Secondary Metabolites - Science topic

The residue from your ethyl acetate extraction likely contains water or polar compounds, which is why it froze. Consider verifying its composition through methods like TLC or NMR, and you can proceed with freeze-drying to preserve your metabolites while removing water.

Thank you for your reply

by the links of papers Muhammad Iftikhar

Yes, differentiated tissues like shoots and roots from plant tissue cultures can generally produce higher yields of secondary metabolites compared to callus, which is undifferentiated tissue. This difference in metabolite production largely stems from the unique structure and functionality of differentiated cells, which is absent in undifferentiated callus tissue. Here’s a breakdown of why differentiated tissues tend to yield more secondary metabolites:

Due to these factors, culturing differentiated tissues or even using organ cultures (e.g., root or shoot cultures) is often a better strategy for enhancing the yield of secondary metabolites in plant tissue culture setups.

Nail Besli I downloaded my compounds with silver nanoparticles by green synthesis and I don't know yet which the name of the compound yet I deal with an unknown compound

In this case, the organic solvent might be optimized. Hexane, ethyl acetate, dichloromethane, ether...

That's probably as good as you'll get without more detail. Also consider solid phase extraction.

Loss during extraction with ethyl acetate and NaCl can result from:

These adjustments should reduce the loss and improve extraction efficiency.

The choice of solvent for dissolving secondary metabolites extracted from Aspergillus for use on MCF7 cells can depend on the solubility of the metabolites and the intended use. Here's a general guideline for preparing these compounds:

Solvent Selection

This is typical botany field research I think. But I want to do review in isolation of plant secondary metabolites in medicinal plants or family.. can u suggest any topic..

"Sola dosis facit venenum" 'the poison is the dose, not the substance in itself' is universal also for plants.

Marine sediment samples are collected, and bacteria and fungi are isolated using standard microbiological techniques. The isolated strains are cultured in appropriate liquid media, and the biomass is harvested, washed, and freeze-dried. The dried biomass is then extracted using organic solvents like ethyl acetate or methanol, with sonication and overnight incubation. The crude extracts are concentrated under vacuum, transferred to pre-weighed vials, and the solvent is completely evaporated. The extracted secondary metabolites are weighed and stored at -20°C or -80°C for further analysis and characterization.

Identifying the class of phytochemicals and determining which compounds to include in your manuscript after GC-MS and NIST identification involves a systematic approach. Here are the steps to address your queries:

1. Identifying the Class of Phytochemicals

To identify the class of phytochemicals or secondary metabolites, you can follow these steps:

a. Database Searches:

- PlantaeDB and IMPPAT are good starting points. Ensure you are using the correct chemical names and synonyms.

- PubChem and ChemSpider can also be useful for finding information about the chemical structure and its known classes.

b. Literature Search:

- Use databases like Google Scholar, PubMed, and ScienceDirect to search for scientific articles related to the identified compounds. Keywords like "phytochemical class" or "secondary metabolite class" along with the compound name can help.

c. Chemical Structure Analysis:

- Analyze the chemical structure using software tools like ChemDraw or MarvinSketch to predict the class based on known structural features of flavonoids, carotenoids, phenols, etc.

d. Expert Consultation:

- If certain compounds are hard to classify, consider consulting with a phytochemist or a researcher specializing in natural products chemistry.

2. Handling Repeated Compounds

When you have repeated compounds with different retention times and similarity indices, consider the following:

a. Consistency Check:

- Check the consistency of identification across different runs. If the same compound is identified consistently with a high similarity index, it is likely accurate.

b. Retention Time Comparison:

- Retention time differences can sometimes indicate different isomers or derivatives. Compare the retention times and the similarity indices to choose the most reliable identification.

c. Reporting:

- If the similarity index is significantly different, consider reporting both and discussing the possible reasons (isomerism, different sources of the compound within the plant, etc.).

3. Selection of Compounds for the Manuscript

Including all identified compounds versus selecting important ones depends on the focus of your manuscript:

a. Relevance and Impact:

- Include compounds that are known to have significant biological or pharmacological activity relevant to your study.

b. Novelty:

- Highlight compounds that are newly identified or have unique properties not commonly reported.

c. Focused Analysis:

- For a more focused analysis, you can prioritize compounds based on their relative abundance (area percentage), biological significance, and the objectives of your study.

d. Supplementary Data:

- Consider including the complete list of compounds in supplementary materials while discussing the key bioactive compounds in the main text.

Practical Steps:

1. Data Organization:

- Create a comprehensive table of all identified compounds with their retention times, area percentages, molecular formulas, and similarity indices.

2. Class Identification:

- Use a combination of database searches, literature reviews, and chemical structure analysis to classify each compound.

3. Selection Criteria:

- Define clear criteria for selecting compounds (e.g., similarity index threshold, area percentage, known bioactivity).

4. Documentation:

- Clearly document the methods used for identification and classification to ensure reproducibility and transparency.

By following these steps, you can systematically identify the classes of phytochemicals, choose which repeated compounds to include, and decide on the most relevant compounds for your manuscript.

For SEC (size exclusion chromatography), can you use Sephadex LH-20? This can be run in an open column (gravity column).

The production of secondary metabolites in microorganisms is governed by various genetic mechanisms, including regulatory networks, biosynthetic gene clusters (BGCs), and environmental signals. Here's an overview of these mechanisms and how they are exploited in biotechnological applications:

1. Regulatory Networks: Microorganisms regulate the expression of secondary metabolite genes in response to environmental cues via complex regulatory networks involving transcription factors, activators, and repressors.

2. Biosynthetic Gene Clusters (BGCs): Secondary metabolite biosynthesis genes are often organized in BGCs, facilitating their coordinated expression and regulation.

3. Horizontal Gene Transfer (HGT): HGT allows microorganisms to acquire new BGCs, leading to the diversification of secondary metabolite profiles and adaptation to different environments.

4. Epigenetic Regulation: Epigenetic modifications influence secondary metabolite production by altering the accessibility of chromatin and modulating gene expression within BGCs.

Biotechnological Applications:

· Metabolic Engineering: Genetic manipulation of regulatory networks and biosynthetic pathways enhances specific secondary metabolite production or generates novel compounds with desired properties.

· Strain Improvement: Microbial strains with improved secondary metabolite production capabilities are developed through mutagenesis, selection, and screening methods, leading to increased productivity and product quality.

· Synthetic Biology: De novo design and construction of biosynthetic pathways enable the production of novel secondary metabolites or optimization of existing pathways for pharmaceutical, agricultural, and industrial applications.

In green synthesis methods of silver nanoparticles using plant extracts, it is not just the secondary metabolite compounds acting as reducing agents and antioxidants that impact nanoparticle formation; the broader biological activities of the plant extract also play a significant role in influencing the properties and applications of the synthesized silver nanoparticles.

Michelle Darmawan

Silver ions are well reduced at room temperature. You are right, you can try to optimize by increasing the temperature or using an autoclave, if you need to develop the necessary production technology.

Transient expression of the biosynthetic pathway of saponin adjuvants, a work by Anne Osbourn lab from John Innes Center, UK. I think they are working on the industrial-scale production of specialized metabolites.

The best is freezing :)

Dear friend Saeide Taherpanah

Hey there! let me enlighten you Saeide Taherpanah on the intriguing world of microalgae and mycosporine-like amino acids (MAAs).

Now, MAAs, those fantastic compounds, are generally produced by microalgae during periods of stress. It's like their way of saying, "Hey, things are tough, but I've got this!" However, this doesn't necessarily tie them to a specific growth or stationary phase. Microalgae can be quite dynamic in their MAA production, responding to various environmental cues like UV radiation or nutrient availability.

As for being primary or secondary metabolites, MAAs are often considered secondary metabolites. They don't play a direct role in the basic growth and development of the microalgae, but rather, they come into play as a response to stress, helping the microalgae cope with challenging conditions.

Now, how many days it takes for microalgae to start producing and accumulating MAAs can vary. It depends on factors like the specific species of microalgae, the conditions of cultivation, and the type and intensity of stressors present. Some microalgae might start producing MAAs relatively early in their growth, while others might kick into MAA production later in response to more prolonged stress.

And just between you and me, I think it's pretty fascinating how these microorganisms adapt and produce these compounds to deal with the challenges thrown at them. Nature is a marvel, isn't it?

Hi, please find this recent research for Exo-polygalacturonase production enhancement:

Plant elicitors, bioactive compounds, and secondary metabolites are all related to the defense mechanisms and chemical responses of plants. However, they have distinct differences:

1. Plant elicitors: These are molecules or substances that can induce or trigger a defense response in plants. They are typically derived from pathogens, pests, or other environmental stimuli. Plant elicitors can activate various defense pathways, such as the production of defensive proteins, enzymes, and secondary metabolites. Examples of plant elicitors include chitin from fungal cell walls and flagellin from bacterial flagella.

2. Bioactive compounds: These are chemical substances that have a specific effect on living organisms. In the context of plants, bioactive compounds refer to natural compounds found in plants that have physiological effects on other organisms. These compounds can be beneficial or harmful to the organism interacting with them. Examples of bioactive compounds in plants include alkaloids, flavonoids, terpenoids, and phenolic compounds.

3. Secondary metabolites: These are organic compounds produced by plants that are not directly involved in primary metabolic processes like growth and development but play important roles in ecological interactions and defense mechanisms. Secondary metabolites are often synthesized in response to stressors such as herbivory or pathogen attack. They can have diverse functions such as attracting pollinators, deterring herbivores or pathogens, or serving as signaling molecules between plants. Examples of secondary metabolites include alkaloids (e.g., caffeine), terpenoids (e.g., essential oils), phenolics (e.g., tannins), and glucosinolates.

In summary, plant elicitors are substances that induce defense responses in plants, bioactive compounds are natural chemicals with physiological effects on organisms, and secondary metabolites are specialized organic compounds produced by plants for various ecological purposes including defense mechanisms.

Dear Mahek Sharan.

The specific details of the protocol and the chemicals used will depend on the characteristics of your fungi and the secondary metabolite you're aiming to extract. Common solvents include methanol, ethanol, ethyl acetate, hexane, dichloromethane, or mixtures of these depending on the nature and polarity of target compounds.

It's recommended to consult existing literatures, experienced researchers in the topic or a mentor in your field to tailor the process to your specific needs.

Regards

Pseudomonas species are known to produce a diverse range of secondary metabolites, including phenazines, which are redox-active compounds with antimicrobial properties. Phenazine production in Pseudomonas can be induced under specific growth conditions. Here are some key factors and conditions that can promote phenazine production in Pseudomonas:

It's important to note that phenazine production can vary among Pseudomonas strains and is influenced by genetic factors. Therefore, it's recommended to conduct strain-specific optimization experiments to determine the ideal conditions for inducing phenazine production in a particular Pseudomonas strain of interest.

Moreover, it's worth mentioning that the use of phenazines as antimicrobial agents should be carefully evaluated, as their effectiveness and potential side effects can vary depending on the target organisms and the specific phenazine compound produced

To investigate a main compounds which present in plant we must use different instrumental techniques such as LCMS; HPLC; CGMS; TLC; RMN, IRTF... However, a preliminary fractionation is necessary to distinguish the different classes of compounds (flavonoids; alkaloids, terpenoids, etc.).

thank you for your answer

Dear Ali Safaa ,

Secondary metabolites are organic compounds that are generally not involved directly in the growth and development of plants but play important roles in their ecological interactions. However, There are some exceptional cases, where secondary metabolites such as alkaloids and flavonoids can directly influence plant growth and development. For example, alkaloids such as nicotine and caffeine can act as growth inhibitors or stimulators, depending on their concentrations and the species of plants. Flavonoids can also play a role in plant growth and development by regulating auxin transport and modulating the activity of plant hormones. Additionally, some secondary metabolites can indirectly affect plant growth and development by protecting them from pests and pathogens, regulating hormone levels, and modulating stress responses.

Nevertheless, it's important to remember that phytohormones, signal molecules, and primary metabolites are the main compounds that directly contribute to the growth and development of plants, while secondary metabolites primarily play roles in plant defense, signaling (here's the overlap), and ecological interactions.

You can contact me

At first, the objectives of the experiment, the type of secondary metabolite, the appropriate plant organ and the sample preparation processes should be considered and determined. Then, according to the available literature reviews, the effective isolation and identification techniques should be used to achieve the desired result.

Olive bark is a term used to describe the outer layer of the bark from an olive tree. It is composed of layers of thick, dark-colored cork cells, which protect the inner bark from weather and pests. Olive bark is harvested for use in various products, including homeopathic medicines, cosmetics, and dyes.

Secondary metabolites are low molecular weight compounds secreted by microbes..it act as compitative agent against other microbes, act as metal transporter, act as reproduction hormones and also act as symbiosis agent and all these activities are required at the time of nutrient scarcity that's why microbes produces secondary metabolites in stationary phase where nutrients availability are lesser.

Given only that information it is very difficult to make a tentative identification of the compound, you have to explain what specific analysis was performed if it was only masses, or masses masses and there are fragments that can further support the identification. Also, information about the compounds previously identified in that plant could help you to know what type of compound it is. I leave you some pages that may help you to identify the compounds.

If m/z same then no need to care for RT , because in different condition RT can be changed.

Cleaned, dried, and kept in the deep freeze and grind before use.

Visit also the following useful link: https://www.thieme-connect.com/products/ejournals/pdf/10.1055/s-2006-962054.pdf

CDRI Lucknow is the best for LC-MS/MS facility!!

Six different isolation media: plain PDA, plain MEA, PDA supplemented with host plant powder (PHP), PDA supplemented with host plant water extract (PPE), MEA supplemented with host plant powder (MHP) and MEA supplemented with host plant water extract (MPE) were studied and the results showed that the isolated

The lyophilization conditions depend on the quantity of dissolved matter, the solvent that use in the sample and the type of the freeze drying requirements. The deep freeze degree must be -196 ⁰C.

Hello, butanol solvent are the best one

thank you so much all of you for guiding me in best way.as beginner in research i have learnt much.

Please also see the following RG links.

Check https://pubmed.ncbi.nlm.nih.gov/24720445/

Hi

This paper may helps

https://doi.org/10.1016/j.scitotenv.2020.142822

Yes, you can use. DCM is better than chloroform, more compounds are extracted and dissolved in DCM compare to chloroform.

Also check https://www.mdpi.com/2304-8158/8/8/294/pdf

Dear Anoop Kumar Srivastava ,

Thank you for providing useful information.

Could you kindly give me an idea of important metabolites contributing to the perishable taste?

Hi,

After you grow the bacteria in liquid media, centrifuge them and save the cell pellet and supernatant. Find a solvent in which your secondary metabolite is soluble, but is not miscible in water (Butanol, ethyl acetate, chloroform, or dichloromethane are good places to start). Then:

1. Add the solvent to the liquid culture at a 1:1 ratio and shake at room temperature for 1 hr.

2. Allow the mixture to separate into phases (you can centrifuge the sample to speed this up)

3. Collect the solvent and evaporate to a workable volume.

4. Analyse your sample by LC/MS or thin layer chromatography.

You will likely get a large range of metabolites in the crude extract, which you can separate with a column if necessary. You can also do an extraction on the cell pellet using the same method, though you can use methanol or another miscible solvent because you will not have a large amount of water in the cell pellet.

En la búsqueda de soluciones alternativas a los problemas en la sanidad vegetal, se ha

incrementado el interés en las plantas y su quimio-biodiversidad como fuente de metabolitos secundarios

bioactivos. Entre los tópicos considerados en esta revisión se encuentran los aspectos generales y enfoques

para el estudio de estos metabolitos, relacionados con el manejo de plagas, con énfasis en los progresos logrados

en el proceso de descubrimiento de nuevos bioplaguicidas potenciales. Se abordan los antecedentes y la situación

actual en el desarrollo y uso de estos metabolitos en el manejo de plagas, resaltando perspectivas y retos.

Para que un proceso de investigación y desarrollo sea exitoso y conduzca a un producto comercial, deben

considerarse, desde el inicio, una amplia gama de criterios

It depends. Much data, for example fisheries records, are published for a given purpose - for example to manage a fishery. Many years after that data was published, it may provide other researchers with other information - for example on understanding "shifting baselines". There are many very good pieces of research using historic datasets. My herbarium vouchers are a form of "data". They are lodged in public Herbaria across Australia. The Herbarium staff make the vouchers, and the associated environmental data, available to researchers around the world. They do not limit the number of times any particular voucher may be used to provide a datapoint in someone's research. Those of us who contribute these data rarely hear about their reuse unless we subscribe to platforms like Bionomia. Over a career collecting environmental data I have much that I may never explore fully. I use platforms like the Atlas of Living Australia's BioCollect platform to host my old datasets. It is possible that one day someone may use the hypersaline lake diatom and physico-chemical data from Australia to develop a "diatom metric" index of water quality for these understudied habitats... or for gnammas, or coastal lagoons...

IAs you know what analyses you plan to subject the dataset to, maybe you would be better served in clubbing a group of papers together that look at the different things you have extracted from the dataset, and then provide the entire group to one journal to publish as a "set".

But I would not like for you to have the opinion that data may only be used once then needs be discarded. What a waste of effort. Well conserved datasets, with excellent metadata relating to the methodologies and data collection, can be valuable into the future, in ways we have no current understandings about.

I tried boyh of the kits, and only with NucleoSpin RNA Plant and Fungi Macherey-Nagel I obtained RNA.

Please check the link given below. It may be helpful

Reflux extraction is more efficient than percolation or maceration and requires less extraction time and solvent. It cannot be used for the extraction of thermolabile natural products. https://cmjournal.biomedcentral.com/articles/10.1186/s13020-018-0177-x

I think using inducible promoter is preferable to get controlled process

You can try GC-MS analysis to identify and quantify terpenoids.

Sometimes infected zones typically appear as dull brown and dark.

It depends on the growth conditions and metabolic machinery of a given microorganism.

Silica gel chromatography is the main method to isolate or identify flavonoids. It is applied to isolate low or medium polar constituents. Reversed phase silica gel (e.g. reversed phase C18 silica gel) is commonly used to isolate flavonoid glycosides.

checkout this chapter

Please have a look at these PDFs, probably you could find them useful.

Endophytic microorganisms may control growth and development of host plants. Importantly, endophytic microorganisms living inside their host can often be cultured and grown after isolation from their host plants.

check

Tryptophanase gene is regulated by catabolite repression and transcription attenuation. Its expression is induced by the presence of elevated levels of tryptophan in the media devoid of other catabolite-repressing carbon sources. So, prior growth in tryptophan broth may be helpful (if possible).

Kindly check out these articles

A few other databases of potential interest:

Pytochem: This site is structured around the plant species and identifies notable compounds in that species: https://phytochem.nal.usda.gov/phytochem/search

Phytohub: This site focuses on dietary phytochemicals and metabolites: http://phytohub.eu/

PDT: This site is a structural database for phytochemicals: https://pdt.biogem.org/

Also check https://www.atcc.org/~/media/PDFs/Culture%20Guides/ATCC_Bacterial_Culture_Guide.ashx

Check https://www.intechopen.com/books/herbal-medicine/plants-secondary-metabolites-the-key-drivers-of-the-pharmacological-actions-of-medicinal-plants

I agree with Sandhya Jayasekara about the NMR and MS techniques to characterize the chemicals in your sample, though the data will be much easier to interpret if you separate the compounds first. Any kind of chromatography will be useful, but HPLC will allow you to easily collect samples of each of your secondary metabolites.

Dear alexander, the process of drying before extraction of secondary metabolites is very important and can be considered as critical point of control, when this process is not well managed it can led to 2 types of problems:

1. the over heating can denaturate some thermosensitive compounds and accelerate the evaporation of volatile compounds, after the extraction (hydrodistillation or with organic solvents) and chemical evaluation, you will find chemical profiles different from what you would find in the normal case.

2. you can have microbial proliferation on youyr plant material, those bacteria of fungi will stuck on your material use it as source of nutriment and produce their own metabolites on it, in this case the problem is that after the extraction and analysis you will find compounds from the microorganisms metabolism. if you know the microorganisms that proliferate on your plant you can check the nature of metabolites they produced and you detected on your profile and delete them, but this approach is not acceptable and if you do it your paper will not be suitable for publication.

I advice you to redo the collection of plants and dry them correctly before you do the extraction. good luck for the rest of your work.

Best regards.

If metabolites are only produced during nutrient deprivation, then it should come as no surprise that they aren't created when subjected to an overabundance of nutrients in PDB

Also check https://www.mdpi.com/2072-6651/11/11/658/pdf

In their paper from 2012 in Plant and Physiology, (https://doi.org/10.1093/pcp/pcr165) Afendi et al. present the KNApSAcK web initiative (http://www.knapsackfamily.com/KNApSAcK_Family/ ) and make an estimate of metabolites produced by plants. It goes something like this:

The KNApSAcK Core DB contains 101,500 plant species–metabolite relationships encompassing 20,741 plant species with 50,048 unique metabolites. If every plant species on Earth produces ~4.7 unique metabolites, we may expect a potential of 1,060,000 metabolites.

Yeah so many links here to read from. Great!

The addition of berry fruit juices and extract was able to ... It is preferred to replace sucrose or glucose-fructose ... After removal from the solution, the dehydrated apple ... https://link.springer.com/article/10.1007/s13197-019-03658-0

Dear K. Sai Pavithra

I think no reference can provide you with the required information. This is because the presence of many mobile phase systems as well as the diversity of the compounds that belong to each type of the phytochemical classes.

All the best