scholarly journals Impact of Extraction Method on the Detection of Quality Biomarkers in Normal vs. DFD Meat

Foods ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1097
Author(s):  
Laura González-Blanco ◽  
Yolanda Diñeiro ◽  
Andrea Díaz-Luis ◽  
Ana Coto-Montes ◽  
Mamen Oliván ◽  
...  
Keyword(s):  
Extraction Method ◽  
Protein Pattern ◽  
Stress Protein ◽  
Electrophoretic Pattern ◽  
Extraction Methods ◽  
Sds Page ◽  
Weight Protein ◽  
Triton X ◽  
Protein Extractability ◽  
Selection Of

The objective of this work was to demonstrate how the extraction method affects the reliability of biomarker detection and how this detection depends on the biomarker location within the cell compartment. Different extraction methods were used to study the sarcoplasmic and myofibrillar fractions of the Longissimus thoracis et lumborum muscle of young bulls of the Asturiana de los Valles breed in two quality grades, standard (Control) or dark, firm, and dry (DFD) meat. Protein extractability and the expression of some of the main meat quality biomarkers—oxidative status (lipoperoxidation (LPO) and catalase activity (CAT)), proteome (SDS-PAGE electrophoretic pattern), and cell stress protein (Hsp70)—were analyzed. In the sarcoplasmic fraction, buffers containing Triton X-100 showed significantly higher protein extractability, LPO, and higher intensity of high-molecular-weight protein bands, whereas the TES buffer was more sensitive to distinguishing differences in the protein pattern between the Control and DFD meat. In the myofibrillar fraction, samples extracted with the lysis buffer showed significantly higher protein extractability, whereas samples extracted with the non-denaturing buffer showed higher results for LPO, CAT, and Hsp70, and higher-intensity bands in the electrophoretic pattern. These findings highlight the need for the careful selection of the extraction method used to analyze the different biomarkers considering their cellular location to adapt the extractive process.

scholarly journals Evaluation of effective protein extraction procedure to profile petiole of Moringa oleifera

2020 ◽  
Vol 7 (2) ◽  
pp. 214
Author(s):  
Zetty Amirah Zulkifli ◽  
Zaidah Rahmat
Keyword(s):  
Moringa Oleifera ◽  
Protein Extraction ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Extraction Procedure ◽  
Electrophoretic Pattern ◽  
Antioxidant Property ◽  
Extraction Methods ◽  
Protein Profiling ◽  
Sds Page

Moringa oleifera is widely known as multipurpose tree since all of its parts confer multiple functions. The leaf is highly favourable among consumers while the petiole is mostly wasted. There are numerous studies on the flavonoid and antioxidant property of the stem and twig. However, study on the petiole has never been done. There-upon, this study was conducted to develop protein profiling of the petiole. In this study, 6 different protein extraction methods were tested on the fresh petiole before its protein quantity and quality were checked via Bradford assay and Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) respectively. The in-solution digestion was then done prior to LC-MS/MS analysis. The protein electrophoretic pattern from the SDS-PAGE proves that method 6 using Tris HCl buffer with incorporation of dithiothreitol (DTT) and phenylmethylsulfonyl fluoride (PMSF) confers the best quality of protein. It produced the highest number of visible individual bands compared to other methods. Meanwhile, 93 proteins were successfully identified via LCMS analysis where the protein, signal response and carbohydrate metabolism categories confer the highest percentage. High quality and content of the protein extracted from the petiole including the antioxidant, anticancer and antidiabetic protein identified suggested that consuming this part of the plant could enhance nutrients of human body.

Association of cumulus–oocyte complexes with the intrafollicular levels of a blood proten in Bubalus bubalis

Zygote ◽  
1994 ◽  
Vol 2 (2) ◽  
pp. 167-178 ◽  
Author(s):  
R. Talevi ◽  
P. Bergamo ◽  
G. Sansone ◽  
A. Savarese ◽  
P. Venditti ◽  
...  
Keyword(s):  
Acrosome Reaction ◽  
Protein Pattern ◽  
Gel Filtration ◽  
Bubalus Bubalis ◽  
Ionophore A23187 ◽  
Sperm Suspension ◽  
Transmission Electron ◽  
Sds Page ◽  
Weight Protein

SummaryThe protein pattern of the follicular fluid (FF) and the ultrastructure of the inner cumulus–oocyte complex (COC) has been analysed in single antral follicles (n = 146) of buffalo B. Bubalis ovaries. The protein population of FF was fractionated by SDS-PAGE; the resulting pattern was Coomassie stained and processed for densitometry. Comparartive analysis of sera and autologous FFs showed a marked difference in the level (measured as the percentage of total proteins) of one 21 kDa polypeptide band, called ‘L’. Concentration of L, which was mainly higher in the serum (2.05 ± 1.5%) than in the surrounding FF(0.98 ± 0.94%), fluctuated widely in fluids from the in the same ovary. On gel filtration of FF and SDS-PAGE of ther factions collected, the L polypeptide was found and eluted together with a 36 kDa polypeptide, called ‘H’, with an exclusion volume lower than that of albumin. The levels of both polypeptides in the eluted fractions were measured by gel densitometry and the same ratio H/L was found (2:1). These data suggest that H and L are subunits of a complex high-molecular-weight protein. The presence of L levels in male sera comparable to those detected in females indicates that this putative protein does not originate in the ovary but is transported from the blood. Moreover, a correlation between the increase in the percentage of Lf (calculated as %L in FF/%L in serum) and atresia was observed. COCs (n = 86) obtained during the collection of the single FF samples were processed for transmission electron microscopy. The ultrastructure of each COC was compared with the SDS-PAGE data of the associated FF. Healthy COCs were found to be related to very low levels of Lf (between 0 and 14% of those measured in serum). COCs with an early atretic ultrastructure undetectable at the dissection microscope, were associated with FFs having Lf levels between 24% and 60%; advanced atresia was associated with Lf values up to 70%. Finally, the acrosome reaction of buffalo precapacitated spermatozoa in vitro was monitored by adding one volume of FF with high (FF +; Lf = 80%) or undetectable (FF - ) values of Lf to the sperm suspension. It was found that 96.2% of spermatozoa treated with FF - showed a normal acrosome reaction, without any change in their motility pattern; spermatozoa treated with FF +, in contrast, exhibited poor motility, and only 66.4% of them underwent the acrosome reaction. The ionophore A23187, in a control experiment, resulted in lower percentages of acrosome reactions (38%). In conclusion, our results suggest that enhanced influx of L from serum into the follicle antrum causes an increase in the polypeptide level in FF. This might be due to a loss of selectivity in the blood-follicle barrier of early atretic follicles. The use of the L polypeptide as a biochemical marker for identifying the earlier stage of follicular atresia is proposed.

scholarly journals Selection of solvent and extraction method for determination of antimicrobial potential of Taxus wallichiana Zucc.

1970 ◽  
pp. 01-09 ◽  
Author(s):  
Priyanka Adhikari, Anita Pandey ◽  
Vasudha Agnihotri ◽  
Veena Pande
Keyword(s):  
Antimicrobial Activity ◽  
Antifungal Activity ◽  
Ethyl Acetate ◽  
Petroleum Ether ◽  
Extraction Method ◽  
Extraction Methods ◽  
Plant Parts ◽  
Antimicrobial Potential ◽  
Selection Of ◽  
Taxus Wallichiana

Antimicrobial potential of different plant parts (needle, stem and bark) of Himalayan yew (Taxus wallichiana Zucc.) has been investigated with particular reference to selection of solvents and extraction methods. Two extraction methods (maceration and soxhlet), seven solvents (methanol, ethanol, acetone, chloroform, ethyl  acetate, di chloro methane and Petroleum ether), and 3 groups of microorganisms (bacteria, actinobacteria and fungi) were considered for detection of antimicrobial activity. While qualitative estimations were done using agar well diffusion method, quantitative analysis was based on dilution method. All the plant part showed significant activity against all 3 groups of microorganisms in qualitative bioassays; maximum being in case of needles. Among solvents, ethanolic extract of needles (maceration) showed highest antibacterial activity (15.33 ± 0.25 mm). Growth of actinobacteria was inhibited maximum (22.0±0.26 mm) by the methanolic extracts of needles (maceration). Ethyl acetate extract of needles (soxhlet) showed higher antifungal activity (7.84±0.21 mm). Antibacterial and antifungal activities were higher in maceration and soxhlet methods, respectively. The most affected group among the test microorganisms was bacteria which may be due to their prokaryotic organization. This was also supported by the low minimum inhibitory concentration (MIC) values. Di chloro methane and petroleum ether did not show any antifungal activity. The antimicrobial activity of various plant parts of T. wallichiana varied with respect to the solvent as well as the extraction method. The study will have implications in selection of the use of solvent and the extraction procedure in obtaining the antimicrobial metabolites from various plant parts of T. wallichiana.

scholarly journals DIMENSIONALITY REDUCTION OF HYPERSPECTRAL IMAGES BY COMBINATION OF NON-PARAMETRIC WEIGHTED FEATURE EXTRACTION (NWFE) AND MODIFIED NEIGHBORHOOD PRESERVING EMBEDDING (NPE)

2014 ◽  
Vol XL-2/W3 ◽  
pp. 31-34
Author(s):  
T. Alipour Fard ◽  
H. Arefi
Keyword(s):  
Feature Extraction ◽  
Extraction Method ◽  
Extraction Methods ◽  
Hyperspectral Images ◽  
Scatter Matrix ◽  
Feature Extraction Method ◽  
Conventional Extraction ◽  
Supervised Feature Extraction ◽  
Number Of Classes ◽  
Selection Of

This paper combine two conventional feature extraction methods (NWFE&NPE) in a novel framework and present a new semi-supervised feature extraction method called Adjusted Semi supervised Discriminant Analysis (ASEDA). The advantage of this method is dominating the Hughes phenomena, automatic selection of unlabelled pixels, extraction of more than L-1(L: number of classes) features and avoidance of singularity or near singularity of within-class scatter matrix. Experimental results on well-known hyperspectral dataset demonstrate that compared to conventional extraction algorithms the overall accuracy of the classification increased.

scholarly journals A NEW METHOD TO EXTRACT PERMANENT SCATTERERS

2020 ◽  
Vol V-1-2020 ◽  
pp. 389-394
Author(s):  
Y. Kang ◽  
Y. Zhang ◽  
H. Wu
Keyword(s):  
Time Series ◽  
Extraction Method ◽  
Surface Deformation ◽  
Extraction Methods ◽  
Deformation Monitoring ◽  
Phase Information ◽  
Final Point ◽  
Point Density ◽  
Permanent Scatterers ◽  
Selection Of

Abstract. At present, time series InSAR technology has been widely used in surface deformation monitoring. The extraction of permanent scatterers is an important part, which is directly related to the accuracy of monitoring results. The existing permanent scatterers extraction methods are mainly based on the amplitude information or the coherence information, there is a problem that the point quality and point density cannot be taken into account, and the selection of the point parameters requires operators to have a wealth of experience. In order to solve the above problems, a permanent scatterers extraction method based on the combination of amplitude and model coherence coefficient is proposed in this paper. This method examines not only the amplitude information of the permanent scatterers, but also the phase information of the point. And the phase quality directly affects the accuracy of deformation inversion. This paper takes Yupu Bridge, Yiqiao Town, Xiaoshan District, Hangzhou City as the experimental area to carry out comparative experiments. The results show that the final point target density extracted by this method is 1.97 times that of the conventional method based on amplitude information, and shows the details of deformation distribution of Yupu Bridge more completely.

The Combining Ability of Glycoproteins IIb, IIIa and Ca2+ in EDTA-Treated Nonaggregable Platelets

1983 ◽  
Vol 50 (04) ◽  
pp. 848-851 ◽  
Author(s):  
Marjorie B Zucker ◽  
David Varon ◽  
Nicholas C Masiello ◽  
Simon Karpatkin
Keyword(s):  
Density Gradient ◽  
Combining Ability ◽  
Density Gradient Centrifugation ◽  
Gradient Centrifugation ◽  
Electrophoretic Pattern ◽  
Sucrose Density Gradient ◽  
Irreversible Loss ◽  
Sucrose Density Gradient Centrifugation ◽  
Crossed Immunoelectrophoresis ◽  
Triton X

SummaryPlatelets deprived of calcium and incubated at 37° C for 10 min lose their ability to bind fibrinogen or aggregate with ADP when adequate concentrations of calcium are restored. Since the calcium complex of glycoproteins (GP) IIb and IIIa is the presumed receptor for fibrinogen, it seemed appropriate to examine the behavior of these glycoproteins in incubated non-aggregable platelets. No differences were noted in the electrophoretic pattern of nonaggregable EDTA-treated and aggregable control CaEDTA-treated platelets when SDS gels of Triton X- 114 fractions were stained with silver. GP IIb and IIIa were extracted from either nonaggregable EDTA-treated platelets or aggregable control platelets with calcium-Tris-Triton buffer and subjected to sucrose density gradient centrifugation or crossed immunoelectrophoresis. With both types of platelets, these glycoproteins formed a complex in the presence of calcium. If the glycoproteins were extracted with EDTA-Tris-Triton buffer, or if Triton-solubilized platelet membranes were incubated with EGTA at 37° C for 30 min, GP IIb and IIIa were unable to form a complex in the presence of calcium. We conclude that inability of extracted GP IIb and IIIa to combine in the presence of calcium is not responsible for the irreversible loss of aggregability that occurs when whole platelets are incubated with EDTA at 37° C.

scholarly journals Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 146
Author(s):  
Catarina Xavier ◽  
Mayra Eduardoff ◽  
Barbara Bertoglio ◽  
Christina Amory ◽  
Cordula Berger ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Extraction Method ◽  
Fragment Size ◽  
Molecular Genetic ◽  
Extraction Methods ◽  
Degraded Dna ◽  
Size Analysis ◽  
Dna Fragments ◽  
Dna Amount

The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille’s overall increased gain of DNA when enough tissue is available and Dabney’s improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.

scholarly journals Molecular analysis of genetic diversity in population of Silybum marianum (L.) Gaertn in Egypt

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Marwa Hamouda
Keyword(s):  
Genetic Diversity ◽  
Electrophoretic Pattern ◽  
Issr Markers ◽  
Silybum Marianum ◽  
Inter Simple Sequence Repeats ◽  
Sds Page ◽  
Dna Pattern ◽  
Pharmaceutical Properties ◽  
High Level ◽  
Rapd And Issr

Abstract Background Silybum marianum L. Gaertn is a medicinal plant of unique pharmaceutical properties in the treatment of liver disorders and diabetic nephropathy. Biochemical (SDS-PAGE) and molecular markers such as randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) technologies were used in this work to detect genetic diversity of 14 collections of Silybum marianum population in Egypt. Results The electrophoretic pattern of seed protein gave different molecular weight bands, ranging from 24 to 111 KDa with the presence of unique bands. RAPD results revealed a high level of polymorphism (73.2%) using 12 RAPD primers, but only eight of them gave reproducible polymorphic DNA pattern. Sixteen primers were used in the ISSR method; only ten of them yielded clearly identifiable bands. The percentage of polymorphism is about 80% of the studied samples. Conclusion The obtained data confirmed that SDS-protein, RAPD, and ISSR markers are important tools for genetic analysis for Silybum marianum and recommended to give accurate results.

scholarly journals Integrated Metabolomics and Transcriptomics Using an Optimised Dual Extraction Process to Study Human Brain Cancer Cells and Tissues

Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 240
Author(s):  
Alison Woodward ◽  
Alina Pandele ◽  
Salah Abdelrazig ◽  
Catherine A. Ortori ◽  
Iqbal Khan ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Extraction Method ◽  
Limit Of Detection ◽  
Rna Extraction ◽  
Extraction Process ◽  
Extraction Methods ◽  
Serum Starvation ◽  
Extraction Techniques ◽  
Metabolic Genes ◽  
Dual Extraction

The integration of untargeted metabolomics and transcriptomics from the same population of cells or tissue enhances the confidence in the identified metabolic pathways and understanding of the enzyme–metabolite relationship. Here, we optimised a simultaneous extraction method of metabolites/lipids and RNA from ependymoma cells (BXD-1425). Relative to established RNA (mirVana kit) or metabolite (sequential solvent addition and shaking) single extraction methods, four dual-extraction techniques were evaluated and compared (methanol:water:chloroform ratios): cryomill/mirVana (1:1:2); cryomill-wash/Econospin (5:1:2); rotation/phenol-chloroform (9:10:1); Sequential/mirVana (1:1:3). All methods extracted the same metabolites, yet rotation/phenol-chloroform did not extract lipids. Cryomill/mirVana and sequential/mirVana recovered the highest amounts of RNA, at 70 and 68% of that recovered with mirVana kit alone. sequential/mirVana, involving RNA extraction from the interphase of our established sequential solvent addition and shaking metabolomics-lipidomics extraction method, was the most efficient approach overall. Sequential/mirVana was applied to study a) the biological effect caused by acute serum starvation in BXD-1425 cells and b) primary ependymoma tumour tissue. We found (a) 64 differentially abundant metabolites and 28 differentially expressed metabolic genes, discovering four gene-metabolite interactions, and (b) all metabolites and 62% lipids were above the limit of detection, and RNA yield was sufficient for transcriptomics, in just 10 mg of tissue.

A Structural Analysis Based Feature Extraction Method for OCR System For Myanmar Printed Document Images

2012 ◽  
Vol 2 (1) ◽  
pp. 16-41 ◽  
Author(s):  
Htwe Pa Pa Win ◽  
Phyo Thu Thu Khine ◽  
Khin Nwe Ni Tun
Keyword(s):  
Feature Extraction ◽  
Structural Analysis ◽  
Character Recognition ◽  
Optical Character Recognition ◽  
Extraction Method ◽  
Recognition Performance ◽  
Extraction Methods ◽  
Support Vector ◽  
Svm Classifier ◽  
Feature Extraction Method

This paper proposes a new feature extraction method for off-line recognition of Myanmar printed documents. One of the most important factors to achieve high recognition performance in Optical Character Recognition (OCR) system is the selection of the feature extraction methods. Different types of existing OCR systems used various feature extraction methods because of the diversity of the scripts’ natures. One major contribution of the work in this paper is the design of logically rigorous coding based features. To show the effectiveness of the proposed method, this paper assumed the documents are successfully segmented into characters and extracted features from these isolated Myanmar characters. These features are extracted using structural analysis of the Myanmar scripts. The experimental results have been carried out using the Support Vector Machine (SVM) classifier and compare the pervious proposed feature extraction method.

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