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Natural Product Drug Discovery - Science topic

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Do you know of any plants or active substances which can be used for wound healing?
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When walnuts is good for reducing LDL and total cholestrol levels in blood,I think we can boil folium layer in kernel of Walnuts in water and use it as a usefull Liquid.
thanks.
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All the nuts, including Walnut are rich in polyunsaturated fatty acids, and reduce total cholesterol and LDL cholesterol.
Although leaves (folium) of walnut tree have been shown to have salutary effect on lipids, no study as such has used the folium of the kernal of the walnut
Have a look at this article in the link:
The Comparative Effects of Aqueous Extract of Walnut ...
3.
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I have tried olive oil as a vehicle but the extract is not also soluble. In fact the extract dissolves in ethanol but crystallizes out on addition of water
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Not more than 1% DMSO
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Most of the researchers working on protease inhibitory assay, they cited the Oyedepo etal, 1995, but I couldn't get the original paper. I followed their protocol, replicated 11 times, but unable to get the readings as absorbance was read very high. Even the Aspirin and Diclofenac sodium at the dose of 10-100 microgram/100 microlitre as well as 1-100 microgram/ml could not give the reading . I am wondering why I can not get the readings even on standard drug following their reported protocol. Does Trypsin (0.06 mg) have any specific concentration in their protocol ?
Oyedepo OO, Femurewa AJ (1995). Anti-protease and membrane
stabilizing activities of extracts of Fagra zanthoxiloides, Olax
subscorpioides and Tetrapleura tetraptera. Int. J. Pharmacog., 33: 65-69.
Please provide any info on the protocol of this paper and suggest another protocol for protease inhibitory assay if possible.
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OK
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where i will get the data base /bank plants having chemopreventive, anticancer, antiproliferative or anti tumor activity. Apart from this is there any lead compound or chemical structure base data base regarding aforsaid activity from vegitation sources?
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My thesis's subject is determination of flavonoids; catechin and quercetin from sea buckthorn leaves with HPLC-DAD. I have extracted the leaves with ethyl acetate 5x12,5ml, and I have now extract about 40ml. I think next step before determination with HPLC is acid hydrolysis, because flavonoids have glucosides and I gues those should dorp out of measurement.
But I have a problem, how should I do the acid hydrolysis? Should I use 4M HCl or weaker, about 2-6M, and should I use reflux 2h at temperature 40C with stirring?
For now I have tried to do this acid hydrolysis like this: 9,5ml ethyl acetate extract + 0,5ml 4M HCl and heated for 5min in waterbath 75°C. The end concentration of sample is 0,6M (I mean extract + HCl). I have found this advice from here page on 47-48
But this doesn't work so well. Am I doing something wrong? I haven't found any good or spefisic advice. So would you guys help me?
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can anyone tell me the Rf value of standard D-quinovose??? I have searched alot but did not find it.
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Dear colleagues, currently I run an academic project dealing with rational discovery of novel antagonists of one of the GPCRs. I performed a hierarchical virtual screening of few libraries (some comprising natural compounds, others - synthetic), and selected few dozens for the evaluation in a cell-based system. In the tests, some compounds showed promising results, and now I am wondering how can I check the newness/patentability of their molecular scaffolds. Have no idea where to start. Are there any specific services for these? Or maybe you can suggest some helpful literature on this topic?
Thanks for any suggestions!
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You can use Chemical Abstract Services like Scifinder, Reaxys, STN on the web, SPRESI (Scientific Chemical Databases) and many more. Chemical Abstract Services keep track of all synthesized compounds.
Ofcourse, there are other online tools also like Chemspider, E-molecule, Chemexpert, Pub chem compound and many more.
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Ethnic medicinal knowledge is precious for the advancement of Drug Discovery, however, there are several challenges in this field like others. What could be the possible opportunities in more practical ways for the economically underdeveloped society from this precious knowledge and how modern scientific tools can be utilised for its optimum utilisation?
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Integration of Orthodox medicine into Traditional Medicine is the sole path towards creating boundless opportunities for underdeveloped countries to achieving sustainability.
Vis a vis the fact that Traditional Medicine services over 60% of populace in rural developing countries , have the prerequisite knowledge and practices, and have a far acceptability by the people in comparison with orthodox medicine.
Hence, when modern scientific tools and precious traditional medicine are integrated, the opportunities are there for the picking.
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I would like to explore the PKS, NRPS and relevant gene diversity in the metagenomic actinobacterial DNA of the mangrove sediment samples to understand the secondary metabolite production pattern. Can some one recommend / provide a simple and efficient protocol to amplify, clone and sequence the PKS, NRPS and relevant gene in the metagenomic DNA pool; specific to actinobacteria?
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Already specific primers are available to screes PKS and NRPS gene from actinobacteria. You can follow that protocol.......
Comprehensive Investigation of Marine Actinobacteria Associated with the Sponge Halichondria panicea
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Can we use Soxhlet for extracting the secondary metabolites from the Actinobacteria fermented broth? Soxhlet is generally being used for dry/solid materials. If we adopt this to actinobacteria does it work?
or the regular solvent extraction is sufficient? Recommend me some rapid and efficient method to maximize the yield of total metabolites.
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Of course you could but you have to select the suitable organic solvents
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Dear all, I have a problem to synthesize the imidazole from isatin and aldehyde using NH4OAc in AcOH. I try several time and the product is not form. Can any buddy help me to figure out the problem.? Thank you in advance. 
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Thank you Michael Pach. I will find that paper. Thanks a lot.
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I am seeking authentic literature (published paper, book etc.) to find out the use of animals against kidney stones. Please share any authentic information if you have in this regard.
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A pubmed search for 'Endothelium Corneum Gigeriae Galli' does yield only 4 articles. However, searching CNKI, China Academic Journals Full-text Database, shows a considerable amount of works in Chinese language:
CNKI chicken gizzard lining (Endothelium Corneum Gigeriae Galli) = jī nèi jīn,
searching ‘雞內金’: Total: 1779 articles.
searching ‘雞內金’ combined with ‘石淋’ (shí lín): Total: 47 articles.
Examples of recent studies with abstracts:
JIN, Lingjia 金伶佳; JIA, Tianzhu 賈天柱 (2015) Ji nei jin de butong paozhipin zhong duotang hanliang bijiao 雞內金的不同炮製品中多糖含量比較 – Comparison of the Polysaccharide Content in Different Processed Products of Inner Membrane of Chicken Gizzard,  in: Zhongguo zhongyiyao xiandai yuancheng jiaoyu  中國中醫藥現代遠程教育 - Chinese Medicine Modern Distance Education of China 13(20): 146-147, 2 tables.
[Abstract: Objective: To study the determination method of polysaccharide of inner membrane of chicken gizzard, and to compare polysaccharide content in different processed products. Methods: The polysaccharide content in different processed products of inner membrane of chicken gizzard was analyzed and compared by phenol- sulfuric acid colorimetry. Results: The total polysaccharide content of different processed products of inner membrane of chicken gizzard of heated with sand was more than raw products which was more than microwave processed products. Conclusion: The total polysaccharide content of sand hot processed products was more than raw product and microwave processed products.
Keywords: 雞內金; 多糖; 苯酚-硫酸比色法; 中藥炮製; inner membrane of chicken gizzard; polysaccharide; phenol-sulfuric acid colorimetry; processing.
Institution:  遼寧省大連市衛生計生培訓中心Health Family Planning Training Center.]
XU, Haohui 許浩輝; FENG, Songjie 馮松傑 (2015) Ji nei jin zhiliao shilin zhi tantao 雞內金治療石淋之探討 – Investigation of Using Endothelium Corneum Gigeriae Galli to Treat Urolithiasis, in: Sichuan zhongyi  四川中醫 - Journal of Sichuan of Traditional Chinese Medicine 33(4): 36-38.
[Abstract: Objective: To explore the mechanism and application about the treatment of urolithiasis with endothelium corneum gigeriae galli. Methods: Papers from 2003 to 2013 journals and professor FENG Songjie about treatment of urolithiasis with endothelium corneum gigeriae galli were retrieved and analyzed. Results: According to relevant papers, professor FENG used endothelium corneum gigeriae galli to treat urolithiasis on the base of high dose of lysimachia chiristinae hance for resolving dampness and removing calculi. Conclusion: Urolithiasis treated by Endothelium corneum gigeriae galli is effective and safe, it is worth further study.
Keywords: 雞內金; 石淋; 化濕消堅; 馮松傑; Endothelium corneum gigeriae galli; Urolithiasis; Resolving dampness and removing calculi; Professor Feng Songjie;
Institution: Nanjing University of Traditional Chinese Medicine 南京中醫藥大學; 江蘇省中醫院.]
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what is the role of plant extracts for the green synthesis of nanoparticles?
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Plant extract act as reducing as well as stabilizing agents.  Polyphenolic compounds act as reducing agents while amino acids as stabilizing agents
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Oral+ demal+inhalation routes simultaneously
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The design of any study depends on the question you are asking. This principle also applies to choosing the route of administration. If the purpose of the study is mechanistic, and the objective is simply to get the test compound into the circulation, then the route of administration is of secondary importance. However, if the objective is risk assessment, it is important to use the route of administration that would mirror actual exposures. For example, if the purpose of the study is to assess the toxicity of a skin lotion that is a personal care product, then the study should employ dermal administration. However, in reality, exposures might occur by multiple routes. Nevertheless, in order to simplify interpretation of results, it may be best to limit exposures to one route of administration at a time. It should also be kept in mind that when a study design employs one route, such as dermal administration, the actual exposures might be mixed if, for example, the animals were able to lick the area of skin to which the substance had been applied then the exposure would be a mix of dermal and oral.
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Can someone help me with with molecular dockings, am working on antidiabetes properties of some plants in vivo?
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First of all find out genes and proteins involved in diabetes. Then download 3d structures pf those proteins which are involve in diabetes. Dock your plants compounds with those proteins in any docking saoftware you can also use online docking servers. Analuze docking results in discovery studio 
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A joint call for research project proposals between Portugal and Algerian scientists / researchers is now available, and invite all local scientists / researchers wishing to participate, to submit their proposals.
The coordination of the program’s activities and its piloting is placed under the responsibility of two focal points: Thematic Agency of Research in Sciences and Technology for the Algerian part and Foundation for Science and Technology for the Portuguese part.
I'm interested to develop a mutual project in the domainof oncology.
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What about including a Belgian guy in your (hopefully wining) team?
I have (and still being) already successfully collaborating with Portugal (see the attached articles) ...
I have (and still being) already successfully collaborating with countries "more or less" in fact "not so far" from Algeria (see the attached articles).
I am eagerly waiting to successfuly enter with a fruitfull Algerian collaboration!
Best regards
Robert
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I have isolated a saponin that is soluble in D2O (~20 mg) but not other solvents. However, no resonances are obtained in two different 400 MHz NMR machines. I only got the solvent resonance! Do I need to change or adjust some parameters in the acquisition setup? 
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Dear Natarajan, the compound looks pure by TLC. I am pretty sure that I have used D2O. Thanks 
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Currently, I am developing a short project to know more about natural products molecules and chemical space of these molecules in order to identify potential drug substances used as research tools for chemoinformatic analysis and systemac review/meta-analysis. Thank you in advance!
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Dear Juan,
I have some expertise with natural products effects one animal models. If you still looking for colaboratos I'm interested.
regards
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I am engineering polyketide synthase III to generate unnatural (novel) Polyketides products.  I would like to test its cytotoxicity. Is there any PKS-III novel product use for cytotoxicity assay (or any other bio-assay)?
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Dear Leonardo,
Thanks much for your information.
I am looking for some Polyketides III products that has cytotoxicity  or any other biological function.
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Dear All,
We have tried some essential oil in some of our solid dosage forms as a natural ingredient. But on analysis, content of essential oil is decreasing significantly.
We have adsorbed essential oil onto Sio2 then added to the compression mix to formulate tablets.
Open for Suggestions please?
Thanks for your time.
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Many essential oils are volatile even at room temperatures. Thermal degradation and loss of low boiling components in known in several essential oils. You may contact Essential Oil Association of India with a large number of manufacturers for sharing their practical experiences.
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How do i determine cytotoxic effect of an extracted compound against human cancer lines?
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Dear Aliyu,
You might be assisted with the following publication for the determination of the cytotoxicity effect of the endophytes you isolated from roots of plants:
Important Paper: (see attached file)
Antonie Van Leeuwenhoek. 2015; 108(2): 267–289.
Published online 2015 Jun 21. doi:  10.1007/s10482-015-0502-7
PMCID: PMC4491368
Endophytic actinobacteria of medicinal plants: diversity and bioactivity
Patrycja Golinska, Magdalena Wypij, Gauravi Agarkar, Dnyaneshwar Rathod, Hanna Dahm, and Mahendra Rai
Author information ► Article notes ► Copyright and License information ►
 
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Abstract
Endophytes are the microorganisms that exist inside the plant tissues without having any negative impact on the host plant. Medicinal plants constitute the huge diversity of endophytic actinobacteria of economical importance. These microbes have huge potential to synthesis of numerous novel compounds that can be exploited in pharmaceutical, agricultural and other industries. It is of prime importance to focus the present research on practical utilization of this microbial group in order to find out the solutions to the problems related to health, environment and agriculture. An extensive characterization of diverse population of endophytic actinobacteria associated with medicinal plants can provide a greater insight into the plant-endophyte interactions and evolution of mutualism. In the present review, we have discussed the diversity of endophytic actinobacteria of from medicinal plants their multiple bioactivities.
Keywords: Actinobacteria, Antimicrobial activity, Bioactive compounds, Endophytes, Medicinal plants
1- Pharm Biol. 2012 Nov;50(11):1416-22. doi: 10.3109/13880209.2012.682118. Epub 2012 Sep 11.
Cytotoxicity effects of various Juglans regia (walnut) leaf extracts in human cancer cell lines.
Salimi M1, Majd A, Sepahdar Z, Azadmanesh K, Irian S, Ardestaniyan MH, Hedayati MH, Rastkari N.
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Abstract
CONTEXT:
Currently, natural products have been shown to present interesting biological and pharmacological activities and are used as chemotherapeutic agents. Plants have historically been used in treating cancer and are recognized for their ability to produce secondary metabolites. Juglans regia L. (Juglandaceae) has medicinal applications to treat a wide range of diseases such as cancer.
OBJECTIVE:
The current study was designed to evaluate the antiproliferative activity of total extract as well as several fractions from the leaves of J. regia.The total phenolics, flavonoids, and condensed tannins content of these extracts were also determined to obtain further information on the correlation between the contents of phenolic compounds and antiproliferative effects as well as the leaf developmental stages.
MATERIALS AND METHODS:
Antiproliferative activity was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and flow cytometry methods against human oral cancer, breast adenocarcinoma and colon adenocarcinoma cell lines. The total phenolics, flavonoids, and condensed tannins were determined by Folin-Ciocalteu, aluminum chloride and butanol-HCl colorimetric methods.
RESULTS:
Our present study has shown that chloroform fraction has the lowest IC(50) values (0.36-0.81 mg/mL) and also induces cell cycle arrest (G0\G1 phase) after a 24 h treatment. The colorimetric methods showed the highest amount of total phenolics, flavonoids, and condensed tannins in the methanol fraction (120.28 ± 2.32, 59.44 ± 0.87, 227.00 ± 4.91 mg/g of dry weight of extract).
DISCUSSION AND CONCLUSION:
The results obtained herein indicate that walnut chloroform fraction may contain effective compounds which can be used as a chemotherapeutic agent.
2-Springerplus. 2015; 4: 127. (see attached file).
Published online 2015 Mar 14. doi:  10.1186/s40064-015-0871-4
PMCID: PMC4374083
Anticancer effect of black tea extract in human cancer cell lines
Katarína Koňariková, Miriam Ježovičová, Ján Keresteš, Helena Gbelcová, Zdeňka Ďuračková, and Ingrid Žitňanová
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Abstract
In this study we investigated effects of natural extract from the black tea Camellia sinensis (BTE) against human colon carcinoma cell line HT-29, human breast carcinoma cell line MCF-7, human alveolar carcinoma cell line A549 and healthy cell line NIH-3T3. We identified concentration range for cytotoxic/antiproliferative effects using MTT assay and the trypan blue assay, gel electrophoresis we employed to determine the type of cell death induced by BTE and DNA damage we determined by comet assay. Different concentrations of the extract (0.00078 - 5 μg/mL) we added to the cultured cells and incubated for 216 h. BTE showed cytotoxic effects against all carcinoma cell lines, however HT-29 and MCF-7 cells were more sensitive than A549. BTE showed no antiproliferative effect against healthy cells NIH-3T3 at tested concentrations. We found no apoptotic cell death in HT-29 and MCF-7 cells after 72 h of incubation in case of single administration of BTE but in case of repetitive administration of BTE (BTE was added to the cells each day) we found apoptotic cell death in HT-29 after 72 h incubation. BTE induced also DNA strand breaks and oxidative damage to DNA in carcinoma cells HT-29 and MCF-7.
Keywords: Camellia sinensis, Black tea, Cancer, Protective effect, Apoptosis
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Introduction
Black tea has a long history of use dating back to China approximately 5,000 years ago. It is made from the dried leaves of Camellia sinensis, a perennial evergreen shrub formerly known as Thea sinensis. It is native to southeastern Asia. Green tea, black tea, and oolong tea are all derived from the same plant. Black tea results from the oxidation of Camellia sinensis leaves. The chemical components in tea include alkaloids (theobromine, caffeine, theophylline), polyphenols, amino acids, polysaccharides, volatile acids, vitamins, lipids as well as inorganic elements (Liang et al. 2013; Xiaorong et al. 2015; Scoparo et al. 2014). Black tea is used for treating headaches, low blood pressure, preventing heart disease, including atherosclerosis and heart attack, preventing Parkinson’s disease, reducing the risk of stomach and colon cancer, lung, ovarian and breast cancers (Lee and Foo 2013). The aim of our study was to evaluate the potential anticancerogenic effect of the black tea extract (BTE) on different types of carcinoma cell lines.
3- Phytomedicine. 2015 Jan 15;22(1):1-4. doi: 10.1016/j.phymed.2014.09.008. Epub 2014 Oct 22.
Cytotoxic effects of stem bark extracts and pure compounds from Margaritaria discoidea on human ovarian cancer cell lines.
Johnson-Ajinwo OR1, Richardson A1, Li WW2.
Author information
 
Abstract
Margaritaria discoidea (Baill.) G. L. Webster (Euphorbiaceae) is a well-known medicinal plant in Africa used for the treatment of various diseases. So far, no cytotoxic effects of plant extracts on cancer cell lines have been reported.
AIM OF THE STUDY:
To evaluate the cytotoxicity against human ovarian cancer cells of extracts of M. discoidea and characterize the major bioactive compounds.
METHODS:
Both organic and aqueous extracts of this plant were obtained by maceration. The sulforhodamine B cell proliferation assay was used for evaluation of their cytotoxic activities and the potential bioactive compounds were characterized by gas chromatography-mass spectrometry.
RESULTS:
The organic extract of M. discoidea showed stronger cytotoxicity than the aqueous extract with IC50 values of 14.4±3.0, 14.2±1.2 and 34.7±0.5µg/ml on OVCAR-8, A2780 and cisplatin-resistant A2780cis ovarian cancer cells, respectively. The organic extract was further subjected to bioassay-guided fractionation by partitioning with n-hexane, ethyl acetate, and n-butanol in water. The ethyl acetate fraction was the most potent on the three ovarian cancer cell lines. A GC-MS analysis of trimethylsilyl derivatives of this fraction indicated the presence of phenolic compounds such as gallic acid and the alkaloid securinine. The IC50 values of these two compounds were determined to be in the range of 3-16µM, which indicated that they could contribute to the cytotoxic activity of the extract of M. discoidea.
CONCLUSIONS:
This study has evaluated the cytotoxicity of stem bark extracts of M. discoidea against ovarian cancer cells and provided a basis of further development of this plant for the treatment of ovarian cancer.
Copyright © 2014 Elsevier GmbH. All rights reserved.
KEYWORDS:
GC–MS; Gallic acid; Margaritaria discoidea; Ovarian cancer; Securinine
4-Nutrients 2015, 7, 2707-2718; doi:10.3390/nu7042707 (see attached file)
nutrients
ISSN 2072-6643
Article
Cytotoxic Activity of Piper cubeba Extract in Breast Cancer
Cell Lines
Potchanapond Graidist 1,2,
*, Mananya Martla 1 and Yaowapa Sukpondma 3
Abstract: This study aimed to evaluate the cytotoxicity of a crude extract of Piper cubeba against normal and breast cancer cell lines. To prepare the extract, P. cubeba seeds were ground, soaked in methanol and dichloromethane and isolated by column chromatography. Fractions were tested for cytotoxicity effects on normal fibroblast (L929), normal breast (MCF-12A) and breast cancer cell lines (MCF-7, MDA-MB-468 and MDA-MB-231). The most effective fraction was selected for DNA fragmentation assay to detect apoptotic activity. The results showed that the methanolic crude extract had a higher cytotoxic activity against MDA-MB-468 and MCF-7 than a dichloromethane crude extract. Then, the methanolic crude extract was separated into six fractions, designated A to F. Fraction C was highly
active against breast cancer cell lines with an IC50 value less than 4 μg/mL. Therefore, Fraction C was further separated into seven fractions, CA to CG. The 1
H-NMR profile showed that Fraction CE was long chain hydrocarbons. Moreover, Fraction CE demonstrated the highest activity against MCF-7 cells with an IC50 value of 2.69 ± 0.09 μg/mL and lower cytotoxicity against normal fibroblast L929 cells with an IC50 value of 4.17 ± 0.77 μg/mL. Finally, DNA fragmentation with a ladder pattern characteristic of apoptosis was observed in MCF-7, MDA-MB-468, MDA-MB-231 and L929 cells, but not in MCF-12A cells.
Hoping this will be helpful,
Rafik
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I would like to do a study in vitro to evaluate any antioxidant activities to protect cells but I do not know if there is any study for the dilution for these extracts in order then to study them, or if anyone did a similar sttudy can suggest to me any protocol..the extracts are : oil obtained after SF-CO2, Aceton, Methanol and water in order.
Thanks a lot
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Hi Husseen, I have published a number of papers investigating the antioxidant activity of seaweed extracts. Try diluting the extracts in water or 1% DMSO. Next you need to determine the possible toxicity of the extracts using the MTT and neutral red assay. These assays will give you the maximum concentration of extract that can be safely used in the cells. Have a look at my attached paper
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Have Done UV, FTIR, HPLC (Qualitative without any standard), LC-Q-TOF-MS, 1H NMR. But dont know how to interpret anything. Is these analysis are enough to find out the compounds with their structures? If not, Kindly suggest me what analysis and all should I do? Its ethanolic extract soluble in methanol and chloroform. 
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I think you should proceed with preparative HPLC both polar and nonpolar column. Collect each fraction. Do the bio-assay invitro first then invio. Identify the mass spectra by LCMS for polar and GCMS profiling for Non-polar volatile compounds. Then you will get preliminary idea about  phytochemicals. Do esterification for non-volatile. Then do the analysis of desired sample like  FTIR, H NMR, C NMR. You will elucidate possible structure with bio-activity.
Best Luck.
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Curcuma amada represents a major source of valuable drugs, pigments and phytochemicals, the major chemical components of Amada include phenolic acids, volatile oils, starch, curcuminoids and terpenoids. I am searching for the pure compound Amadaldehyde for UV vis study. Could anyone help and give me suggestions regarding availability of Standard Amadaldehyde.
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Dear Dr. Sarma,
I have not been able to find a source for pure amadaldehyde. I do not think Extrasynthese has one for sale. I have enclosed the reference to the article that describes in detail the sequential extraction, and the identification of the structure of amadaldehyde by UV, IR, 1H and 13C NMR, and MS. It list all the experimental details, spectral data, including the UV max. You might want to contact the authors to see if they could share a pure sample with you. Best wishes in your research!
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I am working on centella asiatica and I want to know what ascension means especially in Malaysian strains.
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Hi Wasiu, YES, location can have profound impact on the metabolites a plant produces. Think simply tomatoes - depending where they grow they will have a different taste. In case of medicinal plants like Centella location is highly important. Many traditional medicinal systems recognize this and often give the same species different vernacular names depending on where the plant grows. Also, healers often go to great lengths to collect always from the same locations, to make sure that they get plants with consistent properties. This is also where harvest time comes in. Many plants change their compound composition during the seasons, and only show efficacy part of the time. Last, the location is an important aspect of climate change - when plants migrate their compound composition might also change, which could make them more or less efficacious, and/or more or less toxic.
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The bacterial strain I was working on showed activity. I ran out of crude so I cultured a new batch and this one showed no activity. I'm hoping there was no human error involved. Any ideas on what may have caused this?
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sometimes the secondary metabolism changes when you repeat the cultivation of the bacteria as it's highly affected with any small change in culturing condition. So, you should compare the chemical profiles of both extracts to figure out what were the metabolites responsible for the activity.
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I need some procedures how to get alkaloid from plant extraction (rich alcaloid extraction), especially tetrandrine alcaloid.
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in addition you can also see.Tetrandrine and related bis-benzylisoquinoline alkaloids
from medicinal herbs: cardiovascular effects
and mechanisms of action.ht tp:/ /www.Chi naPhar.com
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I extracted fungal extract (extra cellular ) with ethyl acetate . I want to do some bioassays for this.Now I want to check cytotoxic effect of this extract. which assay will be effective for crude extract?  how is brine shrimp lethality assay?....do I need to dissolve extract in new solvent or ethyl acetate is ok?
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Dear colleague, we have done a lot of Brine Shrimp assays over the years, and there are a couple of problems to consider:
1. Most importantly, make sure your brine shrimp are actually hatched in seawater.  Many protocols simply indicate that you can make your own saltwater solution (e.g. using (NaCl), but this does not work well. Brine Shrimp in a regular salt solution are normally weakened, and die quickly even if you do not add an extract. The only way to be sure your Brine Shrimp die from your extract is using real (sterilized) seawater or a solution prepared based on seawater.
2. You need to either remove any solvent and dissolve your extract in the same solution the Brine Shrimp are hatched in, or run a pre-assay with in your case ethyl acetate, which will kill Brine Shrimp on itself, to determine lethality without your extract. However. it would be much better to remove the solvent and reconstitute in saltwater.
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I am investigating the hepatoprotective effect of some medicinal plant on chronic carbon tetrachloride induced liver injury. I observed that although some of the medicinal plants increased the antioxidant enzyme (SOD, CAT and GSH) level in rats co-exposed to CCl4 and the extracts while they also increased lipid peroxidation and markers of hepatic injury such as ALT and AST.Has anyone experienced something similar? If yes, what are the likely reasons why this happened?
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Dear Ifeoluwa T Oyeyemi
I am attaching literature on the anticancer properties. I hope they will be useful to you.
I recommend the fruit of Rhus coriaria L. (Anacardiaceae) for your research.
Good luck.
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I want to see the insulin secreting action of the crude plants extract over cell line as well as consumption of glucose by the cell lines.
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Dear Nrip Kishore Pankaj
Here I attach the list of different cell lines. It might be useful for you. Please find the attachment  and refer page number 11 of this Doc file where you find different cell lines which are responsive to insulin, hydrocortisone and dexamethasone  etc . I f you find it suitable for your resarch protocol than contact with NCCS Pune for placing order for these particular cell lines.  
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for example: DDMP or β-D-glucopyranose which can refer to Ginsenoside Rd or Ginsenoside F2 (two plant saponin)
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Saponins are non volatile compounds, so you can't use GC- MS to determine them, you should use HPLC- MS.
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oleanolic acid has Different types such as oleanolic acid glucuronic, oleanolic acid glycosides and free oleanolic acid. How can measure different types of acid? And how can we distinguish them?
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I think the alternative should be GC-MS after derivatization if necessary. It's a very useful technique for both determination and quantification.
HPLC-DAD could be also used but less sensible and less accurate for isomer identification. LC-MC techniques could afford sensibility but the problem for separation could not be solved. At least, you should consider UHPLC-MS/MS techniques for both sensibility and efficiency for structural identification.
The good choice will depend on several considerations such as quantity of available material, techniques availability, needed acuracy, etc...
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Please help me to find research papers published recently taked in consideration plants family Agavaceae and their anticancer activity.
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You have to view following on Researchgate .
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we want to use it for soft gel encapsulation.
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As per my knowledge, this is the only way.  If any other method is there, I don't know.. 
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I have 10 MDR isolates (five each of gram positive and gram negative bacteria) including metallo beta lactamase producer isolated from clinical samples and I want to test antimicrobial effect of plant extract against these organism. So could anybody suggest me in using ATCC culture that can be used as standard. 
( I have  ATCC culture that can be used for media testing but need name of ATCC that should be used in testing antimicrobial compounds against MDR organisms) 
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S.aureus NCTC6571, Ps. aeruginosa NCTC10662, A. baumannii
ATCC19606 and E.coli NCTC10418. Please check your email.
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Would you please express your valuable comments about this study in order to improve our project. We are going to investigate the effects of some Iran's medicinal plants and its phytochemical compounds on cell cytotoxicity and discovering new anticancer drugs.
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You should use cancer cells and non-malignant cells, and evaluate if your compounds improve the selectivity of the standard anticancer drugs. The following articles describe a simple protocol:
A simple and reliable approach for assessing anticancer activity in vitro (Curr Med Chem. 2015;22(11):1324-34).
Two preclinical tests to evaluate anticancer activity and to help validate drug candidates for clinical trials (Oncoscience. 2015 Feb 20;2(2):91-8)
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In traditional methods we can see some plant latex in drugs.
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The blood red latex of sangre de drago (Croton lechleri) continues to be used in traditional healing in South America. A proanthocyanidin derivative of the latex recently became the first botanical drug (Fulyzaq) allowed for prescription in the U.S. As for an ecological role, when the smooth outer bark is cut, the latex that exudes from the tree serves to seal and protect the wound. In Peru, indigenous peoples use the latex for the same purpose of healing skin wounds.
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For in vivo tests on mice, the test compound is insoluble in water, although it is soluble in DMSO (dimethyl sulfoxide) which has reported toxic effects and side-effects. It has been advised to use 0.25% CMC (carboxymethylcellulose), 20% peg (polyethylene glycol) or tween 80, 50% propylene glycol and 30 % deionised water.
But how much qty of each of the above given solvents should be taken and
are there any other preferable non-toxic solvents?
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Hi Ravi, normally you have to know a minimum on your test drug. What kind of reactive function, type of molecules etc..you have on your drug formula to target the best solvent. Sometimes you need to esterify to make water soluble if you have acidic function; sometimes iol preparation are useful for lipylic substance etc...as more or less indicated by other contributors before me
You have to know that except water (and be careful even with water if you use injectable water and not serum physiologic because you can have side effect due to local hemolytic chock!) , all solvent present a risk of toxicity or side effect (more or less but real!) and it is often important to know them and to control and test them adside your drug.
Depending of the experiment you have to do and if your local rules allow it), you can use DMSO. By example, if you have just to test biological effect to make a sceening, you could use DMSO one time without any deleterious effect on animals (be careful for human manipulator who have a risk by manipulating a lot of animals and use adapted gloves and air aspiration to let animals because DMSO pass in the lung and is expired in air rapidly!). To minimize DMSO dosage, you can test subsequent dilution by water or alcool.: i.e.You induce solubilization in DMSO then you can often continue with other solvent less toxic. Always think to have an administration test of DMSO (or of the solve nt you think to use finally) alone in case of possible side effect on the function you need to observe.
Nevertheless, if you need to do repeated test on the same animal, yes, it will be preferable to change for another solvent.
Good luck Ravi
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I am working with four different species of plant to find their anti-ulcerant activity. i have found one species is very potent. Now I need to identify the chemical group that might be causing this activity. But I have only two weeks to submit this paper. Please somebody show me a short way.
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I think you can do fractional extraction by using from non polar  to semi polar solvent (e.g. hexane, CH2Cl2, Acetone, Methanol). Test each of  the  fraction for its activity, than fraction that have activity can be further  analyzed using GC-MS or LC-MS or LC-NMR. Identity of the compounds can be predicted by using some on line date base (e.g. Metlin or NIST etc.).
Good luck.
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I prepared crude saponins using the following protocol: heat 5g of plant extract in 30 ml of 20% methanol in 4 hrs in a water bath to reduce volume to 15 mls. I added 20 mls diethyl ether to separate organic portion from the aqueous. The organic portion was discarded. I added 15ml butanol to the methanolic fraction to obtain 30ml methanol/n-butanol fraction. The latter was washed with 50 ml 5% Nacl solution and the the aqueous fraction discarded. The methanol/n-butanol fraction obtained was washed for the second time with another 50ml of 5% Nacl and there was  no separation into methanol/n-butanol fraction and aqueous fraction. I therefore evaporated both mixture of methanol/n-butanol fraction and aqueous solution to dryness to obtain a crystalline soapy extract. Is my protocol right? What have done wrong here?  somebody help me!
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I work with ginseng saponins and ultrasonication based extraction with 100% methanol works the best in my case, even though 70% methanolic solutions are just as fine.You may try extraction using a particular methanolic solution apt for you. Try partitioning with di-ethyl ether using an aqueous phase rather than the methanolic solution. After removal of organic layer, you may try water saturated butanol for partitioning. The butanolic extract may be evaporated in vaccuum to obtain a crude saponin mixture.   
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I have put 16000 ligands on Discovery Studio for virtual Screening.
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ITS DEPEND UPON YOUR SERVER AND SYSTEM USED. USUALLY ITS TAKE  TWO WEEK AT SERVER .
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While rotary evaporating plant extract(80% Ethanol) my sample boils. I am very worried that this boiling can affect the properties of my extract? I reduce the pressure very slowly but the problem occurs i would be more than grateful if anyone could help me regarding this issue
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If 40 °C in the water bath of the rotary evaporator is not a danger for your compounds (usually it is not) then the rest ist physics. The effect may be caused by saponins, that cause foaming. With a standard membrane pump going down to ca. 10 mbar  even the removal of water should not be a problem at all.
A practical hint for foaming solutions is to concentrate them in a rather LARGE flask, e.g. then you use a 2 L flask for 500 ml solution, i.e. a rather "empty" flask instead of a up to 50% filled one.
Note: Freeze-drying is only a good idea for purely aqueous solutions without any organic liquids, hence: for 80% ethanol and 20% water ist is not to recommend.
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The sources of drug discoveries has been a synthetic chemical pools and the natural resources including microbes, proteins, plants and animals. The worms especially the intestinal helminths has been neglected and I am wondering if anyone has any experience in this area including isolation, characterisation and biological activies-protocols and findings would be appreciated?
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Thank you all for your comments. Prof Russell, how have you been doing? I saw one of your paper on insect fungi. I have made a request and would appreciate if you could also give a link to related works of yours.  Thank you.
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D-limonene is in many essential oils and has many biological function. In many cases D-limonene conent in the essential oil correlates with biological functions. For drug development, it is important to ensure high content of D-limonene in an essential oil.
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Dear Dr. Ping,
Normally scientists followed seasonal variations to see the highest yield or percent of specific constituent in essential oils. Some times it helped to get highest percentage of specific constituents. Otherway, you need to develop a high yielding variety ( through genetic engening techniques-firstly identified a specific gene which helps to produce specific compound in plants) which produce maximum percent of your desire compound (In this case D-limonene). This is extensively hard and also time consuming. But you can try. Best of luck.
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I am isolating compounds from plant. i have got 2 types of crystals,one is needle like and another cubic in shape in a vial. now from here how can i separate them? any technique??
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Good thing is you good crystals. Looks like you have sorted out by shapes. You can do X-Ray crystallography for both the crystals and see if they are same or different compounds. If you don't have that, you can run through GCMS to see if they have same masses. If you don't have GCMS/GC, reduce the volume you have obtained in excess MeOH or separately dissolve in CHCl3/MeOH (1:1) mixture and run the TLC. Even if it is isomers or enantiomers, if you re-run the sample TLC plate-twice, it should separate if they are different compound.
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Please assist I am working in this area
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Dear Kibonde,
I prepared new article about conservation framework especially for forest ecosystems. Because is not easy questin. We must specified the concrete species and know management of all ecosystems. I can send you my article, but huge part is in czech language. But I think you can find there some information in english too. After printing I send you this article.
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I am doing reducing power assay of plant extracts. but after centrifuge of  3000 rpm as per suggested by all protocols that take upper part of layer, 
but i am not getting any layer formation in this case. 
If any body has done this experiment please give me your suggestion.
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i know this, paper but my problem why there is not any layer formation.
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Anti  cancer study in wistar rats after chemically inducing tumour with DMBA.
I was planning for an anti cancer study of my plant extracts with hydro ethanolic solvent(1:1), but i couldnt find any reference with mixed solvents. All the studies were those of pure solvents. Is there any technical error or something with this type of study?
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With my experience, I can say that It is better to consider this situation:
Plant extract should always be prepared in different/desired solvent(s)-extraction medium- separately for getting the targetted compound classes.
For good extraction use different dilution 10%, 20% 50% 70% 90% 100% in case of water soluble solvents separately, then freeze dry the extract to get concentrated extract/powder form
@Anu
Why not you do do study this
1. Plant extracts prepared using  individual solvents and 
2. Plant extracts prepared using mixture of solvents
And then do LCMSMS or NMR spectral analysis to see what you get in each situation and what you loose-qualitatively and quantitatively- when mixture is used
Explore nanoparticles encapsulation in case of non-water soluble residues for targeted delivary of the compound at the site
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Pinus gerardiana  is plant which contains very delicious seeds locally called Chilgoza/ Shangthi/Rhe in Kinnaur district of Himachal Pradesh INDIA. The price of this seed is very high (600 to 1000 rupees per Kg ). I want to know that is there any medicinal property this  plant contains  ? 
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Seeds of Chilgoja Pine (Pinus gerardiana) occurring in western Himalayas are one of the calorie-rich edible nuts. They comprise of numerous health promoting phyto-chemicals, vitamins, antioxidants, and minerals. Medically seeds are regarded as energetic, carminative, expectorant, anodyne and stimulant. Oil from the seeds is used as a dressing on wounds and ulcers, It is also used externally in the treatment of head diseases. Like all other Pine trees, the turpentine obtained from the resin is antiseptic, diuretic, rubefacient and vermifuge. It is a valuable remedy used internally in the treatment of kidney and bladder complaints and is used both internally and as a rub and steam bath in the treatment of rheumatic affections. It is also very beneficial to the respiratory system and so is useful in treating diseases of the mucous membranes and respiratory complaints such as coughs, colds, influenza and TB. Externally it is a very beneficial treatment for a variety of skin complaints, wounds, sores, burns, boils etc and is used in the form of liniment plasters, poultices, herbal steam baths and inhalers. According to Ayurveda it is sweet in taste, heavy in digestion, nutrient, tonic and aphrodisiac. It reduces Vata and elevates Pitta and Kapha humors. It is useful in chronic arthritis along with honey. Indeed, the nuts, especially rich in mono-unsaturated fatty acids like oleic acid (18:1 undifferentiated fat) that helps to lower LDL or “bad cholesterol” and increases HDL or “good-cholesterol” in the blood. Research studies suggest that Mediterranean diet, which contains good amounts of monounsaturated fatty acids, vitamins and antioxidants, helps to prevent coronary artery disease and strokes by favoring healthy blood lipid profile. Pine nuts contain essential fatty acid (ω-6 fat), pinolenic acid. Recent research has shown its potential use in weight loss by curbing the appetite. Pinolenic acid triggers the release of hunger-suppressant enzymes cholecystokinin and glucagon-like peptide-1 (GLP-1) in the gut. In addition, pinolenic acid was thought to have LDL-lowering properties by enhancing hepatic LDL uptake. Like almonds, pines are an excellent source of vitamin E; contain about 9.33 mg per 100 g (about 62% of RDA). Vitamin E is a powerful lipid soluble antioxidant, required for maintaining the integrity of cell membrane of mucus membranes and skin by protecting it from harmful oxygen-free radicals. Pine nuts are an excellent source of B-complex group of vitamins such as thiamin, riboflavin, niacin, pantothenic acid, vitamin B-6 (pyridoxine) and folates. These vitamins work as co-factors for enzymes in cellular substrate metabolism inside the human body. Furthermore, pine nuts contain healthy amounts of essential minerals like manganese, potassium, calcium, iron, magnesium, zinc and selenium. Pines are one of the richest sources of manganese which is an all-important co-factor for antioxidant enzyme, superoxide dismutase.
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I am searching for that protocol that clearly distinguish those plant extracts having beta lactamase inhibitory component not just having antibiotic property. I have performed iodometric assay and now I am looking for agar cup assay for confirmation of positive ones.
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Nitrocefin is a chromogenic substrate for beta-lactamases. It turns red upon hydrolysis
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I am doing project based on the study of antimicrobial properties of different plant extracts (leaves and bark) in different solvent like ethanol,aqueous,petroleum ether and chloroform : methanol.I had Lyophilized my aqueous plant extract but they are in somewhat sticky form and rest of the extract had been dried using water bath.There is a problem regarding addition of DMSO amount (mg/ml) which need to be added for the preservation.There is also variation in weight of of different dried extract.Can anyone tell me about the amount and concentration of DMSO (mg/ml) for the preservation.
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DMSO is an excellent solvent when working on human or animal cells.  The main problem is that it is practically impossible to remove the DMSO due to its very high  boiling point (189 C) to regain your sample.  
For antimicrobial work acetone is a much better solvent.  It is very easy to remove the solvent from a solution, it is less toxic that ethanol to humans, it mixes with water and non-polar solvents like hexane and it is less toxic than other solvents to five fungi.  The percentage that fungi can withstand are:  acetone 51%, DMSO 45%, methanol 32% and ethanol 30%. (Eloff, JN et al. 2007, Resistance of animal fungal pathogens to solvents used in bioassays. South African Journal of Botany 73, 667-669).  See also  (ELOFF, J N 1998 Which extractant should be used for the screening and isolation of antimicrobial components from plants? Journal of Ethnopharmacology 60, 1-8)
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In aromatic plants' literature both these terms have been used to express the recovery of essential oil (as a percentage) from fresh or dry biomass of aromatic plants. In field experiments agronomists, soil scientists and plant breeders have expressed the essential oil yield (kg or lit per hectare or acre) by multiplying the biomass yield/ha or ac with essential oil content and density/specific gravity of the oil. Any suggestions or remarks?
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I find the discuccion somewhat hairsplitting. Yield is always what you can isolate from the material by various methods (water distillation, extraction for essentila oil compounds) and what you finally have in your hand; the yield for essential oils is normally given as mL/100 g (dry or fresh material).Because the different methods result in different yields, every information on a yield should be accompanied by the method used (e.g.: 5 mL/100 g dry material by watersteam distillation).
Content is the real content of (here) an essentuial oil of the relative plant (part). Often it is not possible to isolate all volative compounds from the plant material (for several reasons, most morphological reasons). Then you may calculate the real content on the basis of moprhological/microscopical characters such as the seize and number of glands, or excretion reservoirs. Also if you use dried plant material, a certain part of the volatiles may alredady be disappeared by evaporation. You may conclude from this information that the real content of any essential oil of a plant/plant part cannot easily be determined.
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kindly provide the detail methods used for the isolation of essential oil from fresh and dried plant tissue.
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Although steam distillation is the most well-known technique for extracting essential oil from plants, there are several other methods that are used to remove and concentrate the aromatic constituents from plant materials. Here is a brief description of each method and their influence on the aromatherapeutic properties and fragrance of the oil. The attached file may provide you further details:-
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We have  some isolated compounds from a medicinal plant.
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This is a review article illustrating several techniques for the in vitro assay of antioxidant activity with the advantages and  disadvantages of each.
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Extraction by means of pressing, heating, solving in solvents etc, which one has best efficiency? 
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I also agree that the method used is determined by the nature and amount of the sample.
I have found hydro-distillation using the Clevenger-type apparatus, a suitable method for extracting essential oils from leaves.
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some essential oils such as Levisticum spp. and eryngium spp. are heavy and we gathered them in the bottom of clevenger apparatus. what are other plants 
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Pandey, do you understand the purpose of ResearchGate? The question was made by Saeid Davazdahemami, not you. Yet when someone contributes an answer, you say  "Thanks & good" (which you have done three times, no less), or "Thanks and Happy New Year". None of us understand how such comments contribute to answering the questioner. You do not need to interject when someone contributes meaningful comments or information to the questioner. 
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Esteemed Colleagues:
I have been working in the field of natural product chemistry and synthetic organic chemistry during the past several years. I welcome extended collaborations with experts in screening/assessing biological/pharmaceutical efficacy of natural products and synthetic chemical entities (mainly heterocycles)  isolated/synthesized in my Lab  against different diseases areas like cancer, microbial infections, malarial, neurodegradative diseases, etc. Besides, I am also keen to work with those working with in silico drug designs and deeply involved in theoretical aspects of molecules (such as molecular dynamics, mechanistic pathways, and molecular docking). I do welcome any suggestions/comments/inquires/proposal from my esteemed colleagues. Best wishes & regards, Goutam (Prof. Dr. Goutam Brahmachari, India)
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Thank you Prof Goutam, we are working on  anxiolytic and antidepressant effect of medicinal plants in my lab. I will like to collaborate with you.My email address is estrarosa@hotmail.com
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Sometimes we have some unsuitable material in biomass of plants. Such as pyrolizidine(alkaloid) in Borage family
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I mean human and also veterinary drugs or food additives containing phytocompounds (plant-derived substances), which are available at the market, and are used against pathogenic bacteria infecting the gut. 
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Numerous  plant metabolite preparations are being produced by pharmacologies as drugs, especially most of the ayurvedic medicines. If you needed the names,the main brands which sell these products in the indian market are Kottakkal arya vaidyasala, Vaidya ratnam, Nagarjuna etc.... please see the links below, which may help you....
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Any info about these constituents in a plant extract? what is their activity: antioxidant, antimicrobial etc....?
2,4-Di-tert-butylphenyl benzoate
6-Monohydroxyflavone
Sterigmatocystin
Actinobolin
Glycitein
Hexestrol
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Dr. Ravi : Is there any reference for this? 
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With an emphasis on the impact of low temperature on sugars and carbohydrates.
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Freezing is probably the best way to store the samples but you should be wary of the impact of thawing. Freezing the sample means that the sample becomes non-homogenous. Usually the last fluid to freeze has the greatest amount of sugar and salt. This is typically in the center of the container. If the entire sample is not melted, you are likely to test liquid that is lower in concentration. But melting the entire sample has its own problems. Once in solution, sugars, especially reducing sugars, can interact with other components in solution. If you freeze your sample but then let it sit on the bench for 3 hours before refreezing it, you may be generating artifacts. The best way to handle this problem is to take your original sample and divide it into aliquots and freeze all the separate aliquots. That way you can ensure that there are no freeze-thaw artifacts in a sample because you will use each sample only once.
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How to be determination of bioactive compounds in aromatic plants ?
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Try with a MSMS analysis. This could indicate what molecules (protein) there are in the extract.
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I am looking for antioxidants activity in some  essential oils.If some one can answer my questions ,it would be grate help for us.
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 Ferric Reducing Antioxidant Potential Assay (FRAP Assay)
The antioxidant capacity was determined following the procedure described by Benzie and Strain [4] with modifications.
The FRAP reagent was freshly prepared by adding 10 mM of 2,4,6-Tris (2-pyridyl)-1,3,5-triazine (TPTZ) (dissolved in 40 mM of HCl), 20 mM of FeCl3 in water and 300 mM of acetate buffer (pH 3.6) in the ratio of 1:1:10. A blank containing sample and solvents only was used for colour correction. The 96-well plates were then incubated at 37˚C for 90 minutes before absorbance was recorded at 600 nm. Vitamin C (L-ascorbic acid), gallic acid and quercetin were used as antioxidant standards and positive controls. The absorbance of the samples were compared to a FeSO4 standard curve and the FRAP values were expressed as Ferrous Equivalent (FE), the concentration of extract or chemical which gives the same absorbance as 1 mmol ferrous ion.
Please go through it following paper which will be useful for your work.
Ferric reducing antioxidant power of essential oils extracted from
Eucalyptus and Curcuma species
Durre Shahwar1*, Muhammad Asam Raza1,2, Sana Bukhariand Gulshan Bukhari3 , Asian Pacific Journal of Tropical Biomedicine (2012) , 1633-1636
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Please only share the published facts (reviews and chapters etc.)
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Here i have enclosed articles for your concern.
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I´m working with hexane:ethyl acetate (7:3) and I have two yellow bands Rf 0,8 and Rf 0,5 but I need a standard.
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Rf value is unique for every solvent system. It can also vary depending upon number of conditions. Its good to purchase standards and try to find out Rf value.    
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Is it important to find out a novel marker, whether it be a phytochemical or a biological, from a herb while working on it? Or the concept of bioactive fraction is more precise in the present context.
In most of the cases, people isolate previously isolated markers from the plant and again report them as confirmation of previous findings. Is it not better to work on some new ideas like fractions rather than markers and relying on them?
As of now, which is more acceptable in scientific community considering the problems that accrue during isolation studies?
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Actually working with standardized bioactive fraction is most appreciated, as it works by multifaceted of action. But many times in bio activity guided fractionation we get pure compound for which activity is governed. Although compound is knowing in other species also and used for some other function. But many times we get new molecule. As we all know just like animal, plant also synthesized basic metabolites of their own importance, which is varies chemotaxonomically between species to species and genus to genus. This creates ambiguity in production of novel marker.
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I am looking for a AChE enzyme inhibitory assay protocol, to be performed in a 96 well micro plate. The AChE enzyme source I'm using is electric eel. If someone knows of a detailed assay protocol with the enzyme concentration please let me know.
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Thanks Lingesh! I did refer this paper.
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Other properties are esteric property and hydrogen bond.
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hi ithis papaer may helpful to you
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I'm seeking published articles which declare marine resources as an anti-urolithiatic agents.
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The Protection of Polysaccharide from the Brown Seaweed Sargassum graminifolium against Ethylene Glycol-Induced Mitochondrial Damage.
Chao-Yan Zhang, Ting-Kong, Wen-Hui Wu and Min-Bo Lan.
Marine Drugs2013, 11, 870-880.
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I want to discover few compounds which can act as inhibitors for a particular protease enzyme. Because random hit and trial assays take a lot of time/money and effort, I want to virtually screen for future inhibitory drug candidates from/among herbal components.
I don't have any knowledge of bioinformatics, but can someone suggest free online software as well as a basic procedure (tutorial) by sharing file/ppt/lecturer?
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ParaDockS (http://www.paradocks.org; see also J Chem Inf Model 2010, 50 (5), pp. 879-89) is another example of freeware suitable for virtual screening approaches.
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I am trying to dock my ligand with some protein that involve in the transportation of cholesterol. But the question is do I need to remove the phospholipid and cholesterol ester in order to dock it?
There is a publication on some ligands mentioning that it acts by displacing the phospholipid and makes cholesterol ester change its conformation. However, I am unsure as to whether this can be proven by molecular modelling since the publication is using crystallography when proving this.
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Aya,
As you mentioned torcetrapib displaces phospholipid, are you expecting ur ligand of interest does the same? If so, you cant study this mechanism in AutoDock. So its better you remove phospholipid while docking.
Reg. cholesterol ester, we cant predict with reliability the conformational changes induced by ligand binding through docking. especially conformational changes induced in other bound ligand.
 
So you can try like:
(a) Find the native stucture of CETP (without bound ligands) and dock your ligand of interest.
(b) Remove the phospholipid and cholesterol ester and perform docking.
(c) Remove the phospholipid ony and retain cholesterol ester then perform docking.
Try to validate docking protocol with torcetrapib also.
Try to understand the conformational changes in protein (unbound and bound state with ligand), I hope there will be substantial difference in key residues.
Try to compare the results and make out the steric hinderance by cholesterol ester. When you compare the results from (a) and (c), you cam come up with significant results.
Once you get the complex from docking, you can carry out molecular dynamics simulations to validate your docking studies.
Obviously, if infrastructure available, Carry out wet lab studies to correlate and justigy your docking studies.
 
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I want to use Soxhlet method for the extraction of different extracts from plant material. but I don't know how long the Soxhlet extraction Should be run for complete extraction of secondary metabolites. I read different paper related to this topic, but different researcher run soxhlet for different periods of time. So, how i can come to know, for how long Soxhlet should be run in order to have complete extraction of compounds from plant material?
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Normally if you count the cycles, then 72 cycles is considered as good criteria for extraction of the soluble constituents. Another simple method to know whether the extraction is complete or not is using a watch glass and collecting the solvent dropping from the extractor. Carefully you can collect few mL of the solvent coming out after extraction. Don't allow it to fall in the round bottom flask. Collect it in a clean watch glass. Allow it to evaporate at room temperature. In another watch glass, take pure solvent being used for extraction. Compare both the watch glasses after drying. If you see a deposit in the former as compared to the latter, your extraction is not yet complete. If both of them are the same, it is an indication that no more extractive will be obtained with the same solvent. It is a sort of indigenous method, might appear a bit hazy but it works and works well. I use it very frequently and results are always accurate.
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One may say it depends on your compound of interest but, in general, which one would be a better choice all together in terms of labour, yield loss, possibility of multi solvent usage?
For example, I am afraid of column chromatography during, overnight auto collection of fractions. What if the auto collector got struck and lose everything? On the other hand, I am afraid of SPE cartridges with possibilities of multi solvent system. What is your opinion?
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Like you mentioned, it depends on your compound. In addition, how pure is the compound? Do you know which compounds you are purifying? In my opinion (please note it is only my opinion!) SPE is better for purifying known compounds that don't have closely eluting impurities, and are good for known compounds. This is why one mostly sees SPE as the clean-up steps for analytical procedures. So if you are purifying a known compound, SPE may work very well for you.
I find column chromatography works better until I know which compound(s) is active in my extract. Once I know which compound I want, I may be able to simplify the purification so an SPE procedure may be more suitable, depending on impurities and how they elute. Once on the SPE cartridge, there is a possibility of solvent savings.
As for over night runs, I find that using one of the automated flash chromatography systems run fast enough that I don't need to do over night runs. They are very well suited for natural products. Alternately, I suspect you might be using one of the "shuttle" type fraction collectors, which i find are prone to jamming. A find a fraction collector that uses an overhead arm tends not to jam, but these require tubing to the fraction collector, where the shuttle fraction collectors can be simply be placed under the column.
As for multi solvent usage, flash chromatography works very well. I use a technique I term "wide polarity range chromatography" for natural products.
Conflict of interest notice: I do work for Teledyne ISCO which makes the items I link to below.
Wide polarity range chromatography:
Automated flash chromatography applications in natural products: