Dyes - Science topic

When dyes are added to an aqueous suspension of nanoparticles, they can perform the following functions

1. adsorb on the surface of nanoparticles and change their spectrum in the visible region

2. act as water pollutants in dye factory wastewater when studying the catalytic properties of nanoparticles.

3. act as a standard of substances in SERS analysis.

4. When mixing dyes and nanoparticles with plasmonic absorption, two types of absorption in the visible part of the spectrum and their interaction can be studied.

Dye photosensitizers assembly involves anchoring dye molecules onto a substrate (e.g., semiconductor) to enhance light absorption in devices like dye-sensitized solar cells (DSSCs). The process typically includes surface separation, dye adsorption washing and optimization such common dyes are ruthenium complexes, organic dyes or porphyrins.

I think the stained blood sample has residual Hoescht and then since Hoechst is cell-permeable the cancer cells stain with residual Hoechst. A few follow-up questions to help.

What is the concentration you are using?

What is the purpose of staining with Hoechst? If it is just to stain the DNA (does not matter if it is dead or alive), then I do not see an issue with the blue color.

Hoechst is cell-permeable. If you are using it on live cells, you would want to use something else that is not permeable without fixation or if the cell is dead, such as Propodium Iodine (PI). What color is your CellTracker? Make sure that the PI and CellTracker excitations do not overlap.

yes, based on the information I found, there are several dyes that can be used to distinguish between live and dead cells without affecting their motility. Here are some of the main options:

1. https://www.thermofisher.cn/order/catalog/product/cn/zh/L34970;

2. https://www.thermofisher.cn/cn/zh/home/life-science/cell-analysis/cell-viability-and-regulation/cell-viability/live-dead-cell-viability-assays.html;

3. https://www.thermofisher.cn/cn/zh/home/life-science/cell-analysis/cell-viability-and-regulation/cell-viability/live-dead-cell-viability-assays.html;

4. https://www.thermofisher.cn/cn/zh/home/life-science/cell-analysis/flow-cytometry/flow-cytometry-assays-reagents/cell-viability-assays-flow-cytometry/fixable-viability-dyes-flow-cytometry.html;

These kits and dyes are specifically designed for cell viability testing, aiming to minimize the impact on live cells while effectively distinguishing between live and dead cells. When selecting dyes that meet your experimental needs, please consider your specific application and experimental conditions.

Silica nano-particles are reported to efficient absorbers for methylene blue?

But just by adsorption not by photocatalytic destruction.

Warming the solution to help the dye dissolve while stirring it should help to reduce the amount of undissolved dye. If there is still some undissolved dye in the solution, you can remove it by passing the solution through a filter membrane, such as an 0.45 micron filter, using a vacuum flask. It may clog if there is a lot of solid, so you may need two filters to get it all through.

Hi. I'm with Thermo Fisher Tech Support. I've also used that dye and other CellTracker dyes when I was in R&D here.

11uM is probably a fine concentration, but 45 minutes seems like a long label time to me. Overlabeling (either too high a concentration and/or too long label time) can lead to toxicity effects. Your labeled, but unimaged, control looks fine, but remember that when you are imaging labeled samples, photobleaching occurs, particularly if you image over a long time, which creates free radicals and singlet oxygen that leads to increased cell toxicity. Some cell lines are more sensitive to others. Another thing to note is the binding mechanism. This dye has a chloromethyl functional group that binds to free thiols on proteins, particularly glutathione, in the cytoplasm. This, too, can lead to effects on cell functionality.

So here are some things to try:

1) reduce your label time and/or concentration, as long as your initial intensity is still sufficient for imaging.

2) reduce photobleaching effects by reducing your light exposure and compensating by increased gain or exposure time settings, reduce the frequency of imaging, or using ProLong Live (a live-cell antifade solution we sell).

3) Try a different dye. We have other colors of CellTrackers. Contact tech support (cellanalysis.support@thermofisher.com) and we can help you choose one and offer a free goodwill replacement with it if you ordered within the past year. Feel free to mention my name. They'll need the catalog and lot number, order date, and any order numbers for your CellTracker Red. Since you are in Germany, our European tech support team will need to process it for you.

Cheers, Jason

May consider using Permai fluorescence dye.

Hi Mohamed, ammonium oxalate is used to prevent precipitation of the dye (the so-called Hucker modification). If you don't intend to store the solution for longer than a few weeks, you can leave the oxalate out but need to keep an eye out for precipitation (perhaps filter before use). The solution for Gram staining is made as follows: dissolve 2 grams of crystal violet in 20 ml ethanol (>95%), add 80 ml of distilled water and mix well until fully dissolved. Filter this solution through coarse filter paper and store in a dark glass bottle.

The (-N-N-) bonds either triple or double bonds make dyes stable and their degradation products are also carcinogenic and mutagenic creating more challenges in degradation.

You may have a chance to exclude dye using Sephadex G10...Its MW is close to the exclusion limit of the resin. Otherwise, you may add a secondary purification step such as reversed phase or anion exchange at pH 2...Ponceu S remains acidic at low pH but even acidic amino acids will be protonated. This will help the adsorb dye. Reversed phase separation could be beneficial to perform a group separation. Only hydrophobic amino acids will be closely eluted, a shallow gradient can efficiently exclude the dye from all amino acids...

May consider using Permai fluorescence dye.

Vishnu Sankar

There is a concept, in the Russian version, adsorption strength reduction during adsorption (P.A. Rebinder effect). It can be associated with adsorption.

May be. Thanks a lot for your reply.

Adnan Shahzaib thanks for the suggestions, well i cannot go with hydrophilic dyes as i want to mimic kinetics with some hydropohobic dye. Adding surfactant worked in my case.

May consider using Permai fluorescence dye.

For an exothermal reaction the reaction enthalpy should be negative because the products should be more stable than the educts. So this is not a big surprise.

Endothermal reactions, so those with a positive reaction enthalpy, need to be favored by entropy so that they can occur and become exergonic.

Dear Haoting Lin ,

I would suggest CellTracker in the version CellTracker™ Red CMTPX if it should be a dye or if you would like to stain only the membranes you might want to try CellLight™ Plasma Membrane-RFP, BacMam 2.0 both from Thermo Fisher. I have used the later with different tags and it worked great for me.

The CellTrackers are really good, the CMAC, CMFDA and CMTPX are all great and should last for days.

Best wishes

Soenke

Dear Doctor

Go To

[Abstract

The term “biomass” encompasses all substances found in the natural world that were once alive or derived from living organisms or their byproducts. These substances consist of organic molecules containing hydrogen, typically oxygen, frequently nitrogen, and small amounts of heavy, alkaline earth and alkali metals. Magnetic biochar refers to a type of material derived from biomass that has been magnetized typically by adding magnetic components such as magnetic iron oxides to display magnetic properties. These materials are extensively applicable in widespread areas like environmental remediation and catalysis. The magnetic properties of these compounds made them ideal for practical applications through their easy separation from a reaction mixture or environmental sample by applying a magnetic field. With the evolving global strategy focused on protecting the planet and moving towards a circular, cost-effective economy, natural compounds, and biomass have become particularly important in the field of biochemistry.

Conclusion

This review focuses on magnetic adsorbents prepared from agricultural waste biomass to remove different dyes from textile wastewater. Adsorption is a desired process for eliminating pollutants thanks to its ease of use, efficacy, energy efficiency, cheapness, lack of harmful by-products, simple design, and magnetic separation capabilities. Recently, magnetic adsorbents have been widely used for dye removal because of their unique surface chemistry containing ketones, aldehydes, carboxylic...]

The behavior of a photocatalyst in adsorbing one cationic dye while degrading another is influenced by various factors, including the structural characteristics and functional groups of both the catalyst and the dyes. Effective adsorption requires favorable interactions between the catalyst's functional groups and the dye, while photocatalytic degradation depends on the catalyst's band gap and the nature of the light used for irradiation.

The pH of the solution is crucial, as it affects charge interactions between the catalyst and the dyes, potentially leading to electrostatic repulsion or attraction. Additionally, the stability of the dye molecules under light exposure is critical; some dyes may undergo structural changes that enhance their degradation, while others may form stable complexes that resist breakdown.

Molecular size and steric hindrance also play important roles, as they can affect how easily dye molecules access the catalyst's active sites, influencing both adsorption and degradation efficiency. Larger dye molecules may struggle to reach these sites, resulting in reduced adsorption and lower degradation efficiency. Bulky groups or complex structures can further obstruct the dye's approach, hindering interaction with the catalyst.

The impact of molecular size and steric hindrance is discussed in section 3.1.4 (BET-BJH analyses) of the following paper, which I highly recommend for a deeper understanding of these dynamics: http://dx.doi.org/10.1016/j.jclepro.2024.141850

Hello Haiyao Ding

Calcein AM is a non-fluorescent cell-permeable derivate of Calcein that is widely used in cell viability measurement. The carboxylic acid groups on Calcein are modified with AM (acetomethoxy) groups, which endows Calcein AM with high hydrophobicity, facilitating its penetration through cell membrane. Once inside the cell, AM groups are hydrolyzed by intracellular esterases. The fluorescent Calcein molecule is restored, which is trapped in the cell and emits strong green fluorescence.

Since dead cells lack esterase activity, only live cells are labeled and detected. The fluorescence intensity will be proportional to esterase activity. Calcein-AM has been proved to be both specific and sensitive for detection and tracking of apoptosis in living cells. The preservation of membrane integrity is one of the most significant features of apoptosis with respect to necrosis. In the presence of membrane defects, Calcein leaks out of the cell and the signal also vanishes in the presence of residual esterase activity.

On the other hand, Propidium iodide (PI) which is a red-fluorescent nuclear stain is not permeant to live cells or cells which are dead but still have an intact membrane (such as the primary apoptotic cells). In late apoptotic and necrotic cells, the integrity of the plasma and nuclear membranes decreases, allowing PI to pass through the membranes, intercalate into nucleic acids, and display red fluorescence.

Calcein generated from esterase in viable cells emits a strong green fluorescence with an excitation and emission maximum at 494nm and 517nm, respectively, while PI once bound to DNA has a maximum emission wavelength at 617nm when excited at 535nm.

There is something that must have gone wrong with your reagent or your process. You may have cells that are either alive or dead, but not both. Cells which are dead but still have an intact membrane (like the primary apoptotic cells), PI is not permeant to these cells.

You may repeat the experiment. Initially, observe the cells in bright field. Then observe the cells in the green fluorescence channel. The live cells will be stained by green, fluorescent Calcein. Follow it by observing the cells in the red fluorescence channel. The dead cells will be stained by the red fluorescent, PI. Then finally you merge the image of green and red channels.

Good Luck!

Using a dialysis membrane with well-known pore sizes can help you estimate the size or molecular weight of organic dyes.

I have some ideas that may help:

-Hydrogen Peroxide Concentration: Choose a ratio where the H₂O₂ concentration is at least twice that of methyl orange. This will enhance the oxidation process.

-UV Light Source: Ensure you have information about your UV lamp, particularly its maximum emission wavelength. Compare this with the molar absorption spectrum of methyl orange, as a high molar absorption could cause it to act as a filter for photons.

-pH Considerations: Work around the point of zero charge (pHzc) of TiO₂, which is about 6.2. Research the pKa of methyl orange, as it is a pH indicator. -Start with a small concentration of dye may also be beneficial 5mg/,10mg/l ...ect .

Some types of dyes are used in PETG filaments : Solvent Dyes, Anthraquinone Dyes, Phthalocyanine Dyes and Disperse Dyes.

The specific dye or colorant used can vary depending on the manufacturer and the desired properties of the filament, such as UV resistance, lightfastness, and thermal stability.

Continuing on Adam B Shapiro answer I will suggest going 10-fold to 100-fold higher in the wells containing fluorescein in the beginning and adding a buffer to the ones that don't. Simply because if a splash occurs it will be of small volume.

10%H2SO4 In EtOH can be used as the dye，after the TLC is done, dry it and then put it into the dye, then use the heating machine to dry it and heat it (200℃), there will be spot on the TLC for sugars.

Considering of the well-established fabrication techniques of optical color filters and photoresists, I would say trying colorants like triarylmethane type dyes (such as crystal violet and Victoria Blue) or pigments (such as Pigment Violet 23) might be good a start. In general, (as I know) pigments are less soluble than dyes; on the other hand, dyes might need extra operations such as photoinitiation. If you use your layer for optical applications and if you also want to further pattern the surface, it is important to select pigments with small size (for Pigment Violet 23, there are many options available starting from a nm to a micron). However, a good dispersion and chemical compatibility with PDMS might be always challenging.

Here I have another idea, too. There is also a way to make the thin layer visible to the naked eye without using any additional additives. Using soft lithography/imprinting lithography, you can patter the PDMS surface with periodic structures (such as grooves). These diffraction gratings offer very colourful appearance under ambient light. However, this will totally change the optical properties of the layer.

Good luck.

Several dyes can be used to stain bacterial cellulose for microscopic analysis or other purposes. Some common dyes include:

### 1. **Calcofluor White**

- **Type**: Fluorescent dye

- **Function**: Binds to β-glucan structures, including cellulose

- **Usage**: Widely used for staining cellulose due to its strong fluorescence under UV light, making it easy to visualize bacterial cellulose in fluorescence microscopy.

### 2. **Congo Red**

- **Type**: Non-fluorescent dye

- **Function**: Binds to cellulose and other polysaccharides

- **Usage**: Often used for staining cellulose in bacterial colonies on agar plates, where cellulose-producing colonies will appear red.

### 3. **Direct Red 23 (Sirius Red)**

- **Type**: Anionic dye

- **Function**: Binds to β-glucan structures

- **Usage**: Used for staining cellulose in histological sections, providing a clear contrast against the background.

### 4. **Acridine Orange**

- **Type**: Fluorescent dye

- **Function**: Can stain both nucleic acids and polysaccharides, but with different emission spectra

- **Usage**: Useful for dual-staining protocols where cellulose and nucleic acids need to be differentiated.

### 5. **Safranin O**

- **Type**: Cationic dye

- **Function**: Stains cellulose and other components

- **Usage**: Often used in combination with other stains in differential staining protocols.

### Staining Procedure with Calcofluor White (Example):

1. **Sample Preparation**: Fix the bacterial cellulose sample on a microscope slide.

2. **Staining**: Apply a few drops of Calcofluor White solution onto the sample.

3. **Incubation**: Let the dye sit on the sample for a few minutes to ensure adequate binding.

4. **Rinsing**: Gently rinse the slide with water to remove excess dye.

5. **Microscopy**: Observe the stained sample under a fluorescence microscope with the appropriate filters for UV excitation.

### General Tips:

- **Fixation**: Ensure proper fixation of the bacterial cellulose to the slide to prevent loss of material during staining and rinsing.

- **Controls**: Include controls to distinguish between specific and non-specific staining.

- **Fluorescence Microscopy**: Use appropriate filters and settings for fluorescent dyes to achieve optimal visualization.

The choice of dye depends on the specific requirements of your experiment, such as the need for fluorescence, the type of microscopy available, and the level of detail required.

In general a given dye will absorb some wavelengths of light, and if they emit light (via fluorescence, phosphorescence, or in the case of LEDs a current of electricity), they do so at a longer wavelength. There are exceptions to this (e.g. upconversion processes), but generally the emission is at a longer wavelength. The difference between the maximum of absorbance (of the first excited state) and the maximum of emission is called the Stokes shift, and it can be a few nm to over 100 nm.

So you could see a dye absorb blue light in the range of say 420-500 nm. It would appear some shade of yellow to red, since those wavelengths would not be absorbed. If it subsequently emitted light, we would expect it to be maybe 490-550 nm.

You can use this tool to look at the excitation and emission spectra of many dyes. Hope that helps!

It is supplied in DMSO which is quite volatile so if it is very old you may have lost some dmso to evaporation and reached the point where it cannot dissolve the dye cold but the dye is more soluble in warm solvent. If you have not used much and if the supplier material sheet gives you the total volume in the vial then you could measure the volume in the vial to see if it is what it is expected to be

The isoelectric point (pI) of ZnO nanoparticles significantly affects the photodegradation of MB (Methylene Blue) dye. Here’s how:

To calculate the isoelectric point of ZnO nanoparticles using the acid-base titration method:

The isoelectric point (pI) is identical to the point of zero charge (pzc). The determination of pzc is detailed in this manuscript.

The isoelectric point of ZnO nanoparticles influences their surface charge and thereby affects their adsorption capacity and photocatalytic activity towards MB dye. Understanding and controlling the isoelectric point is crucial for optimizing ZnO nanoparticle-based systems for efficient photodegradation of MB dye pollutants.

I hope this helps. Regards, Pramod

unidentifiable

DNA ladder is usually not mixed with the loading dye and transferred directly to the well. For samples, I personally used 7:3 ratio of sample and the loading dye and it gave me good results.

I don't doubt the UV light source. I think that the UV light might be absorbed by the glass of the beaker. So, no UV light reaches the inside and the degradation cannot take. But I don't know.

Sircol is a sirius red based collagen assay. The wash buffer is most likely PBS or something very close. Release of dye from collagen is induced by treatment with a basic solution like 0.1 M NaOH. You can look on Google scholar for sirius red collagen assay and find many papers describing it.

As Julie Ann Dougherty says it probably won't make much difference. Nevertheless since you have to use the same conditions for all the qPCRs to compare, I'd rather repeat this one with the correct quantities.

Regeneration, often referred to as reactivation, is a method of thermally processing the activated carbon to destroy the adsorbed components contained on its surface. In regeneration, the adsorbed components are almost completely removed, yielding a regenerated carbon that can again function as an adsorbent.

Since it's reactive to amine, I'm not sure if it will bind to any free amine group on the antibodies that bind to the surface receptors. I would test that if you have to do live/dead after surface stain before fixation. I have used another kit LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit that is also amine-reactive kit. I always use it before surface staining and stain in PBS for 10min at RT, then wash and do surface stain, and then fix my cells for intracellular staining.

In summary, the ability of methyl orange to absorb visible light, facilitate electron transfer, and provide stable, cost-effective sensitization makes it the preferred choice in many photodegradation studies compared to other dyes that may lack these beneficial properties.

To prepare a 100 ppm (parts per million) methylene blue stock solution in 1 liter of water, you need to know the molecular weight of methylene blue and apply the definition of ppm.

Definition and Calculation

- 1 ppm means 1 mg of solute per liter of solution.

- Therefore, 100 ppm means 100 mg of solute per liter of solution.

Given:

- Desired concentration: 100 ppm

- Volume of solution: 1 liter

Steps to Calculate the Required Weight

1. Determine the amount of methylene blue needed:

- Since 100 ppm is 100 mg/L, you need 100 mg of methylene blue per liter.

2. Convert mg to grams:

100mg = 0.1g

Weighing the Dye

Weigh out 0.1 grams of methylene blue dye accurately using an analytical balance.

Preparing the Solution

1. Weigh the dye:

- Use an analytical balance to weigh 0.1 grams of methylene blue dye.

2. Dissolve the dye:

- Add the weighed dye to a 1-liter volumetric flask.

3. Add water:

- Fill the flask with distilled or deionized water up to the 1-liter mark.

4. Mix thoroughly:

- Stir or shake the solution until the dye is completely dissolved.

To make a 100 ppm methylene blue stock solution in 1 liter of water, weigh out 0.1 grams of methylene blue dye and dissolve it in 1 liter of distilled or deionized water.

Hello Farah Mousli, please find the attached document with protocol for your above question.

Wish you good luck.

Debabrata Chakraborty - but in the case of reabsorption, decay time would not change?

Muhammad Sami - you may send me figures if you wish, may be it becomes more clear (but I am not sure...)

Repeated cycles can lead to cracks or enlarged pores which decrease rejection and increases flux. adding some plasticizers or blending could help

May consider using Permai fluorescence dye.

Start with one well

The first step is to determine the volume of sample to be used for 20ug of protein. Then, use the total volume of each well to derive the amount of loading dye. Finally, subtract the sample volume and the amount of loading dye from the total volume to know how much lysis buffer to add.

Then, depending on the number of wells needed and the amount of extra volume to be retained for loading, multiply the sample volume, loading dye dosage, and lysimetric buffer. in your case it is 2(duplicate)*1.1(10% more)=2.2. Multiply all volumes by 2.2 from one well calculations.

Hi mister

You can try with the natural non-toxic coloring which is curcumin

Good luck

Does it have to be fluorescent?

Dear Noor ul Ain, you didn't specified the type of polymer and its mechanism of action. I will talk about flocculants. These are polar and charged ionic polymers of four types: polar/neutral, anionic, cationic, and zwetterionic (+ & -). Flocculants help disperded substances to associate/agglomerate so that they settle down by gravity. They do so mainly by two mechanisms: charge neutralization and bridging. My Regards

Hi Priyanka,

I am wondering if you have figured out how to do it? It is hard to find an established protocol for this.

Thank you!

In a dye adsorption study, you will need to construct separate calibration curves at each pH level if the dye's absorbance or other properties vary significantly with pH. This ensures that accurate concentrations of the dye are determined during the adsorption experiments.

May consider using Permai fluorescence dye.

The DAPI excitation peak is at 359 nm and the emission peak is at 457 nm. The Calcium Orange excitation peak is at 549 nm and the emission peak is at 574 nm. (There needs to be esterase activity present to cleave the AM ester off the calcium orange.) Therefore, the fluorescence ranges can be separated by flow cytometry and fluorescence microscopy optical filters, allowing the two dyes to be used together.

Thank you Muhammad Shahid Malik

Hello Sofya Landynya

Yes.

Before treating the cells, the medium must be removed so that the cells are exposed to a uniform treatment.

Before adding the MTT dye, it is necessary to remove the medium because when you remove the medium containing the drug, it ensures that there is no interference of the drug with the MTT reagent, and that all the cells are treated in the same manner during the MTT assay.

Best.

May consider using Permai fluorescence dye.

May consider using Permai fluorescence dye.

May consider using Permai fluorescence dye.

All enzymes that work on DNA have Mg2+ as a cofactor. So, I think the EDTA you have in your buffer will already do the job, as it complexes the Mg2+. Concerning proteins bound to DNA, an alternative to phenol extraction is to use proteinase K for the deproteinization of the samples.

If the 30% concentration refers to the weight of H₂O₂ per 100 mL of solution (w/v), the calculation requires knowing its molecular mass, which is 34.0 g/mole.

30% (w/v) is 300 g/L

(300 g/L)/(34 g/mol) = 8.82 mol/L.

1 millimole = 0.001 mol

0.001 mol/(8.82 mol/L)=0.000113 L = 113 µL of 30% (w/v)

For 1 L of a 1 millimolar solution, add 113 µL of 30% (w/v) H₂O₂ to 1 L of water.

However, according to the Sigma catalog, they supply 30% H₂O₂ as a (w/w) solution, rather than a (w/v) solution, so the above calculation would be a little bit off, because the density of a 30% H₂0₂ solution is greater than the density of water, since the density of H₂O₂ is 1.45 g/mL.

In fact, a 30% H₂O₂ listing at Millipore-Sigma gives the density of 30% H₂O₂ as 1.11 g/mL, so 100 mL of the solution weighs 111 g, and 100 g of solution has a volume of 100/111 = 90.1 mL. (Caveat: this particular listing did not specify w/v or w/w.)

Therefore, the 30% (w/w) solution contains 30 g of H₂O₂ per 90.1 mL of solution.

(30 g/90.1 mL) = 0.333 g/mL = 333 g/L

(333 g/L)/(34 g/mol) = 9.79 mol/L

For 1 millimole: (0.001 mol)/(9.79 mol/L) = 0.00102 L = 102 µL

For 1 L of a 1 millimolar solution, add 102 µL of 30% (w/w) H₂O₂ to 1 L of water.

If you can't find out whether you are using a (w/w) or (w/v) solution, at least you know that 1 millimole is contained in either 102 or 113 µL.

In case of every catalytic reaction, the removal step has to be performed in order to remove the added catalyst from the reaction. The type of methodology implemented to achieve this will depend upon the nature of catalyst, size of catalyst, and reaction medium phase. The centrifugation is the most commonly used methodology for the nanosized catalyst removal from aqueous medium while flocculation/sedimentation can be applied for higher size of the catalyst. You can modify the catalyst by depositing it on the membrane to avoid the removal step as well.

May consider using Permai fluorescence dye.

Define the amount of one component to calculate them all. I'd consider the amount of water (H2O). Do you need 1 uL, 23 mL, 41 billion L? You should easily find out how much mol H2O are within this amount and then use the ratio to calculate the amount of the other components. Good luck.

May consider using Permai fluorescence dye.

Hi, I am not sure what your study is about. Before proceeding, in my opinion, you should conduct your preliminary study to determine the optimal dye concentration for your research. To do that, you should plot a concentration or dose (dye)-response (cells) graph. The type of response data you'll be recording will be up to you based on your study objectives.

Covalent interaction between a polymer dye and a cotton fabric is possible thanks to several mechanisms. Here are a few possibilities:

1- Covalent grafting reaction: In this reaction, functional groups present on the polymer dye react with functional groups present on the cotton fibers. For example, hydroxyl groups (-OH) on the cotton fibers can react with appropriate functional groups on the polymer dye to form covalent bonds.

2- Copolymerization reaction: If the polymer dye contains monomers that can polymerize with the monomers present in the cotton, a copolymerization reaction can occur. In this case, the polymer dye monomers bond covalently with the cellulose monomers present in the cotton.

3- Oxidation reaction: Some polymer dyes can undergo oxidation reactions in the presence of oxidizing agents such as hydrogen peroxide. These reactions can lead to the formation of covalent bonds between the polymer dye and the cotton fibers.

4- Condensation reaction: Some polymer dyes may contain functional groups capable of reacting with functional groups present on cotton fibers to form covalent bonds by a condensation reaction. For example, amine groups (-NH2) present in the polymer dye can react with carbonyl groups (-CO) present in the cotton fibers to form amide bonds.

These mechanisms are general examples and the precise nature of the covalent interaction would depend on the specific chemical structures of the polymer dye and the cotton fibres, as well as the reaction conditions.

Check the adsorption and desorption properties of your absorbent. If the desorption capability is low that absorbent will not leave the adsorbed pollutant from its surface.

Fluorescein is a cheap dye that is water soluble at pH >6. It's innocuous as far as I know. It's also fluorescent, so you can detect it at very low concentrations, if necessary.

Phenol red is the red dye that is added to cell culture media as a pH indicator, so it must be pretty innocuous. It is red at neutral pH, pinkish at alkaline pH and yellow at acid pH.

Those dye stuffs weren't bound with adsorbent, you can't stop them from being separated when you do filtration. Actually, they weren't adsorbed. You have to subtract those values from your total percentage of removal.

May consider using Permai fluorescence dye.

Did you find the answer? I am also wondering if I can use two primary antibodies, from different species, together.

The cell seeding density of 200-300 cells per 6 well is probably to low. iPSC like adjacent cells for better survival. You could try 48 or 24 well plates and/or more cells. The thawing AND freezing protocol should be optimized. iPSC should be frozen approximately 2-4 days after passaging. Freezing them significantly later after the last passaging, strongly decreases cell survival after thawing. Please find further information attached.

Looking at the structure of methyl orange, the N=N bond can be cis or trans (E or Z). If you started with one pure isomer, it is likely the absorbent is equilibrating the two isomers. I have synthesized similar dyes and have had to deal with isolating each isomer. Both are dyes but they absorb at different wavelengths.

A second explanation could depend on the pH. Since it is a pH indicator dye, you could be at a pH where the basic and acidic forms are in equilibrium. It is red below 3.1 and yellow above 4.1. Both species should exist in equalibrium in a pH range around those values.

This reference points out that cis -methyl orange fluoresence originates through initial absorbtion around 375 nm so I think the first explanation holds water. https://www.sciencedirect.com/science/article/abs/pii/S1386142514001991

Dear Muhammad Younis ,

Thank you for your answer.

How many cycles of pcr are you running and how much dna (ng) are you amplifying in each pcr reaction?

The cheapest fluorescent dye is fluorescein. It is highly water soluble and very bright. Its main disadvantage is poor photostability, meaning that it photobleaches quickly when exposed to light. Pyranine is another relatively inexpensive, bright fluorescent dye that is highly water soluble and probably more photostable than fluorescein.

It has been demonstrated that removing dangerous organic species from water can be accomplished with the use of H2O2 and photocatalyst. H2O2 can promote the generation of hydroxyl radicals and impede the surface recombination of electron-hole pairs.H2O2 increases the concentration of the ·OH and ·O2 radicals in photocatalytic systems by its reactivity with the valence band holes and conduction band electrons. Further radicals can be produced by the reaction of H2O2 with ·OH, HO2·, or ·O2 radicals . To form O2, the oxidative species interact with one other or with the holes they make. Additionally, hydroxyl radicals are formed when H2O2 is exposed to UV-vis radiations.

Costa, E. P. et al. New trend on open solar photoreactors to treat micropollutants by photo-Fenton at circumneutral pH: Increasing optical pathway. Chem. Eng. J. 385, 123982 (2020).