splicing. As compared to the translatome (polysome-bound RNA) of untreated cells, the radiation-induced translatome contained 280 splice events of which only 24 were overlapping with the radiation-induced transcriptome. These results suggest that radiation not only modifies alternative splicing of precursor mRNA, but also results in the selective association of existing mRNA isoforms with polysomes. Comparison of radiation-induced alternative transcripts to radiation-induced gene expression in total RNA revealed little overlap (about 3%). In contrast, in the radiation-induced translatome, about 38% of the induced alternative transcripts corresponded to genes whose expression level was affected in the translatome. This study suggests that whereas radiation induces alternate splicing, the alternative transcripts present at the time of irradiation may play a role in the radiation-induced translational control of gene expression and thus cellular radioresponse.

  17. Response Surface Optimized Extraction of Total Triterpene Acids ...

    African Journals Online (AJOL)

    Tropical Journal of Pharmaceutical Research May 2014; 13 (5): 787-792 ... surface method were used to optimize the extraction process, while antioxidant activity was evaluated in vitro using α ... Response surface methodology is increasingly.

  18. Optimization of phenol extraction procedures for preparation of RNA from mammalian lymphoid organs

    Energy Technology Data Exchange (ETDEWEB)

    Griffin, G.D.; Sellin, H.G.; Novelli, G.D.

    1978-07-01

    Methods have been developed to optimize the extraction of RNA from mammalian lymphoid organs (spleen) with respect to both quantity and quality of RNA and with minimal DNA contamination. Nuclease inhibitors, including diethyl pyrocarbonate, polyvinyl sulfate, and bentonite were used in the initial disruption of the tissue, which was accomplished by blender, Dounce homogenizer, or preparation of a cell suspension. Seven buffer systems, varying with respect to pH, detergent, and NaCl concentration, were used in the initial extraction with phenol, and the temperature of extraction was also varied. Protocols involving the selective use of naphthalene 1.5-disulfonic acid and sodium dodecyl sulfate were developed to provide an initial RNA extract with minimal DNA content. Dounce homogenization, followed by separate treatment of nuclear and cytosol fractions, was found to be the most effective technique, both in terms of RNA yield (averaging 76%) and the quality of RNA recovered (as judged by gel electrophoresis). RNA from blender preparations contained larger amounts of DNA and RNA yield was decreased to 54%. RNA extracted from spleen cell suspensions was of poor quality and gave very poor yield (27%).

  19. rich extract on total polyphenols and antioxidant activity obtained by ...

    African Journals Online (AJOL)

    Z. Ghouila

    ABSTRACT: Conventional and non-conventional extraction methods were applied in the first time for the ... The heating of the matrix internally and externally without thermal gradient gives numerous advantages to microwave ... Once in laboratory, the clusters were washed with distilled and de-ionized water, then dried and ...

  20. Urinary extracellular vesicles for RNA extraction: optimization of a protocol devoid of prokaryote contamination

    Directory of Open Access Journals (Sweden)

    Dorota Tataruch-Weinert

    2016-06-01

    Full Text Available Background: Urinary extracellular vesicles (UEVs represent an ideal platform for biomarker discovery. They carry different types of RNA species, and reported profile discrepancies related to the presence/absence of 18s and 28s rRNA remain controversial. Moreover, sufficient urinary RNA yields and respective quality RNA profiles are still to be fully established. Methods: UEVs were enriched by hydrostatic filtration dialysis, and RNA content was extracted using 7 different commercially available techniques. RNA quantity was assessed using spectrophotometry and fluorometry, whilst RNA quality was determined by capillary electrophoresis. Results: The presence of prokaryotic transcriptome was stressed when cellular RNA, as a control, was spiked into the UEVs samples before RNA extraction. The presence of bacteria in hydrostatic filtration dialysis above 1,000 kDa molecular weight cut-off and in crude urine was confirmed with growth media plates. The efficiency in removing urinary bacteria was evaluated by differential centrifugation, filtration (0.22 µm filters and chemical pretreatment (water purification tablet. For volumes of urine >200 ml, the chemical treatment provides ease of handling without affecting vesicle integrity, protein and RNA profiles. This protocol was selected to enrich RNA with 7 methods, and its respective quality and quantity were assessed. The results were given as follows: (a Fluorometry gave more repeatability and reproducibility than spectrophotometry to assess the RNA yields, (b UEVs were enriched with small RNA, (c Ribosomal RNA peaks were not observed for any RNA extraction method used and (d RNA yield was higher for column-based method designed for urinary exosome, whilst the highest relative microRNA presence was obtained using TRIzol method. Conclusion: Our results show that the presence of bacteria can lead to misidentification in the electrophoresis peaks. Fluorometry is more reliable than spectrophotometry. RNA

  1. Comparison of RNA Extraction Methods for the Identification of Grapevine fan leaf virus

    Directory of Open Access Journals (Sweden)

    Z. Gholampour

    2016-06-01

    Full Text Available Introduction: To now, more than 70 viral diseases have been reported from grapevine. Serological methods are regular diagnostic tools of grapevine viruses, however, their sensitivity has affected by seasonal fluctuations of the virus. Reverse transcription polymerase chain reaction provides significant improvement in detection of grapevine viruses. Extraction of high-quality RNA is essential for the successful application of many molecular techniques, such as RT-PCR. Extraction of high-quality RNA from the leaves of woody plants, such as grapevine, is particularly challenging because of high concentrations of polysaccharides, polyphenols, and other secondary metabolites. Some RNA extraction methods yield pellets that are poorly soluble, indicating the presence of unknown contaminants, whereas others are gelatinous, indicating the presence of polysaccharides. RNA can make complexes with polysaccharides and phenolic compounds render the RNA unusable for applications such as reverse transcription. Grapevine fanleaf virus is a member of the genus Nepovirus in the family Secoviridae. The GFLV genome consists of two positive-sense single stranded RNAs. The genome has a poly (A tail at the 3´ terminus and a covalently linked VPG protein at the 5´ terminus. Several extraction methods had been reported to be used for identification of GFLV in grapevine. Some of them require harmful chemical material; disadvantages of other are high costs. Immunocapture-RT-PCR requires preparation of specific antibody and direct binding RT-PCR (DB-RT-PCR has a high contamination risk. In this study, four RNA extraction protocols were compared with a commercial isolation kit to explore the most efficient RNA isolation method for grapevines. Material and Methods: 40 leaf samples were randomly collected during the growing season of 2011-2012. GFLV was detected in leaf samples by enzyme linked immunosorbent assay (ELISA Using specific antibodies raised against Iranian

  2. Efficient RNA extraction protocol for the wood mangrove species Laguncularia racemosa suited for next-generation RNA sequencing

    International Nuclear Information System (INIS)

    Wilwerth, M. W.; Rossetto, P.

    2016-01-01

    Mangrove flora and habitat have immeasurable importance in marine and coastal ecology as well as in the economy. Despite their importance, they are constantly threatened by oil spill accidents and environmental contamination; therefore, it is crucial to understand the changes in gene expression to better predict toxicity in these plants. Among the species of Atlantic coast mangrove (Americas and Africa), Laguncularia racemosa, or white mangrove, is a conspicuous species. The wide distribution of L. racemosa in areas where marine oil exploration is rapidly increasing make it a candidate mangrove species model to uncover the impact of oil spills at the molecular level with the use of massive transcriptome sequencing. However, for this purpose, the RNA extraction protocol should ensure low levels of contaminants and structure integrity. In this study, eight RNA extraction methods were tested and analysed using downstream applications. The InviTrap Spin Plant RNA Mini Kit performed best with regard to purity and integrity. Moreover, the obtained RNA was submitted to cDNA synthesis and RT-PCR, successfully generating amplification products of the expected size. These Results show the applicability of the RNA obtained here for downstream methodologies, such as the construction of cDNA libraries for the Illumina Hi-seq platform. (author)

  3. 64 original article optimization of rna extraction in mycobacterium

    African Journals Online (AJOL)

    Dr Oboro VO

    ... on thick 7H10 agar plates supplemented with 10% oleic acid- ... RNA lysis solution (0.15 M sucrose, 10 mM sodium acetate [pH 5.2] .... medium was discarded and the infected macrophage ..... Clin Invest 1995, 96(1):245-249. 18. Buchmeier ...

  4. Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method

    Directory of Open Access Journals (Sweden)

    Chijioke O. Elekwachi

    2017-09-01

    Full Text Available Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction. However, for studies using rumen content there is no consensus on (1 the amount of rumen digesta to use or (2 the amount of TRIzol reagent to be used in RNA extraction procedures. This study evaluated the effect of using various quantities of ground rumen digesta and of TRIzol reagent on the yield and quality of extracted RNA. It also investigated the possibility of using lower masses of solid-phase rumen digesta and lower amounts of TRIzol reagent than is used currently, for extraction of RNA for metatranscriptomic studies. We found that high quality RNA could be isolated from 2 g of ground rumen digesta sample, whilst using 0.6 g of ground matter for RNA extraction and using 3 mL (a 5:1 TRIzol : extraction mass ratio of TRIzol reagent. This represents a significant savings in the cost of RNA isolation. These lower masses and volumes were then applied in the RNA-Seq analysis of solid-phase rumen samples obtained from 6 Angus X Hereford beef heifers which had been fed a high forage diet (comprised of barley straw in a forage-to-concentrate ratio of 70:30 for 102 days. A bioinformatics analysis pipeline was developed in-house that generated relative abundance values of archaea, protozoa, fungi and bacteria in the rumen and also allowed the extraction of individual rRNA variable regions that could be analyzed in downstream molecular ecology programs. The average relative abundances of rRNA transcripts of archaea, bacteria

  5. Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method.

    Science.gov (United States)

    Elekwachi, Chijioke O; Wang, Zuo; Wu, Xiaofeng; Rabee, Alaa; Forster, Robert J

    2017-01-01

    Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction. However, for studies using rumen content there is no consensus on (1) the amount of rumen digesta to use or (2) the amount of TRIzol reagent to be used in RNA extraction procedures. This study evaluated the effect of using various quantities of ground rumen digesta and of TRIzol reagent on the yield and quality of extracted RNA. It also investigated the possibility of using lower masses of solid-phase rumen digesta and lower amounts of TRIzol reagent than is used currently, for extraction of RNA for metatranscriptomic studies. We found that high quality RNA could be isolated from 2 g of ground rumen digesta sample, whilst using 0.6 g of ground matter for RNA extraction and using 3 mL (a 5:1 TRIzol : extraction mass ratio) of TRIzol reagent. This represents a significant savings in the cost of RNA isolation. These lower masses and volumes were then applied in the RNA-Seq analysis of solid-phase rumen samples obtained from 6 Angus X Hereford beef heifers which had been fed a high forage diet (comprised of barley straw in a forage-to-concentrate ratio of 70:30) for 102 days. A bioinformatics analysis pipeline was developed in-house that generated relative abundance values of archaea, protozoa, fungi and bacteria in the rumen and also allowed the extraction of individual rRNA variable regions that could be analyzed in downstream molecular ecology programs. The average relative abundances of rRNA transcripts of archaea, bacteria, protozoa and fungi in

  6. Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria

    Directory of Open Access Journals (Sweden)

    Lindblad Peter

    2009-08-01

    Full Text Available Abstract Background The validity and reproducibility of gene expression studies depend on the quality of extracted RNA and the degree of genomic DNA contamination. Cyanobacteria are gram-negative prokaryotes that synthesize chlorophyll a and carry out photosynthetic water oxidation. These organisms possess an extended array of secondary metabolites that impair cell lysis, presenting particular challenges when it comes to nucleic acid isolation. Therefore, we used the NHM5 strain of Nostoc punctiforme ATCC 29133 to compare and improve existing phenol based chemistry and procedures for RNA extraction. Results With this work we identify and explore strategies for improved and lower cost high quality RNA isolation from cyanobacteria. All the methods studied are suitable for RNA isolation and its use for downstream applications. We analyse different Trizol based protocols, introduce procedural changes and describe an alternative RNA extraction solution. Conclusion It was possible to improve purity of isolated RNA by modifying protocol procedures. Further improvements, both in RNA purity and experimental cost, were achieved by using a new extraction solution, PGTX.

  7. Total Phenolics and Total Flavonoids Contents and Hypnotic Effect in Mice of Ziziphus mauritiana Lam. Seed Extract

    Directory of Open Access Journals (Sweden)

    Aye Moh Moh San

    2013-01-01

    Full Text Available The seeds of Ziziphus mauritiana Lam. have been traditionally used for treatment of various complications including insomnia and anxiety. They are popularly used as sedative and hypnotic drugs in China, Korea, Myanmar, Vietnam, and other Asian countries. However, no scientific proof on hypnotic activity of Z. mauritiana seeds (ZMS was reported. In this study, the hypnotic activity of 50% ethanolic extract from ZMS was observed on the loss of righting reflex in mice using pentobarbital-induced sleep mice method. The contents of total phenolics and total flavonoids in the extract were also determined. The results showed that the 50% ethanolic extract from ZMS contained total phenolics  mg gallic acid equivalent (GAE/g extract and total flavonoids  mg quercetin equivalent (QE/g extract. Oral administration of the extract at the dose of 200 mg/kg significantly increased the sleeping time in mice intraperitoneally administered with sodium pentobarbital (50 mg/kg body weight. These results supported the traditional use of ZMS for the treatment of insomnia. The seeds of Z. mauritiana should be further developed as an alternative sedative and/or hypnotic product.

  8. Improving Griffith's protocol for co-extraction of microbial DNA and RNA in adsorptive soils

    DEFF Research Database (Denmark)

    Paulin, Mélanie Marie; Nicolaisen, Mette Haubjerg; Jacobsen, Carsten Suhr

    2013-01-01

    Quantification of microbial gene expression is increasingly being used to study key functions in soil microbial communities, yet major limitations still exist for efficient extraction of nucleic acids, especially RNA for transcript analysis, from this complex matrix. We present an improved......-time PCR on both the RNA (after conversion to cDNA) and the DNA fraction of the extracts. Non-adsorptive soils were characterized by low clay content and/or high phosphate content, whereas adsorptive soils had clay contents above 20% and/or a strong presence of divalent Ca in combination with high p......H. Modifications to the co-extraction protocol improved nucleic acid extraction efficiency from all adsorptive soils and were successfully validated by DGGE analysis of the indigenous community based on 16S rRNA gene and transcripts in soils representing low biomass and/or high clay content. This new approach...

  9. Optimization of Total Flavonoids Extraction from Coreopsis tinctoria Nutt. by Response Surface Methodology

    Directory of Open Access Journals (Sweden)

    Liu, X. F.

    2014-11-01

    Full Text Available Response surface methodology (RSM was applied to predict optimum conditions for extraction of flavonoid from Coreopsis tinctoria Nutt. A central composite design (CCD was used to monitor the effect of extraction temperature, extraction time, and water-to-material ratio on yield of total flavonoids. The optimal extraction conditions were obtained as water-to-material ratio of 55 ml g−1, extraction temperature of 80 °C and extraction time of 70 minutes. Under these conditions, the average total flavonoids yield, according to the mass of raw material, was 9.0 ± 0.6 %, which corresponds to the predicted value of 8.9 %. Thus, the extraction method was applied successfully to extract total flavonoids from C. tinctoria.

  10. Phosphogypsum analysis: total content and extractable element concentrations

    International Nuclear Information System (INIS)

    Gennari, Roseli F.; Medina, Nilberto H.; Garcia, Isabella; Silveira, Marcilei A.G.

    2011-01-01

    Phosphogypsum stand for the chemical origin gypsum generated in fertilizers production, in which phosphate rock is attacked by sulfuric acid resulting in phosphoric acid (H 3 PO 4 ) and phosphate fertilizers. Phosphogypsum is not a commercial product and it is stocked in large open areas or accumulated in lakes inducing to a major environmental problem due to the presence of toxic and radioactive elements. The increasing world agricultural demand is the real responsible for the severity of this environmental problem. Nevertheless, there are some possibilities for the application of this reject material, such as civil construction, waste water treatment, and in cultivated lands, etc. In the agriculture the phosphogypsum is commonly used as a nutrient source due to its large amounts of phosphorus, calcium and sulfur. However, there are still some environmental questions related to the use of this by-product since phosphogypsum is classified as TENORM (Technologically Enhanced Naturally Occurring Radioactive Material), which is a solid waste containing heavy metals and naturally occurring radioactive elements from the rock matrix. In this work, Plasma Mass Spectrometry (ICP-MS) was used to study phosphogypsum samples. Several acid solutions for samples digestion were evaluated in order to be feasible the chemical analysis. BCR sequential extractions were also performed. The results showed analyte concentrations are highly dependent on the acid solution used. The BCR guidelines could not be applied as used for soil, since the phosphogypsum solubility is different. So, it would be necessary to use different mass aliquots in the extractions, to be feasible an environmental evaluation. (author)

  11. Ultrasound-Assisted Extraction of Total Flavonoids from Corn Silk and Their Antioxidant Activity

    Directory of Open Access Journals (Sweden)

    Ling-Li Zheng

    2016-01-01

    Full Text Available Object. Ultrasound-assisted extraction of total flavonoids from corn silk and their antioxidant activities were studied. Methods. Response surface methodology was adopted to optimize the extraction conditions and antioxidant activities of the extracted total flavonoids were detected through ferric reducing antioxidant power (FRAP assay. Results. Through a three-level, three-variable Box-Behnken design of response surface methodology (RSM adopting yield as response, the optimal conditions were determined as follows: ultrasonic power 500 W, extraction time 20 min, material solvent ratio 1 : 20, and ethanol concentration 30%. Under the optimum conditions, the extraction yield of total flavonoids was 1.13%. FRAP value of total flavonoids extracted from corn silk was 467.59 μmol/L. Conclusion. The total flavonoids of corn silk could be developed as food natural antioxidant reagents.

  12. Comparison of Total RNA Isolation Methods for Analysis of Immune-Related microRNAs in Market Milks.

    Science.gov (United States)

    Oh, Sangnam; Park, Mi Ri; Son, Seok Jun; Kim, Younghoon

    2015-01-01

    Bovine milk provides essential nutrients, including immunologically important molecules, as the primary source of nutrition to newborns. Recent studies showed that RNAs from bovine milk contain immune-related microRNAs (miRNA) that regulate various immune systems. To evaluate the biological and immunological activity of miRNAs from milk products, isolation methods need to be established. Six methods for extracting total RNAs from bovine colostrums were adopted to evaluate the isolating efficiency and expression of miRNAs. Total RNA from milk was presented in formulation of small RNAs, rather than ribosomal RNAs. Column-combined phenol isolating methods showed high recovery of total RNAs, especially the commercial columns for biofluid samples, which demonstrated outstanding efficiency for recovering miRNAs. We also evaluated the quantity of five immune-related miRNAs (miR-93, miR-106a, miR-155, miR-181a, miR-451) in milk processed by temperature treatments including low temperature for long time (LTLT, 63℃ for 30 min)-, high temperature for short time (HTST, 75℃ for 15 s)-, and ultra heat treatment (UHT, 120-130℃ for 0.5-4 s). All targeted miRNAs had significantly reduced levels in processed milks compared to colostrum and raw mature milk. Interestingly, the amount of immune-related miRNAs from HTST milk was more resistant than those of LTLT and UHT milks. Our present study examined defined methods of RNA isolation and quantification of immune-specific miRNAs from small volumes of milk for use in further analysis.

  13. Novel extraction strategy of ribosomal RNA and genomic DNA from cheese for PCR-based investigations.

    Science.gov (United States)

    Bonaïti, Catherine; Parayre, Sandrine; Irlinger, Françoise

    2006-03-15

    Cheese microorganisms, such as bacteria and fungi, constitute a complex ecosystem that plays a central role in cheeses ripening. The molecular study of cheese microbial diversity and activity is essential but the extraction of high quality nucleic acid may be problematic: the cheese samples are characterised by a strong buffering capacity which negatively influenced the yield of the extracted rRNA. The objective of this study is to develop an effective method for the direct and simultaneous isolation of yeast and bacterial ribosomal RNA and genomic DNA from the same cheese samples. DNA isolation was based on a protocol used for nucleic acids isolation from anaerobic digestor, without preliminary washing step with the combined use of the action of chaotropic agent (acid guanidinium thiocyanate), detergents (SDS, N-lauroylsarcosine), chelating agent (EDTA) and a mechanical method (bead beating system). The DNA purification was carried out by two washing steps of phenol-chloroform. RNA was isolated successfully after the second acid extraction step by recovering it from the phenolic phase of the first acid extraction. The novel method yielded pure preparation of undegraded RNA accessible for reverse transcription-PCR. The extraction protocol of genomic DNA and rRNA was applicable to complex ecosystem of different cheese matrices.

  14. 16S rRNA Gene Sequence Analysis of Drinking Water Using RNA and DNA Extracts as Targets for Clone Library Development

    Science.gov (United States)

    The bacterial composition of chlorinated drinking water was analyzed using 16S rRNA gene clone libraries derived from DNA extracts of 12 samples and compared to clone libraries previously generated using RNA extracts from the same samples. Phylogenetic analysis of 761 DNA-based ...

  15. Anti-tumor potential of total alkaloid extract of Prosopis juliflora DC ...

    African Journals Online (AJOL)

    The total alkaloid extract from Prosopis juliflora DC. leaves was obtained using acid/base modified extraction method. The in vitro anti-tumor potential of the extract was evaluated using MTT (3-(4,5- dimethythiazol-2yl)2,5-diphenyl tetrazolium bromide) based cytotoxicity monitoring after 24, 48 and 72 h exposure of the ...

  16. Effect of extraction solvent on total phenol content, total flavonoid content, and antioxidant activity of Limnophila aromatica

    Directory of Open Access Journals (Sweden)

    Quy Diem Do

    2014-09-01

    Full Text Available Limnophila aromatica is commonly used as a spice and a medicinal herb in Southeast Asia. In this study, water and various concentrations (50%, 75%, and 100% of methanol, ethanol, and acetone in water were used as solvent in the extraction of L. aromatica. The antioxidant activity, total phenolic content, and total flavonoid content of the freeze-dried L. aromatica extracts were investigated using various in vitro assays. The extract obtained by 100% ethanol showed the highest total antioxidant activity, reducing power and DPPH (2,2-diphenyl-1-picrylhydrazyl radical scavenging activity. The same extract also exhibited the highest phenolic content (40.5 mg gallic acid equivalent/g of defatted L. aromatica and the highest flavonoid content (31.11 mg quercetin equivalent/g of defatted L. aromatica. The highest extraction yield was obtained by using 50% aqueous acetone. These results indicate that L. aromatica can be used in dietary applications with a potential to reduce oxidative stress.

  17. JUICE EXTRACTION FOR TOTAL SOLUBLE SOLIDS CONTENT DETERMINATION IN MELON

    Directory of Open Access Journals (Sweden)

    Paulo Sérgio Lima e Silva

    2006-01-01

    Full Text Available The total soluble solids content (TSSC shows high positive correlation with sugars content, and therefore is generally accepted as an important quality trait of fruits. In melon, this evaluation is usually done by grinding a slice of the fruit's pulp in a household food processor, straining the ground material and then proceeding the TSSC determination in the resulting juice. This evaluation is labor-intensive and takes a long time to complete. An alternative process was delineated for obtaining the juice: the pulp of the fruit slice would be transversally cut one or more times, and longitudinally pressed by hand to obtain the juice. The objective of this work was to compare processes for obtaining juice to evaluate TSSC in melons. Fifty, 15, and 15 fruits of the Galia, Yellow, and Cantaloupe type melons were evaluated, respectively. Each fruit was considered as a block, and was longitudinally split into six fractions with similar sizes, which corresponded to the plots. The following treatments were evaluated: fraction without cuts, fractions with one, three, five, or seven transversal cuts, and the fraction treated by the conventional process. It was concluded that the procedure by which the melon slices of Galia, Yellow and Cantaloupe types are pressed for obtaining the juice to evaluate TSSC can overestimate this content. This would probably be due to the fact that the most internal section of the mesocarp presents greater TSSC than the portions closer to the epicarp.

  18. 34A, miRNA-944, miRNA-101 and miRNA-218 in cervical cancer

    African Journals Online (AJOL)

    RNAs (21 - 24 nucleotides in length) that are critical for many important processes such as development, ... RNA extraction and reverse transcription. Total RNA was extracted from each of the experimental groups using ... used as an endogenous control to normalize the expression of miRNA-143, miRNA-34A, miRNA-.

  19. Ultrasound-Assisted Extraction of Total Flavonoids from Corn Silk and Their Antioxidant Activity

    OpenAIRE

    Zheng, Ling-Li; Wen, Guan; Yuan, Min-Yong; Gao, Feng

    2016-01-01

    Object. Ultrasound-assisted extraction of total flavonoids from corn silk and their antioxidant activities were studied. Methods. Response surface methodology was adopted to optimize the extraction conditions and antioxidant activities of the extracted total flavonoids were detected through ferric reducing antioxidant power (FRAP) assay. Results. Through a three-level, three-variable Box-Behnken design of response surface methodology (RSM) adopting yield as response, the optimal conditions we...

  20. In vitro antimicrobial activity of total extracts of the leaves of Petiveria alliacea L. (Anamu

    Directory of Open Access Journals (Sweden)

    Ania Ochoa Pacheco

    2013-06-01

    Full Text Available The antimicrobial activity of 13 total extracts was evaluated, 10 soft extracts (B and 3 blended extracts (E prepared from dry and fresh leaves of Petiveria alliacea L. Various solvents were used for their preparation: hydroalcoholic solution at 30%, 80% and isopropyl alcohol. The antimicrobial effect of the extracts was tested by means of the method of Kirby-Bauer, using four bacterial strains from the ATCC collection (Escherichia coli, Staphylococcus aureus, Enterococcus faecalis and Pseudomonas aeruginosa and a leveduriform fungus (Candida albicans. The following quality control parameters were determined for most active extracts: physical, physical-chemical and chemical parameters. The results were: nine extracts showed antibacterial activity, being the most concentrated (B8 and E3, the ones with the highest activity in the presence of the bacteria tested; the effect of blended extracts (E1, E2 and E3 was greater in the presence of P. aeruginosa. Blended extracts are considered more potent and active than soft extracts. No antifungal activity was obtained for both types of extracts. The Minimum Inhibitory Concentration (MIC and Minimum Bactericidal Concentration (MBC were determined for both extracts, with the following results: MIC-soft extracts (>100 mg/mL, blended extracts (>50 mg/mL; MBC-soft extracts (≥400 mg/mL, blended extracts (≥200 mg/mL based on fresh leaves.

  1. How Severely Is DNA Quantification Hampered by RNA Co-extraction?

    Science.gov (United States)

    Sanchez, Ignacio; Remm, Matthieu; Frasquilho, Sonia; Betsou, Fay; Mathieson, William

    2015-10-01

    The optional RNase digest that is part of many DNA extraction protocols is often omitted, either because RNase is not provided in the kit or because users do not want to risk contaminating their laboratory. Consequently, co-eluting RNA can become a "contaminant" of unknown magnitude in a DNA extraction. We extracted DNA from liver, lung, kidney, and heart tissues and established that 28-52% of the "DNA" as assessed by spectrophotometry is actually RNA (depending on tissue type). Including an RNase digest in the extraction protocol reduced 260:280 purity ratios. Co-eluting RNA drives an overestimation of DNA yield when quantification is carried out using OD 260 nm spectrophotometry, or becomes an unquantified contaminant when spectrofluorometry is used for DNA quantification. This situation is potentially incompatible with the best practice guidelines for biobanks issued by organizations such as the International Society for Biological and Environmental Repositories, which state that biospecimens should be accurately characterized in terms of their identity, purity, concentration, and integrity. Consequently, we conclude that an RNase digest must be included in DNA extractions if pure DNA is required. We also discuss the implications of unquantified RNA contamination in DNA samples in the context of laboratory accreditation schemes.

  2. Antinociceptive and Anti-Inflammatory Effects of Total Alkaloid Extract from Fumaria capreolata

    Directory of Open Access Journals (Sweden)

    Noureddine Bribi

    2015-01-01

    Full Text Available Fumaria capreolata is used in traditional medicine in North Africa for its gastrointestinal and anti-inflammatory activities. The present study investigates the effects of total alkaloids extracted from the aerial parts of Fumaria capreolata (AFC on LPS-induced production of proinflammatory mediators (IL-6, IL-1β, iNOS, TNF-α, COX-2, and MIP-2 in RAW264.7 cells. AFC significantly reduced the inflammatory response inhibiting the production of nitric oxide (NO and IL-6 in a dose-dependent manner, without affecting the viability of cells, and downregulated mRNA expression of proinflammatory key players: IL-6, IL-1β, iNOS, TNF-α, and COX-2. AFC antinociceptive and anti-inflammatory properties were also evaluated on the acetic acid- and formalin-induced pain models in mice. AFC oral administration significantly inhibited acetic acid-induced writhes and reduced formalin-induced paw licking time. Therefore, AFC may be a potential candidate for the treatment of inflammatory diseases, such as colitis and arthritis.

  3. Antioxidant properties of cumin (Bunium persicum Boiss.) extract and its protective role against abiotic stress tested by microRNA markers

    OpenAIRE

    Katarína Ražná; Nishonoy Khasanova; Eva Ivanišová; Davranov Qahramon; Miroslav Habán

    2018-01-01

    Bunium persicum Boiss. seeds have been used for medicinal and nutritional properties such as antioxidant, antihelmetic and antimicrobial activity. The aim of this study was to to tested protective role of cumin extract against abiotic stress by microRNA markers. Secondary also was to evaluate antioxidant activity as well as total polyphenol, flavonoid and phenolic acid content of cumin extract. We observed that cumin DNA itself has not been damaged by sonication teratment. This protective im...

  4. Extraction of High Quality RNA from Cannabis sativa Bast Fibres: A Vademecum for Molecular Biologists

    Directory of Open Access Journals (Sweden)

    Gea Guerriero

    2016-07-01

    Full Text Available In plants there is no universal protocol for RNA extraction, since optimizations are required depending on the species, tissues and developmental stages. Some plants/tissues are rich in secondary metabolites or synthesize thick cell walls, which hinder an efficient RNA extraction. One such example is bast fibres, long extraxylary cells characterized by a thick cellulosic cell wall. Given the economic importance of bast fibres, which are used in the textile sector, as well as in biocomposites as green substitutes of glass fibres, it is desirable to better understand their development from a molecular point of view. This knowledge favours the development of biotechnological strategies aimed at improving specific properties of bast fibres. To be able to perform high-throughput analyses, such as, for instance, transcriptomics of bast fibres, RNA extraction is a crucial and limiting step. We here detail a protocol enabling the rapid extraction of high quality RNA from the bast fibres of textile hemp, Cannabis sativa L., a multi-purpose fibre crop standing in the spotlight of research.

  5. A Rapid and Efficient Method for Purifying High Quality Total RNA from Peaches (Prunus persica for Functional Genomics Analyses

    Directory of Open Access Journals (Sweden)

    LEE MEISEL

    2005-01-01

    Full Text Available Prunus persica has been proposed as a genomic model for deciduous trees and the Rosaceae family. Optimized protocols for RNA isolation are necessary to further advance studies in this model species such that functional genomics analyses may be performed. Here we present an optimized protocol to rapidly and efficiently purify high quality total RNA from peach fruits (Prunus persica. Isolating high-quality RNA from fruit tissue is often difficult due to large quantities of polysaccharides and polyphenolic compounds that accumulate in this tissue and co-purify with the RNA. Here we demonstrate that a modified version of the method used to isolate RNA from pine trees and the woody plant Cinnamomun tenuipilum is ideal for isolating high quality RNA from the fruits of Prunus persica. This RNA may be used for many functional genomic based experiments such as RT-PCR and the construction of large-insert cDNA libraries.

  6. Ultrasound-Assisted Extraction of Total Phenolic Compounds from Inula helenium

    Directory of Open Access Journals (Sweden)

    Jin Wang

    2013-01-01

    Full Text Available Ultrasound-assisted extraction (UAE of phenolic compounds from Inula helenium was studied. Effects of ethanol concentration, ultrasonic time, solid-liquid ratio, and number of extractions were investigated. An orthogonal array was constructed to optimize UAE process. The optimized extraction conditions were as follows: ethanol concentration, 30%; solid-liquid ratio, 1 : 20; number of extractions, 2 times; extraction time, 30 min. Under the optimal conditions, the yield of total phenolic compounds and chlorogenic acid was 6.13±0.58 and 1.32±0.17 mg/g, respectively. The results showed that high amounts of phenolic compounds can be extracted from I. helenium by ultrasound-assisted extraction technology.

  7. Free radical scavenging and total antioxidant capacity of root extracts of Anchomanes difformis Engl. (Araceae).

    Science.gov (United States)

    Aliyu, Abubakar B; Ibrahim, Mohammed A; Musa, Aliyu M; Musa, Aisha O; Kiplimo, Joyce J; Oyewale, Adebayo O

    2013-01-01

    Antioxidants activities from plants sources have attracted a wide range of interest across the world in recent times. This is due to growing concern for safe and alternative sources of antioxidants. The free radical scavenging activity using 1,1-diphenyl-2-picrylhydrazyl radical (DPPH), reducing power assay, total antioxidant capacity of the phosphomolybdenum method and the total phenolics content using the Folin-Ciocalteu reagent were carried out on the acetone, n-butanol and methanol root extracts of Anchomanes difformis. The results of the total phenolics content expressed in mg/100 g of gallic acid equivalent (GAE) showed that the n-butanol extract has significantly (p extracts. All the extracts displayed strong concentration dependent radical scavenging activity. It was also observed that the n-butanol extract showed higher activity of 70.87% and 78.59% at low concentrations of 31.25 microg/mL and 62.5 microg/mL, respectively, than methanol and acetone extracts. The results also showed that the n-butanol extract has strongest reducing ability which is comparable to that of gallic acid at all the concentrations tested. Phytochemical screening on the extracts revealed the presence of flavonoids, saponins, and tannins. The results suggest that n-butanol extract of the plant is very rich in antioxidant compounds worthy of further investigations.

  8. A study of extraction process and in vitro antioxidant activity of total ...

    African Journals Online (AJOL)

    The study investigated the extraction method of Rhizoma Imperatae and its antioxidant activity, and provided a basis for its rational development. The extraction method of Rhizoma Imperatae was determined using orthogonal design test and by total phenol content, its hydroxyl radical scavenging ability was measured by ...

  9. The use of carrier RNA to enhance DNA extraction from microfluidic-based silica monoliths.

    Science.gov (United States)

    Shaw, Kirsty J; Thain, Lauren; Docker, Peter T; Dyer, Charlotte E; Greenman, John; Greenway, Gillian M; Haswell, Stephen J

    2009-10-12

    DNA extraction was carried out on silica-based monoliths within a microfluidic device. Solid-phase DNA extraction methodology was applied in which the DNA binds to silica in the presence of a chaotropic salt, such as guanidine hydrochloride, and is eluted in a low ionic strength solution, such as water. The addition of poly-A carrier RNA to the chaotropic salt solution resulted in a marked increase in the effective amount of DNA that could be recovered (25ng) compared to the absence of RNA (5ng) using the silica-based monolith. These findings confirm that techniques utilising nucleic acid carrier molecules can enhance DNA extraction methodologies in microfluidic applications.

  10. TOTAL PHENOLIC CONTENT, ANTIOXIDANT AND ANTIBACTERIAL ACTIVITIES OF THE EXTRACT OF EPHEDRA PROCERA FISCH. ET MEY.

    Science.gov (United States)

    Dehkordi, Naser Vahed; Kachouie, Mehrdad Ataie; Pirbalouti, Abdollah Ghasemi; Malekpoor, Fatemeh; Rabei, Mohammad

    2015-01-01

    Ephedra prcera belonging to the family Ephedraceae is a poison and medicinal plant. The main aim of present study was to determine total phenolic content and antioxidant and antibacterial activities of ethanolic extract from the aerial parts of E. procera collected from a natural habitat in Chaharmahal va Bakhtiari province, Southwestern Iran. The total phenolic content of the extract by Folin-Ciocalteu method and the antioxidant activity using DPPH assay were determined. The antibacterial activity, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) of the extract were evaluated against five bacteria, including Proteus vulgaris, Pseudomonas aeruginosa, Enteobacter aeogenes, Bacillus ceirus and Staphylococcus aureus. Total phenolic content in the extract of E. procera was 0.718 mg tannic acid/g dry weight extract. The results indicated that the ethanolic extract of E. piocera exhibited radical scavenging activity. In addition, the results of this study confirmed that the ethanolic extract of E. procera exhibited antibacterial activity. In conclusion, the extract of E. piocera could be an important source of phenolic components with antioxidant capacity and antibacterial activity.

  11. 16S rRNA Gene Sequence Analysis of Drinking Water Using RNA and DNA Extracts as Targets for Clone Library Development - Poster

    Science.gov (United States)

    We examined the bacterial composition of chlorinated drinking water using 16S rRNA gene clone libraries derived from RNA and DNA extracted from twelve water samples collected in three different months (June, August, and September of 2007). Phylogenetic analysis of 1234 and 1117 ...

  12. Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics.

    Science.gov (United States)

    Stark, Lucy; Giersch, Tina; Wünschiers, Röbbe

    2014-10-01

    Understanding the microbial population in anaerobic digestion is an essential task to increase efficient substrate use and process stability. The metabolic state, represented e.g. by the transcriptome, of a fermenting system can help to find markers for monitoring industrial biogas production to prevent failures or to model the whole process. Advances in next-generation sequencing make transcriptomes accessible for large-scale analyses. In order to analyze the metatranscriptome of a mixed-species sample, isolation of high-quality RNA is the first step. However, different extraction methods may yield different efficiencies in different species. Especially in mixed-species environmental samples, unbiased isolation of transcripts is important for meaningful conclusions. We applied five different RNA-extraction protocols to nine taxonomic diverse bacterial species. Chosen methods are based on various lysis and extraction principles. We found that the extraction efficiency of different methods depends strongly on the target organism. RNA isolation of gram-positive bacteria was characterized by low yield whilst from gram-negative species higher concentrations can be obtained. Transferring our results to mixed-species investigations, such as metatranscriptomics with biofilms or biogas plants, leads to the conclusion that particular microorganisms might be over- or underrepresented depending on the method applied. Special care must be taken when using such metatranscriptomics data for, e.g. process modeling. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Extracting microRNA-gene relations from biomedical literature using distant supervision.

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    Andre Lamurias

    Full Text Available Many biomedical relation extraction approaches are based on supervised machine learning, requiring an annotated corpus. Distant supervision aims at training a classifier by combining a knowledge base with a corpus, reducing the amount of manual effort necessary. This is particularly useful for biomedicine because many databases and ontologies have been made available for many biological processes, while the availability of annotated corpora is still limited. We studied the extraction of microRNA-gene relations from text. MicroRNA regulation is an important biological process due to its close association with human diseases. The proposed method, IBRel, is based on distantly supervised multi-instance learning. We evaluated IBRel on three datasets, and the results were compared with a co-occurrence approach as well as a supervised machine learning algorithm. While supervised learning outperformed on two of those datasets, IBRel obtained an F-score 28.3 percentage points higher on the dataset for which there was no training set developed specifically. To demonstrate the applicability of IBRel, we used it to extract 27 miRNA-gene relations from recently published papers about cystic fibrosis. Our results demonstrate that our method can be successfully used to extract relations from literature about a biological process without an annotated corpus. The source code and data used in this study are available at https://github.com/AndreLamurias/IBRel.

  14. A study of extraction process and in vitro antioxidant activity of total phenols from Rhizoma Imperatae.

    Science.gov (United States)

    Zhou, Xian-rong; Wang, Jian-hua; Jiang, Bo; Shang, Jin; Zhao, Chang-qiong

    2013-01-01

    The study investigated the extraction method of Rhizoma Imperatae and its antioxidant activity, and provided a basis for its rational development. The extraction method of Rhizoma Imperatae was determined using orthogonal design test and by total phenol content, its hydroxyl radical scavenging ability was measured by Fenton reaction, and potassium ferricyanide reduction method was used to determine its reducing power. The results showed that the optimum extraction process of Rhizoma Imperatae was a 50-fold volume of water, 30 °C, three times of extraction with 2 h each. Its IC50 for scavenging of hydroxyl radicals was 0.0948 mg/mL, while IC50 of ascorbic acid was 0.1096 mg/mL; in the ferricyanide considerable reduction method, the extract exhibited reducing power comparable to that of the ascorbic acid. The study concluded that Rhizoma Imperatae extract contains relatively large amount of polyphenols, and has a good anti-oxidation ability.

  15. Chemical Composition of the Essential Oil, Total Phenolics, Total Flavonoids and Antioxidant Activity of Methanolic Extracts of Satureja montana L.

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    Avni Hajdari

    2016-05-01

    Full Text Available Aerial parts of Satureja montana L. (Lamiaceae were collected from seven growing wild populations (four populations in Kosovo, two in Albania and one in Montenegro in 2013 with the aim of assessing the natural variation in the chemical composition of the essential oils, total flavonoids, total phenolics and the antioxidant activity of their methanolic extracts. Essential oils were obtained by steam distillation and analysed using GC-FID and GC-MS, whereas total flavonoids, total phenolics and antioxidant activities were determined using spectrophotometric methods. Sixty-one volatile constituents were identified. The main constituents were myrcene, p-cymene, γ-terpinene, linalool, thymol, carvacrol and viridiflorol. Total phenolics ranged from 68.1 to 102.6 mg/g dry mass, the total flavonoid content ranged from 38.3 to 67.0 mg/g dm, and the antioxidant activity according to the DPPH assay ranged from 253.3 to 342.9 mg TE/g dm and according to the FRAP assay ranged from 8.9 to 11.4 mg TE/g dm. Hierarchical cluster analysis and principal component analyses were used to assess the geographical variations in the essential oil composition. Statistical analysis revealed that the analysed populations are grouped into four main clusters that appear to reflect the environmental impact on the chemical composition, which is influenced by differences in habitat composition, altitude and microclimatic conditions.

  16. Optimization of supercritical carbon dioxide extraction of Piper Betel Linn leaves oil and total phenolic content

    Science.gov (United States)

    Aziz, A. H. A.; Yunus, M. A. C.; Arsad, N. H.; Lee, N. Y.; Idham, Z.; Razak, A. Q. A.

    2016-11-01

    Supercritical Carbon Dioxide (SC-CO2) Extraction was applied to extract piper betel linn leaves. The piper betel leaves oil was used antioxidant, anti-diabetic, anticancer and antistroke. The aim of this study was to optimize the conditions of pressure, temperature and flowrate for oil yield and total phenolic content. The operational conditions of SC-CO2 studied were pressure (10, 20, 30 MPa), temperature (40, 60, 80 °C) and flowrate carbon dioxide (4, 6, 8 mL/min). The constant parameters were average particle size and extraction regime, 355pm and 3.5 hours respectively. First order polynomial expression was used to express the extracted oil while second order polynomial expression was used to express the total phenolic content and the both results were satisfactory. The best conditions to maximize the total extraction oil yields and total phenolic content were 30 MPa, 80 °C and 4.42 mL/min leading to 7.32% of oil and 29.72 MPa, 67.53 °C and 7.98 mL/min leading to 845.085 mg GAE/g sample. In terms of optimum condition with high extraction yield and high total phenolic content in the extracts, the best operating conditions were 30 MPa, 78 °C and 8 mL/min with 7.05% yield and 791.709 mg gallic acid equivalent (GAE)/g sample. The most dominant condition for extraction of oil yield and phenolic content were pressure and CO2 flowrate. The results show a good fit to the proposed model and the optimal conditions obtained were within the experimental range with the value of R2 was 96.13% for percentage yield and 98.52% for total phenolic content.

  17. Determination of total triterpenoid acids in different part and extract of Ganoderma lucidum

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    FENG Huiqin

    2013-04-01

    Full Text Available Aim To develop a method for determination of total triterpenoid acids in different part and extracts of Ganoderma lucidum. Method The samples of Ganoderma lucidum were extracted with ethanol and successively extracted with CHCl3 and 5% NaHCO3,the NaHCO3 layer was acidified to pH 3 with 2 mol/L HCl,the resulting precipitates were dissolved in CHCl3 and evaporated in vacuo then weighed. The total triterpenoid acids were obtained. Result The total triterpenoid acids of Ganoderma lucidum fruitbody,spore and mycelium were (8.58±0.25 mg/g,(3.48±0.03 mg/g and (1.75 ±0.09 mg/g respectively. The total triterpenoid acids of pileus and stipe were (12.62±0.22 mg/g and (7.66±0.08 mg/g. The range of total triterpenoid acid content among 10 batches of Ganoderma lucidum fruitbody purchased from the market was between 4.34 to 16.39 mg/g. The highest content fro/8/8/88/ m Ganoderma lucidum fruiting body with alcohol - water extracting was (208.70±5.54 mg/g and the lowest content with alkaline solution extracting was (123.07±4.99 mg/g. The composition of total triterpenoid acid from fruitbody,spores and extract of fruitbody analyzed by HPLC were almost the same. This method is reliable for determination of total triterpenoid acid in the fruiting body and its extracts,spore and mycelium from Ganoderma lucidum,which provides an indicator for the quality of Ganoderma lucidum product.

  18. Efficient recovery of whole blood RNA - a comparison of commercial RNA extraction protocols for high-throughput applications in wildlife species

    Directory of Open Access Journals (Sweden)

    Schwochow Doreen

    2012-06-01

    Full Text Available Abstract Background Since the emergence of next generation sequencing platforms, unprecedented opportunities have arisen in the study of natural vertebrate populations. In particular, insights into the genetic and epigenetic mechanisms of adaptation can be revealed through study of the expression profiles of genes. However, as a pre-requisite to expression profiling, care must be taken in RNA preparation as factors like DNA contamination, RNA integrity or transcript abundance can affect downstream applications. Here, we evaluated five commonly used RNA extraction methods using whole blood sampled under varying conditions from 20 wild carnivores. Results Despite the use of minute starting volumes, all methods produced quantifiable RNA extracts (1.4 – 18.4 μg with varying integrity (RIN 4.6 - 7.7, the latter being significantly affected by the storage and extraction method used. We observed a significant overall effect of the extraction method on DNA contamination. One particular extraction method, the LeukoLOCK™ filter system, yielded high RNA integrity along with low DNA contamination and efficient depletion of hemoglobin transcripts highly abundant in whole blood. In a proof of concept sequencing experiment, we found globin RNA transcripts to occupy up to ¼ of all sequencing reads if libraries were not depleted of hemoglobin prior to sequencing. Conclusion By carefully choosing the appropriate RNA extraction method, whole blood can become a valuable source for high-throughput applications like expression arrays or transcriptome sequencing from natural populations. Additionally, candidate genes showing signs of selection could subsequently be genotyped in large population samples using whole blood as a source for RNA without harming individuals from rare or endangered species.

  19. Surfactant mediated extraction of total phenolic contents (TPC) and antioxidants from fruits juices.

    Science.gov (United States)

    Sharma, Shweta; Kori, Shivpoojan; Parmar, Ankush

    2015-10-15

    The aim of this study was to enhance the extraction of total phenolic contents (TPC) and antioxidants from fruit juices by the application of surfactants formulations instead of conventional solvents (methanol, ethanol and acetone). A variety of fruit infusions: apple red delicious (apple (rd)) (Malus domestica), Mcintosh apple (apple (i)) (Malus pumila), sweet lemon (Citrus limetta) and mango (Magnifera indica) were studied. Effect of water, organic solvents and five different aqueous surfactant formulations viz. SDS, Brij-35, Brij-58, Triton X-100 and Span-40 were explored for the extraction of TPC and determining the antioxidant activity (AA). The TPC and AA (%) were determined using Folin-Ciocalteu (FCA) and DPPH assay, respectively. The effect of surfactant type, concentration and common organic solvents on the extraction of TPC and AA (%) was studied using UV-visible spectrophotometric technique. Among all the extracting systems employed, Brij-58 showed the highest extraction efficiency. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Solid-Liquid Extraction Kinetics of Total Phenolic Compounds (TPC from Red Dates

    Directory of Open Access Journals (Sweden)

    Bee Lin Chua

    2018-01-01

    Full Text Available Red dates are one of the most famous herbal plants in making traditional Chinese medicine. They contain large amount of bioactive compounds. The objectives of this research were to optimise the crude extract yield and total phenolic compounds (TPC yield from red dates using response surface methodology (RSM and model the extraction kinetics of TPC yield from red dates. Date fruits were dried in an oven under temperatures 50°C, 60°C, 70°C and 80°C until a constant weight was obtained. The optimum drying temperature was 60°C as it gave the highest crude extract yield and TPC yield. Besides that, single factor experiments were used to determine the optimum range of four extraction parameters which were: liquid-solid ratio (10-30 ml/g; ultrasonic power (70-90%; extraction temperature (50-70°C; and extraction time (40-60min. The optimum range of the four parameters were further optimised using the Box-Behken Design (BBD of RSM. The extraction conditions that gave the highest crude extract yield and TPC yield were chosen. The optimum value for liquid-solid ratio, ultrasonic power, extraction temperature and extraction time were 30ml/g, 70%, 60°C and 60 min respectively. The two equations generated from RSM were reliable and can be used to predict the crude extract yield and TPC yield. The higher the extraction temperature, liquid-solid ratio, and extraction time and lower ultrasonic power, the higher the crude extract and TPC yield. Finally, the results of TPC yield versus time based on the optimum extraction parameters from RSM optimisation were fitted into three extraction kinetic models (Peleg’s model, Page’s model and Ponomaryov’s model. It was found that the most suitable kinetic model to represent the extraction process of TPC from red dates was Page’s model due to its coefficient of determination (R2 was the closest to unity, 0.9663 while its root mean square error (RMSE was the closest to zero, 0.001534.

  1. Comparative study of the total phenol content and antioxidant activity of some medicinal herbal extracts

    Directory of Open Access Journals (Sweden)

    H. Hajimehdipoor

    2014-08-01

    Full Text Available Herbal medicines can be used as the potential sources of anti-oxidative compounds to help the treatment of diseases associated to oxidative stress. In this paper, the Ferric Reducing Antioxidant Power (FRAP activity of four Lamiaceae herbal extracts, which traditionally applied in oxidative stress related diseases, has been evaluated and total phenolics contents of these extracts determined by using Folin-Ciocalteu reagent. The aqueous methanol extracts were prepared by percolation method and investigated for antioxidant properties and total phenolics content evaluation. All the extracts showed antioxidant effect from 123.6±4.6 mmol of FeSO4.7H2Oequivalent/100 g dried extract in Scutellaria tornefortii to 551.5±16.0 mmol of FeSO4.7H2Oequivalent/100 g dried extract in Satureja sahendica. Interestingly, although Satureja sahendica exhibited the most antioxidant activity, the highest content of polyphenolics belonged to Stachys byzantina. Taking together, antioxidant activity of the mentioned medicinal plants is not necessarily associated with polyphenolic compounds and might be partially due to the presence of other polar constituents like terpenoid-glycosides in aqueous extracts that traditionally used as decoction.

  2. Total phenolic content, antioxidant and antimicrobial activities of Blepharis edulis extracts

    Directory of Open Access Journals (Sweden)

    Mohaddese Mahboubi

    2013-02-01

    Full Text Available Blepharis edulis is traditionally used as an antiseptic, purgative, aphrodisiac and anti-inflammatory agent. The extractsof plant aerial parts were screened for total phenolic content (TPC gallic acid equivalents (GAE, total flavonoid compound(TFC quercetin equivalents (QE, antioxidant capacity and its antimicrobial activity by micro broth dilution assay. The 50%-inhibition values of BHT and 70% (v/v aqueous ethanol, 70% (v/v aqueous methanol, methanol, and water extracts of B.edulis according to the DPPH method were found to be 19.6, 71.2, 73.7, 81.4, and 218.4 g/ml, respectively. TPC ranged from38.9 to 102.7 mg GAE/g dry extracts. The antimicrobial activity showed that yeast and fungi were sensitive and resistantmicroorganisms to the extracts. The 70%-methanol extract showed more drastic antimicrobial activity than the others. Theantimicrobial activity of ethanolic extract is the same as of the methanolic extract; water extract had the weakest antimicrobialactivity.

  3. COMPARISON OF DIFFERENT EXTRACTION METHODS REPRESENTING AVAILABLE AND TOTAL CONCENTRATIONS OF Cd, Cu, Fe, Mn and Zn IN SOIL

    Directory of Open Access Journals (Sweden)

    Vladimir Ivezić

    2013-06-01

    Full Text Available Various extraction methods are used to predict plant uptake of trace metals. Most commonly it is total concentration that is used for risk assessment and evaluation of trace metal availability. However, recent studies showed that total concentration is a poor indicator of availability while concentrations in soil solution show good correlation with plant uptake. Present study was conducted on magricultural soils with low levels of trace metals where 45 soil samples were collected from different soil types. The main objective was to compare four different extraction methods and examine how total and reactive (EDTA trace metal concentrations correlate ,with soil solution concentration (in this study determined by water extraction. The samples were analyzed by four extraction methods: strong acid extraction (ultra-pure HNO3 extraction and aqua regia, weak acid extraction by EDTA and the most available fraction, fraction in soil solution, were represented by water extraction (weakest extractant. Five elements were investigated (Cd, Cu, Fe, Mn and Zn. Water extraction significantly correlated with EDTA extraction for Cu, Fe and Mn, while total extraction (HNO3 extraction and aqua regia correlated significantly with water extraction only for Cu. No correlation between water extraction and total extraction confirmed poor role of total concentration as an indicator of availability. EDTA extraction can be used to represent reactive pool of trace metals in soil but it should be also taken with caution when using it to describe available fraction.

  4. A CTAB Procedure Of Total Genomic DNA Extraction For Medicinal Mushrooms

    International Nuclear Information System (INIS)

    Azhar Mohamad; Muhammad Hussaini Mohd Mustafa; Muhammad Hanif Azhari Noor; Rosnani Abdul Rashid; Hasan Hamdani Hasan Mutaat; Meswan Meskom; Mat Rasol Awang

    2014-01-01

    Medicinal mushroom is defined as mushrooms used in medicine or medical research. Isolation of intact, high-molecular-mass genomic DNA is essential for many molecular biology applications including Polymerase Chain Reaction (PCR), endonuclease restriction digestion, Southern blot analysis, and genomic library construction. The most important and prerequisite towards reliable molecular biology work is the total genomic DNA of a sample must be in good quality. Five freshly samples of medicinal mushroom were used in this work known as Auriculariapolytricha, Lentinus edode, Pleurotus sayorcaju, Sczhizopyllum commune and Ganodermalucidum. 5 mg of each sample were used to extraction the DNA, prepared in 3 replications and repeated twice. PCR based technique by using ISSR markers were used in checking the amplification ability of the total genomic extraction. A standard Doyle and Doyle protocol for genomic DNA extraction was modified in optimizing the total genomic DNA from the medicinal mushroom.The modification parameters were percentage of CTAB, incubation period and temperature. The results reveal that each sample required a certain combinations of time and period of incubation. Besides, percentage of CTAB in the buffer was found significant in giving a high yielding of extracted total genomic DNA. The extracted total genomic DNA from the medicinal mushroom yielded from 39.7 ng/ μl to 919.1 ng/ μl. The different yield among the samples found to be corresponded to polysaccharide content in the medicinal mushrooms. The objective of this works is to optimize total genomic DNA extraction of medicinal mushrooms towards a high quality intact genomic DNA for molecular activities. (author)

  5. [Evaluation of the total biological activity and allergenic composition of allergenic extracts].

    Science.gov (United States)

    Lombardero, M; González, R; Duffort, O; Juan, F; Ayuso, R; Ventas, P; Cortés, C; Carreira, J

    1986-01-01

    In the present study, a complete procedure is presented in order to standardize allergenic extracts, the meaning of which is the measurement of the total allergenic activity and the determination of the allergenic composition. The measurement of the biological activity comprises 2 steps: Preparation of Reference Extracts and determination of their "in vivo" activity. Evaluation of the total allergenic activity of extracts for clinical use. Reference extracts were prepared from the main allergens and their "in vivo" biological activity was determined by a quantitative skin prick test in a sample of at least 30 allergic patients. By definition, the protein concentration of Reference Extract that produces, in the allergic population, a geometric mean wheal of 75 mm.2 has an activity of 100 biological units (BUs). The determination of the biological activity of a problem extract is made by RAST inhibition. The sample is compared with the corresponding Reference Extract by this technique and, from this comparison, it is possible to quantify the activity of the problem extract in biologic units (BUs) with clinical significance. Likewise, different techniques have been used to determine the allergenic composition of extracts. These techniques comprise 2 steps: Separation of the components of the extract. Identification of the components that bind specific human IgE. The separation of the components of the extract has been carried out by isoelectric focusing (IEF) and electrophoresis in the presence of sodium dodecyl sulphate (SDS-PAGE). In order to identify the allergenic components, an immunoblotting technique has been employed. The separated components in the IEF gel or SDS-PAGE gel are transferred to a nitrocellulose sheet and later on, this membrane is overlaid with a serum pool from allergic patients and a mouse monoclonal anti-human IgE, labelled with 125I. Finally, the autoradiography of the nitrocellulose membrane is obtained. In this way it is possible to compare

  6. [Effects of lipopolysaccharides extracted from Porphyromonas endodontalis on the expression of IL-1beta mRNA and IL-6 mRNA in osteoblasts].

    Science.gov (United States)

    Yang, Di; Li, Ren; Qiu, Li-Hong; Li, Chen

    2009-04-01

    To quantify the IL-1 beta mRNA and IL-6 mRNA expression induced by lipopolysaccharides (LPS)extracted from Porphyromonas endodontalis(P.e) in osteoblasts, and to relate P.e-LPS to bone absorption pathogenesis in lesions of chronical apical periodontitis. MG63 was treated with different concentrations of P.e-LPS(0-50 microg/mL) for different hours(0-24h). The expression of IL-1 beta mRNA and IL-6 mRNA was detected by reverse transcription polymerase chain reaction (RT-PCR).Statistical analysis was performed using one- way ANOVA and Dunnett t test with SPSS11.0 software package. The level of IL-1 beta mRNA and IL-6 mRNA increased significantly after treatment with P.e-LPS at more than 5 microg/mL (P<0.01)and for more than 1 hour (P<0.01), which indicated that P.e-LPS induced osteoblasts to express IL-1 beta mRNA and IL-6 mRNA in dose and time dependent manners. P.e-LPS may promote bone resorption in lesions of chronical apical periodontitis by inducing IL-1 beta mRNA and IL-6 mRNA expression in osteoblasts.

  7. Antioxidant, Cytotoxic, and Antiproliferative Activities and Total Polyphenol Contents of the Extracts of Geissospermum reticulatum Bark

    Directory of Open Access Journals (Sweden)

    Joanna J. Sajkowska-Kozielewicz

    2016-01-01

    Full Text Available Geissospermum species are medically important plants due to their health-promoting effects. The objective of this study was to determine the antioxidant ability and antiproliferative and cytotoxic effects of infusions, tinctures, and ethanolic extracts of Geissospermum reticulatum barks in relation to the contents of total phenolics and flavonoids. Seven samples of barks were collected in various regions of Peruvian Amazonia. We found that the amount of total phenolics in the studied products varied from 212.40 ± 0.69 to 1253.92 ± 11.20 mg GAE/kg. In our study there is a correlation (R2=0.7947 between the results of antioxidants assays: FRAP and ORAC for tinctures, infusions, and ethanolic extracts of G. reticulatum barks. We have also observed antiproliferative activities of the ethanolic extracts on normal T-cells. These extracts have caused death on malignant cell lines (THP-1 and HL-60 and this data correlates well with their antioxidant capacity measured by ORAC method. Interestingly, the highest concentration of the ethanolic extract was not toxic in the zebrafish embryo developmental assay. Our results indicate that G. reticulatum is rich in antioxidants and have cytotoxic and antiproliferative properties. The data suggests potential immunosuppressive role of the extracts. This is the first study presenting the results of chemical and biological analysis of multiple preparations from G. reticulatum.

  8. Monocytic microRNA profile associated with coronary collateral artery function in chronic total occlusion patients.

    Science.gov (United States)

    Hakimzadeh, Nazanin; Elias, Joëlle; Wijntjens, Gilbert W M; Theunissen, Ruud; van Weert, Angela; Smulders, Martijn W; van den Akker, Nynke; Moerland, Perry D; Verberne, Hein J; Hoebers, Loes P; Henriques, Jose P S; van der Laan, Anja M; Ilhan, Mustafa; Post, Mark; Bekkers, Sebastiaan C A M; Piek, Jan J

    2017-05-08

    An expansive collateral artery network is correlated with improved survival in case of adverse cardiac episodes. We aimed to identify cellular microRNAs (miRNA; miR) important for collateral artery growth. Chronic total occlusion (CTO) patients (n = 26) were dichotomized using pressure-derived collateral flow index (CFI p ) measurements; high collateral capacity (CFI p  > 0.39; n = 14) and low collateral (CFI p  collateral capacity patients. Validation by real-time polymerase chain reaction demonstrated significantly decreased expression of miR339-5p in all stimulated monocyte phenotypes of low collateral capacity patients. MiR339-5p showed significant correlation with CFI p values in stimulated monocytes. Ingenuity pathway analysis of predicted gene targets of miR339-5p and differential gene expression data from high versus low CFI p patients (n = 20), revealed significant association with STAT3 pathway, and also suggested a possible regulatory role for this signaling pathway. These results identify a novel association between miR339-5p and coronary collateral function. Future work examining modulation of miR339-5p and downstream effects on the STAT3 pathway and subsequent collateral vessel growth are warranted.

  9. Multivessel supercritical fluid extraction of food items in Total Diet Study.

    Science.gov (United States)

    Hopper, M L; King, J W; Johnson, J H; Serino, A A; Butler, R J

    1995-01-01

    An off-line, large capacity, multivessel supercritical fluid extractor (SFE) was designed and constructed for extraction of large samples. The extractor can simultaneously process 1-6 samples (15-25 g) by using supercritical carbon dioxide (SC-CO2), which is relatively nontoxic and nonflammable, as the solvent extraction medium. Lipid recoveries for the SFE system were comparable to those obtained by blending or Soxhlet extraction procedures. Extractions at 10,000 psi, 80 degrees C, expanded gaseous CO2 flow rates of 4-5 L/min (35 degrees C), and 1-3 h extraction times gave reproducible lipid recoveries for pork sausage (relative standard deviation [RSD], 1.32%), corn chips (RSD, 0.46%), cheddar cheese (RSD, 1.14%), and peanut butter (RSD, 0.44%). In addition, this SFE system gave reproducible recoveries (> 93%) for butter fortified with cis-chlordane and malathion at the 100 ppm and 0.1 ppm levels. Six portions each of cheddar cheese, saltine crackers, sandwich cookies, and ground hamburger also were simultaneously extracted with SC-CO2 and analyzed for incurred pesticide residues. Results obtained with this SFE system were reproducible and comparable with results from organic-solvent extraction procedures currently used in the Total Diet Study; therefore, use and disposal of large quantities of organic solvents can be eliminated.

  10. A single-step method for rapid extraction of total lipids from green microalgae.

    Directory of Open Access Journals (Sweden)

    Martin Axelsson

    Full Text Available Microalgae produce a wide range of lipid compounds of potential commercial interest. Total lipid extraction performed by conventional extraction methods, relying on the chloroform-methanol solvent system are too laborious and time consuming for screening large numbers of samples. In this study, three previous extraction methods devised by Folch et al. (1957, Bligh and Dyer (1959 and Selstam and Öquist (1985 were compared and a faster single-step procedure was developed for extraction of total lipids from green microalgae. In the single-step procedure, 8 ml of a 2∶1 chloroform-methanol (v/v mixture was added to fresh or frozen microalgal paste or pulverized dry algal biomass contained in a glass centrifuge tube. The biomass was manually suspended by vigorously shaking the tube for a few seconds and 2 ml of a 0.73% NaCl water solution was added. Phase separation was facilitated by 2 min of centrifugation at 350 g and the lower phase was recovered for analysis. An uncharacterized microalgal polyculture and the green microalgae Scenedesmus dimorphus, Selenastrum minutum, and Chlorella protothecoides were subjected to the different extraction methods and various techniques of biomass homogenization. The less labour intensive single-step procedure presented here allowed simultaneous recovery of total lipid extracts from multiple samples of green microalgae with quantitative yields and fatty acid profiles comparable to those of the previous methods. While the single-step procedure is highly correlated in lipid extractability (r² = 0.985 to the previous method of Folch et al. (1957, it allowed at least five times higher sample throughput.

  11. Anti-tumor potential of total alkaloid extract of Prosopis juliflora DC ...

    African Journals Online (AJOL)

    Jane

    2011-08-15

    Aug 15, 2011 ... Cancer is the second leading cause of death in the world. (Madhusudan and .... formula and from that the percentage of cytotoxicity and IC50 values ... complete media were treated as positive and negative controls, .... Cytotoxic effect of total alkaloid extract of P. juliflora leaves against cancer (black bars).

  12. Total phenol content and antioxidant activity of water solutions of plant extracts

    Directory of Open Access Journals (Sweden)

    Mirela Kopjar

    2009-01-01

    Full Text Available Water solutions of extracts were investigated for total phenol content, flavonoid content and antioxidant activity. Susceptibility to degradation of water solutions of plant extracts, under light and in the dark, during storage at room temperature was investigated in order to determine their stability prior to their application for fortification of food products. Large dispersion of total phenol (TP content in the investigated model solutions of selected extracts (olive leaves, green tea, red grape, red wine, pine bark PE 5:1, pine bark PE 95 %, resveratrol, ranging from 11.10 mg GAE/100 mL to 92.19 mg GAE/100 mL was observed. Consequently, large dispersion of total flavonoids (TF content (8.89 mg to 61.75 mg CTE/100 mL was also observed. Since phenols have been mostly responsible for antioxidant activity of extracts, in most cases, antioxidant activity followed the TP content. That was proven by estimation of correlation coefficient between the total phenol content and antioxidant activity. Correlation coefficients between investigated parameters ranged from 0.5749 to 0.9604. During storage of 5 weeks at room temperature loss of phenols and flavonoids occurred. Antioxidant activity decreased with the decrease of TP and TF content. Degradations of phenols and flavonoids were more pronounced in samples stored at light.

  13. Use of solvent mixtures for total lipid extraction of Chlorella vulgaris and gas chromatography FAME analysis.

    Science.gov (United States)

    Moradi-Kheibari, Narges; Ahmadzadeh, Hossein; Hosseini, Majid

    2017-09-01

    Lipid extraction is the bottleneck step for algae-based biodiesel production. Herein, 12 solvent mixture systems (mixtures of three non-polar and two polar organic solvents) were examined to evaluate their effects on the total lipid yield from Chlorella vulgaris (C. vulgaris). Moreover, the extraction yields of three solvent systems with maximum extraction efficiency of esterifiable lipids were determined by acidic transesterification and GC-FID analysis. Three solvent systems, which resulted in a higher extraction yield, were further subjected to fatty acid methyl ester (FAME) analysis. The total lipid extraction yields (based on dry biomass) were (38.57 ± 1.51), (25.33 ± 0.58), and (25.17 ± 1.14) %, for chloroform-methanol (1:2) (C1M2), hexane-methanol (1:2) (H1M2), and chloroform-methanol (2:1) (C2M1), respectively. The extraction efficiency of C1M2 was approximately 1.5 times higher than H1M2 and C2M1, whereas the FAME profile of extracted lipids by H1M2 and C1M2 were almost identical. Moreover, the esterifiable lipid extraction yields of (18.14 ± 2.60), (16.66 ± 0.35), and (13.22 ± 0.31) % (based on dry biomass) were obtained for C1M2, H1M2, and C2M1 solvent mixture systems, respectively. The biodiesel fuel properties produced from C. vulgaris were empirically predicted and compared to that of the EN 14214 and ASTM 6751 standard specifications.

  14. RNA.

    Science.gov (United States)

    Darnell, James E., Jr.

    1985-01-01

    Ribonucleic acid (RNA) converts genetic information into protein and usually must be processed to serve its function. RNA types, chemical structure, protein synthesis, translation, manufacture, and processing are discussed. Concludes that the first genes might have been spliced RNA and that humans might be closer than bacteria to primitive…

  15. Two cases of laparoscopic total colectomy with natural orifice specimen extraction and review of the literature.

    Science.gov (United States)

    Gundogan, Ersin; Aktas, Aydin; Kayaalp, Cuneyt; Gonultas, Fatih; Sumer, Fatih

    2017-09-01

    We present two cases of natural orifice specimen extraction (NOSE) after laparoscopic total colectomy and ileorectal anastomosis (TC-IRA), and we also review all of the previously reported cases. Our aim was to focus on patient selection for NOSE after TC-IRA. The PubMed and Google Scholar databases were scanned. Demographic features, surgical indications, and techniques were analyzed. Basic calculations were used for statistical analysis. A total of 13 cases were detected in addition to our 2 cases. All of the specimens were removed through the natural orifices successfully. No case required a diverting ileostomy. No patients were converted to open surgery or to conventional laparoscopy. Complications were reported in three patients. Transanal extractions were performed in 12 cases (10 colonic inertia, 2 polyposis), and transvaginal extractions were performed in 3 cases (2 malignancy, 1 colonic inertia). Both transanal and transvaginal specimen extractions after laparoscopic TC-IRA can be preferred. However, transanal extraction seems to be feasible in cases of TC for benign disease with a limited mesenteric-omental resection. If the indication is a malignancy requiring a mesenteric-omental resection, a transvaginal route should be preferred for a voluminous specimen.

  16. Validation of an HPLC method for quantification of total quercetin in Calendula officinalis extracts

    International Nuclear Information System (INIS)

    Muñoz Muñoz, John Alexander; Morgan Machado, Jorge Enrique; Trujillo González, Mary

    2015-01-01

    Introduction: calendula officinalis extracts are used as natural raw material in a wide range of pharmaceutical and cosmetic preparations; however, there are no official methods for quality control of these extracts. Objective: to validate an HPLC-based analytical method for quantification total quercetin in glycolic and hydroalcoholic extracts of Calendula officinalis. Methods: to quantify total quercetin content in the matrices, it was necessary to hydrolyze flavonoid glycosides under optimal conditions. The chromatographic separation was performed on a C-18 SiliaChrom 4.6x150 mm 5 µm column, adapted to a SiliaChrom 5 um C-18 4.6x10 mm precolumn, with UV detection at 370 nm. The gradient elution was performed with a mobile phase consisting of methanol (MeOH) and phosphoric acid (H 3 PO 4 ) (0.08 % w/v). The quantification was performed through the external standard method and comparison with quercetin reference standard. Results: the studied method selectivity against extract components and degradation products under acid/basic hydrolysis, oxidation and light exposure conditions showed no signals that interfere with the quercetin quantification. It was statistically proved that the method is linear from 1.0 to 5.0 mg/mL. Intermediate precision expressed as a variation coefficient was 1.8 and 1.74 % and the recovery percentage was 102.15 and 101.32 %, for glycolic and hydroalcoholic extracts, respectively. Conclusions: the suggested methodology meets the quality parameters required for quantifying total quercetin, which makes it a useful tool for quality control of C. officinalis extracts. (author)

  17. Studies on total polyphenols and reducing power of aqueous extracts from selected lamiaceae species

    Directory of Open Access Journals (Sweden)

    Maria Cioroi

    2010-08-01

    Full Text Available Certain phytochemicals in species are attracting increased attention because of a wide range of biological activities especially the possible cancer preventive properties. Polyphenols, the naturalantioxidants are present in plant extracts and they play a key role in antioxidative defence mechanisms in biological systems and they act as free radicals scavenging agents. Polyphenols might thereforeinhibit development of coronary heart disease and cancers. Basil, oregano and sage are highly fragrant plants whose leaves are used as a seasoning herb for many different types of foods. Aqueous extractswere prepared from basil (Ocimum basilicum L., oregano (Origanum vulgare L. and sage (Salvia officinalis L.. To check the phenols presence, the UV-VIS spectrum was made. The amount of polyphenolic compounds from selected Lamiaceae species was determined by spectrophotometry method using the Folin - Ciocalteau reagent and gallic acid as standard. The range of polyphenols total was between 516,352 mg/100g dried species and 859,617 mg/100g dried species.Reducing power has been established by measuring the redox potential of aqueous extracts. Antioxidant activity was directly correlated with the total amount of polyphenols in the species extracts.The free reducing sugars in aqueous extracts from species were analyzed and correlated to the total content of polyphenols.

  18. A simple and efficient total genomic DNA extraction method for individual zooplankton.

    Science.gov (United States)

    Fazhan, Hanafiah; Waiho, Khor; Shahreza, Md Sheriff

    2016-01-01

    Molecular approaches are widely applied in species identification and taxonomic studies of minute zooplankton. One of the most focused zooplankton nowadays is from Subclass Copepoda. Accurate species identification of all life stages of the generally small sized copepods through molecular analysis is important, especially in taxonomic and systematic assessment of harpacticoid copepod populations and to understand their dynamics within the marine community. However, total genomic DNA (TGDNA) extraction from individual harpacticoid copepods can be problematic due to their small size and epibenthic behavior. In this research, six TGDNA extraction methods done on individual harpacticoid copepods were compared. The first new simple, feasible, efficient and consistent TGDNA extraction method was designed and compared with the commercial kit and modified available TGDNA extraction methods. The newly described TGDNA extraction method, "Incubation in PCR buffer" method, yielded good and consistent results based on the high success rate of PCR amplification (82%) compared to other methods. Coupled with its relatively consistent and economical method the "Incubation in PCR buffer" method is highly recommended in the TGDNA extraction of other minute zooplankton species.

  19. An optimised method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7

    Directory of Open Access Journals (Sweden)

    Ashleigh eHolmes

    2014-06-01

    Full Text Available Analysis of microbial gene expression during host colonisation provides valuable information on the nature of interaction, beneficial or pathogenic, and the adaptive processes involved. Isolation of bacterial mRNA for in planta analysis can be challenging where host nucleic acid may dominate the preparation, or inhibitory compounds affect downstream analysis, e.g. qPCR, microarray or RNA-seq. The goal of this work was to optimise the isolation of bacterial mRNA of food-borne pathogens from living plants. Reported methods for recovery of phytopathogen-infected plant material, using hot phenol extraction and high concentration of bacterial inoculation or large amounts of infected tissues, were found to be inappropriate for plant roots inoculated with Escherichia coli O157:H7. The bacterial RNA yields were too low and increased plant material resulted in a dominance of plant RNA in the sample. To improve the yield of bacterial RNA and reduce the number of plants required, an optimised method was developed which combines bead beating with directed bacterial lysis using SDS and lysozyme. Inhibitory plant compounds, such as phenolics and polysaccharides, were counteracted with the addition of HMW-PEG and CTAB. The new method increased the total yield of bacterial mRNA substantially and allowed assessment of gene expression by qPCR. This method can be applied to other bacterial species associated with plant roots, and also in the wider context of food safety.

  20. Phytochemicals Screening, Total Phenol Estimation, Antioxidant Activity of Blainvillea Acmella Leaf and Stem Successive Extracts

    International Nuclear Information System (INIS)

    Sharma, P.; Sharma, G.N.; Shrivastava, B.; Jadhav, H.R.

    2014-01-01

    The aim of present work was to investigate antioxidant potential of different extracts of Blainvillea acmella leaf and stem. The successive extraction of individual plant part was carried out using solvents of different polarity viz. n-hexane, ethyl acetate, methanol and water. Preliminary phyto chemical screening of all the extracts was done. The present total phenolic contents were estimated by Folin-Ciocalteu reagent method and expressed as μg/ mg of gallic acid equivalent. The antioxidant potential and reducing power of all the prepared extracts were measured against DPPH, as compared to standard ascorbic acid, and BHA respectively. The result data indicate that the phenolic contents were higher in methanolic extracts of leaf (73.67 ± 0.38 mg/ g) followed by ethyl acetate (29.08 ± 0.38 mg/ g), aqueous (21.50 ± 0.28 mg/ g), and n-Hexane (9.29 ± 0.38 mg/ g); gallic acid equivalent. The similar pattern in stem part was also observed for example methanolic extracts (41.90 ± 0.45 mg/ g), ethyl acetate (21.92 ± 0.28 mg/ g), aqueous (15.13 ± 0.18 mg/ g), and n-Hexane (3.69 ± 0.28 mg/ g). The antioxidant capacity of methanolic extract of both the part for example leaf and stem was found to be maximum, as IC50 values were 226.49 ± 0.16, 402.05 ± 1.10 respectively. The reducing power was also highest in methanol extract of both parts. The result data conclude that the higher antioxidant as well as reducing power may be due to present phenolic contents. (author)

  1. Polyethylene glycol and polyvinylpirrolidone effect on bacterial rRNA extraction and hybridization from cells exposed to tannins.

    OpenAIRE

    ARCURI, P.B.; THONNEY, M.L.; SCHOFIELD, P.; PELL, A.N.

    2003-01-01

    In order to detect fluctuations in ruminal microbial populations due to forage tannins using 16S ribosomal RNA (rRNA) probes, recovery of intact rRNA is required. The objective of this work was to evaluate the effect of polyethylene glycol (PEG) and polyvinylpirrolidone (PVP) on extraction of bacterial rRNA, in the presence of tannins from tropical legume forages and other sources, that hybridize with oligonucleotide probes. Ruminococcus albus 8 cells were exposed to 8 g/L tannic acid or 1 g/...

  2. Total phenolic and flavonoid contents and biological activities of Cachrys cristata DC. extracts

    Directory of Open Access Journals (Sweden)

    Matejić Jelena S.

    2014-01-01

    Full Text Available The total phenolic/flavonoid contents and antioxidant potential of the methanol, ethyl-acetate, acetone and water extracts obtained from the aerial parts and fruits of Cachrys cristata DC.(Apiaceae were compared. The total phenolic contents of the tested extracts were determined using Folin-Ciocalteu’s reagent. The amounts per g of dry plant extract of gallic acid (GA and quercetin (Qu ranged between 22.60-166.97 mg, and 8.91-46.02 mg, respectively. The antioxidant activity, expressed as IC50, ranged from 1.784-17.621 mg/mL and from 1.01-3.42 mg L(+-ascorbic acid (Vitamin C/g when tested with 2,2-diphenyl-1-picrylhydrazyl (DPPH and ABTS, respectively. The antimicrobial activity of the extracts was investigated by the microwell dilution assay, for the most common human gastrointestinal pathogenic bacterial strains: Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 9027, Salmonella enteritidis ATCC 13076, Bacillus cereus ATCC 10876, Listeria monocytogenes ATCC15313, Staphylococcus aureus ATCC 25923 and yeast Candida albicans ATCC 10231. The results indicate that C. cristata can be regarded as a potential source of antioxidant and antimicrobial agents. [Projekat Ministarstva nauke Republike Srbije, br. 173029

  3. A novel technology coupling extraction and foam fractionation for separating the total saponins from Achyranthes bidentata.

    Science.gov (United States)

    Ding, Linlin; Wang, Yanji; Wu, Zhaoliang; Liu, Wei; Li, Rui; Wang, Yanyan

    2016-10-02

    A novel technology coupling extraction and foam fractionation was developed for separating the total saponins from Achyranthes bidentata. In the developed technology, the powder of A. bidentata was loaded in a nylon filter cloth pocket with bore diameter of 180 µm. The pocket was fixed in the bulk liquid phase for continuously releasing saponins. Under the optimal conditions, the concentration and the extraction rate of the total saponins in the foamate by the developed technology were 73.5% and 416.2% higher than those by the traditional technology, respectively. The foamates obtained by the traditional technology and the developed technology were analyzed by ultraperformance liquid chromatography-mass spectrometry to determine their ingredients, and the results appeared that the developed technology exhibited a better performance for separating saponins than the traditional technology. The study is expected to develop a novel technology for cost effectively separating plant-derived materials with surface activity.

  4. Evaluation of different pulverisation methods for RNA extraction in squash fruit: lyophilisation, cryogenic mill and mortar grinding.

    Science.gov (United States)

    Román, Belén; González-Verdejo, Clara I; Peña, Francisco; Nadal, Salvador; Gómez, Pedro

    2012-01-01

    Quality and integrity of RNA are critical for transcription studies in plant molecular biology. In squash fruit and other high water content crops, the grinding of tissue with mortar and pestle in liquid nitrogen fails to produce a homogeneous and fine powered sample desirable to ensure a good penetration of the extraction reagent. To develop an improved pulverisation method to facilitate the homogenisation process of squash fruit tissue prior to RNA extraction without reducing quality and yield of the extracted RNA. Three methods of pulverisation, each followed by the same extraction protocol, were compared. The first approach consisted of the lyophilisation of the sample in order to remove the excess of water before grinding, the second one used a cryogenic mill and the control one a mortar grinding of frozen tissue. The quality of the isolated RNA was tested by carrying out a quantitative real time downstream amplification. In the three situations considered, mean values for A(260) /A(280) indicated minimal interference by proteins and RNA quality indicator (RQI) values were considered appropriate for quantitative real-time polymerase chain reaction (qRT-PCR) amplification. Successful qRT-PCR amplifications were obtained with cDNA isolated with the three protocols. Both apparatus can improve and facilitate the grinding step in the RNA extraction process in zucchini, resulting in isolated RNA of high quality and integrity as revealed by qRT-PCR downstream application. This is apparently the first time that a cryogenic mill has been used to prepare fruit samples for RNA extraction, thereby improving the sampling strategy because the fine powder obtained represents a homogeneous mix of the organ tissue. Copyright © 2012 John Wiley & Sons, Ltd.

  5. Robust microwave-assisted extraction protocol for determination of total mercury and methylmercury in fish tissues

    Energy Technology Data Exchange (ETDEWEB)

    Reyes, L. Hinojosa; Rahman, G.M. Mizanur [Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282 (United States); Kingston, H.M. Skip [Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282 (United States)], E-mail: kingston@duq.edu

    2009-01-12

    A rapid and efficient closed vessel microwave-assisted extraction (MAE) method based on acidic leaching was developed and optimized for the extraction of total mercury (Hg), inorganic mercury (Hg{sup 2+}) and methylmercury (CH{sub 3}Hg{sup +}) from fish tissues. The quantitative extraction of total Hg and mercury species from biological samples was achieved by using 5 mol L{sup -1} HCl and 0.25 mol L{sup -1} NaCl during 10 min at 60 deg. C. Total Hg content was determined using inductively coupled plasma mass spectrometry (ICP-MS). Mercury species were measured by liquid chromatography hyphenated with inductively coupled plasma mass spectrometry (LC-ICP-MS). The method was validated using biological certified reference materials ERM-CE464, DOLT-3, and NIST SRM-1946. The analytical results were in good agreement with the certified reference values of total Hg and CH{sub 3}Hg{sup +} at a 95% confidence level. Further, accuracy validation using speciated isotope-dilution mass spectrometry (SIDMS, as described in the EPA Method 6800) was carried out. SIDMS was also applied to study and correct for unwanted species transformation reactions during and/or after sample preparation steps. For the studied reference materials, no statistically significant transformation between mercury species was observed during the extraction and determination procedures. The proposed method was successfully applied to fish tissues with good agreement between SIDMS results and external calibration (EC) results. Interspecies transformations in fish tissues were slightly higher than certified reference materials due to differences in matrix composition. Depending on the type of fish tissue, up to 10.24% of Hg{sup 2+} was methylated and up to 1.75% of CH{sub 3}Hg{sup +} was demethylated to Hg{sup 2+}.

  6. Extraction and quantitation of total cholesterol, dolichol and dolichyl phosphate from mammalian liver

    International Nuclear Information System (INIS)

    Crick, D.C.; Carroll, K.K.

    1987-01-01

    A procedure is described for the determination of total cholesterol, dolichol and dolichyl phosphate (Dol-P) in mammalian liver. It is based on extraction of these compounds into diethyl ether after alkaline saponification of the tissue. Extractability is affected by the length of saponification and concentration of potassium hydroxide (KOH) in the saponification mixture. After extraction, total cholesterol and dolichol are quantitated directly by reverse-phase high pressure liquid chromatography (HPLC) on C18. Dol-P requires further purification before quantitation by HPLC, this is accomplished by chromatography on silicic acid. These methods gave recoveries of over 90% for cholesterol and dolichol and about 60% for Dol-P, using [4- 14 C]cholesterol, a polyprenol containing 15 isoprene units, and [1- 14 C]Dol-P as recovery standards. Concentrations of total cholesterol, dolichol and Dol-P in livers from one month-old-CBA mice were found to be 5.7 +/- 0.7 mg/g, 66.3 +/- 1.2 micrograms/g and 3.7 +/- 0.3 micrograms/g, respectively

  7. Optimization of extraction conditions of total phenolics, antioxidant activities, and anthocyanin of oregano, thyme, terebinth, and pomegranate.

    Science.gov (United States)

    Rababah, Taha M; Banat, Fawzi; Rababah, Anfal; Ereifej, Khalil; Yang, Wade

    2010-09-01

    The purpose of this study was to evaluate the total phenolic extracts and antioxidant activity and anthocyanins of varieties of the investigated plants. These plants include oregano, thyme, terebinth, and pomegranate. The optimum extraction conditions including temperature and solvent of the extraction process itself were investigated. Total phenolic and anthocyanin extracts were examined according to Folin-Ciocalteu assay and Rabino and Mancinelli method, respectively. The effect of different extracting solvents and temperatures on extracts of phenolic compounds and anthocyanins were studied. Plant samples were evaluated for their antioxidant chemical activity by 2, 2-diphenyl-1-picrylhydrazl assay, to determine their potential as a source of natural antioxidant. Results showed that all tested plants exhibited appreciable amounts of phenolic compounds. The methanolic extract (60 °C) of sour pomegranate peel contained the highest phenolic extract (4952.4 mg/100 g of dry weight). Terebinth green seed had the lowest phenolic extract (599.4 mg/100 g of dry weight). Anthocyanins ranged between 3.5 (terebinth red seed) and 0.2 mg/100 g of dry material (thyme). Significant effect of different extracting solvents and temperatures on total phenolics and anthocyanin extracts were found. The methanol and 60 °C of extraction conditions found to be the best for extracting phenolic compounds. The distilled water and 60 °C extraction conditions found to be the best for extracting anthocyanin.

  8. Extract of Stellerachamaejasme L(ESC) inhibits growth and metastasis of human hepatocellular carcinoma via regulating microRNA expression.

    Science.gov (United States)

    Liu, Xiaoni; Wang, Shuang; Xu, Jianji; Kou, Buxin; Chen, Dexi; Wang, Yajie; Zhu, Xiaoxin

    2018-03-20

    MicroRNAs(miRNAs)are involved in the initiation and progression of hepatocellular carcinoma. ESC, an extract of Stellerachamaejasme L, had been confirmed as a potential anti-tumor extract of Traditional Chinese Medicine. In light of the important role of miRNAs in hepatocellular carcinoma, we questioned whether the inhibitory effects of ESC on hepatocellular carcinoma (HCC) were associated with miRNAs. The proliferation inhibition of ESC on HCC cells was measured with MTT assay. The migration inhibition of ESC on HCC cells was measured with transwell assay. The influences of ESC on growth and metastasis inhibition were evaluated with xenograft tumor model of HCC. Protein expressions were measured with western blot and immunofluorescence methods and miRNA profiles were detected with miRNA array. Differential miRNA and target mRNAs were verified with real-time PCR. The results showed that ESC could inhibit proliferation and epithelial mesenchymal transition (EMT) in HCC cells in vitro and tumor growth and metastasis in xenograft models in vivo. miRNA array results showed that 69 differential miRNAs in total of 429 ones were obtained in MHCC97H cells treated by ESC. hsa-miR-107, hsa-miR-638, hsa-miR-106b-5p were selected to be validated with real-time PCR method in HepG2 and MHCC97H cells. Expressions of hsa-miR-107 and hsa-miR-638 increased obviously in HCC cells treated by ESC. Target genes of three miRNAs were also validated with real-time PCR. Interestingly, only target genes of hsa-miR-107 changed greatly. ESC downregulated the MCL1, SALL4 and BCL2 gene expressions significantly but did not influence the expression of CACNA2D1. The findings suggested ESC regressed growth and metastasis of human hepatocellular carcinoma via regulating microRNAs expression and their corresponding target genes.

  9. Sample preparation for avian and porcine influenza virus cDNA amplification simplified: Boilign vs. conventional RNA extraction

    International Nuclear Information System (INIS)

    Fereidouni, S.R.; Starick, E.; Ziller, M.; Harder, T.C.; Unger, H.; Hamilton, K.; Globig, A.

    2016-01-01

    Full text: RNA extraction and purification is a fundamental step that allows for highly sensitive amplification of specific RNA targets in PCR applications. However, commercial extraction kits that are broadly used because of their robustness and high yield of purified RNA are expensive and labor-intensive. In this study, boiling in distilled water or a commerical lysis buffer of different sample matrices containing avian or porcine influenza viruses was tested as an alternative. Real-time PCR (RTaPCR) for nucleoprotein gene fragment was used as read out. Results were compared with freshly extracted RNA by use of a commercial extraction kit. Different batches of virus containing material materials, including diluted virus positive allontoic fluid or cell culture supernatnat, and avian faecal, cloacal or oropharyngeal swab samples were used in this study. Simple boiling of samples without any additional purification steps can be used as an alternative RNA preparation method to detect influenza A virus nucleoprotein RNA in oropharyngeal swab samples, allantoic fluid or cell-culture supernatant. The boiling method is not applicable for sample matrices containing faecal material. (author)

  10. Digestion of chrysanthemum stunt viroid by leaf extracts of Capsicum chinense indicates strong RNA-digesting activity.

    Science.gov (United States)

    Iraklis, Boubourakas; Kanda, Hiroko; Nabeshima, Tomoyuki; Onda, Mayu; Ota, Nao; Koeda, Sota; Hosokawa, Munetaka

    2016-08-01

    CSVd could not infect Nicotiana benthamiana when the plants were pretreated with crude leaf extract of Capsicum chinense 'Sy-2'. C. chinense leaves were revealed to contain strong RNA-digesting activity. Several studies have identified active antiviral and antiviroid agents in plants. Capsicum plants are known to contain antiviral agents, but the mechanism of their activity has not been determined. We aimed to elucidate the mechanism of Capsicum extract's antiviroid activity. Chrysanthemum stunt viroid (CSVd) was inoculated into Nicotiana benthamiana plants before or after treating the plants with a leaf extract of Capsicum chinense 'Sy-2'. CSVd infection was determined using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) 3 weeks after inoculation. When Capsicum extract was sprayed or painted onto N. benthamiana before inoculation, it was effective in preventing infection by CSVd. To evaluate CSVd digestion activity in leaf extracts, CSVd was mixed with leaf extracts of Mirabilis, Phytolacca, Pelargonium and Capsicum. CSVd-digesting activities were examined by quantifying undigested CSVd using qRT-PCR, and RNA gel blotting permitted visualization of the digested CSVd. Only Capsicum leaf extract digested CSVd, and in the Capsicum treatment, small digested CSVd products were detected by RNA gel blot analysis. When the digesting experiment was performed for various cultivars and species of Capsicum, only cultivars of C. chinense showed strong CSVd-digesting activity. Our observations indicated that Capsicum extract contains strong RNA-digesting activity, leading to the conclusion that this activity is the main mechanism for protection from infection by CSVd through spraying or painting before inoculation. To our knowledge, this is the first report of a strong RNA-digesting activity by a plant extract.

  11. Evaluation of Antioxidant Activity, Total Flavonoids, Tannins and Phenolic Compounds in Psychotria Leaf Extracts

    Directory of Open Access Journals (Sweden)

    Anelise Samara Nazari Formagio

    2014-11-01

    Full Text Available The antioxidant activity of Psychotria carthagenensis, P. leiocarpa, P. capillacea and P. deflexa (Rubiaceae extracts were investigated, and the concentrations of total phenolics, flavonoids, condensed tannins and flavonols were determined. The chemical compositions of the extracts were investigated using the high performance liquid chromatography (HPLC/PAD method. We used 1,1-diphenyl-1-picrylhydrazyl free radical (DPPH, β-Carotene bleaching and 2,2-azinobis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS radical cations to determine antioxidant activity. The ability to scavenge radical was measured in these experiments by the discoloration of the solution. Concentrations of constituents were measured spectrophotometrically. P. carthagenensis and P. capillacea exhibited the highest antioxidant activity, in the DPPH test, β-carotene bleaching and ABTS system. The highest phenolic, flavonoid, condensed tannin and flavonol concentration was found in P. carthagenensis and P. capillacea extracts. HPLC-PDA analysis of P. carthagenensis and P. capillacea revealed hydroxycinnamic acid (p-coumaric acid. This is the first report on the antioxidant properties and constituent analysis of these Psychotria extracts.

  12. Evaluation of Antibacterial Activity and Total Phenol Compounds of Punica granatum Hydro-Alcoholic Extract

    Directory of Open Access Journals (Sweden)

    Elahe Ahmadi

    2016-12-01

    Full Text Available Background & Objectives: Punica granatum is a non-productive form of a plant and is used for the treatment of diseases in traditional medicine. In this study, we evaluate the antibacterial activity and the total phenol compounds of Punica granatum. Materials & Methods: Disk and well diffusion methods and MIC were used to evaluate the antibacterial activity of hydro-alcoholic extract on S. aureus and E. coli compared to standard commercial antibiotic disks. Measurement of phenol compounds were performed by Seevers and Daly colorimetric methods (Folin-ciocalteu indicator. Results: 35 and 29 mm inhibition zones in S. aureus and 22 and 17 mm inhibition zones in E. coli were shown by disk and well diffusion method, respectively. Also, 7.8 mg/ml concentration of extract showed the MIC points for two bacteria. Phenol compound of extract was 233.15±5.1 mg/g of extraction. Conclusion: Antibacterial effect of Punica granatum compared to antibiotics indicates the strong activity against examined bacteria. Extensive antibacterial study of Punica granatum is suggested.

  13. Total flavonoids content in the raw material and aqueous extractives from Bauhinia monandra Kurz (Caesalpiniaceae).

    Science.gov (United States)

    Fernandes, Ana Josane Dantas; Ferreira, Magda Rhayanny Assunção; Randau, Karina Perrelli; de Souza, Tatiane Pereira; Soares, Luiz Alberto Lira

    2012-01-01

    The aim of this work was to evaluate the spectrophotometric methodology for determining the total flavonoid content (TFC) in herbal drug and derived products from Bauhinia monandra Kurz. Several analytical parameters from this method grounded on the complex formed between flavonoids and AlCl₃ were evaluated such as herbal amount (0.25 to 1.25 g); solvent composition (ethanol 40 to 80%, v/v); as well as the reaction time and AlCl₃ concentration (2 to 9%, w/v). The method was adjusted to aqueous extractives and its performance studied through precision, linearity and preliminary robustness. The results showed an important dependence of the method response from reaction time, AlCl₃ concentration, sample amount, and solvent mixture. After choosing the optimized condition, the method was applied for the matrixes (herbal material and extractives), showing precision lower than 5% (for both parameters repeatability and intermediate precision), coefficient of determination higher than 0.99, and no important influence could be observed for slight variations from wavelength or AlCl₃ concentration. Thus, it could be concluded that the evaluated analytical procedure was suitable to quantify the total flavonoid content in raw material and aqueous extractives from leaves of B. monandra.

  14. Anti-pseudomonas activity of essential oil, total extract, and proanthocyanidins of Pinus eldarica Medw. bark.

    Science.gov (United States)

    Sadeghi, Masoud; Zolfaghari, Behzad; Jahanian-Najafabadi, Ali; Abtahi, Seyed Reza

    2016-01-01

    Pinus eldarica Medw. (Iranian pine) is native to Transcaucasian region and has been vastly planted in Iran, Afghanistan, and Pakistan. Various parts of this plant have been widely used in traditional medicine for the treatment of various diseases including infectious conditions (e.g. infectious wounds). In this study we aimed to investigate the antibacterial activity of P. eldarica bark extract, essential oil and proanthocyanidins on three important bacteria, Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. Antibacterial analysis was performed using standard disk diffusion method with different concentrations of essential oil, bark total hydroalcoholic extract, and bark proanthocyanidins (0.5, 1, 2 and 3 mg/ml). After incubation at 37°C for 24 h, the antibacterial activity was assessed by measuring the zone of growth inhibition surrounding the disks. The results indicated that the essential oil, total hydroalcoholic extract, and proanthocyanidins of the bark of the P. eldarica were effective against the gram negative bacteria, P. aeruginosa, and significantly inhibited its growth in disk diffusion method (Pessential oil had the most potent inhibitory effect. However, none of the bark preparations could significantly inhibit the growth of S. aureus or E. coli. Our findings showed that P. eldarica bark components have significant anti-pseudomonas activity having potentials for new sources of antibacterial agents or antibacterial herbal preparations.

  15. Screening of immunomodulatory activity of total and protein extracts of some Moroccan medicinal plants.

    Science.gov (United States)

    Daoudi, Abdeljlil; Aarab, Lotfi; Abdel-Sattar, Essam

    2013-04-01

    Herbal and traditional medicines are being widely used in practice in many countries for their benefits of treating different ailments. A large number of plants in Morocco were used in folk medicine to treat immune-related disorders. The objective of this study is to evaluate the immunomodulatory activity of protein extracts (PEs) of 14 Moroccan medicinal plants. This activity was tested on the proliferation of immune cells. The prepared total and PEs of the plant samples were tested using MTT (3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazolium bromide) assay on the splenocytes with or without stimulation by concanavalin-A (Con-A), a mitogenic agent used as positive control. The results of this study indicated different activity spectra. Three groups of activities were observed. The first group represented by Citrullus colocynthis, Urtica dioica, Elettaria cardamomum, Capparis spinosa and Piper cubeba showed a significant immunosuppressive activity. The second group that showed a significant immunostimulatory activity was represented by Aristolochia longa, Datura stramonium, Marrubium vulgare, Sinapis nigra, Delphynium staphysagria, Lepidium sativum, Ammi visnaga and Tetraclinis articulata. The rest of the plant extracts did not alter the proliferation induced by Con-A. This result was more important for the PE than for the total extract. In conclusion, this study revealed an interesting immunomodulating action of certain PEs, which could explain their traditional use. The results of this study may also have implications in therapeutic treatment of infections, such as prophylactic and adjuvant with cancer chemotherapy.

  16. Total Flavonoids Content in the Raw Material and Aqueous Extractives from Bauhinia monandra Kurz (Caesalpiniaceae

    Directory of Open Access Journals (Sweden)

    Ana Josane Dantas Fernandes

    2012-01-01

    Full Text Available The aim of this work was to evaluate the spectrophotometric methodology for determining the total flavonoid content (TFC in herbal drug and derived products from Bauhinia monandra Kurz. Several analytical parameters from this method grounded on the complex formed between flavonoids and AlCl3 were evaluated such as herbal amount (0.25 to 1.25 g; solvent composition (ethanol 40 to 80%, v/v; as well as the reaction time and AlCl3 concentration (2 to 9%, w/v. The method was adjusted to aqueous extractives and its performance studied through precision, linearity and preliminary robustness. The results showed an important dependence of the method response from reaction time, AlCl3 concentration, sample amount, and solvent mixture. After choosing the optimized condition, the method was applied for the matrixes (herbal material and extractives, showing precision lower than 5% (for both parameters repeatability and intermediate precision, coefficient of determination higher than 0.99, and no important influence could be observed for slight variations from wavelength or AlCl3 concentration. Thus, it could be concluded that the evaluated analytical procedure was suitable to quantify the total flavonoid content in raw material and aqueous extractives from leaves of B. monandra.

  17. Phytochemical screening, total phenolic content and phytotoxic activity of corn (Zea mays) extracts against some indicator species.

    Science.gov (United States)

    Ahmed, Hiwa M

    2018-03-01

    Allelopathic effects of corn (Zea mays) extracts was studied, against seed germination and seedling growth of Phalaris minor, Helianthus annuus, Triticumaestivum, Sorghum halepense, Z. mays. Bioassay results showed that aqueous extracts of corn root and shoot, markedly affected seed germination, and other parameters compared with related controls. Preliminary phytochemical screening revealed the presence of various phytochemicals such as tannins, phlobatannins, flavonoids, terpenoids and alkaloids in both roots and shoot aqueous extracts. However, saponins were only present in the shoot aqueous extract, while in shoot ethanol extracts, only terpenoids and alkaloids were detected. Additionally, total polyphenolic (TPC) content in aqueous extracts of corn root and shoot, plus ethanol extracts of corn shoot were determined using an Ultraviolet-visible spectroscopy. Results revealed TPC content of the corn shoot aqueous extract showed the highest yield, compared to other extracts. These findings suggest that phytochemicals present in Z. mays extracts may contribute to allelopathy effect.

  18. Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR.

    Science.gov (United States)

    Tatti, Enrico; McKew, Boyd A; Whitby, Corrine; Smith, Cindy J

    2016-06-11

    Real Time Polymerase Chain Reaction also known as quantitative PCR (q-PCR) is a widely used tool in microbial ecology to quantify gene abundances of taxonomic and functional groups in environmental samples. Used in combination with a reverse transcriptase reaction (RT-q-PCR), it can also be employed to quantify gene transcripts. q-PCR makes use of highly sensitive fluorescent detection chemistries that allow quantification of PCR amplicons during the exponential phase of the reaction. Therefore, the biases associated with 'end-point' PCR detected in the plateau phase of the PCR reaction are avoided. A protocol to quantify bacterial 16S rRNA genes and transcripts from coastal sediments via real-time PCR is provided. First, a method for the co-extraction of DNA and RNA from coastal sediments, including the additional steps required for the preparation of DNA-free RNA, is outlined. Second, a step-by-step guide for the quantification of 16S rRNA genes and transcripts from the extracted nucleic acids via q-PCR and RT-q-PCR is outlined. This includes details for the construction of DNA and RNA standard curves. Key considerations for the use of RT-q-PCR assays in microbial ecology are included.

  19. Effect of temperature, time, and milling process on yield, flavonoid, and total phenolic content of Zingiber officinale water extract

    Science.gov (United States)

    Andriyani, R.; Kosasih, W.; Ningrum, D. R.; Pudjiraharti, S.

    2017-03-01

    Several parameters such as temperature, time of extraction, and size of simplicia play significant role in medicinal herb extraction. This study aimed to investigate the effect of those parameters on yield extract, flavonoid, and total phenolic content in water extract of Zingiber officinale. The temperatures used were 50, 70 and 90°C and the extraction times were 30, 60 and 90 min. Z. officinale in the form of powder and chips were used to study the effect of milling treatment. The correlation among those variables was analysed using ANOVA two-way factors without replication. The result showed that time and temperature did not influence the yield of extract of Powder simplicia. However, time of extraction influenced the extract of simplicia treated without milling process. On the other hand, flavonoid and total phenolic content were not influenced by temperature, time, and milling treatment.

  20. Microwave-assisted extraction and a new determination method for total steroid saponins from Dioscorea zingiberensis C.H. Wright.

    Science.gov (United States)

    Ren, Yao; Chen, Yu; Hu, Bohan; Wu, Hui; Lai, Furao; Li, Xiaofeng

    2015-12-01

    An efficient microwave-assisted extraction (MAE) technique was applied to isolate total steroid saponins from Dioscorea zingiberensis C.H. Wright (DZW). The optimal extracting conditions were established as 75% ethanol as solvent, ratio of solid/liquid 1:20 (g/ml), temperature 75 °C, irradiation power 600 W and three extraction cycles of 6 min each. Scanning electron microscopy (SEM) images of DZW processed by four different extractions provided visual evidence of the disruption effect on DZW. Diosgenin was quantified by HPLC and examined further by LC-ESI/MS after acid hydrolysis. Total steroid saponins were calculated using diosgenin from total steroid saponins. The MAE procedure was optimized, validated and compared with other conventional extraction processes. This report provides a convenient technology for the extraction and quantification of total saponins of DZW combining MAE with HPLC and LC-ESI/MS for the first time. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Hippophae leaf extract (SBL-1) countered radiation induced dysbiosis in jejunum of total body 60Cobalt gamma - irradiated mice

    International Nuclear Information System (INIS)

    Beniwal, C.S.; Madhu Bala

    2014-01-01

    Single dose of SBL-1 administered at the rate 30 mg/kg body weight (b.w.) 30 min prior to whole body 60 Co-gamma-irradiation at lethal dose (10 Gy), rendered >90% survival in comparison to zero survival in the non-SBL-1 treated 60 Co-gamma-irradiated (10 Gy) mice population (J Herbs Spices Med Plants, 2009; 15(2): 203-215). Present study investigated the effect of SBL-1 on jejunal microbiota in lethally irradiated mice. Study was performed with inbred Swiss albino Strain 'A' male mice (age 9 weeks) weighing 28±2 g. The animals were maintained under controlled environment at 26±2℃; 12 h light/dark cycle and offered standard animal food (Golden feed, Delhi) as well as tap water ad libitum. Metagenomic DNA was extracted, purified and quantified from jejunum of the mice. Universal primers (27f and 1492r) were used to amplify the 16S rRNA DNA from the metagenomic DNA. Amplicons were sequenced, vector contamination and chimeras were removed. The sequences (GenBank Accession No: KF681283 to KF681351) were taxonomically classified by using Sequence Match program, Ribosomal Database Project as well as by nucleotide-BLAST (E-value: 10, database: 16S rRNA gene sequences, Bacteria and Archea). Phylogenetic Tree was prepared using MEGA 5.2 package, using maximum likelihood algorithm after sequence alignment by MUSCLE. Thermus aquaticus was used as out-group to construct rooted tree. Branch stability was assessed by bootstrap analysis. Untreated animals and the animals treated with SBL-1 had 100% Lactobacillus; 60 Co gamma-irradiated animals had 55% Cohaesibacter (Alphaproteobacteria); 27% Mycoplasma (Tenericutes) and only 18% Lactobacillus; animals treated with SBL-1 prior to irradiation had 89% Lactobacillus and 11% Clostridium. This study demonstrated that treatment with SBL-1 at radioprotective doses before total body irradiation with lethal dose (10 Gy) countered the jejunal dysbiosis. (author)

  2. RT-PCR amplification of RNA extracted from formalin-fixed, paraffin-embedded oral cancer sections: analysis of p53 pathway.

    Science.gov (United States)

    Tachibana, Masatsugu; Shinagawa, Yasuhiro; Kawamata, Hitoshi; Omotehara, Fumie; Horiuchi, Hideki; Ohkura, Yasuo; Kubota, Keiichi; Imai, Yutaka; Fujibayashi, Takashi; Fujimori, Takahiro

    2003-01-01

    We present a new approach towards the detection of the mRNAs in formalin-fixed, paraffin-embedded samples using a reverse transcriptase (RT)-polymerase chain reaction (PCR). The total RNAs were extracted from 10-micron-thick sections and were reverse-transcribed, then the RT-products were subjected to PCR amplification of GAPDH mRNA for screening the mRNA degradation. Next, nested PCR was performed for examining the expression of p53-related genes, p21WAF1, MDM2, p33ING1 and p14ARF. GAPDH mRNA expression was detectable in 12 out of 21 oral squamous cell carcinoma (SCC) samples. p21WAF1 mRNA expression was detectable in 5 out of 12 SCC samples, MDM2 mRNA expression was detectable in 5 our of 12 SCC samples and p33ING1 mRNA expression was detectable in 6 out of 12 SCC samples. However, the expression of p14ARF mRNA was not detectable in any of the samples. Seven out of 12 oral SCC samples showed abnormal nuclear accumulation of p53 protein by immunohistochemical staining, whereas 5 out of 12 oral SCCs showed negative staining for p53 protein. Of of p33ING1 mRNA. One of these was a verrucous carcinoma in which the p53 gene products might be inactivated by the oncoprotein E6 of human papilloma virus. Thus, the p53 tumor suppressor pathway was disrupted in most oral SCCs at the cellular levels, due to either an abnormality in p53 itself or loss of expression of p53 regulatory factors. This method would assist in making diagnosis, determining therapeutic strategy and predicting the prognosis of various cancers including oral SCCs.

  3. Evaluation of a low-cost procedure for sampling, long-term storage, and extraction of RNA from blood for qPCR analyses

    DEFF Research Database (Denmark)

    Mærkedahl, Rasmus Baadsgaard; Frøkiær, Hanne; Lauritzen, Lotte

    2015-01-01

    Abstract Background: In large clinical trials, where RNA cannot be extracted immediately after sampling, preserving RNA in whole blood is a crucial initial step in obtaining robust qPCR data. The current golden standard for RNA preservation is costly and designed for time-consuming column-based RNA....../binding solution over time and between samples stored and extracted by the two systems. Conclusions: The MagMAX system can be used for storage of human blood for up to 4 months and is equivalent to the PAXgene system for RNA extraction. It furthermore, provides a means for significant cost reduction in large...

  4. Sensitive radioimmunoassay of total thyroxine (T4) in horses using a simple extraction method.

    Science.gov (United States)

    Tangyuenyong, Siriwan; Nambo, Yasuo; Nagaoka, Kentaro; Tanaka, Tomomi; Watanabe, Gen

    2017-07-28

    Most thyroid hormone determinations in animals are based on immunoassays adapted from those used to test human samples, which may not reflect the actual values of thyroid hormone in horses because of the presence of binding proteins. The aims of the present study were i) to establish a novel radioimmunoassay (RIA) using a more simple and convenient method to separate binding proteins for the measurement of total thyroxine (T4) in horses and ii) to validate the assay by comparing total T4 concentrations in yearling horses raised in different climates. Blood samples were collected from trained yearlings in Hokkaido (temperate climate) and Miyazaki (subtropical climate) in Japan and from adult horses in estrus and diestrus. T4 was extracted from both serum and plasma using modified acid ethanol cryo-precipitation and sodium acetate ethanol methods. Circulating total T4 concentrations were determined by RIA. T4 concentration by sodium acetate ethanol was appropriately detectable rather than sodium salicylate method and was the same as for acid ethanol method. Furthermore, this sodium acetate ethanol method required fewer extraction steps than the other methods. Circulating T4 concentrations in yearlings were 225.98 ± 20.89 ng/ml, which was higher than the previous reference values. With respect to climate, T4 levels in Hokkaido yearlings tended to be higher than those in Miyazaki yearlings throughout the study period. These results indicated that this RIA protocol using a modified sodium acetate ethanol separation technique might be an appropriate tool for specific measurement of total T4 in horses.

  5. Total phenols and antioxidant activities of leaf and stem extracts from coriander, mint and parsley grown in Saudi Arabia

    International Nuclear Information System (INIS)

    Al-Juhaimi, F.; Ghafoorr, K.

    2011-01-01

    Leaves and stems of three different herbs from two different families were used to extract phenolic compounds and the bioactivity of the extracts was evaluated by using 1, 1-diphenyl-2-picrylhydrazyl or DPPH scavenging ability or their antioxidant activities. Extract from leaves of mint, which belongs to Lamiaceae family contained 1.24 mgGAE/100 mL of total phenolic compounds and 34.21% antioxidant activity which were significantly higher than those in extracts from coriander and parsley, both of which belong to Apiaceae family. Extracts of leaves from these herbs showed more quantity of total phenols and higher antioxidant activities than extracts from stem parts, however both leaves and stems of these three herbs grown in Saudi Arabia contained good quantities of total phenols (>1.02 mgGAE/100 mL) and showed more than 18.3% free radical scavenging activity. (author)

  6. [Studies on preparative technology and quantitative determination for extracts of total saponin in roof of Panax japonicus].

    Science.gov (United States)

    He, Yu-min; Lu, Ke-ming; Yuan, Ding; Zhang, Chang-cheng

    2008-11-01

    To explore the optimum extraction and purification condition of the total saponins in the root of Panax japonicus (RPJ), and establish its quality control methods. Designed L16 (4(5)) orthogonal test with the extraction rate of total saponins as index, to determine the rational extraction process, and the techniques of water-saturated n-butanol extraction and acetone precipitation were applied to purify the alcohol extract of RPJ. Total saponins were detected by spectrophotometry and its triterpenoidal sapogenin oleanolic acid detected by HPLC. The optimum conditions of total saponins from RPJ was as follows: the material was pulverized, dipped in 60% ethanol aqueous solution as extract solvent at 10 times of volume, and refluxed 3 times for 3 h each time. Extractant of water-saturated n-butanol with extraction times of 3 and precipitant of acetone with precipitation amount of 4-5 times were included in the purification process, which would obtain the quality products. The content of total saponins could reach to 83.48%, and oleanolic acid to 38.30%. The optimized preparative technology is stable, convenient and practical. The extract rate of RPJ was high and steady with this technology, which provided new evidence for industrializing production of the plant and developing new drug.

  7. Cellular and Molecular Mechanisms in Vascular Smooth Muscle Cells by which Total Saponin Extracted from Tribulus Terrestris Protects Against Artherosclerosis

    Directory of Open Access Journals (Sweden)

    Mengquan Li

    2013-11-01

    Full Text Available Background/Aims: Total saponin extracted from Tribulus terrestris (TSETT has been reported to protect against atherosclerosis. We here investigate the cellular and molecular mechanisms of TSETT underlying protection against atherosclerosis. Methods: Cell proliferation was measured with Methyl thiazolyl tetrazolium (MTT; Intracellular H2O2 was measured with DCFH-DA, a fluorescent dye; Intracellular free Ca2+ was measured with a confocal laser scanning microscopy; Genes expression was measured with gene array and real-time quantitative polymerase chain reaction (RT-PCR; Phosphorylation of extracellular signal-regulated kinase 1/2 (phospho-ERK1/2 was measured with cell-based enzyme-linked immunosorbent assay (ELISA and western blotting. Results: TSETT significantly suppressed the increase in cells proliferation induced by angiotensin II, significantly suppressed the increase in the intracellular production of H2O2 induced by angiotensin II, significantly inhibited the increase in intracellular free Ca2+ induced by H2O2, significantly inhibited the increase in phospho-ERK1/2 induced by angiotensin II; significantly inhibited the increase in mRNA expression of c-fos, c-jun and pkc-α induced by angiotensin II. Conclusion: These findings provide a new insight into the antiatherosclerotic properties of TSETT and provide a pharmacological basis for the clinical application of TSETT in anti-atherosclerosis.

  8. Cellular and molecular mechanisms in vascular smooth muscle cells by which total saponin extracted from Tribulus terrestris protects against artherosclerosis.

    Science.gov (United States)

    Li, Mengquan; Guan, Yue; Liu, Jiaqi; Zhai, Fengguo; Zhang, Xiuping; Guan, Lixin

    2013-01-01

    Total saponin extracted from Tribulus terrestris (TSETT) has been reported to protect against atherosclerosis. We here investigate the cellular and molecular mechanisms of TSETT underlying protection against atherosclerosis. Cell proliferation was measured with Methyl thiazolyl tetrazolium (MTT); Intracellular H2O2 was measured with DCFH-DA, a fluorescent dye; Intracellular free Ca(2+) was measured with a confocal laser scanning microscopy; Genes expression was measured with gene array and real-time quantitative polymerase chain reaction (RT-PCR); Phosphorylation of extracellular signal-regulated kinase 1/2 (phospho-ERK1/2) was measured with cell-based enzyme-linked immunosorbent assay (ELISA) and western blotting. TSETT significantly suppressed the increase in cells proliferation induced by angiotensin II, significantly suppressed the increase in the intracellular production of H2O2 induced by angiotensin II, significantly inhibited the increase in intracellular free Ca(2+) induced by H2O2, significantly inhibited the increase in phospho-ERK1/2 induced by angiotensin II; significantly inhibited the increase in mRNA expression of c-fos, c-jun and pkc-α induced by angiotensin II. These findings provide a new insight into the antiatherosclerotic properties of TSETT and provide a pharmacological basis for the clinical application of TSETT in anti-atherosclerosis. © 2013 S. Karger AG, Basel.

  9. Automated, simple, and efficient influenza RNA extraction from clinical respiratory swabs using TruTip and epMotion.

    Science.gov (United States)

    Griesemer, Sara B; Holmberg, Rebecca; Cooney, Christopher G; Thakore, Nitu; Gindlesperger, Alissa; Knickerbocker, Christopher; Chandler, Darrell P; St George, Kirsten

    2013-09-01

    Rapid, simple and efficient influenza RNA purification from clinical samples is essential for sensitive molecular detection of influenza infection. Automation of the TruTip extraction method can increase sample throughput while maintaining performance. To automate TruTip influenza RNA extraction using an Eppendorf epMotion robotic liquid handler, and to compare its performance to the bioMerieux easyMAG and Qiagen QIAcube instruments. Extraction efficacy and reproducibility of the automated TruTip/epMotion protocol was assessed from influenza-negative respiratory samples spiked with influenza A and B viruses. Clinical extraction performance from 170 influenza A and B-positive respiratory swabs was also evaluated and compared using influenza A and B real-time RT-PCR assays. TruTip/epMotion extraction efficacy was 100% in influenza virus-spiked samples with at least 745 influenza A and 370 influenza B input gene copies per extraction, and exhibited high reproducibility over four log10 concentrations of virus (extraction were also positive following TruTip extraction. Overall Ct value differences obtained between TruTip/epMotion and easyMAG/QIAcube clinical extracts ranged from 1.24 to 1.91. Pairwise comparisons of Ct values showed a high correlation of the TruTip/epMotion protocol to the other methods (R2>0.90). The automated TruTip/epMotion protocol is a simple and rapid extraction method that reproducibly purifies influenza RNA from respiratory swabs, with comparable efficacy and efficiency to both the easyMAG and QIAcube instruments. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Total Lactic Acid Bacteria (LAB), Antioxidant Activity, and Acceptance of Synbiotic Yoghurt with Binahong Leaf Extract (Anredera cordifolia (Ten.) Steenis)

    Science.gov (United States)

    Lestari, R. P.; Nissa, C.; Afifah, D. N.; Anjani, G.; Rustanti, N.

    2018-02-01

    Alternative treatment for metabolic syndrome can be done by providing a diet consist of functional foods or beverages. Synbiotic yoghurt containing binahong leaf extract which high in antioxidant, total LAB and fiber can be selected to reduce the risk of metabolic syndrome. The effect of binahong leaf extract in synbiotic yoghurt against total LAB, antioxidant activity, and acceptance were analyzed. The experiment was done with complete randomized design with addition of binahong leaf extract 0% (control); 0.12%; 0.25%; 0.5% in synbiotic yoghurt. Analysis of total LAB using Total Plate Count test, antioxidant activity using DPPH, and acceptance were analyzed by hedonic test. The addition of binahong leaf extract in various doses in synbiotic yoghurt decreased total LAB without significant effect (p=0,145). There was no effect of addition binahong leaf extract on antioxidant activity (p=0,297). The addition of binahong leaf extract had an effect on color, but not on aroma, texture and taste. The best result was yoghurt synbiotic with addition of 0,12% binahong leaf extract. Conclusion of the research was the addition of binahong leaf extract to synbiotic yogurt did not significantly affect total LAB, antioxidant activity, aroma, texture and taste; but had a significant effect on color.

  11. EFFECTS OF STORAGE, RNA EXTRACTION, GENECHIP TYPE, AND DONOR SEX ON GENE EXPRESSION PROFILING OF HUMAN WHOLE BLOOD

    Science.gov (United States)

    Background: Gene expression profiling of whole blood may be useful for monitoring toxicological exposure and for diagnosis and monitoring of various diseases. Several methods are available that can be used to transport, store, and extract RNA from whole blood, but it is not clear...

  12. Study of total phenol, flavonoids contents and phytochemical screening of various leaves crude extracts of locally grown Thymus vulgaris.

    Science.gov (United States)

    Hossain, Mohammad Amzad; AL-Raqmi, Khulood Ahmed Salim; AL-Mijizy, Zawan Hamood; Weli, Afaf Mohammed; Al-Riyami, Qasim

    2013-09-01

    To prepare various crude extracts using different polarities of solvent and to quantitatively evaluate their total phenol, flavonoids contents and phytochemical screening of Thymus vulgaris collected from Al Jabal Al Akhdar, Nizwa, Sultanate of Oman. The leave sample was extracted with methanol and evaporated. Then it was defatted with water and extracted with different polarities organic solvents with increasing polarities. The prepare hexane, chloroform, ethyl acetate, butanol and methanol crude extracts were used for their evaluation of total phenol, flavonoids contents and phytochemical screening study. The established conventional methods were used for quantitative determination of total phenol, flavonoids contents and phytochemical screening. Phytochemical screening for various crude extracts were tested and shown positive result for flavonoids, saponins and steroids compounds. The result for total phenol content was the highest in butanol and the lowest in methanol crude extract whereas the total flavonoids contents was the highest in methanol and the lowest hexane crude extract. The crude extracts from locally grown Thymus vulgaris showed high concentration of flavonoids and it could be used as antibiotics for different curable and uncurable diseases.

  13. Short Communication An efficient method for simultaneous extraction of high-quality RNA and DNA from various plant tissues.

    Science.gov (United States)

    Oliveira, R R; Viana, A J C; Reátegui, A C E; Vincentz, M G A

    2015-12-29

    Determination of gene expression is an important tool to study biological processes and relies on the quality of the extracted RNA. Changes in gene expression profiles may be directly related to mutations in regulatory DNA sequences or alterations in DNA cytosine methylation, which is an epigenetic mark. Correlation of gene expression with DNA sequence or epigenetic mark polymorphism is often desirable; for this, a robust protocol to isolate high-quality RNA and DNA simultaneously from the same sample is required. Although commercial kits and protocols are available, they are mainly optimized for animal tissues and, in general, restricted to RNA or DNA extraction, not both. In the present study, we describe an efficient and accessible method to extract both RNA and DNA simultaneously from the same sample of various plant tissues, using small amounts of starting material. The protocol was efficient in the extraction of high-quality nucleic acids from several Arabidopsis thaliana tissues (e.g., leaf, inflorescence stem, flower, fruit, cotyledon, seedlings, root, and embryo) and from other tissues of non-model plants, such as Avicennia schaueriana (Acanthaceae), Theobroma cacao (Malvaceae), Paspalum notatum (Poaceae), and Sorghum bicolor (Poaceae). The obtained nucleic acids were used as templates for downstream analyses, such as mRNA sequencing, quantitative real time-polymerase chain reaction, bisulfite treatment, and others; the results were comparable to those obtained with commercial kits. We believe that this protocol could be applied to a broad range of plant species, help avoid technical and sampling biases, and facilitate several RNA- and DNA-dependent analyses.

  14. Recent Developments in Solid-Phase Extraction for Near and Attenuated Total Reflection Infrared Spectroscopic Analysis

    Directory of Open Access Journals (Sweden)

    Christian W. Huck

    2016-05-01

    Full Text Available A review with more than 100 references on the principles and recent developments in the solid-phase extraction (SPE prior and for in situ near and attenuated total reflection (ATR infrared spectroscopic analysis is presented. New materials, chromatographic modalities, experimental setups and configurations are described. Their advantages for fast sample preparation for distinct classes of compounds containing different functional groups in order to enhance selectivity and sensitivity are discussed and compared. This is the first review highlighting both the fundamentals of SPE, near and ATR spectroscopy with a view to real sample applicability and routine analysis. Most of real sample analyses examples are found in environmental research, followed by food- and bioanalysis. In this contribution a comprehensive overview of the most potent SPE-NIR and SPE-ATR approaches is summarized and provided.

  15. Changes in total phenol, flavonoid contents and anti-Lactobacillus activity of Callisia fragrans due to extraction solvent

    Science.gov (United States)

    Le, Thom; Cao, Diem Kieu; Pham, Thanh Vy; Huynh, Tan Dat; Ta, Nhat Thuy Anh; Nguyen, Ngoc Thao Linh; Nguyen, Huu Thanh; Le, Hue Huong; Bui, Anh Vo; Truong, Dieu-Hien

    2018-04-01

    Callisia fragrans is a wonder herb with many medicinal properties such as burn, dental diseases, cancer diseases and arthritis in folk medicine. It is noted that the phytochemical constituents and antimicrobial activity of traditional plants depend on not only the extracting method but also the solvent used for extraction. In this study, the effect of five extraction solvents (i.e., distilled water, 80% methanol, 80% ethanol, 80% ethyl acetate, and 80% chloroform) on yield, total phenolic content (TPC) and total flavonoid content (TFC) of Callisia leaves was determined. Besides, changes in anti-Lactobacillus fermentum activity of C. fragrans freeze-dried extract was also evaluated using disk-diffusion method. The recovery percentage of extractable yield of fresh leaves are ranged from 11.93% w/w for distilled water extract to 16.60% w/w for aqueous ethanol extracts. The yield of 80% aqueous methanol extract (16.27% w/w) is only slightly less than that of the ethanol extract. Significant differences were observed among TPC and TFC obtaining by 80% methanol (0.0522% and 0.0335% w/w, respectively) compared to other solvents (p < 0.05). TPC and TFC of C. fragrans extracts increase in the following order: distilled water < 80% chloroform < 80% ethyl acetate < 80% ethanol < 80% methanol. The results revealed that 80% aqueous methanol Calissia extracts has moderate inhibition (9.0 mm of inhibition zone for 1.5 mg/mL of extracts) of L. fermentum compared to standard antibacterial agent. Based on the study results, it can be concluded that the yield, TPC and TFC of C. frgrans extract varied with the extracting solvent. It also showed that Callisia extracts can prevent dental caries by inhibiting the growth of L. fermentum, towards new insights for treatment of dental caries.

  16. Crataegus Special Extract WS 1442 Effects on eNOS and microRNA 155.

    Science.gov (United States)

    Wang, Xinwen; Liang, Yan; Shi, Jian; Zhu, Hao-Jie; Bleske, Barry E

    2018-04-16

    Increased expression of microRNA 155 (miR-155) results in a decrease in endothelial nitric oxide synthase (eNOS) expression and impaired endothelial function. Factors that have been shown to increase expression of miR-155 may be mitigated by WS 1442, an extract of hawthorn leaves and flowers ( Crataegus special extract) that contains a range of pharmacologically active substances including oligomeric proanthocyanidins and flavonoids. The purpose of this study is to determine the effect of WS 1442 on the expression of miR-155 and eNOS in the presence of tumor necrosis factor (TNF- α ). Human umbilical vein endothelial cells (HUVECs) were studied after the exposure to TNF- α , with or without simvastatin (positive control) and WS 1442. The expression levels of eNOS, phosphorylated eNOS, and miR-155 in the different HUVEC treatment groups were determined by western blot and quantitative real-time polymerase chain reaction, respectively. To evaluate the effect of WS 1442 on the eNOS activity, the medium and intracellular nitrate/nitrite (NO) concentrations were also analyzed using a colorimetric Griess assay kit. The results demonstrated that TNF- α upregulated miR-155 expression and decreased eNOS expression and NO concentrations. WS 1442 also increased miR-155 expression and decreased eNOS expression but, unlike TNF- α , increased phosphorylated eNOS expression and NO concentrations. Surprisingly, WS 1442 increased miR-155 expression; however, WS 1442 mitigated the overall negative effect of miR-155 on decreasing eNOS expression by increasing expression of phosphorylated eNOS and resulting in an increase in NO concentrations. In the setting where miR-155 may be expressed, WS 1442 may offer vascular protection by increasing the expression of phosphorylated eNOS. Georg Thieme Verlag KG Stuttgart · New York.

  17. Antioxidant properties of cumin (Bunium persicum Boiss. extract and its protective role against abiotic stress tested by microRNA markers

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    Katarína Ražná

    2018-02-01

    Full Text Available Bunium persicum Boiss. seeds have been used for medicinal and nutritional properties such as antioxidant, antihelmetic and antimicrobial activity. The aim of this study was to to tested protective role of cumin extract against abiotic stress by microRNA markers. Secondary also was to evaluate antioxidant activity as well as total polyphenol, flavonoid and phenolic acid content of cumin extract. We observed that cumin DNA itself has not been damaged by sonication teratment. This protective impact indicates that cumin antioxidant properties can efficiently quench free radicals induced by sonication. On the other side, ultrasound-mediated formation of reactive oxygen species did induce the DNA polymorphism of lettuce samples which was detected by miRNAs-based markers. The range of sonication impact was time-dependent. Markers based of miRNA-DNA sequences has proven to be an effective tool. We have confirmed statistically significant differences (p ≤0.01 in miRNAs markers ability to detect the polymorphism due to sonication treatment.  The antioxidant activity was determined by a method using DPPH radical and phosphomolybdenum method, total polyphenol content with Folin - Ciocalteu reagent, total flavonoid with aluminium-chloride mehod and total phenolic acid with Arnova reagent. Results showed that cumin is rich for biologically active substances and can be used more in different kind of industry as a cheap source of these substances. Antioxidant activity with DPPH method was 1.18 mg TEAC.g-1 (TEAC - Trolox equivalent antioxidant capacity per g of sample and by phosphomolybdenum method 45.23 mg TEAC.g-1. Total polyphenol content achieved value 4.22 mg GAE.g-1 (GAE - gallic acid equivalent per g of sample, total flavonoid content value 10.91 mg QE.g-1 (QE - quercetin equivalent per g of sample and total phenolic acid content value 5.07 mg CAE.g-1 (CAE - caffeic acid equivalent per g of sample.

  18. Protocol: A simple phenol-based method for 96-well extraction of high quality RNA from Arabidopsis

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    Coustham Vincent

    2011-03-01

    Full Text Available Abstract Background Many experiments in modern plant molecular biology require the processing of large numbers of samples for a variety of applications from mutant screens to the analysis of natural variants. A severe bottleneck to many such analyses is the acquisition of good yields of high quality RNA suitable for use in sensitive downstream applications such as real time quantitative reverse-transcription-polymerase chain reaction (real time qRT-PCR. Although several commercial kits are available for high-throughput RNA extraction in 96-well format, only one non-kit method has been described in the literature using the commercial reagent TRIZOL. Results We describe an unusual phenomenon when using TRIZOL reagent with young Arabidopsis seedlings. This prompted us to develop a high-throughput RNA extraction protocol (HTP96 adapted from a well established phenol:chloroform-LiCl method (P:C-L that is cheap, reliable and requires no specialist equipment. With this protocol 192 high quality RNA samples can be prepared in 96-well format in three hours (less than 1 minute per sample with less than 1% loss of samples. We demonstrate that the RNA derived from this protocol is of high quality and suitable for use in real time qRT-PCR assays. Conclusion The development of the HTP96 protocol has vastly increased our sample throughput, allowing us to fully exploit the large sample capacity of modern real time qRT-PCR thermocyclers, now commonplace in many labs, and develop an effective high-throughput gene expression platform. We propose that the HTP96 protocol will significantly benefit any plant scientist with the task of obtaining hundreds of high quality RNA extractions.

  19. [Optimization of ultrasonic-assisted extraction of total flavonoids from leaves of the Artocarpus heterophyllus by response surface methodology].

    Science.gov (United States)

    Wang, Hong-wu; Liu, Yan-qing; Wang, Yuan-hong

    2011-07-01

    To investigate the ultrasonic-assisted extract on of total flavonoids from leaves of the Artocarpus heterophyllus. Investigated the effects of ethanol concentration, extraction time, and liquid-solid ratio on flavonoids yield. A 17-run response surface design involving three factors at three levels was generated by the Design-Expert software and experimental data obtained were subjected to quadratic regression analysis to create a mathematical model describing flavonoids extraction. The optimum ultrasonic assisted extraction conditions were: ethanol volume fraction 69.4% and liquid-solid ratio of 22.6:1 for 32 min. Under these optimized conditions, the yield of flavonoids was 7.55 mg/g. The Box-Behnken design and response surface analysis can well optimize the ultrasonic-assisted extraction of total flavonoids from Artocarpus heterophyllus.

  20. The ability of Abelmoschus manihot L. leaf extract in scavenging of free radical DPPH and total flavonoid determination

    Science.gov (United States)

    Sudewi, S.; Lolo, W. A.; Warongan, M.; Rifai, Y.; Rante, H.

    2017-11-01

    Abelmoschus manihot L. has reported to have flavonoids content. This study aims were to determine the ability of A. manihot extract in counteracting free radical DPPH and determine the content of total flavonoids. A. manihot leaf was taken from 2 regions in North Sulawesi, namely Tomohon and Kotamobagu. The maceration was carried out to extract the active compound in a 96% ethanol solvent. Free radical scavenging analysis was carried out by DPPH and determination of its total flavonoid in the extract was measured using spectrophotometri method. The results showed that A. manihot extract from Tomohon and Kotamobagu could counteract free radical of DPPH with value of free radical activity of 88.151 and 88.801 %, respectively. A. manihot leaf from Kotamobagu has higher total flavonoids content 61.763 mg/g compare to Tomohon 46.679 mg/g which presented as quercetin. A. manihot has antioxidant activity.

  1. In vitro antioxidant evaluation and total phenolics of methanolic leaf extracts of Nyctanthes arbor-tristis L.

    Science.gov (United States)

    Michael, J Savarimuthu; Kalirajan, A; Padmalatha, C; Singh, A J A Ranjit

    2013-09-01

    To investigate the in vitro antioxidant activity and total phenolic content of the methanolic leaf extract of Nyctanthes arbor-tristis L. (NA). The sample was tested using five in vitro antioxidant methods (1, 1-diphenyl-2-picryl hydrazine radical scavenging activity (DPPH), hydroxyl radical-scavenging activity (-OH), nitric oxide scavenging activity (NO), superoxide radical-scavenging activity, and total antioxidant activity) to evaluate the in vitro antioxidant potential of NA and the total phenolic content (Folin-Ciocalteu method). The extract showed good free radical scavenging property which was calculated as an IC50 value. IC50 (Half maximal inhibitory concentration) of the methanolic extract was found to be 57.93 μg·mL(-1) for DPPH, 98.61 μg·mL(-1) for -OH, 91.74 μg·mL(-1) for NO, and 196.07 μg·mL(-1) for superoxide radical scavenging activity. Total antioxidant capacity of the extract was found to be (1198 ± 24.05) mg ascorbic acid for the methanolic extract. Free radical scavenging activity observed in the extracts of NA showed a concentration-dependent reaction. The in vitro scavenging tested for free radicals was reported to be due to high phenolic content in the leaf extract. The leaf extract of NA showed the highest total phenolic content with a value of 78.48 ± 4.2 equivalent mg TAE/g (tannic acid equivalent). N. arbor-tristis leaf extract exhibited potent free radical scavenging activity. The finding suggests that N. arbor-tristis leaves could be a potential source of natural antioxidant. Copyright © 2013 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

  2. Sequential Combination of Microwave- and Ultrasound-Assisted Extraction of Total Flavonoids from Osmanthus fragrans Lour. Flowers

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    Jianfeng Yu

    2017-12-01

    Full Text Available Microwave-assisted and ultrasound-assisted extraction assays were used to isolate total flavonoids (TF from Osmanthus fragrans flowers. The effects of the solid-liquid ratio, ethanol concentration, microwave power, microwave extraction time, ultrasonic power and ultrasonic extraction time on the yield of TF were studied. A sequential combination of microwave- and ultrasound-assisted extraction (SC-MUAE methods was developed, which was subsequently optimized by Box-Behnken design-response surface methodology (BBD-RSM. The interaction effects of the ethanol concentration (40–60%, microwave extraction time (5–7 min, ultrasonic extraction time (8–12 min and ultrasonic power (210–430 W on the yield of TF were investigated. The optimum operating parameters for the extraction of TF were determined to be as follows: ethanol concentration (48.15%, microwave extraction time (6.43 min, ultrasonic extraction time (10.09 min and ultrasonic power (370.9 W. Under these conditions, the extraction yield of TF was 7.86 mg/g.

  3. Total flavonoid extract from Coreopsis tinctoria Nutt. protects rats against myocardial ischemia/reperfusion injury.

    Science.gov (United States)

    Zhang, Ya; Yuan, Changsheng; Fang, He; Li, Jia; Su, Shanshan; Chen, Wen

    2016-09-01

    This study aimed to evaluate the protective effects of total flavonoid extract from Coreopsis tinctoria Nutt. (CTF) against myocardial ischemia/reperfusion injury (MIRI) using an isolated Langendorff rat heart model. Left ventricular developed pressure (LVDP) and the maximum rate of rise and fall of LV pressure (±dp/dtmax) were recorded. Cardiac injury was assessed by analyzing lactate dehydrogenase (LDH) and creatine kinase (CK) released in the coronary effluent. Superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and malondialdehyde (MDA) levels were determined. Myocardial inflammation was assessed by monitoring tumor necrosis factor-alpha (TNF-α), C-reactive protein (CRP), interleukin-8 (IL-8), and interleukin-6 (IL-6) levels. Myocardial infarct size was estimated. Cell morphology was assessed by 2,3,5-triphenyltetrazolium chloride and hematoxylin and eosin (HE) staining. Cardiomyocyte apoptosis was determined by terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) staining. Pretreatment with CTF significantly increased the heart rate and increased LVDP, as well as SOD and GSH-Px levels. In addition, CTF pretreatment decreased the TUNEL-positive cell ratio, infarct size, and levels of CK, LDH, MDA, TNF-α, CRP, IL-6, and IL-8. These results suggest that CTF exerts cardio-protective effects against MIRI via anti-oxidant, anti-inflammatory, and anti-apoptotic activities.

  4. The extraction of total lipids from parsley: Petroselinum crispum (mill. Nym. Ex. A.W. Hill seeds

    Directory of Open Access Journals (Sweden)

    Stanković Mihajlo Z.

    2004-01-01

    Full Text Available The kinetics of extraction of total lipids from ground parsley (Petroselinum crispum (Mill. Nym. ex. A.W. Hill seeds with a mixture of ethanol or methanol with non-polar organic solvents, chloroform, carbon tetrachloride, trichloroethylene and petroleum ether, at various temperatures were studied. The maceration technique with reflux was used. The kinetic parameters were determined in extraction kinetic equations, as well as the optimal operation conditions for total lipids extraction. The maximum total lipids yield under optimal conditions was 33.7 g per 100 g of dry parsley seeds. Nine lipid fractions of the total lipids were separated by thin layer chromatography among which were phospholipids, sterol, mono-, di- and triacylglycerol, free fatty acids and carbohydrates.

  5. Total flavonoid content and antioxidant activity in leaves and stems extract of cultivated and wild tabat barito (Ficus deltoidea Jack)

    Science.gov (United States)

    Manurung, Hetty; Kustiawan, Wawan; Kusuma, Irawan W.; Marjenah

    2017-02-01

    Tabat barito (Ficus deltoidea Jack) is a name given by Dayak Tribe who lived in Borneo-Kalimantan and it is belongs to the moraceae. Almost all of the parts of F. deltoidea plant is widely used as a medicinal property. The total flavonoid content (TFC) and antioxidant activity from cultivated and wild F. deltoidea leaves and stems extract were assessed. Total flavonoid content was estimated by using Aluminium chloride colorimetric method and expressed as catechin equivalents (mg CE g-1 extract) and the antioxidant activity by the DPPH (2,2-diphenyl-1-picryl hydrazyl) method. The content of total flavonoid of leaves and stems (430.77 and 371.80 µg CE mg-1 extract) of cultivated F. deltoidea were higher than in the wild leaves and stems (114.82 and 66.67 µg CE mg-1 extract). The IC50 of leaves extract of cultivated and wild F. deltoidea, based on the DPPH assay, has a strong antioxidant activity (34.19 and 39.31 µg mL-1 extract) as compared to stems extract. These results showed that the cultivated F. deltoidea are suitable source for medicinal properties and the leaves could be exploited as source of natural antioxidants.

  6. Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils.

    Science.gov (United States)

    Gill, Aman S; Lee, Angela; McGuire, Krista L

    2017-08-15

    New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation ( cbbL-R [ cbbL gene, red-like subunit] and apsA ), nitrogen cycling ( noxZ and amoA ), and contaminant degradation ( bphA ); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants. IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a

  7. A simple and rapid infrared-assisted self enzymolysis extraction method for total flavonoid aglycones extraction from Scutellariae Radix and mechanism exploration.

    Science.gov (United States)

    Wang, Liping; Duan, Haotian; Jiang, Jiebing; Long, Jiakun; Yu, Yingjia; Chen, Guiliang; Duan, Gengli

    2017-09-01

    A new, simple, and fast infrared-assisted self enzymolysis extraction (IRASEE) approach for the extraction of total flavonoid aglycones (TFA) mainly including baicalein, wogonin, and oroxylin A from Scutellariae Radix is presented to enhance extraction yield. Extraction enzymolysis temperature, enzymolysis liquid-to-solid ratio, enzymolysis pH, enzymolysis time and infrared power, the factors affecting IRASEE procedure, were investigated in a newly designed, temperature-controlled infrared-assisted extraction (TC-IRAE) system to acquire the optimum analysis conditions. The results illustrated that IRASEE possessed great advantages in terms of efficiency and time compared with other conventional extraction techniques. Furthermore, the mechanism of IRASEE was preliminarily explored by observing the microscopic change of the samples surface structures, studying the main chemical compositions change of the samples before and after extraction and investigating the kinetics and thermodynamics at three temperature levels during the IRASEE process. These findings revealed that IRASEE can destroy the surface microstructures to accelerate the mass transfer and reduce the activation energy to intensify the chemical process. This integrative study presents a simple, rapid, efficient, and environmental IRASEE method for TFA extraction which has promising prospects for other similar herbal medicines. Graphical Abstract ᅟ.

  8. Rapid determination of carbohydrates, ash, and extractives contents of straw using attenuated total reflectance fourier transform mid-infrared spectroscopy.

    Science.gov (United States)

    Tamaki, Yukihiro; Mazza, Giuseppe

    2011-06-22

    Analysis of the chemical components of lignocellulosic biomass is essential to understanding its potential for utilization. Mid-infrared spectroscopy and partial least-squares regression were used for rapid measurement of the carbohydrate (total glycans; glucan; xylan; galactan; arabinan; mannan), ash, and extractives content of triticale and wheat straws. Calibration models for total glycans, glucan, and extractives showed good and excellent predictive performance on the basis of slope, r², RPD, and R/SEP criteria. The xylan model showed good and acceptable predictive performance. However, the ash model was evaluated as providing only approximate quantification and screening. The models for galactan, arabinan, and mannan indicated poor and insufficient prediction for application. Most models could predict both triticale and wheat straw samples with the same degree of accuracy. Mid-infrared spectroscopic techniques coupled with partial least-squares regression can be used for rapid prediction of total glycans, glucan, xylan, and extractives in triticale and wheat straw samples.

  9. Determination of in vitro total phenolic, flavonoid contents and antioxidant capacity of the methanolic extract of Echium amoenum L.

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    Fathi H

    2016-06-01

    Full Text Available Introduction: In traditional and modern medicine, active ingredients of medicinal plants have many applications in food, pharmaceutical, medical and industry. Antioxidants are compounds that prevent the oxidation process in the cell. Echium amoenum L. is a plant which grows in the mountainous regions of Mazandaran. This plant has different biological effects such as sedation, anti-inflammation, antidepressant and cancer preventive properties in traditional medicine. The aim of this study was to determine the total phenolic, flavonoid contents and antioxidant capacity of the methanolic extract of E.amoenum plant. Methods:In this experimental laboratory study the content of total phenolic Using the folin-siokalatio reactive at 760 nm wavelength and flavonoid With the use of aluminum chloride reagent at 420nm of E.amoenum extract were measured and antioxidant capacities of different concentrations of the extract were evaluated. Results: The results showed that total phenolic content of the extract was 429±2μg gallic acid equivalent/ml and flavonoid content was 148.56±1.52μg quercetin equivalent/ml, respectively. The radical scavenging activity by 2, 2-diphenyl-1-picryl-hydrazyl hydrate (DPPH,inhibitory concentration of 50%(IC50,was determined 178.11 μg/ml. Assessment of the reducing ability of extract showed that the extract had more activity than vitamin C. The percent nitric oxide trap inhibition of the extract was 57.89% and power iron chelating properties was 51.74%,that showed statistically significant difference in comparison with vitamin C and Quercetin (P=0.0473 and (P=0.0096 respectively. Conclusion: According to the results, E.amoenum extract had remarkable antioxidant capacity and can be proposed as an antioxidant compound used in the manufacture of food and pharmaceutical products.

  10. Phytochemical screening, total phenolics and antioxidant activities of bark and leaf extracts of Goniothalamus velutinus (Airy Shaw from Brunei Darussalam

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    Erum Iqbal

    2015-07-01

    Full Text Available Goniothalamus velutinus Airy Shaw belongs to the family Annonaceae which is known to have anticancer, antitumor and many other bioactivities. Natives of Sabah and Sarawak use root decoction of G. velutinus for the treatment of headache and food poisoning while the bark was used as a mosquito repellent. Bark and leaf extracts of this plant, obtained from Brunei Darussalam, were tested for phytochemical and antioxidant activities. Phytochemical screening of plant extracts revealed the presence of alkaloids, steroids, terpenoids and cardiac glycosides. Quantitative determination of total phenolics, total flavonoids, and various in vitro antioxidant activities (DPPH, ABTS and FRAP of methanolic extract was carried out using colorimetric methods. The total phenolic content, expressed as mg of gallic acid equivalent (GAE per gram of extract, was found to be 68 mg GAE/g and 78 mg GAE/g for bark and leaves respectively. The radical scavenging activity measurement, expressed in terms of EC50 (effective concentration of extract in μg/mL that reduces DPPH absorbance to 50% as compared to negative control, for leaf and bark extracts was found to be 155 μg/mL and 204 μg/mL respectively. Standards trolox and ascorbic acid show EC50 value of 5 μg/mL and 4 μg/mL respectively. Trolox equivalent antioxidant capacity (TEAC was measured using the ABTS and FRAP method. Result for bark and leaf extracts was 79 mg and 106 mg trolox equivalent (TE/g respectively for the ABTS method. For FRAP assay, results for bark and leaf extracts were 80 and 89 mg TE/g respectively.

  11. Effect of ultrasonic treatment on total phenolic extraction from Lavandula pubescens and its application in palm olein oil industry.

    Science.gov (United States)

    Rashed, Marwan M A; Tong, Qunyi; Abdelhai, Mandour H; Gasmalla, Mohammed A A; Ndayishimiye, Jean B; Chen, Long; Ren, Fei

    2016-03-01

    The aims of the current study were to evaluate the best technique for total phenolic extraction from Lavandula pubescens (Lp) and its application in vegetable oil industries as alternatives of synthetic food additives (TBHQ and BHT). To achieve these aims, three techniques of extraction were used: ultrasonic-microwave (40 kHz, 50 W, microwave power 480 W, 5 min), ultrasonic-homogenizer (20 kHz, 150 W, 5 min) and conventional maceration as a control. By using the Folin-Ciocalteu method, the total phenolic contents (TPC) (mg gallic acid equivalent/g dry matter) were found to be 253.87, 216.96 and 203.41 for ultrasonic-microwave extract, ultrasonic-homogenizer extract and maceration extract, respectively. The ultrasonic-microwave extract achieved the higher scavenger effect of DPPH (90.53%) with EC50 (19.54 μg/mL), and higher inhibition of β-carotene/linoleate emulsion deterioration (94.44%) with IC50 (30.62 μg/mL). The activity of the ultrasonic-microwave treatment could prolong the induction period (18.82 h) and oxidative stability index (1.67) of fresh refined, bleached and deodorized palm olein oil (RBDPOo) according to Rancimat assay. There was an important synergist effect between citric acid and Lp extracts in improving the oxidative stability of fresh RBDPOo. The results of this work also showed that the ultrasonic-microwave assisted extract was the most effective against Gram-positive and Gram-negative strains that were assessed in this study. The uses of ultrasonic-microwave could induce the acoustic cavitation and rupture of plant cells, and this facilitates the flow of solvent into the plant cells and enhances the desorption from the matrix of solid samples, and thus would enhance the efficiency of extraction based on cavitation phenomenon. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Determination of total lipids and characterization of marigold flower extracts (Calendula officinalis

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    Novković Vesna M.

    2005-01-01

    Full Text Available Bioactive extracts from marigold flower are important ingredients for parapharmaceutical and cosmetic preparations. Their antiflogistic holeretic.antimicrobic, antidermatic and anticancer effects are due to the presence of flavonoids, carotenoids, etheric oils, and terpenoids. This study presents the results of spectrophotometric investigation for the overall carotene content calculated as (3-caroten (442 nm, visual and physico-chemical characteristics according to Ph.Jug. V in oil extracts of marigold flower obtained by maceration (room temperature and 70°C and percolation (room temperature with olive oil and sunflower oil by original procedures.The largest content of (3-carotene (57.5 mg/kg of oil extracts is in the oil extract obtained by maceration for 72 hours with olive oil (solvomodulus 1:5 m/m at room temperature.

  13. A Novel Microfluidic Device for Fully Automated Extraction of RNA from Cell Cultures, Phase I

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    National Aeronautics and Space Administration — Differential gene expression by RNA profiling is a universal and critical step in space biology experiments, which seek to link specific molecular events with...

  14. A Novel Microfluidic Device for Fully Automated Extraction of RNA from Cell Cultures, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Obtaining high quality, intact RNA from cells is an ubiquitous need in the pursuit of space biology. Our overall objective is to develop and commercialize a...

  15. Evaluation of five methods for total DNA extraction from western corn rootworm beetles.

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    Hong Chen

    Full Text Available BACKGROUND: DNA extraction is a routine step in many insect molecular studies. A variety of methods have been used to isolate DNA molecules from insects, and many commercial kits are available. Extraction methods need to be evaluated for their efficiency, cost, and side effects such as DNA degradation during extraction. METHODOLOGY/PRINCIPAL FINDINGS: From individual western corn rootworm beetles, Diabrotica virgifera virgifera, DNA extractions by the SDS method, CTAB method, DNAzol reagent, Puregene solutions and DNeasy column were compared in terms of DNA quantity and quality, cost of materials, and time consumed. Although all five methods resulted in acceptable DNA concentrations and absorbance ratios, the SDS and CTAB methods resulted in higher DNA yield (ng DNA vs. mg tissue at much lower cost and less degradation as revealed on agarose gels. The DNeasy kit was most time-efficient but was the costliest among the methods tested. The effects of ethanol volume, temperature and incubation time on precipitation of DNA were also investigated. The DNA samples obtained by the five methods were tested in PCR for six microsatellites located in various positions of the beetle's genome, and all samples showed successful amplifications. CONCLUSION/SIGNIFICANCE: These evaluations provide a guide for choosing methods of DNA extraction from western corn rootworm beetles based on expected DNA yield and quality, extraction time, cost, and waste control. The extraction conditions for this mid-size insect were optimized. The DNA extracted by the five methods was suitable for further molecular applications such as PCR and sequencing by synthesis.

  16. Influence of different extracts addition on total phenols, anthocyanin content and antioxidant activity of blackberry juice during storage

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    Blanka Bilić

    2011-01-01

    Full Text Available The aim of this study was investigation of influence of different extracts addition on total phenols, anthocyanin content, antioxidant activity and percent of polymeric colour of blackberry juice during storage of 52 days at 4 °C. Anthocyanin content of control sample (blackberry juice without extracts addition was 149.91 mg/L. Samples with addition of extracts (olive leaf, pine bark PE 5:1, pine bark PE 95 %, green tea, red wine PE 30 %, red wine PE 4:1 and bioflavonoids had higher anthocyanin content (from 152.42 to 161.19 mg/L in comparison to control sample. Sample with addition of bioflavonoids had the highest anthocyanin content. Samples with addition of extracts had much higher total phenol content and antioxidant activity than control sample, what was expected since extracts are rich in phenols. During storage decrease of phenols, anthocyanins and antioxidant activity occurred in higher or lesser extent, depending on extract type addition. Anthocyanin content in control sample was 119.85 mg/L. Samples with addition of bioflavonoids, olive leaf, pine bark PE 5:1 and red wine PE 4:1 had lower (from 103.44 to 118.84 mg/L, while other samples had higher (from 131.99 to 135.57 mg/L anthocyanin content than control sample. After storage, decrease of anthocyanins was followed with increase of percent of polymeric colour, with exception of samples with addition of green tea.

  17. Evaluating the impact of extraction and cleanup parameters on the yield of total petroleum hydrocarbons in soil

    Energy Technology Data Exchange (ETDEWEB)

    Saari, Eija; Peraemaeki, Paavo; Jalonen, Jorma [University of Oulu, Department of Chemistry (Finland)

    2008-11-15

    Interlaboratory comparisons for the analysis of mineral oil in polluted soil using the GC-FID method indicate that extraction and cleanup conditions have significant effects on the analytical results. In this investigation a ruggedness test was performed on the extraction and cleanup method for the determination of total petroleum hydrocarbons in soil. A two-level Plackett-Burman design was utilized to study the effect of 11 different method parameters on the extraction recovery of total petroleum hydrocarbons (TPH) in soil. Both qualitative and quantitative factors were investigated. The results indicate that total petroleum hydrocarbons can be relatively reliably monitored through strict implementation of the ISO and CEN draft standards. However, variation in certain method parameters readily affects the validity of the results. The most critical factors affecting TPH recovery were the solvent and co-solvent used for extraction, the extraction time, adsorbent and its weight and sample TPH concentration. Because adaptation of the draft standards especially with respect to these factors easily leads to TPH recoveries higher than 200% or lower than 70%, the validity of the adapted method should always be verified. A proper estimate of the expanded uncertainty should also be appended to TPH results, because only then can the reliability of the results be guaranteed and further justification is gained to support the end-use of the data. This also supports the credibility of the analytical services and prevents the data end-users from drawing misleading conclusions concerning the environmental risks and potential remediation requirements. (orig.)

  18. siRNA-like double-stranded RNAs are specifically protected against degradation in human cell extract.

    Directory of Open Access Journals (Sweden)

    John A H Hoerter

    Full Text Available RNA interference (RNAi is a set of intracellular pathways in eukaryotes that controls both exogenous and endogenous gene expression. The power of RNAi to knock down (silence any gene of interest by the introduction of synthetic small-interfering (siRNAs has afforded powerful insight into biological function through reverse genetic approaches and has borne a new field of gene therapeutics. A number of questions are outstanding concerning the potency of siRNAs, necessitating an understanding of how short double-stranded RNAs are processed by the cell. Recent work suggests unmodified siRNAs are protected in the intracellular environment, although the mechanism of protection still remains unclear. We have developed a set of doubly-fluorophore labeled RNAs (more precisely, RNA/DNA chimeras to probe in real-time the stability of siRNAs and related molecules by fluorescence resonance energy transfer (FRET. We find that these RNA probes are substrates for relevant cellular degradative processes, including the RNase H1 mediated degradation of an DNA/RNA hybrid and Dicer-mediated cleavage of a 24-nucleotide (per strand double-stranded RNA. In addition, we find that 21- and 24-nucleotide double-stranded RNAs are relatively protected in human cytosolic cell extract, but less so in blood serum, whereas an 18-nucleotide double-stranded RNA is less protected in both fluids. These results suggest that RNAi effector RNAs are specifically protected in the cellular environment and may provide an explanation for recent results showing that unmodified siRNAs in cells persist intact for extended periods of time.

  19. Comparative analysis of three different of extraction protocols of total nucleic acids of squash (Cucurbita moschata) for the diagnosis from geminivirus

    International Nuclear Information System (INIS)

    Hernandez Jimenez, Eduardo

    2008-01-01

    The geminivirus constitute an important group of plant pathogens, characterized by an unusual morphology of the viral particle and its DNA. They have a paired icosahedral cover and a small circular genome of DNA simple band that is replicated, by DNA double band, in the nucleus of the infected cell of the plant. Many researchers have focused on the development and optimization of protocols for obtaining DNA or RNA of interest, because of rapid advances in molecular biology during the second half of the XX century and the beginning of XXI century, and to that the extraction and purification of nucleic acids is the first step mainly of the procedures in this area. The objective is to compare, by means of molecular techniques, the DNA purification in squash from different ways of storage and extraction protocols of total nucleic acids of the plant, in order to improve the quality and amount of genetic matters whereupon the detection and characterization of geminivirus are realised. Three methods were compared: i. Dellaporta and collaborators (1983), ii.- Doyle and Doyle (1990) and iii.- Jose and Usha (2000). The operation of the three methods scaled downward (15 milligrams of leaf tissue) and two ways of storage were evaluated: 1.- tubes with silica gel (SG, a desiccant) and 2.- frozen to -70 degrees Celsius. The method of Jose and Usha (2000) presented technical difficulties that not permitted to scale downward, for which it should work with the purification from a gram of foliar tissue. The integrity of the total DNA was verified superior in the material stored to -70 degrees celsius for all the methods, by means of electrophoresis in gels of agarose, besides that the protocol of Dellaporta et al. (1983) tends to enrich the RNA. The readings were similar for the methods of Dellaporta et al. (1983) and Doyle and Doyle (1993), this was evidenced upon quantifying the total DNA and that is extracted at least a 30% more of DNA from material in the desiccant with respect

  20. Determination of total and extractable hydrogen peroxide in organic and aqueous solutions of uranyl nitrate

    International Nuclear Information System (INIS)

    Goodall, Ph.

    1999-01-01

    The development of a spectrophotometric method for the determination of hydrogen peroxide in uranyl nitrate solutions is reported. The method involves the measurement of the absorbance at 520 mm of a vanadyl peroxide species. This species was formed by the addition of a reagent consisting of vanadium (V) (50 mmol x dm -3 ) in dilute sulphuric acid (2 mol x dm -3 H 2 SO 4 ). This reagent, after dilution, was also used as an extractant for organic phase samples. The method is simple and robust and tolerant of nitric acid and U(VI). Specificity and accuracy were improved by the application of solid phase extraction techniques to remove entrained organic solvents and Pu(VI). Reverse phase solid phase extraction was used to clean-up aqueous samples or extracts which were contaminated with entrained solvent. A solid phase extraction system based upon an extraction chromatography system was used to remove Pu(IV). Detection limits of 26 μmol x dm -3 (0.88 μg x cm -3 ) or 7 μmol x dm -3 (0.24 μg x cm -3 ) for, respectively, a 1 and 4 cm path length cell were obtained. Precisions of RSD = 1.4% and 19.5% were obtained at the extremes of the calibration curve (5 mmol x dm -3 and 50 μmol x dm -3 H 2 O 2 , 1 cm cell). The introduction of the extraction and clean-up stages had a negligible effect upon the precision of the determination. The stability of an organic phase sample was tested and no loss of analyte could be discerned over a period of at least 5 days. (author)

  1. Quantitative Analysis of Total Petroleum Hydrocarbons in Soils: Comparison between Reflectance Spectroscopy and Solvent Extraction by 3 Certified Laboratories

    Directory of Open Access Journals (Sweden)

    Guy Schwartz

    2012-01-01

    Full Text Available The commonly used analytic method for assessing total petroleum hydrocarbons (TPH in soil, EPA method 418.1, is usually based on extraction with 1,1,2-trichlorotrifluoroethane (Freon 113 and FTIR spectroscopy of the extracted solvent. This method is widely used for initial site investigation, due to the relative low price per sample. It is known that the extraction efficiency varies depending on the extracting solvent and other sample properties. This study’s main goal was to evaluate reflectance spectroscopy as a tool for TPH assessment, as compared with three commercial certified laboratories using traditional methods. Large variations were found between the results of the three commercial laboratories, both internally (average deviation up to 20%, and between laboratories (average deviation up to 103%. Reflectance spectroscopy method was found be as good as the commercial laboratories in terms of accuracy and could be a viable field-screening tool that is rapid, environmental friendly, and cost effective.

  2. Comparação de três protocolos distintos para extração de RNA de amostras fixadas em formalina e emblocadas em parafina Comparison of three different protocols for extracting RNA from formalin-fixed paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    Gisele Rodrigues Gouveia

    2011-12-01

    Full Text Available INTRODUÇÃO: Tecidos fixados em formalina e emblocados em parafina (FFEP são importantes fontes de amostras para estudos retrospectivos. Apesar de sua capacidade de preservação de proteínas e morfologia celular, a formalina interfere negativamente em testes de biologia molecular por fragmentar e modificar quimicamente os ácidos nucleicos, particularmente o ácido ribonucleico (RNA. OBJETIVO: Comparar a eficiência de três diferentes protocolos de extração de RNA para análise de expressão gênica de tecidos FFEP. MATERIAL E MÉTODOS: Amostras de linfonodo humano FEEP foram submetidas à extração de RNA utilizando-se os kits Ambion e Arcturus Bioscience e o método clássico de Trizol. Após a extração, o RNA foi quantificado e testado quanto à sua capacidade de amplificaç��o pela reação em cadeia da polimerase em tempo real (RT-PCR utilizando primers do gene endógeno gliceraldeído-3 fosfato desidrogenase (GAPDH. DISCUSSÃO/CONCLUSÃO: Todos os protocolos testados produziram quantidades adequadas e suficientes de RNA total, entretanto, somente os protocolos com uso dos kits Ambion e Arcturus produziram RNA capaz de ser amplificado pela PCR.INTRODUCTION: Formalin fixed paraffin embedded (FFPE tissues are an important sample source for retrospective studies. Despite its ability to preserve proteins and cell morphology, formalin hinders Molecular Biology tests once it fragments and chemically modifies nucleic acids, particularly RNA. OBJECTIVE: To compare the efficiency of three different RNA extraction protocols for gene expression analysis of FFEP tissues. MATERIAL AND METHODS: RNA was extracted from FFPE samples of human lymph by means of Ambion and Arcturus Bioscience kits and the classical Trizol method. After extraction, RNA was quantified and tested for amplification through real time polymerase chain reaction (RT-PCR using glyceraldehydes-3 phosphate dehydrogenase (GAPDH endogenous gene primers. DISCUSSION

  3. The extraction of φ-N total cross section from d(γ,pK+K-)n

    International Nuclear Information System (INIS)

    Qian, X.; Chen, W.; Gao, H.; Hicks, K.; Kramer, K.; Laget, J.M.; Mibe, T.; Stepanyan, S.; Tedeschi, D.J.; Xu, W.; Adhikari, K.P.; Amaryan, M.; Anghinolfi, M.; Baghdasaryan, H.; Ball, J.; Battaglieri, M.; Batourine, V.; Bedlinskiy, I.; Bellis, M.; Biselli, A.S.

    2009-01-01

    We report on the first measurement of the differential cross section of φ-meson photoproduction for the d(γ,pK + K - )n exclusive reaction channel. The experiment was performed using a tagged-photon beam and the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab. A combined analysis using data from the d(γ,pK + K - )n channel and those from a previous publication on coherent φ production on the deuteron has been carried out to extract the φ-N total cross section, σ φN . The extracted φ-N total cross section favors a value above 20 mb. This value is larger than the value extracted using vector-meson dominance models for φ photoproduction on the proton.

  4. Statistical mixture design selective extraction of compounds with antioxidant activity and total polyphenol content from Trichilia catigua.

    Science.gov (United States)

    Lonni, Audrey Alesandra Stinghen Garcia; Longhini, Renata; Lopes, Gisely Cristiny; de Mello, João Carlos Palazzo; Scarminio, Ieda Spacino

    2012-03-16

    Statistical design mixtures of water, methanol, acetone and ethanol were used to extract material from Trichilia catigua (Meliaceae) barks to study the effects of different solvents and their mixtures on its yield, total polyphenol content and antioxidant activity. The experimental results and their response surface models showed that quaternary mixtures with approximately equal proportions of all four solvents provided the highest yields, total polyphenol contents and antioxidant activities of the crude extracts followed by ternary design mixtures. Principal component and hierarchical clustering analysis of the HPLC-DAD spectra of the chromatographic peaks of 1:1:1:1 water-methanol-acetone-ethanol mixture extracts indicate the presence of cinchonains, gallic acid derivatives, natural polyphenols, flavanoids, catechins, and epicatechins. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Evaluation of Antioxidant Activity of Total Extract of Onopordon leptolepis L. in Vitro

    Directory of Open Access Journals (Sweden)

    Einollah Valizadeh

    2015-08-01

    Full Text Available Background and objectives : Medicinal plants are valuable natural resources that have been considered nowadays in developed countries as raw materials for converting into safe drugs for human. Antioxidants are compounds that effectively prevent oxygen free radical reactions and reduce damage or cell death, cardiovascular diseases and cancer. Material and Methods : After extraction of floral and vegetative parts of Onopordon leptolepis plant, antioxidant potential was determined by two testes: 1. 1diphenyl-2-picrylhydrazyl (DPPH free radical-scavenging and ferric-reducing antioxidant power (FRAP. Results : The hydro-alcohol extract (methanol 70% of floral and vegetative parts of O. leptolepis plant was found as the most active in scavenging DPPH radicals and in FRAP. The antioxidant potential of hydro-alcohol (H.A70% extracts of the floral part of O.leptolepis showed weak effect than the extract of vegetative of O.leptolepis plant. Conclusion : Results showed that the hydro-alcohol extract (methanol 70% of vegetative part can be considered for medicinal and food industries due to the high antioxidant properties.

  6. In vitro activity of total aqueous ethanol leaf extracts of Ricinus communis on Leishmania major promastigotes

    International Nuclear Information System (INIS)

    Okech, B.G.A.; Irungu, L.W.; Anjili, C.O.; Munyua, J.K.; Njagi, E.N.M.; Rukungu, G.

    2006-01-01

    The activity of aqueous and ethanol extracts of Ricinus communis was tested on Leishmania promastigotes in cell-free culture media. Serial dilutions of the extracts ranging from 500μg/ml, 250 μg/ml and 62.5μg/ml were prepared in triplicate using Schneiders Drosophila medium supplemented with 20% fetal bovine serum in the absence of antibiotics and the growth of approximately 1x 10 (power 6) parasites monitored every two days for a period of 8 days. Parasite density was estimated every two days using the Neuabeur counting chamber. At the end of the 8-day period cell morphology was observed and photographed. Significant growth inihibitory effect was observed on the promastigotes by the aqueous and ethanol extracts especially at high concentrations. However, there was an enhanced growth effect initially thereafter leading to to a rapid decline in promastigote cell population. Flagellar motility was also greatly affected at high concentration and it appeared that there was a linear relationship between flagellar motilities and the level of concentrations. Parasite morphology was affected severely. Most of the cultures observed appeared to have abnormal round morphology. Rosseting was also evident in the extract treated cultures. The aqueous leaf extract interfered with parasite morphology but this was dose dependent. The importance of R. communis plant as a potential source for chemotypes with antileishmanial activity is discussed. (author)

  7. Quantification of total and water extractable essential elements in medicinal plants used for stomach problems

    International Nuclear Information System (INIS)

    Sahito, S.R.; Kazi, T.G.; Shar, G.Q.; Mangrio, A.M; Shaikh, M.S.

    2004-01-01

    The role of elements particularly trace elements in health and disease is well known. Present study has been undertaken in our laboratories to quantify the commonly occurring elements in three medicinal plans. Peganum harmala Linn, Phyllanthus emblica Linn, Tamarix dioca used for stomach problems using atomic absorption spectrophotometer. Wet digestion method has been used to extract the acid extractable metals. Samples were boiled in water to obtain water extractable metals. The validation of the method was checked with the NBS-1570 (Spinach) as Standard Reference Material. Levels of essential elements were found high as compared to concentration of toxic elements. The considerable amounts of essential such as calcium, magnesium, potassium, zinc and iron were found in all these plant samples. (author)

  8. Optimisation of pressurised liquid extraction (PLE) for rapid and efficient extraction of superficial and total mineral oil contamination from dry foods.

    Science.gov (United States)

    Moret, Sabrina; Scolaro, Marianna; Barp, Laura; Purcaro, Giorgia; Sander, Maren; Conte, Lanfranco S

    2014-08-15

    Pressurised liquid extraction (PLE) represents a powerful technique which can be conveniently used for rapid extraction of mineral oil saturated (MOSH) and aromatic hydrocarbons (MOAH) from dry foods with a low fat content, such as semolina pasta, rice, and other cereals. Two different PLE methods, one for rapid determination of superficial contamination mainly from the packaging, the other for efficient extraction of total contamination from different sources, have been developed and optimised. The two methods presented good performance characteristics in terms of repeatability (relative standard deviation lower than 5%) and recoveries (higher than 95%). To show their potentiality, the two methods have been applied in combination on semolina pasta and rice packaged in direct contact with recycled cardboard. In the case of semolina pasta it was possible to discriminate between superficial contamination coming from the packaging, and pre-existing contamination (firmly enclosed into the matrix). Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. RNA Polymerase II Second Largest Subunit Molecular Identification of Boletus griseipurpureus Corner From Thailand and Antibacterial Activity of Basidiocarp Extracts.

    Science.gov (United States)

    Aung-Aud-Chariya, Amornrat; Bangrak, Phuwadol; Lumyong, Saisamorn; Phupong, Worrapong; Aggangan, Nelly Siababa; Kamlangdee, Niyom

    2015-03-01

    Boletus griseipurpureus Corner, an edible mushroom, is a putative ectomycorrhizal fungus. Currently, the taxonomic boundary of this mushroom is unclear and its bitter taste makes it interesting for evaluating its antibacterial properties. The purpose of this study was to identify the genetic variation of this mushroom and also to evaluate any antibacterial activities. Basidiocarps were collected from 2 north-eastern provinces, Roi Et and Ubon Ratchathani, and from 2 southern provinces, Songkhla and Surat Thani, in Thailand. Genomic DNA was extracted and molecular structure was examined using the RNA polymerase II (RPB2) analysis. Antibacterial activities of basidiocarp extracts were conducted with Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 29523 and methicillin-resistant Staphylococcus aureus (MRSA) 189 using the agar-well diffusion method. All the samples collected for this study constituted a monophyletic clade, which was closely related with the Boletus group of polypore fungi. For the antibacterial study, it was found that the crude methanol extract of basidiomes inhibited the growth of all bacteria in vitro more than the crude ethyl acetate extract. Basidomes collected from four locations in Thailand had low genetic variation and their extracts inhibited the growth of all tested bacteria. The health benefits of this edible species should be evaluated further.

  10. In situ, real-time catabolic gene expression: Extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater

    International Nuclear Information System (INIS)

    Wilson, M.S.; Bakermans, C.; Madsen, E.L.

    1999-01-01

    The authors developed procedures for isolating and characterizing in situ-transcribed mRNA from groundwater microorganisms catabolizing naphthalene at a coal tar waste-contaminated site. Groundwater was pumped through 0.22-microm-pore-size filters, which were then frozen to dry ice-ethanol. RNA was extracted from the frozen filters by boiling sodium dodecyl sulfate lysis and acidic phenol-chloroform extraction. Transcript characterization was performed with a series of PCR primers designed to amplify nahAc homologs. Several primer pairs were found to amplify nahAc homologs representing the entire diversity of the naphthalene-degrading genes. The environmental RNA extract was reverse transcribed, and the resultant mixture of cDNAs was amplified by PCR. A digoxigenin-labeled probe mixture was produced by PCR amplification of groundwater cDNA. This probe mixture hybridized under stringent conditions with the corresponding PCR products from naphthalene-degrading bacteria carrying a variety of nahAc homologs, indicating that diverse dioxygenase transcripts had been retrieved from groundwater. Diluted and undiluted cDNA preparations were independently amplified, and 28 of the resulting PCR products were cloned and sequenced. Sequence comparisons revealed two major groups related to the dioxygenase genes ndoB and dntAc, previously cloned from Pseudomonas putida NCIB 9816-4 and Burkholderia sp. strain DNT, respectively. A distinctive subgroup of sequences was found only in experiments performed with the undiluted cDNA preparation. To the authors' knowledge, these results are the first to directly document in situ transcription of genes encoding naphthalene catabolism at a contaminated site by indigenous microorganisms. The retrieved sequences represent greater diversity than has been detected at the study site by culture-based approaches

  11. Investigation of Total Phenolic and Flavonoid Contents, and Evaluation of Antimicrobial and Antioxidant Activities from Baeckea frutescens Extracts

    Science.gov (United States)

    Nisa, K.; Nurhayati, S.; Apriyana, W.; Indrianingsih, A. W.

    2017-12-01

    Baeckea frutescens L. is a medicinal plant endemic to the tropical area and it has been used by locals for topical and oral ailments. This study investigated total phenolic and flavonoid contents and also evaluated in vitro antimicrobial and antioxidant activities of of Baeckea frutescens crude extracts. These extracts were assessed for their antibacterial activities against strains of Escherichia coli, Staphylococcus aureus, Salmonella thypii, and Pseudomonas aureginosa by the broth micro-dilution methods using a modified tetrazolium-based colorimetric assay (3-(4, 5-dimethylthiazol)-2, 5-diphenyl tetrazolium bromide (MTT) assay). Baeckea frutescens crude extracts were also tested against the stable DPPH (2,2-diphenyl-1-picryl-hydrazyl-hydrate) free-radical. The results indicated that Baeckea frutescens water and ethanol extracts possesed remarkable antibacterial activity with the minimum inhibitory concentration less than 100 μg/ml against Escherichia coli and Salmonella thypi. On the evaluation of the antioxidant activity via DPPH assay, Baeckea frutescens ethanol extracts exhibited a good antioxidant activity with IC50 less than 50 μg/ml and Baeckea frutescens water extracts showed a moderate antioxidant activity with IC50 less than 100 μg/ml.

  12. Effects of extracted soy isoflavones alone on blood total and LDL cholesterol: Meta-analysis of randomized controlled trials

    Directory of Open Access Journals (Sweden)

    Kyoko Taku

    2008-07-01

    Full Text Available Kyoko Taku1, Keizo Umegaki1, Yoshiko Ishimi2, Shaw Watanabe31Information Center, National Institute of Health and Nutrition, Tokyo, Japan; 2Nutritional Epidemiology Program, National Institute of Health and Nutrition, Tokyo, Japan; 3Nutritional Education Program, National Institute of Health and Nutrition, Tokyo, JapanAbstract: When provided concurrently with soy protein for 1–3 months, soy isoflavones exert synergistic or additive cholesterol-lowering effects. This meta-analysis was performed to evaluate the effects of extracted soy isoflavones alone (not ingested concurrently with soy protein on total and low density lipoprotein (LDL cholesterol. MEDLINE (1966–2007, EMBASE (1966–2007, CENTRAL (1966–2007, ICHUSHI (1983–2008, and CNKI (1979–2007 were searched for randomized placebo-controlled trials published in English, Japanese, and Chinese, describing the changes in lipid profiles in adult humans resulting from ingestion of extracted soy isoflavones for 1–3 months. Reference lists of relevant systematic reviews and meta-analyses were hand-searched. Meta-analysis of 10 and 9 trials with usable information using REVMAN found that an average of 70 mg soy isoflavones/day (27–132 mg, as the aglycone form alone had a nonsignificant effect on total (0.01 mmol/L [95% CI: –0.12, 0.14]; P = 0.86 and LDL (0.03 mmol/L [95% CI: –0.11, 0.16]; P = 0.71 cholesterol in menopausal women, respectively. It is concluded that ingestion of about 70 mg extracted soy isoflavones/day alone for 1–3 months does not improve total and LDL cholesterol levels in normocholesterolemic menopausal women; further studies are needed to verify the effects of extracted soy isoflavones.Keywords: extracted soy isoflavones, lipid, total cholesterol, LDL cholesterol

  13. A method for high-quality RNA extraction from tall fescue

    African Journals Online (AJOL)

    Jane

    2011-07-20

    Jul 20, 2011 ... but most of those methods are time-consuming (Li et al.,. 2008). Since RNA ... forage and seed (Wang and Ge, 2004; Huang et al.,. 2008). ..... Malnoy M, Reynoird JP, Mourgues F, Chevreau E, Simoneau P (2001). A method ...

  14. Intragraft interleukin 2 mRNA expression during acute cellular rejection and left ventricular total wall thickness after heart transplantation

    NARCIS (Netherlands)

    de Groot-Kruseman, H A; Baan, C C; Hagman, E M; Mol, W M; Niesters, H G; Maat, A P; Zondervan, P E; Weimar, W; Balk, A H

    OBJECTIVE: To assess whether diastolic graft function is influenced by intragraft interleukin 2 (IL-2) messenger RNA (mRNA) expression in rejecting cardiac allografts. DESIGN: 16 recipients of cardiac allografts were monitored during the first three months after transplantation. The presence of IL-2

  15. Statistically extracted fundamental watershed variables for estimating the loads of total nitrogen in small streams

    Science.gov (United States)

    Kronholm, Scott C.; Capel, Paul D.; Terziotti, Silvia

    2016-01-01

    Accurate estimation of total nitrogen loads is essential for evaluating conditions in the aquatic environment. Extrapolation of estimates beyond measured streams will greatly expand our understanding of total nitrogen loading to streams. Recursive partitioning and random forest regression were used to assess 85 geospatial, environmental, and watershed variables across 636 small (monitoring may be beneficial.

  16. Determination of Total Phenolics, Flavonoids and Antioxidant Capacity of Methanolic Extracts of Some Brassica Seeds

    Directory of Open Access Journals (Sweden)

    Maria Doiniţa Borş

    2014-11-01

    Full Text Available Cruciferous vegetables are rich in nutrients and bioactive compounds. Seeds are highly nutritious and they are becoming more and more popular in nowadays diets. In the present study various types of radish and mustard seeds were evaluated on the basis of the total phenolic content (TPC, total flavonoid content (TFC and the antioxidant potential, using simple spectrophotometric methods.

  17. Total lactic acid bacteria, antioxidant activity, and acceptance of synbiotic yoghurt with red ginger extract (Zingiberofficinale var. rubrum)

    Science.gov (United States)

    Larasati, B. A.; Panunggal, B.; Afifah, D. N.; Anjani, G.; Rustanti, N.

    2018-02-01

    Antioxidant related to oxidative stress can caused the metabolic disorders. A functional food that high in antioxidant can be use as the alternative prevention. The addition of red ginger extract in yoghurt could form a functional food, that high in antioxidant, synbiotic and fiber. The influence of red ginger extract on yoghurt synbiotic against lactic acid bacteria, antioxidant activity and acceptance were analyzed. This was an experimental research with one factor complete randomized design, specifically the addition of red ginger extract 0%; 0,1%; 0,3% and 0,5% into synbiotic yoghurt. Total plate count method used to analyze the lactic acid bacteria, 1-1-diphenyl-2-picrylhydrazyl (DPPH) method for antioxidant activity, and acceptance analyzed with hedonic test. The higher the dose of extract added to synbiotic yoghurt, the antioxidant activity got significantly increased (ρ=0,0001), while the lactic acid bacteria got insignificantly decreased (ρ=0,085). The addition of 0,5% red ginger extract obtained the antioxidant activity of 71% and 4,86 × 1013 CFU/ml on lactic acid bacteria, which the requirement for probiotic on National Standard of Indonesia is >107 CFU/ml. The addition of extract had a significant effect on acceptance (ρ=0,0001) in flavor, color, and texture, but not aroma (ρ=0,266). The optimal product in this research was the yoghurt synbiotic with addition of 0,1% red ginger extract. To summarize, the addition of red ginger extract in synbiotic yoghurt had significant effect on antioxidant activity, flavor, color, and texture, but no significant effect on lactic acid bacteria and aroma.

  18. The Effects of Vitex agnus castus Total Extract on Spermatogenesis of Balb/C Mice

    Directory of Open Access Journals (Sweden)

    M Ramezani

    2008-12-01

    Full Text Available ABSTRACT Introduction & Objective: Vitex agnus castus (Verbenaceae is a phytoestrogeic herb native to the Middle East and southern Europe. It has clinical usage in so many countries. In this research, the effects of Vitex agnus castus extract was investigated on spermatogenesis of male Balb/C mice. Materials & Methods: This is an experimental study in which adult male mice were chosen and divided into 3 groups: control, vehicle, and experimental. Animals were daily injected (i.p. with 65, 165 265, 365, and 465 mg/kg of seed extract for ten consecutive days. Then the animals were weighed and eventually killed by cervical dislocation 2 weeks after the last injection. The caudal part of the right epididymis was used for sperm counting. After macroscopic investigation (weight, diameter and volume of testes tissues were fixed in Buin's fixative. Tissues were cut at 5 µm, stained with Hematoxylin and Eosin (H& E.Ccollected data was analyzed by the SPSS software by using one-way ANOVA. Results: No significant differences in body weight, volume, weight and diameter of testes was seen. Light microscopic studies showed a significant reduction in germinal epithelium in doses of 265 and 365 mg/kg and increased of interstitial tissue area in doses of 265, 365, and 465 mg/kg of extract. There was no significant difference in epithelium thickness and of the diameter of the epididymis. Germinal cells contained pyknotic nuclei and several holes that were found scattered in the tubules. Testis also showed a general disarrangement in various germinal elements of seminiferous tubules. Result of sperms count indicated a significant decreasing of spermatozoa in animals which received 265 and 365 mg/kg of extract. Conclusion: Vitex agnus castus contains essential oils, iridoid glycosides, flavonoids diterpenes, and essential fatty acids. The results suggest that its contraceptive effects is related to its flavonoids and essential fatty acids but further studies is

  19. Studies on total polyphenols and reducing power of aqueous extracts from selected lamiaceae species

    OpenAIRE

    Maria Cioroi; Daniela Dumitriu

    2010-01-01

    Certain phytochemicals in species are attracting increased attention because of a wide range of biological activities especially the possible cancer preventive properties. Polyphenols, the naturalantioxidants are present in plant extracts and they play a key role in antioxidative defence mechanisms in biological systems and they act as free radicals scavenging agents. Polyphenols might thereforeinhibit development of coronary heart disease and cancers. Basil, oregano and sage are highly fragr...

  20. Areca nut extract up-regulates prostaglandin production, cyclooxygenase-2 mRNA and protein expression of human oral keratinocytes.

    Science.gov (United States)

    Jeng, J H; Ho, Y S; Chan, C P; Wang, Y J; Hahn, L J; Lei, D; Hsu, C C; Chang, M C

    2000-07-01

    There are about 600 million betel quid (BQ) chewers in the world. BQ chewing is associated with increased incidence of oral cancer and submucous fibrosis. In this study, areca nut (AN) extract (200-800 microg/ml) induced the prostaglandin E(2) (PGE(2)) production by 1. 4-3.4-fold and 6-keto-PGF(1 alpha) production by 1.1-1.7-fold of gingival keratinocytes (GK), respectively, following 24 h of exposure. Exposure of GK to AN extract (>400 microg/ml) led to cell retraction and intracellular vacuoles formation. At concentrations of 800 and 1200 microg/ml, AN extract induced cell death at 21-24 and 32-52% as detected by MTT assay and cellular lactate dehydrogenase release, respectively. Interestingly, AN-induced morphological changes of GK are reversible. GK can still proliferate following exposure to AN extract. Cytotoxicity of AN extract cannot be inhibited by indomethacin (1 microM) and aspirin (50 microM), indicating that prostaglandin (PG) production is not the major factor responsible for AN cytotoxicity. PGE(2) exhibited little effect on the growth of GK at concentrations ranging from 100-1000 pg/ml. Stimulating GK production of PGs by AN extract could be due to induction of cyclooxygenase-2 (COX-2) mRNA expression and protein production. These results suggest that AN ingredients are critical in the pathogenesis of oral submucous fibrosis and oral cancer via their stimulatory effects on the PGs, COX-2 production and associated tissue inflammatory responses. AN cytotoxicity to GK is not directly mediated by COX-2 stimulation and PG production.

  1. Comparison of total and cold-extractable uranium in stream sediments of the southwestern Karoo supergroup, South Africa

    International Nuclear Information System (INIS)

    Jakob, W.R.O.; Smit, M.C.B.; Murphy, G.C.

    1979-01-01

    In order to evaluate the usefullness of cold-extractable uranium as a tool of uranium prospecting in stream sediments of the southwestern Karoo, South Africa, ten orientation studies were conducted near known mineralisation jointly by the Atomic Energy Board and the Geological Survey of South Africa. These indicate that the topography determines the nature of the dispersion. In areas of moderate to high relief the total uranium content of the stream sediment gives dispersion trains up to about 500 m from the mineralisation, and peak-to-background ratios of about 3. The use of cold-extractable uranium doubles the length of the dispersion, and peak-to-background ratios are greater than 10 and may be as high as 35. In areas of low relief, the total uranium content of the sediment gives low anomalies, with short dispersion downstream. Cold-extractable uranium gives anomalies 500-1 000 m from the mineralisation. This is interpreted to be due to the longer residence time of the clay minerals in the stream. In order to test the applicability of cold-extractable uranium on a regional scale, 720 samples were collected at a density of one sample per square kilometre. Statistical treatment of the data shows the U content of the stream sediments, to be log-normally distributed. For cold-extractable uranium, polymodal distributions, apparently representing background and anomalous samples, can be separated with a high rate of success, and meaningful threshold values can be assigned. This is not the case for the total uranium content of the stream sediments [af

  2. TOTAL AND HOT-WATER EXTRACTABLE CARBON RELATIONSHIP IN CHERNOZEM SOIL UNDER DIFFERENT CROPPING SYSTEMS AND LAND USE

    Directory of Open Access Journals (Sweden)

    Srdjan Šeremešić

    2013-12-01

    Full Text Available A study was conducted to determine the hot water extractable organic carbon (HWOC in 9 arable and 3 non arable soil samples on Haplic Chernozem. The hot water extractable carbon represents assimilative component of the total organic matter (OM that could contain readily available nutrients for plant growth. The obtained fraction of organic carbon (C makes up only a small percentage of the soil OM and directly reflects the changes in the rhizosphere. This labile fraction of the organic matter was separated by hot water extraction at 80°C. In our study the HWOC content in different samples ranged from 125 mg g-1 to 226 mg g-1. On the plots that are under native vegetation, higher values were determined (316 mg g-1 to 388 mg g-1. Whereas samples from arable soils were lower in HWOC. It was found that this extraction method can be successfully used to explain the dynamics of the soil OM. Soil samples with lower content of the total OM had lower HWOC content, indicating that the preservation of the OM depends on the renewal of its labile fractions.

  3. Total Phenolic, Flavonoid, Tomatine, and Tomatidine Contents and Antioxidant and Antimicrobial Activities of Extracts of Tomato Plant

    Science.gov (United States)

    Silva-Beltrán, Norma Patricia; Ruiz-Cruz, Saul; Cira-Chávez, Luis Alberto; Estrada-Alvarado, María Isabel; Ornelas-Paz, José de Jesús; López-Mata, Marco Antonio; Del-Toro-Sánchez, Carmen Lizette; Ayala-Zavala, J. Fernando; Márquez-Ríos, Enrique

    2015-01-01

    The purpose of this study was to evaluate the antioxidant and antimicrobial properties of extracts of different fractions of two tomato plant cultivars. The stems, roots, leaves, and whole-plant fractions were evaluated. Tomatine and tomatidine were identified by HPLC-DAD. The leaf extracts from the two varieties showed the highest flavonoids, chlorophyll, carotenoids, and total phenolics contents and the highest antioxidant activity determined by DPPH, ABTS, and ORAC. A positive correlation was observed between the antioxidant capacities of the extracts and the total phenolic, flavonoid, and chlorophyll contents. The Pitenza variety extracts inhibited the growth of pathogens such as E. coli O157:H7, Salmonella Typhimurium, Staphylococcus aureus, and Listeria ivanovii, yielding inhibition halos of 8.0 to 12.9 mm in diameter and MIC values of 12.5 to 3.125 mg/mL. These results suggest that tomato plant shows well potential as sources of various bioactive compounds, antioxidants, and antimicrobials. PMID:26609308

  4. Effects of certain polyphenols and extracts on furans and acrylamide formation in model system, and total furans during storage.

    Science.gov (United States)

    Oral, Rasim Alper; Dogan, Mahmut; Sarioglu, Kemal

    2014-01-01

    Using a glucose-glycine and asparagine-fructose system as a Maillard reaction model, the effects of seven polyphenols and solid phase extracts of three plants on the formation of furans and acrylamide were investigated. The polyphenols and extracts were used in biscuit formulation and acrylamide formation was observed. They were used for the storage of the glycine-glucose model system at three different temperatures. The addition of some of the extracts and polyphenols significantly decreased furan formation to different extents. All phenolic compounds and plant extracts decreased in the range of 30.8-85% in the model system except for oleuropein, and all of them decreased in the range of 10.3-19.2% in biscuit. Total furan formation was inhibited by caffeic acid, punicalagin, epicatechin, ECE and PPE during storage. This study evaluated and found the inhibitory effect on the formation of furans and acrylamide in Maillard reactions by the use of some plant extracts and polyphenols. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Structural Features and Potent Antidepressant Effects of Total Sterols and β-sitosterol Extracted from Sargassum horneri

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    Donghai Zhao

    2016-06-01

    Full Text Available The purified total sterols and β-sitosterol extracted from Sargassum horneri were evaluated for their antidepressant-like activity using the forced swim test (FST and tail suspension test (TST in mice. Total sterols and β-sitosterol significantly reduced the immobility time in the FST and TST. Total sterols were administered orally for 7 days at doses of 50, 100, and 200 mg/kg, and β-sitosterol was administered intraperitoneally at doses of 10, 20, and 30 mg/kg. β-sitosterol had no effect on locomotor activity in the open field test. In addition, total sterols and β-sitosterol significantly increased NE, 5-HT, and the metabolite 5-HIAA in the mouse brain, suggesting that the antidepressant-like activity may be mediated through these neurotransmitters.

  6. Determination of total phenolic content and antioxidant activitity of methanol extract of Maranta arundinacea L fresh leaf and tuber

    Science.gov (United States)

    Kusbandari, A.; Susanti, H.

    2017-11-01

    Maranta arundinacea L is one of herbaceous plants in Indonesia which have flavonoid content. Flavonoids has antioxidants activity by inhibition of free radical oxidation reactions. The study aims were to determination total phenolic content and antioxidant activity of methanol extract of fresh leaf and tuber of M. arundinacea L by UV-Vis spectrophotometer. The methanol extracts were obtained with maceration and remaseration method of fresh leaves and tubers. The total phenolic content was assayed with visible spectrophotometric using Folin Ciocalteau reagent. The antioxidant activity was assayed with 1,1-diphenyl-2-picrilhidrazil (DPPH) compared to gallic acid. The results showed that methanol extract of tuber and fresh leaf of M. arundinacea L contained phenolic compound with total phenolic content (TPC) in fresh tuber of 3.881±0.064 (% GAE) and fresh leaf is 6.518±0.163 (% b/b GAE). IC50 value from fresh tuber is 1.780±0.0005 μg/mL and IC50 fresh leaf values of 0.274±0.0004 μg/mL while the standard gallic acid is IC50 of 0.640±0.0002 μg/mL.

  7. Aloe vera extract reduces 8-oxo-2'-deoxyguanosine levels and improves total antioxidants in streptozotocin-induced diabetic rats

    Directory of Open Access Journals (Sweden)

    Wulan Christijanti

    2017-04-01

    Full Text Available Background Diabetes mellitus is a chronic disease caused by lack of insulin production in the pancreas or by insulin resistance, the disease being characterized by elevated blood glucose levels. Hyperglycemia in diabetes could lead to oxidative stress due to the rise in 8-oxo-2'-deoxyguanosine (8-oxo-dG levels and the decrease in levels of total antioxidant status (TAS. The purpose of this study was to assess the effect Aloe vera extract on 8-oxo-dG level and total antioxidant status in diabetic rat testis.   Methods This was an experimental laboratory study with 20 rat samples which were divided into 4 groups (1 control group and 3 treatment groups. Diabetes was induced in the rats by streptozotocin (STZ at 65 mg/kgBW. The diabetic rats were then treated for 28 days with Aloe vera extract at 0 mg (P0, 200 mg rind (P1, 200 mg pulp (P2, respectively. The level of 8 -oxo-dG was measured by ELISA and total antioxidant status with 2,2' -azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS. Data were analyzed with ANOVA and Least Significant Difference Advanced Test at P<0.05.   Results 8-Oxo-dG levels were significantly different between the control group and both P0 and P2, but not between the control group and P1. Among the treatment groups the 8-oxo-dG levels were significantly different. Mean total antioxidant status was significantly different between control and treatment groups, and also between treatment groups (p<0.05.   Conclusions Aloe vera extract reduced free radicals (level of 8-oxo-dG and increased the total antioxidant status in diabetic rat testis.

  8. Relationship between circulating microRNA-30c with total- and LDL-cholesterol, their circulatory transportation and effect of statins.

    Science.gov (United States)

    Sodi, Ravinder; Eastwood, Jarlath; Caslake, Muriel; Packard, Chris J; Denby, Laura

    2017-03-01

    Small non-coding microRNAs (miR) have important regulatory roles and are used as biomarkers of disease. We investigated the relationship between lipoproteins and circulating miR-30c, evaluated how they are transported in circulation and determined whether statins altered the circulating concentration of miR-30c. To determine the relationship between lipoproteins and circulating miR-30c, serum samples from 79 subjects recruited from a lipid clinic were evaluated. Ultracentrifugation and nanoparticle tracking analysis was used to evaluate the transportation of miR-30c in the circulation by lipoproteins and extracellular vesicles in three healthy volunteers. Using archived samples from previous studies, the effects of 40mg rosuvastatin (n=22) and 40mg pravastatin (n=24) on miR-30c expression was also examined. RNA extraction, reverse transcription-quantitative real-time polymerase chain reaction was carried out using standard procedures. When stratified according to total cholesterol concentration, there was increased miR-30c expression in the highest compared to the lowest tertile (p=0.035). There was significant positive correlation between miR-30c and total- (r=0.367; p=0.002) and LDL-cholesterol (r=0.391; p=0.001). We found that miR-30c was transported in both exosomes and on HDL3. There was a 3.8-fold increased expression of circulating miR-30c after pravastatin treatment for 1year (p=0.005) but no significant change with atorvastatin after 8weeks (p=0.145). This study shows for the first-time in humans that circulating miR-30c is significantly, positively correlated with total- and LDL-cholesterol implicating regulatory functions in lipid homeostasis. We show miR-30c is transported in both exosomes and on HDL3 and pravastatin therapy significantly increased circulating miR-30c expression adding to the pleiotropic dimensions of statins. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Determination of As concentration in earthworm coelomic fluid extracts by total-reflection X-ray fluorescence spectrometry

    Science.gov (United States)

    Allegretta, Ignazio; Porfido, Carlo; Panzarino, Onofrio; Fontanella, Maria Chiara; Beone, Gian Maria; Spagnuolo, Matteo; Terzano, Roberto

    2017-04-01

    Earthworms are often used as sentinel organisms to study As bioavailability in polluted soils. Arsenic in earthworms is mainly sequestrated in the coelomic fluids whose As content can therefore be used to asses As bioavalability. In this work, a method for determining As concentration in coelomic fluid extracts using total-reflection X-ray fluorescence spectrometry (TXRF) is presented. For this purpose coelomic fluid extracts from earthworms living in three polluted soils and one non-polluted (control) soil have been collected and analysed. A very simple sample preparation was implemented, consisting of a dilution of the extracts with polyvinyl alcohol (PVA) using a 1:8 ratio and dropwise deposition of the sample on the reflector. A detection limit of 0.2 μg/l and quantification limit of 0.6 μg/l was obtained in the diluted samples, corresponding to 2 μg/l and 6 μg/l in the coelomic fluid extracts, respectively. This allowed to quantify As concentration in coelomic fluids extracted from earthworms living in soils polluted with As at concentrations higher than 20 mg/kg (considered as a pollution threshold for agricultural soils). The TXRF method has been validated by comparison with As concentrations in standards and by analysing the same samples by ICP-MS, after acid digestion of the sample. The low limit of detection, the proven reliability of the method and the little sample preparation make TXRF a suitable, cost-efficient and "green" technique for the analysis of As in earthworm coelomic fluid extracts for bioavailability studies.

  10. Evaluation of total phenols, total flavonoids and antioxidant activity of the leaves crude extracts of locally grown pigeon pea traditionally used in Sultanate of Oman for the treatment of jaundice and diabetes

    Directory of Open Access Journals (Sweden)

    Asma Hamood Al-Saeedi

    2015-04-01

    Full Text Available Objective: To determine the total phenols, total flavonoids and evaluate the antioxidant activity of crude extracts from the leaves of pigeon pea native to Sultanate of Oman by a popular method. Methods: The powdered leaves samples from pigeon pea were used for extraction by maceration method with methanol solvent. The methanol free crude extract by maceration method was suspended in water and successively extracted with different polarities of solvents. The obtained crude extracts with different polarities were used for the determination of total phenols and flavonoids contents by using Folin-Ciocalteu reagent and aluminum chloride methods. The antioxidant activity of six crude extracts from pigeon pea was determined by α, α-diphenyl-β-picrylhydrazyl method. Results: The different polarities leaves crude extracts showed a significant amount of total phenols content ranging from 97.80 to 256.00 mg of GAE/g of crude extract. The same leaves crude extracts also showed good amount of total flavonoids content ranging from 1.38 to 8.51 mg QE/g plant material. The six crude extracts from the leaves displayed significant α, α- diphenyl-β-picrylhydrazyl free radical scavenging activity with highest value in chloroform extract followed by methanol, butanol, ethyl acetate, hexane and water crude extracts (98.13%, 89.26%, 88.82%, 86.41%, 79.95% and 69.44%, respectively. Conclusions: Leaves crude extracts from pigeon pea have high contents of total phenols and flavonoids. In this regards, it could be used as a medicine for the treatment of different diseases.

  11. Comparison of inductively coupled plasma mass spectrometry and colorimetric determination of total and extractable phosphorus in soils

    International Nuclear Information System (INIS)

    Ivanov, Krasimir; Zaprjanova, Penka; Petkova, Milena; Stefanova, Violeta; Kmetov, Veselin; Georgieva, Deyana; Angelova, Violina

    2012-01-01

    The most widely used method for determination of total phosphorus in soils is perchloric acid digestion, followed by a colorimetric assay to measure the concentration of P in solution. The first part of this study compares an alternative digestion method, using aqua regia (ISO 11466 and EPA Method 3052), with perchloric acid digestion procedure, and also compares inductively coupled plasma mass spectroscopy (ICP-MS) with colorimetry for the measurement of P on the basis of five internationally certified standard soils and 20 real-life soils with widely different extractability of phosphorus. The phosphorus concentration was determined by means of the reduced phosphomolybdenum blue and ICP-MS. The relationship between methods has been examined statistically. Good agreement of the results from colorimetry and ICP-MS was established for all certified soils. The microwave-assisted digestion with aqua regia was comparable, both in precision and accuracy, with the hot plate aqua regia method. The phosphorus concentration found with the HF + HClO 4 digestion method was in good agreement with the certified mean values, while the superiority in extracting phosphorus, when compared to other methods, was obvious. Soil testing for plant-available phosphorus in Bulgaria and many European countries is most commonly conducted using acid Ca-lactate extraction (Egner–Riehm test) and alkaline sodium bicarbonate extraction (BDS ISO 11263:2002), based on Olsen test, followed by a colorimetric assay to measure the concentration of P in solution. The second part of this study reports the differences between Egner–Riehm test and BDS ISO 11263:2002 measured colorimetrically and by ICP-MS. Fifty soils were selected from South Bulgaria to represent a wide range of soil properties. It was established that ICP-MS consistently yielded significantly higher P concentrations than the colorimetric method in both extraction tests, and the relative differences were greatest in soils with lower P

  12. Comparison of inductively coupled plasma mass spectrometry and colorimetric determination of total and extractable phosphorus in soils

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, Krasimir, E-mail: kivanov1@abv.bg [Department of Chemistry, University of Agriculture, Plovdiv (Bulgaria); Zaprjanova, Penka [Tobacco and Tobacco Products Institute, Plovdiv (Bulgaria); Petkova, Milena [Department of Chemistry, University of Agriculture, Plovdiv (Bulgaria); Stefanova, Violeta; Kmetov, Veselin; Georgieva, Deyana [Department of Analytical Chemistry, Plovdiv University ' Paisii Hilendarski,' Plovdiv (Bulgaria); Angelova, Violina [Department of Chemistry, University of Agriculture, Plovdiv (Bulgaria)

    2012-05-15

    The most widely used method for determination of total phosphorus in soils is perchloric acid digestion, followed by a colorimetric assay to measure the concentration of P in solution. The first part of this study compares an alternative digestion method, using aqua regia (ISO 11466 and EPA Method 3052), with perchloric acid digestion procedure, and also compares inductively coupled plasma mass spectroscopy (ICP-MS) with colorimetry for the measurement of P on the basis of five internationally certified standard soils and 20 real-life soils with widely different extractability of phosphorus. The phosphorus concentration was determined by means of the reduced phosphomolybdenum blue and ICP-MS. The relationship between methods has been examined statistically. Good agreement of the results from colorimetry and ICP-MS was established for all certified soils. The microwave-assisted digestion with aqua regia was comparable, both in precision and accuracy, with the hot plate aqua regia method. The phosphorus concentration found with the HF + HClO{sub 4} digestion method was in good agreement with the certified mean values, while the superiority in extracting phosphorus, when compared to other methods, was obvious. Soil testing for plant-available phosphorus in Bulgaria and many European countries is most commonly conducted using acid Ca-lactate extraction (Egner-Riehm test) and alkaline sodium bicarbonate extraction (BDS ISO 11263:2002), based on Olsen test, followed by a colorimetric assay to measure the concentration of P in solution. The second part of this study reports the differences between Egner-Riehm test and BDS ISO 11263:2002 measured colorimetrically and by ICP-MS. Fifty soils were selected from South Bulgaria to represent a wide range of soil properties. It was established that ICP-MS consistently yielded significantly higher P concentrations than the colorimetric method in both extraction tests, and the relative differences were greatest in soils with lower

  13. Evaluation of extracts and essential oil from Callistemon viminalis leaves: antibacterial and antioxidant activities, total phenolic and flavonoid contents.

    Science.gov (United States)

    Salem, Mohamed Z M; Ali, Hayssam M; El-Shanhorey, Nader A; Abdel-Megeed, Ahmed

    2013-10-01

    To investigate antioxidant and antibacterial activities of Callistemon viminalis (C. viminalis) leaves. The essential oil of C. viminalis leaves obtained by hydro-distillation was analyzed by GC/MS. Different extracts were tested for total phenolic and flavonoid contents and in vitro antioxidant (DPPH assay) and antibacterial (agar disc diffusion and 96-well micro-plates methods) actives. Fourteen components were identified in the essential oil, representing 98.94% of the total oil. The major components were 1,8-cineole (64.53%) and α-pinene (9.69%). Leaf essential oil exhibited the highest antioxidant activity of (88.60±1.51)% comparable to gallic acid, a standard compound [(80.00±2.12)%]. Additionally, the biggest zone of inhibitions against the studied bacterial strains was observed by the essential oil when compared to the standard antibiotic (tetracycline). The crude methanol extract and ethyl acetate fraction had a significant antibacterial activity against the tested bacterial strains. It can be suggested that C. viminalis is a great potential source of antibacterial and antioxidant compounds useful for new antimicrobial drugs from the natural basis. The present study revealed that the essential oil as well as the methanol extracts and ethyl acetate fraction of C. viminalis leaves exhibited highly significant antibacterial activity against the tested bacterial strains. Copyright © 2013 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

  14. Extraction and purification of total flavonoids from pine needles of Cedrus deodara contribute to anti-tumor in vitro.

    Science.gov (United States)

    Shi, Xiaofeng; Liu, Dongyan; Zhang, Junmin; Hu, Pengbin; Shen, Wei; Fan, Bin; Ma, Quhuan; Wang, Xindi

    2016-07-26

    Cedrus deodara is one of the traditional Chinese medicinal herbs that exhibits a line of biological activities. The current study extracted the total flavonoids from the pine needles of Cedrus deodara (TFPNCD), and investigated its anti-cancer effects in tumor cell lines. The total flavonoids was extracted from pine needles of Cedrus deodara by ethanol hot refluxing and purified by HPD722 macroporous resin. The contents of total flavonoids and the active ingredients of TFPNCD were analyzed through UV and HPLC. MTT assay was used to investigate its inhibitory effect on tumor cell lines. The flow cytometry was employed to determine the apoptosis and cell cycle distribution after treated TFPNCD on HepG2 cells. The TFPNCD, in which the contents of total flavonoid reached up to 54.28 %, and the major ingredients of myricetin, quercetin, kaempferol and isorhamnetin in TFPNCD were 1.89, 2.01, 2.94 and 1.22 mg/g, respectively. The MTT assays demonstrated that TFPNCD inhibited the growth of HepG2 cells in a dose-dependent manner, with the IC50 values of 114.12 μg/mL. By comparison, TFPNCD inhibited the proliferation to a less extent in human cervical carcinoma HeLa, gastric cancer MKN28 cells, glioma SHG-44 cells and lung carcinoma A549 than HepG2 cells. We found that even at the lower doses, the total flavonoids effectively inhibited the proliferation of HepG2 cells. Comparison of IC50 values implicated that HepG2 cells might be more sensitive to the treatment with total flavonoids. TFPNCD was able to increase the population of HepG2 cells in G0 /G1 phase. Meanwhile, TFPNCD treatment increased the percentage of apoptotic HepG2 cells. These data suggested that TFPNCD might have therapeutic potential in cancer through the regulation of cell cycle and apoptosis.

  15. Ultrasound-assisted extraction for total sulphur measurement in mine tailings

    International Nuclear Information System (INIS)

    Khan, Adnan Hossain; Shang, Julie Q.; Alam, Raquibul

    2012-01-01

    Highlights: ► We develop a total sulphur measuring procedure of mine tailings. ► Ultrasound is used in the sample pre-treatment process. ► Full factorial design is applied to identify the best level of effecting factors. - Abstract: A sample preparation method for percentage recovery of total sulphur (%S) in reactive mine tailings based on ultrasound-assisted digestion (USAD) and inductively coupled plasma-optical emission spectroscopy (ICP-OES) was developed. The influence of various methodological factors was screened by employing a two-level and three-factor (2 3 ) full factorial design and using KZK-1, a sericite schist certified reference material (CRM), to find the optimal combination of studied factors and %S. Factors such as the sonication time, temperature and acid combination were studied, with the best result identified as 20 min of sonication, 80 °C temperature and 1 ml of HNO 3 :1 ml of HCl, which can achieve 100% recovery for the selected CRM. Subsequently a fraction of the 2 3 full factorial design was applied to mine tailings. The percentage relative standard deviation (%RSD) for the ultrasound method is less than 3.0% for CRM and less than 6% for the mine tailings. The investigated method was verified by X-ray diffraction analysis. The USAD method compared favorably with existing methods such as hot plate assisted digestion method, X-ray fluorescence and LECO™-CNS method.

  16. Mechanical properties and total hydroxycinnamic derivative release of starch/glycerol/Melissa officinalis extract films

    Directory of Open Access Journals (Sweden)

    Letícia Mello Rechia

    2010-09-01

    Full Text Available The aim of this study was to investigate the mechanical properties of starch/glycerol/Melissa officinalis, a topical drug delivery system for labial herpes treatment. Four films were prepared with different concentrations of starch, glycerol, and Melissa officinalis extract. The results revealed that increasing the glycerol concentration in the film reduced elasticity modulus and tensile strength, exhibiting a plasticizing effect. The increase in free volume resulted in increased release of hydroxycinnamic derivatives expressed as rosmarinic acid.O objetivo deste trabalho foi estudar as propriedades mecânicas e o mecanismo de liberação de um sistema tópico de liberação prolongada para o tratamento do Herpes labial a partir de filmes de amido/glicerol/extrato de Melissa officinalis, planta com comprovada atividade antiviral. Foram obtidos quatro filmes poliméricos com diferentes concentrações de amido, glicerol e extrato de Melissa officinalis os quais foram caracterizados mecanicamente e determinado o perfil de liberação de derivados hidroxicinâmicos. Os resultados demonstraram que o aumento da concentração de glicerol no filme produz uma redução no módulo de elasticidade e na tensão de deformação como conseqüência do efeito plastificante. O aumento no volume livre do polímero resultou em aumento da liberação dos derivados hidroxicinâmicos expressos como ácido rosmarínico.

  17. High-throughput sequencing of nematode communities from total soil DNA extractions

    DEFF Research Database (Denmark)

    Sapkota, Rumakanta; Nicolaisen, Mogens

    2015-01-01

    nematodes without the need for enrichment was developed. Using this strategy on DNA templates from a set of 22 agricultural soils, we obtained 64.4% sequences of nematode origin in total, whereas the remaining sequences were almost entirely from other metazoans. The nematode sequences were derived from...... in previous sequence-based studies are not nematode specific but also amplify other groups of organisms such as fungi and plantae, and thus require a nematode enrichment step that may introduce biases. Results: In this study an amplification strategy which selectively amplifies a fragment of the SSU from...... a broad taxonomic range and most sequences were from nematode taxa that have previously been found to be abundant in soil such as Tylenchida, Rhabditida, Dorylaimida, Triplonchida and Araeolaimida. Conclusions: Our amplification and sequencing strategy for assessing nematode diversity was able to collect...

  18. Ultrasound-assisted extraction for total sulphur measurement in mine tailings

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Adnan Hossain, E-mail: ad_li2@yahoo.com [Department of Civil and Environmental Engineering, University of Western Ontario (Canada); Shang, Julie Q.; Alam, Raquibul [Department of Civil and Environmental Engineering, University of Western Ontario (Canada)

    2012-10-15

    Highlights: Black-Right-Pointing-Pointer We develop a total sulphur measuring procedure of mine tailings. Black-Right-Pointing-Pointer Ultrasound is used in the sample pre-treatment process. Black-Right-Pointing-Pointer Full factorial design is applied to identify the best level of effecting factors. - Abstract: A sample preparation method for percentage recovery of total sulphur (%S) in reactive mine tailings based on ultrasound-assisted digestion (USAD) and inductively coupled plasma-optical emission spectroscopy (ICP-OES) was developed. The influence of various methodological factors was screened by employing a two-level and three-factor (2{sup 3}) full factorial design and using KZK-1, a sericite schist certified reference material (CRM), to find the optimal combination of studied factors and %S. Factors such as the sonication time, temperature and acid combination were studied, with the best result identified as 20 min of sonication, 80 Degree-Sign C temperature and 1 ml of HNO{sub 3}:1 ml of HCl, which can achieve 100% recovery for the selected CRM. Subsequently a fraction of the 2{sup 3} full factorial design was applied to mine tailings. The percentage relative standard deviation (%RSD) for the ultrasound method is less than 3.0% for CRM and less than 6% for the mine tailings. The investigated method was verified by X-ray diffraction analysis. The USAD method compared favorably with existing methods such as hot plate assisted digestion method, X-ray fluorescence and LECO Trade-Mark-Sign -CNS method.

  19. A study on the total phenols content and antioxidant activity of essential oil and different solvent extracts of endemic plant Merremia borneensis

    Directory of Open Access Journals (Sweden)

    M. Amzad Hossain

    2015-01-01

    Full Text Available This study is planned to determine the antioxidant activity and total phenols content of the essential oil and different solvent extracts of the endemic plant Merremia borneensis. The antioxidant activities of the extracts were examined by three different methods, DPPH, β-carotene and reducing power assays. In all methods, aqueous ethanol extract exhibited a higher activity potential than that of other extracts (hexane, chloroform, ethyl acetate and butanol and the essential oil. As assumed, the amount of total phenolics was very high in this extract. Chloroform extract has been found to be rich in flavonoids. A positive result was observed between the antioxidant activity potential and total flavonoid levels of the extracts.

  20. Total Contents and Sequential Extraction of Heavy Metals in Soils Irrigated with Wastewater, Akaki, Ethiopia

    Science.gov (United States)

    Fitamo, Daniel; Itana, Fisseha; Olsson, Mats

    2007-02-01

    The Akaki River, laden with untreated wastes from domestic, industrial, and commercial sources, serves as a source of water for irrigating vegetable farms. The purpose of this study is to identify the impact of waste-water irrigation on the level of heavy metals and to predict their potential mobility and bioavailability. Zn and V had the highest, whereas Hg the lowest, concentrations observed in the soils. The average contents of As, Co, Cr, Cu, Ni, Zn, V, and Hg of both soils; and Pb and Se from Fluvisol surpassed the mean + 2 SD of the corresponding levels reported for their uncontaminated counterparts. Apparently, irrigation with waste water for the last few decades has contributed to the observed higher concentrations of the above elements in the study soils (Vertisol and Fluvisol) when compared to uncontaminated Vertisol and Fluvisol. On the other hand, Vertisol accommodated comparatively higher average levels of Cr, Cu, Ni, Zn, etc V, and Cd, whereas high contents of Pb and Se were observed in Fluvisol. Alternatively, comparable levels of Co and Hg were found in either soil. Except for Ni, Cr, and Cd in contaminated Vertisol, heavy metals in the soils were not significantly affected by the depth (0-20 and 30-50 cm). When the same element from the two soils was compared, the levels of Cr, Cu, Ni, Pb, Se, Zn, V, Cd at 0-20 cm; and Cr, Ni, Cu, Cd, and Zn at 30-50 cm were significantly different. Organic carbon (in both soils), CEC (Fluvisol), and clay (Vertisol) exhibited significant positive correspondences with the total heavy metal levels. Conversely, Se and Hg contents revealed perceptible associations with carbonate and pH. The exchangeable fraction was dominated by Hg and Cd, whereas the carbonate fraction was abounded with Cd, Pb, and Co. conversely, V and Pb displayed strong affinity to reducible fraction, where as Cr, Cu, Zn, and Ni dominated the oxidizable fraction. Cr, Hg, Se, and Zn (in both soils) showed preference to the residual fraction

  1. Anthocyanin Characterization, Total Phenolic Quantification and Antioxidant Features of Some Chilean Edible Berry Extracts

    Directory of Open Access Journals (Sweden)

    Anghel Brito

    2014-07-01

    Full Text Available The anthocyanin composition and HPLC fingerprints of six small berries endemic of the VIII region of Chile were investigated using high resolution mass analysis for the first time (HR-ToF-ESI-MS. The antioxidant features of the six endemic species were compared, including a variety of blueberries which is one of the most commercially significant berry crops in Chile. The anthocyanin fingerprints obtained for the fruits were compared and correlated with the antioxidant features measured by the bleaching of the DPPH radical, the ferric reducing antioxidant power (FRAP, the superoxide anion scavenging activity assay (SA, and total content of phenolics, flavonoids and anthocyanins measured by spectroscopic methods. Thirty one anthocyanins were identified, and the major ones were quantified by HPLC-DAD, mostly branched 3-O-glycosides of delphinidin, cyanidin, petunidin, peonidin and malvidin. Three phenolic acids (feruloylquinic acid, chlorogenic acid, and neochlorogenic acid and five flavonols (hyperoside, isoquercitrin, quercetin, rutin, myricetin and isorhamnetin were also identified. Calafate fruits showed the highest antioxidant activity (2.33 ± 0.21 μg/mL in the DPPH assay, followed by blueberry (3.32 ± 0.18 μg/mL, and arrayán (5.88 ± 0.21, respectively.

  2. Ultrasound-assisted extraction for total sulphur measurement in mine tailings.

    Science.gov (United States)

    Khan, Adnan Hossain; Shang, Julie Q; Alam, Raquibul

    2012-10-15

    A sample preparation method for percentage recovery of total sulphur (%S) in reactive mine tailings based on ultrasound-assisted digestion (USAD) and inductively coupled plasma-optical emission spectroscopy (ICP-OES) was developed. The influence of various methodological factors was screened by employing a two-level and three-factor (2(3)) full factorial design and using KZK-1, a sericite schist certified reference material (CRM), to find the optimal combination of studied factors and %S. Factors such as the sonication time, temperature and acid combination were studied, with the best result identified as 20 min of sonication, 80°C temperature and 1 ml of HNO(3):1 ml of HCl, which can achieve 100% recovery for the selected CRM. Subsequently a fraction of the 2(3) full factorial design was applied to mine tailings. The percentage relative standard deviation (%RSD) for the ultrasound method is less than 3.0% for CRM and less than 6% for the mine tailings. The investigated method was verified by X-ray diffraction analysis. The USAD method compared favorably with existing methods such as hot plate assisted digestion method, X-ray fluorescence and LECO™-CNS method. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Total phytosterol content in drug materials and extracts from roots of Acanthospermum hispidum by UV-VIS spectrophotometry

    Directory of Open Access Journals (Sweden)

    Larissa B. D. C. Araújo

    Full Text Available Acanthospermum hispidum DC., Asteraceae, is widely used in folk medicine in Brazil to treat respiratory diseases; this biological property has been attributed to its phytosterol content. This study evaluated the spectrophotometric assay method to quantify the total phytosterol content in raw materials and extracts from roots of A. hispidum. The procedure was based on the quantification at 625 nm after the Liebermann-Burchard reaction. The method was evaluated for linearity, repeatability, intermediate precision, accuracy and robustness. The date indicated that the procedure is a valid analytical tool for materials and herbal derivatives from A. hispidum.

  4. Investigating of the antimicrobial effect of total extract of Tribulus terrestris against some gram positive and negative bacteria and candida spp.

    Directory of Open Access Journals (Sweden)

    Mojdeh Hakemi Vala

    2014-08-01

    Full Text Available Introduction: In the recent years, due to the wide spread of resistant bacteria on one side and several different reports about the side effects of chemical drugs on the other side, vast researches on the medicinal plants have been started. In this study, antimicrobial effect of total extract of Tribulus terrestris L. and its fraction containing Benzoxazine derivative (Terresoxazine was studied for the first time in Iran.Materials and methods: Total aqueous extract of aerial parts of the plant was prepared and in order to separate the components of aqueous extract, liquid/liquid extraction with Petroleum ether was used. Formation of three layers was the result of this extraction. Layers included water fraction, Petroleum ether fraction and a third layer which was formed at the interface of water and petroleum ether. LC/MS system proved the existence of Benzixazine derivative in the water fraction and the thirds fraction. Antimicrobial effects of total extract, water fraction and the third fraction (which were the layers formed after the extraction process were examined against 10 Gram positive and negative and candida spp by cup plate method and Disk diffusion method. Also, the MIC and MBC were determined by micro dilution method.Results: Of 8 evaluated bacteria and 2 Candida spp, the total extract showed antibacterial effect only against E.coli, P.aeruginosa and B.subtilis. Size of the zone of inhibitation increased with increasing the concentration of the extract. Fraction containing Benzoxazine derivative had no effect against tested microbes. MIC and MBC determination showed that B.subtilis had the least sensitivity to the total extract, comparing to other microorganisms. Besides, comparing the zone of inhibitation of Penicillin 200 mg/ml and the zone of inhibitation of the total aqueous extract shows that the solution of total extract in water with 1000 mg/ml concentration and the solution of total extract in DMSO10% with 750 mg/ml density

  5. Intake of branched-chain amino acids influences the levels of MAFbx mRNA and MuRF-1 total protein in resting and exercising human muscle.

    Science.gov (United States)

    Borgenvik, Marcus; Apró, William; Blomstrand, Eva

    2012-03-01

    Resistance exercise and amino acids are two major factors that influence muscle protein turnover. Here, we examined the effects of resistance exercise and branched-chain amino acids (BCAA), individually and in combination, on the expression of anabolic and catabolic genes in human skeletal muscle. Seven subjects performed two sessions of unilateral leg press exercise with randomized supplementation with BCAA or flavored water. Biopsies were collected from the vastus lateralis muscle of both the resting and exercising legs before and repeatedly after exercise to determine levels of mRNA, protein phosphorylation, and amino acid concentrations. Intake of BCAA reduced (P exercising legs, respectively. The level of MuRF-1 mRNA was elevated (P exercising leg two- and threefold under the placebo and BCAA conditions, respectively, whereas MuRF-1 total protein increased by 20% (P exercising muscle. In conclusion, BCAA ingestion reduced MAFbx mRNA and prevented the exercise-induced increase in MuRF-1 total protein in both resting and exercising leg. Further-more, resistance exercise differently influenced MAFbx and MuRF-1 mRNA expression, suggesting both common and divergent regulation of these two ubiquitin ligases.

  6. Antioxidant activity, phenolic and flavonoids total of ethanolic extract of Ipomoea batata L. leaves (white, yellow, orange, and purple)

    Science.gov (United States)

    Dewijanti, Indah Dwiatmi; Banjarnahor, Sofna D.; Triyuliani, Maryani, Faiza; Meilawati, Lia

    2017-11-01

    Antioxidant activity, phenolic and total flavonoids from sweet potato ethanol extract (Ipomea batatas L.) of different varieties (white, yellow, orange and purple) were studied. Sweet potatoes were collected from Research Centre for Chemistry. Sweet potato leaves have been used for numerous oxidative-associated diseases such as cancer, allergy, aging, HIV and cardiovascular. 1,1-diphenyl-2-picryl hydrazyl (DPPH) method was used to investigate antioxidant activity in leaves, in which the yellow and purple varieties showed the highest and the lowest scavenging activities of 47.65 µg/ ml (IC50) and 87.402 µg/ ml (IC50), respectively. In this study, the yellow leaves showed the highest concentrations of total phenolic and flavonoids contents at 11.293 µg/g and 44.963 µg/g, respectively. Therefore, sweet potato leaves can be used as a prospective natural antioxidant.

  7. Optimization of ultrasonic-assisted extraction of total carotenoids from peach palm fruit (Bactris gasipaes) by-products with sunflower oil using response surface methodology.

    Science.gov (United States)

    Ordóñez-Santos, Luis Eduardo; Pinzón-Zarate, Lina Ximena; González-Salcedo, Luis Octavio

    2015-11-01

    The present study reports on the extraction of total carotenoids from peach palm fruit by-products with sunflower oil. Response surface methodology (RSM) was used to investigate the effect of process variables on the ultrasound-assisted extraction (UAE). Three independent variables including ultrasonic intensity (764-1528, W/m(2)), temperature (25-45°C), and the extraction time (10-30 min). According to the results, the optimal UAE condition was obtained with an ultrasonic intensity of 1528 W/m(2), extraction temperature of 35°C and extraction time of 30 min. At these conditions, extraction maximum extraction of total carotenoids as 163.47 mg/100 g dried peel. The experimental values under optimal condition were in good consistent with the predicted values. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Splicing of a C. elegans myosin pre-mRNA in a human nuclear extract

    Energy Technology Data Exchange (ETDEWEB)

    Ogg, S C; Anderson, P; Wickens, M P [Univ. of Wisconsin, Madison (USA)

    1990-01-11

    Splicing of mammalian introns requires that the intron possess at least 80 nucleotides. This length requirement presumably reflects the constraints of accommodating multiple snRNPs simultaneously in the same intro. In the free-living nematode, C. elegans, introns typically are 45 to 55 nucleotides in length. In this report, the authors determine whether C. elegans introns can obviate the mammalian length requirement by virtue of their structure or sequence. They demonstrate that a 53 nucleotide intron from the unc-54 gene of C. elegans does not undergo splicing in a mammalian (HeLa) nuclear extract. However, insertion of 31 nucleotides of foreign, prokaryotic sequence into the same intron results in efficient splicing. The observed splicing proceeds by the same two-step mechanism observed with mammalian introns, and exploits the same 3{prime} and 5{prime} sites as are used in C. elegans. The branch point used lies in the inserted sequences. They conclude that C. elegans splicing components are either fewer in number or smaller than their mammalian counterparts.

  9. A rapid silica spin column-based method of RNA extraction from fruit trees for RT-PCR detection of viruses.

    Science.gov (United States)

    Yang, Fan; Wang, Guoping; Xu, Wenxing; Hong, Ni

    2017-09-01

    Efficient recovery of high quality RNA is very important for successful RT-PCR detection of plant RNA viruses. High levels of polyphenols and polysaccharides in plant tissues can irreversibly bind to and/or co-precipitate with RNA, which influences RNA isolation. In this study, a silica spin column-based RNA isolation method was developed by using commercially available silica columns combined with the application of a tissue lysis solution, and binding and washing buffers with high concentration guanidinium thiocyanate (GuSCN, 50% w/v), which helps remove plant proteins, polysaccharides and polyphenolic compounds. The method was successfully used to extract high quality RNA from citrus (Citrus aurantifolia), grapevine (Vitis vinifera), peach (Prunus persica), pear (Pyrus spp.), taro (Colocosia esculenta) and tobacco (Nicotiana benthamiana) samples. The method was comparable to conventional CTAB method in RNA isolation efficiency, but it was more sample-adaptable and cost-effective than commercial kits. High quality RNA isolated using silica spin column-based method was successfully used for the RT-PCR and/or multiplex RT-PCR amplification of woody fruit tree viruses and a viroid. The study provided a useful tool for the detection and characterization of plant viruses. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. A need for standardization in drinking water analysis – an investigation of DNA extraction procedure, primer choice and detection limit of 16S rRNA amplicon sequencing

    DEFF Research Database (Denmark)

    Brandt, Jakob; Nielsen, Per Halkjær; Albertsen, Mads

    have been made to illuminate the effects specifically related to bacterial communities in drinking water. In this study, we investigated the impact of the DNA extraction and primer choice on the observed community structure, and we also estimated the detection limit of the 16S rRNA amplicon sequencing...

  11. Olea europaea leaf extract improves the treatment response of GBM stem cells by modulating miRNA expression.

    Science.gov (United States)

    Tezcan, Gulcin; Tunca, Berrin; Bekar, Ahmet; Budak, Ferah; Sahin, Saliha; Cecener, Gulsah; Egeli, Unal; Taskapılıoglu, Mevlut Ozgur; Kocaeli, Hasan; Tolunay, Sahsine; Malyer, Hulusi; Demir, Cevdet; Tumen, Gulendam

    2014-01-01

    The stem-like cells of Glioblastoma multiforme (GBM) tumors (GSCs) are one of the important determinants of recurrence and drug resistance. The aims of the current study were to evaluate the anticancer effect of Olea europaea leaf extract (OLE) on GBM cell lines, the association between OLE and TMZ responses, and the effect of OLE and the OLE-TMZ combination in GSCs and to clarify the molecular mechanism of this effect on the expression of miRNAs related to cell death. The anti-proliferative activity of OLE and the effect of the OLE-TMZ combination were tested in the T98G, U-138MG and U-87MG GBM cell lines using WST-1 assay. The mechanism of cell death was analyzed with Annexin V/FITC and TUNEL assays. The effects of OLE on the expression levels of miR-181b, miR-153, miR-145 and miR-137 and potential mRNA targets were analyzed in GSCs using RT-qPCR. OLE exhibited anti-proliferative effects via apoptosis and necrosis in the GBM cell lines. In addition, OLE significantly induced the expression of miR-153, miR-145, and miR-137 and decreased the expression of the target genes of these miRNAs in GSCs (p GBM cells with different TMZ responses, and this effect is synergistically increased when the cells are treated with a combination of OLE and TMZ. This is the first study to indicate that OLE may interfere with the pluripotency of GSCs by modulating miRNA expression. Further studies are required, but we suggest that OLE may have a potential for advanced therapeutic cancer drug studies in GBM.

  12. A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts.

    Science.gov (United States)

    Hoover, Malachia; Adamian, Yvess; Brown, Mark; Maawy, Ali; Chang, Alexander; Lee, Jacqueline; Gharibi, Armen; Katz, Matthew H; Fleming, Jason; Hoffman, Robert M; Bouvet, Michael; Doebler, Robert; Kelber, Jonathan A

    2017-01-24

    Next-generation sequencing (NGS) can identify and validate new biomarkers of cancer onset, progression and therapy resistance. Substantial archives of formalin-fixed, paraffin-embedded (FFPE) cancer samples from patients represent a rich resource for linking molecular signatures to clinical data. However, performing NGS on FFPE samples is limited by poor RNA purification methods. To address this hurdle, we developed an improved methodology for extracting high-quality RNA from FFPE samples. By briefly integrating a newly-designed micro-homogenizing (mH) tool with commercially available FFPE RNA extraction protocols, RNA recovery is increased by approximately 3-fold while maintaining standard A260/A280 ratios and RNA quality index (RQI) values. Furthermore, we demonstrate that the mH-purified FFPE RNAs are longer and of higher integrity. Previous studies have suggested that pancreatic ductal adenocarcinoma (PDAC) gene expression signatures vary significantly under in vitro versus in vivo and in vivo subcutaneous versus orthotopic conditions. By using our improved mH-based method, we were able to preserve established expression patterns of KRas-dependency genes within these three unique microenvironments. Finally, expression analysis of novel biomarkers in KRas mutant PDAC samples revealed that PEAK1 decreases and MST1R increases by over 100-fold in orthotopic versus subcutaneous microenvironments. Interestingly, however, only PEAK1 levels remain elevated in orthotopically grown KRas wild-type PDAC cells. These results demonstrate the critical nature of the orthotopic tumor microenvironment when evaluating the clinical relevance of new biomarkers in cells or patient-derived samples. Furthermore, this new mH-based FFPE RNA extraction method has the potential to enhance and expand future FFPE-RNA-NGS cancer biomarker studies.

  13. Use of 60Co gamma radiation in increased levels of total polyphenol extracts of bark of Schinus terebinthifolius Raddi

    International Nuclear Information System (INIS)

    Santos, Gustavo H.F.; Silva, Edvane B.; Silva, Hianna A.M.F.; Amorin, Elba L.C.; Peixoto, Tadeu J.S.; Yara, Ricardo; Lima, Claudia S.A.

    2013-01-01

    Schinus terebinthifolius Raddi (Anacardiaceae) is well known as sources of phenolic compounds. Known as mastic pepper, red pepper tree is a plant native to midsize coast of Brazil. Some of its structures have proven antibacterial, anti-inflammatory, antifungal and healing. The aim of this study was to evaluate the difference in the phenol contents of crude extracts that were measured after irradiating the barks of S. terebinthifolius using gamma radiation from 60 Co. The crude extract were divided into a control group and eight experimental groups, which were separated based on the doses of gamma radiation to which they were exposed: 2.5, 5.0, 7.5, 10.0, 12.5, 15.0, 20.0 and 50.0 kGy (Assays were performed in triplicate). The results allow observe that gamma radiation promoted in extracts of bark of S. terebinthifolius, many percents increase (p> 0.05) of total polyphenol content between 2.5 kGy (41.93%) and 50.0 kGy (44.52%) compared to 0 kGy (30.07%), with the same gradual to 10.0 kGy, and reaching peak maximum at 10.0 kGy (68.44%). However, the study puts the process of gamma radiation from 60 Co as an alternative significant increase in the percentage of some natural substances of plant material, and subsequently contribute to the augmentation of various therapeutic applications to which they are assigned. (author)

  14. Use of {sup 60}Co gamma radiation in increased levels of total polyphenol extracts of bark of Schinus terebinthifolius Raddi

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Gustavo H.F.; Silva, Edvane B.; Silva, Hianna A.M.F.; Amorin, Elba L.C.; Peixoto, Tadeu J.S.; Yara, Ricardo; Lima, Claudia S.A., E-mail: santosghf@hotmail.com, E-mail: edvborges@yahoo.com, E-mail: amdemelo@hotmail.com, E-mail: claudia.salima@gmail.com, E-mail: ricardo.yara@gmail.com, E-mail: tadeu1903@yahoo.com.br, E-mail: elba@ufpe.br [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil)

    2013-07-01

    Schinus terebinthifolius Raddi (Anacardiaceae) is well known as sources of phenolic compounds. Known as mastic pepper, red pepper tree is a plant native to midsize coast of Brazil. Some of its structures have proven antibacterial, anti-inflammatory, antifungal and healing. The aim of this study was to evaluate the difference in the phenol contents of crude extracts that were measured after irradiating the barks of S. terebinthifolius using gamma radiation from {sup 60}Co. The crude extract were divided into a control group and eight experimental groups, which were separated based on the doses of gamma radiation to which they were exposed: 2.5, 5.0, 7.5, 10.0, 12.5, 15.0, 20.0 and 50.0 kGy (Assays were performed in triplicate). The results allow observe that gamma radiation promoted in extracts of bark of S. terebinthifolius, many percents increase (p> 0.05) of total polyphenol content between 2.5 kGy (41.93%) and 50.0 kGy (44.52%) compared to 0 kGy (30.07%), with the same gradual to 10.0 kGy, and reaching peak maximum at 10.0 kGy (68.44%). However, the study puts the process of gamma radiation from {sup 60}Co as an alternative significant increase in the percentage of some natural substances of plant material, and subsequently contribute to the augmentation of various therapeutic applications to which they are assigned. (author)

  15. Protective effect of Asparagus racemosus root extract against lethal total - body electron beam radiation induced damage in Swiss albino mice

    International Nuclear Information System (INIS)

    Sharmila, K.P.; Bhandary, B. Satheesh Kumar; Suchetha Kumari, N.; Bhat, Vadish S.; Shetty, Jayaram; Peter, Alex John; Jose, Jerish M.; Fernandes, Ronald

    2016-01-01

    To investigate the protective effect of Asparagus Racemosus Root ethanolic extract (ARE) in Swiss albino mice against acute lethal total - body Electron beam irradiation. Swiss Albino mice were used for the assessment of radiation induced sickness and 30 day survival analysis. Survival studies were determined using the Kaplan-Meier survival curves. The maximum survival was observed in the experimental mice pretreated with 200 mg/kg.b.wt. of ARE which also reduced the radiation sickness characteristics. This dose was considered as an optimal dose for radioprotection. Treatment of mice with ARE before irradiation delayed the onset of mortality as compared with the untreated irradiated controls. Present findings demonstrate the potential of ARE in mitigating radiation-induced mortality, which may be attributed to its free radical scavenging and increased antioxidant potential

  16. In vitro total phenolics, flavonoids contents and antioxidant activity of essential oil, various organic extracts from the leaves of tropical medicinal plant Tetrastigma from Sabah.

    Science.gov (United States)

    Hossain, M Amzad; Shah, Muhammad Dawood; Gnanaraj, Charles; Iqbal, Muhammad

    2011-09-01

    To detect the in vitro total phenolics, flavonoids contents and antioxidant activity of essential oil, various organic extracts from the leaves of tropical medicinal plant Tetrastigma from Sabah. The dry powder leaves of Tetrastigma were extracted with different organic solvent such as hexane, ethyl acetate, chloroform, butanol and aqueous methanol. The total phenolic and total flavonoids contents of the essential oil and various organic extracts such as hexane, ethyl acetate, chloroform, butanol and aqueous ethanol were determined by Folin - Ciocalteu method and the assayed antioxidant activity was determined in vitro models such as antioxidant capacity by radical scavenging activity using α, α-diphenyl- β-picrylhydrazyl (DPPH) method. The total phenolic contents of the essential oil and different extracts as gallic acid equivalents were found to be highest in methanol extract (386.22 mg/g) followed by ethyl acetate (190.89 mg/g), chloroform (175.89 mg/g), hexane (173.44 mg/g), and butanol extract (131.72 mg/g) and the phenolic contents not detected in essential oil. The antioxidant capacity of the essential oil and different extracts as ascorbic acid standard was in the order of methanol extract > ethyl acetate extract >chloroform> butanol > hexane extract also the antioxidant activity was not detected in essential oil. The findings show that the extent of antioxidant activity of the essential oil and all extracts are in accordance with the amount of phenolics present in that extract. Leaves of Tetrastigma being rich in phenolics may provide a good source of antioxidant. Copyright © 2011 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

  17. Polyethylene glycol and polyvinylpirrolidone effect on bacterial rRNA extraction and hybridization from cells exposed to tannins Efeito de polietilenoglicol e polivinilpirrolidona na extração e hibridização de rRNA bacteriano de células expostas a taninos

    Directory of Open Access Journals (Sweden)

    Pedro Braga Arcuri

    2003-09-01

    Full Text Available In order to detect fluctuations in ruminal microbial populations due to forage tannins using 16S ribosomal RNA (rRNA probes, recovery of intact rRNA is required. The objective of this work was to evaluate the effect of polyethylene glycol (PEG and polyvinylpirrolidone (PVP on extraction of bacterial rRNA, in the presence of tannins from tropical legume forages and other sources, that hybridize with oligonucleotide probes. Ruminococcus albus 8 cells were exposed to 8 g/L tannic acid or 1 g/L condensed tannins extracted from Acacia angustissima, banana (Musa sp. skin, Desmodium ovalifolium, red grape (Vitis vinifera skin and Inga edulis, or no tannins. Cells were rinsed with Tris buffer pH 7 containing either 8% PEG or 6% PVP prior to cell lysis. Total RNA samples rinsed with either PEG or PVP migrated through denaturing agarose gels. The 16S rRNA bands successfully hybridized with a R. albus species-specific oligonucleotide probe, regardless of tannin source. The effect of rinsing buffers on the density of 16S rRNA bands, as well as on the hybridization signals was compared. There were significant effects (PA recuperação de RNA ribossômico (rRNA intacto é necessária para a detecção de flutuações na população microbiana ruminal decorrentes dos taninos de forrageiras, utilizando-se sondas para 16S rRNA. O objetivo deste trabalho foi avaliar o efeito de polietilenoglicol (PEG e polivinilpirrolidona (PVP na extração de rRNA bacteriano, em presença de taninos de leguminosas forrageiras tropicais e de outras fontes, que possa ser hibridizado com sondas de oligonucleotídeos. Culturas de Ruminococcus albus 8 foram expostas ou não a 8 g/L de ácido tânico ou a 1 g/L de taninos condensados, extraídos de Acacia angustissima, casca de banana (Musa sp., Desmodium ovalifolium, cascas de uvas vermelhas (Vitis vinifera e Inga edulis. As culturas foram lavadas com tampão Tris pH 7 contendo 8% PEG ou 6% PVP antes do rompimento das c

  18. Changes in rRNA levels during stress invalidates results from mRNA blotting: Fluorescence in situ rRNA hybridization permits renormalization for estimation of cellular mRNA levels

    DEFF Research Database (Denmark)

    Hansen, M.C.; Nielsen, A.K.; Molin, Søren

    2001-01-01

    obtained by these techniques are compared between experiments in which differences in growth rates, strains, or stress treatments occur, the normalization procedure may have a significant impact on the results. In this report we present a solution to the normalization problem in RNA slot blotting...... the relative level of rRNA per cell, and slot blotting to rRNA probes, which estimates the level of rRNA per extracted total RNA, the amount of RNA per cell was calculated in a series of heat shock experiments with the gram-positive bacterium Lactococcus lactis. It was found that the level of rRNA per cell...... decreased to 30% in the course of the heat shock. This lowered ribosome level led to a decrease in the total RNA content, resulting in a gradually increasing overestimation of the mRNA levels throughout the experiment. Using renormalized cellular mRNA levels, the HrcA-mediated regulation of the genes...

  19. An improved and reproducible protocol for the extraction of high quality fungal RNA from plant biomass substrates

    NARCIS (Netherlands)

    Patyshakuliyeva, Aleksandrina; Mäkelä, Miia R; Sietiö, Outi-Maaria; de Vries, Ronald P; Hildén, Kristiina S; van den Brink, J.

    2014-01-01

    Isolation of high quantity and quality RNA is a crucial step in the detection of meaningful gene expression data. Obtaining intact fungal RNA from complex lignocellulosic substrates is often difficult, producing low integrity RNA which perform poorly in downstream applications. In this study we

  20. Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays

    Directory of Open Access Journals (Sweden)

    Heather D. Kissel

    2013-01-01

    Full Text Available Identifying molecular markers of endometrial hyperplasia (neoplasia progression is critical to cancer prevention. To assess RNA and DNA quantity and quality from routinely collected endometrial samples and evaluate the performance of RNA- and DNA-based arrays across endometrial tissue types, we collected fresh frozen (FF Pipelle, FF curettage, and formalin-fixed paraffin-embedded (FFPE hysterectomy specimens (benign indications from eight women. Additionally, neoplastic and uninvolved tissues from 24 FFPE archival hysterectomy specimens with endometrial hyperplasias and carcinomas were assessed. RNA was extracted from 15 of 16 FF and 51 of 51 FFPE samples, with yields >1.2 μg for 13/15 (87% FF and 50/51 (98% FFPE samples. Extracted RNA was of high quality; all samples performed successfully on the Illumina whole-genome cDNA-mediated annealing, selection, extension, and ligation (WG-DASL array and performance did not vary by tissue type. While DNA quantity from FFPE samples was excellent, quality was not sufficient for successful performance on the Affymetrix SNP Array 6.0. In conclusion, FF Pipelle samples, which are minimally invasive, yielded excellent quantity and quality of RNA for gene expression arrays (similar to FF curettage and should be considered for use in genomic studies. FFPE-derived DNA should be evaluated on new rapidly evolving sequencing platforms.

  1. Total flavonoid and phenolic contents of n-butanol extract of Samanea saman leaf and the antibacterial activity towards Escherichia coli and Staphylococcus aureus

    Science.gov (United States)

    Rita, Wiwik Susanah; Swantara, I. Made Dira; Asih, I. A. Raka Astiti; Sinarsih, Ni Ketut; Suteja, I. Kadek Pater

    2016-03-01

    Total flavonoid and phenolic contents in some natural products was suspected of having a positive correlation to its activity in inhibiting the growth of bacteria. The aim of this study was to determine the total flavonoid and phenolic contents of n-butanol extract of Samanea saman leaf, and to evaluate the antibacterial activity towards Escherechia coli and Staphylococcus aureus. Extraction of compounds was done by ethanol 96%, followed by fractionation into n-hexane, ethyl acetate, and n-butanol. Determination of total flavonoid and phenolic contents was done by UV-Vis Spectrophotometer using standard of quersetin and galic acid respectively. In addition, antibacterial activity was evaluated by agar disc diffusion method. Extraction of 1000 g of Samanea saman leaf was obtained 80 g of ethanol extracts, fractionation of the extract was obtained 8.02 g of n-hexane extracts, 7.11 g of ethyl acetate extracts, 13.5 g of n-butanol extracts, and 14.16 g of aqueous extracts. Phytochemical screening of the n-butanol extracts revealed the presence of flavonoid and phenolic compounds. Total flavonoid and phenolic contents were successively 43.5798 mg QE/100g and 34.0180 mg GAE/100g. The butanol extracts inhibited the growth of S.aureus higher than the growth of E.coli. At the concentration of 2, 4, 6, 8 % (b/v), and positive control (meropenem μg/disc), inhibition zone towards S. aureus was successively 5.67, 9.33, 10.33, 12.00, and 32.33 mm, while the inhibition zone towards E. coli was1.33, 3.33, 4.33, 5.43, and 34.00 mm.

  2. Antioxidant activity, the content of total phenols and flavonoids in the ethanol extracts of Mentha longifolia (L. Hudson dried by the use of different techniques

    Directory of Open Access Journals (Sweden)

    Stanisavljević Dragana M.

    2012-01-01

    Full Text Available In this study, we have examined the yield of extracted substances obtained by means of extraction using 70 % ethanol (v/v, the content of total phenols and flavonoids, as well as the antioxidant activity of the extracts obtained from the samples of the herbs dried by means of different techniques. Wild mint Mentha longifolia (L. Hudson was dried naturally in a laboratory oven at a temperature of 45 °C and in an absorptive low temperature condensation oven at 35°C. The highest yield of extracts was obtained from the naturally dried herbs and the lowest from the herbs dried in the low temperature condensation drying oven. The content of total phenols and flavonoids was determined by spectrophotometric methods with an FC reagent and by the complexation reaction with aluminium-chloride, respectively. The extract of the naturally dried herbs had the highest overall content of phenols (113.8±2.0 mg of gallic acid/g of the dry extract and flavonoids (106.7±0.3 mg of rutin/g of the dry extract. The highest antioxidant activity determined by the FRAP and DPPH assay was determined in the extracts obtained from naturally dried herbs (2.76±0.15 mmol Fe2+/mg of the dry extract and EC50=0.022±0.001 mg/ml, while the lowest was obtained from the extracts of herbs dried in the laboratory oven (1.13±0.11 mmol Fe2+/mg of the dry extract and EC50=0.033±0.001 mg/ml. The HPLC-DAD analysis result show that the greatest content of phenolic compounds show extract obtained from naturally dried plant material. The dominant phenolic component in the all extracts is Kaempferol 3-O-glucoside. The content of all phenolic compound strongly depend on the drying conditions.

  3. Epigenomics of Total Acute Sleep Deprivation in Relation to Genome-Wide DNA Methylation Profiles and RNA Expression

    OpenAIRE

    Nilsson, Emil K.; Bostr?m, Adrian E.; Mwinyi, Jessica; Schi?th, Helgi B.

    2016-01-01

    Abstract Despite an established link between sleep deprivation and epigenetic processes in humans, it remains unclear to what extent sleep deprivation modulates DNA methylation. We performed a within-subject randomized blinded study with 16 healthy subjects to examine the effect of one night of total sleep deprivation (TSD) on the genome-wide methylation profile in blood compared with that in normal sleep. Genome-wide differences in methylation between both conditions were assessed by applyin...

  4. Epigenomics of Total Acute Sleep Deprivation in Relation to Genome-Wide DNA Methylation Profiles and RNA Expression.

    Science.gov (United States)

    Nilsson, Emil K; Boström, Adrian E; Mwinyi, Jessica; Schiöth, Helgi B

    2016-06-01

    Despite an established link between sleep deprivation and epigenetic processes in humans, it remains unclear to what extent sleep deprivation modulates DNA methylation. We performed a within-subject randomized blinded study with 16 healthy subjects to examine the effect of one night of total sleep deprivation (TSD) on the genome-wide methylation profile in blood compared with that in normal sleep. Genome-wide differences in methylation between both conditions were assessed by applying a paired regression model that corrected for monocyte subpopulations. In addition, the correlations between the methylation of genes detected to be modulated by TSD and gene expression were examined in a separate, publicly available cohort of 10 healthy male donors (E-GEOD-49065). Sleep deprivation significantly affected the DNA methylation profile both independently and in dependency of shifts in monocyte composition. Our study detected differential methylation of 269 probes. Notably, one CpG site was located 69 bp upstream of ING5, which has been shown to be differentially expressed after sleep deprivation. Gene set enrichment analysis detected the Notch and Wnt signaling pathways to be enriched among the differentially methylated genes. These results provide evidence that total acute sleep deprivation alters the methylation profile in healthy human subjects. This is, to our knowledge, the first study that systematically investigated the impact of total acute sleep deprivation on genome-wide DNA methylation profiles in blood and related the epigenomic findings to the expression data.

  5. A comparison of two colorimetric assays, based upon Lowry and Bradford techniques, to estimate total protein in soil extracts

    OpenAIRE

    Redmile-Gordon, M.A.; Armenise, E.; White, R.P.; Hirsch, P.R.; Goulding, K.W.T.

    2013-01-01

    Soil extracts usually contain large quantities of dissolved humified organic material, typically reflected by high polyphenolic content. Since polyphenols seriously confound quantification of extracted protein, minimising this interference is important to ensure measurements are representative. Although the Bradford colorimetric assay is used routinely in soil science for rapid quantification protein in soil-extracts, it has several limitations. We therefore investigated an alternative colori...

  6. Evaluation of automated RNA-extraction technology and a qualitative HCV assay for sensitivity and detection of HCV RNA in pool-screening systems

    NARCIS (Netherlands)

    Beld, M.; Habibuw, M. R.; Rebers, S. P.; Boom, R.; Reesink, H. W.

    2000-01-01

    BACKGROUND: The objective of this study was the evaluation of NAT technology for the detection of HCV RNA in plasma pools according to the recommendations of the Paul Ehrlich Institute (5000 IU/mL/donation) and the Committee for Proprietary Medical Products (100 IU/mL/manufacturing pool). STUDY

  7. Screening of Six Medicinal Plant Extracts Obtained by Two Conventional Methods and Supercritical CO₂ Extraction Targeted on Coumarin Content, 2,2-Diphenyl-1-picrylhydrazyl Radical Scavenging Capacity and Total Phenols Content.

    Science.gov (United States)

    Molnar, Maja; Jerković, Igor; Suknović, Dragica; Bilić Rajs, Blanka; Aladić, Krunoslav; Šubarić, Drago; Jokić, Stela

    2017-02-24

    Six medicinal plants Helichrysum italicum (Roth) G. Don, Angelica archangelica L., Lavandula officinalis L., Salvia officinalis L., Melilotus officinalis L., and Ruta graveolens L. were used. The aim of the study was to compare their extracts obtained by Soxhlet (hexane) extraction, maceration with ethanol (EtOH), and supercritical CO₂ extraction (SC-CO₂) targeted on coumarin content (by high performance liquid chromatography with ultraviolet detection, HPLC-UV), 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) scavenging capacity, and total phenols (TPs) content (by Folin-Ciocalteu assay). The highest extraction yields were obtained by EtOH, followed by hexane and SC-CO₂. The highest coumarin content (316.37 mg/100 g) was found in M. officinalis EtOH extracts, but its SC-CO₂ extraction yield was very low for further investigation. Coumarin was also found in SC-CO₂ extracts of S. officinalis , R. graveolens , A. archangelica , and L. officinalis . EtOH extracts of all plants exhibited the highest DPPH scavenging capacity. SC-CO₂ extracts exhibited antiradical capacity similar to hexane extracts, while S. officinalis SC-CO₂ extracts were the most potent (95.7%). EtOH extracts contained the most TPs (up to 132.1 mg gallic acid equivalents (GAE)/g from H. italicum ) in comparison to hexane or SC-CO₂ extracts. TPs content was highly correlated to the DPPH scavenging capacity of the extracts. The results indicate that for comprehensive screening of different medicinal plants, various extraction techniques should be used in order to get a better insight into their components content or antiradical capacity.

  8. Screening of Six Medicinal Plant Extracts Obtained by Two Conventional Methods and Supercritical CO2 Extraction Targeted on Coumarin Content, 2,2-Diphenyl-1-picrylhydrazyl Radical Scavenging Capacity and Total Phenols Content

    Directory of Open Access Journals (Sweden)

    Maja Molnar

    2017-02-01

    Full Text Available Six medicinal plants Helichrysum italicum (Roth G. Don, Angelica archangelica L., Lavandula officinalis L., Salvia officinalis L., Melilotus officinalis L., and Ruta graveolens L. were used. The aim of the study was to compare their extracts obtained by Soxhlet (hexane extraction, maceration with ethanol (EtOH, and supercritical CO2 extraction (SC-CO2 targeted on coumarin content (by high performance liquid chromatography with ultraviolet detection, HPLC-UV, 2,2-diphenyl-1-picrylhydrazyl radical (DPPH scavenging capacity, and total phenols (TPs content (by Folin–Ciocalteu assay. The highest extraction yields were obtained by EtOH, followed by hexane and SC-CO2. The highest coumarin content (316.37 mg/100 g was found in M. officinalis EtOH extracts, but its SC-CO2 extraction yield was very low for further investigation. Coumarin was also found in SC-CO2 extracts of S. officinalis, R. graveolens, A. archangelica, and L. officinalis. EtOH extracts of all plants exhibited the highest DPPH scavenging capacity. SC-CO2 extracts exhibited antiradical capacity similar to hexane extracts, while S. officinalis SC-CO2 extracts were the most potent (95.7%. EtOH extracts contained the most TPs (up to 132.1 mg gallic acid equivalents (GAE/g from H. italicum in comparison to hexane or SC-CO2 extracts. TPs content was highly correlated to the DPPH scavenging capacity of the extracts. The results indicate that for comprehensive screening of different medicinal plants, various extraction techniques should be used in order to get a better insight into their components content or antiradical capacity.

  9. Extraction of high-quality epidermal RNA after ammonium thiocyanate-induced dermo-epidermal separation of 4 mm human skin biopsies

    DEFF Research Database (Denmark)

    Clemmensen, Anders; Thomassen, Mads; Clemmensen, Ole

    2009-01-01

    To obtain a separation of the epidermal and dermal compartments to examine compartment specific biological mechanisms in the skin, we incubated 4 mm human skin punch biopsies in ammonium thiocyanate. We wanted to test (i) the histological quality of the dermo-epidermal separation obtained...... by different incubation times; (ii) the amount and quality of extractable epidermal RNA and (iii) its impact on sample RNA expression profiles assessed by large-scale gene expression microarray analysis in both normal and inflamed skin. At 30-min incubation, the split between dermis and epidermis...... and almost completely separated from the dermis of 4 mm skin biopsies by 30 min incubation in 3.8% ammonium thiocyanate combined with curettage of the dermal surface, producing high-quality RNA suitable for transcriptional analysis. Our refined method of dermo-epidermal separation will undoubtedly prove...

  10. Sequential Total Variation Denoising for the Extraction of Fetal ECG from Single-Channel Maternal Abdominal ECG.

    Science.gov (United States)

    Lee, Kwang Jin; Lee, Boreom

    2016-07-01

    Fetal heart rate (FHR) is an important determinant of fetal health. Cardiotocography (CTG) is widely used for measuring the FHR in the clinical field. However, fetal movement and blood flow through the maternal blood vessels can critically influence Doppler ultrasound signals. Moreover, CTG is not suitable for long-term monitoring. Therefore, researchers have been developing algorithms to estimate the FHR using electrocardiograms (ECGs) from the abdomen of pregnant women. However, separating the weak fetal ECG signal from the abdominal ECG signal is a challenging problem. In this paper, we propose a method for estimating the FHR using sequential total variation denoising and compare its performance with that of other single-channel fetal ECG extraction methods via simulation using the Fetal ECG Synthetic Database (FECGSYNDB). Moreover, we used real data from PhysioNet fetal ECG databases for the evaluation of the algorithm performance. The R-peak detection rate is calculated to evaluate the performance of our algorithm. Our approach could not only separate the fetal ECG signals from the abdominal ECG signals but also accurately estimate the FHR.

  11. Evaluation of RNA extraction methods and identification of putative reference genes for real-time quantitative polymerase chain reaction expression studies on olive (Olea europaea L.) fruits.

    Science.gov (United States)

    Nonis, Alberto; Vezzaro, Alice; Ruperti, Benedetto

    2012-07-11

    Genome wide transcriptomic surveys together with targeted molecular studies are uncovering an ever increasing number of differentially expressed genes in relation to agriculturally relevant processes in olive (Olea europaea L). These data need to be supported by quantitative approaches enabling the precise estimation of transcript abundance. qPCR being the most widely adopted technique for mRNA quantification, preliminary work needs to be done to set up robust methods for extraction of fully functional RNA and for the identification of the best reference genes to obtain reliable quantification of transcripts. In this work, we have assessed different methods for their suitability for RNA extraction from olive fruits and leaves and we have evaluated thirteen potential candidate reference genes on 21 RNA samples belonging to fruit developmental/ripening series and to leaves subjected to wounding. By using two different algorithms, GAPDH2 and PP2A1 were identified as the best reference genes for olive fruit development and ripening, and their effectiveness for normalization of expression of two ripening marker genes was demonstrated.

  12. Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples

    LENUS (Irish Health Repository)

    Mee, Blanaid C.

    2011-12-29

    The Saint James\\'s Hospital Biobank was established in 2008, to develop a high-quality breast tissue BioResource, as a part of the breast cancer clinical care pathway. The aims of this work were: (1) to ascertain the quality of RNA, DNA, and protein in biobanked carcinomas and normal breast tissues, (2) to assess the efficacy of AllPrep® (Qiagen) in isolating RNA, DNA, and protein simultaneously, (3) to compare AllPrep with RNEasy® and QIAamp® (both Qiagen), and (4) to examine the effectiveness of Allprotect® (Qiagen), a new tissue stabilization medium in preserving DNA, RNA, and proteins. One hundred eleven frozen samples of carcinoma and normal breast tissue were analyzed. Tumor and normal tissue morphology were confirmed by frozen sections. Tissue type, tissue treatment (Allprotect vs. no Allprotect), extraction kit, and nucleic acid quantification were analyzed by utilizing a 4 factorial design (SPSS PASW 18 Statistics Software®). QIAamp (DNA isolation), AllPrep (DNA, RNA, and Protein isolation), and RNeasy (RNA isolation) kits were assessed and compared. Mean DNA yield and A260\\/280 values using QIAamp were 33.2 ng\\/μL and 1.86, respectively, and using AllPrep were 23.2 ng\\/μL and 1.94. Mean RNA yield and RNA Integrity Number (RIN) values with RNeasy were 73.4 ng\\/μL and 8.16, respectively, and with AllPrep were 74.8 ng\\/μL and 7.92. Allprotect-treated tissues produced higher RIN values of borderline significance (P=0.055). No discernible loss of RNA stability was detected after 6 h incubation of stabilized or nonstabilized tissues at room temperature or 4°C or in 9 freeze-thaw cycles. Allprotect requires further detailed evaluation, but we consider AllPrep to be an excellent option for the simultaneous extraction of RNA, DNA, and protein from tumor and normal breast tissues. The essential presampling procedures that maintain the diagnostic integrity of pathology specimens do not appear to compromise the quality of molecular isolates.

  13. The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing.

    Science.gov (United States)

    Kennedy, Nicholas A; Walker, Alan W; Berry, Susan H; Duncan, Sylvia H; Farquarson, Freda M; Louis, Petra; Thomson, John M; Satsangi, Jack; Flint, Harry J; Parkhill, Julian; Lees, Charlie W; Hold, Georgina L

    2014-01-01

    Determining bacterial community structure in fecal samples through DNA sequencing is an important facet of intestinal health research. The impact of different commercially available DNA extraction kits upon bacterial community structures has received relatively little attention. The aim of this study was to analyze bacterial communities in volunteer and inflammatory bowel disease (IBD) patient fecal samples extracted using widely used DNA extraction kits in established gastrointestinal research laboratories. Fecal samples from two healthy volunteers (H3 and H4) and two relapsing IBD patients (I1 and I2) were investigated. DNA extraction was undertaken using MoBio Powersoil and MP Biomedicals FastDNA SPIN Kit for Soil DNA extraction kits. PCR amplification for pyrosequencing of bacterial 16S rRNA genes was performed in both laboratories on all samples. Hierarchical clustering of sequencing data was done using the Yue and Clayton similarity coefficient. DNA extracted using the FastDNA kit and the MoBio kit gave median DNA concentrations of 475 (interquartile range 228-561) and 22 (IQR 9-36) ng/µL respectively (p<0.0001). Hierarchical clustering of sequence data by Yue and Clayton coefficient revealed four clusters. Samples from individuals H3 and I2 clustered by patient; however, samples from patient I1 extracted with the MoBio kit clustered with samples from patient H4 rather than the other I1 samples. Linear modelling on relative abundance of common bacterial families revealed significant differences between kits; samples extracted with MoBio Powersoil showed significantly increased Bacteroidaceae, Ruminococcaceae and Porphyromonadaceae, and lower Enterobacteriaceae, Lachnospiraceae, Clostridiaceae, and Erysipelotrichaceae (p<0.05). This study demonstrates significant differences in DNA yield and bacterial DNA composition when comparing DNA extracted from the same fecal sample with different extraction kits. This highlights the importance of ensuring that samples

  14. EXTRACT

    DEFF Research Database (Denmark)

    Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra

    2016-01-01

    The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have the...... and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed.Database URL: https://extract.hcmr.gr/......., organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual...

  15. Epithelial-mesenchymal transition and cancer stem cells, mediated by a long non-coding RNA, HOTAIR, are involved in cell malignant transformation induced by cigarette smoke extract

    International Nuclear Information System (INIS)

    Liu, Yi; Luo, Fei; Xu, Yuan; Wang, Bairu; Zhao, Yue; Xu, Wenchao; Shi, Le; Lu, Xiaolin; Liu, Qizhan

    2015-01-01

    The incidence of lung diseases, including cancer, caused by cigarette smoke is increasing, but the molecular mechanisms of gene regulation induced by cigarette smoke remain unclear. This report describes a long noncoding RNA (lncRNA) that is induced by cigarette smoke extract (CSE) and experiments utilizing lncRNAs to integrate inflammation with the epithelial-mesenchymal transition (EMT) in human bronchial epithelial (HBE) cells. The present study shows that, induced by CSE, IL-6, a pro-inflammatory cytokine, leads to activation of STAT3, a transcription activator. A ChIP assay determined that the interaction of STAT3 with the promoter regions of HOX transcript antisense RNA (HOTAIR) increased levels of HOTAIR. Blocking of IL-6 with anti-IL-6 antibody, decreasing STAT3, and inhibiting STAT3 activation reduced HOTAIR expression. Moreover, for HBE cells cultured in the presence of HOTAIR siRNA for 24 h, the CSE-induced EMT, formation of cancer stem cells (CSCs), and malignant transformation were reversed. Thus, IL-6, acting on STAT3 signaling, which up-regulates HOTAIR in an autocrine manner, contributes to the EMT and to CSCs induced by CSE. These data define a link between inflammation and EMT, processes involved in the malignant transformation of cells caused by CSE. This link, mediated through lncRNAs, establishes a mechanism for CSE-induced lung carcinogenesis. - Highlights: • STAT3 directly regulates the levels of LncRNA HOTAIR. • LncRNA HOTAIR mediates the link between inflammation and EMT. • LncRNA HOTAIR is involved in the malignant transformation of cells caused by CSE

  16. Optimization of Ultrasonic-Assisted Enzymatic Extraction Conditions for Improving Total Phenolic Content, Antioxidant and Antitumor Activities In Vitro from Trapa quadrispinosa Roxb. Residues.

    Science.gov (United States)

    Li, Feng; Mao, Yi-Dan; Wang, Yi-Fan; Raza, Aun; Qiu, Li-Peng; Xu, Xiu-Quan

    2017-03-06

    Stems are the important residues of Trapa quadrispinosa Roxb., which are abundant in phenolic compounds. Ultrasonic-assisted enzymatic extraction (UAEE) is confirmed as a novel extraction technology with main advantages of enhancing extraction yield and physiological activities of the extracts from various plants. In this study, UAEE was applied to obtain the highest yield of phenolic content, strongest antioxidant, and antitumor activities and to optimize the extraction conditions using response surface methodology (RSM). The extracts from the stems of T. quadrispinosa were characterized by determination of their antioxidant activities through 2,2-azinobis(3-ethylbenzthiazoline)-6-sulfonic acid (ABTS), 1,1-Diphenyl-2-picrylhydrazxyl (DPPH) radical scavenging, total antioxidant capacity (TAC), ferric reducing antioxidant capacity (FRAC) methods and of their antitumor activity by MTT method. The selected key independent variables were cellulase concentration ( X ₁: 1.5%-2.5%), extraction time ( X ₂: 20-30 min) and extraction temperature ( X ₃: 40-60 °C). The optimal extraction conditions for total phenolic content (TPC) value of the extracts were determined as 1.74% cellulase concentration, 25.5 min ultrasonic extraction time and 49.0 °C ultrasonic temperature. Under these conditions, the highest TPC value of 53.6 ± 2.2 mg Gallic acid equivalent (GAE)/g dry weight (DW) was obtained, which agreed well with the predicted value (52.596 mg GAE/g·DW. Furthermore, the extracts obtained from UAEE presented highest antioxidant activities through ABTS, DPPH, TAC and FRAC methods were of 1.54 ± 0.09 mmol Trolox equivalent (TE)/g·DW; 1.45 ± 0.07 mmol·TE/g·DW; 45.2 ± 2.2 mg·GAE/g·DW; 50.4 ± 2.6 μmol FeSO₄ equivalent/g·DW and lowest IC 50 values of 160.4 ± 11.6 μg/mL, 126.1 ± 10.8 μg/mL, and 178.3 ± 13.1 μg/mL against Hela, HepG-2 and U251 tumor cells, respectively. The results indicated that the UAEE was an efficient alternative to improve

  17. Protective effects of total extracts of Averrhoa carambola L. (Oxalidaceae) roots on streptozotocin-induced diabetic mice.

    Science.gov (United States)

    Xu, Xiaohui; Liang, Tao; Wen, Qingwei; Lin, Xing; Tang, Jingzhi; Zuo, Qiaoyun; Tao, Liqun; Xuan, Feifei; Huang, Renbin

    2014-01-01

    In Chinese culture, the roots of Averrhoa carambola L. have long been used for medical purposes due to their potent pharmaceutical activities, such as improving digestive function and treating diabetes. Recently, we prepared extracts of Averrhoa carambola L. root (EACR), which were isolated from Averrhoa carambola L. roots using ethanol or water. This study was designed to investigate the potential effects of EACR on streptozotocin (STZ) diabetic mice and to explore the underlying mechanism of these effects. Male mice were injected with STZ through the tail vein (120 mg/kg body weight) and were identified as a diabetic mouse model when the level of blood glucose was ≥11.1 mmol/L. Subsequently, the mice were administered EACR (150, 300, 600, 1200 mg/kg body weight/d) and metformin (320 mg/kg body weight/d) via intragastric gavage for three weeks. The results indicated that EACR significantly decreased the serum levels of blood glucose, total cholesterol (TC), triglycerides (TGs) and free fatty acids (FFAs), whereas the content of serum insulin was elevated. In addition, the expressions of apoptosis-related regulators (including caspase-3, caspase-8 and caspase-9) and the apoptosis-induced protein Bax were markedly down-regulated by EACR, whereas the expression of the anti-apoptotic Bcl-2 protein was notably increased. Furthermore, EACR could protect the diabetic mice against the STZ-induced apoptosis of pancreatic β cells. Taken together, these findings indicate that EACR plays an effective hyperglycemic role that is associated with ameliorating metabolic functions and with inhibiting apoptosis in pancreas tissue. © 2014 S. Karger AG, Basel.

  18. Protective Effects of Total Extracts of Averrhoa carambola L. (Oxalidaceae Roots on Streptozotocin-Induced Diabetic Mice

    Directory of Open Access Journals (Sweden)

    Xiaohui Xu

    2014-04-01

    Full Text Available Background: In Chinese culture, the roots of Averrhoa carambola L. have long been used for medical purposes due to their potent pharmaceutical activities, such as improving digestive function and treating diabetes. Methods: Recently, we prepared extracts of Averrhoa carambola L. root (EACR, which were isolated from Averrhoa carambola L. roots using ethanol or water. This study was designed to investigate the potential effects of EACR on streptozotocin (STZ diabetic mice and to explore the underlying mechanism of these effects. Male mice were injected with STZ through the tail vein (120 mg/kg body weight and were identified as a diabetic mouse model when the level of blood glucose was ≥11.1 mmol/L. Subsequently, the mice were administered EACR (150, 300, 600, 1200 mg/kg body weight/d and metformin (320 mg/kg body weight/d via intragastric gavage for three weeks. Results: The results indicated that EACR significantly decreased the serum levels of blood glucose, total cholesterol (TC, triglycerides (TGs and free fatty acids (FFAs, whereas the content of serum insulin was elevated. In addition, the expressions of apoptosis-related regulators (including caspase-3, caspase-8 and caspase-9 and the apoptosis-induced protein Bax were markedly down-regulated by EACR, whereas the expression of the anti-apoptotic Bcl-2 protein was notably increased. Furthermore, EACR could protect the diabetic mice against the STZ-induced apoptosis of pancreatic β cells. Conclusion: Taken together, these findings indicate that EACR plays an effective hyperglycemic role that is associated with ameliorating metabolic functions and with inhibiting apoptosis in pancreas tissue.

  19. Assessment of efficacy and safety of various adjuvant formulations with a total soluble extract of Trichinella spiralis

    Directory of Open Access Journals (Sweden)

    Aucouturier J.

    2001-06-01

    Full Text Available Trichinellosis, a re-emerging zoonosis in several countries and pig, is the main species responsible for its transmission to human. Vaccination of swine could be an alternative to prevent the risk of human contamination. In order to develop an efficient and safe inactivate vaccine, the choice of the adjuvant is an important issue. The aim of this study was to develop and select potent and safe adjuvants by screening them in an experimental model with a crude soluble antigen from L1 muscular larvae (ML of Trichinella spiralis (Ts. The efficacy was checked by the quantification of specific antibody levels. Specific and non-specific IgE antibody levels were also assessed. Safety was checked by the assessment of the local reaction at the injection site.Various Montanide® ISA adjuvant formulations including water in oil, oil in water and multiphasic emulsions, but also nanoparticles or microbeads were tested. The results clearly showed differences between the antibody responses induced by the adjuvants and demonstrated the necessity to use an adjuvant to obtain a specific IgG (IgG1or lgG2a response directed against the total soluble extract of Ts. All the formulations enhanced the humoral immune response. The origin of the oil contained in the emulsions played an important role on the efficacy. Indeed emulsions based on mineral oils were more efficient than those based on metabolisable oils. However it was linked with stronger local reactions. Multiphasic and oil in water emulsions but also nanoparticles failed to induce 1gG2a antibody levels. Microbeads and water in oil formulations based on mineral oils were more efficient. This experimentation allowed then the selection of several adjuvants which efficacy will be further Investigated by a challenge test and an analysis of the cellular populations involved in the mechanism of the immune response.

  20. A Metabolism-Based Synergy for Total Coumarin Extract of Radix Angelicae Dahuricae and Ligustrazine on Migraine Treatment in Rats

    Directory of Open Access Journals (Sweden)

    Shan Feng

    2018-04-01

    Full Text Available Radix Angelicae dahuricae, containing coumarins, which might affect cytochrome P450 enzyme (CYP450 activity, has been co-administered with ligustrazine, a substrate of CYP450s, for the clinical treatment of migraine. However, whether a pharmacokinetic-based synergy exists between Radix Angelicae dahuricae and ligustrazine is still unknown. In this study, the total coumarin extract (TCE of Radix Angelicae dahuricae (50 mg/kg, orally reinforced the anti-migraine activity of ligustrazine by declining head scratching, plasma calcitonin gene-related peptide, and serum nitric oxide, as well as increasing plasma endothelin levels in rats (p < 0.05. Moreover, the pharmacokinetic study reflected that TCE potentiated the area under the concentration–time curve of ligustrazine and prolonged its mean retention time in rats (p < 0.05. Besides, the IC50 for TCE, imperatorin and isoimperatorin inhibiting ligustrazine metabolism were 5.0 ± 1.02, 1.35 ± 0.46, 4.81 ± 1.14 µg/mL in human liver microsomes, and 13.69 ± 1.11, 1.19 ± 1.09, 1.69 ± 1.17 µg/mL in rat liver microsomes, respectively. Moreover, imperatorin and isoimperatorin were CYP450s inhibitors with IC50 < 10 µM for CYP1A2, 2C9, 2D6, and 3A4. Therefore, this study concluded that Radix Angelicae dahuricae could increase ligustrazine plasma concentration and then reinforce its pharmacological effect by inhibiting its metabolism through interference with CYP450s. This could be one mechanism for the synergy between Radix Angelicae dahuricae and ligustrazine on migraine treatment.

  1. Effects of total glucosides of peony on AQP-5 and its mRNA expression in submandibular glands of NOD mice with Sjogren's syndrome.

    Science.gov (United States)

    Wu, G-L; Pu, X-H; Yu, G-Y; Li, T-Y

    2015-01-01

    The aim of this study was to observe the effects of total glucosides of peony (TGP) on pathological change, Aquaporin-5 (AQP-5) and its mRNA expression in submandibular glands of non-obese diabetic (NOD) mice with Sjogren's Syndrome, to investigate its regulation on secretion of salivary glands. 40 NOD mice were randomly divided into model group, TGP group, hydroxychloroquine group, combination group (n = 10). For TGP group, the mice were intragastrically administrated with 0.4 ml TGP dilution per day in accordance with 300 g/kg dose; for hydroxychloroquine group, the mice were intragastrically administrated with 0.4 ml hydroxychloroquine per day in accordance with 60 mg/kg dose; for the combination group, the mice were intragastrically administrated with 0.4 ml TGP dilution and 0.4 ml hydroxychloroquine. 8 weeks later, the mice were sacrificed, and submandibular glands were collected by anatomy. Pathological changes of submandibular gland were observed under a light microscope; AQP-5 protein in submandibular glands was detected by immunohistochemical staining; and AQP-5 mRNA expression in submandibular glands was detected by RT-PCR. The lymphocytic infiltration score of model mice was significantly higher than that of other groups. The pathological morphology and score of NOD mice were significantly improved after administration, and the combination group was superior to the hydroxychloroquine group and TGP group (p TGP group and the combination group were higher than the hydroxychloroquine group (p TGP may improve pathological damage of submandibular glands of NOD mouse with Sjogren's syndrome by upregulating AQP-5 and its mRNA expression in submandibular glands.

  2. Theoretical analysis of the distribution of isolated particles in totally asymmetric exclusion processes: Application to mRNA translation rate estimation

    Science.gov (United States)

    Dao Duc, Khanh; Saleem, Zain H.; Song, Yun S.

    2018-01-01

    The Totally Asymmetric Exclusion Process (TASEP) is a classical stochastic model for describing the transport of interacting particles, such as ribosomes moving along the messenger ribonucleic acid (mRNA) during translation. Although this model has been widely studied in the past, the extent of collision between particles and the average distance between a particle to its nearest neighbor have not been quantified explicitly. We provide here a theoretical analysis of such quantities via the distribution of isolated particles. In the classical form of the model in which each particle occupies only a single site, we obtain an exact analytic solution using the matrix ansatz. We then employ a refined mean-field approach to extend the analysis to a generalized TASEP with particles of an arbitrary size. Our theoretical study has direct applications in mRNA translation and the interpretation of experimental ribosome profiling data. In particular, our analysis of data from Saccharomyces cerevisiae suggests a potential bias against the detection of nearby ribosomes with a gap distance of less than approximately three codons, which leads to some ambiguity in estimating the initiation rate and protein production flux for a substantial fraction of genes. Despite such ambiguity, however, we demonstrate theoretically that the interference rate associated with collisions can be robustly estimated and show that approximately 1% of the translating ribosomes get obstructed.

  3. The BUME method: a new rapid and simple chloroform-free method for total lipid extraction of animal tissue.

    Science.gov (United States)

    Löfgren, Lars; Forsberg, Gun-Britt; Ståhlman, Marcus

    2016-06-10

    In this study we present a simple and rapid method for tissue lipid extraction. Snap-frozen tissue (15-150 mg) is collected in 2 ml homogenization tubes. 500 μl BUME mixture (butanol:methanol [3:1]) is added and automated homogenization of up to 24 frozen samples at a time in less than 60 seconds is performed, followed by a 5-minute single-phase extraction. After the addition of 500 μl heptane:ethyl acetate (3:1) and 500 μl 1% acetic acid a 5-minute two-phase extraction is performed. Lipids are recovered from the upper phase by automated liquid handling using a standard 96-tip robot. A second two-phase extraction is performed using 500 μl heptane:ethyl acetate (3:1). Validation of the method showed that the extraction recoveries for the investigated lipids, which included sterols, glycerolipids, glycerophospholipids and sphingolipids were similar or better than for the Folch method. We also applied the method for lipid extraction of liver and heart and compared the lipid species profiles with profiles generated after Folch and MTBE extraction. We conclude that the BUME method is superior to the Folch method in terms of simplicity, through-put, automation, solvent consumption, economy, health and environment yet delivering lipid recoveries fully comparable to or better than the Folch method.

  4. The BUME method: a new rapid and simple chloroform-free method for total lipid extraction of animal tissue

    Science.gov (United States)

    Löfgren, Lars; Forsberg, Gun-Britt; Ståhlman, Marcus

    2016-06-01

    In this study we present a simple and rapid method for tissue lipid extraction. Snap-frozen tissue (15-150 mg) is collected in 2 ml homogenization tubes. 500 μl BUME mixture (butanol:methanol [3:1]) is added and automated homogenization of up to 24 frozen samples at a time in less than 60 seconds is performed, followed by a 5-minute single-phase extraction. After the addition of 500 μl heptane:ethyl acetate (3:1) and 500 μl 1% acetic acid a 5-minute two-phase extraction is performed. Lipids are recovered from the upper phase by automated liquid handling using a standard 96-tip robot. A second two-phase extraction is performed using 500 μl heptane:ethyl acetate (3:1). Validation of the method showed that the extraction recoveries for the investigated lipids, which included sterols, glycerolipids, glycerophospholipids and sphingolipids were similar or better than for the Folch method. We also applied the method for lipid extraction of liver and heart and compared the lipid species profiles with profiles generated after Folch and MTBE extraction. We conclude that the BUME method is superior to the Folch method in terms of simplicity, through-put, automation, solvent consumption, economy, health and environment yet delivering lipid recoveries fully comparable to or better than the Folch method.

  5. A comparison of two colorimetric assays, based upon Lowry and Bradford techniques, to estimate total protein in soil extracts.

    Science.gov (United States)

    Redmile-Gordon, M A; Armenise, E; White, R P; Hirsch, P R; Goulding, K W T

    2013-12-01

    Soil extracts usually contain large quantities of dissolved humified organic material, typically reflected by high polyphenolic content. Since polyphenols seriously confound quantification of extracted protein, minimising this interference is important to ensure measurements are representative. Although the Bradford colorimetric assay is used routinely in soil science for rapid quantification protein in soil-extracts, it has several limitations. We therefore investigated an alternative colorimetric technique based on the Lowry assay (frequently used to measure protein and humic substances as distinct pools in microbial biofilms). The accuracies of both the Bradford assay and a modified Lowry microplate method were compared in factorial combination. Protein was quantified in soil-extracts (extracted with citrate), including standard additions of model protein (BSA) and polyphenol (Sigma H1675-2). Using the Lowry microplate assay described, no interfering effects of citrate were detected even with concentrations up to 5 times greater than are typically used to extract soil protein. Moreover, the Bradford assay was found to be highly susceptible to two simultaneous and confounding artefacts: 1) the colour development due to added protein was greatly inhibited by polyphenol concentration, and 2) substantial colour development was caused directly by the polyphenol addition. In contrast, the Lowry method enabled distinction between colour development from protein and non-protein origin, providing a more accurate quantitative analysis. These results suggest that the modified-Lowry method is a more suitable measure of extract protein (defined by standard equivalents) because it is less confounded by the high polyphenolic content which is so typical of soil extracts.

  6. Chemical composition, total phenolic and flavonoid contents, and in vitro antimicrobial and antioxidant activities of crude extracts from red chilli seeds (Capsicum frutescens L.

    Directory of Open Access Journals (Sweden)

    Neelam Gurnani

    2016-07-01

    Full Text Available The objectives of present study were to assess the antimicrobial and antioxidant potential of Capsicum frutescens L. seeds and to characterize the chemical constituents of the crude extracts. The n-hexane and chloroform extracts were analyzed using gas chromatography–mass spectroscopy (GC–MS, which showed the presence of many biologically important volatile constituents, including heterocyclic compounds, β-diketones, hydrocarbons, long chain aliphatic carboxylic acids, and their derivatives, such as esters, hydroxy ester, and aromatic compounds. The amounts of the total phenolic content and the total flavonoid content in same the extracts were in the ranges of 7.95–26.15 gallic acid equivalents (GAE mg/g and 4.64–12.84 rutin equivalents (RU mg/g of dry weight of extract, respectively. In the determination of the in vitro antimicrobial activity, seed extracts prevented the growth of most of the tested pathogens by forming significant inhibition zones. The inhibitory activity was especially remarkable (inhibition zone ≥ 13 mm against Pesudomaonas aeruginosa, Klebsilla pneumonae, Staphylococcus aureus and Candida albicans. During the evaluation of the in vitro antioxidant activity via DPPH assay, n-hexane and chloroform extracts showed 26.9% and 30.9% free radical scavenging abilities, respectively, at the concentration of 1 mg/mL. Considering these results, C. frutescens seeds can be used as a source of novel antimicrobial and antioxidant compounds.

  7. Monitoring of the antiviral potential of bee venom and wax extracts against Adeno-7 (DNA) and Rift Valley fever virus (RNA) viruses models.

    Science.gov (United States)

    Hassan, Mostafa I; Mohamed, Aly F; Amer, Moner A; Hammad, Kotb M; Riad, Saber A

    2015-04-01

    This study monitored the antiviral potential of bee venom and four wax extracts, ethanol white and black beeswax (EWW/EBW) and acetone white and black beeswax (AWW/ABW) extracts. Two different virus models namely Adeno-7 as DNA model and RVFV as RNA virus models. End point calculation assay was used to calculate virus depletion titer. The depletion of viral infectivity titer of ABW to Adeno-7 virus showed strong antiviral activity recorded a depletion of viral infectivity titer (1.66 log (10)/ ml) that gave equal action with bee venom and more than interferon IFN (1 log (10)/ ml). On the other hand, antiviral activity of EBW showed a moderate potential, while AWW showed no antiviral activity. Finally EWW showed synergetic activity against Adeno-7 virus activity. Thus, activity of wax extracts to RVFV was arranged in order of IFN bee venom > AWW & EBW > EWW and ABW recorded 3.34, 0.65, 0.5, 0.34 respectively. It is the first time to study the beeswax effect against DNA and RNA virus' models; acetone black beeswax recorded a depletion titer 1.66 log (10)/ml.

  8. Modifying a standard method allows simultaneous extraction of RNA and protein, enabling detection of enzymes in the rat retina with low expressions and protein levels.

    Science.gov (United States)

    Agardh, Elisabet; Gustavsson, Carin; Hagert, Per; Nilsson, Marie; Agardh, Carl-David

    2006-02-01

    The aim of the study was to evaluate messenger RNA and protein expression in limited amounts of tissue with low protein content. The Chomczynski method was used for simultaneous extraction of RNA, and protein was modified in the protein isolation step. Template mass and cycling time for the complementary DNA synthesis step of real-time reverse transcription-polymerase chain reaction (RT-PCR) for analysis of catalase, copper/zinc superoxide dismutase, manganese superoxide dismutase, the catalytic subunit of glutamylcysteine ligase, glutathione peroxidase 1, and the endogenous control cyclophilin B (CypB) were optimized before PCR. Polymerase chain reaction accuracy and efficacy were demonstrated by calculating the regression (R2) values of the separate amplification curves. Appropriate antibodies, blocking buffers, and running conditions were established for Western blot, and protein detection and multiplex assays with CypB were performed for each target. During the extraction procedure, the protein phase was dissolved in a modified washing buffer containing 0.1% sodium dodecyl sulfate, followed by ultrafiltration. Enzyme expression on real-time RT-PCR was accomplished with high reliability and reproducibility (R2, 0.990-0.999), and all enzymes except for glutathione peroxidase 1 were detectable in individual retinas on Western blot. Western blot multiplexing with CypB was possible for all targets. In conclusion, connecting gene expression directly to protein levels in the individual rat retina was possible by simultaneous extraction of RNA and protein. Real-time RT-PCR and Western blot allowed accurate detection of retinal protein expressions and levels.

  9. Correlation Between Total Flavonoid Contents and Macrophage Phagocytosis Activity of Fractions From Faloak (Sterculia quadrifida R.Br. Barks Ethanolic Extract In Vitro

    Directory of Open Access Journals (Sweden)

    Rima Munawaroh

    2018-04-01

    Full Text Available On Timor island, Nusa Tenggara Timur, faloak barks (Sterculia quadrifida R.Br. has been used empirically to restore stamina. Faloak bark ethanolic extract proved to have immunomodulatory activity in vitro, which can increase macrophage phagocytosis activity. This research aimed: (i to determine the immunomodulatory active fraction of faloak bark ethanolic extract, (ii to determine the total flavonoid contents of faloak extract and fractions, and (iii to evaluate the correlation of the total flavonoid contents of those extract and fractions with their macrophage phagocytosis activity. The simplisia powder is macerated with 96% ethanol. The extract was dissolved in methanol:water (9:1v/v was then subsequently partitioned with n-hexane, ethyl acetate, and water to obtain n-hexane fraction, ethyl acetate fraction, water fraction, and insoluble fraction. Faloak extract and fractions at concentration 62,5; 125; 250; 500μg/mL were tested for their effect on the peritoneal macrophage phagocytosis of Balb/c mice in vitro by the latex beads method. Phagocytosis capacity and phagocytosis index were analyzed using one-way anova and post hoc Tukey HSD test with 95% confidence level. The results showed that ethyl acetate fraction had the highest macrophage phagocytosis capacity and the highest total flavonoid content compared to other fractions. The highest macrophage phagocytosis capacity of ethyl acetate fraction at concentration of 250 μg/mL was 51,94±4,67%, this value was significantly different from cell control (7,50±1,29%, negative controls of 0,0625% dimethylsulphoxide (6,25±0,36%, as well as positive control of 200 μg/mL echinaceae extract syrup® (9,97±0,33%. The total flavonoid content of ethyl acetate fraction determined by aluminum chloride method was 4,290±0.029 mg of quercetin equivalent/g fraction. There was a positive and strong correlation between the total flavonoid content of these extract and fractions with their macrophage

  10. Total milk fat extraction and quantification of polar and neutral lipids of cow, goat, and ewe milk by using a pressurized liquid system and chromatographic techniques.

    Science.gov (United States)

    Castro-Gómez, M P; Rodriguez-Alcalá, L M; Calvo, M V; Romero, J; Mendiola, J A; Ibañez, E; Fontecha, J

    2014-11-01

    Although milk polar lipids such as phospholipids and sphingolipids located in the milk fat globule membrane constitute 0.1 to 1% of the total milk fat, those lipid fractions are gaining increasing interest because of their potential beneficial effects on human health and technological properties. In this context, the accurate quantification of the milk polar lipids is crucial for comparison of different milk species, products, or dairy treatments. Although the official International Organization for Standardization-International Dairy Federation method for milk lipid extraction gives satisfactory results for neutral lipids, it has important disadvantages in terms of polar lipid losses. Other methods using mixtures of solvents such as chloroform:methanol are highly efficient for extracting polar lipids but are also associated with low sample throughput, long time, and large solvent consumption. As an alternative, we have optimized the milk fat extraction yield by using a pressurized liquid extraction (PLE) method at different temperatures and times in comparison with those traditional lipid extraction procedures using 2:1 chloroform:methanol as a mixture of solvents. Comparison of classical extraction methods with the developed PLE procedure were carried out using raw whole milk from different species (cows, ewes, and goats) and considering fat yield, fatty acid methyl ester composition, triacylglyceride species, cholesterol content, and lipid class compositions, with special attention to polar lipids such as phospholipids and sphingolipids. The developed PLE procedure was validated for milk fat extraction and the results show that this method performs a complete or close to complete extraction of all lipid classes and in less time than the official and Folch methods. In conclusion, the PLE method optimized in this study could be an alternative to carry out milk fat extraction as a routine method. Copyright © 2014 American Dairy Science Association. Published by

  11. Establishment of five cover crops and total soil nutrient extraction in a humid tropical soil in the Peruvian Amazon

    Science.gov (United States)

    In order to evaluate the establishment of five cover crops and their potential to increase soil fertility through nutrient extraction, an experiment was installed in the Research Station of Choclino, San Martin, Peru. Five cover crops were planted: Arachis pintoi Krapov. & W.C. Greg, Calopogonium m...

  12. Evaluation of FTA(®) card for the rescue of infectious foot-and-mouth disease virus by chemical transfection of extracted RNA in cultured cells.

    Science.gov (United States)

    Biswal, Jitendra K; Subramaniam, Saravanan; Ranjan, Rajeev; Pattnaik, Bramhadev

    2016-08-01

    Foot-and-mouth disease (FMD) is a highly contagious epidemic disease of transboundary importance. Inadequate storage and shipment of suspected clinical samples can compromise the ability to detect and characterise FMD virus (FMDV) in endemic countries, thereby, leading to the loss of valuable virological and epidemiological data. This study, investigates the potential of using FTA(®) cards for dry transportation of clinical samples and subsequent recovery of infectious FMDV by chemical transfection of FTA(®) card fixed RNA as an alternative to the conventional cell culture based virus isolation method. A higher proportion of infectious FMDV was rescued from clinical samples (cell culture isolates, tongue epithelial suspension and impression smears) by the FTA(®) card fixed RNA transfection method (76%) compared to the conventional cell culture based virus isolation (56%), suggesting a better performance of the current RNA transfection procedure. Furthermore, it was possible to rescue live virus by the transfection of RNA extracted from FTA(®) card impregnated with clinical samples that had been stored at varying temperature (4-37 °C) up to a period of six weeks. The VP1 sequence data and antigenic relationships with the vaccine strains, between viruses rescued by FTA(®) card fixed RNA transfection and conventional cell culture, were comparable. Therefore, these results support the use of the FTA(®) card for the economic, dry, non-hazardous transport of FMD suspected clinical samples from the site of collection to national/international reference laboratories. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Effect of domestic processing on total and extractable calcium and zinc content of bathua (Chenopodium album) and fenugreek (Trigonella foenum graecum) leaves.

    Science.gov (United States)

    Yadav, S K; Sehgal, S

    1999-01-01

    Bathua (Chenopodium album) and fenugreek (Trigonellafoenum graecum) stored in polyethylene bags and without packaging for 24 or 48 hours in a refrigerator at 5 or 30 degrees C in polyethylene bags. The fresh leaves were also dried (oven and sun); blanched (5, 10 or 15 min) and cooked in an open pan and a pressure cooker. The processed leaves were analyzed for total and extractable calcium and zinc content. The Ca and Zn content of these leaves varied from 970 to 2230 and 10.50 to 12.30 mg/100 g DM and the percentage HCl-extractability was 80.34 to 83.04 and 82.43 to 83.90, respectively. Non significant effects of drying and storage were observed on total Ca and Zn content and HCl-extractability while blanching and cooking resulted in significant improvement of HCl-extractability of these two minerals. Thus, cooking and blanching are good ways to improve the HCl-extractability of Ca and Zn.

  14. Optimization of dynamic-microwave assisted enzymatic hydrolysis extraction of total ginsenosides from stems and leaves of panax ginseng by response surface methodology.

    Science.gov (United States)

    Wang, Xiao-Yan; Ren, Hui

    2018-03-21

    Ginseng stems and leaves (GSAL) are abundant in ginsenosides compounds. For efficient utilization of GSAL and the enhancement of total ginsenosides (TG) compound yields in GSAL, TG from GSAL were extracted, using dynamic-microwave assisted extraction coupled with enzymatic hydrolysis (DMAE-EH) method. The extraction process has been simulated and its main influencing factors such as ethanol concentration, microwave temperature, microwave time and pump flow rate have been optimized by response surface methodology coupled with a Box-Behnken design(BBD). The experimental results indicated that optimal extraction conditions of TG from GSAL were as follows: ethanol concentration of 75%, microwave temperature of 60°C, microwave time of 20 min and pump flow rate of 38 r/min. After experimental verification, the experimental yields of TG was 60.62 ± 0.85 mg g -1 , which were well agreement with the predicted by the model. In general, the present results demonstrated that DMAE-EH method was successfully used to extract total ginsenosides in GSAL.

  15. Effects of process parameters on supercritical CO2 extraction of total phenols from strawberry (Arbutus unedo L.) fruits: An optimization study.

    Science.gov (United States)

    Akay, Seref; Alpak, Ilknur; Yesil-Celiktas, Ozlem

    2011-08-01

    The aim of this work was to optimize total phenolic yield of Arbutus unedo fruits using supercritical fluid extraction. A Box-Behnken statistical design was used to evaluate the effect of various values of pressure (50-300 bar), temperature (30-80°C) and concentration of ethanol as co-solvent (0-20%) by CO2 flow rate of 15 g/min for 60 min. The most effective variable was co-solvent ratio (p<0.005). Evaluative criteria for both dependent variables (total phenols and radical scavenging activity) in the model were assigned maximum. Optimum extraction conditions were elicited as 60 bar, 48°C and 19.7% yielding 25.72 mg gallic acid equivalent (GAE) total phenols/g extract and 99.9% radical scavenging capacity, which were higher than the values obtained by conventional water (24.89 mg/g; 83.8%) and ethanol (15.12 mg/g; 95.8%) extractions demonstrating challenges as a green separation process with improved product properties for industrial applications. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Extraction of total polyphenols from hibiscus (Hibiscus sabdariffa L. and waxweed / ‘sete-sangrias’ (Cuphea carthagenensis and evaluation of their antioxidant potential

    Directory of Open Access Journals (Sweden)

    Daniele Begmeier

    2014-02-01

    Full Text Available Current research investigates the extraction process of total polyphenols from hibiscus (Hibiscus sabdariffa L. and waxweed (Brazilian name: ‘sete-sangrias’ (Cuphea carthagenensis and evaluates the antioxidant potential of their extracts. The extraction stage comprised investigation on the following parameters: i solvents (acetone and ethanol pure and fractioned with water; ii variables (temperature, stirring, solvent ratio, time and pH. Total polyphenols were quantified by Folin-Ciocalteau reagent and antioxidant activity was determined by ABTS•+ (2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid and DPPH (2,2-diphenyl-1-picrylhydrazyl radical scavenging assay. Results showed that, depending on experimental conditions, total phenolic contents for hibiscus and waxweed ranged between 460.86 mg GAE 100 g-1 and 5012.54 mg GAE 100 g-1 and between 462.86 mg GAE 100 g-1 and 4215.99 mg GAE 100 g-1, respectively. Waxweed had a higher antioxidant activity when compared to that of hibiscus by both ABTS•+ and DPPH. Data showed that hibiscus and waxweed have a significant amount of polyphenols which may be extracted in mild processing conditions and then employed as natural antioxidant sources in industrial processes.

  17. Surfactant-enhanced spectrofluorimetric determination of total aflatoxins from wheat samples after magnetic solid-phase extraction using modified Fe3O4 nanoparticles

    Science.gov (United States)

    Manafi, Mohammad Hanif; Allahyari, Mehdi; Pourghazi, Kamyar; Amoli-Diva, Mitra; Taherimaslak, Zohreh

    2015-07-01

    The extraction and preconcentration of total aflatoxins (including aflatoxin B1, B2, G1, and G2) using magnetic nanoparticles based solid phase extraction (MSPE) followed by surfactant-enhanced spectrofluorimetric detection was proposed. Ethylene glycol bis-mercaptoacetate modified silica coated Fe3O4 nanoparticles as an efficient antibody-free adsorbent was successfully applied to extract aflatoxins from wheat samples. High surface area and strong magnetization properties of magnetic nanoparticles were utilized to achieve high enrichment factor (97), and satisfactory recoveries (92-105%) using only 100 mg of the adsorbent. Furthermore, the fast separation time (less than 10 min) avoids many time-consuming cartridge loading or column-passing procedures accompany with the conventional SPE. In determination step, signal enhancement was performed by formation of Triton X-100 micelles around the analytes in 15% (v/v) acetonitrile-water which dramatically increase the sensitivity of the method. Main factors affecting the extraction efficiency and signal enhancement of the analytes including pH of sample solution, desorption conditions, extraction time, sample volume, adsorbent amount, surfactant concentration and volume and time of micelle formation were evaluated and optimized. Under the optimum conditions, wide linear range of 0.1-50 ng mL-1 with low detection limit of 0.03 ng mL-1 were obtained. The developed method was successfully applied to the extraction and preconcentration of aflatoxins in three commercially available wheat samples and the results were compared with the official AOAC method.

  18. Faecal excretion of total and acid extractable phosphorus in dairy cows fed rations with different levels of phosphorus.

    Science.gov (United States)

    Nordqvist, Maria; Spörndly, Rolf; Holtenius, Kjell

    2016-03-15

    The phosphorus (P) originating from livestock operations causes eutrophication. Determination of acid extractable P (AEP) in cattle faeces has been proposed as a tool to identify excessive P feeding. The method has not yet been evaluated in controlled studies with cows subjected to individual recording of P intake. Thus the present study focused on investigating the relationship between different P fractions in faeces from cows fed rations with varying P content. The study also investigated whether AEP in faeces could be used to estimate dietary P intake in relation to the P requirement. The results showed that acid extractable P predicted P overfeeding. P fed in excess of requirements was largely excreted as acid extractable P. The unavailable and/or inevitably lost P fractions in the diets were smaller than assumed. This study demonstrates in experimental studies a positive relationship between measured AEP and indirectly calculated regulated P. Any P fed in excess of requirements was largely excreted as AEP. This fraction is thought to be the most mobile P fraction with regard to potential runoff losses. However, the unavailable and/or inevitably lost P fractions in the diets were smaller than assumed. © 2015 Society of Chemical Industry.

  19. Optimization of Conditions for Extraction of Polyphenols and the Determination of the Impact of Cooking on Total Polyphenolic, Antioxidant, and Anticholinesterase Activities of Potato

    Science.gov (United States)

    Laib, Imen; Barkat, Malika

    2018-01-01

    In this work we optimized the cooking and extraction conditions for obtaining high yields of total polyphenols from potato and studied the effect of three domestic methods of cooking on total phenols, antioxidant activity, and anticholinesterase activities. The optimization of the experiment was carried out by the experimental designs. The extraction of the polyphenols was carried out by maceration and ultrasonication. Determination of the polyphenols was performed by using the Folin-Ciocalteau reagent method. The antioxidant activity was evaluated by three methods: 1,1-diphenyl-2-picryl-hydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), and CUPRAC(Cupric reducing antioxidant capacity), the anticholinesterase activity was evaluated by the method of Elmann. The optimum of total phenolic obtained was: 4.668 × 104, 1.406 × 104, 3357.009, 16,208.99 µg Gallic Acid Equivalent (GAE)/g of dry extract for crude potato, steamed potatoes, in boiling water, and by microwave, respectively. The three modes of cooking cause a decrease in the total polyphenol contents, antioxidant and anticholinesterase activities. PMID:29522482

  20. Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification.

    Science.gov (United States)

    Yang, Qi; Franco, Christopher M M; Zhang, Wei

    2015-10-01

    Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.

  1. Polyphenolic extracts from cowpea (Vigna unguiculata) protect colonic myofibroblasts (CCD18Co cells) from lipopolysaccharide (LPS)-induced inflammation--modulation of microRNA 126.

    Science.gov (United States)

    Ojwang, Leonnard O; Banerjee, Nivedita; Noratto, Giuliana D; Angel-Morales, Gabriela; Hachibamba, Twambo; Awika, Joseph M; Mertens-Talcott, Susanne U

    2015-01-01

    Cowpea (Vigna unguiculata) is a drought tolerant crop with several agronomic advantages over other legumes. This study evaluated varieties from four major cowpea phenotypes (black, red, light brown and white) containing different phenolic profiles for their anti-inflammatory property on non-malignant colonic myofibroblasts (CCD18Co) cells challenged with an endotoxin (lipopolysaccharide, LPS). Intracellular reactive oxygen species (ROS) assay on the LPS-stimulated cells revealed antioxidative potential of black and red cowpea varieties. Real-time qRT-PCR analysis in LPS-stimulated cells revealed down-regulation of proinflammatory cytokines (IL-8, TNF-α, VCAM-1), transcription factor NF-κB and modulation of microRNA-126 (specific post-transcriptional regulator of VCAM-1) by cowpea polyphenolics. The ability of cowpea polyphenols to modulate miR-126 signaling and its target gene VCAM-1 were studied in LPS-stimulated endothelial cells transfected with a specific inhibitor of miR-126, and treated with 10 mg GAE/L black cowpea extract where the extract in part reversed the effect of the miR-126 inhibitor. This suggests that cowpea may exert their anti-inflammatory activities at least in part through induction of miR-126 that then down-regulate VCAM-1 mRNA and protein expressions. Overall, Cowpea therefore is promising as an anti-inflammatory dietary component.

  2. Optimization of ultrasound-assisted extraction of crude oil from winter melon (Benincasa hispida) seed using response surface methodology and evaluation of its antioxidant activity, total phenolic content and fatty acid composition.

    Science.gov (United States)

    Bimakr, Mandana; Rahman, Russly Abdul; Taip, Farah Saleena; Adzahan, Noranizan Mohd; Sarker, Md Zaidul Islam; Ganjloo, Ali

    2012-10-08

    In the present study, ultrasound-assisted extraction of crude oil from winter melon seeds was investigated through response surface methodology (RSM). Process variables were power level (25-75%), temperature (45-55 °C) and sonication time (20-40 min). It was found that all process variables have significant (p yield (108.62 mg-extract/g-dried matter). The antioxidant activity, total phenolic content and fatty acid composition of extract obtained under optimized conditions were determined and compared with those of oil obtained by the Soxhlet method. It was found that crude extract yield (CEY) of ultrasound-assisted extraction was lower than that of the Soxhlet method, whereas antioxidant activity and total phenolic content of the extract obtained by ultrasound-assisted extraction were clearly higher than those of the Soxhlet extract. Furthermore, both extracts were rich in unsaturated fatty acids. The major fatty acids of the both extracts were linoleic acid and oleic acid.

  3. Sensing cocaine in saliva with attenuated total reflection infrared (ATR-IR) spectroscopy combined with a one-step extraction method

    Science.gov (United States)

    Hans, Kerstin M.-C.; Gianella, Michele; Sigrist, Markus W.

    2012-03-01

    On-site drug tests have gained importance, e.g., for protecting the society from impaired drivers. Since today's drug tests are majorly only positive/negative, there is a great need for a reliable, portable and preferentially quantitative drug test. In the project IrSens we aim to bridge this gap with the development of an optical sensor platform based on infrared spectroscopy and focus on cocaine detection in saliva. We combine a one-step extraction method, a sample drying technique and infrared attenuated total reflection (ATR) spectroscopy. As a first step we have developed an extraction technique that allows us to extract cocaine from saliva to an almost infrared-transparent solvent and to record ATR spectra with a commercially available Fourier Transform-infrared spectrometer. To the best of our knowledge this is the first time that such a simple and easy-to-use one-step extraction method is used to transfer cocaine from saliva into an organic solvent and detect it quantitatively. With this new method we are able to reach a current limit of detection around 10 μg/ml. This new extraction method could also be applied to waste water monitoring and controlling caffeine content in beverages.

  4. Study on the change of total fat content and fatty acid composition of the ethanol extract from cooking drips of thunnus thynnus by ionizing irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Hee Sub; Choi, Jong Il; Kim, Hyun Joo; Kim, Jin Kyu; Byun, Myung Woo; Lee, Ju Woon [Team for Radiation Food Science and Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup (Korea, Republic of); Yoo, Cheon Woo; Kim, Ju Bong [Dongwon Research and Development Center, Seongnam (Korea, Republic of); Hwang, Young Jung [Division of Food Science, Jinju International University, Jinju (Korea, Republic of); Chung, Young Jin [Dept. of Food and Nutrition, Chungnam National University, Daejeon (Korea, Republic of)

    2008-05-15

    This study was conducted to examine the effect of a gamma irradiation (GM) and an electron-beam irradiation (EB) on the total fat content and fatty acid composition of ethanol extract from cooking drips of Thunnus thynnus (ECT). The total fat content of samples were determined by fat extraction (Folch method) and fatty acid composition was by gas chromatography mass spectrometry (GC-MS) after fat extraction. The results showed that total fat contents were not changed by GM and EB up to the dose of 50 kGy. The content of unsaturated fatty acids (USFA) such as vaccenic acid and DHA, was decreased by irradiation. But, the content of palmitoleic acid was not changed by GM. In contrast, the content of saturated fatty acids(SFA) such as myristic acid and palmitic acid, was increased by the irradiation. But, the content of stearic acid was decreased with the increase of irradiation dose. Also, it has been shown that the GM had further affected the change of fatty acid content than EB.

  5. Study on the change of total fat content and fatty acid composition of the ethanol extract from cooking drips of thunnus thynnus by ionizing irradiation

    International Nuclear Information System (INIS)

    Lee, Hee Sub; Choi, Jong Il; Kim, Hyun Joo; Kim, Jin Kyu; Byun, Myung Woo; Lee, Ju Woon; Yoo, Cheon Woo; Kim, Ju Bong; Hwang, Young Jung; Chung, Young Jin

    2008-01-01

    This study was conducted to examine the effect of a gamma irradiation (GM) and an electron-beam irradiation (EB) on the total fat content and fatty acid composition of ethanol extract from cooking drips of Thunnus thynnus (ECT). The total fat content of samples were determined by fat extraction (Folch method) and fatty acid composition was by gas chromatography mass spectrometry (GC-MS) after fat extraction. The results showed that total fat contents were not changed by GM and EB up to the dose of 50 kGy. The content of unsaturated fatty acids (USFA) such as vaccenic acid and DHA, was decreased by irradiation. But, the content of palmitoleic acid was not changed by GM. In contrast, the content of saturated fatty acids(SFA) such as myristic acid and palmitic acid, was increased by the irradiation. But, the content of stearic acid was decreased with the increase of irradiation dose. Also, it has been shown that the GM had further affected the change of fatty acid content than EB

  6. Averrhoa carambola free phenolic extract ameliorates nonalcoholic hepatic steatosis by modulating mircoRNA-34a, mircoRNA-33 and AMPK pathways in leptin receptor-deficient db/db mice.

    Science.gov (United States)

    Pang, Daorui; You, Lijun; Zhou, Lin; Li, Tong; Zheng, Bisheng; Liu, Rui Hai

    2017-12-13

    The objective of the present study is to investigate the hepatic steatosis relieving effect of Averrhoa carambola free phenolic extract (ACF) on leptin receptor-deficient (db/db) mice and elucidate the modulation hepatic lipogenesis mechanisms. The serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) assays, accompanying hematoxylin and eosin (H&E) staining, were applied to identify the alleviation of liver histopathological changes. Serum and hepatic lipid assays, combined with oil red O staining, were used to investigate the amelioration of lipid accumulation. Further assessments by quantitative real-time PCR and western blot assays were used to elucidate the suppression of the fatty acid and triglyceride (TG) synthesis mechanisms underlying ACF protection. These results indicated that ACF treatment significantly reduced the liver TG of db/db mice (p < 0.05). The mechanisms are partly through phosphorylation of AMPK α and down-regulation of SREBP-1c expression, and further down-regulation of FAS and SCD1 (p < 0.05). In addition, the expression levels of mircoRNA-34a and mircoRNA-33, which modulate this signaling pathway, were significantly down-regulated by ACF treatment (p < 0.05). Collectively, these results revealed that ACF exhibited a potent hepatic steatosis relieving effect partly by inhibiting the signal transduction of hepatic lipogenesis.

  7. Polyethylene glycol and polyvinylpirrolidone effect on bacterial rRNA extraction and hybridization from cells exposed to tannins Efeito de polietilenoglicol e polivinilpirrolidona na extração e hibridização de rRNA bacteriano de células expostas a taninos

    OpenAIRE

    Pedro Braga Arcuri; Michael Larry Thonney; Peter Schofield; Alice Nelson Pell

    2003-01-01

    In order to detect fluctuations in ruminal microbial populations due to forage tannins using 16S ribosomal RNA (rRNA) probes, recovery of intact rRNA is required. The objective of this work was to evaluate the effect of polyethylene glycol (PEG) and polyvinylpirrolidone (PVP) on extraction of bacterial rRNA, in the presence of tannins from tropical legume forages and other sources, that hybridize with oligonucleotide probes. Ruminococcus albus 8 cells were exposed to 8 g/L tannic acid or 1 g/...

  8. FORTRAN 4 programs for the extraction of potential well parameters from the energy dependence of total elastic scattering cross sections

    Science.gov (United States)

    Labudde, R. A.

    1972-01-01

    An attempt has been made to keep the programs as subroutine oriented as possible. Usually only the main programs are directly concerned with the problem of total cross sections. In particular the subroutines POLFIT, BILINR, GASS59/MAXLIK, SYMOR, MATIN, STUDNT, DNTERP, DIFTAB, FORDIF, EPSALG, REGFAL and ADSIMP are completely general, and are concerned only with the problems of numerical analysis and statistics. Each subroutine is independently documented.

  9. Supplementation with Watermelon Extract Reduces Total Cholesterol and LDL Cholesterol in Adults with Dyslipidemia under the Influence of the MTHFR C677T Polymorphism.

    Science.gov (United States)

    Massa, Nayara M L; Silva, Alexandre S; de Oliveira, Caio V C; Costa, Maria J C; Persuhn, Darlene C; Barbosa, Carlos V S; Gonçalves, Maria da C R

    2016-08-01

    Dyslipidemia and genetic polymorphisms are associated with increased risk for developing cardiovascular diseases, and watermelon appears to have the potential to improve hyperlipidemia due to the presence of nutrients such as arginine and citrulline. To test the hypolipidemic effect of watermelon extract (Citrullus lanatus) and the influence of the methylenetetrahydrofolate reductase genotype (MTHFR C677T) on supplementation response. This is an experimental clinical phase II randomized and double-blind study. Forty-three subjects with dyslipidemia were randomly divided into 2 groups: experimental (n = 22) and control (n = 21) groups. The subjects were supplemented daily for 42 days with 6 g of watermelon extract or a mixture of carbohydrates (sucrose/glucose/fructose). The use of watermelon extract reduced plasma total cholesterol (p watermelon extract in reducing plasma levels of lipids in humans. The MTHFR C677T polymorphism did not affect the plasma lipid concentration but made individuals more responsive to treatment with watermelon. The consumption of this functional food represents an alternative therapy in the combined treatment of patients with dyslipidemia, promoting health and minimizing the development of risk factors for cardiovascular diseases.

  10. Effect of Pistacia Atlantica Extract on Glutathione Peroxidase Tissue Levels and Total Oxidative Capacity of Liver and Plasma Lipid Profile of Rats

    Directory of Open Access Journals (Sweden)

    Parvin Farzanegi

    2013-11-01

    Full Text Available Background: Exercise causes increased oxygen consumption, leaving cells exposed to oxidative stress. Antioxidants may have a protective effect by inhibiting lipid peroxidation. Thus, this study aims to examine the effect of Pistacia atlantica extract on glutathione peroxidase levels and total oxidative capacity of liver and plasma lipid profile of rats. Materials and Methods: In this experimental study, 28 female rats’ weight 155.8±2.7 grams were randomly and equally divided into 4 groups of exercise-saline, control-saline, exercise-mastic, and control-mastic. The exercise groups exercised for 8 weeks (5 days per week, 60 minutes daily, 25 meters per minute, on a zero degree slope. The rats received equal volumes of mastic and saline orally for 4 weeks. Blood and tissue samples were taken 72 hours after the last exercise session. Data were analyzed using one-way variance analysis (ANOVA.Results: Consumption of Pistacia atlantica extract together with endurance exercising for 8 weeks did not significantly affect glutathione peroxidase concentration, total oxidative capacity, LDL, triglyceride, or cholesterol, but significantly reduced HDL (p=0.002.Conclusion: Results showed that antioxidant and lipid profile levels were not affected by consumption of supplements and endurance exercising. However, further studies are required to assess the long term effects of this herbal extract.

  11. Novel determination of the total phenolic content in crude plant extracts by the use of 1H NMR of the -OH spectral region

    International Nuclear Information System (INIS)

    Nerantzaki, A.A.; Tsiafoulis, C.G.; Charisiadis, P.; Kontogianni, V.G.; Gerothanassis, I.P.

    2011-01-01

    A novel method for the determination of the total phenolic content using 1 H NMR spectroscopy in the -OH spectral region is presented. The use of DMSO-d 6 , which is an aprotic and strongly hydrogen bonding solvent, allows the 'appearance' of the relative sharp resonances of phenolic hydroxyl protons in the region of 8-14 ppm. The determination of the total phenolic -OH content requires three steps: (i) a 1D 1 H NMR spectrum is obtained in DMSO-d 6 ; (ii) a subsequent 1D 1 H NMR spectrum is recorded with irradiation of the residual water signal which results in the elimination or reduction of the phenolic -OH groups, due to proton exchange; and (iii) 1D 1 H NMR spectra are recorded with the addition of a progressively increased amount of salt, NaHCO 3 , which results in extensive linebroadening of the COOH resonances thus allowing the discrimination of the phenolic from the carboxylic acid signals. Integration, with respect to the internal standard TSP-d 4 , of the signal resonances between 14 and 8 ppm in spectrum (i) which are either eliminated or reduced in intensity in steps (ii) and (iii) allows the quantitation of the total phenolic content. The method was applied to model compounds, a mixture of them and several extracts of natural products. The results of the proposed 1 H NMR method were compared to the Folin-Ciocalteu (FC) reagent method. Additionally, since 1 H NMR refers to the total phenolic hydroxyl protons, a reaction factor, A e , is proposed that corresponds to the hydroxyl reactivity. The 1 H NMR method is rapid and accurate bearing the inherent advantages of the NMR spectroscopy and can be applied directly in complex extracts. Furthermore, it can be applied in a wide range of matrixes from crude plant extracts and food products to biological samples.

  12. The effect of hydro-ethanolic extract of Curcuma longa rhizome and curcumin on total and differential WBC and serum oxidant, antioxidant biomarkers in rat model of asthma.

    Science.gov (United States)

    Shakeri, Farzaneh; Soukhtanloo, Mohammad; Boskabady, Mohammad Hossein

    2017-02-01

    The effects of Curcuma longa ( C. longa ) and curcumin on total and differential WBC count and oxidant, antioxidant biomarkers, in rat model of asthma were evaluated. Total and differential WBC count in the blood, NO 2 , NO 3 , MDA, SOD, CAT and thiol levels in serum were examined in control, asthma, Asthmatic rats treated with C. longa (0.75, 1.50, and 3.00 mg/ml), curcumin (0.15, 0.30, and 0.60 mg/ml), and dexamethasone (1.25 μg/ml) rats. Total and most differential WBC count, NO 2 , NO 3 and MDA were increased but lymphocytes, SOD, CAT and thiol were decreased in asthmatic animals compared to controls ( P longa and curcumin compared to asthmatic group ( P longa and curcumin ( P longa extract and its constituent curcumin in animal model of asthma was observed which suggest a therapeutic potential for the plant and its constituent on asthma.

  13. Turmeric (Curcuma longa L.) extract may prevent the deterioration of spatial memory and the deficit of estimated total number of hippocampal pyramidal cells of trimethyltin-exposed rats.

    Science.gov (United States)

    Yuliani, Sapto; Mustofa; Partadiredja, Ginus

    2018-01-01

    Protection of neurons from degeneration is an important preventive strategy for dementia. Much of the dementia pathology implicates oxidative stress pathways. Turmeric (Curcuma longa L.) contains curcuminoids which has anti-oxidative and neuro-protective effects. These effects are considered to be similar to those of citicoline which has been regularly used as one of standard medications for dementia. This study aimed at investigating the effects of turmeric rhizome extract on the hippocampus of trimethyltin (TMT)-treated Sprague-Dawley rats. The rats were divided randomly into six groups, i.e., a normal control group (N); Sn group, which was given TMT chloride; Sn-Cit group, which was treated with citicoline and TMT chloride; and three Sn-TE groups, which were treated with three different dosages of turmeric rhizome extract and TMT chloride. Morris water maze test was carried out to examine the spatial memory. The estimated total number of CA1 and CA2-CA3 pyramidal cells was calculated using a stereological method. The administration of turmeric extract at a dose of 200 mg/kg bw has been shown to prevent the deficits in the spatial memory performance and partially inhibit the reduction of the number of CA2-CA3 regions pyramidal neurons. TMT-induced neurotoxic damage seemed to be mediated by the generation of reactive oxygen species and reactive nitrogen species. Turmeric extract might act as anti inflammatory as well as anti-oxidant agent. The effects of turmeric extract at a dose of 200 mg/kg bw seem to be comparable to those of citicoline.

  14. [Effect of total hypothermia on the fatty acid composition of blood phospholipids of rats and sousliks and light irradiation on chemical processes in lipid extract].

    Science.gov (United States)

    Zabelinskiĭ, S A; Chebotareva, M A; Kalandarov, A M; Feĭzulaev, B A; Klichkhanov, N K; Krivchenko, A I; Kazennov, A M

    2011-01-01

    Effect of hypothermia on the fatty acid composition of rat and souslik blood phospholipids is studied. Different reaction of these animals to cooling is revealed: in rats no changes were observed in the fatty acid composition of blood phospholipids, whereas in the hibernating there were significant changes in the content of individual fatty acids (FA). The content of monoenic acids in sousliks decreased almost by 50%, while the content of saturated acid (C18) and of polyenic acids C18 : 2omega6 and C20 : 4omega6 rose significantly. Such changes seem to be the mechanism that promotes maintenance of the organism viability under conditions of a decreased level of metabolism, heart rhythm, and body temperature and is evolutionarily acquired. At the same time, the observed changes in the content of individual FA do not lead to sharp changes in such integrative parameters as the total non-saturation of phospholipids, which determines liquid properties of chylomicrons and other lipolipoprotein transport particles of the souslik blood. There are studied absorption spectra of blood lipid extracts of rats and sousliks under effect of light as well as effect of light upon the FA composition of lipid extracts of these animals. The FA composition of lipid extracts has been established to remain practically constant, whereas the character of changes of spectra under action of light indicates the presence in the extracts of oxidation-reduction reactions. The obtained data allow suggesting that in the lipid extract there occurs cooperation both of the phospholipid molecules themselves and of them with other organic molecules, which makes it possible for fatty acids to participate in processes of transport both of electrons and of protons. This novel role of FA as a participant of the electron transfer might probably be extrapolated to chemical reactions (processes) occurring inside the membrane.

  15. Optimization of microwave-assisted extraction of total extract, stevioside and rebaudioside-A from Stevia rebaudiana (Bertoni) leaves, using response surface methodology (RSM) and artificial neural network (ANN) modelling.

    Science.gov (United States)

    Ameer, Kashif; Bae, Seong-Woo; Jo, Yunhee; Lee, Hyun-Gyu; Ameer, Asif; Kwon, Joong-Ho

    2017-08-15

    Stevia rebaudiana (Bertoni) consists of stevioside and rebaudioside-A (Reb-A). We compared response surface methodology (RSM) and artificial neural network (ANN) modelling for their estimation and predictive capabilities in building effective models with maximum responses. A 5-level 3-factor central composite design was used to optimize microwave-assisted extraction (MAE) to obtain maximum yield of target responses as a function of extraction time (X 1 : 1-5min), ethanol concentration, (X 2 : 0-100%) and microwave power (X 3 : 40-200W). Maximum values of the three output parameters: 7.67% total extract yield, 19.58mg/g stevioside yield, and 15.3mg/g Reb-A yield, were obtained under optimum extraction conditions of 4min X 1 , 75% X 2 , and 160W X 3 . The ANN model demonstrated higher efficiency than did the RSM model. Hence, RSM can demonstrate interaction effects of inherent MAE parameters on target responses, whereas ANN can reliably model the MAE process with better predictive and estimation capabilities. Copyright © 2017. Published by Elsevier Ltd.

  16. Characterization, antibacterial, total antioxidant, scavenging, reducing power and ion chelating activities of green synthesized silver, copper and titanium dioxide nanoparticles using Artemisia haussknechtii leaf extract.

    Science.gov (United States)

    Alavi, Mehran; Karimi, Naser

    2017-12-12

    Recently, major problem related to pathogenic bacteria is augmentation of antibiotic resistance which has been changed treatment and recovery of millions of infectious patients. The present study reports an eco-friendly, rapid and easy method for synthesis of silver (Ag), copper (Cu) and titanium dioxide (TiO 2 ) nanoparticles (NPs) using Artemisia haussknechtii leaf aqueous extract with antibacterial activities against multi-drug resistance (MDR) bacteria species. Three different concentrations (0.001, 0.01 and 0.1 M) of AgNO 3 , CuSO 4 and TiO (OH) 2 were investigated for obtaining optimum NPs green synthesis. Total phenolic content, total flavonoid content of leaf extract and total antioxidant activity (DPPH) assay were determined as radical scavenging methods. UV-Visible spectroscopy, Fourier transform infrared spectroscopy analysis, X-ray diffraction, energy dispersive X-ray spectroscopy, field emission scanning electron microscope and atomic force microscopy (AFM) were used due to NPs characterization. The size average of the Ag, Cu and TiO 2 NPs obtained were respectively 10.69 ± 5.55, 35.36 ± 44.4 and 92.58 ± 56.98 nm. In the case of antibacterial assay, disc diffusion assay, minimum inhibitory concentration, minimum bactericidal concentration, bacterial growth and morphology of four MDR species Staphylococcus aureus ATCC 43300, Staphylococcus epidermidis ATCC 12258, Serratia marcescens ATTC13880 and Escherichia coli ATCC 25922 were evaluated. Results of this study demonstrated that A. haussknechtii leaf extract with various groups of phytochemicals such as phenols and flavonoids had suitable ability in green synthesis of Ag, Cu and TiO 2 NPs. Also, Ag and Cu NPs had more antibacterial activities compared to TiO 2 NPs.

  17. Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags.

    Science.gov (United States)

    Peng, Xin; Yu, Ke-Qiang; Deng, Guan-Hua; Jiang, Yun-Xia; Wang, Yu; Zhang, Guo-Xia; Zhou, Hong-Wei

    2013-12-01

    Low cost and high throughput capacity are major advantages of using next generation sequencing (NGS) techniques to determine metagenomic 16S rRNA tag sequences. These methods have significantly changed our view of microorganisms in the fields of human health and environmental science. However, DNA extraction using commercial kits has shortcomings of high cost and time constraint. In the present study, we evaluated the determination of fecal microbiomes using a direct boiling method compared with 5 different commercial extraction methods, e.g., Qiagen and MO BIO kits. Principal coordinate analysis (PCoA) using UniFrac distances and clustering showed that direct boiling of a wide range of feces concentrations gave a similar pattern of bacterial communities as those obtained from most of the commercial kits, with the exception of the MO BIO method. Fecal concentration by boiling method affected the estimation of α-diversity indices, otherwise results were generally comparable between boiling and commercial methods. The operational taxonomic units (OTUs) determined through direct boiling showed highly consistent frequencies with those determined through most of the commercial methods. Even those for the MO BIO kit were also obtained by the direct boiling method with high confidence. The present study suggested that direct boiling could be used to determine the fecal microbiome and using this method would significantly reduce the cost and improve the efficiency of the sample preparation for studying gut microbiome diversity. © 2013 Elsevier B.V. All rights reserved.

  18. Effect of Green Tea Extract on Systemic Metabolic Homeostasis in Diet-Induced Obese Mice Determined via RNA-Seq Transcriptome Profiles

    Directory of Open Access Journals (Sweden)

    Ji-Young Choi

    2016-10-01

    Full Text Available Green tea (GT has various health effects, including anti-obesity properties. However, the multiple molecular mechanisms of the effects have not been fully determined. The aim of this study was to elucidate the anti-obesity effects of GT via the analysis of its metabolic and transcriptional responses based on RNA-seq profiles. C57BL/6J mice were fed a normal, high-fat (60% energy as fat, or high-fat + 0.25% (w/w GT diet for 12 weeks. The GT extract ameliorated obesity, hepatic steatosis, dyslipidemia, and insulin resistance in diet-induced obesity (DIO mice. GT supplementation resulted in body weight gain reduction than mice fed high-fat through enhanced energy expenditure, and reduced adiposity. The transcriptome profiles of epididymal white adipose tissue (eWAT suggested that GT augments transcriptional responses to the degradation of branched chain amino acids (BCAAs, as well as AMP-activated protein kinase (AMPK signaling, which suggests enhanced energy homeostasis. Our findings provide some significant insights into the effects of GT for the prevention of obesity and its comorbidities. We demonstrated that the GT extract contributed to the regulation of systemic metabolic homeostasis via transcriptional responses to not only lipid and glucose metabolism, but also amino acid metabolism via BCAA degradation in the adipose tissue of DIO mice.

  19. New method to determine the total carbonyl functional group content in extractable particulate organic matter by tandem mass spectrometry.

    Science.gov (United States)

    Dron, J; Zheng, W; Marchand, N; Wortham, H

    2008-08-01

    A functional group analysis method was developed to determine the quantitative content of carbonyl functional groups in atmospheric particulate organic matter (POM) using constant neutral loss scanning-tandem mass spectrometry (CNLS-MS/MS). The neutral loss method consists in monitoring the loss of a neutral fragment produced by the fragmentation of a precursor ion in a collision cell. The only ions detected are the daughter ions resulting from the loss of the neutral fragment under study. Then, scanning the loss of a neutral fragment characteristic of a functional group enables the selective detection of the compounds bearing the chemical function under study within a complex mixture. The selective detection of carbonyl functional groups was achieved after derivatization with pentafluorophenylhydrazine (PFPH) by monitoring the neutral loss of C(6)F(5)N (181 amu), which was characteristic of a large panel of derivatized carbonyl compounds. The method was tested on 25 reference mixtures of different composition, all containing 24 carbonyl compounds at randomly determined concentrations. The repeatability and calibration tests were satisfying as they resulted in a relative standard deviation below 5% and a linear range between 0.01 and 0.65 mM with a calculated detection limit of 0.0035 mM. Also, the relative deviation induced by changing the composition of the mixture while keeping the total concentration of carbonyl functional groups constant was less than 20%. These reliability experiments demonstrate the high robustness of the developed procedure for accurate carbonyl functional group measurement, which was applied to atmospheric POM samples. Copyright (c) 2008 John Wiley & Sons, Ltd.

  20. A novel solid phase extraction procedure on Amberlite XAD-1180 for speciation of Cr(III), Cr(VI) and total chromium in environmental and pharmaceutical samples

    International Nuclear Information System (INIS)

    Narin, Ibrahim; Kars, Ayse; Soylak, Mustafa

    2008-01-01

    Due to the toxicity of chromium, species depend on their chemical properties and bioavailabilities, speciation of chromium is very important in environmental samples. A speciation procedure for chromium(III), chromium(VI) and total chromium in environmental samples is presented in this work, prior to flame atomic absorption spectrometric determination of chromium. The procedure is based on the adsorption of Cr(III)-diphenylcarbazone complex on Amberlite XAD-1180 resin. After oxidation of Cr(III), the developed solid phase extraction system was applied to determinate the total chromium. Cr(III) was calculated as the difference between the total Cr content and the Cr(VI) content. The analytical conditions for the quantitative recoveries of Cr(VI) on Amberlite XAD-1180 resin were investigated. The effects of some alkaline, earth alkaline, metal ions and also some anions were also examined. Preconcentration factor was found to be 75. The detection limits (LOD) based on three times sigma of the blank (N: 21) for Cr(VI) and total chromium were 7.7 and 8.6 μg/L, respectively. Satisfactory results for the analysis of total chromium in the stream sediment (GBW7310) certified reference material for the validation of the presented method was obtained. The procedure was applied to food, water and pharmaceutical samples successfully

  1. DPPH RADICAL SCAVENGING ACTIVITY, TOTAL PHENOLICS AND FLAVONOIDS OF WATER SOLUBLE EXTRACTS DERIVED FROM LEAVES AND FRUIT OF Ficus carica L. AND Ficus parietalis Bl.

    Directory of Open Access Journals (Sweden)

    Oktavia Tri Wahyuni

    2016-08-01

    Full Text Available Ficus carica L and Ficus parietalis Bl. (Moraceae are closely related plants which also known in Indonesia as Figs L. Considering the wide therapeutic value of Figs, this research was aimed to evaluate the DPPH-radical scavenging activity of both plants as well as their total phenolic and flavonoids. Extracts were produced by using boiled water and diluted to gain the desired concentration. Analyses were performed by using UV-vis spectrophotometer. Radical scavenging activity testing was done by using radical of DPPH (2,2-diphenyl-1-pycrylhydrazyl to determine the IC50s. The determination of total phenolic was conducted by using Folin-Ciocalteau method and calculated as Gallic Acid Equivalence (GAE. The total flavonoid was measured by using AlCl3-reagents, and calculated as Rutin Equivalence (RE. Afterwards, the radical scavenging activity was correlated to the total phenolic and flavonoids contents. The results showed that the water soluble extract of F. carica fruit had the best IC50 value of 33.38 mg/mL, followed successively by the F. parietalis fruit (35.69 mg/mL, F. parietalis leaves (44.01 mg/mL and the F. carica leaves (76.38 mg/mL. The highest content of total phenolic was shown by the leaves of F. parietalis (1.46% w/w GAE and the lowest was in the fruit or F. carica (0.36% w/w GAE. The highest flavonoid content was detected in the leaves of F. carica (1.42% w/w RE and the lowest was in the F. parietalis fruit (0.20% w/w RE. Correlation analyses of the IC50 values vs. the total phenolic and the flavonoids contents resulted in a positive slope having R2 values as 0.5362 and 0.9895, respectively. As a conclusion, the total flavonoid content influenced the DPPH radical scavenging activity by 98.95%, while the total phenolic content influence was only 53.62%.

  2. Neuroprotective Effect of Total and Sequential Extract of Scrophularia striata Boiss. in Rat Cerebellar Granule Neurons Following Glutamate- Induced Neurotoxicity: An In-vitro Study

    Science.gov (United States)

    Salavati, Parvin; Ramezani, Mina; Monsef-Esfahani, Hamid R; Hajiagha, Reza; Parsa, Maliheh; Tavajohi, Shoreh; Ostad, Seyed Nasser

    2013-01-01

    Neuroprotective effect of the extract from aerial parts of Scrophularia striata Boiss (Scrophulariaceae) was investigated against glutamate-induced neurotoxicity on cultured rat pups Cerebellar Granule Neurons (CGNs). CGNs from 8 days old Sprague-Dawley rat were prepared and cultured. The experiments were performed after 8 days in culture. The plant was collected from the northeastern part (Ruin region) of Iran and air-dried at room temperature. The total extract was prepared with maceration of prepared powder in ethanol 80% for three times. Sequential extracts were obtained using dried and powdered aerial parts with increasingly polar solvents: petroleum ether, chloroform, ethyl acetate and methanol 80% solution. Cultured cells were exposed to 125 μM of glutamate for 12 h following a 24 h of incubation with test fractions at concentration of 10 mcg/mL. Morphological assay was performed using invert light microscope after fixation and staining with haematoxylin. Neuronal viability was measured using MTT assay. Statistical analysis was done using SPSS software. One way analysis of variance (ANOVA) was performed by Tukey post-hoc test. Values were considered statistically significant when p-value ≤ 0.05. Results of this study showed a significant neuroprotective activity of high polarity methanolic fraction of aerial parts of Scrophularia striata against glutamate-induced neurotoxicity in a dosedependent manner. Treatment with 10 mcg/mL of the fractions showed the best result. PMID:24250613

  3. Association Mapping of Total Carotenoids in Diverse Soybean Genotypes Based on Leaf Extracts and High-Throughput Canopy Spectral Reflectance Measurements.

    Directory of Open Access Journals (Sweden)

    Arun Prabhu Dhanapal

    Full Text Available Carotenoids are organic pigments that are produced predominantly by photosynthetic organisms and provide antioxidant activity to a wide variety of plants, animals, bacteria, and fungi. The carotenoid biosynthetic pathway is highly conserved in plants and occurs mostly in chromoplasts and chloroplasts. Leaf carotenoids play important photoprotective roles and targeted selection for leaf carotenoids may offer avenues to improve abiotic stress tolerance. A collection of 332 soybean [Glycine max (L. Merr.] genotypes was grown in two years and total leaf carotenoid content was determined using three different methods. The first method was based on extraction and spectrophotometric determination of carotenoid content (eCaro in leaf tissue, whereas the other two methods were derived from high-throughput canopy spectral reflectance measurements using wavelet transformed reflectance spectra (tCaro and a spectral reflectance index (iCaro. An association mapping approach was employed using 31,253 single nucleotide polymorphisms (SNPs to identify SNPs associated with total carotenoid content using a mixed linear model based on data from two growing seasons. A total of 28 SNPs showed a significant association with total carotenoid content in at least one of the three approaches. These 28 SNPs likely tagged 14 putative loci for carotenoid content. Six putative loci were identified using eCaro, five loci with tCaro, and nine loci with iCaro. Three of these putative loci were detected by all three carotenoid determination methods. All but four putative loci were located near a known carotenoid-related gene. These results showed that carotenoid markers can be identified in soybean using extract-based as well as by high-throughput canopy spectral reflectance-based approaches, demonstrating the utility of field-based canopy spectral reflectance phenotypes for association mapping.

  4. Determination of total arsenic and arsenic(III) in phosphate fertilizers by hydride generation atomic absorption spectrometry after ultrasound-assisted extraction based on a control acid media.

    Science.gov (United States)

    Rezende, Helen Cristine; Coelho, Nivia Maria Melo

    2014-01-01

    An ultrasound-assisted extraction procedure was developed for determination of inorganic arsenic (As) in phosphate fertilizer by hydride generation atomic absorption spectrometry. The variables that affect the hydride generation step were optimized, including the reducer, acid, sample flow rate, and concentrations of the acid and reducer. The determination of As(lll) was performed through the simple control of solution pH with a 0.5 M citric acid-sodium citrate buffer solution at pH 4.5, and total As was determined after a pre-reduction reaction with 1.0% (w/v) thiourea. Ultrasound-assisted acid extraction was performed, and the parameters sonication time and acid and Triton X-114 concentrations were optimized using a 23 factorial design and central composite design. LODs for As(lll) and total As were 0.029 and 0.022 microg/L, respectively. The accuracy of the method was confirmed with certified reference materials. The method was successfully applied in the determination of inorganic As in phosphate fertilizer samples.

  5. Lead isotopic signatures in Antarctic marine sediment cores: A comparison between 1 M HCl partial extraction and HF total digestion pre-treatments for discerning anthropogenic inputs

    International Nuclear Information System (INIS)

    Townsend, A.T.; Snape, I.; Palmer, A.S.; Seen, A.J.

    2009-01-01

    Sensitive analytical techniques are typically required when dealing with samples from Antarctica as even low concentrations of contaminants can have detrimental environmental effects. Magnetic Sector ICP-MS is an ideal technique for environmental assessment as it offers high sensitivity, multi-element capability and the opportunity to determine isotope ratios. Here we consider the Pb isotope record of five marine sediment cores collected from three sites in the Windmill Islands area of East Antarctica: Brown Bay adjacent to the current Australian station Casey, Wilkes near the abandoned US/Australian Station and McGrady Cove lying midway between the two. Two sediment pre-treatment approaches were considered, namely partial extraction with 1 M HCl and total dissolution involving HF. Lead isotope ratio measurements made following sediment partial extraction provided a more sensitive indication of Pb contamination than either Pb concentrations alone (irrespective of sample pre-treatment method) or isotope ratios made after HF digestion, offering greater opportunity for discrimination between impacted and natural/geogenic samples and sites. Over 90% of the easily extractable Pb from sediments near Casey was anthropogenic in origin, consisting of Pb from major Australian deposits. At Wilkes impact from discarded batteries with a unique isotopic signature was found to be a key source of Pb contamination to the marine environment with ∼ 70-80% of Pb being anthropogenic in origin. The country and source of origin of these batteries remain unknown. Little evidence was found suggesting contamination at Wilkes by Pb originating from the major US source, Missouri. No definitive assessment could be made regarding Pb impact at McGrady Cove as the collected sediment core was of insufficient depth. Although Pb isotope ratio signatures may indicate anthropogenic input, spatial concentration gradients at nearby Brown Bay suggest contamination at McGrady Cove is unlikely. We

  6. A new estimation of the total flavonoids in silkworm cocoon sericin layer through aglycone determination by hydrolysis-assisted extraction and HPLC-DAD analysis

    Directory of Open Access Journals (Sweden)

    Jin-Ge Zhao

    2016-03-01

    Full Text Available Background: Silk sericin and a few non-protein components isolated from the cocoon layer including two silk proteins in silkworm Bombyx mori has many bioactivities. The dietary sericin possess antinatural oxidation, anticancer, antihyperlipidemic, and antidiabetic activities. The non-protein components surrounding the sericin layer involve in wax, pigments mainly meaning flavonoids, sugars, and other impurities. However, very few investigations have reported the estimation of the total flavonoids derived from the cocoon layer. The flavonoids are commonly present in their glycosylated forms and mostly exist as quercetin glycosides in the sericin layers of silkworm cocoons. Objective: The aim of this study was to find a more accurate method to estimate the level of the total flavonoids in silkworm cocoons. Design: An efficient procedure of hydrolysis-assisted extraction (HAE was first established to estimate the level of the total flavonoids through the determination of their aglycones, quercetin, and kaempferol. Then, a comparison was made between traditional colorimetric method and our method. In addition, the antioxidant activities of hydrolysis-assisted extract sample were determined. Results: The average contents of quercetin and kaempferol were 1.98 and 0.42 mg/g in Daizo cocoon. Their recoveries were 99.56 and 99.17%. The total sum of quercetin and kaempferol was detected to be 2.40±0.07 mg/g by HAE-HPLC, while the total flavonoids (2.59±0.48 mg/g estimated by the traditional colorimetric method were only equivalent to 1.28±0.04 mg/g of quercetin. The HAE sample also exhibits that IC50 values of scavenging ability of diphenyl picryl hydrazinyl (DPPH radical and hydroxyl radical (HO· are 243.63 µg/mL and 4.89 mg/mL, respectively. Conclusions: These results show that the HAE-HPLC method is specificity of cocoon and far superior to the colorimetric method. Therefore, this study has profound significance for the comprehensive utilization

  7. Bienzymatic sensor based on the use of redox enzymes and chitosan-MWCNT nanocomposite. Evaluation of total phenolic content in plant extracts

    International Nuclear Information System (INIS)

    Diaconu, M.; Litescu, S.C.; Radu, G.L.

    2011-01-01

    We are presenting a bienzymatic sensor for the determination of polyphenols. An ITO electrode was modified with multiwalled carbon nanotubes, and the enzymes laccase and tyrosinase were co-entrapped into a chitosan matrix. The resulting biosensor was calibrated at -50 mV (vs. the Ag/AgCl reference electrode) using rosmarinic acid, caffeic acid and gallic acid as the substrates. The new biosensor resulted in a 10.7-fold increase in response sensitivity and a considerable improvement of the detection limit (42 nM for rosmarinic acid). Fouling of the surface of the biosensor was prevented by applying the surfactant Tween 20. The data recorded in surfactant medium revealed a significant improvement of the operational stability and an enlarged linear concentration ranges (up to 12 μM for rosmarinic acid). The sensor was used to evaluate the total phenolic content from extracts of Salvia officinalis and cultures of Basilicum callus. (author)

  8. Effects of different enzyme treatments in extraction of total folate from infant formula, baby foods and other food products prior to microbiological assay and radioassay

    International Nuclear Information System (INIS)

    De Souza, S.C.

    1988-01-01

    Four different enzyme treatments-conjugase alone, conjugase and alpha-amylase, conjugase and Pronase reg-sign and a triple enzyme combination of conjugase, Pronase reg-sign and alpha-amylase were applied in the extraction of total folate from infant formula, baby foods and various other foods by microbiological and radioassay methods. Significant increases (P < 0.05) in measurable folate were obtained using the triple enzyme system in spinach, Camembert cheese, soy-based infant formula and cereal-based, meat-based and fruit-based infant foods over the use of conjugase alone by the microbiological method. Increases were also observed in many of the same foods using Pronase reg-sign or alpha-amylase in addition to conjugase alone. Increases obtained by microbiological assay were confirmed by radioassay in a number of foods studied

  9. In growing pigs, the true ileal and total tract digestibility of acid hydrolyzed ether extract in extracted corn oil is greater than in intact sources of corn oil or soybean oil.

    Science.gov (United States)

    Kim, B G; Kil, D Y; Stein, H H

    2013-02-01

    An experiment was conducted to determine the true ileal digestibility (TID) and the true total tract digestibility (TTTD) of acid-hydrolyzed ether extract (AEE) in extracted corn oil, high-oil corn, distillers dried grains with solubles (DDGS), corn germ, and high protein distillers dried grains (HP DDG) and to compare these values to the TID and TTTD of AEE in full-fat soybeans. Nineteen barrows with an initial BW of 52.2 kg (SD = 3.8) were fitted with a T-cannula in the distal ileum and allotted to a 19 × 11 Youden square design with 19 diets and 11 periods. A basal diet based on cornstarch, casein, sucrose, and corn bran was formulated. Eighteen additional diets were formulated by adding 3 levels of extracted corn oil, high-oil corn, DDGS, corn germ, HP DDG, or full-fat soybeans to the basal diet. The apparent ileal and the apparent total tract digestibility of AEE were calculated for each diet. The endogenous flow of AEE associated with each ingredient and values for TID and TTTD were calculated using the regression procedure. Results indicated that digested AEE in ileal digesta and feces linearly increased as AEE intake increased regardless of ingredient (P 0.77). However, the ileal and fecal endogenous losses of AEE were different (P oil, HP DDG, and full-fat soybeans. The TID of AEE was greater (P oil (95.4%) than for all other ingredients. The TID of AEE in HP DDG (76.5%) was not different from the TID of AEE in full-fat soybeans (85.2%) but greater (P oil corn, DDGS, and corn germ (53.0, 62.1, and 50.1%, respectively). The TTTD of AEE was greater (P oil (94.3%) than for all other ingredients, and the TTTD in full-fat soybeans (79.7%) was greater (P oil corn, DDGS, corn germ, and HP DDG (41.4, 51.9, 43.9, and 70.2%, respectively). The TTTD of AEE in HP DDG was also greater (P oil corn, DDGS, and corn germ. In conclusion, the intact sources of oil originating from high-oil corn, DDGS, corn germ, or HP DDG are much less digestible than extracted corn oil

  10. Effect of the Total Extract of Averrhoacarambola (Oxalidaceae Root on the Expression Levels of TLR4 and NF-κB in Streptozotocin-Induced Diabetic Mice

    Directory of Open Access Journals (Sweden)

    Xiaohui Xu

    2015-07-01

    Full Text Available Background: Averrhoacarambola L., which is a folk medicine used in diabetes mellitus (DM in ancient China, has been reported to have anti-diabetic efficacy. Aims: The aim of this study was to evaluate the hypoglycemic effect of the extract of Averrhoacarambola L. root (EACR on the regulation of the Toll-like receptor 4 (TLR4-Nuclear-factor kappa B (NF-κB pathway in B pathway in streptozotocin (STZ-induced diabetic mice. Methods: the mice were injected with STZ (120 mg/kg body weight via a tail vein. After 72 h, the mice with FBG = 11.1 mmol/L were confirmed as having diabetes. Subsequently, the mice were treated intragastrically with EACR (300, 600, 1200 mg/kg body weight/d and metformin (320 mg/kg body weight/d for 14 days. Results: As a result the serum fasting blood glucose (FBG, interleukin-6 (IL-6 and tumor necrosis factor-a (TNF-a levels were decreased following EACR administration. Immunohistochemical analysis revealed that the pancreatic tissue expression levels of TLR4 and NF-κB were downregulated after EACR administration. EACR suppressed pancreatic mRNA expression level of TLR4 and blocked the downstream NF-κB pathway in the pancreas. According to Western blot analysis EACR suppressed pancreatic TLR4 and NF-κB protein expression levels. Histopathological examination of the pancreas showed that STZ-induced pancreas lesions were alleviated by the EACR treatment. Conclusion: These findings suggest that the modulation of the IL-6 and TNF-a inflammatory cytokines and the suppression of the TLR4-NF-κB pathway are most likely involved in the anti-hyperglycemic effect of EACR in STZ-induced diabetic mice.

  11. A technical assessment of the porcine ejaculated spermatozoa for a sperm-specific RNA-seq analysis.

    Science.gov (United States)

    Gòdia, Marta; Mayer, Fabiana Quoos; Nafissi, Julieta; Castelló, Anna; Rodríguez-Gil, Joan Enric; Sánchez, Armand; Clop, Alex

    2018-04-26

    The study of the boar sperm transcriptome by RNA-seq can provide relevant information on sperm quality and fertility and might contribute to animal breeding strategies. However, the analysis of the spermatozoa RNA is challenging as these cells harbor very low amounts of highly fragmented RNA, and the ejaculates also contain other cell types with larger amounts of non-fragmented RNA. Here, we describe a strategy for a successful boar sperm purification, RNA extraction and RNA-seq library preparation. Using these approaches our objectives were: (i) to evaluate the sperm recovery rate (SRR) after boar spermatozoa purification by density centrifugation using the non-porcine-specific commercial reagent BoviPure TM ; (ii) to assess the correlation between SRR and sperm quality characteristics; (iii) to evaluate the relationship between sperm cell RNA load and sperm quality traits and (iv) to compare different library preparation kits for both total RNA-seq (SMARTer Universal Low Input RNA and TruSeq RNA Library Prep kit) and small RNA-seq (NEBNext Small RNA and TailorMix miRNA Sample Prep v2) for high-throughput sequencing. Our results show that pig SRR (~22%) is lower than in other mammalian species and that it is not significantly dependent of the sperm quality parameters analyzed in our study. Moreover, no relationship between the RNA yield per sperm cell and sperm phenotypes was found. We compared a RNA-seq library preparation kit optimized for low amounts of fragmented RNA with a standard kit designed for high amount and quality of input RNA and found that for sperm, a protocol designed to work on low-quality RNA is essential. We also compared two small RNA-seq kits and did not find substantial differences in their performance. We propose the methodological workflow described for the RNA-seq screening of the boar spermatozoa transcriptome. FPKM: fragments per kilobase of transcript per million mapped reads; KRT1: keratin 1; miRNA: micro-RNA; miscRNA: miscellaneous

  12. COMPARATION OF SEVERAL PLANTS EXTRACT AND VITAMIN C INHIBITION ACTIVITY TO TYROSINE PHOTODEGRADATION INDUCED BY KETOPROFEN AND ITS TOTAL PHENOLIC COMPOUNDS

    Directory of Open Access Journals (Sweden)

    Tatang Irianti

    2016-12-01

    Full Text Available Antioxidant is known to inhibit free radical reaction. Tyrosine photodegradation can be caused by radical reaction. Nowadays, plant with antioxidants are widely used to inhibit free radical reaction. Study of inhibition of photodegradation used four groups. Those groups are: P1 consisted of 2mL tyrosine 0,05 %; P2 consisted of 2 mL tyrosine 0,05 %, and 600 μL Rhetoflam (topical ketoprofen 1 %; P3 consisted of 2 mL tyrosine 0,05 %, 60μL Rhetoflam 1 %, and 100 μL tea leaf water ekstract 0,15 %; P4 consisted of 2 mL tyrosine 0,05 %, 600 μL Rhetoflam 1 %, and 100 μL mahkota dewa fruit water ekstract 0,15 %; P5 consisted of 2 mL tyrosine 0,05 %, 600 μL Rhetoflam 1 %, and 100 μL finger root etanolic ekstract 0,15 %; P6 consisted of 2 mL tyrosine 0,05 %, 600 μL Rhetoflam 1 %, and 100 μL vitamin C 0,15 %; each group is added with aquadest up to 5,0 mL and illuminated with mercuric lamp for four hours. Level of remaining tyrosine was measured with visible spectrophotometric method. We used ANOVA to analyse the data with convidence level of 0,95 and then continued by Tukey (HSD. Follin-Ciocalteu method with galic acid calibration curve was used to determine total phenolic level. The level of total phenolic of tea leaf aquoeus extract, mahkota dewa fruit aquoeus extract, fingerroot ethanolic extract were 29.64±0.86 %; 8.29 % 0.27 %; and 7.11 %, 0.15 %, respectively. Our investigation also found gallic acid equivalent (GAE with the inhibition activity of 4.03; 1.58; and 2.09 and they were bigger than Vitamin C with the same concentration of 0.15 %.

  13. Effects of dietary onion ( extract supplementation on performance, apparent total tract retention of nutrients, blood profile and meat quality of broiler chicks

    Directory of Open Access Journals (Sweden)

    Siska Aditya

    2017-02-01

    Full Text Available Objective This study was conducted to investigate the effect of dietary onion (Allium cepa extract (OE supplementation on growth performance, apparent total tract retention (ATTR, blood profile, carcass characteristics and meat quality in broilers. Methods Four hundred male broiler chicks (Ross 308, 3-d old were randomly allocated to four dietary treatments for 28 d feeding trial. Each treatment has five replications with 20 birds each. Four dietary treatments were designated according to the OE supplementation levels (0 as control, 5, 7.5, and 10 g of OE per kg of basal diet respectively. On d 28, a total of 20 birds from each treatment were subjected for ATTR, serum biochemical assay, carcass characteristic and organ weight measurement. Results Overall weight gain of OE 7.5 g/kg group was higher (p = 0.04 than control group. The ATTRs of dietary energy (p<0.01 and ether extract (p = 0.04 linearly increased with increasing levels of dietary OE. However, no difference in ATTR of dry matter and crude protein was evident. Furthermore, serum IgG concentration increased linearly (p<0.01 and quadratically (p = 0.03 with increasing OE supplementation. No differences in carcass dressing weight and amount of abdominal fat by treatments were observed. Also, the weight of organ including immune organ was not different among the treatments. The TBARS values of 10 d stored breast meat decreased linearly (p<0.01 and quadratically (p<0.01 with increasing dietary OE levels. The meat color was also affected, with lower (p<0.01 redness score in meats from OE supplemented groups. This study showed that dietary OE improved broiler weight gain presumably by increasing feed intake and ATTR of both energy and ether extract. The dietary OE increased serum IgG level and meat anti-oxidation capacity. Conclusion This study implies that the recommended level of dietary OE supplementation could be beneficial for improving broiler performance and meat quality.

  14. Blood cell mRNAs and microRNAs: optimized protocols for extraction and preservation.

    Science.gov (United States)

    Eikmans, Michael; Rekers, Niels V; Anholts, Jacqueline D H; Heidt, Sebastiaan; Claas, Frans H J

    2013-03-14

    Assessing messenger RNA (mRNA) and microRNA levels in peripheral blood cells may complement conventional parameters in clinical practice. Working with small, precious samples requires optimal RNA yields and minimal RNA degradation. Several procedures for RNA extraction and complementary DNA (cDNA) synthesis were compared for their efficiency. The effect on RNA quality of freeze-thawing peripheral blood cells and storage in preserving reagents was investigated. In terms of RNA yield and convenience, quality quantitative polymerase chain reaction signals per nanogram of total RNA and using NucleoSpin and mirVana columns is preferable. The SuperScript III protocol results in the highest cDNA yields. During conventional procedures of storing peripheral blood cells at -180°C and thawing them thereafter, RNA integrity is maintained. TRIzol preserves RNA in cells stored at -20°C. Detection of mRNA levels significantly decreases in degraded RNA samples, whereas microRNA molecules remain relatively stable. When standardized to reference targets, mRNA transcripts and microRNAs can be reliably quantified in moderately degraded (quality index 4-7) and severely degraded (quality index <4) RNA samples, respectively. We describe a strategy for obtaining high-quality and quantity RNA from fresh and stored cells from blood. The results serve as a guideline for sensitive mRNA and microRNA expression assessment in clinical material.

  15. Optimization of Ultrasound-Assisted Extraction of Crude Oil from Winter Melon (Benincasa hispida Seed Using Response Surface Methodology and Evaluation of Its Antioxidant Activity, Total Phenolic Content and Fatty Acid Composition

    Directory of Open Access Journals (Sweden)

    Md. Zaidul Islam Sarker

    2012-10-01

    Full Text Available In the present study, ultrasound-assisted extraction of crude oil from winter melon seeds was investigated through response surface methodology (RSM. Process variables were power level (25–75%, temperature (45–55 °C and sonication time (20–40 min. It was found that all process variables have significant (p < 0.05 effects on the response variable. A central composite design (CCD was used to determine the optimum process conditions. Optimal conditions were identified as 65% power level, 52 °C temperature and 36 min sonication time for maximum crude yield (108.62 mg-extract/g-dried matter. The antioxidant activity, total phenolic content and fatty acid composition of extract obtained under optimized conditions were determined and compared with those of oil obtained by the Soxhlet method. It was found that crude extract yield (CEY of ultrasound-assisted extraction was lower than that of the Soxhlet method, whereas antioxidant activity and total phenolic content of the extract obtained by ultrasound-assisted extraction were clearly higher than those of the Soxhlet extract. Furthermore, both extracts were rich in unsaturated fatty acids. The major fatty acids of the both extracts were linoleic acid and oleic acid.

  16. A standardized seabuckthorn leaf extract (SBL-1) counters radiation induced renal histopathology, oxidative stress as well as changes in mRNA levels

    International Nuclear Information System (INIS)

    Saini, Manu; Madhu Bala; Prasad, Jagdish; Farooqi, Humaira; Abdin, M.Z.

    2014-01-01

    Hippophae rhamnoides L., (common name Seabuckthorn; Family: Elaeagnaceae) is a plant growing naturally as well as cultivated in North-West Himalayas at 7000-15,000 feet. It is known for antioxidant and medicinal properties. Our earlier studies showed that administration of SBL-1 (30 mg/kg body weight), 30 minutes before 60 Co-γ-radiation (10 Gy, lethal dose) rendered > 90% survival in mice population. The present study was planned to investigate the effects of radioprotective dose (30 mg/kg body weight) dose of SBL-1 treatment in kidneys of irradiated and control animals. Strain 'A' male mice (weighing 28±2 g) were irradiated without or 30 minutes after administration of SBL-1. Animals were sacrificed at different days (1, 2, 3, 5, 7 and 15) after the treatment. Histopathology and biochemical assays were performed using standardized procedures. Gene expression study was performed by PCR of mRNA. The 60 Co γ-irradiated animals showed a significant reduction in total thiol (T-SH) content till day 5 (p< 0.05), activity of catalase, superoxide dismutase (SOD) (p<0.01) and glutathione-s-transferase (GST) (p<0.05) and significant increase in LPx, ALP and free iron content (p<0.05) on all study days. Histopathology showed Glomeruli shrinkage, nuclear degeneration, tubular dilations, widening of tubular lumen and collapsing of cellular architecture which increased from day 2 till day 7. Significant alterations in mRNA levels of some of the key genes involved in acute renal failure were observed. In animals treated with SBL-1 before irradiation the T-SH increased significantly at day 2, 3 and 5, activity of catalase, SOD and GST decreased significantly (p<0.05) only at day 2 and 3 respectively. Significant increase in (p<0.05) LPx was observed till day 3, ALP levels only at day 3 while free iron content till day 5. Only mild changes in the tissues histology were observed at day 2, 5 and 7. By day 10 no significant difference was observed in comparison to

  17. Vertical distribution of soil extractable organic C and N contents and total C and N stocks in 78-year-old tree plantations in subtropical Australia.

    Science.gov (United States)

    Zhou, Xiaoqi; Dong, Haibo; Lan, Zhongming; Bacon, Gary; Hao, Yanbin; Chen, Chengrong

    2017-10-01

    Few studies have focused on the effects of long-term forest plantations on the soil profile of carbon (C) and nitrogen (N) stocks. In this study, we selected 78-year-old tree plantations that included three coniferous tree species (i.e., slash pine, hoop pine and kauri pine) and a Eucalyptus species in subtropical Australia. We measured soil extractable organic C (EOC) and N (EON) contents and total C and N stocks under different tree species on the forest floor and along a soil profile to 100 cm depth. The results showed that Eucalyptus had significantly higher soil EOC contents (3.3 Mg ha -1 ) than the other tree species (EOC of 1.9-2.3 Mg ha -1 ) and had significantly higher EON (156 kg ha -1 ) contents than slash pine (107 kg ha -1 ). Eucalyptus had significantly higher soil C (58.9 Mg ha -1 ) and N (2.03 Mg ha -1 ) stocks than the other tree species (22.3-27.6 Mg C ha -1 and 0.71-1.23 Mg N ha -1 ) at 0-100 cm depth. There were no differences in soil C stocks at the 0-100 cm depth among the coniferous tree species. Forest floor C stocks had stronger effects on mineral soil total N stocks than fine root biomass, whereas fine root biomass exerted stronger effects on soil total C stocks at the 0-100 cm depth than forest floor C and N stocks. Our results addressed large differences in soil C and N stocks under different tree species, which can provide useful information for local forest management practices in this region.

  18. A sensitive method for determining total vanadium in water samples using colorimetric-solid-phase extraction-fiber optic reflectance spectroscopy

    International Nuclear Information System (INIS)

    Filik, Hayati; Yanaz, Zeynep

    2009-01-01

    A selective colorimetric-solid-phase extraction (C-SPE) method for the determination of total vanadium in water samples was developed. This method introduced a new variation of C-SPE. The colour reaction is based on the reaction of vanadium(V) ternary complex formed with 1-(2-Pyridylazo)-2-naphtol (PAN) in the presence hydrogen peroxide (H 2 O 2 ). In this technique, the target analytes in samples are extracted onto solid matrix loaded with a colorimetric reagent and then quantified directly on the adsorbent surface by using a miniature fiber optic reflectance spectrometer. The measurements were carried out at a wavelength of 589.4 nm since it yielded the largest divergence different in reflectance spectra before and after reaction with the vanadium. The overall time required for the C-SPE procedure was ∼20 min. The amount of concentrated V is then determined in a few seconds by using miniature reflectance spectrometer. At the optimal conditions, a calibration curve was constructed, revealing a linear range of 0.05-0.52 mg L -1 and a detection limit as low as 0.01 mg L -1 while the RSD lower than 2.8%. In order to verify the accuracy of the method, a certified reference water samples (TMDA) were analysed and the results obtained were in good agreement with the certified values. The proposed method was applied to the determination of vanadium in tap water, seawater samples with a recovery for the spiked samples in the range of 98-102%.

  19. Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize.

    Science.gov (United States)

    Thiebaut, Flávia; Rojas, Cristian A; Grativol, Clícia; Motta, Mariana Romeiro; Vieira, Tauan; Regulski, Michael; Martienssen, Robert A; Farinelli, Laurent; Hemerly, Adriana S; Ferreira, Paulo C G

    2014-09-06

    Small RNA (sRNA) has been described as a regulator of gene expression. In order to understand the role of maize sRNA (Zea mays-hybrid UENF 506-8) during association with endophytic nitrogen-fixing bacteria, we analyzed the sRNA regulated by its association with two diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense. Deep sequencing analysis was done with RNA extracted from plants inoculated with H. seropedicae, allowing the identification of miRNA and siRNA. A total of 25 conserved miRNA families and 15 novel miRNAs were identified. A dynamic regulation in response to inoculation was also observed. A hypothetical model involving copper-miRNA is proposed, emphasizing the fact that the up-regulation of miR397, miR398, miR408 and miR528, which is followed by inhibition of their targets, can facilitate association with diazotrophic bacteria. Similar expression patterns were observed in samples inoculated with A. brasilense. Moreover, novel miRNA and siRNA were classified in the Transposable Elements (TE) database, and an enrichment of siRNA aligned with TE was observed in the inoculated samples. In addition, an increase in 24-nt siRNA mapping to genes was observed, which was correlated with an increase in methylation of the coding regions and a subsequent reduction in transcription. Our results show that maize has RNA-based silencing mechanisms that can trigger specific responses when plants interact with beneficial endophytic diazotrophic bacteria. Our findings suggest important roles for sRNA regulation in maize, and probably in other plants, during association with diazotrophic bacteria, emphasizing the up-regulation of Cu-miRNA.

  20. Andrographolide antagonizes cigarette smoke extract-induced inflammatory response and oxidative stress in human alveolar epithelial A549 cells through induction of microRNA-218.

    Science.gov (United States)

    Li, Ying-jie; Yu, Chang-hai; Li, Jing-bo; Wu, Xi-ya

    2013-12-01

    Andrographolide is a major bioactive labdane diterpenoid isolated from Andrographis paniculata and has protective effects against cigarette smoke (CS)-induced lung injury. This study was done to determine whether such protective effects were mediated through modulation of microRNA (miR)-218 expression. Therefore, we exposed human alveolar epithelial A549 cells to cigarette smoke extract (CSE) with or without andrographolide pretreatment and measured the level of glutathione, nuclear factor-kappaB (NF-κB) activation, proinflammatory cytokine production, and miR-218 expression. We found that andrographolide pretreatment significantly restored the glutathione level in CSE-exposed A549 cells, coupled with reduced inhibitor κB (IκB)-α phosphorylation and p65 nuclear translocation and interleukin (IL)-8 and IL-6 secretion. The miR-218 expression was significantly upregulated by andrographolide pretreatment. To determine the biological role of miR-218, we overexpressed and downregulated its expression using miR-218 mimic and anti-miR-218 inhibitor, respectively. We observed that miR-218 overexpression led to a marked reduction in IκB-α phosphorylation, p65 nuclear accumulation, and NF-κB-dependent transcriptional activity in CSE-treated A549 cells. In contrast, miR-218 silencing enhanced IκB-α phosphorylation and p65 nuclear accumulation in cells with andrographolide pretreatment and reversed andrographolide-mediated reduction of IL-6 and IL-8 production. In addition, depletion of miR-218 significantly reversed the upregulation of glutathione levels in A549 cells by andrographolide. Taken together, our results demonstrate that andrographolide mitigates CSE-induced inflammatory response in A549 cells, largely through inhibition of NF-κB activation via upregulation of miR-218, and thus has preventive benefits in CS-induced inflammatory lung diseases.

  1. RNA precursor pool metabolism and RNA synthesis in X-irradiated Tetrahymena

    International Nuclear Information System (INIS)

    Stephens, R.E.; Paul, I.J.; Zimmerman, A.M.

    1976-01-01

    The incorporation of a radioactive RNA precursor ( 3 H-uridine) has been used in many studies as an index for measuring the synthesis of RNA, yet there is a distinct possibility that the results so obtained were significantly influenced by radiation-induced effects on the metabolism of this precursor into UTP (the primary immediate precursor of RNA) before its incorporation into RNA. A direct examination was therefore undertaken of the effects of X-irradiation on the metabolism of 3 H-uridine and its relationship to RNA synthesis as determined by incorporation. X-irradiation of logarithmically growing Tetrahymena pyriformis caused a dose-dependent depression of total cellular RNA synthesis. Ribosomal RNA (which comprises about 80 per cent of total cellular RNA) synthesis was also depressed by X-irradiation in a dose-dependent manner. Measurements of the levels of radioactivity present in the UTP precursor pool of both irradiated and unirradiated cells were obtained by means of DEAE-cellulose column chromatography of the extracted free nucleotides. Metabolism of 3 H-uridine into UMP, UDP and UTP was depressed by 40%, 26% and 27% respectively, whereas incorporation of 3 H-uridine into RNA was depressed by 77%. The results show that about one-third of the observed (apparent) depression in RNA synthesis was due to radiation-induced effects on the precursor pool, and the remaining two-thirds due to some definite effect of radiation at the transcription level leading to depressed synthesis of RNA. (U.K.)

  2. Development of solid lipid nanoparticles containing total flavonoid extract from Dracocephalum moldavica L. and their therapeutic effect against myocardial ischemia-reperfusion injury in rats.

    Science.gov (United States)

    Tan, Mei-E; He, Cheng-Hui; Jiang, Wen; Zeng, Cheng; Yu, Ning; Huang, Wei; Gao, Zhong-Gao; Xing, Jian-Guo

    2017-01-01

    Total flavonoid extract from Dracocephalum moldavica L. (TFDM) contains effective components of D. moldavica L. that have myocardial protective function. However, the cardioprotection function of TFDM is undesirable due to its poor solubility. In order to improve the solubility and efficacy of TFDM, we developed TFDM-loaded solid lipid nanoparticles (TFDM-SLNs) and optimized the formulation of TFDM-SLNs using central composite design and response surface methodology. The physicochemical properties of TFDM-SLNs were characterized, and the pharmacodynamics was investigated using the myocardial ischemia-reperfusion injury model in rats. The nanoparticles of optimal formulation for TFDM-SLNs were spherical in shape with the average particle size of 104.83 nm and had a uniform size distribution with the polydispersity index value of 0.201. TFDM-SLNs also had a negative zeta potential of -28.7 mV to ensure the stability of the TFDM-SLNs emulsion system. The results of pharmacodynamics demonstrated that both TFDM and TFDM-SLN groups afforded myocardial protection, and the protective effect of TFDM-SLNs was significantly superior to that of TFDM alone, based on the infarct area, histopathological examination, cardiac enzyme levels and inflammatory factors in serum. Due to the optimal quality and the better myocardial protective effect, TFDM-SLNs are expected to become a safe and effective nanocarrier for the oral delivery of TFDM.

  3. Determination of calcium, potassium, manganese, iron, copper and zinc levels in representative samples of two onion cultivars using total reflection X-ray fluorescence and ultrasound extraction procedure

    International Nuclear Information System (INIS)

    Alvarez, J.; Marco, L.M.; Arroyo, J.; Greaves, E.D.; Rivas, R.

    2003-01-01

    The chemical characterization of onion cultivar samples is an important tool for the enhancement of their productivity due to the fact that chemical composition is closed related to the quality of the products. A new sample preparation procedure for elemental characterization is proposed, involving the acid extraction of the analytes from crude samples by means of an ultrasonic bath, avoiding the required digestion of samples in vegetable tissue analysis. The technique of total reflection X-ray fluorescence (TXRF) was successfully applied for the simultaneous determination of the elements Ca, K, Mn, Fe, Cu and Zn. The procedure was compared with the wet ashing and dry ashing procedures for all the elements using multivariate analysis and the Scheffe test. The technique of flame atomic absorption spectrometry (FAAS) was employed for comparison purposes and accuracy evaluation of the proposed analysis method. A good agreement between the two techniques was found when using the dry ashing and ultrasound leaching procedures. The levels of each element found for representative samples of two onion cultivars (Yellow Granex PRR 502 and 438 Granex) were also compared by the same method. Levels of K, Mn and Zn were significantly higher in the 438 Granex cultivar, while levels of Ca, Fe and Cu were significantly higher in the Yellow Granex PRR 502 cultivar

  4. An improved method for RNA isolation and cDNA library construction from immature seeds of Jatropha curcas L

    Directory of Open Access Journals (Sweden)

    Kaur Jatinder

    2010-05-01

    Full Text Available Abstract Background RNA quality and quantity is sometimes unsuitable for cDNA library construction, from plant seeds rich in oil, polysaccharides and other secondary metabolites. Seeds of jatropha (Jatropha curcas L. are rich in fatty acids/lipids, storage proteins, polysaccharides, and a number of other secondary metabolites that could either bind and/or co-precipitate with RNA, making it unsuitable for downstream applications. Existing RNA isolation methods and commercial kits often fail to deliver high-quality total RNA from immature jatropha seeds for poly(A+ RNA purification and cDNA synthesis. Findings A protocol has been developed for isolating good quality total RNA from immature jatropha seeds, whereby a combination of the CTAB based RNA extraction method and a silica column of a commercial plant RNA extraction kit is used. The extraction time was reduced from two days to about 3 hours and the RNA was suitable for poly(A+ RNA purification, cDNA synthesis, cDNA library construction, RT-PCR, and Northern hybridization. Based on sequence information from selected clones and amplified PCR product, the cDNA library seems to be a good source of full-length jatropha genes. The method was equally effective for isolating RNA from mustard and rice seeds. Conclusions This is a simple CTAB + silica column method to extract high quality RNA from oil rich immature jatropha seeds that is suitable for several downstream applications. This method takes less time for RNA extraction and is equally effective for other tissues where the quality and quantity of RNA is highly interfered by the presence of fatty acids, polysaccharides and polyphenols.

  5. Fasting decreases apolipoprotein B mRNA editing and the secretion of small molecular weight apoB by rat hepatocytes: Evidence that the total amount of apoB secreted is regulated post-transcriptionally

    International Nuclear Information System (INIS)

    Leighton, J.K.; Joyner, J.; Zamarripa, J.; Deines, M.; Davis, R.A.

    1990-01-01

    Two different molecular weight forms of apoB are produced from a common initial transcript via editing of a Gln codon (CAA) to a stop codon (UAA), leading to a truncated translation product (apo BS) that consists of the amino terminal half of the larger form (apoBL). Previous studies have shown that fasting coordinately decreases lipogenesis and the secretion of very low density lipoprotein (VLDL) lipids and apoBS. Secretion of the apoBL is unaffected by fasting. We studied whether editing of apoB RNA is repressed by fasting, thus accounting for the selective decreased secretion of apoBS. Column chromatography of [35S]methionine-labeled lipoproteins secreted by hepatocytes from fed rats showed that essentially all of apoBL is secreted in the VLDL fraction, whereas a significant amount (15%) of apoBS is secreted associated as lipoproteins eluting in the HDL fractions. Fasting decreased the relative amount of apoBS that eluted in the VLDL fractions and increased the amount secreted in the HDL fractions. Consistent with previous results, hepatocytes from fasted rats show a selective twofold decrease in apoBS secretion. Fasting did not affect the relative abundance of apoB RNA, determined by slot blot hybridization assays using two different 32P-labeled cDNA probes coding either for both molecular weight forms or for only the large molecular weight form. However, quantitative of the editing of apoB RNA showed that fasting caused a 60% decrease in the amount of apoB RNA possessing the stop codon. These data show that the editing of apoB RNA is sensitive to metabolic state (i.e., fasting) resulting in a selective decrease in the secretion of apoBS. However, since the total secretion of apoB was decreased by fasting, while apoB mRNA levels remained constant, additional (post-transcriptional) mechanisms play a role in regulating apoB secretion

  6. Determination of As(III) and total inorganic As in water samples using an on-line solid phase extraction and flow injection hydride generation atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Sigrist, Mirna, E-mail: msigrist@fiq.unl.edu.ar [Laboratorio Central, Facultad de Ingenieria Quimica, Universidad Nacional del Litoral, Santiago del Estero 2654-Piso 6, (3000) Santa Fe (Argentina); Albertengo, Antonela; Beldomenico, Horacio [Laboratorio Central, Facultad de Ingenieria Quimica, Universidad Nacional del Litoral, Santiago del Estero 2654-Piso 6, (3000) Santa Fe (Argentina); Tudino, Mabel [Laboratorio de Analisis de Trazas, Departamento de Quimica Inorganica, Analitica y Quimica Fisica/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Pabellon II, Ciudad Universitaria (1428), Buenos Aires (Argentina)

    2011-04-15

    A simple and robust on-line sequential injection system based on solid phase extraction (SPE) coupled to a flow injection hydride generation atomic absorption spectrometer (FI-HGAAS) with a heated quartz tube atomizer (QTA) was developed and optimized for the determination of As(III) in groundwater without any kind of sample pretreatment. The method was based on the selective retention of inorganic As(V) that was carried out by passing the filtered original sample through a cartridge containing a chloride-form strong anion exchanger. Thus the most toxic form, inorganic As(III), was determined fast and directly by AsH{sub 3} generation using 3.5 mol L{sup -1} HCl as carrier solution and 0.35% (m/v) NaBH{sub 4} in 0.025% NaOH as the reductant. Since the uptake of As(V) should be interfered by several anions of natural occurrence in waters, the effect of Cl{sup -}, SO{sub 4}{sup 2-}, NO{sub 3}{sup -}, HPO{sub 4}{sup 2-}, HCO{sub 3}{sup -} on retention was evaluated and discussed. The total soluble inorganic arsenic concentration was determined on aliquots of filtered samples acidified with concentrated HCl and pre-reduced with 5% KI-5% C{sub 6}H{sub 8}O{sub 6} solution. The concentration of As(V) was calculated by difference between the total soluble inorganic arsenic and As(III) concentrations. Detection limits (LODs) of 0.5 {mu}g L{sup -1} and 0.6 {mu}g L{sup -1} for As(III) and inorganic total As, respectively, were obtained for a 500 {mu}L sample volume. The obtained limits of detection allowed testing the water quality according to the national and international regulations. The analytical recovery for water samples spiked with As(III) ranged between 98% and 106%. The sampling throughput for As(III) determination was 60 samples h{sup -1}. The device for groundwater sampling was especially designed for the authors. Metallic components were avoided and the contact between the sample and the atmospheric oxygen was carried to a minimum. On-field arsenic species

  7. Determination of As(III) and total inorganic As in water samples using an on-line solid phase extraction and flow injection hydride generation atomic absorption spectrometry

    International Nuclear Information System (INIS)

    Sigrist, Mirna; Albertengo, Antonela; Beldomenico, Horacio; Tudino, Mabel

    2011-01-01

    A simple and robust on-line sequential injection system based on solid phase extraction (SPE) coupled to a flow injection hydride generation atomic absorption spectrometer (FI-HGAAS) with a heated quartz tube atomizer (QTA) was developed and optimized for the determination of As(III) in groundwater without any kind of sample pretreatment. The method was based on the selective retention of inorganic As(V) that was carried out by passing the filtered original sample through a cartridge containing a chloride-form strong anion exchanger. Thus the most toxic form, inorganic As(III), was determined fast and directly by AsH 3 generation using 3.5 mol L -1 HCl as carrier solution and 0.35% (m/v) NaBH 4 in 0.025% NaOH as the reductant. Since the uptake of As(V) should be interfered by several anions of natural occurrence in waters, the effect of Cl - , SO 4 2- , NO 3 - , HPO 4 2- , HCO 3 - on retention was evaluated and discussed. The total soluble inorganic arsenic concentration was determined on aliquots of filtered samples acidified with concentrated HCl and pre-reduced with 5% KI-5% C 6 H 8 O 6 solution. The concentration of As(V) was calculated by difference between the total soluble inorganic arsenic and As(III) concentrations. Detection limits (LODs) of 0.5 μg L -1 and 0.6 μg L -1 for As(III) and inorganic total As, respectively, were obtained for a 500 μL sample volume. The obtained limits of detection allowed testing the water quality according to the national and international regulations. The analytical recovery for water samples spiked with As(III) ranged between 98% and 106%. The sampling throughput for As(III) determination was 60 samples h -1 . The device for groundwater sampling was especially designed for the authors. Metallic components were avoided and the contact between the sample and the atmospheric oxygen was carried to a minimum. On-field arsenic species separation was performed through the employ of a serial connection of membrane filters and

  8. Phosphatidic acid produced by phospholipase D promotes RNA replication of a plant RNA virus.

    Directory of Open Access Journals (Sweden)

    Kiwamu Hyodo

    2015-05-01

    Full Text Available Eukaryotic positive-strand RNA [(+RNA] viruses are intracellular obligate parasites replicate using the membrane-bound replicase complexes that contain multiple viral and host components. To replicate, (+RNA viruses exploit host resources and modify host metabolism and membrane organization. Phospholipase D (PLD is a phosphatidylcholine- and phosphatidylethanolamine-hydrolyzing enzyme that catalyzes the production of phosphatidic acid (PA, a lipid second messenger that modulates diverse intracellular signaling in various organisms. PA is normally present in small amounts (less than 1% of total phospholipids, but rapidly and transiently accumulates in lipid bilayers in response to different environmental cues such as biotic and abiotic stresses in plants. However, the precise functions of PLD and PA remain unknown. Here, we report the roles of PLD and PA in genomic RNA replication of a plant (+RNA virus, Red clover necrotic mosaic virus (RCNMV. We found that RCNMV RNA replication complexes formed in Nicotiana benthamiana contained PLDα and PLDβ. Gene-silencing and pharmacological inhibition approaches showed that PLDs and PLDs-derived PA are required for viral RNA replication. Consistent with this, exogenous application of PA enhanced viral RNA replication in plant cells and plant-derived cell-free extracts. We also found that a viral auxiliary replication protein bound to PA in vitro, and that the amount of PA increased in RCNMV-infected plant leaves. Together, our findings suggest that RCNMV hijacks host PA-producing enzymes to replicate.

  9. Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

    Directory of Open Access Journals (Sweden)

    Olivier Laroche

    2017-05-01

    Full Text Available Sequencing environmental DNA (eDNA is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene and eukaryotic (18S ribosomal RNA gene eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand. Macro-infauna (visual classification of benthic invertebrates and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs, by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from

  10. Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

    KAUST Repository

    Laroche, Olivier

    2017-05-17

    Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil

  11. Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities.

    Science.gov (United States)

    Laroche, Olivier; Wood, Susanna A; Tremblay, Louis A; Lear, Gavin; Ellis, Joanne I; Pochon, Xavier

    2017-01-01

    Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil

  12. Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format.

    Science.gov (United States)

    Salvo-Chirnside, Eliane; Kane, Steven; Kerr, Lorraine E

    2011-12-02

    The increasing popularity of systems-based approaches to plant research has resulted in a demand for high throughput (HTP) methods to be developed. RNA extraction from multiple samples in an experiment is a significant bottleneck in performing systems-level genomic studies. Therefore we have established a high throughput method of RNA extraction from Arabidopsis thaliana to facilitate gene expression studies in this widely used plant model. We present optimised manual and automated protocols for the extraction of total RNA from 9-day-old Arabidopsis seedlings in a 96 well plate format using silica membrane-based methodology. Consistent and reproducible yields of high quality RNA are isolated averaging 8.9 μg total RNA per sample (~20 mg plant tissue). The purified RNA is suitable for subsequent qPCR analysis of the expression of over 500 genes in triplicate from each sample. Using the automated procedure, 192 samples (2 × 96 well plates) can easily be fully processed (samples homogenised, RNA purified and quantified) in less than half a day. Additionally we demonstrate that plant samples can be stored in RNAlater at -20°C (but not 4°C) for 10 months prior to extraction with no significant effect on RNA yield or quality. Additionally, disrupted samples can be stored in the lysis buffer at -20°C for at least 6 months prior to completion of the extraction procedure providing a flexible sampling and storage scheme to facilitate complex time series experiments.

  13. Development of solid lipid nanoparticles containing total flavonoid extract from Dracocephalum moldavica L. and their therapeutic effect against myocardial ischemia–reperfusion injury in rats

    Directory of Open Access Journals (Sweden)

    Tan ME

    2017-04-01

    Full Text Available Mei-e Tan,1–3,* Cheng-hui He,3,* Wen Jiang,4 Cheng Zeng,2–4 Ning Yu,3 Wei Huang,2 Zhong-gao Gao,2 Jian-guo Xing3 1Key Laboratory of Xinjiang Endemic Phytomedicine Resources of Ministry of Education, School of Pharmacy, Shihezi University, Shihezi, 2State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of Pharmaceutics, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 3Xinjiang Key Laboratory of Uighur Medicines, Xinjiang Institute of Materia Medica, 4Xinjiang Medical University, Urumqi, People’s Republic of China *These authors contributed equally to this work Abstract: Total flavonoid extract from Dracocephalum moldavica L. (TFDM contains effective components of D. moldavica L. that have myocardial protective function. However, the cardioprotection function of TFDM is undesirable due to its poor solubility. In order to improve the solubility and efficacy of TFDM, we developed TFDM-loaded solid lipid nanoparticles (TFDM-SLNs and optimized the formulation of TFDM-SLNs using central composite design and response surface methodology. The physicochemical properties of TFDM-SLNs were characterized, and the pharmacodynamics was investigated using the myocardial ischemia–reperfusion injury model in rats. The nanoparticles of optimal formulation for TFDM-SLNs were spherical in shape with the average particle size of 104.83 nm and had a uniform size distribution with the polydispersity index value of 0.201. TFDM-SLNs also had a negative zeta potential of -28.7 mV to ensure the stability of the TFDM-SLNs emulsion system. The results of pharmacodynamics demonstrated that both TFDM and TFDM-SLN groups afforded myocardial protection, and the protective effect of TFDM-SLNs was significantly superior to that of TFDM alone, based on the infarct area, histopathological examination, cardiac enzyme levels and inflammatory factors in serum. Due to the optimal

  14. Effects of aqueous extract of Portulaca oleracea L. on oxidative stress and liver, spleen leptin, PARα and FAS mRNA expression in high-fat diet induced mice.

    Science.gov (United States)

    Chen, Bendong; Zhou, Haining; Zhao, Wenchao; Zhou, Wenyan; Yuan, Quan; Yang, Guangshun

    2012-08-01

    We reported that an aqueous extract of Portulaca oleracea L. inhibited high-fat-diet-induced oxidative injury in a dose-dependent manner. Male kunming mice (5-weeks-old, 24 g) were used in this experiment. After a 4-day adaptation period, animals were randomly divided into four groups (n = 10 in each group); Group 1: animals received normal powdered rodent diet; Group 2: animals received high fat diet; Groups 3 and 4: animals received high fat diet and were fed by gavage to mice once a day with aqueous extract at the doses of 100 and 200 mg/kg body weight, respectively. In mice fed with high-fat diet, blood and liver lipid peroxidation level was significantly increased, whereas antioxidant enzymes activities were markedly decreased compared to normal control mice. Administration of an aqueous extract of P. oleracea L. significantly dose-dependently reduced levels of blood and liver lipid peroxidation and increased the activities of blood and liver antioxidant enzymes activities in high fat mice. Moreover, administration of an aqueous extract of P. oleracea L. significantly dose-dependently increase liver Leptin/β-actin (B), and Liver PPARα/β-actin, decrease liver, spleen FAS mRNA, p-PERK and p-PERK/PERK protein expression levels. Taken together, these data demonstrate that aqueous extract of P. oleracea L. can markedly alleviate high fat diet-induced oxidative injury by enhancing blood and liver antioxidant enzyme activities, modulating Leptin/β-actin (B), and Liver PPARα/β-actin, decrease liver, spleen FAS mRNA, p-PERK and p-PERK/PERK protein expression levels in mice.

  15. Determination of total ribonucleotide pool in plant materials by high-pH anion-exchange high-performance liquid chromatography following extraction with potassium hydroxide.

    Science.gov (United States)

    Riondet, Christophe; Morel, Sylvain; Alcaraz, Gérard

    2005-06-10

    A new, improved method that only requires a potassium hydroxide extraction procedure is presented for the analysis of a full nucleotide pool in plant materials. Quantification was performed by high-pH anion-exchange chromatography (HPAEC) with UV detection after a potassium hydroxide extraction, and allowed the quantification of 13 linear ribonucleotides in a single run. The method has been validated by comparison of six extraction methods and also by measurement of the intracellular nucleotide levels of three plant species (cell cultures and leaves). The evolution of the nucleotide pool of Nicotiana tabacum cell culture during growth has also been measured, and showed an increase in the pool until the fifth day, where the growth rate reaches a maximum, after which a decrease was observed.

  16. RNA Crystallization

    Science.gov (United States)

    Golden, Barbara L.; Kundrot, Craig E.

    2003-01-01

    RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

  17. Epigenetic silencing of miR-218 by the lncRNA CCAT1, acting via BMI1, promotes an altered cell cycle transition in the malignant transformation of HBE cells induced by cigarette smoke extract

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Lu; Xu, Hui; Luo, Fei; Liu, Xinlu; Lu, Xiaolin; Yang, Qianlei; Xue, Junchao; Chen, Chao; Shi, Le; Liu, Qizhan, E-mail: drqzliu@hotmail.com

    2016-08-01

    Cigarette smoking is the strongest risk factor for the development of lung cancer, the leading cause of cancer-related deaths. However, the molecular mechanisms leading to lung cancer are largely unknown. A long-noncoding RNA (lncRNA), CCAT1, regarded as cancer-associated, has been investigated extensively. Moreover, the molecular mechanisms of lncRNAs in regulation of microRNAs (miRNAs) induced by cigarette smoke remain unclear. In the present investigation, cigarette smoke extract (CSE) caused an altered cell cycle and increased CCAT1 levels and decreased miR-218 levels in human bronchial epithelial (HBE) cells. Depletion of CCAT1 attenuated the CSE-induced decreases of miR-218 levels, suggesting that miR-218 is negatively regulated by CCAT1 in HBE cells exposed to CSE. The CSE-induced increases of BMI1 levels and blocked by CCAT1 siRNA were attenuated by an miR-218 inhibitor. Moreover, in CSE-transformed HBE cells, the CSE-induced cell cycle changes and elevated neoplastic capacity were reversed by CCAT1 siRNA or BMI1 siRNA. This epigenetic silencing of miR-218 by CCAT1 induces an altered cell cycle transition through BMI1 and provides a new mechanism for CSE-induced lung carcinogenesis. - Highlights: • CSE exposure induces increases of CCAT1 levels and decreases of miR-218 levels. • CCAT1 negatively regulates miR-218 expression. • CCAT1, regulated by miR-218, via BMI1, is involved in the CSE-induced altered cell cycle transition.

  18. Epigenetic silencing of miR-218 by the lncRNA CCAT1, acting via BMI1, promotes an altered cell cycle transition in the malignant transformation of HBE cells induced by cigarette smoke extract

    International Nuclear Information System (INIS)

    Lu, Lu; Xu, Hui; Luo, Fei; Liu, Xinlu; Lu, Xiaolin; Yang, Qianlei; Xue, Junchao; Chen, Chao; Shi, Le; Liu, Qizhan

    2016-01-01

    Cigarette smoking is the strongest risk factor for the development of lung cancer, the leading cause of cancer-related deaths. However, the molecular mechanisms leading to lung cancer are largely unknown. A long-noncoding RNA (lncRNA), CCAT1, regarded as cancer-associated, has been investigated extensively. Moreover, the molecular mechanisms of lncRNAs in regulation of microRNAs (miRNAs) induced by cigarette smoke remain unclear. In the present investigation, cigarette smoke extract (CSE) caused an altered cell cycle and increased CCAT1 levels and decreased miR-218 levels in human bronchial epithelial (HBE) cells. Depletion of CCAT1 attenuated the CSE-induced decreases of miR-218 levels, suggesting that miR-218 is negatively regulated by CCAT1 in HBE cells exposed to CSE. The CSE-induced increases of BMI1 levels and blocked by CCAT1 siRNA were attenuated by an miR-218 inhibitor. Moreover, in CSE-transformed HBE cells, the CSE-induced cell cycle changes and elevated neoplastic capacity were reversed by CCAT1 siRNA or BMI1 siRNA. This epigenetic silencing of miR-218 by CCAT1 induces an altered cell cycle transition through BMI1 and provides a new mechanism for CSE-induced lung carcinogenesis. - Highlights: • CSE exposure induces increases of CCAT1 levels and decreases of miR-218 levels. • CCAT1 negatively regulates miR-218 expression. • CCAT1, regulated by miR-218, via BMI1, is involved in the CSE-induced altered cell cycle transition.

  19. A Rapid Protocol of Crude RNA/DNA Extraction for RT-qPCR Detection and Quantification of 'Candidatus Phytoplasma prunorum'.

    Science.gov (United States)

    Minguzzi, Stefano; Terlizzi, Federica; Lanzoni, Chiara; Poggi Pollini, Carlo; Ratti, Claudio

    2016-01-01

    Many efforts have been made to develop a rapid and sensitive method for phytoplasma and virus detection. Taking our cue from previous works, different rapid sample preparation methods have been tested and applied to Candidatus Phytoplasma prunorum ('Ca. P. prunorum') detection by RT-qPCR. A duplex RT-qPCR has been optimized using the crude sap as a template to simultaneously amplify a fragment of 16S rRNA of the pathogen and 18S rRNA of the host plant. The specific plant 18S rRNA internal control allows comparison and relative quantification of samples. A comparison between DNA and RNA contribution to qPCR detection is provided, showing higher contribution of the latter. The method presented here has been validated on more than a hundred samples of apricot, plum and peach trees. Since 2013, this method has been successfully applied to monitor 'Ca. P. prunorum' infections in field and nursery. A triplex RT-qPCR assay has also been optimized to simultaneously detect 'Ca. P. prunorum' and Plum pox virus (PPV) in Prunus.

  20. MicroRNA alterations in Barrett′s esophagus, esophageal adenocarcinoma, and esophageal adenocarcinoma cell lines following cranberry extract treatment: Insights for chemoprevention

    Directory of Open Access Journals (Sweden)

    Laura A Kresty

    2011-01-01

    Full Text Available Background: Aberrant expression of small noncoding endogenous RNA molecules known as microRNAs (miRNAs is documented to occur in multiple cancer types including esophageal adencarcinoma (EAC and its only known precursor, Barrett′s esophagus (BE. Recent studies have linked dysregulation of specific miRNAs to histological grade, neoplastic progression and metastatic potential. Materials and Methods: Herein, we present a summary of previously reported dysregulated miRNAs in BE and EAC tissues as well as EAC cell lines and evaluate a cranberry proanthocyanidin rich extract′s (C-PAC ability to modulate miRNA expression patterns of three human EAC cell lines (JHEso-Ad-1, OE33 and OE19. Results: A review of 13 published studies revealed dysregulation of 87 miRNAs in BE and EAC tissues, whereas 52 miRNAs have been reported to be altered in BE or EAC cell lines, with 48% overlap with miRNA changes reported in tissues. We report for the first time C-PAC-induced modulation of five miRNAs in three EAC cell lines resulting in 26 validated gene targets and identification of key signaling pathways including p53, angiogenesis, T-cell activation and apoptosis. Additionally, mutiple cancer related networks were ideintified as modulated by C-PAC utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG, Protein Analysis Through Evolutionary Relationships (PANTHER, and MetaCore analysis tools. Conclusions: Study results support the cancer inhibitory potential of C-PAC is in part attributable to C-PAC′s ability to modify miRNA profiles within EAC cells. A number of C-PAC-modulated miRNAs have been been identified as dysregulated in BE and EAC. Further insights into miRNA dysregulation and modulation by select cancer preventive agents will support improved targeted interventions in high-risk cohorts.

  1. [Correlation between five RNA markers of rat's skin and PMI at different temperatures].

    Science.gov (United States)

    Pan, Hui; Zhang, Heng; Lü, Ye-hui; Ma, Jian-long; Ma, Kai-jun; Chen, Long

    2014-08-01

    To explore the correlation between postmortem interval (PMI) and five RNA markers of rat's skin--β-actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S ribosomal RNA(18S rRNA), 5S ribosomal RNA (5S rRNA), and microRNA-203 (miR-203), at different temperatures. Eighteen SD rats were randomly divided into three environmental temperature groups: 4 °C, 15 °C and 35 °C, respectively. Skin samples were taken at 11 time points from 0 h to 120 h post-mortem. The total RNA was extracted from the skin samples and the five RNA levels were detected by real-time fluorescent quantitative PCR. Proper internal reference was selected by geNorm software. Regression analysis of the RNA markers was conducted by GraphPad software. 5S rRNA and miR-203 were most suitable internal references. A good linear relationship between PMI and RNA levels (β-actin and GAPDH) was observed in two groups (4 °C and 15 °C), whereas the S type curve relationship between the expression levels of the two markers (β-actin and GAPDH) and PMI was observed in the 35 °C group. The partial linear relationship between 18S rRNA and PMI was observed in the groups (15 °C and 35 °C). Skin could be a suitable material for extracting RNA. The RNA expression levels of β-actin and GAPDH correlate well with PMI, and these RNA markers of skin tissue could be additional indice for the estimation of PMI.

  2. Acute phase protein mRNA expressions and enhancement of antioxidant defense system in Black-meated Silkie Fowls supplemented with clove (Eugenia caryophyllus extracts under the influence of chronic heat stress

    Directory of Open Access Journals (Sweden)

    Alhassan Usman Bello

    2016-11-01

    Full Text Available Abstract Background The current study investigates the anti-stress effects of clove (Eugenia caryophyllus extracts (0, 200, 400, and 600 mg/kg on serum antioxidant biomarkers, immune response, immunological organ growth index, and expression levels of acute phase proteins (APPs; ovotransferrin (OVT, ceruloplasmin (CP, ceruloplasmin (AGP, C-reactive protein (CRP, and serum amyloid-A (SAA mRNA in the immunological organs of 63-d-old male black-meated Silkie fowls subjected to 21 d chronic heat stress at 35 ± 2 °C. Results The results demonstrated that clove extract supplementation in the diet of Silkie fowls subjected to elevated temperature (ET improve growth performance, immune responses, and suppressed the activities of glutathion peroxidase (GSH-Px, superoxide dismutase (SOD, catalase (CAT, and thioredoxin reductase (TXNRD; reduced serum malonaldehyde (MDA and glutathione (GSH concentrations when compared with fowls raised under thermoneutral condition (TC. Upon chronic heat stress and supplementation of clove extracts, the Silkie fowls showed a linear increase in GSH-Px, SOD, CAT, and TXNRD activities (P = 0.01 compared with fowls fed diets without clove extract. ET decreased (P < 0.05 the growth index of the liver, spleen, bursa of Fabricius and thymus. However, the growth index of the liver, spleen, bursa of Fabricius and thymus increased significantly (P < 0.05 which corresponded to an increase in clove supplemented levels. The expression of OVT, CP, AGP, CRP, and SAA mRNA in the liver, spleen, bursa of Fabricius and thymus were elevated (P < 0.01 by ET compared with those maintained at TC. Nevertheless, clove mitigates heat stress-induced overexpression of OVT, CP, AGP, CRP and SAA mRNA in the immune organs of fowls fed 400 mg clove/kg compared to other groups. Conclusions The results showed that clove extracts supplementation decreased oxidative stress in the heat-stressed black-meated fowls by alleviating

  3. Polyadenylated mRNA from the photosynthetic procaryote Rhodospirillum rubrum

    International Nuclear Information System (INIS)

    Majumdar, P.K.; McFadden, B.A.

    1984-01-01

    Total cellular RNA extracted from Rhodospirillum rubrum cultured in butyrate-containing medium under strict photosynthetic conditions to the stationary phase of growth has been fractionated on an oligodeoxy-thymidylic acid-cellulose column into polyadenylated [poly(A) + ] RNA and poly(A) - RNA fractions. The poly(A) + fraction was 9 to 10% of the total bulk RNA isolated. Analysis of the poly(A) + RNA on a denaturing urea-polyacrylamide gel revealed four sharp bands of RNA distributed in heterodisperse fashion between 16S and 9S. Similar fractionation of the poly(A) - RNA resulted in the separation of 23, 16, and 5S rRNAs and 4S tRNA. Poly(A) + fragments isolated after combined digestion with pancreatic A and T 1 RNases and analysis by denaturing gel electrophoresis demonstrated two major components of 80 and 100 residues. Alkaline hydrolysis of the nuclease-resistant, purified residues showed AMP-rich nucleotides. Through the use of snake venom phosphodiesterase, poly(A) tracts were placed at the 3' end of poly(A) + RNA. Stimulation of [ 3 H]leucine incorporation into hot trichloroacetic acid-precipitable polypeptides in a cell-free system from wheat germ primed by the poly(A) + RNA mixture was found to be 220-fold higher than that for poly(A) - RNAs (on a unit mass basis), a finding which demonstrated that poly(A) + RNAs in R. rubrum are mRNAs. Gel electrophoretic analysis of the translation mixture revealed numerous 3 H-labeled products including a major band (M/sub r/, 52,000). The parent protein was precipitated by antibodies to ribulose bisphosphate carboxylase-oxygenase and comprised 6.5% of the total translation products

  4. RNA Origami

    DEFF Research Database (Denmark)

    Sparvath, Steffen Lynge

    introducerede vores gruppe den enkeltstrengede RNA-origami metode, der giver mulighed for cotranscriptional foldning af veldefinerede nanostrukturer, og er en central del af arbejdet præsenteret heri. Denne ph.d.-afhandling udforsker potentielle anvendelser af RNA-origami nanostrukturer, som nanomedicin eller...... biosensorer. Afhandlingen består af en introduktion til RNA-nanoteknologi feltet, en introduktion af enkeltstrenget RNA-origami design, og fire studier, der beskriver design, produktion og karakterisering af både strukturelle og funktionelle RNA-origamier. Flere RNA-origami designs er blevet undersøgt, og...... projekterne, der indgår i denne afhandling, inkluderer de nyeste fremskridt indenfor strukturel RNA-nanoteknologi og udvikling af funktionelle RNA-baserede enheder. Det første studie beskriver konstruktion og karakterisering af en enkeltstrenget 6-helix RNA-origami stuktur, som er den første demonstration af...

  5. Towards a “Sample-In, Answer-Out” Point-of-Care Platform for Nucleic Acid Extraction and Amplification: Using an HPV E6/E7 mRNA Model System

    Directory of Open Access Journals (Sweden)

    Anja Gulliksen

    2012-01-01

    Full Text Available The paper presents the development of a “proof-of-principle” hands-free and self-contained diagnostic platform for detection of human papillomavirus (HPV E6/E7 mRNA in clinical specimens. The automated platform performs chip-based sample preconcentration, nucleic acid extraction, amplification, and real-time fluorescent detection with minimal user interfacing. It consists of two modular prototypes, one for sample preparation and one for amplification and detection; however, a common interface is available to facilitate later integration into one single module. Nucleic acid extracts (n=28 from cervical cytology specimens extracted on the sample preparation chip were tested using the PreTect HPV-Proofer and achieved an overall detection rate for HPV across all dilutions of 50%–85.7%. A subset of 6 clinical samples extracted on the sample preparation chip module was chosen for complete validation on the NASBA chip module. For 4 of the samples, a 100% amplification for HPV 16 or 33 was obtained at the 1 : 10 dilution for microfluidic channels that filled correctly. The modules of a “sample-in, answer-out” diagnostic platform have been demonstrated from clinical sample input through sample preparation, amplification and final detection.

  6. Attenuation of the Disruptive Effect induced by the Insecticide Fenvalerate on Total Monoamine Content and Testosterone Level in Adult Male Albino Rats Using Salvia aegyptiaca Extract

    International Nuclear Information System (INIS)

    Abdel Kader, S.M.; Aly, M.A.S.

    2008-01-01

    Administration of fenvalerate (90 mg/kg) to rats resulted in a significant decrease in dopamine (OA) content in most of brain areas under investigation. Its content in pons + medulla oblongata was the most affected recording - 62.98 %, on day 7, compared to control. Furthermore, norepinephrine (NE) content gradually decreased in different brain areas showing its maximal decrease in cerebellum with percentage change -64.89% on day 7. Serotonin (5-HT) and its metabolite 5-hydroxyindoleacetic acid (5-HIAA) showed maximal significant decrease, in the cortex with percentage differences -78.33 and -72.61%, respectively. Similarly, fen valerate resulted in a gradual decrease in serum testosterone level recording its maximal effect (-46. 58 %) at the end of the experimental period. On the other hand, administration of Salvia aegyptiaca (2 g/kg) caused a significant increase in monoamine contents (DA, NE, 5-HT and 5- HlAA) in most of the brain areas under investigation, throughout the experimental period. Moreover, Salvia extract administration resulted in a significant elevation in serum testosterone level, one day after administration, recording its maximal effect (55.75%) on day 7. Animals that received the combined treatment (Salvia extract one hour after fen valerate administration) showed that monoamine contents in most of the brain areas were more or less near to the control values. Furthermore, no significant change was noticed in serum testosterone level throughout the experiment in the combined treatment. From the present study, it can be concluded that Salvia aegyptiaca extract seems to be potentially promising for attenuating the disruption that occurred in monoamine and testosterone levels. This could highly recommend Salvia aegyptiaca to be a potential herb for further studies in the future for extracting compounds of medical use

  7. Automated Purification and Suspension Array Detection of 16S rRNA from Soil and Sediment Extracts by Using Tunable Surface Microparticles

    OpenAIRE

    Chandler, Darrell P.; Jarrell, Ann E.

    2004-01-01

    Autonomous, field-deployable molecular detection systems require seamless integration of complex biochemical solutions and physical or mechanical processing steps. In an attempt to simplify the fluidic requirements for integrated biodetection systems, we used tunable surface microparticles both as an rRNA affinity purification resin in a renewable microcolumn sample preparation system and as the sensor surface in a flow cytometer detector. The tunable surface detection limits in both low- and...

  8. The effect of hydro-ethanolic extract of Curcuma longa rhizome and curcumin on total and differential WBC and serum oxidant, antioxidant biomarkers in rat model of asthma

    OpenAIRE

    Farzaneh Shakeri; Mohammad Soukhtanloo; Mohammad Hossein Boskabady

    2017-01-01

    Objective(s): The effects of Curcuma longa (C. longa) and curcumin on total and differential WBC count and oxidant, antioxidant biomarkers, in rat model of asthma were evaluated. Materials and Methods: Total and differential WBC count in the blood, NO2, NO3, MDA, SOD, CAT and thiol levels in serum were examined in control, asthma, Asthmatic rats treated with C. longa (0.75, 1.50, and 3.00 mg/ml), curcumin (0.15, 0.30, and 0.60 mg/ml), and dexamethasone (1.25 ?g/ml) rats. Results: Total and mo...

  9. Determining the better solvent and time for extracting soil by soxhlet in TPH (Total Petroleum Hydrocarbon) gravimetric method; A determinacao de qual o melhor solvente e o melhor tempo de extracao de sedimento em aparato Soxhlet na metodologia do TPH (Total Petroleum Hydrocarbon) gravimetrico

    Energy Technology Data Exchange (ETDEWEB)

    Koike, Renato S.; Lima, Guilherme; Baisch, Paulo R. [Fundacao Universidade Federal do Rio Grande (FURG), RS (Brazil)

    2004-07-01

    There are several methods of TPH (Total Petroleum Hydrocarbons) analysis of petroleum hydrocarbons contaminants in sediment. The TPH gravimetric has been widely used in many studies and in oil spill monitoring case. The present work examined three different solvents (DCM, DCM/N-HEX and N-HEX), in three different times, to the purpose to optimize the contaminants extraction using USEPA 9071 and 3540 reference method. Then was realized analysis of Total Organic Carbon (TOC) for monitoring the reproducible extracts. The sediments used in this experiment was collected in the Cavalos Island, localized in the city of Rio Grande, RS-Brasil. The sediment was 'washed' and after then contaminated with petroleum. The extracts were realized in Soxhlet apparatus, in three different times (4, 8 and 12 hours), and TOC analysis were realized before and after the extraction. The result demonstrated that eight hours with DCM/N-HEX solvent is more indicated for TPH gravimetric in sediment analysis with high concentration of petroleum hydrocarbons. TOC analysis demonstrated inappropriate for monitoring extract reproducibility. (author)

  10. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

    DEFF Research Database (Denmark)

    Lever, Mark; Torti, Andrea; Eickenbusch, Philip

    2015-01-01

    tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world...... DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample...

  11. Measurement of total alpha activity of neptunium, plutonium, and americium in highly radioactive Hanford waste by iron hydroxide precipitation and 2-heptanone solvent extraction

    International Nuclear Information System (INIS)

    Maiti, T.C.; Kaye, J.H.

    1992-06-01

    An improved method has been developed to concentrate the major alpha-emitting actinide elements neptunium, plutonium, and americium from samples with high salt content such as those resulting from efforts to characterize Hanford storage tank waste. Actinide elements are concentrated by coprecipitation of their hydroxides using iron carrier. The iron is removed by extraction from 8M HCI with 2-heptanone. The actinide elements remain in the aqueous phase free from salts, iron, and long-lived fission products. Recoveries averaged 98 percent

  12. Preparation and quantification of the total phenolic products in Citrus fruit using solid-phase extraction coupled with high-performance liquid chromatography with diode array and UV detection.

    Science.gov (United States)

    Zeng, Honglian; Liu, Zhenli; Zhao, Siyu; Shu, Yisong; Song, Zhiqian; Wang, Chun; Dong, Yunzhuo; Ning, Zhangchi; He, Dan; Wang, Menglei; Lu, Cheng; Liu, Yuanyan; Lu, Aiping

    2016-10-01

    Citrus fruit is an important health-promoting food that is rich in dietary phenolic metabolites. Traditional Chinese medicines, such as Zhishi and Zhiqiao, come from young and immature fruits of Citrus cultivars. The preparation of diversified bioactive phenolic products and establishment of the corresponding quality control methodology are challenging and necessary. In the current study, four types of solid-phase extraction sorbents for the enrichment and clean-up of the phenolic matrix were evaluated. A solid-phase extraction column coated with Strata-X was finally used in the procedure. Twenty phenolic compounds were selected to evaluate the extraction performances of the sorbents using high-performance liquid chromatography analysis. Under the optimized conditions, good linearities were obtained with R 2 more than 0.9996 for all analytes with LODs of 0.04-1.012 μg/g. Intra- and interday relative standard deviation values were less than 3%, and the recovery was equal to or higher than 90.02%. Compared to non-solid-phase extraction process, the content of total phenolic products was elevated 35.55-68.48% with solid-phase extraction. Finally, the developed and validated method was successfully applied to the discrimination of Zhishi samples from different species as well as Zhishi and Zhiqiao samples in different development stages. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. A comparison of various "housekeeping" probes for northern analysis of normal and osteoarthritic articular cartilage RNA.

    Science.gov (United States)

    Matyas, J R; Huang, D; Adams, M E

    1999-01-01

    Several approaches are commonly used to normalize variations in RNA loading on Northern blots, including: ethidium bromide (EthBr) fluorescence of 18S or 28S rRNA or autoradiograms of radioactive probes hybridized with constitutively expressed RNAs such as elongation factor-1alpha (ELF), glyceraldehyde-3-phosphate dehydrogenase (G3PDH), actin, 18S or 28S rRNA, or others. However, in osteoarthritis (OA) the amount of total RNA changes significantly and none of these RNAs has been clearly demonstrated to be expressed at a constant level, so it is unclear if any of these approaches can be used reliably for normalizing RNA extracted from osteoarthritic cartilage. Total RNA was extracted from normal and osteoarthritic cartilage and assessed by EthBr fluorescence. RNA was then transferred to a nylon membrane hybridized with radioactive probes for ELF, G3PDH, Max, actin, and an oligo-dT probe. The autoradiographic signal across the six lanes of a gel was quantified by scanning densitometry. When compared on the basis of total RNA, the coefficient of variation was lowest for 28S ethidium bromide fluorescence and oligo-dT (approximately 7%), followed by 18S ethidium bromide fluorescence and G3PDH (approximately 13%). When these values were normalized to DNA concentration, the coefficient of variation exceeded 50% for all signals. Total RNA and the signals for 18S, 28S rRNA, and oligo-dT all correlated highly. These data indicate that osteoarthritic chondrocytes express similar ratios of mRNA to rRNA and mRNA to total RNA as do normal chondrocytes. Of all the "housekeeping" probes, G3PDH correlated best with the measurements of RNA. All of these "housekeeping" probes are expressed at greater levels by osteoarthritic chondrocytes when compared with normal chondrocytes. Thus, while G3PDH is satisfactory for evaluating the amount of RNA loaded, its level of expression is not the same in normal and osteoarthritic chondrocytes.

  14. Optimized methods for total nucleic acid extraction and quantification of the bat white-nose syndrome fungus, Pseudogymnoascus destructans, from swab and environmental samples.

    Science.gov (United States)

    Verant, Michelle L; Bohuski, Elizabeth A; Lorch, Jeffery M; Blehert, David S

    2016-03-01

    The continued spread of white-nose syndrome and its impacts on hibernating bat populations across North America has prompted nationwide surveillance efforts and the need for high-throughput, noninvasive diagnostic tools. Quantitative real-time polymerase chain reaction (qPCR) analysis has been increasingly used for detection of the causative fungus, Pseudogymnoascus destructans, in both bat- and environment-associated samples and provides a tool for quantification of fungal DNA useful for research and monitoring purposes. However, precise quantification of nucleic acid from P. destructans is dependent on effective and standardized methods for extracting nucleic acid from various relevant sample types. We describe optimized methodologies for extracting fungal nucleic acids from sediment, guano, and swab-based samples using commercial kits together with a combination of chemical, enzymatic, and mechanical modifications. Additionally, we define modifications to a previously published intergenic spacer-based qPCR test for P. destructans to refine quantification capabilities of this assay. © 2016 The Author(s).

  15. Optimized methods for total nucleic acid extraction and quantification of the bat white-nose syndrome fungus, Pseudogymnoascus destructans, from swab and environmental samples

    Science.gov (United States)

    Verant, Michelle; Bohuski, Elizabeth A.; Lorch, Jeffrey M.; Blehert, David

    2016-01-01

    The continued spread of white-nose syndrome and its impacts on hibernating bat populations across North America has prompted nationwide surveillance efforts and the need for high-throughput, noninvasive diagnostic tools. Quantitative real-time polymerase chain reaction (qPCR) analysis has been increasingly used for detection of the causative fungus, Pseudogymnoascus destructans, in both bat- and environment-associated samples and provides a tool for quantification of fungal DNA useful for research and monitoring purposes. However, precise quantification of nucleic acid fromP. destructans is dependent on effective and standardized methods for extracting nucleic acid from various relevant sample types. We describe optimized methodologies for extracting fungal nucleic acids from sediment, guano, and swab-based samples using commercial kits together with a combination of chemical, enzymatic, and mechanical modifications. Additionally, we define modifications to a previously published intergenic spacer–based qPCR test for P. destructans to refine quantification capabilities of this assay.

  16. A Simple Paper-Based Microfluidic Device for the Determination of the Total Amino Acid Content in a Tea Leaf Extract

    Science.gov (United States)

    Cai, Longfei; Wu, Yunying; Xu, Chunxiu; Chen, Zefeng

    2013-01-01

    An experiment was developed to demonstrate a microfluidic device in the analytical chemistry (instrumental analysis) laboratory. Students made the paper-based microfluidic device with a wax pen and a piece of filter paper and used it to determine the total quantity of amino acids in a green tea leaf

  17. Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants

    Directory of Open Access Journals (Sweden)

    Charith Raj Adkar-Purushothama

    2015-12-01

    Full Text Available In order to analyze the production of small RNA (sRNA by viroids upon infecting the plants, the tomato plants (Solanum lycopersicum cultivar Rutgers were inoculated with the variants of Potato spindle tuber viroid (PSTVd. After 21-days of postinoculation, total RNA was extracted and subjected for deep-sequencing using Illumina HiSeq platform. The primers were trimmed and only 21- to 24-nt long sRNAs were filtered after quality check of the raw data. The filtered sRNA population was then mapped against both the genomic (+ and antigenomic (− strands of the respective PSTVd variants using standard pattern-matching algorithm. The profiling of viroid derived sRNA (vd-sRNA revealed that the viroids are susceptible to host RNA silencing mechanism. High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO database under accession number GSE69225.

  18. Evaluation of cost-effective total nucleic acids extraction protocols for cultured Mycobacterium tuberculosis; a comparison by PCR amplification of genes associated with drug resistance

    Directory of Open Access Journals (Sweden)

    Gyamfi Oti K

    2010-02-01

    Full Text Available Abstract Background The emergence of drug resistant strains of Mycobacterium tuberculosis complex has made the management of tuberculosis difficult. Also, Mycobacterium species has a peculiar cell wall, made of an impermeable complex structure rich in mycolate, making the lyses of its cell difficult. In order to apply a radio-labelled-probe based detection of mutations in selected genes leading to drug resistance, we concede that the evaluation and modifications of nucleic acid extraction protocols that are less sophisticated and less prone to contamination would be useful in the management of tuberculosis in a resource-constrained setting. Findings The average amount of nucleic acids was determined for different extraction treatments. High temperature treatment only, yielded the lowest amount of nucleic acids, i.e. 15.7 ± 3.2 μg. The average amount of nucleic acids obtained with the addition of TE and triton-X100, was 133.7 ± 8.9 μg, while that obtained with the addition of TE only, and TE and SDS were 68.4 ± 22.7 μg and 70.4 ± 20.3 μg respectively. Other treatments yielded 28.8 ± 6.7 μg, 32.5 ± 2.4 μg and 36.9 ± 15.5 μg. The average amount of nucleic acids obtained with high temperature treatment in TE, and that obtained by freezing prior to high temperature treatment, successfully amplified for the genes of interest (rpoB, KatG, rrs. Conclusion We strongly recommend the use of 1× TE buffer, and freezing and heating for improved lysis of cultured M. tuberculosis, and therefore, as an effective method for the preparation of M. tuberculosis nucleic acid useful for PCR.

  19. Fenólicos totais e atividade antioxidante do extrato aquoso de broto de feijão-mungo (Vigna radiata L. Total phenolics and antioxidant activity of the aqueous extract of mung bean sprout (Vigna radiata L.

    Directory of Open Access Journals (Sweden)

    Vera Lúcia Arroxelas Galvão de Lima

    2004-03-01

    Full Text Available OBJETIVO: Considerando a importância dos compostos fenólicos em alimentos e que o broto de feijão-mungo vem sendo incluído na culinária brasileira, este estudo teve como objetivo quantificar o teor de fenólicos totais deste vegetal e avaliar a ação antioxidante do seu extrato aquoso. MÉTODOS: Os compostos fenólicos foram extraídos por quatro sistemas de solventes e dois métodos de extração, os quais foram diferenciados no tempo (2 e 1h e número de extrações (2 e 3 extrações. Os fenólicos totais dos extratos foram quantificados por método espectrofotométrico. RESULTADOS: Os extratos obtidos com água à temperatura ambiente (28ºC, nos dois métodos de extração, foram os que apresentaram maior quantidade de fenólicos totais, sem contudo apresentar diferença significativa entre eles. O método II, que consistiu de três extrações em 1h, pode ser considerado o melhor por ter utilizado menor tempo de extração. O extrato aquoso em sistema modelo b-caroteno/ácido linoléico exibiu ação antioxidante (48,07% de inibição da oxidação, entretanto foi inferior ao padrão BHT. CONCLUSÃO: O broto de feijão-mungo possui considerável quantidade de fenólicos totais, compostos responsáveis por sua ação antioxidante, cujo consumo pode proporcionar efeitos benéficos à saúde.OBJECTIVE: Considering the importance of phenolic compounds in foods and the increasing consumption of mung bean sprouts in Brazil, this study had the objective of quantifying the total phenolic content in this vegetable and to assess the antioxidant activity of its aqueous extract. METHODS: The phenolic compounds were extracted by four solvent systems and two extraction methods, which were different in time (2 and 1h and in number of extractions (2 and 3 extractions. The total phenolic content of the extracts were quantified by the spectrophotometric method. RESULTS: The extracts obtained with water at room temperature (28ºC in both extraction

  20. Simultaneous separation of five major ribonucleic acids by capillary electrophoresis with laser-induced fluorescence in the presence of electroosmotic flow: application to the rapid screening of 5S rRNA from ovarian cancer cells.

    Science.gov (United States)

    Shih, Ya-Chu; Liao, Ching-Ru; Chung, I-Che; Chang, Yu-Sun; Chang, Po-Ling

    2014-10-17

    RNA integrity is important in RNA studies because poor RNA quality may impact downstream methodologies. This study proposes a rapid and cost-effective method for the determination of RNA integrity based on CE-LIF in the presence of electroosmotic flow. The proposed method uses poly(ethylene) oxide (Mavg=4,000,000 Da) as a sieving matrix for total RNA separation. Ethidium bromide (μg mL(-1)) was dissolved in a polymer solution as an interchelating dye for on-column fluorescent labeling. The 28S rRNA, 18S rRNA, 5.8S rRNA, 5S rRNA and tRNA from the total human RNA extracted from the cells were fully separated using the proposed method. The lowest detectable concentration of total RNA achieved was 100 pg μL(-1) with a 6 min sample injection followed by on-column concentration. In addition, the temperature-induced degradation of total RNA was observed by CE-LIF. The electropherograms revealed more fragmentation of 28S and 18S rRNAs by temperature-induced hydrolysis compared with the 5.8S rRNA, 5S rRNA and tRNA. Therefore, the results indicated that RNA degradation should be considered for long-term, high-temperature incubations in RNA-related experiments involving RNA hybridization. The proposed method is furthermore, applied to the determination of 5S rRNA overexpressed in ovarian cancer cells as compared to the cervical cancer cells. Overall, CE-LIF is highly promising for rapid screening of ovarian cancers without tedious pre-amplification steps. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Low-level lasers on microRNA and uncoupling protein 2 mRNA levels in human breast cancer cells

    Science.gov (United States)

    Canuto, K. S.; Teixeira, A. F.; Rodrigues, J. A.; Paoli, F.; Nogueira, E. M.; Mencalha, A. L.; Fonseca, A. S.

    2017-06-01

    MicroRNA is short non-coding RNA and is a mediator of post-transcriptional regulation of gene expression. In addition, uncoupling proteins (UCPs) regulate thermogenesis, metabolic and energy balance, and decrease reactive oxygen species production. Both microRNA and UCP2 expression can be altered in cancer cells. At low power, laser wavelength, frequency, fluence and emission mode deternube photobiological responses, which are the basis of low-level laser therapy. There are few studies on miRNA and UCP mRNA levels after low-level laser exposure on cancer cells. In this work, we evaluate the micrRNA (mir-106b and mir-15a) and UCP2 mRNA levels in human breast cancer cells exposed to low-level lasers. MDA-MB-231 human breast cancer cells were exposed to low-level red and infrared lasers, total RNA was extracted for cDNA synthesis and mRNA levels by real time quantitative polymerase chain reaction were evaluated. Data show that mir-106b and mir-15a relative levels are not altered, but UCP2 mRNA relative levels are increased in MDA-MB-231 human breast cancer cells exposed to low-level red and infrared lasers at fluences used in therapeutic protocols.

  2. Identification of messenger RNA of fetoplacental source in maternal plasma of women with normal pregnancies and pregnancies with intrauterine growth restriction.

    Science.gov (United States)

    Ayala Ramírez, Paola; García Robles, Reggie; Rojas, Juan Diego; Bermúdez, Martha; Bernal, Jaime

    2012-07-01

    to quantify placenta-specific RNA in plasma of women carrying foetuses with intrauterine growth restriction and pregnant women with normal pregnancies. 8 pregnant women with foetuses with intrauterine growth restriction were studied as well as 18 women with uncomplicated pregnancies in the third pregnancy trimester. Total free RNA was quantified in maternal plasma by spectrophotometry and the gene expression of hPL (Human Placental Lactogen) at the messenger RNA level through technical Real Time-Chain Reaction Polymerase. plasma RNA of fetoplacental origin was successfully detected in 100% of pregnant women. There were no statistically significant differences between the values of total RNA extracted from plasma (p= 0.5975) nor in the messenger RNA expression of hPL gene (p= 0.5785) between cases and controls. messenger RNA of fetoplacental origin can be detected in maternal plasma during pregnancy.

  3. Posttranscriptional silencing of the lncRNA MALAT1 by miR-217 inhibits the epithelial–mesenchymal transition via enhancer of zeste homolog 2 in the malignant transformation of HBE cells induced by cigarette smoke extract

    International Nuclear Information System (INIS)

    Lu, Lu; Luo, Fei; Liu, Yi; Liu, Xinlu; Shi, Le; Lu, Xiaolin; Liu, Qizhan

    2015-01-01

    Lung cancer is regarded as the leading cause of cancer-related deaths, and cigarette smoking is one of the strongest risk factors for the development of lung cancer. However, the mechanisms for cigarette smoke-induced lung carcinogenesis remain unclear. The present study investigated the effects of an miRNA (miR-217) on levels of an lncRNA (MALAT1) and examined the role of these factors in the epithelial–mesenchymal transition (EMT) induced by cigarette smoke extract (CSE) in human bronchial epithelial (HBE) cells. In these cells, CSE caused decreases of miR-217 levels and increases in lncRNA MALAT1 levels. Over-expression of miR-217 with a mimic attenuated the CSE-induced increase of MALAT1 levels, and reduction of miR-217 levels by an inhibitor enhanced expression of MALAT1. Moreover, the CSE-induced increase of MALAT1 expression was blocked by an miR-217 mimic, indicating that miR-217 negatively regulates MALAT1 expression. Knockdown of MALAT1 reversed CSE-induced increases of EZH2 (enhancer of zeste homolog 2) and H3K27me3 levels. In addition to the alteration from epithelial to spindle-like mesenchymal morphology, chronic exposure of HBE cells to CSE increased the levels of EZH2, H3K27me3, vimentin, and N-cadherin and decreased E-cadherin levels, effects that were reversed by MALAT1 siRNA or EZH2 siRNA. The results indicate that miR-217 regulation of EZH2/H3K27me3 via MALAT1 is involved in CSE-induced EMT and malignant transformation of HBE cells. The posttranscriptional silencing of MALAT1 by miR-217 provides a link, through EZH2, between ncRNAs and the EMT and establishes a mechanism for CSE-induced lung carcinogenesis. - Highlights: • CSE exposure decreases miR-217 levels and increases MALAT1 levels. • miR-217 negatively regulates MALAT1 expression. • MALAT1, via EZH2, is involved in the EMT of CSE-transformed HBE cells.

  4. Quantitative analysis of unconjugated and total bisphenol A in human urine using solid-phase extraction and UPLC-MS/MS: method implementation, method qualification and troubleshooting.

    Science.gov (United States)

    Buscher, Brigitte; van de Lagemaat, Dick; Gries, Wolfgang; Beyer, Dieter; Markham, Dan A; Budinsky, Robert A; Dimond, Stephen S; Nath, Rajesh V; Snyder, Stephanie A; Hentges, Steven G

    2015-11-15

    The aim of the presented investigation was to document challenges encountered during implementation and qualification of a method for bisphenol A (BPA) analysis and to develop and discuss precautions taken to avoid and to monitor contamination with BPA during sample handling and analysis. Previously developed and published HPLC-MS/MS methods for the determination of unconjugated BPA (Markham et al. Journal of Analytical Toxicology, 34 (2010) 293-303) [17] and total BPA (Markham et al. Journal of Analytical Toxicology, 38 (2014) 194-203) [20] in human urine were combined and transferred into another laboratory. The initial method for unconjugated BPA was developed and evaluated in two independent laboratories simultaneously. The second method for total BPA was developed and evaluated in one of these laboratories to conserve resources. Accurate analysis of BPA at sub-ppb levels is a challenging task as BPA is a widely used material and is ubiquitous in the environment at trace concentrations. Propensity for contamination of biological samples with BPA is reported in the literature during sample collection, storage, and/or analysis. Contamination by trace levels of BPA is so pervasive that even with extraordinary care, it is difficult to completely exclude the introduction of BPA into biological samples and, consequently, contamination might have an impact on BPA biomonitoring data. The applied UPLC-MS/MS method was calibrated from 0.05 to 25ng/ml. The limit of quantification was 0.1ng/ml for unconjugated BPA and 0.2ng/ml for total BPA, respectively, in human urine. Finally, the method was applied to urine samples derived from 20 volunteers. Overall, BPA can be analyzed in human urine with acceptable recovery and repeatability if sufficient measures are taken to avoid contamination throughout the procedure from sample collection until UPLC-MS/MS analysis. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  5. Data set on the effects of conifer control and slash burning on soil carbon, total N, organic matter and extractable micro-nutrients

    Directory of Open Access Journals (Sweden)

    Jonathan D. Bates

    2017-10-01

    Full Text Available Conifer control in sagebrush steppe of the western United States causes various levels of site disturbance influencing vegetation recovery and resource availability. The data set presented in this article include growing season availability of soil micronutrients and levels of total soil carbon, organic matter, and N spanning a six year period following western juniper (Juniperus occidentalis spp. occidentalis reduction by mechanical cutting and prescribed fire of western juniper woodlands in southeast Oregon. These data can be useful to further evaluate the impacts of conifer woodland reduction to soil resources in sagebrush steppe plant communities.

  6. [Correlation between RNA Expression Level and Early PMI in Human Brain Tissue].

    Science.gov (United States)

    Lü, Y H; Ma, K J; Li, Z H; Gu, J; Bao, J Y; Yang, Z F; Gao, J; Zeng, Y; Tao, L; Chen, L

    2016-08-01

    To explore the correlation between the expression levels of several RNA markers in human brain tissue and early postmortem interval (PMI). Twelve individuals with known PMI (range from 4.3 to 22.5 h) were selected and total RNA was extracted from brain tissue. Eight commonly used RNA markers were chosen including β -actin, GAPDH, RPS29, 18S rRNA, 5S rRNA, U6 snRNA, miRNA-9 and miRNA-125b, and the expression levels were detected in brain tissue by real-time fluorescent quantitative PCR. The internal reference markers with stable expression in early PMI were screened using geNorm software and the relationship between its expression level and some relevant factors such as age, gender and cause of death were analyzed. RNA markers normalized by internal reference were inserted into the mathematic model established by previous research for PMI estimation using R software. Model quality was judged by the error rate calculated with estimated PMI. 5S rRNA, miRNA-9 and miRNA-125b showed quite stable expression and their expression levels had no relation with age, gender and cause of death. The error rate of estimated PMI using β -actin was 24.6%, while GAPDH was 41.0%. 5S rRNA, miRNA-9 and miRNA-125b are suitable as internal reference markers of human brain tissue owing to their stable expression in early PMI. The expression level of β -actin correlates well with PMI, which can be used as an additional index for early PMI estimation. Copyright© by the Editorial Department of Journal of Forensic Medicine

  7. Extracellular plasma RNA from colon cancer patients is confined in a vesicle-like structure and is mRNA-enriched

    Science.gov (United States)

    García, José Miguel; García, Vanesa; Peña, Cristina; Domínguez, Gemma; Silva, Javier; Diaz, Raquel; Espinosa, Pablo; Citores, Maria Jesús; Collado, Manuel; Bonilla, Félix

    2008-01-01

    Little is yet known about the origin and protective mechanism of free nucleic acids in plasma. We investigated the possibility of these free nucleic acids being particle associated. Plasma samples from colon cancer patients and cell culture media were subjected to various antibody incubations, ultracentrifugation, and RNA extraction protocols for total RNA, epithelial RNA, and mRNA. Flow cytometry using a Ber-EP4 antibody and confocal laser microscopy after staining with propidium iodide were also performed. mRNA levels of the LISCH7 and SDHA genes were determined in cells and in culture media. Ber-EP4 antibody and polystyrene beads coated with oligo dT sequences were employed. We observed that, after incubation, total RNA and mRNA were always detected after membrane digestion, and that epithelial RNA was detected before this procedure. In ultracentrifugation, mRNA was caught in the supernatant only if a former lysis mediated or in the pellet if there was no previous digestion. Flow cytometry determinations showed that antibody-coated microbeads keep acellular structures bearing epithelial antigens apart. Confocal laser microscopy made 1- to 2-μm-diameter particles perceptible in the vicinity of magnetic polystyrene beads. Relevant differences were observed between mRNA of cells and culture media, as there was a considerable difference in LISCH7 mRNA levels between HT29 and IMR90 cell co-cultures and their culture media. Our results support the view that extracellular RNA found in plasma from cancer patients circulates in association with or is protected in a multiparticle complex, and that an active release mechanism by tumor cells may be a possible origin. PMID:18456845

  8. Total protein

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003483.htm Total protein To use the sharing features on this page, please enable JavaScript. The total protein test measures the total amount of two classes ...

  9. In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS Genes

    Directory of Open Access Journals (Sweden)

    Csengele E. Barta

    2017-10-01

    Full Text Available Mature oak (Quercus spp. leaves, although abundantly available during the plants’ developmental cycle, are rarely exploited as viable sources of genomic DNA. These leaves are rich in metabolites difficult to remove during standard DNA purification, interfering with downstream molecular genetics applications. The current work assessed whether in situ dark adaptation, to deplete sugar reserves and inhibit secondary metabolite synthesis could compensate for the difficulties encountered when isolating DNA from mature leaves rich in secondary metabolites. We optimized a rapid, commercial kit based method to extract genomic DNA from dark- and light-adapted leaves. We demonstrated that in situ dark adaptation increases the yield and quality of genomic DNA obtained from mature oak leaves, yielding templates of sufficiently high quality for direct downstream applications, such as PCR amplification and gene identification. The quality of templates isolated from dark-adapted pin oak leaves particularly improved the amplification of larger fragments in our experiments. From DNA extracts prepared with our optimized method, we identified for the first time partial segments of the genes encoding 18S rRNA and isoprene synthase (IspS from pin oak (Quercus palustris, whose full genome has not yet been sequenced.

  10. Prognostic and Clinical Significance of miRNA-205 in Endometrioid Endometrial Cancer.

    Directory of Open Access Journals (Sweden)

    Milosz Wilczynski

    Full Text Available Endometrial cancer is one of the most common malignancies of the reproductive female tract, with endometrioid endometrial cancer being the most frequent type. Despite the relatively favourable prognosis in cases of endometrial cancer, there is a necessity to evaluate clinical and prognostic utility of new molecular markers. MiRNAs are small, non-coding RNA molecules that take part in RNA silencing and post-transcriptional regulation of gene expression. Altered expression of miRNAs may be associated with cancer initiation, progression and metastatic capabilities. MiRNA-205 seems to be one of the key regulators of gene expression in endometrial cancer. In this study, we investigated clinical and prognostic role of miRNA-205 in endometrioid endometrial cancer. After total RNA extraction from 100 archival formalin-fixed paraffin-embedded tissues, real-time quantitative RT-PCR was used to define miRNA-205 expression levels. The aim of the study was to evaluate miRNA-205 expression levels in regard to patients' clinical and histopathological features, such as: survival rate, recurrence rate, staging, myometrial invasion, grading and lymph nodes involvement. Higher levels of miRNA-205 expression were observed in tumours with less than half of myometrial invasion and non-advanced cancers. Kaplan-Maier analysis revealed that higher levels of miRNA-205 were associated with better overall survival (p = 0,034. These results indicate potential clinical utility of miRNA-205 as a prognostic marker.

  11. Supplementary data: Materials and methods RNA expression ...

    Indian Academy of Sciences (India)

    ritt8

    Supplementary data: Materials and methods. RNA expression analysis. Freshly collected tissue was taken in TRIzol reagent for total RNA isolation according to the manufacturer's protocol. The cDNA synthesis was carried out in 1 μg total RNA using Random hexamer (Invitrogen, Carlsbad, USA) and Superscript III ...

  12. High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature.

    Science.gov (United States)

    Sergeant, Martin J; Constantinidou, Chrystala; Cogan, Tristan; Penn, Charles W; Pallen, Mark J

    2012-01-01

    The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing. Although considerable effort has been devoted to identifying the most informative region of the 16S gene and the optimal informatics procedures to process the data, little attention has been paid to the PCR step, in particular annealing temperature and primer length. To address this, amplicons derived from 16S-rDNA were generated from chicken caecal content DNA using different annealing temperatures, primers and different DNA extraction procedures. The amplicons were pyrosequenced to determine the optimal protocols for capture of maximum bacterial diversity from a chicken caecal sample. Even at very low annealing temperatures there was little effect on the community structure, although the abundance of some OTUs such as Bifidobacterium increased. Using shorter primers did not reveal any novel OTUs but did change the community profile obtained. Mechanical disruption of the sample by bead beating had a significant effect on the results obtained, as did repeated freezing and thawing. In conclusion, existing primers and standard annealing temperatures captured as much diversity as lower annealing temperatures and shorter primers.

  13. The effects of black garlic ethanol extract on the spatial memory and estimated total number of pyramidal cells of the hippocampus of monosodium glutamate-exposed adolescent male Wistar rats.

    Science.gov (United States)

    Hermawati, Ery; Sari, Dwi Cahyani Ratna; Partadiredja, Ginus

    2015-09-01

    Monosodium glutamate (MSG) is believed to exert deleterious effects on various organs, including the hippocampus, likely via the oxidative stress pathway. Garlic (Alium sativum L.), which is considered to possess potent antioxidant activity, has been used as traditional remedy for various ailments since ancient times. We have investigated the effects of black garlic, a fermented form of garlic, on spatial memory and estimated the total number of pyramidal cells of the hippocampus in adolescent male Wistar rats treated with MSG. Twenty-five rats were divided into five groups: C- group, which received normal saline; C+ group, which was exposed to 2 mg/g body weight (bw) of MSG; three treatment groups (T2.5, T5, T10), which were treated with black garlic extract (2.5, 5, 10 mg/200 g bw, respectively) and MSG. The spatial memory test was carried out using the Morris water maze (MWM) procedure, and the total number of pyramidal cells of the hippocampus was estimated using the physical disector design. The groups treated with black garlic extract were found to have a shorter path length than the C- and C+ groups in the escape acquisition phase of the MWM test. The estimated total number of pyramidal cells in the CA1 region of the hippocampus was higher in all treated groups than that of the C+ group. Based on these results, we conclude that combined administration of black garlic and MSG may alter the spatial memory functioning and total number of pyramidal neurons of the CA1 region of the hippocampus of rats.

  14. RNA-SSPT: RNA Secondary Structure Prediction Tools.

    Science.gov (United States)

    Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

    2013-01-01

    The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

  15. Total algorithms

    NARCIS (Netherlands)

    Tel, G.

    We define the notion of total algorithms for networks of processes. A total algorithm enforces that a "decision" is taken by a subset of the processes, and that participation of all processes is required to reach this decision. Total algorithms are an important building block in the design of

  16. Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format

    Directory of Open Access Journals (Sweden)

    Salvo-Chirnside Eliane

    2011-12-01

    Full Text Available Abstract The increasing popularity of systems-based approaches to plant research has resulted in a demand for high throughput (HTP methods to be developed. RNA extraction from multiple samples in an experiment is a significant bottleneck in performing systems-level genomic studies. Therefore we have established a high throughput method of RNA extraction from Arabidopsis thaliana to facilitate gene expression studies in this widely used plant model. We present optimised manual and automated protocols for the extraction of total RNA from 9-day-old Arabidopsis seedlings in a 96 well plate format using silica membrane-based methodology. Consistent and reproducible yields of high quality RNA are isolated averaging 8.9 μg total RNA per sample (~20 mg plant tissue. The purified RNA is suitable for subsequent qPCR analysis of the expression of over 500 genes in triplicate from each sample. Using the automated procedure, 192 samples (2 × 96 well plates can easily be fully processed (samples homogenised, RNA purified and quantified in less than half a day. Additionally we demonstrate that plant samples can be stored in RNAlater at -20°C (but not 4°C for 10 months prior to extraction with no significant effect on RNA yield or quality. Additionally, disrupted samples can be stored in the lysis buffer at -20°C for at least 6 months prior to completion of the extraction procedure providing a flexible sampling and storage scheme to facilitate complex time series experiments.

  17. The effects of frozen tissue storage conditions on the integrity of RNA and protein.

    Science.gov (United States)

    Auer, H; Mobley, J A; Ayers, L W; Bowen, J; Chuaqui, R F; Johnson, L A; Livolsi, V A; Lubensky, I A; McGarvey, D; Monovich, L C; Moskaluk, C A; Rumpel, C A; Sexton, K C; Washington, M K; Wiles, K R; Grizzle, W E; Ramirez, N C

    2014-10-01

    Unfixed tissue specimens most frequently are stored for long term research uses at either -80° C or in vapor phase liquid nitrogen (VPLN). There is little information concerning the effects such long term storage on tissue RNA or protein available for extraction. Aliquots of 49 specimens were stored for 5-12 years at -80° C or in VPLN. Twelve additional paired specimens were stored for 1 year under identical conditions. RNA was isolated from all tissues and assessed for RNA yield, total RNA integrity and mRNA integrity. Protein stability was analyzed by surface-enhanced or matrix-assisted laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS, MALDI-TOF-MS) and nano-liquid chromatography electrospray ionization tandem mass spectrometry (nLC-ESI-MS/MS). RNA yield and total RNA integrity showed significantly better results for -80° C storage compared to VPLN storage; the transcripts that were preferentially degraded during VPLN storage were these involved in antigen presentation and processing. No consistent differences were found in the SELDI-TOF-MS, MALDI-TOF-MS or nLC-ESI-MS/MS analyses of specimens stored for more than 8 years at -80° C compared to those stored in VPLN. Long term storage of human research tissues at -80° C provides at least the same quality of RNA and protein as storage in VPLN.

  18. Conifers have a unique small RNA silencing signature.

    Science.gov (United States)

    Dolgosheina, Elena V; Morin, Ryan D; Aksay, Gozde; Sahinalp, S Cenk; Magrini, Vincent; Mardis, Elaine R; Mattsson, Jim; Unrau, Peter J

    2008-08-01

    Plants produce small RNAs to negatively regulate genes, viral nucleic acids, and repetitive elements at either the transcriptional or post-transcriptional level in a process that is referred to as RNA silencing. While RNA silencing has been extensively studied across the different phyla of the animal kingdom (e.g., mouse, fly, worm), similar studies in the plant kingdom have focused primarily on angiosperms, thus limiting evolutionary studies of RNA silencing in plants. Here we report on an unexpected phylogenetic difference in the size distribution of small RNAs among the vascular plants. By extracting total RNA from freshly growing shoot tissue, we conducted a survey of small RNAs in 24 vascular plant species. We find that conifers, which radiated from the other seed-bearing plants approximately 260 million years ago, fail to produce significant amounts of 24-nucleotide (nt) RNAs that are known to guide DNA methylation and heterochromatin formation in angiosperms. Instead, they synthesize a diverse population of small RNAs that are exactly 21-nt long. This finding was confirmed by high-throughput sequencing of the small RNA sequences from a conifer, Pinus contorta. A conifer EST search revealed the presence of a novel Dicer-like (DCL) family, which may be responsible for the observed change in small RNA expression. No evidence for DCL3, an enzyme that matures 24-nt RNAs in angiosperms, was found. We hypothesize that the diverse class of 21-nt RNAs found in conifers may help to maintain organization of their unusually large genomes.

  19. Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling

    Directory of Open Access Journals (Sweden)

    Brenton James D

    2004-01-01

    Full Text Available Abstract Background Expression microarrays have evolved into a powerful tool with great potential for clinical application and therefore reliability of data is essential. RNA amplification is used when the amount of starting material is scarce, as is frequently the case with clinical samples. Purification steps are critical in RNA amplification and labelling protocols, and there is a lack of sufficient data to validate and optimise the process. Results Here the purification steps involved in the protocol for indirect labelling of amplified RNA are evaluated and the experimentally determined best method for each step with respect to yield, purity, size distribution of the transcripts, and dye coupling is used to generate targets tested in replicate hybridisations. DNase treatment of diluted total RNA samples followed by phenol extraction is the optimal way to remove genomic DNA contamination. Purification of double-stranded cDNA is best achieved by phenol extraction followed by isopropanol precipitation at room temperature. Extraction with guanidinium-phenol and Lithium Chloride precipitation are the optimal methods for purification of amplified RNA and labelled aRNA respectively. Conclusion This protocol provides targets that generate highly reproducible microarray data with good representation of transcripts across the size spectrum and a coefficient of repeatability significantly better than that reported previously.

  20. An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing.

    Science.gov (United States)

    Amini, Parisa; Ettlin, Julia; Opitz, Lennart; Clementi, Elena; Malbon, Alexandra; Markkanen, Enni

    2017-08-23

    Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA-protein crosslinking and RNA fragmentation, both of which heavily impact on RNA quantity and quality for downstream analysis. With very small sample sizes, e.g. when performing Laser-capture microdissection (LCM) to isolate specific subpopulations of cells, recovery of sufficient RNA for analysis with reverse-transcription quantitative PCR (RT-qPCR) or next-generation sequencing (NGS) becomes very cumbersome and difficult. We excised matched cancer-associated stroma (CAS) and normal stroma from clinical specimen of FFPE canine mammary tumours using LCM, and compared the commonly used protease-based RNA isolation procedure with an adapted novel technique that additionally incorporates a focused ultrasonication step. We successfully adapted a protocol that uses focused ultrasonication to isolate RNA from small amounts of deparaffinised, stained, clinical LCM samples. Using this approach, we found that total RNA yields could be increased by 8- to 12-fold compared to a commonly used protease-based extraction technique. Surprisingly, RNA extracted using this new approach was qualitatively at least equal if not superior compared to the old approach, as Cq values in RT-qPCR were on average 2.3-fold lower using the new method. Finally, we demonstrate that RNA extracted using the new method performs comparably in NGS as well. We present a successful isolation protocol for extraction of RNA from difficult and limiting FFPE tissue samples that enables successful analysis of small sections of clinically relevant specimen. The possibility to study gene expression signatures in specific small sections of archival FFPE tissue, which often entail large amounts of highly relevant clinical follow-up data, unlocks a new dimension of hitherto difficult-to-analyse samples which now

  1. MicroRNA profiling in intraocular medulloepitheliomas.

    Directory of Open Access Journals (Sweden)

    Deepak P Edward

    Full Text Available To study the differential expression of microRNA (miRNA profiles between intraocular medulloepithelioma (ME and normal control tissue (CT.Total RNA was extracted from formalin fixed paraffin embedded (FFPE intraocular ME (n=7 and from age matched ciliary body controls (n=8. The clinical history and phenotype was recorded. MiRNA profiles were determined using the Affymetrix GeneChip miRNA Arrays analyzed using expression console 1.3 software. Validation of significantly dysregulated miRNA was confirmed by quantitative real-time PCR. The web-based DNA Intelligent Analysis (DIANA-miRPath v2.0 was used to perform enrichment analysis of differentially expressed (DE miRNA gene targets in Kyoto Encyclopedia of Genes and Genomes (KEGG pathway.The pathologic evaluation revealed one benign (benign non-teratoid, n=1 and six malignant tumors (malignant teratoid, n=2; malignant non-teratoid, n = 4. A total of 88 miRNAs were upregulated and 43 miRNAs were downregulated significantly (P<0.05 in the tumor specimens. Many of these significantly dysregulated miRNAs were known to play various roles in carcinogenesis and tumor behavior. RT-PCR validated three significantly upregulated miRNAs and three significantly downregulated miRNAs namely miR-217, miR-216a, miR-216b, miR-146a, miR-509-3p and miR-211. Many DE miRNAs that were significant in ME tumors showed dysregulation in retinoblastoma, glioblastoma, and precursor, normal and reactive human cartilage. Enriched pathway analysis suggested a significant association of upregulated miRNAs with 15 pathways involved in prion disease and several types of cancer. The pathways involving significantly downregulated miRNAs included the toll-like receptor (TLR (p<4.36E-16 and Nuclear Factor kappa B (NF-κB signaling pathways (p<9.00E-06.We report significantly dysregulated miRNAs in intraocular ME tumors, which exhibited abnormal profiles in other cancers as well such as retinoblastoma and glioblastoma. Pathway analysis

  2. Elevated levels of circulating microRNA-200 family members correlate with serous epithelial ovarian cancer

    Directory of Open Access Journals (Sweden)

    Kan Casina WS

    2012-12-01

    Full Text Available Abstract Background There is a critical need for improved diagnostic markers for high grade serous epithelial ovarian cancer (SEOC. MicroRNAs are stable in the circulation and may have utility as biomarkers of malignancy. We investigated whether levels of serum microRNA could discriminate women with high-grade SEOC from age matched healthy volunteers. Methods To identify microRNA of interest, microRNA expression profiling was performed on 4 SEOC cell lines and normal human ovarian surface epithelial cells. Total RNA was extracted from 500 μL aliquots of serum collected from patients with SEOC (n = 28 and age-matched healthy donors (n = 28. Serum microRNA levels were assessed by quantitative RT-PCR following preamplification. Results microRNA (miR-182, miR-200a, miR-200b and miR-200c were highly overexpressed in the SEOC cell lines relative to normal human ovarian surface epithelial cells and were assessed in RNA extracted from serum as candidate biomarkers. miR-103, miR-92a and miR -638 had relatively invariant expression across all ovarian cell lines, and with small-nucleolar C/D box 48 (RNU48 were assessed in RNA extracted from serum as candidate endogenous normalizers. No correlation between serum levels and age were observed (age range 30-79 years for any of these microRNA or RNU48. Individually, miR-200a, miR-200b and miR-200c normalized to serum volume and miR-103 were significantly higher in serum of the SEOC cohort (P  Conclusions We identified serum microRNAs able to discriminate patients with high grade SEOC from age-matched healthy controls. The addition of these microRNAs to current testing regimes may improve diagnosis for women with SEOC.

  3. RNA-Based Vaccines in Cancer Immunotherapy

    Directory of Open Access Journals (Sweden)

    Megan A. McNamara

    2015-01-01

    Full Text Available RNA vaccines traditionally consist of messenger RNA synthesized by in vitro transcription using a bacteriophage RNA polymerase and template DNA that encodes the antigen(s of interest. Once administered and internalized by host cells, the mRNA transcripts are translated directly in the cytoplasm and then the resulting antigens are presented to antigen presenting cells to stimulate an immune response. Alternatively, dendritic cells can be loaded with either tumor associated antigen mRNA or total tumor RNA and delivered to the host to elicit a specific immune response. In this review, we will explain why RNA vaccines represent an attractive platform for cancer immunotherapy, discuss modifications to RNA structure that have been developed to optimize mRNA vaccine stability and translational efficiency, and describe strategies for nonviral delivery of mRNA vaccines, highlighting key preclinical and clinical data related to cancer immunotherapy.

  4. Totally James

    Science.gov (United States)

    Owens, Tom

    2006-01-01

    This article presents an interview with James Howe, author of "The Misfits" and "Totally Joe". In this interview, Howe discusses tolerance, diversity and the parallels between his own life and his literature. Howe's four books in addition to "The Misfits" and "Totally Joe" and his list of recommended books with lesbian, gay, bisexual, transgender,…

  5. RNA oxidation

    DEFF Research Database (Denmark)

    Kjaer, L. K.; Cejvanovic, V.; Henriken, T.

    2015-01-01

    .9 significant hazard ratio for death compared with the quartile with the lowest 8oxoGuo excretion when adjusted for age, sex, BMI, smoker status, s-HbA1c, urine protein excretion and s-cholesterol. We conclude that it is now established that RNA oxidation is an independent risk factor for death in type 2...

  6. Immunoprecipitation of Tri-methylated Capped RNA.

    Science.gov (United States)

    Hayes, Karen E; Barr, Jamie A; Xie, Mingyi; Steitz, Joan A; Martinez, Ivan

    2018-02-05

    Cellular quiescence (also known as G 0 arrest) is characterized by reduced DNA replication, increased autophagy, and increased expression of cyclin-dependent kinase p27 Kip1 . Quiescence is essential for wound healing, organ regeneration, and preventing neoplasia. Previous findings indicate that microRNAs (miRNAs) play an important role in regulating cellular quiescence. Our recent publication demonstrated the existence of an alternative miRNA biogenesis pathway in primary human foreskin fibroblast (HFF) cells during quiescence. Indeed, we have identified a group of pri-miRNAs (whose mature miRNAs were found induced during quiescence) modified with a 2,2,7-trimethylguanosine (TMG)-cap by the trimethylguanosine synthase 1 (TGS1) protein and transported to the cytoplasm by the Exportin-1 (XPO1) protein. We used an antibody against (TMG)-caps (which does not cross-react with the (m 7 G)-caps that most pri-miRNAs or mRNAs contain [Luhrmann et al ., 1982]) to perform RNA immunoprecipitations from total RNA extracts of proliferating or quiescent HFFs. The novelty of this assay is the specific isolation of pri-miRNAs as well as other non-coding RNAs containing a TMG-cap modification.

  7. How the RNA isolation method can affect microRNA microarray results

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Kaczkowski, Bogumil; Litman, Thomas

    2011-01-01

    RNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results...... that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.......The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform micro...

  8. Changes of microRNA profile and microRNA-mRNA regulatory network in bones of ovariectomized mice.

    Science.gov (United States)

    An, Jee Hyun; Ohn, Jung Hun; Song, Jung Ah; Yang, Jae-Yeon; Park, Hyojung; Choi, Hyung Jin; Kim, Sang Wan; Kim, Seong Yeon; Park, Woog-Yang; Shin, Chan Soo

    2014-03-01

    Growing evidence shows the possibility of a role of microRNAs (miRNA) in regulating bone mass. We investigated the change of miRNAs and mRNA expression profiles in bone tissue in an ovariectomized mice model and evaluated the regulatory mechanism of bone mass mediated by miRNAs in an estrogen-deficiency state. Eight-week-old female C3H/HeJ mice underwent ovariectomy (OVX) or sham operation (Sham-op), and their femur and tibia were harvested to extract total bone RNAs after 4 weeks for microarray analysis. Eight miRNAs (miR-127, -133a, -133a*, -133b, -136, -206, -378, -378*) were identified to be upregulated after OVX, whereas one miRNA (miR-204) was downregulated. Concomitant analysis of mRNA microarray revealed that 658 genes were differentially expressed between OVX and Sham-op mice. Target prediction of differentially expressed miRNAs identified potential targets, and integrative analysis using the mRNA microarray results showed that PPARγ and CREB pathways are activated in skeletal tissues after ovariectomy. Among the potential candidates of miRNA, we further studied the role of miR-127 in vitro, which exhibited the greatest changes after OVX. We also studied the effects of miR-136, which has not been studied in the context of bone mass regulation. Transfection of miR-127 inhibitor has enhanced osteoblastic differentiation in UAMS-32 cells as measured by alkaline phosphatase activities and mRNA expression of osteoblast-specific genes, whereas miR-136 precursor has inhibited osteoblastic differentiation. Furthermore, transfection of both miR-127 and miR-136 inhibitors enhanced the osteocyte-like morphological changes and survival in MLO-Y4 cells, whereas precursors of miR-127 and -136 have aggravated dexamethasone-induced cell death. Both of the precursors enhanced osteoclastic differentiation in bone marrow macrophages, indicating that both miR-127 and -136 are negatively regulating bone mass. Taken together, these results suggest a novel insight into the

  9. Isotopic diagnosis and molecular identification of cucumber mosaic virus and satellite RNA infecting tomato in Shanghai

    International Nuclear Information System (INIS)

    Zhang Huarong; Du Zhiyou; Liao Qiansheng; Zhang Hen

    2006-01-01

    In summer of 2004 and 2005, typical viral disease symptoms were found on field tomato from Shanghai, which remarkably reduced the yield of tomato. Total RNA of tomato leaves and purified virions were detected by hybridization with 32 P probes conducted with partial sequence of CMV RNA3 and full cDNA of CMV satRNA. Viruses were also confirmed by analyzing dsRNA extracted from tomato leaves. Full sequence of CMV RNA3 was gained by RT-PCR and the result of sequencing indicated that genomic RNA3 belongs to subgroup II. Two 15nt complementary ssDNA as amplification primers. Phylogenetic analysis showed that the identity of this 383nt satellite and some documented satRNAs was 72.6 to 99.5% at the nucleotide level. Several mutation sites were found at the 3' terminus of the newly discovered satRNA. By Isotopic diagnosis and molecular Identification, variation of CMV and its satRNA were found in Tomato from Shanghai, Which may influence the viral disease prevalence and the emergence of new symptom. (authors)

  10. Diverging affinity of tospovirus RNA silencing suppressor proteins, NSs, for various RNA duplex molecules.

    Science.gov (United States)

    Schnettler, Esther; Hemmes, Hans; Huismann, Rik; Goldbach, Rob; Prins, Marcel; Kormelink, Richard

    2010-11-01

    The tospovirus NSs protein was previously shown to suppress the antiviral RNA silencing mechanism in plants. Here the biochemical analysis of NSs proteins from different tospoviruses, using purified NSs or NSs containing cell extracts, is described. The results showed that all tospoviral NSs proteins analyzed exhibited affinity to small double-stranded RNA molecules, i.e., small interfering RNAs (siRNAs) and micro-RNA (miRNA)/miRNA* duplexes. Interestingly, the NSs proteins from tomato spotted wilt virus (TSWV), impatiens necrotic spot virus (INSV), and groundnut ringspot virus (GRSV) also showed affinity to long double-stranded RNA (dsRNA), whereas tomato yellow ring virus (TYRV) NSs did not. The TSWV NSs protein was shown to be capable of inhibiting Dicer-mediated cleavage of long dsRNA in vitro. In addition, it suppressed the accumulation of green fluorescent protein (GFP)-specific siRNAs during coinfiltration with an inverted-repeat-GFP RNA construct in Nicotiana benthamiana. In vivo interference of TSWV NSs in the miRNA pathway was shown by suppression of an enhanced GFP (eGFP) miRNA sensor construct. The ability to stabilize miRNA/miRNA* by different tospovirus NSs proteins in vivo was demonstrated by increased accumulation and detection of both miRNA171c and miRNA171c* in tospovirus-infected N. benthamiana. All together, these data suggest that tospoviruses interfere in the RNA silencing pathway by sequestering siRNA and miRNA/miRNA* molecules before they are uploaded into their respective RNA-induced silencing complexes. The observed affinity to long dsRNA for only a subset of the tospoviruses studied is discussed in light of evolutional divergence and their ancestral relation to the animal-infecting members of the Bunyaviridae.

  11. Black ginseng extract ameliorates hypercholesterolemia in rats.

    Science.gov (United States)

    Saba, Evelyn; Jeon, Bo Ra; Jeong, Da-Hye; Lee, Kija; Goo, Youn-Kyoung; Kim, Seung-Hyung; Sung, Chang-Keun; Roh, Seong-Soo; Kim, Sung Dae; Kim, Hyun-Kyoung; Rhee, Man-Hee

    2016-04-01

    Ginseng (Panax ginseng Meyer) is a well-characterized medicinal herb listed in the classic oriental herbal dictionary as "Shin-nong-bon-cho-kyung." Ginseng has diverse pharmacologic and therapeutic properties. Black ginseng (BG, Ginseng Radix nigra) is produced by repeatedly steaming fresh ginseng nine times. Studies of BG have shown that prolonged heat treatment enhances the antioxidant activity with increased radical scavenging activity. Several recent studies have showed the effects of BG on increased lipid profiles in mice. In this study report the effects of water and ethanol extracts of BG on hypercholesterolemia in rats. To our knowledge, this is the first time such an effect has been reported. Experiments were conducted on male Sprague Dawley rats fed with a high-cholesterol diet supplemented with the water and ethanol extracts of BG (200 mg/kg). Their blood cholesterol levels, serum white blood cell levels, and cholesterol-metabolizing marker genes messenger RNA (mRNA) expression were determined. Liver and adipose tissues were histologically analyzed. We found that BG extracts efficiently reduced the total serum cholesterol levels, low-density lipoprotein (LDL) levels with increased food efficiency ratio and increased number of neutrophil cells. It also attenuated the key genes responsible for lipogenesis, that is, acetyl-coenzyme A (CoA) acetyltransferase 2, 3-hydroxy-3-methyl-glutaryl-CoA reductase, and sterol regulatory element-binding protein 2, at the mRNA level inside liver cells. Furthermore, the BG extract also reduced the accumulation of fat in adipose tissues, and inhibited the neutral fat content in liver cells stained with hematoxylin and eosin and oil red O. Administration of BG extracts to Sprague Dawley rats fed with high-cholesterol diet ameliorated hypercholesterolemia, which was mediated via modulation of cholesterol-metabolizing marker genes. This data throw a light on BG's cardioprotective effects.

  12. Optimization of miRNA-seq data preprocessing.

    Science.gov (United States)

    Tam, Shirley; Tsao, Ming-Sound; McPherson, John D

    2015-11-01

    The past two decades of microRNA (miRNA) research has solidified the role of these small non-coding RNAs as key regulators of many biological processes and promising biomarkers for disease. The concurrent development in high-throughput profiling technology has further advanced our understanding of the impact of their dysregulation on a global scale. Currently, next-generation sequencing is the platform of choice for the discovery and quantification of miRNAs. Despite this, there is no clear consensus on how the data should be preprocessed before conducting downstream analyses. Often overlooked, data preprocessing is an essential step in data analysis: the presence of unreliable features and noise can affect the conclusions drawn from downstream analyses. Using a spike-in dilution study, we evaluated the effects of several general-purpose aligners (BWA, Bowtie, Bowtie 2 and Novoalign), and normalization methods (counts-per-million, total count scaling, upper quartile scaling, Trimmed Mean of M, DESeq, linear regression, cyclic loess and quantile) with respect to the final miRNA count data distribution, variance, bias and accuracy of differential expression analysis. We make practical recommendations on the optimal preprocessing methods for the extraction and interpretation of miRNA count data from small RNA-sequencing experiments. © The Author 2015. Published by Oxford University Press.

  13. High-performance liquid chromatography - Ultraviolet method for the determination of total specific migration of nine ultraviolet absorbers in food simulants based on 1,1,3,3-Tetramethylguanidine and organic phase anion exchange solid phase extraction to remove glyceride.

    Science.gov (United States)

    Wang, Jianling; Xiao, Xiaofeng; Chen, Tong; Liu, Tingfei; Tao, Huaming; He, Jun

    2016-06-17

    The glyceride in oil food simulant usually causes serious interferences to target analytes and leads to failure of the normal function of the RP-HPLC column. In this work, a convenient HPLC-UV method for the determination of the total specific migration of nine ultraviolet (UV) absorbers in food simulants was developed based on 1,1,3,3-tetramethylguanidine (TMG) and organic phase anion exchange (OPAE) SPE to efficiently remove glyceride in olive oil simulant. In contrast to the normal ion exchange carried out in an aqueous solution or aqueous phase environment, the OPAE SPE was performed in the organic phase environments, and the time-consuming and challenging extraction of the nine UV absorbers from vegetable oil with aqueous solution could be readily omitted. The method was proved to have good linearity (r≥0.99992), precision (intra-day RSD≤3.3%), and accuracy(91.0%≤recoveries≤107%); furthermore, the lower limit of quantifications (0.05-0.2mg/kg) in five types of food simulants(10% ethanol, 3% acetic acid, 20% ethanol, 50% ethanol and olive oil) was observed. The method was found to be well suited for quantitative determination of the total specific migration of the nine UV absorbers both in aqueous and vegetable oil simulant according to Commission Regulation (EU) No. 10/2011. Migration levels of the nine UV absorbers were determined in 31 plastic samples, and UV-24, UV-531, HHBP and UV-326 were frequently detected, especially in olive oil simulant for UV-326 in PE samples. In addition, the OPAE SPE procedure was also been applied to efficiently enrich or purify seven antioxidants in olive oil simulant. Results indicate that this procedure will have more extensive applications in the enriching or purification of the extremely weak acidic compounds with phenol hydroxyl group that are relatively stable in TMG n-hexane solution and that can be barely extracted from vegetable oil. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Estrogen receptor mRNA in mineralized tissues of rainbow trout: calcium mobilization by estrogen.

    Science.gov (United States)

    Armour, K J; Lehane, D B; Pakdel, F; Valotaire, Y; Graham, R; Russell, R G; Henderson, I W

    1997-07-07

    RT-PCR was undertaken on total RNA extracts from bone and scales of the rainbow trout, Oncorhynchus mykiss. The rainbow trout estrogen receptor (ER)-specific primers used amplified a single product of expected size from each tissue which, using Southern blotting, strongly hybridized with a 32P-labelled rtER probe under stringent conditions. These data provide the first in vivo evidence of ER mRNA in bone and scale tissues of rainbow trout and suggest that the effects of estrogen observed in this study (increased bone mineral and decreased scale mineral contents, respectively) may be mediated directly through ER.

  15. Total fluorine, extractable organic fluorine, perfluorooctane sulfonate and other related fluorochemicals in liver of Indo-Pacific humpback dolphins (Sousa chinensis) and finless porpoises (Neophocaena phocaenoides) from South China

    Energy Technology Data Exchange (ETDEWEB)

    Yeung, L.W.Y. [Centre for Coastal Pollution and Conservation, Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong (China); National Institute of Advanced Industrial Science and Technology (AIST), Onogawa 16-1, Tsukuba, Ibaraki 305-8569 (Japan); Miyake, Y. [National Institute of Advanced Industrial Science and Technology (AIST), Onogawa 16-1, Tsukuba, Ibaraki 305-8569 (Japan); Wang, Y. [Centre for Coastal Pollution and Conservation, Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong (China); National Institute of Advanced Industrial Science and Technology (AIST), Onogawa 16-1, Tsukuba, Ibaraki 305-8569 (Japan); Taniyasu, S. [National Institute of Advanced Industrial Science and Technology (AIST), Onogawa 16-1, Tsukuba, Ibaraki 305-8569 (Japan); Yamashita, N. [National Institute of Advanced Industrial Science and Technology (AIST), Onogawa 16-1, Tsukuba, Ibaraki 305-8569 (Japan)], E-mail: nob.yamashita@aist.go.jp; Lam, P.K.S. [Centre for Coastal Pollution and Conservation, Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong (China)], E-mail: bhpksl@cityu.edu.hk

    2009-01-15

    The concentrations of 10 PFCs (perfluorinated compounds: PFOS, PFHxS, PFOSA, N-EtFOSA, PFDoDA, PFUnDA, PFDA, PFNA, PFOA, and PFHpA) were measured in liver samples of Indo-Pacific humpback dolphins (Sousa chinensis) (n = 10) and finless porpoises (Neophocaena phocaenoides) (n = 10) stranded in Hong Kong between 2003 and 2007. PFOS was the dominant PFC in the tissues at concentrations ranging at 26-693 ng/g ww in dolphins and 51.3-262 ng/g ww in porpoises. A newly developed combustion ion chromatography for fluorine was applied to measure total fluorine (TF) and extractable organic fluorine (EOF) in these liver samples to understand PFC contamination using the concept of mass balance analysis. Comparisons between the amounts of known PFCs and EOF in the livers showed that a large proportion ({approx}70%) of the organic fluorine in both species is of unknown origin. These investigations are critical for a comprehensive assessment of the risks of these compounds to humans and other receptors. - Comparison between the amounts of known PFCs and EOF in the livers of Indo-Pacific humpback dolphin and finless porpoise in South China showed that a large proportion ({approx}70%) of the organofluorine is of unknown origin.

  16. Total fluorine, extractable organic fluorine, perfluorooctane sulfonate and other related fluorochemicals in liver of Indo-Pacific humpback dolphins (Sousa chinensis) and finless porpoises (Neophocaena phocaenoides) from South China

    International Nuclear Information System (INIS)

    Yeung, L.W.Y.; Miyake, Y.; Wang, Y.; Taniyasu, S.; Yamashita, N.; Lam, P.K.S.

    2009-01-01

    The concentrations of 10 PFCs (perfluorinated compounds: PFOS, PFHxS, PFOSA, N-EtFOSA, PFDoDA, PFUnDA, PFDA, PFNA, PFOA, and PFHpA) were measured in liver samples of Indo-Pacific humpback dolphins (Sousa chinensis) (n = 10) and finless porpoises (Neophocaena phocaenoides) (n = 10) stranded in Hong Kong between 2003 and 2007. PFOS was the dominant PFC in the tissues at concentrations ranging at 26-693 ng/g ww in dolphins and 51.3-262 ng/g ww in porpoises. A newly developed combustion ion chromatography for fluorine was applied to measure total fluorine (TF) and extractable organic fluorine (EOF) in these liver samples to understand PFC contamination using the concept of mass balance analysis. Comparisons between the amounts of known PFCs and EOF in the livers showed that a large proportion (∼70%) of the organic fluorine in both species is of unknown origin. These investigations are critical for a comprehensive assessment of the risks of these compounds to humans and other receptors. - Comparison between the amounts of known PFCs and EOF in the livers of Indo-Pacific humpback dolphin and finless porpoise in South China showed that a large proportion (∼70%) of the organofluorine is of unknown origin

  17. Enrichment of total steroidal saponins from the extracts of Trillium tschonoskii Maxim by macroporous resin and the simultaneous determination of eight steroidal saponins in the final product by HPLC.

    Science.gov (United States)

    Zhou, Yulan; Gao, Xin; Fu, Qiang; Guo, Pengqi; Xu, Xinya; Zhang, Ting; Ge, Yanhui; Zhang, Bilin; Wang, Mingchan; Zeng, Aiguo; Luo, Zhimin; Chang, Chun

    2017-03-01

    An effective and simple method was established for the separation and enrichment of steroidal saponins from Trillium tschonoskii Maxim. The adsorption and desorption properties of seven macroporous resins were investigated. Among the tested resins, AB-8 resin showed the best adsorption and desorption capacities. The adsorption of steroidal saponins on AB-8 at 25°C was quite consistent with both the Freundlich isotherm model and the pseudo-second-order kinetics model. By optimizing the dynamic adsorption and desorption parameters, the content of steroidal saponins increased from 5.20% in the crude extracts to 51.93% in the final product, with a recovery yield of 86.67%. Furthermore, by scale-up separation, the concentration and recovery of total steroidal saponins were 43.8 and 85.5%, respectively, which suggested that AB-8 resin had great industrial and pharmaceutical potential because of its high efficiency and cost-effectiveness. In addition, a high-performance liquid chromatography method for the simultaneous determination of eight steroidal saponins was established for the first time, which was employed to qualitatively and quantitatively analyze the final product. Based on the methodological validation results, the high-performance liquid chromatography method can be widely applied to the quality control of steroidal saponins from Trillium tschonoskii Maxim due to its excellent accuracy, stability, and repeatability. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Structure and function of initiator methionine tRNA from the mitochondria of Neurospora crassa

    International Nuclear Information System (INIS)

    Heckman, J.E.; Hecker, L.I.; Schwartzbach, S.D.; Barnett, W.E.; Baumstark, B.; RajBhandary, U.L.

    1978-01-01

    Initiator methionine tRNA from the mitochondria of Neurospora crassa has been purified and sequenced. This mitochondrial tRNA can be aminoacylated and formylated by E. coli enzymes, and is capable of initiating protein synthesis in E. coli extracts. The nucleotide composition of the mitochondrial initiator tRNA (the first mitochondrial tRNA subjected to sequence analysis) is very rich in A + U, like that reported for total mitochondrial tRNA. In two of the unique features which differentiate procaryotic from eucaryotic cytoplasmic initiator tRNAs, the mitochondrial tRNA appears to resemble the eucaryotic initiator tRNAs. Thus unlike procaryotic initiator tRNAs in which the 5' terminal nucleotide cannot form a Watson-Crick base pair to the fifth nucleotide from 3' end, the mitochondrial tRNA can form such a base pair; and like the eucaryotic cytoplasmic initiator tRNAs, the mitochondrial initiator tRNA lacks the sequence - T psiCG(or A) in loop IV. The corresponding sequence in the mitochondrial tRNA, however, is -UGCA- and not -AU(or psi)CG- as found in all eucaryotic cytoplasmic initiator tRNAs. In spite of some similarity of the mitochondrial initiator tRNA to both eucaryotic and procaryotic initiator tRNAs, the mitochondrial initiator tRNA is basically different from both these tRNAs. Between these two classes of initiator tRNAs, however, it is more homologous in sequence to procaryotic (56 to 60%) than to eucaryotic cytoplasmic initiator tRNAs

  19. (Lamiaceae) root extracts

    African Journals Online (AJOL)

    Purpose: To evaluate the larvicidal, nematicidal, antifeedant, and antifungal effects of 10 solvent extracts of Mentha spicata root. Methods: Ten solvent extracts were investigated for their total flavonoid and phenolic content and screened for larvicidal, nematicidal, antifeedant, and antifungal activities. The total phenolic ...

  20. Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins

    Science.gov (United States)

    de Beauchene, Isaure Chauvot; de Vries, Sjoerd J.; Zacharias, Martin

    2016-01-01

    Abstract Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the docking of single-stranded RNA (ssRNA). We have developed a fragment-based approach to model the structure of ssRNA bound to a protein, based on only the protein structure, the RNA sequence and conserved contacts. The conformational diversity of each RNA fragment is sampled by an exhaustive library of trinucleotides extracted from all known experimental protein–RNA complexes. The method was applied to ssRNA with up to 12 nucleotides which bind to dimers of the RNA recognition motifs (RRMs), a highly abundant eukaryotic RNA-binding domain. The fragment based docking allows a precise de novo atomic modeling of protein-bound ssRNA chains. On a benchmark of seven experimental ssRNA–RRM complexes, near-native models (with a mean heavy-atom deviation of <3 Å from experiment) were generated for six out of seven bound RNA chains, and even more precise models (deviation < 2 Å) were obtained for five out of seven cases, a significant improvement compared to the state of the art. The method is not restricted to RRMs but was also successfully applied to Pumilio RNA binding proteins. PMID:27131381

  1. The use of 125iodine-labeled RNA for detection of the RNA binding to ribosomes

    International Nuclear Information System (INIS)

    Mori, Tomohiko; Fukuda, Mitsuru

    1975-01-01

    The in vitro labeling of RNA with radioactive iodine is the efficient method to obtain the RNA with high specific activity. The present paper reports on the application of this technique to the production of iodine-labeled RNA for use in the experiment of binding RNA to ribosomes. Tobacco mosaic virus (TMV) RNA was used as natural mRNA, and E. coli S-30 preparation was used as a source of ribosomes. The TMV-RNA was prepared by bentonite-phenol extraction from TMV, and the method used for the iodation of RNA was based on the procedure described by Getz et al. The iodine-labeled RNA was incubated in a cell-free protein synthesizing system (S-30) prepared from E. coli K-12. After the incubation, the reaction mixture was layered onto sucrose gradient, centrifuged, and fractionated into 18 fractions. Optical density at 260 nm was measured, and radioactivity was counted, for each fraction. The binding of mRNA to ribosomes occurred even at 0 deg C, and the occurrence of the nonspecific binding was also shown. Consequently, the specific binding, i.e. the formation of the initiation complex being involved in amino acid incorporation, may be estimated by subtracting the radioactivity associated with monosomes in the presence of both rRNA and ATA from that in the presence of rRNA only. It was shown that the iodine-labeled RNA can be used for the studies of binding RNA to ribosomes. (Kako, I.)

  2. Chromosomal loop/nuclear matrix organization of transcriptionally active and inactive RNA polymerases in HeLa nuclei.

    Science.gov (United States)

    Roberge, M; Dahmus, M E; Bradbury, E M

    1988-06-05

    The relative distribution of transcriptionally active and inactive RNA polymerases I and II between the nuclear matrix/scaffold and chromosomal loops of HeLa cells was determined. Total RNA polymerase was assessed by immunoblotting and transcribing RNA polymerase by a photoaffinity labeling technique in isolated nuclei. Nuclear matrix/scaffold was isolated by three methods using high-salt, intermediate-salt or low-salt extraction. The distribution of RNA polymerases I and II were very similar within each of the methods, but considerable differences in distributions were found between the different preparation methods. Either intermediate-salt or high-salt treatment of DNase I-digested nuclei showed significant association of RNA polymerases with the nuclear matrix. However, intermediate-salt followed by high-salt treatment released all transcribing and non-transcribing RNA polymerases. Nuclear scaffolds isolated with lithium diiodosalicylate (low-salt) contained very little of the RNA polymerases. This treatment, however, caused the dissociation of RNA polymerase II transcription complexes. These results show unambiguously that RNA polymerases, both in their active and inactive forms, are not nuclear matrix proteins. The data support models in which the transcriptional machinery moves around DNA loops during transcription.

  3. Biological Activities of Aerial Parts Extracts of Euphorbia characias

    Directory of Open Access Journals (Sweden)

    Maria Barbara Pisano

    2016-01-01

    Full Text Available The aim of the present study was to evaluate antioxidant, antimicrobial, anti-HIV, and cholinesterase inhibitory activities of aqueous and alcoholic extracts from leaves, stems, and flowers of Euphorbia characias. The extracts showed a high antioxidant activity and were a good source of total polyphenols and flavonoids. Ethanolic extracts from leaves and flowers displayed the highest inhibitory activity against acetylcholinesterase and butyrylcholinesterase, showing potential properties against Alzheimer’s disease. Antimicrobial assay showed that leaves and flowers extracts were active against all Gram-positive bacteria tested. The ethanolic leaves extract appeared to have the strongest antibacterial activity against Bacillus cereus with MIC value of 312.5 μg/mL followed by Listeria monocytogenes and Staphylococcus aureus that also exhibited good sensitivity with MIC values of 1250 μg/mL. Moreover, all the extracts possessed anti-HIV activity. The ethanolic flower extract was the most potent inhibitor of HIV-1 RT DNA polymerase RNA-dependent and Ribonuclease H with IC50 values of 0.26 and 0.33 μg/mL, respectively. The LC-DAD metabolic profile showed that ethanolic leaves extract contains high levels of quercetin derivatives. This study suggests that Euphorbia characias extracts represent a good source of natural bioactive compounds which could be useful for pharmaceutical application as well as in food system for the prevention of the growth of food-borne bacteria and to extend the shelf-life of processed foods.

  4. Measuring influenza RNA quantity after prolonged storage or multiple freeze/thaw cycles.

    Science.gov (United States)

    Granados, Andrea; Petrich, Astrid; McGeer, Allison; Gubbay, Jonathan B

    2017-09-01

    In this study, we aim to determine what effects prolonged storage and repeated freeze/thaw cycles have on the stability of influenza A(H1N1)pdm09 (influenza A/H1N1)RNA. Cloned influenza A/H1N1 RNA transcripts were serially diluted from 8.0-1.0 log 10 copies/μl. RT-qPCR was used to measure RNA loss in transcripts stored at -80°C, -20°C, 4°C and 25°C for up to 84days or transcripts undergoing a total of 10 freeze/thaw cycles. Viral load was measured in clinical specimens stored at-80°C for three years (n=89 influenza A RNA extracts; n=35 primary specimens) and in 10 clinical specimens from the 2015/2016 influenza season that underwent 7 freeze/thaw cycles. RNA stored at -80°C, -20°C, 4°C and 25°C is stable for up to 56, 56, 21, and 7days respectively or up to 9 freeze/thaw cycles when stored at -80°C. There is no difference in viral load in clinical specimens that have been stored for up to three years at -80°C if they are re-extracted. Similarly, clinical specimens undergoing up to 7 freeze/thaw cycles are stable if they are re-extracted between cycles. Influenza specimens can be stored for up to three years at -80°C or undergo up to 7 freeze/thaw cycles without loss of RNA quantity if re-extracted. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Total Thyroidectomy

    Directory of Open Access Journals (Sweden)

    Lopez Moris E

    2016-06-01

    Full Text Available Total thyroidectomy is a surgery that removes all the thyroid tissue from the patient. The suspect of cancer in a thyroid nodule is the most frequent indication and it is presume when previous fine needle puncture is positive or a goiter has significant volume increase or symptomes. Less frequent indications are hyperthyroidism when it is refractory to treatment with Iodine 131 or it is contraindicated, and in cases of symptomatic thyroiditis. The thyroid gland has an important anatomic relation whith the inferior laryngeal nerve and the parathyroid glands, for this reason it is imperative to perform extremely meticulous dissection to recognize each one of these elements and ensure their preservation. It is also essential to maintain strict hemostasis, in order to avoid any postoperative bleeding that could lead to a suffocating neck hematoma, feared complication that represents a surgical emergency and endangers the patient’s life.It is essential to run a formal technique, without skipping steps, and maintain prudence and patience that should rule any surgical act.

  6. RAID: a comprehensive resource for human RNA-associated (RNA–RNA/RNA–protein) interaction

    Science.gov (United States)

    Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong

    2014-01-01

    Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA–RNA/RNA–protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA–RNA interactions and 1619 RNA–protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA–RNA/RNA–protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA–RNA/RNA–protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. PMID:24803509

  7. Corn silk extract improves cholesterol metabolism in C57BL/6J mouse fed high-fat diets.

    Science.gov (United States)

    Cha, Jae Hoon; Kim, Sun Rim; Kang, Hyun Joong; Kim, Myung Hwan; Ha, Ae Wha; Kim, Woo Kyoung

    2016-10-01

    Corn silk (CS) extract contains large amounts of maysin, which is a major flavonoid in CS. However, studies regarding the effect of CS extract on cholesterol metabolism is limited. Therefore, the purpose of this study was to determine the effect of CS extract on cholesterol metabolism in C57BL/6J mouse fed high-fat diets. Normal-fat group fed 7% fat diet, high-fat (HF) group fed 25% fat diet, and high-fat with corn silk (HFCS) group were orally administered CS extract (100 mg/kg body weight) daily. Serum and hepatic levels of total lipids, triglycerides, and total cholesterol as well as serum free fatty acid, glucose, and insulin levels were determined. The mRNA expression levels of acyl-CoA: cholesterol acyltransferase (ACAT), cholesterol 7-alpha hydroxylase (CYP7A1), farnesoid X receptor (FXR), lecithin cholesterol acyltransferase (LCAT), low-density lipoprotein receptor, 3-hyroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase), adiponectin, leptin, and tumor necrosis factor α were determined. Oral administration of CS extract with HF improved serum glucose and insulin levels as well as attenuated HF-induced fatty liver. CS extracts significantly elevated mRNA expression levels of adipocytokines and reduced mRNA expression levels of HMG-CoA reductase, ACAT, and FXR. The mRNA expression levels of CYP7A1 and LCAT between the HF group and HFCS group were not statistically different. CS extract supplementation with a high-fat diet improves levels of adipocytokine secretion and glucose homeostasis. CS extract is also effective in decreasing the regulatory pool of hepatic cholesterol, in line with decreased blood and hepatic levels of cholesterol though modulation of mRNA expression levels of HMG-CoA reductase, ACAT, and FXR.

  8. MysiRNA-designer: a workflow for efficient siRNA design.

    Directory of Open Access Journals (Sweden)

    Mohamed Mysara

    Full Text Available The design of small interfering RNA (siRNA is a multi factorial problem that has gained the attention of many researchers in the area of therapeutic and functional genomics. MysiRNA score was previously introduced that improves the correlation of siRNA activity prediction considering state of the art algorithms. In this paper, a new program, MysiRNA-Designer, is described which integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. It also features the MysiRNA score, a highly ranked correlated siRNA efficacy prediction score for ranking the designed siRNAs, in addition to top scoring models Biopredsi, DISR, Thermocomposition21 and i-Score, and integrates them in a unique siRNA score-filtration technique. This multi-score filtration layer filters siRNA that passes the 90% thresholds calculated from experimental dataset features. MysiRNA-Designer takes an accession, finds conserved regions among its transcript space, finds accessible regions within the mRNA, designs all possible siRNAs for these regions, filters them based on multi-scores thresholds, and then performs SNP and off-target filtration. These strict selection criteria were tested against human genes in which at least one active siRNA was designed from 95.7% of total genes. In addition, when tested against an experimental dataset, MysiRNA-Designer was found capable of rejecting 98% of the false positive siRNAs, showing superiority over three state of the art siRNA design programs. MysiRNA is a freely accessible (Microsoft Windows based desktop application that can be used to design siRNA with a high accuracy and specificity. We believe that MysiRNA-Designer has the potential to play an important role in this area.

  9. Reproducible pattern of microRNA in normal human skin

    DEFF Research Database (Denmark)

    Holst, Line; Kaczkowski, Bogumil; Gniadecki, Robert

    2010-01-01

    RNA expression pattern in normal human skin. Here we investigated miRNA expression profiles from skin biopsies of 8 healthy volunteers taken from sun protected and mildly photo damaged skin using the modified protocol for miRNA extraction. We were able to show a constant pattern of miRNA expression between......MicroRNAs (miRNAs) regulate cell growth, differentiation and apoptosis via specific targeting of messenger RNA (mRNA). Aberrant mRNA expression contributes to pathological processes such as carcinogenesis. To take advantage of miRNA profiling in skin disease it is essential to investigate mi...... different individuals. We did not find any significant differences in miRNA expression between sun protected and mildly photodamaged skin. These results may be valuable for future design of studies on miRNA expression in skin disease....

  10. Reproducible pattern of microRNA in normal human skin

    DEFF Research Database (Denmark)

    Holst, Line; Kaczkowski, Bogumil; Gniadecki, Robert

    2010-01-01

    RNA expression pattern in normal human skin. Here we investigated miRNA expression profiles from skin biopsies of 8 healthy volunteers taken from sun protected and mildly photo damaged skin using the modified protocol for miRNA extraction. We were able to show a constant pattern of miRNA expression between...... different individuals. We did not find any significant differences in miRNA expression between sun protected and mildly photodamaged skin. These results may be valuable for future design of studies on miRNA expression in skin disease.......MicroRNAs (miRNAs) regulate cell growth, differentiation and apoptosis via specific targeting of messenger RNA (mRNA). Aberrant mRNA expression contributes to pathological processes such as carcinogenesis. To take advantage of miRNA profiling in skin disease it is essential to investigate mi...

  11. Extracellular RNA Communication (ExRNA)

    Data.gov (United States)

    Federal Laboratory Consortium — Until recently, scientists believed RNA worked mostly inside the cell that produced it. Some types of RNA help translate genes into proteins that are necessary for...

  12. Nucleic acid protocols: Extraction and optimization

    Directory of Open Access Journals (Sweden)

    Saeed El-Ashram

    2016-12-01

    Full Text Available Yield and quality are fundamental features for any researchers during nucleic acid extraction. Here, we describe a simplified, semi-unified, effective, and toxic material free protocol for extracting DNA and RNA from different prokaryotic and eukaryotic sources exploiting the physical and chemical properties of nucleic acids. Furthermore, this protocol showed that DNA and RNA are under triple protection (i.e. EDTA, SDS and NaCl during lysis step, and this environment is improper for RNase to have DNA liberated of RNA and even for DNase to degrade the DNA. Therefore, the complete removal of RNA under RNase influence is achieved when RNase is added after DNA extraction, which gives optimal quality with any protocols. Similarly, DNA contamination in an isolated RNA is degraded by DNase to obtain high-quality RNA. Our protocol is the protocol of choice in terms of simplicity, recovery time, environmental safety, amount, purity, PCR and RT-PCR applicability.

  13. Detection and comparison of microRNA expression in the serum of Doberman Pinschers with dilated cardiomyopathy and healthy controls.

    Science.gov (United States)

    Steudemann, Carola; Bauersachs, Stefan; Weber, Karin; Wess, Gerhard

    2013-01-17

    Dilated cardiomyopathy (DCM) is the most common heart disease in Doberman Pinschers. MicroRNAs (miRNAs) are short non-coding RNAs playing important roles in gene regulation. Different miRNA expression patterns have been described for DCM in humans and might represent potential diagnostic markers. There are no studies investigating miRNA expression profiles in canine DCM. The aims of this study were to screen the miRNA expression profile of canine serum using miRNA microarray and to compare expression patterns of a group of Doberman Pinschers with DCM and healthy controls. Eight Doberman Pinschers were examined by echocardiography and 24-hour-ECG and classified as healthy (n=4) or suffering from DCM (n=4). Total RNA was extracted from serum and hybridized on a custom-designed 8x60k miRNA microarray (Agilent) containing probes for 1368 individual miRNAs. Although total RNA concentrations were very low in serum samples, 404 different miRNAs were detectable with sufficient signal intensity on miRNA microarray. 22 miRNAs were differentially expressed in the two groups (p1.5), but did not reach statistical significance after multiple testing correction (false discovery rate adjusted p>0.05). Five miRNAs were selected for further analysis using quantitative Real-Time RT-PCR (qPCR) assays. No significant differences were found using specific miRNA qPCR assays (p>0.05). Numerous miRNAs can be detected in canine serum. Between healthy and DCM dogs, miRNA expression changes could be detected, but the results did not reach statistical significance most probably due to the small group size. miRNAs are potential new circulating biomarkers in veterinary medicine and should be investigated in larger patient groups and additional canine diseases.

  14. RNA-seq analysis of early hepatic response to handling and confinement stress in rainbow trout.

    Directory of Open Access Journals (Sweden)

    Sixin Liu

    Full Text Available Fish under intensive rearing conditions experience various stressors which have negative impacts on survival, growth, reproduction and fillet quality. Identifying and characterizing the molecular mechanisms underlying stress responses will facilitate the development of strategies that aim to improve animal welfare and aquaculture production efficiency. In this study, we used RNA-seq to identify transcripts which are differentially expressed in the rainbow trout liver in response to handling and confinement stress. These stressors were selected due to their relevance in aquaculture production. Total RNA was extracted from the livers of individual fish in five tanks having eight fish each, including three tanks of fish subjected to a 3 hour handling and confinement stress and two control tanks. Equal amount of total RNA of six individual fish was pooled by tank to create five RNA-seq libraries which were sequenced in one lane of Illumina HiSeq 2000. Three sequencing runs were conducted to obtain a total of 491,570,566 reads which were mapped onto the previously generated stress reference transcriptome to identify 316 differentially expressed transcripts (DETs. Twenty one DETs were selected for qPCR to validate the RNA-seq approach. The fold changes in gene expression identified by RNA-seq and qPCR were highly correlated (R(2 = 0.88. Several gene ontology terms including transcription factor activity and biological process such as glucose metabolic process were enriched among these DETs. Pathways involved in response to handling and confinement stress were implicated by mapping the DETs to reference pathways in the KEGG database.Raw RNA-seq reads have been submitted to the NCBI Short Read Archive under accession number SRP022881.All customized scripts described in this paper are available from Dr. Guangtu Gao or the corresponding author.

  15. Correlation between RNA Degradation Patterns of Rat's Brain and Early PMI at Different Temperatures.

    Science.gov (United States)

    Lü, Y H; Li, Z H; Tuo, Y; Liu, L; Li, K; Bian, J; Ma, J L; Chen, L

    2016-06-01

    To explore the correlation between early postmortem interval (PMI) and eight RNA markers of rat's brain at different temperatures. Total 222 SD rats were randomly divided into control group (PMI=0 h) and four experimental groups. And the rats in the experimental groups were sacrificed by cervical dislocation and respectively kept at 5 ℃, 15 ℃, 25 ℃ and 35 ℃ in a controlled environment chamber. The RNA was extracted from brain tissues, which was taken at 9 time points from 1 h to 24 h postmortem. The expression levels of eight markers, β-actin, GAPDH, RPS29, 18S rRNA, 5S rRNA, U6 snRNA, miRNA-9 and miRNA-125b, were detected using real-time fluorescent quantitative PCR, respectively. Proper internal reference was selected by geNorm software. Regression analysis of normalized RNA markers was performed by SPSS software. Mathematical model for PMI estimation was established using R software. Another 6 SD rats with known PMI were used to verify the mathematical model. 5S rRNA, miR-9 and miR-125b were suitable as internal reference markers for their stable expression. Both β-actin and GAPDH had well time-dependent degradation patterns and degraded continually with prolongation of PMI in 24 h postmortem. The mathematical model of the variation of ΔCt values with PMI and temperature was set up by R software and the model could be used for PMI estimation. The average error rates of model validation using β-actin and GAPDH were 14.1% and 22.2%, respectively. The expression levels of β-actin and GAPDH are well correlated with PMI and environmental temperature. The mathematical model established in present study can provide references for estimating early PMI under various temperature conditions. Copyright© by the Editorial Department of Journal of Forensic Medicine

  16. Association of microRNA-200c expression levels with clinicopathological factors and prognosis in endometrioid endometrial cancer.

    Science.gov (United States)

    Wilczynski, Milosz; Danielska, Justyna; Domanska-Senderowska, Daria; Dzieniecka, Monika; Szymanska, Bozena; Malinowski, Andrzej

    2018-05-01

    MicroRNAs (miRNAs) are regulators of gene expression, which play an important role in many critical cellular processes including apoptosis, proliferation and cell differentiation. Aberrant miRNA expression has been reported in a variety of human malignancies. Therefore, miRNAs may be potentially used as cancer biomarkers. miRNA-200c, which is a member of the miRNA-200 family, might play an essential role in tumor progression. The purpose of this study was to evaluate the prognostic and clinical significance of miRNA-200c in women with endometrioid endometrial cancer. Total RNA extraction from 90 archival formalin-fixed paraffin-embedded tissue samples of endometri-oid endometrial cancer and 10 normal endometrium samples was performed. After cDNA synthesis, real-time polymerase chain reaction was conducted and relative expression of miRNA-200c was assessed. Then, miRNA-200c expression levels were evaluated with regard to clinicopathological characteristics. The expression levels of miRNA-200c were significantly increased in endometrioid endometrial cancer samples. Expression of miRNA-200c maintained at significantly higher levels in the early stage endometrioid endometrial cancer compared with more advanced stages. In the Kaplan-Meier analysis, lower levels of miRNA-200c expression were associated with inferior survival. Expression levels of miRNA-200c might be associated with clinicopathological factors and survival in endometrioid endometrial cancer. © 2018 Nordic Federation of Societies of Obstetrics and Gynecology.

  17. European interlaboratory comparison of Schmallenberg virus (SBV) real-time RT-PCR detection in experimental and field samples: The method of extraction is critical for SBV RNA detection in semen

    NARCIS (Netherlands)

    Schulz, C.; Poel, van der W.H.M.; Ponsart, C.; Cay, A.B.; Steinbach, F.; Zientara, S.; Beer, M.; Hoffmann, B.

    2015-01-01

    Molecular methods for the detection of Schmallenberg virus (SBV) RNA were rapidly developed after the emergence of this novel orthobunyavirus in Europe. The SBV epizootic wave has declined, but infectious SBV in SBV RNA–positive semen remains a possible risk for the distribution of SBV. However, the

  18. Profiling of RNA degradation for estimation of post mortem [corrected] interval.

    Directory of Open Access Journals (Sweden)

    Fernanda Sampaio-Silva

    Full Text Available An estimation of the post mortem interval (PMI is frequently touted as the Holy Grail of forensic pathology. During the first hours after death, PMI estimation is dependent on the rate of physical observable modifications including algor, rigor and livor mortis. However, these assessment methods are still largely unreliable and inaccurate. Alternatively, RNA has been put forward as a valuable tool in forensic pathology, namely to identify body fluids, estimate the age of biological stains and to study the mechanism of death. Nevertheless, the attempts to find correlation between RNA degradation and PMI have been unsuccessful. The aim of this study was to characterize the RNA degradation in different post mortem tissues in order to develop a mathematical model that can be used as coadjuvant method for a more accurate PMI determination. For this purpose, we performed an eleven-hour kinetic analysis of total extracted RNA from murine's visceral and muscle tissues. The degradation profile of total RNA and the expression levels of several reference genes were analyzed by quantitative real-time PCR. A quantitative analysis of normalized transcript levels on the former tissues allowed the identification of four quadriceps muscle genes (Actb, Gapdh, Ppia and Srp72 that were found to significantly correlate with PMI. These results allowed us to develop a mathematical model with predictive value for estimation of the PMI (confidence interval of ±51 minutes at 95% that can become an important complementary tool for traditional methods.

  19. nduced hyperlipidemic rats. Methods: Column chromatographic fractionation of butanol fraction of total methanol extract of leaves of Bauhinia variegata (Linn. yields four sub-fractions (sub-fraction A-D. All sub-fractions tested for their anti-hyperlipidemic activity. Sub-fractions administered at a dose of 65 mg/kg (oral to the Triton WR-1339 induced hyperlipidemic rats and total cholesterol, triglycerides, HDL, LDL and VLDL

    Directory of Open Access Journals (Sweden)

    Deepak Kumar

    2012-10-01

    Full Text Available Objective: To investigate the effect and evaluation of Anti-hyperlipidemic activity guided subfraction isolated from total methanolic extract of Bauhinia variegata (Linn. leaves on Triton WR-1339 induced hyperlipidemic rats. Methods: Column chromatographic fractionation of butanol fraction of total methanol extract of leaves of Bauhinia variegata (Linn. yields four subfractions (sub-fraction A-D. All sub-fractions tested for their anti-hyperlipidemic activity. Subfractions administered at a dose of 65 mg/kg (oral to the Triton WR-1339 induced hyperlipidemic rats and total cholesterol, triglycerides, HDL, LDL and VLDL level in the blood were checked. Results: Sub-fraction D showed significant reduction (P<0.05 among four sub-fraction in comparison with standard drug fenofibrate. Conclusions: From the above study it could be concluded that butanol sub-fraction D of Bauhinia variegata (Linn. not only have resulted in significant reduction in cholesterol, triglyceride, LDL, VLDL level but also increases the HDL level at a reduced dose level.

  20. RNA Thermodynamic Structural Entropy.

    Science.gov (United States)

    Garcia-Martin, Juan Antonio; Clote, Peter

    2015-01-01

    Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  1. RNA Thermodynamic Structural Entropy.

    Directory of Open Access Journals (Sweden)

    Juan Antonio Garcia-Martin

    Full Text Available Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs. However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  2. Carbon nanotube-polyamidoamine dendrimer hybrid-modified electrodes for highly sensitive electrochemical detection of microRNA24.

    Science.gov (United States)

    Li, Fengye; Peng, Jing; Zheng, Qiong; Guo, Xiang; Tang, Hao; Yao, Shouzhuo

    2015-01-01

    A simple and ultrasensitive microRNA (miRNA) electrochemical biosensor employing multiwalled carbon nanotube (MWCNT)-polyamidoamine (PAMAM) dendrimer and methylene blue (MB) redox indicator is reported in this work. The assay utilizes a glass carbon (GC) electrode modified with MWCNT-PAMAM, on which the oligonucleotide capture probes are immobilized. The electrochemical detection of miRNAs is completed by measuring the reduction signal change of MB before and after the probe hybridization with target miRNA (miRNA24 is used as a model case). The MWCNT-PAMAM/GC electrode shows greatly enhanced signal to MB reduction in contrast to bare GC electrode. The functionalization of MWCNT with PAMAM maintains the electrochemical property of MWCNT to MB reduction but minimizes the undesired adsorption of MB on the MWCNT surface. The effect of experimental variables on the miRNA detection is investigated and optimized. A detection limit of 0.5 fM and a linear peak current density-concentration relationship up to 100 nM are obtained following 60 min hybridization. The proposed assay is successfully used to detect miRNA24 in total RNA sample extracted from HeLa cells.

  3. Comparative study of the anti-oxidant activity of the total polyphenols extracted from Hibiscus Sabdariffa L., Glycine max L. Merr., yellow tea and red wine through reaction with DPPH free radicals

    Directory of Open Access Journals (Sweden)

    T. Andzi Barhé

    2016-01-01

    Full Text Available The present study is part of the evaluation of extracts of Glycine max L. Merr and Hibiscus L. Sabdariffa as antioxidants. A comparative study was performed with extracts of yellow tea and commercial red wine, two foods known for their antioxidant activity. The method applied is free radical scavenging using the 1,1-diphenyl-2-picrylhydrazyl (DPPH°. The antioxidant properties were identified and measured by the determining the anti-radical activity reducing index, expressed in percentage % RSA (Radical Scavenger Activity, and by the determination of the colouring intensity (IC50. All results are compared to those of ascorbic acid as reference antioxidant. The results indicate the following order for the antioxidant power of the extracts tested. % RSA (tea > % RSA (Glycine max % > RSA (red wine % > RSA (Sabdariffa Hibiscus, and colouring intensities (IC50 ranging from 4.62 μM (ascorbic acid to 1.10 μM (Hibiscus sabdariffa correlated with their chemical structure and the content of phenolic compounds.

  4. Combinatorics of RNA-RNA interaction

    DEFF Research Database (Denmark)

    Li, Thomas J X; Reidys, Christian

    2012-01-01

    RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...

  5. Alterations in messenger RNA and small nuclear RNA metabolism resulting from fluorouracil incorporation

    International Nuclear Information System (INIS)

    Armstrong, R.D.; Cadman, E.C.

    1985-01-01

    Studies were completed to examine the effect of 5-fluorouracil (FUra) incorporation on messenger RNA (mRNA) and small molecular weight nuclear RNA (SnRNA) metabolism. Studies of mRNA were completed using cDNA-mRNA hybridization methods to specifically examine dihydrofolate reductase (DHFR) mRNA. C 3 -L5178Y murine leukemia cells which are gene-amplified for DHFR, were exposed to FUra for 6, 12 or 24 hr, and the nuclear and cytoplasmic levels of DHFR-mRNA determined by hybridization with 32 P-DHFR-cDNA. FUra produced a dose-dependent increase in nuclear DHFR-mRNA levels, while total cytoplasmic DHFR-mRNA levels appeared to be unchanged. To examine only mRNA synthesized during FUra exposure, cells were also treated concurrently with [ 3 H] cytidine, and the [ 3 H]mRNA-cDNA hybrids measured following S 1 -nuclease treatment. FUra produced a concentration-dependent increase in nascent nuclear DHFR-mRNA levels, and a decrease in nascent cytoplasmic DHFR-mRNAs levels. These results suggest that FUra produces either an inhibition of mRNA processing, or an inhibition of nuclear-cytoplasmic transport. Preliminary experiments to examine ATP-dependent mRNA transport were completed with isolated nuclei from cells treated with FUra for 1 or 24 hr and then pulse-labeled for 1 hr with [ 3 H] cytidine. The results demonstrate a FUra-concentration and time-dependent inhibition of ATP-mediated mRNA efflux

  6. Lower FOXO3 mRNA expression in granulosa cells is involved in unexplained infertility.

    Science.gov (United States)

    Yamamoto, Hikaru; Yamashita, Yoshiki; Saito, Natsuho; Hayashi, Atsushi; Hayashi, Masami; Terai, Yoshito; Ohmichi, Masahide

    2017-06-01

    The aim of this study was to investigate whether FOXO1 and FOXO3 mRNA expression in granulosa cells is the cause of unexplained infertility. Thirty-one patients aged infertility and 18 with male partner infertility as a control group) whose serum anti-Müllerian hormone level was >0.5 ng/μL were enrolled in the study. All patients underwent oocyte retrieval under a short protocol from June 2012 to October 2013. Real-time PCR was carried out using mRNA extracted from granulosa cells retrieved from mature follicles. We compared FOXO1 and FOXO3 mRNA expression ratios in granulosa cells between the unexplained infertility group and the male infertility group. The relation between FOXO1 and FOXO3 mRNA expression ratios in granulosa cells and assisted reproduction technology clinical outcome was also examined. FOXO3 mRNA expression ratio was significantly lower in the unexplained infertility group than in the male infertility group. Moreover, FOXO3 mRNA expression ratio showed a positive correlation with both the number of retrieved oocytes and serum anti-Müllerian hormone level. A positive correlation was also identified between FOXO1 mRNA expression and total dose of hMG. As well, the number of retrieved oocytes in the unexplained infertility group was statistically lower than that in the male infertility group. A lower FOXO3 mRNA expression in granulosa cells leads to poor oocyte development in patients with unexplained infertility undergoing controlled ovarian stimulation for in vitro fertilization-embryo transfer. © 2017 Japan Society of Obstetrics and Gynecology.

  7. Efeitos da inclusão do extrato oleoso de urucum em rações de poedeiras com substituição total ou parcial do milho pelo sorgo de baixo tanino = Effects of oily anatto extract inclusion in laying hens rations with total or partial replacement of maize by low tannin sorghum

    Directory of Open Access Journals (Sweden)

    Fernando Guilherme Perazzo Costa

    2006-10-01

    Full Text Available Este trabalho foi conduzido com o objetivo de avaliar o efeito da adição do extrato oleoso de urucum na s rações de poedeiras com substituição do milho pelo sorgo de baixo tanino. Foram utilizadas 324 aves em um delineament o inteiramente casualizado, com nove tratamentos, sendo uma ração controle e um fatorial 2 x 4 (dois níveis de sorgo e quatro níveis de extrato oleoso de urucum, com seis repetições de seis aves por unidade experimental. A substituição do milho pelo sorgo não alterou o desempenho das aves (P>0,05, porém a inclusão do sorgo reduziu o peso do albúmen e aumentou o peso e aporcentagem da casca (PThe aim of this work was to evaluate the effect of oily anatto extract addition on laying hens rations with replacement of maize by low tannin sorghum. Three hundred and twenty four birds were used in a completely randomized design, with nine treatments, a control diet and a 2 x 4 factorial (two sorghum levels and four levels of oily anatto extract, and six replicates of six birds each experimental unit. Replacement of maize by sorghum did not alter birds performance (P>0.05, however, sorghum inclusion decreased albumen weight andincreased shell weight and percentage (P<0.05. There was a linear effect on yolk weight when anatto extract was added to rations with 100% of sorghum. It was verified that inclusion of 0.15% of anatto extract on sorghum ration promotes yolk coloration score similar to the one observed for maize ration.

  8. RNA modifications by oxidation

    DEFF Research Database (Denmark)

    Poulsen, Henrik E; Specht, Elisabeth; Broedbaek, Kasper

    2012-01-01

    to encompass various classes of novel regulatory RNAs, including, e.g., microRNAs. It is well known that DNA is constantly oxidized and repaired by complex genome maintenance mechanisms. Analogously, RNA also undergoes significant oxidation, and there are now convincing data suggesting that oxidation......The past decade has provided exciting insights into a novel class of central (small) RNA molecules intimately involved in gene regulation. Only a small percentage of our DNA is translated into proteins by mRNA, yet 80% or more of the DNA is transcribed into RNA, and this RNA has been found......, and the consequent loss of integrity of RNA, is a mechanism for disease development. Oxidized RNA is found in a large variety of diseases, and interest has been especially devoted to degenerative brain diseases such as Alzheimer disease, in which up to 50-70% of specific mRNA molecules are reported oxidized, whereas...

  9. Exportin-5 mediates nuclear export of SRP RNA in vertebrates.

    Science.gov (United States)

    Takeiwa, Toshihiko; Taniguchi, Ichiro; Ohno, Mutsuhito

    2015-04-01

    The signal recognition particle is a ribonucleoprotein complex that is essential for the translocation of nascent proteins into the endoplasmic reticulum. It has been shown that the RNA component (SRP RNA) is exported from the nucleus by CRM1 in the budding yeast. However, how SRP RNA is exported in higher species has been elusive. Here, we show that SRP RNA does not use the CRM1 pathway in Xenopus oocytes. Instead, SRP RNA uses the same export pathway as pre-miRNA and tRNA as showed by cross-competition experiments. Consistently, the recombinant Exportin-5 protein specifically stimulated export of SRP RNA as well as of pre-miRNA and tRNA, whereas an antibody raised against Exportin-5 specifically inhibited export of the same RNA species. Moreover, biotinylated SRP RNA can pull down Exportin-5 but not CRM1 from HeLa cell nuclear extracts in a RanGTP-dependent manner. These results, taken together, strongly suggest that the principal export receptor for SRP RNA in vertebrates is Exportin-5 unlike in the budding yeast. © 2015 The Authors. Genes to Cells published by Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

  10. Absolute and direct microRNA quantification using DNA-gold nanoparticle probes.

    Science.gov (United States)

    Degliangeli, Federica; Kshirsagar, Prakash; Brunetti, Virgilio; Pompa, Pier Paolo; Fiammengo, Roberto

    2014-02-12

    DNA-gold nanoparticle probes are implemented in a simple strategy for direct microRNA (miRNA) quantification. Fluorescently labeled DNA-probe strands are immobilized on PEGylated gold nanoparticles (AuNPs). In the presence of target miRNA, DNA-RNA heteroduplexes are formed and become substrate for the endonuclease DSN (duplex-specific nuclease). Enzymatic hydrolysis of the DNA strands yields a fluorescence signal due to diffusion of the fluorophores away from the gold surface. We show that the molecular design of our DNA-AuNP probes, with the DNA strands immobilized on top of the PEG-based passivation layer, results in nearly unaltered enzymatic activity toward immobilized heteroduplexes compared to substrates free in solution. The assay, developed in a real-time format, allows absolute quantification of as little as 0.2 fmol of miR-203. We also show the application of the assay for direct quantification of cancer-related miR-203 and miR-21 in samples of extracted total RNA from cell cultures. The possibility of direct and absolute quantification may significantly advance the use of microRNAs as biomarkers in the clinical praxis.

  11. RNA-Based Assessment of Diversity and Composition of Active Archaeal Communities in the German Bight

    Directory of Open Access Journals (Sweden)

    Bernd Wemheuer

    2012-01-01

    Full Text Available Archaea play an important role in various biogeochemical cycles. They are known extremophiles inhabiting environments such as thermal springs or hydrothermal vents. Recent studies have revealed a significant abundance of Archaea in moderate environments, for example, temperate sea water. Nevertheless, the composition and ecosystem function of these marine archaeal communities is largely unknown. To assess diversity and composition of active archaeal communities in the German Bight, seven marine water samples were taken and studied by RNA-based analysis of ribosomal 16S rRNA. For this purpose, total RNA was extracted from the samples and converted to cDNA. Archaeal community structures were investigated by pyrosequencing-based analysis of 16S rRNA amplicons generated from cDNA. To our knowledge, this is the first study combining next-generation sequencing and metatranscriptomics to study archaeal communities in marine habitats. The pyrosequencing-derived dataset comprised 62,045 archaeal 16S rRNA sequences. We identified Halobacteria as the predominant archaeal group across all samples with increased abundance in algal blooms. Thermoplasmatales (Euryarchaeota and the Marine Group I (Thaumarchaeota were identified in minor abundances. It is indicated that archaeal community patterns were influenced by environmental conditions.

  12. Transcriptional profiling of cells sorted by RNA abundance

    NARCIS (Netherlands)

    Klemm, Sandy; Semrau, Stefan; Wiebrands, Kay; Mooijman, Dylan; Faddah, Dina A; Jaenisch, Rudolf; van Oudenaarden, Alexander

    We have developed a quantitative technique for sorting cells on the basis of endogenous RNA abundance, with a molecular resolution of 10-20 transcripts. We demonstrate efficient and unbiased RNA extraction from transcriptionally sorted cells and report a high-fidelity transcriptome measurement of

  13. Working with RNA

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    Working with RNA is not a special discipline in molecular biology. However, RNA is chemically and structurally different from DNA and a few simple work rules have to be implemented to maintain the integrity of the RNA. Alkaline pH, high temperatures, and heavy metal ions should be avoided when po...

  14. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

    DEFF Research Database (Denmark)

    Theis, Corinna; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

    2013-01-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general...... comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22495 3D modules in all PDB files results in 977 internal loop...

  15. Extraction process

    International Nuclear Information System (INIS)

    Rendall, J.S.; Cahalan, M.J.

    1979-01-01

    A process is described for extracting at least two desired constituents from a mineral, using a liquid reagent which produces the constituents, or compounds thereof, in separable form and independently extracting those constituents, or compounds. The process is especially valuable for the extraction of phosphoric acid and metal values from acidulated phosphate rock, the slurry being contacted with selective extractants for phosphoric acid and metal (e.g. uranium) values. In an example, uranium values are oxidized to uranyl form and extracted using an ion exchange resin. (U.K.)

  16. Solvent extraction

    Energy Technology Data Exchange (ETDEWEB)

    Coombs, D.M.; Latimer, E.G.

    1988-01-05

    It is an object of this invention to provide for the demetallization and general upgrading of heavy oil via a solvent extracton process, and to improve the efficiency of solvent extraction operations. The yield and demetallization of product oil form heavy high-metal content oil is maximized by solvent extractions which employ either or all of the following techniques: premixing of a minor amount of the solvent with feed and using countercurrent flow for the remaining solvent; use of certain solvent/free ratios; use of segmental baffle tray extraction column internals and the proper extraction column residence time. The solvent premix/countercurrent flow feature of the invention substantially improves extractions where temperatures and pressures above the critical point of the solvent are used. By using this technique, a greater yield of extract oil can be obtained at the same metals content or a lower metals-containing extract oil product can be obtained at the same yield. Furthermore, the premixing of part of the solvent with the feed before countercurrent extraction gives high extract oil yields and high quality demetallization. The solvent/feed ratio features of the invention substanially lower the captial and operating costs for such processes while not suffering a loss in selectivity for metals rejection. The column internals and rsidence time features of the invention further improve the extractor metals rejection at a constant yield or allow for an increase in extract oil yield at a constant extract oil metals content. 13 figs., 3 tabs.

  17. Cloning and characterization of DNA complementary to the canine distemper virus mRNA encoding matrix, phosphoprotein, and nucleocapsid protein

    International Nuclear Information System (INIS)

    Rozenblatt, S.; Eizenberg, O.; Englund, G.; Bellini, W.J.

    1985-01-01

    Double-stranded cDNA synthesized from total polyadenylate-containing mRNA, extracted from monkey kidney cells infected with canine distemper virus (CDV), has been cloned into the PstI site of Escherichia coli plasmid pBR322. Clones containing canine distemper virus DNA were identified by hybridization to a canine distemper virus-specific, 32 P-labeled cDNA. Four specific clones containing different classes of sequences have been identified. The cloned plasmids contain inserts of 800 (clone 44-80), 960 (clone 74-16), 1700 (clone 364), and 950 (clone 40-9) base pairs. The sizes of the mRNA species complementary to these inserts are 1500, 1850, 1850 and 2500 nucleotides, respectively, as determined by the Northern technique. Three of the cloned DNA fragments were further identified as the reverse transcripts of the mRNA coding for the matrix, phosphoprotein, and nucleocapsid protein of CDV

  18. Cloning and characterization of DNA complementary to the canine distemper virus mRNA encoding matrix, phosphoprotein, and nucleocapsid protein

    Energy Technology Data Exchange (ETDEWEB)

    Rozenblatt, S.; Eizenberg, O.; Englund, G.; Bellini, W.J.

    1985-02-01

    Double-stranded cDNA synthesized from total polyadenylate-containing mRNA, extracted from monkey kidney cells infected with canine distemper virus (CDV), has been cloned into the PstI site of Escherichia coli plasmid pBR322. Clones containing canine distemper virus DNA were identified by hybridization to a canine distemper virus-specific, /sup 32/P-labeled cDNA. Four specific clones containing different classes of sequences have been identified. The cloned plasmids contain inserts of 800 (clone 44-80), 960 (clone 74-16), 1700 (clone 364), and 950 (clone 40-9) base pairs. The sizes of the mRNA species complementary to these inserts are 1500, 1850, 1850 and 2500 nucleotides, respectively, as determined by the Northern technique. Three of the cloned DNA fragments were further identified as the reverse transcripts of the mRNA coding for the matrix, phosphoprotein, and nucleocapsid protein of CDV.

  19. Methods for RNA Analysis

    DEFF Research Database (Denmark)

    Olivarius, Signe

    of the transcriptome, 5’ end capture of RNA is combined with next-generation sequencing for high-throughput quantitative assessment of transcription start sites by two different methods. The methods presented here allow for functional investigation of coding as well as noncoding RNA and contribute to future...... RNAs rely on interactions with proteins, the establishment of protein-binding profiles is essential for the characterization of RNAs. Aiming to facilitate RNA analysis, this thesis introduces proteomics- as well as transcriptomics-based methods for the functional characterization of RNA. First, RNA...

  20. Relation of type-C RNA virus infectivity and leukemogenesis in rats and mice

    International Nuclear Information System (INIS)

    Nagao, Kenji; Ito, Takaaki; Yokoro, Kenjiro

    1976-01-01

    Observation was made as to movement of type-C RNA virus infectivity in the process of leukemogensis induced by Gross virus, N-nitrosoethylurea (NEU), or, x-ray. Total dose of 680 R in 4 times was given to the whole body or parts of the body at intervals of 5 days. Thymic leukemia occurred in 100% or rats which were inoculated with type-C RNA virus at the period of newborn 64 days after, on the average. Infectious titer of virus rose only in thymus toward leukemogenesis. Thymic leukemia was induced 100% in mice by NEU 122 days after, but its incidence was 9% of mice of which thymus was extracted. Leukemia virus was not detected in non-extracted thymus of mice, and pattern of virus infectivity in other organs did not show any difference with that of mice of which thymus was extracted. Virus showed high infectious titer in uterus of mice of both groups. Leukemia occurred 87% in the whole body irradiated mice, 15% in partially irradiated mice, and 39% in mice of which thymus was extracted and the whole body was irradiated. Virus did not show any homeostatic infectious titer in three kinds of leukemia, but it showed high infectious titer in uterus. (Kanao, N.)

  1. Cytoplasmic Z-RNA

    International Nuclear Information System (INIS)

    Zarling, D.A.; Calhoun, C.J.; Hardin, C.C.; Zarling, A.H.

    1987-01-01

    Specific immunochemical probes for Z-RNA were generated and characterized to search for possible Z-RNA-like double helices in cells. Z-RNA was detected in the cytoplasm of fixed protozoan cells by immunofluorescence microscopy using these anti-Z-RNA IgCs. In contrast, autoimmune or experimentally elicited anti-DNA antibodies, specifically reactive with B-DNA or Z-DNA, stained the nuclei. Pre-or nonimmune IgGs did not bind to the cells. RNase A or T1 digestion eliminated anti-Z-RNA IgG binding to cytoplasmic determinants; however, DNase I or mung bean nuclease had no effect. Doxorubicin and ethidium bromide prevented anti-Z-RNA antibody binding; however, actinomycin D, which does not bind double-stranded RNA, did not. Anti-Z-RNA immunofluorescence was specifically blocked in competition assays by synthetic Z-RNA but not Z-DNA, A-RNA, or single-stranded RNAs. Thus, some cytoplasmic sequences in fixed cells exist in the left-handed Z-RNA conformation

  2. A Rapid and Cost-Effective Method for DNA Extraction from Archival Herbarium Specimens.

    Science.gov (United States)

    Krinitsina, A A; Sizova, T V; Zaika, M A; Speranskaya, A S; Sukhorukov, A P

    2015-11-01

    Here we report a rapid and cost-effective method for the extraction of total DNA from herbarium specimens up to 50-90-year-old. The method takes about 2 h, uses AMPure XP magnetic beads diluted by PEG-8000- containing buffer, and does not require use of traditional volatile components like chloroform, phenol, and liquid nitrogen. It yields up to 4 µg of total nucleic acid with high purity from about 30 mg of dry material. The quality of the extracted DNA was tested by PCR amplification of 5S rRNA and rbcL genes (nuclear and chloroplast DNA markers) and compared against the traditional chloroform/isoamyl alcohol method. Our results demonstrate that the use of the magnetic beads is crucial for extraction of DNA suitable for subsequent PCR from herbarium samples due to the decreasing inhibitor concentrations, reducing short fragments of degraded DNA, and increasing median DNA fragment sizes.

  3. Hepatitis C virus translation preferentially depends on active RNA replication.

    Directory of Open Access Journals (Sweden)

    Helene Minyi Liu

    Full Text Available Hepatitis C virus (HCV RNA initiates its replication on a detergent-resistant membrane structure derived from the endoplasmic reticulum (ER in the HCV replicon cells. By performing a pulse-chase study of BrU-labeled HCV RNA, we found that the newly-synthesized HCV RNA traveled along the anterograde-membrane traffic and moved away from the ER. Presumably, the RNA moved to the site of translation or virion assembly in the later steps of viral life cycle. In this study, we further addressed how HCV RNA translation was regulated by HCV RNA trafficking. When the movement of HCV RNA from the site of RNA synthesis to the Golgi complex was blocked by nocodazole, an inhibitor of ER-Golgi transport, HCV protein translation was surprisingly enhanced, suggesting that the translation of viral proteins occurred near the site of RNA synthesis. We also found that the translation of HCV proteins was dependent on active RNA synthesis: inhibition of viral RNA synthesis by an NS5B inhibitor resulted in decreased HCV viral protein synthesis even when the total amount of intracellular HCV RNA remained unchanged. Furthermore, the translation activity of the replication-defective HCV replicons or viral RNA with an NS5B mutation was greatly reduced as compared to that of the corresponding wildtype RNA. By performing live cell labeling of newly synthesized HCV RNA and proteins, we further showed that the newly synthesized HCV proteins colocalized with the newly synthesized viral RNA, suggesting that HCV RNA replication and protein translation take place at or near the same site. Our findings together indicate that the translation of HCV RNA is coupled to RNA replication and that the both processes may occur at the same subcellular membrane compartments, which we term the replicasome.

  4. Lysosomal putative RNA transporter SIDT2 mediates direct uptake of RNA by lysosomes.

    Science.gov (United States)

    Aizawa, Shu; Fujiwara, Yuuki; Contu, Viorica Raluca; Hase, Katsunori; Takahashi, Masayuki; Kikuchi, Hisae; Kabuta, Chihana; Wada, Keiji; Kabuta, Tomohiro

    2016-01-01

    Lysosomes are thought to be the major intracellular compartment for the degradation of macromolecules. We recently identified a novel type of autophagy, RNautophagy, where RNA is directly taken up by lysosomes in an ATP-dependent manner and degraded. However, the mechanism of RNA translocation across the lysosomal membrane and the physiological role of RNautophagy remain unclear. In the present study, we performed gain- and loss-of-function studies with isolated lysosomes, and found that SIDT2 (SID1 transmembrane family, member 2), an ortholog of the Caenorhabditis elegans putative RNA transporter SID-1 (systemic RNA interference deficient-1), mediates RNA translocation during RNautophagy. We also observed that SIDT2 is a transmembrane protein, which predominantly localizes to lysosomes. Strikingly, knockdown of Sidt2 inhibited up to ˜50% of total RNA degradation at the cellular level, independently of macroautophagy. Moreover, we showed that this impairment is mainly due to inhibition of lysosomal RNA degradation, strongly suggesting that RNautophagy plays a significant role in constitutive cellular RNA degradation. Our results provide a novel insight into the mechanisms of RNA metabolism, intracellular RNA transport, and atypical types of autophagy.

  5. Extraction method

    International Nuclear Information System (INIS)

    Stary, J.; Kyrs, M.; Navratil, J.; Havelka, S.; Hala, J.

    1975-01-01

    Definitions of the basic terms and of relations are given and the knowledge is described of the possibilities of the extraction of elements, oxides, covalent-bound halogenides and heteropolyacids. Greatest attention is devoted to the detailed analysis of the extraction of chelates and ion associates using diverse agents. For both types of compounds detailed conditions are given of the separation and the effects of the individual factors are listed. Attention is also devoted to extractions using mixtures of organic agents, the synergic effects thereof, and to extractions in non-aqueous solvents. The effects of radiation on extraction and the main types of apparatus used for extractions carried out in the laboratory are described. (L.K.)

  6. Comparison of microRNA expression using different preservation methods of matched psoriatic skin samples

    DEFF Research Database (Denmark)

    Løvendorf, Marianne B; Zibert, John R; Hagedorn, Peter H

    2012-01-01

    MicroRNAs are non-coding RNA molecules modulating gene expression post-transcriptionally. Formalin-fixed, paraffin-embedding (FFPE) is a standard preservation method often used in clinical practices, but induces RNA degradation. Extracting high-quality RNA from human skin can be challenging as skin...

  7. RNA decay by messenger RNA interferases

    DEFF Research Database (Denmark)

    Christensen-Dalsgaard, Mikkel; Overgaard, Martin; Winther, Kristoffer Skovbo

    2008-01-01

    Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mR...... cleaving enzymes such as RelE of Escherichia coli and the corresponding antitoxin RelB. In particular, we describe a set of plasmid vectors useful for the detailed analysis of cleavage sites in model mRNAs.......Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mRNA...

  8. Vacuum extraction

    DEFF Research Database (Denmark)

    Maagaard, Mathilde; Oestergaard, Jeanett; Johansen, Marianne

    2012-01-01

    Objectives. To develop and validate an Objective Structured Assessment of Technical Skills (OSATS) scale for vacuum extraction. Design. Two-part study design: Primarily, development of a procedure-specific checklist for vacuum extraction. Hereafter, validation of the developed OSATS scale for vac...

  9. Electromembrane extraction

    DEFF Research Database (Denmark)

    Huang, Chuixiu; Chen, Zhiliang; Gjelstad, Astrid

    2017-01-01

    Electromembrane extraction (EME) was inspired by solid-phase microextraction and developed from hollow fiber liquid-phase microextraction in 2006 by applying an electric field over the supported liquid membrane (SLM). EME provides rapid extraction, efficient sample clean-up and selectivity based...

  10. Diverging affinity of tospovirus RNA silencing suppressor proteins, NSs, for various RNA duplex molecules

    NARCIS (Netherlands)

    Schnettler, E.; Hemmes, J.C.; Huisman, R.; Goldbach, R.W.; Prins, M.W.; Kormelink, R.J.M.

    2010-01-01

    The tospovirus NSs protein was previously shown to suppress the antiviral RNA silencing mechanism in plants. Here the biochemical analysis of NSs proteins from different tospoviruses, using purified NSs or NSs containing cell extracts, is described. The results showed that all tospoviral NSs

  11. Comparison of the extraction and determination of serum exosome and miRNA in serum and the detection of miR-27a-3p in serum exosome of ALS patients.

    Science.gov (United States)

    Xu, Qian; Zhao, Yuying; Zhou, Xiaoyan; Luan, Jing; Cui, Yazhou; Han, Jinxiang

    2018-02-01

    Amyotrophic Lateral Sclerosis (ALS) is a muscle-bone degenerative disease, which lacks a specific index for diagnosis. In our previous studies, we found that exosomes mediated the interaction mechanism between muscle and bone at the cellular level, and myoblast exosomes can transfer miR-27a-3p to promote osteoblast mineralization. Therefore, we suppose that the expression of miR-27a-3p in the serum exosomes of ALS patients also changes. In this study, we used healthy human serum as a sample to find out the conditions and methods for extraction and detection. Then through comparison of the expression of miR-27a-3p in the serum exosomes of 10 ALS patients and healthy subjects, we found that in the ALS patients miR-27a-3p was down-regulated, and may be involved in the development of ALS, and therefore has potential as a reference for the diagnosis of ALS in the clinic.

  12. High Quality RNA Isolation from Leaf, Shell, Root Tissues and Callus of Hazelnut (Corylus avellana L.

    Directory of Open Access Journals (Sweden)

    Hossein Khosravi

    2017-12-01

    Full Text Available Extraction of high quality RNA is a critical step in molecular genetics studies. Hazelnut is one of the most important nuts plants in the world. The presence of the taxol and other taxanes in hazelnut plant necessitates explaining their biosynthesis pathway and identifying the candidate genes. Therefore, an easy and practical method is necessary for RNA extraction from hazelnuts. Hazelnut has high levels of phenolic compounds. High amounts of polyphenolic and polysaccharide compounds in plants could be causing problems in RNA extraction procedures.  To avoid these problems, a simple and efficient method can be used based on cetyltrimethylammonium bromide (CTAB extraction buffer and lithium chloride for extraction of high quality RNA from different parts of hazelnut plant. Using this method, a high-quality RNA sample (light absorbed in the A260/A280 was 2.04

  13. The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism.

    Science.gov (United States)

    Wang, Na; Wang, Ruoqing; Wang, Renkai; Tian, Yongsheng; Shao, Changwei; Jia, Xiaodong; Chen, Songlin

    2017-01-01

    Albinism, a phenomenon characterized by pigmentation deficiency on the ocular side of Japanese flounder (Paralichthys olivaceus), has caused significant damage. Limited mRNA and microRNA (miRNA) information is available on fish pigmentation deficiency. In this study, a high-throughput sequencing strategy was employed to identify the mRNA and miRNAs involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05). The next target prediction discovered a variety of putative target genes, of which, 134 genes including Tyrosinase (TYR), Tyrosinase-related protein 1 (TYRP1), Microphthalmia-associated transcription factor (MITF) were overlapped with differentially expressed genes derived from RNA-seq. These target genes were significantly enriched to 254 GO terms and 103 KEGG pathways (p<0.001). Of those, tyrosine metabolism, lysosomes, phototransduction pathways, etc., attracted considerable attention due to their involvement in regulating skin pigmentation. Expression patterns of differentially expressed mRNA and miRNAs were validated in 10 mRNA and 10 miRNAs by qRT-PCR. With high-throughput mRNA and miRNA sequencing and analysis, a series of interested mRNA and miRNAs involved in fish

  14. Topology of RNA-RNA interaction structures

    DEFF Research Database (Denmark)

    Andersen, Jørgen Ellegaard; Huang, Fenix Wenda; Penner, Robert

    2012-01-01

    Abstract The topological filtration of interacting RNA complexes is studied, and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that, for two interacting RNAs, called interaction structures, there exist...

  15. Altered expression of four miRNA (miR-1238-3p, miR-202-3p, miR-630 and miR-766-3p) and their potential targets in peripheral blood from vitiligo patients.

    Science.gov (United States)

    Shang, Zhiwei; Li, Hongwen

    2017-10-01

    Vitiligo is an acquired skin disease with pigmentary disorder. Autoimmune destruction of melanocytes is thought to be major factor in the etiology of vitiligo. miRNA-based regulators of gene expression have been reported to play crucial roles in autoimmune disease. Therefore, we attempt to profile the miRNA expressions and predict their potential targets, assessing the biological functions of differentially expressed miRNA. Total RNA was extracted from peripheral blood of vitiligo (experimental group, n = 5) and non-vitiligo (control group, n = 5) age-matched patients. Samples were hybridized to a miRNA array. Box, scatter and principal component analysis plots were performed, followed by unsupervised hierarchic