Science topic

Carbohydrates - Science topic

The largest class of organic compounds, including STARCH; GLYCOGEN; CELLULOSE; POLYSACCHARIDES; and simple MONOSACCHARIDES. Carbohydrates are composed of carbon, hydrogen, and oxygen in a ratio of Cn(H2O)n.
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I am looking for seed coat mucilage deglycosylation simple method for identify the carbohydrates
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You should treat your sample separately or tandemly for each N-linked and O-linked saccharide profile...You may follow endoglycosidase such as PNGase F for the enzymatic procedure at N-linked release. Beta alkaline elimination on the other hand is a chemical approach for O-linked...You may find many reagents and protocols on the Ludger website for glycan release. This would be the way for protein-bound carbohydrates. You can also unconjugate the bound carbohydrate variants by acid hydrolysis. But I am not sure this could reflect the whole spectrum.
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What i mean by the path to obesity, is the type of excess calories that led to this obese state: someone can get obese on a ketogenic diet (very low carbohydrate) Vs. someone on a low fat high carbohydrate diet, etc.
What i am after is the knowledge of the effect of these two factors:
[1] The state of obesity
[2] Long term dietary habits,
on obesity related chronic diseases.
Is there any study on obese people that were complying with a long term low carb diet as a tradition for example, in relation to obesity related chronic diseases?
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several factors can play role in obesity, diet is only one factor other factors such as environment, certain medicine, heredity, eating junk food, etc etc . more research needs to find on what is the exact and major causes of obesity. prevention and treatment
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Does anybody know where can I find the information on the relative content of different sugars (such as glucose, galactose, mannose, fructose, xylose, etc.) in animal cells?
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Many thanks for your reply; if I find something, I'll let you know.
Best, Jacques
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Hello everybody,
I just started with MD simulations to find out more about the interaction of a carbohydrate substrate with my enzyme than I can see from simply docking the substrate into the active site.
I followed the Protein-Ligand Complex tutorial (http://www.mdtutorials.com/gmx/complex/index.html) for GROMACS and got a decent looking simulation (as far as I can tell). However, CGenFF says "CGenFF should NOT be used for biological macromolecules! Only use CGenFF for small organic molecules".
So I would like to use the GLYCAM_06j force field to generate a topology for my ligand. I also used the carbohydrate builder from the GLYCAM website (http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1) to generate my ligand for the docking. I used tleap from AmberTools19 to generate the topology and coordinate files using the following commands:
tleap -f leaprc.GLYCAM_06j-1
> lig = loadpdb ligand.pdb
> saveamberparm lig ligand.prmtop ligand.inpcrd
Running the loadpdb command returned the following:
Loading PDB file: ./ligand.pdb
total atoms in file: 71
Leap added 40 missing atoms according to residue templates:
40 H / lone pairs
Then, I used the acpype.py script (https://github.com/alanwilter/acpype) to convert the amber topology into a GROMACS topology using the following command:
python3 acpype.py -x ligand.inpcrd -p ligand.prmtop -o gmx
After that, I followed the GROMACS tutorial again creating a topol.top and a protein.gro file using pdb2gmx with the amber14sb force field.Then, I including the ligand_GMX.top file into the topol.top file by adding the following after the ";Include Position restraint file" term:
; Include ligand topology
#include "ligand_GMX.top"
I also added the ligand to the [ molecules ] entry. I copied the coordinates together in a complex.gro file, created a dodecahedron box and added the water molecules. However, when I get to the step to add the ions using the ions.mdp file provided in the tutorial using this command:
gmx grompp -f ions.mdp -c solv.gro -p topol.top
I get the following error:
ERROR 1 [file topol.top, line 35334]:
No default Improper Dih. types
ERROR 2 [file topol.top, line 35454]:
No default Improper Dih. types
-------------------------------------------------------
Program: gmx grompp, version 2019.4
Source file: src/gromacs/gmxpreprocess/topio.cpp (line 607)
Fatal error:
Syntax error - File ligand.top, line 3
Last line read:
'[ defaults ]'
Invalid order for directive defaults
I already found, that I can only have one [ defaults ] entry in my topology and that there is another one in the forcefield.itp file of the amber14sb force field which is included in the topol.top file. If I simply remove the [ defaults ] entry in the ligand.top file, I get the same error for the [ atomtypes ], which is also present in the ffnonbonded.itp file (included in the forcefield.itp file).
I know, that in GLYCAM_06j, the atom types are intentionally different from those in the amber14sb force field. I also thought about including the atomtypes from my ligand topology into the ffnonbonded.itp file from the amber14sb force field, but the columns have different names in these files.
I read through every tutorial and manual I could find to get to this point, but now I seem to be stuck. Could anyone give me some advice on how to solve this problem. Or is my first simulation already sufficient using CGenFF to prepare the ligand (it's either a tetra- or hexamer). If you need any more information to answer this question, please feel free to ask.
Thank you very much in advance!
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Hi Aditya,
here are my topol.top and my ligand_GMX.top/.itp files. As I mentioned above, I remove the defauls, system and molecules entries from the ligand_GMX.top file and rename it into ligand_GMX.itp. As you can see in the topol.top file, I only included the updated ligand_GMX.itp file so you don't have to copy everything into the topology.
For my case, I also created a small bash script to simplify the preparation of the ligand file (bash_prepare_1ligand(.sh) <- for some reason I had to remove the .sh extension to be able to upload it here). It automatically runs tleap, acpype, removes the defauls, system and molecules entries and saves the output as an itp file which you can then include in your topology. Maybe that helps in your case as well. If you have any further questions, please let me know.
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Dear all,
I am busy with my thesis (chemical engineering) in enzyme discovery and have established that my one candidate has b-1,6 galactosidase activity. For my report, I wish to discuss some of the practical applications that this could have in industry. I am hoping to find some application relevant to biofuels, but really just want to find out for which carbohydrates b-1,6 galactosidase activity could be beneficial (in breaking the carbohydrate down).
For example, larch arabinogalactan has b-1,6 galactose substituents and thus my enzyme could in theory increase the efficiency by which this polymer could be broken down into galactose monomers, and subsequently fermented into ethanol using yeast.
Does anyone have any idea of other carbohydrates/substrates where this activity could have practical applications? (or could point me to resources to help this pursuit)
Would really appreciate any assistance!
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Thanks for your reply Frank Höger
I don't think I explained myself too well. What I meant is that I'm looking for substrates that I can use for a purely theoretical discussion. I have also tested my enzyme on allolactose and it does work, but I'm more so looking for natural substrates which I could discuss in my thesis as a possible industrial application - if that makes sense?? The ability to break down allolactose doesn't really serve much industrial relevance, hence I'm trying to look for industrially-relevant substrates with b-1,6 galactose substituents.
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Dear,
I want to perform a Molecular Dinamics simulation in a protein with 5 molecules of NAG attached to it.
Since the covalent bond between the carbohydrate and the protein creates an unusual bond, the GROMACS page shows that I should change something in the specbond.dat, but nothing more...
Are there any tutorials explaining how to prepare the system to perform the simulation using the GROMACS software (or could someone explain)?
Thanks for your help.
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Thank you for your answer.
It works fine in the CHARMM-GUI, but I want to understand how to perform the whole steps in the GROMACS.
I tried to use the pdb2gmx (with charmm36 and amber99sb-ildn), but it showed me some errors, including the NAG that was not found in the FF files, I've tried to use the PDB generated by the CHARMM-GUI, but it still getting some errors. It also showed me to make changes in the residuetypes.dat.
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I'm working on carbohydrates.
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Jyoti
Better to give out the structure for better answer!
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I have digested the polysaccharides with HCl. Can I inject digested content (with acid) into the LCMS column for detection of individual mono or disaccharides ?
Any suggestion or advice, those who are working on carbohydrates
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Thank you for your answer
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I am currently working on analyzing the association of dietary intake and microbiome with type 2 diabetes (T2D). I plan to validate my findings using publicly available databases and was wondering if there are such studies/cohorts that enrolled T2D cases and controls and have macronutrient (protein, fiber, carbohydrate, and fat) and/or gut microbiome data. It would also be great if the study focuses on an Asian population.
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I am a beginner in molecular docking. And I want to know is the active pocket of the receptor the same for all ligands? Or will there be different active pockets for different ligand receptors? I want to do a hydrolase docking with a small carbohydrate molecule, I want to know exactly (or roughly) which part of the active pocket is in (I hope that the binding energy will be lower after docking), so how do I determine which range the active pocket of the receptor is in before docking? Looking forward to your response!
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This's an interesting question. There are several ways to find the binding site of proteins.
1- As the respected colleagues answered, using online databases, you can do it.
2- For all crystallographic structures available in the PDB database, the binding site of target proteins can be accessed through the paper that published the relevant protein. In this case, you can search for your protein in PDB to find its binding site.
3- Using blind docking. Blind docking is a procedure in which you can dock several ligands with different backbones into target receptors to evaluable the possible interaction between these ligands and protein surfaces in different areas. Based on docking energies, you can categorize your ligands and find relevant sites that are the most important locations for interactions of your ligands. This method, in some cases, works fine, and it is a reliable way to find the binding site of proteins.
4- Using the PDBbind database. PDBbind database consists of many experimentally assayed binding modes of ligands and receptors. You can download it and check its content for relevant data.
5- Using text-mining approaches. This method will enable you to use artificial neural networks to excavate the literature to find the binding mode of ligands into your target receptors. In this way, you can find many papers dealing with your project and use their content to predict the binding site of your protein.
6- Using PSI-BLAST. This method is a time-consuming procedure but returns validated results. For this case, you can blast the sequence of your query against the PDB database and find more similar proteins. Based on the location of other protein active sites that showed similarity with your protein sequence, you can find some binding sites in your protein structure. Please note that the alignment output can be submitted to ENDsprit software to compare the results and align the studied sequences' binding site.
Helpful papers:
These papers can help you to know more about the prediction of protein active sites:
Good Luck
Rasouli. H
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That is, only synthesize nutrients in laboratories using compounds that are not digestible, if the answer is yes, how is it done, and can it cover all the food demand that a person needs? I would appreciate if you share articles with me!
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I have to simulate carbohydrate-protein complex on GROMACS. I have used GLYCAM webserver to generate a trisaccharide. Then I used acpype of Ambertools21 to prepare carbohydrate ligand using GLYCAM_06j force field. It is giving me outputs as .gro and .top file. I need .itp file to run it on GROMACS. If I use .top then it gives me the following error (attach file). I am new to MD simulations. Is there a way to convert .pdb or .top file to itp? Pdb2gmx is useless in this matter.
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If you open the .top file you posted you will find the parameters for your molecule, starting with
[ moleculetype ]
and closing with the values under
[ dihedrals ] ; impropers
that is, excluding what comes from [ system ] and later on. Try to open a .itp file of GROMACS, you'll see that the structure is the same. I think you can just copy paste these sections into an .itp file, then build the .top file of your system by properly including (#include statement) the forcefield parameters and the .itp file for your ligand.
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How can I estimate fructose in my sample by spectrophotometer method like carbohydrates estimation. Is there any spectrophotometer method for it.
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2/24/22
Dear Karisma,
Here is an enzymatic method that works.
I have used it. It is easy to do and works very well. I hope this helps you.
Bill Colonna
Iowa State University, Ames, Iowa, USA wcolonna@iastate.edu
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In case of carbohydrates and training there are many variaties, such as train low, sleep low, train high, sleep low...
Carb loading is ingesting low carbohydrates for some days, followed by intensive ingestion of carbohydrates ingestion to create some kind of super compensation of glycogen stored in muscle. It should be combined with training, mostly with less training near the high carbohydrates intake.
My question is if the same can be done with low protein intake and a supercompenstion mechanism with protein.
I do not have literature at hand, but many articles are about carb loading.
The second part is about the fact cyclist train with different training methods (intensive/extensive) and different nutritional methods (Full glycogen, empty glycogen stores (till some extend) and such.
With resistance training this is lacking.
Would the same be possible in case of resistance training? 
=training with different begin status in stead of always looking at maximum performance. For instance no pre-workout, low glycogen, or maybe a day no protein?
Would the same be possible with protein to some extent? 
=is there some basic in a form of protein loading, to break throught some barriers or plateaus?
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Interesting
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From defeated Finger millet flour how to remove carbohydrates to get a pure protein? Want to know the protocol?
If anyone know so plz tell me?
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Hello Divya Singh , check this paper DOI: 10.3920/JIFF2021.0017
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I am trying to study on minerals, amino acids, vitamins and enzymes of different fruit juices/natural syrups. However, because of a high concentration of polysaccharides and sugars (e.g., glucose and fructose), it is difficult to get high concentrations of the interested above compounds. Moreover, most of available procedures are performed under intensive conditions (e.g., using acidic and alkaline conditions) or expensive (e.g., HPLC). Could you please guide me in this respect?
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What worked for me in the past was to treat the sample with a cation exchanger. Any compound interacting with the cation exchange resin will be retained, while the carbohydrates will pass. Then elute the "cationic" species of the resin and perform the analytical determination you need.
Treatment with an anion exchanger will work similarly if you keep the sample pH below 12. Most carbohydrates deprotonate at pH > 12 and would therefore be retained. We used commercially available ion exchange resin in bulk and prepacked SPE cartridges depending on the specific workflow demands.
To create a proof of principle, I'd suggest the bulk approach first - usually less expensive. Once you know the general route to take for your sample, switch to the SPE cartridges - I would suggest.
I hope this helps!
Good luck with your research!
Cheers
Detlef.
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Can you tell me the changing pattern of protein and carbohydrate during different period of storage in chickpea? and why?
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My research aims to study Lectin-Carbohydrate interaction. However, I can't do the titration at the ITC, as I don't know the number of binding domains of the lectin.
Lectins are isolated from plants (by my research group) and carbohydrates are N-acetyl-D-Glucosamine.
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Hello dear researchers
Would you please introduce a Widely used and suitable database for protein, carbohydrate, RNA, and DNA sequences?
The purpose of my model is to predict protein with peptides, DNA, RNA, and carbohydrates
Thank you
I am waiting for your guidance
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Also check EMBL
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Is it necessary to neutralize enzymes in the obtained hydrolysates before the carbohydrates analysis by HPLC?
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Probably a good practice is to remove all foreign matter, especially proteins, other polymers, and any insolubles in your HPLC buffer, to circumvent plumbing problems, and also spurious signals.
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All opinions and answers are welcomed with appreciation to all
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Complex carbohydrates are present in foods such as bread and pasta. Simple carbohydrates are in foods such as table sugar and syrups. Complex carbohydrates contain longer chains of sugar molecules than simple carbohydrates. The body converts these sugar molecules into glucose, which it uses for energy. https://www.medicalnewstoday.com/articles/325171
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I want to know standard concentration of phenol and H2SO4 which is used in phenol sulfuric acid test.
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Dear
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The glycemic index is a system of assigning a number to carbohydrate-containing foods according to how much each food increases blood sugar. The glycemic index itself is not a diet plan but one of various tools — such as calorie counting or carbohydrate counting — for guiding food choices.
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Kindly check the following RG link:
In which it discusses the most relevant methodological considerations and highlights specific recommendations regarding many aspects as well as calculation of glycaemic response area under the curve.
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#research #biotechnology #spectroscopy
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Molecular fluorescence spectroscopy is one of the most sensitive and highly selective spectroscopic methods, which can detect extremely low amounts of chemical substances. In the milk industry, it is used for the determination of vitamins, fatty acids, residual amounts of antibiotics, and the identification of different milk species in dairy products.
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We are going to do an RNA-seq analysis to study transcriptomes\ profile of different organs in terrestrial orchid species within genera including Dactylorhiza, Ophrys, Himantoglossum, and Orchis but their underground fleshy tubers contain high content of glucomannan (a carbohydrate which gives special rheological features to products obtained from Salep) and it's difficult to obtain a pure RNA in presence of such contaminations. Is there any special and home-developed protocol to extract a pure RNA sample suitable for RNA-seq analysis from such tissues?
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Sanaan Fathi thanks for your answer. We usually use Ethanol and Isopropanol in the RNA extraction protocol. The first one washing the resulted pellet and removing extraction solution or other contamination in the final step and the second one for precipitation of RNA molecules.
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give definitions of both without telling their properties , uses , source. define these two groups as if u are explaining to a 6th grade kid.
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I am measuring the total carbohydrates of Agave americana fermented beverages. The absorbance value of my blanks is so different between each measure. Is this problem normal?
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By using the regression equation, Y=mX+C, whether to take C=0 or not in this calculation?
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I plot my standard curves in Microsoft excel and it generates the y=mx+c equation for the curve automatically with the appropriate value for c. I then use the standard curve equation to solve for the unknown concentration. Hope this helps.
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Seed carbohydrate composition as affected by some soil or foliar applied substance
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Thank you
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Protein extraction, wastewater treatment, anaerobic bioreactor
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hope so the following link might be of help to you please have a look and comment and am sure this is what you were looing for as well
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I would like to know what method authorized by the AOC is used to determine carbohydrates in fish muscle, since I have read that regularly only lipids and proteins are determined
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Can any give suggestions regarding to the calculation of estimation of Total soluble sugars or total carbohydrates by anthrone method.
Please help me
Thanking you.
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Hi everyone,
Actually, I am doing some research about modifying edible films by crosslinking them, which are based on carbohydrates such as carboxymethyl cellulose, etc, but I am looking for the best cross-linker, which can improve these films.
Thanks in advance.
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Dear Shahriyar Valizadeh, it seems dialdehyde is one of the best choices, citric acid is also used. Please check the following documents. My Regards
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Hello together,
I am conducting the established assay for carbohydrate detection with anthrone reagent in an aquatic organism. Normally, the color changes like expected from yellow to green, or stays yellow when no sugar is in my sample.
But in my last assays with (differently) treated organisms, the color changed from yellow to brown instead. I already renewed the reagent and all chemicals I use in the assay, but the color always changed to brown. During my last try, I examined treated and, as control for the color change, freshly caught organisms. Suprisingly, the color changed for the freshly caught to green and for the others to brown. So the assay must have worked.
Does anyone know, how this color change to brown could happen? Were you able to observe such a color change in your assays? Is it possible that my treated organisms are so much weakened that somethings else was produced consuming the sugars?
Many thanks for your ideas.
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If we know the dextrose equivalent value in carbohydrates, from DE how we can calculate the monosaccharides of that glucose?
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I am currently working on a project on bifidobacteria growth tests on various prebiotic substrates, and I am having difficulty analyzing the fermentation activity qualitatively, I use bromocresol purple to see a change in pH in the medium mrs agar with an indicator of a change in color, but after doing it many times, the results do not show significant color change what should I do? should i use mrs broth instead
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There are many methods for determining carbohydrates from plant extracts, but what is the most appropriate method for total extraction of carbohydrates from grape pomace.
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A method for the determination of carbohydrates in plant samples is described, in which the plants are frozen in dry ice as soon as they are cut and portions extracted with 8004 alcohol in an Elco Homogenizer and the carbohydrate estimated by the anthrone reaction. https://onlinelibrary.wiley.com/doi/pdf/10.1002/jsfa.2740091104
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I wish to inquire how the energy produced for someone starving can be compared with another person not starving when a biomolecule nutrient like carbohydrates is considered when all energy production pathways are operational?
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Look up Autophagy, it is well established science.
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I am a research scholar working on heavy metal stress on plants. I will be doing biochemical characterisation( protein, carbohydrate, proline, antioxidant enzymes and many more assays) at interval of 30 days until harvest in root, leaf and shoot. . (The tests will be repeated 5-6 times). Each time the plant has to be uprooted. Each of these assays demands fresh sample, however the availability of sample is less and time available is less. Can someone please suggest ow can the time be manged. Or how to simultaneously run these experiments.?
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I am a research scholar working on heavy metal stress on plants. I will be doing biochemical characterisation( protein, carbohydrate, proline, antioxidant enzymes and many more assays) at interval of 30 days until harvest in root, leaf and shoot. . (The tests will be repeated 5-6 times). Each time the plant has to be uprooted. Each of these assays demands fresh sample, however the availability of sample is less and time available is less. Can someone please suggest ow can the time be manged. Or how to simultaneously run these experiments.?
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If you want to study 30 days dynamics of analytes like protein, carbohydrate, antioxidants, and many more assays, there are many many ways available.
Depends on what relly you want to detect the quality, quantity structure the verious methods can be used.
Protein detection
Non-specific methods that detect total protein only
  • Absorbance: Read at 280 or 215 nm. Can be very inaccurate. Detection in the range of 100 μg/mL to 1 mg/mL.
  • Bradford protein assay: Detection in the range of ~1 mg/mL
  • Biuret Test Derived Assays:
    • Bicinchoninic acid assay (BCA assay): Detection down to 0.5 μg/mL
    • Lowry Protein assay: Detection in the range of 0.01–1.0 mg/mL
  • Fluorescamine: Quantifies proteins and peptides in the solution
  • Amido black: Detection in the range of 1-12 μg/mL
  • Colloidal gold: Detection in the range of 20 - 640 ng/mL
  • Nitrogen detection
    • Kjeldahl method
    • Dumas method
    Specific methods which can detect the amount of a single protein
    • High-performance liquid chromatography
    • Liquid chromatography-mass spectrometry
  • Antibody-dependent methods
    • Enzyme-linked immunosorbent assay
    • Protein immunoprecipitation
    • Immunoelectrophoresis
    • Western blot
    • Protein immunostaining
Carbohydrate analysis methods
  • Chromatographic and Electrophoretic methods
  • Chemical methods
  • Titration Methods
  • Gravimetric Methods
  • Colorimetric Methods
  • Enzymatic Methods
  • Polarimetry
  • Refractive Index
  • Infrared
  • Immunoassays
Proline detection methods
  • HPLC UV or FLU with a post or pre-column derivatization
  • ELIZA method
  • Voltammetric sensor-based method
  • Multilayer paper-based microfluidic sensor method
  • Ultrasound assisted-cloud point extraction and spectrophotometry method
  • Chemosensor fluorescence quencher Ag+ method
Antioxidant activity detection methods
  • Peroxide value detection methods
  • Diene conjugation
  • Kreis test
  • ABTS + assay
  • Phycoerythrin assay
  • Electron spin resonance spin-trap test
  • FRAP assay
Hope this info will help you.
Good luck
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Can anyone -who may have hands-on experience in analytical chemistry or photochemistry- help me how can I quantitatively analyze a sample with carbohydrate content?
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I am not sure what setting you are doing your experiments in. In case you are measuring starch content of a solution you can employ fluorescent microscopy Where starch glows bright red. If you use this along with software they can analyze The ratio between things that are not glowing versus things that are glowing red then you can tell what your content of starch would be.
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now i am doing the catalytic conversion of carbohydrate into lactic acid in alkaline aqueous solution .... then i need to find a method ( sample preparation ) to quantify the resulted lactic acid inside the solution ( pure dist.water solution ) by GC-Mass .
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How to analyse the qualitative and nutritive values in baby corn in the laboratory such as sugar content, starch content, carbohydrate and protein content etc.
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I downloaded the PDB file of receptors from the RCSB PDB site, but most of them are glycosylation, meaning that several groups of carbohydrates are attached to it, should these carbohydrates be removed for docking ?? Or should this glycosylation be naturally present in the receptor ??
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In most of the communities especially are owned by lower socioeconomic status.Diet contains more of carbohydrate than protein and fat. More carbohydrate after catabolism produce more saturated fatty acids. This may disturb the level of LDL( high ) lead to atherosclerosis.
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Diet contains more of carbohydrate than protein and fat. More carbohydrate after catabolism produce more saturated fatty acids. This may disturb the level of LDL( high ) lead to atherosclerosis.
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Prosopis juliflora is considered a noxious weed but its eradication is very costly inhivitive if no impossible ! We have very strong openion that it's spread could be chacked only if it's pods are crushed with seed to process livestock feed ! Pods/ seeds are very protein , carbohydrates and mneral rich and we have demonstrated through R&D that they are absolutely safe for livstock and human consumption ! Livestock feed processing is very simple ! Our work in this direction could be very helpful , especially for Africa , where countries are facing lot of problems due to this species ! Comments and views from learned researchers are welcome !
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Kamlesh Pareek Exact is a very important species within an ecosystem.
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Hi Everyone,
I am trying to characterize the microstructure (localization of carbohydrates, fats, and proteins) of coconut milk powder using confocal microscopy. From the review of the available literature, I have found that fats and proteins can be non covalently labeled using fluorescent dyes. However, I am having trouble deciding the labeling protocol for the carbohydrate. Two common methods that I have seen in the papers are as follows:
1. Use antibodies or lectins conjugated with fluorophores to label carbohydrates
2. Covalent labeling of carbohydrates with FITC
If I use the first method, the signal from antibodies or lectins may interfere with the signal from protein present in the sample.
In the second method, the FITC (probe used for covalent labeling) also shows an affinity for proteins. So, I am afraid that the use of such a probe may also interfere with the protein signal (from the food sample). Is there any other probe available that I can use?
What would be the best way to label carbohydrates such that I can simultaneously image three components in the food mixture?
Thanks.
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Thank you all for your help :) I will read the articles that you have shared.
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Hi All,
I have build the model of cellulose polymer using xleap and hemicellulose polymer using glycam carbohydrate builder. Now, I need to place the two polymer chain parallel two each other. How can I do it? Any suggestion would be appreciated.
Thanks.
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Ra.Jabbar Sh
Thank you. Do you know how to apply tensile loading on a polymer in AMBER?
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We are looking for articles, on lipid to carbhydrate ratios in fishfeeds, with static protein and energy levels. We have found some literature but we are looking for your recommendations.
Any help is much appreciated
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Looking for suggestion for making carbohydrate complex which is stable.
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I believe it is sucrose. It is more inert than maltose.
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1- How can we calculate monosaccharides of carbohydrates (Sorbitol , glucose) practically , using dextrose equivalent value?
Explain indetails
Thank you!
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Dear colleagues,
We are interested in extracting carbohydrates fro E. coli and the protocol we've seen so far include too many hours in a sonicator. Does anyone has suggestions or experinece in isolating this kind of component?
Thank you for your attention.
Best regards,
Cláudia
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I am working with a complex plant material and I want to test different enzymes on it and measure the changes in carbohydrates and proteins fraction compared to untreated material. I got no experience on such assays and I would like to address some questions:
a) Is the activity assay mandatory for such experiments? Or declared activity is sufficient?
b) Since the material is in a form of sludge, what pretreatment is needed? Do I just add X ml of enzyme (enzymes are in aqueous solutions)?
c) Do you recomend pH adjustment with acid/base or buffer solution?
Thank you in advance.
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i) Enzyme assays are the established methods used for testing enzymes on a substrate or substrates. They are used to characterize a an enzyme by measuring its various parameters like activity, temperature and pH stability, Km and Ki etc.
ii) The pretreatment is required in case the material is insoluble.
iii) The pH adjustment can be done with both acid as well as base in different samples. That is going to depend upon the pH Optima of the enzyme being tested.
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I need to know, if the temperature around 60°C-70°C can efficiently kill the enzymes that involve in non-structural carbohydrate cleavage.
In one experiment we´ve boiled root samples in 50% ethanol for at least 15 min at 80°C and we´re sure that the enzymes were killed as we compared the results with liquid nitrogen and subsequent lyophilization procedure and it was comparable. We´ve also tried a procedure where it was only put into 50% ethanol in ambient temperature without boiling and only the total sum of carbohydrates was comparable with that of liquid nitrogen treatment and the ratio of free sugars to polysaccharides was different, so it implies that the enzymes were not killed immediately.
What will happen if we boil it in 50% ethanol, but the temperature is lower – 60/70°C? Is the standard 80°C :
1) the lowest possible for the enzyme denaturing?
2) kind of „excessive“ just to be sure that the enzymes are killed and also the best for the extraction of carbohydrates (the highest yield)?
Does ethanol by itself stop the enzymes?
I´ve searched in the literature and for the temperature 60-70°C, I´ve found only air-drying treatments which are not efficient for the enzyme stopping. And in case of putting the samples into liquid solutes, I´ve found temperatures >80°C. Most of the studies used pure water or 80% ethanol instead of 50 % as a medium.
I´ve found 1 paper where they discuss the lethal temperature for woody tissue in case of fire and it was 60°C. But they mentioned that the mitochondries are killed, I´m not sure if also the carbohydrate splitting enzymes are stopped (fructanases, sucrase, amylase, α-galactosidase etc.). When I searched for the information about individual enzymes in vivo, I found only treatments with t>80°C. And in case of commercial enzymes I found that these enzymes work the best around 40-60°C and then the activity decreases (which does not mean that they´re killed, I assume) and that they become unstable. But most of these commercial enzymes were of microbial or fungal origin.
Does anybody have an idea? Or is it necessary to try it experimentally...
Thank you!
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Chinaza Godswill Awuchi Thank you for the links, but they don´t really respond to my questions, one is a review and the second uses 75°C air drying instead od boiling in a solute. I´ll search more. Best regards. Zuzana
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WHO recommends a fat intake of no less than 15% of the daily caloric requirements (https://www.who.int/dietphysicalactivity/publications/trs916/en/).
However, imagine a catastrophic situation in which a population somehow lost access to fat-rich foods for several years, while still having access to a good supply of carbohydrates, protein and micronutrients. Is there a point at which nutritional problems would arise if the consumption of fat was near zero? Would people survive if this was the case? what if the consumption was 5% or 10% of the total caloric intake?
Could the body survive via its own capacity to synthesize fats from carbohydrates?
-Please assume that essential fatty acid consumption (linoleic and alpha linoleic) is covered in this scenario-
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Current Dietary Fat Intake Recommendations for Adults by WHO (Fats and fatty acids in human nutrition Report of an expert consultation. FAO Food Nutr Pap. 2010;91) -
Total: 20-35%, Saturated: <10%, Trans: <1%, n-6 PUFA: 2.5-9%, n-3 PUFA: 0.5-2%.
Lichtenstein & Van Horn (1998) defined "a very low fat diet is defined as one in which ≤15% of total calories are derived from fat (33 g for a 2000-calorie diet, 50 g for a 3000-calorie diet) with fat calories distributed approximately equally among saturated, monounsaturated, and polyunsaturated fatty acids. Approximately 15% of total daily calories consumed should be derived from protein and ≥70% from carbohydrates."
In contrast, at this time, no health benefits and possible harmful effects can be predicted from adherence to very low fat diets in certain subgroups. In addition to young children, the elderly, pregnant women, and persons with eating disorders should not attempt a very low fat diet. Persons with insulin-dependent diabetes mellitus, elevated TG levels, and carbohydrate malabsorption illnesses should also avoid such a diet.
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When I compare the results obtained from the oxidation of carbohydrates using this equation with the data obtained with the respiratory quotient (RQ) table, I obtain very different results.
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Hi
Dear Colleagues,
Could anyone explain an optimized protocol to extract total RNA from plasma samples? We would like to extract total RNA from plasma samples through Trizol, however, after the washing step with 75% cold ethanol, there are a high amount of reagent components such as phenol or carbohydrate (260/230 < 0.7). What do you suggest to get rid of these components?
Thanks in advance
#RNA_extraction #Tizol #Plasma #phenol or carbohydrate contamination
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hello there
you can use less amount of reagent at the first step or high amount of isopropanol at the next step!!
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Hello,
Is it possible to dissolve non-hydrolyzed lecithin powder in water without oil content (or oil phase such as in emulsion). Is carbohydrate content or glucose content of non-hydrolyzed lecithin effective in the dissolving power of lecithin in water?
I would be grateful for receiving your answers.
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Alireza Shirkhani Lecithin dissolves in water to form micelles, liposomes. Of course, their formation begins with the dissolution of the molecule, and then, with an increase in concentration, micelles are formed. See Wikipedia.
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Either it is just like crop equivalant yield or else different. If any formula available or reference paper that have procedure to calculate kindly share
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I am looking at gender differences in fat and carbohydrate oxidation during endurance cycling. They (male and female) completed two trials each, one with a water placebo and another with a carbohydrate solution. I am currently thinking a repeated measures ANOVA?
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The one-way analysis of variance (ANOVA) is used to determine whether there are any statistically significant differences between the means of two or more independent (unrelated) groups (although you tend to only see it used when there are a minimum of three, rather than two groups). https://statistics.laerd.com/spss-tutorials/one-way-anova-using-spss-statistics.php
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Please provide procedure for sample preparation as well as to carry out analysis.
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90C is OK. Regarding analytical techniques, all depends on what you have. The Dionex IC system (with ECD detector) is very robust, but LC-MS can do that as well.
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I used gravimetric analysis to determine microalgal lipid content after lipid extract in my lab. Now we need to determine both protein and carbohydrate content. We have a Velp TKN digestion-distillation which can be used to determine the estimated protein content of any sample. So, I am thinking if we extract lipid, then determine protein and subtract to find the carbohydrate content of microalgae sample, is this okay? Or
Is there any other direct method to determine lipid, protein, and carbohydrate?
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The most popular methods for the estimation of lipid, protein, and carbohydrates in microalgae are:
Lipid: Bligh and Dyer method 1959
Protein: LOWRY et al., 1951
Carbohydrate: Phenol–sulphuric acid method by Dubois et al., 1956
E.G. BLIGH, W.J. DYER, A rapid method of total lipid extraction and purification., Canadian Journal of Biochemistry and Physiology. 37 (1959) 911–917. https://doi.org/10.1139/o59-099.
LOWRY, O.H., ROSEBROUGH, N.J., FARR, A.L., RANDALL, R.J., 1951. Protein measurement with the Folin phenol reagent. The Journal of biological chemistry 193, 265–275. https://doi.org/10.1016/0922-338X(96)89160-4
Dubois M, Gilles KA, Hamilton JK, Rebers PA, Smith F. Colorimetric Method for Determination of Sugars and Related Substances. Analytical Chemistry 1956; 28: 350–356.
I think this might help you
Thank you
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aptamers are short nucleotides meant for the specific binding with targets ranging from small molecules to proteins, carbohydrates, lipids and almost everything in nature.
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Any luck finding a database?
I'm about to put together my own application specific database
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I need to find out structural carbohydrate and lignin of my sample which is a mix of the wheat husk (particle size less than 5mm)+cow dung+anaerobic digester sludge+sewage sludge+granular activated carbon (size 2-5mm). I am more interested in change rather than the absolute value of these parameters. What are suitable methods other than NREL?
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Thank you!
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Hi everyone! Can you help me with this answer? I need to know what is the average N,P,K, Carbohydrate content in Eucalyptus sp. plants for leaves and bark.. And if you have any papers to recommend me... Thank you at all!
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Also, you can try this database: https://phyllis.nl/
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What are the advantages and disadvantages of consuming sugars?
What are the health benefits?
What are the consequences?
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Some of the inputs here are scary. I'm glad my consumption rate of sugar is quite low. Thanks for sharing this research.
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Probably COVID-19 contain modifying lectins to hide itself from host immune cells and some carbohydrates.
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Yes, a Covid-19 can produce new strains that can defeat the host's cell.
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In part I’m wondering if protein carbohydrates complexes can stabize the reaction in a biologically relevant medium.
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Dear Sir
What is you mean? polymeric carbohydrates, folded proteins or glycoproteins?
Regards
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FTIR gives you clues regarding the functional groups, but still not so comprehensive regarding the exact matter I guess. Further, quantification is not possible. Any other methods to identify and quantify the same?
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To the best of my knowledge,the LC willgive us same information about organic
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The batch study was done by the varying ID of microalgae (50 mg/L, 100mg/L, 400 mg/L, and 700 mg/L ) to check its effect on the accumulation of proteins and carbohydrates cultivated in synthetic tertiary WW.
Light intensity, temperature, pH, nutrient concentration were remained constant throughout the study.
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If I understand correctly, Bahram Barati's explanation is almost correct, except for the carbohydrate content. Carbohydrates and lipids are reserve compounds and so accumulated in greater quantity in the stationary growth phase (or on nitrogen deplete).
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All digested carbohydrates are converted to glucose and metabolized. We know that the mechanisms. But, is there anyone knowing the specific reason for glucose?
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Dear
I am very happy for the question and i want to tell you a specific answer.
all living mostly made of five element like C, H, O, N and P in which C, H and O is primary elements. three element mostly conserved in our body system and glucose have balanced ratio of three element composition. the chemical composition of glucose in living system is a important key to play all activity in the living system as well as help of respiration (exchange O2 and CO2) for survival in nature. Various kind of by product of glucose during metabolism its help to cyclic approach for molecules regeneration or alternative sources in living system.
Dear your query
Why is only glucose completely metabolized in the body?
Because glucose have three common carbon, hydrogen and oxygen in certain ratio, they element contribute to any kind of other glucose molecules and easily change into glucose get to energy in cells.
Thank You
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EPS constituents have the anionic functional groups and can bind the metal ions hence leads the corrosion. Which constituent (carbohydrate, protein, lipid, uronic acid, etc.) is responsible for MIC?
Can anybody provide me a paper entitled "Microbial polysaccharides and corrosion" by Iwona B.Beech?
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Dear Dr. Reena Sachan,
I suggest you to have a look at the following interesting paper:
- Microbial influenced corrosion by thermophilic bacteria (Review article)
Suman Lata, Chhaya Sharma and Ajay Singh
Cent. Eur. J. Eng., 2 (1) pp. 113-122 (2012)
Best regards, Pierluigi Traverso
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Lectins are carbohydrate-binding proteins. they can, therefore, be purified using affinity chromatography, however, the lectin loses its activity once bound to the carbohydrate of choice in the process. This is because the carbohydrate-binding domain of the lectin is already occupied by the sugar employed in the purification. if the downstream target for the purification required the lectin to have a free carbohydrate-binding domain, there is a need to unbound the lectin from the sugar.
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Thanks so much, this will be helpful
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There is a need to ensure extraction yield of the soluble coffee process, thus we need a method to analyze carbohydrate degradation products produced after hydrolisys of polysaccharides due to high temperatures used during extraction. It is important to measure in process the extraction efficiency to fine tune the process. Which secondary rapid method could be used to measure carbohydrate degradation products in the liquid phase and how can it be calibrated on primary methods?
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Dear Giulia,
Near infrared (NIR) and Raman spectroscopies have already demonstrated their potential for in-situ analysis. It is nevertheless difficult to say in advance which one would be the best for this specific application. it must therefore be tested.
Best regards,
Ludovic.
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Can anyone help me to find the best esterification method between carbohydrate and bulky amine?
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Hello Mohammed,
Talking from experience. What you can do is to convert the sugar to (Ac3)GlcNAc-Asn by Staudinger reaction and then couple it to RAM (Rink Amide Resin) for instance. Thereafter, couple the drug and then take the acetyl group off the sugar and cleave off the target molecule from the resin. Should you consider this worthy of trial, let me know for more details on how you can do it?
Regards.
Jude
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The last few days i have determined reduced sugar content from grass that was both hydrolyzed with sulfuric acid as from grass extracted with distilled water. Because the calculated concentrations of both extractions did not differ from each other, i decided to do a test where i used maltose and fructose as a positive control and dextrose as the standards set. This test was intended to verify if the method used is valid. The determination of reducing sugars is performed using dinitrosalicyclic acid method. Is there a reference value for both fructose and maltose in the literature?
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Sugar Meal Composition of Five North Central Florida Mosquito Species (Diptera: Culicidae) as Determined by Gas Chromatography
  • July 1999
  • Journal of Medical Entomology 36(4):462-7
  • DOI: 10.1093/jmedent/36.4.462
  • D A Burkett
  • D L Kline
  • 📷David Arthur Carlson
  • This publication describes GC analysis of sugar meals in wild mosquitoes.
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I wish to look at glycogen accumulation in cardiac tissue using PAS staining on frozen sections of tissue. I am using formalin fixative, followed by a sucrose gradient until the tissue sinks, then standard freezing, cutting and staining. I am wondering if the use of sucrose may generate false positives as it's a carbohydrate? Is there some merit to this? my histology experience is extreamly limited so any suggestions would be terrific :)
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Dear Micah,