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Plant Biochemistry - Science topic

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I have been working on Cupressus arizonica. one of most noted things is a layer of glaucous covers almost entire tree body. Still, I did not find any mentions relating to the purpose or causes of this layer in those books or papers.
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epicuticular waxes are reported to be a common answer of desert/dry climates plants to drought. It is supposed to limit evapo-transpiration. However closeby are usually found thriving plants with no such waxes. And waxy plants can also be found in wet habitats. As usual the question is probably more "why does this not disadvantage them" rather than "how does it benefit them?
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In our lab we usually dry arabidopsis seeds(Col-0) in 37 degree incubator after haversting. But I found several protocols in which drying seeds in room-temperature. So im worried about whether 37 degree is too high for arabidopsis seeds?
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As Yuan-Yeu Yau wrote, it leads to heat shock and that definitely alters the expression profile. Thus, if you do it, you must do it for all the seeds that you're going to use in the experiment, unless the drying temperature is part of the treatment in your experimental design, and explicitly mention it in the material & methods.
Although the seeds are most likely viable after drying at 37°C, it's not the method that ensures the highest viability and germination rate. You must also consider the ecotypes and eventual mutations. For example, seeds of the abscisic acid-insensitive (ABI) mutants fail to degrade chlorophyll during maturation and show no dormancy, leading to low desiccation tolerance and poor longevity.
According to the Arabidopsis protocols, the recommended method is to air-dry the seeds at room temperature and about 20% RH for 1–3 weeks. I stop watering my plants for the 1-2 weeks after they developed the siliques and afterward I harvest them. Then you pack the seeds in cryovials and store them at 4°C at max 30% RH for up to 2 years or at -20°C and max 20% RH for longer. You also must make sure that they dry well after sterilisation. Whether is better to sterilise them immediately or only before immediate use it's debated. Seed moisture content should be around 5% and there are several methods of measuring it.
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Is it that chlorophyll content and protein level are significantly affected under drought?
Do drought-tolerant genotypes produce specific secondary metabolites? If yes what are the secondary metabolites?
What should one look for (in terms of biochemical parameters) when studying drought tolerance or sensitivity in legume or cereal genotypes.
Please see the link below:
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I am trying to design an agricultural and horticultural calendar for Karbi Anglong and Dima Hasao districts of Assam, India. What are the steps that I should begin with?
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I'm going to use half strength MS media for root initiation for indica rice cultivar. What will be it's composition when I'm using MS salt, sucrose and agar without growth regulators
Thanks in Advance
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Half strength of MS medium means the use of half the quantity of macro and micronutrients including sucrose. The gelling agent will remain in the same quantity.
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Is BRASSINOSTEROID INSENSITIVE 1-Associated receptor Kinase 1 (BAK1) a plant resistance (R) gene?
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Brasinosteroids, defined as the sixth plant hormone after the classic plant hormones auxin, gibberellins, cytokinin, abscisic acid and ethylene, are analogous to animal steroid hormones in structure. BR-insensitive (BRI) is the receptor for BR. BRI1-associated kinase 1 (BAK1) is another enzyme.
BRI1 and BAK1 interacted with each other in vitro and in vivo, which contributed to BR signalling 
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Can the hypersensitive response occur as part of PAMP-Triggered Immunity (PTI) as well as Effector-Triggered Immunity (ETI)?
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Dear @Ruby Metzner
The ubiquity of hypersensitive response among higher plants despite its costs suggests that it is an extremely effective component of the plant immune system. Please check the following links, and attached pdfs; hope, these could be useful to you.
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Are resistance (R) genes expressed in response to pathogen attack - or only defense genes - as part of the plant immune response? R proteins act as receptors to recognize pathogen effectors and an interaction between R protein and effector stimulates Effector Triggered Immunity (ETI) which itself involves the expression of defense related genes. However, are R genes also expressed as part of ETI?
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Dear Ruby Metzner Plants have developed a complex defense system against diverse pests and pathogens. Once pathogens overcome mechanical barriers to infection, plant receptors initiate signaling pathways driving the expression of defense response genes. I have attached some PDFs; hope these will provide useful insight regarding answer to your question.
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I'd like to know about the antibacterial compounds of those species. Can you suggest any previous researches?
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Dear Emerson
Thank you for your interest
Betel leaf has two major compound Hydroxychavicol and eugenol
Both compound has antibacterial activity.
Best wishes
Atikul
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for oxalate, i used 1g sample, 75ml 0f 3M H2SO4 to soak it. filtered and took 25ml aliquot and warm and titrate against 0,05M KMnO4. (1ml KMnO4=2.2mg).
for phytate, i used 2g sample, soak with 100ml 0f 2%HCl, filter and took 25ml aliquot and to it, 53.5ml dH20 was added. 10ml 0.3% ammonium thiocyanate soln was added and titrated against standard iron III chloride containing 0.00195n iron/ml.
 how do i determine these values in mg/100g?
thanks. swift response is anticipated
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Are plant pathogenesis-related protein genes, mlo genes, and SNARE protein defense genes classified as resistance (R) genes? Or do they fall into a different category?
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Yes protien genes,mlo genes and SNAR protein classified resistence R gene
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How well understood is pathogen response MAPK signalling in plants?
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Just download both papers and check references therein
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How does MAPK signalling work in plants in response to pathogen infection?
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This topic is well explored and there is a huge literature resource and review articles available. You just need to find and focus on reading and understanding it.
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Hi I am trying to express my protein R in tobacco leaves and do a CoIP, but I can't detect the protein R in CoIP input.
I took the same tissue and added 8M Urea plus LDS protein buffer, protein R shows as a distinct band at the correct size. But when I grind the tissue and put in CoIP lysis buffer, after centrifugation, I put the input in LDS, I couldn't detect my protein, I only see a smear.
Does anyone know what went wrong?
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ok, we´re working with the Plant Protease Inhibitor cocktail from Sigma (P9599).
This works also fine.
Best and good luck furthermore!
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The production of amino acids in plant depends on the enzymes. Amino and carboxyl group are components of protein.
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We are trying to isolate the mesophyll protoplasts from dicot leaves. So we are using an enzyme combination of cellulase onozuka R-10 and macerozyme R-10. The problem we are currently having is we can even hardly release the cells from the plant tissues. Using the microscope to observe every 1 hour for several hours, we didn't find any significant difference. My understanding is macerozyme R-10 is mainly aimed at releasing the cells from the plant tissues and cellulase onozuka R-10 is mainly aimed at digesting the cell walls. So based on the current problem, should we increase the amount of macerozyme R-10 to enhance the release of the cells? We are also considering to use pectolyase Y-23, so will this help? My last question is if the plant protoplasts are always round shaped or they can be elongated shaped? Any advice and experience about these questions will be greatly appreciated. Thank you very much in advance.
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For protoplasm realization you need to have certain osmotic pressure. It is better to replace enzyme with modified W5 solution. And thereafter shake plates. This will help. also, pH of the enzyme solution must be low (5.1-5,2 as compromise) bacuse enzyme activity were maximal at low pH. 4-5 mM MES at pH 5,1 is OK.
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I want built a small biochemistry lab for research purpose ( Phytochemical Study).
Phytochemical screening
 It refers to the extraction, screening and identification of the medicinally active substances found in plants. Some of the bioactive substances that can be derived from plants are flavonoids, alkaloids, carotenoids, tannin, antioxidants and phenolic compounds.
Please give me some guideline and references for built a small laboratory.
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Hi,
as
Sebastian Schmitt
mentioned, it is indeed necessary to provide a more specific question in this case. Depending on the machines available in your lab it could be possible to perform an analysis more than another. Of course some basic chemicals are in every lab, but to avoid misleading you it could be better to receive more information about the type of research you want to carry.
Please have a look at the following link:
Best regards
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If I have a powdered or ground plant, how can I make a petroleum ether extract of it?
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i am doing plant leaf [fine powder] extraction by soxhlet using petroleum ether as solvent..i am facing problem like
1 smoke on condensor
2 slow extraction process
3 grease like solvent extract in round bottom flask
4 Even on 0 degree celsius it is giving more vapours making smoke on condensor and giving vapours through condensor as water is cold also
5 i have been running it for around 8 hours now ,on even little bit heat extract in round bottom flask is giving black foam like something
please help...
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Dear Colleagues/Editors/Reviewers,
Comment those journals which are going to receive its first impact factor in JUNE 2020 and currently indexed in ESCI, SCOPUS, PubMed, etc.
Journals must be related to plant physiology, plant biology, plant sciences, agriculture, and biotechnology, etc.
Note. Please don't comment any predatory journals. Thanks in advance.
Regards
Ali
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i have got my mass spectrometry results on excel file but now i want to know how could i identify which proteins can be determined (identified) and which can't be identified? and on what criteria? qnd if there is any software that can help me in doing this?
thanks in advance.
regards.
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Knowing which columns are in your Excel file and what mass spectrometer/analysis type they come from would be helpful prior to recommending anything. Assuming you need sequencing info, I agree with Luke V Schneider, but there are many other open source resources, it is just the matter of selecting the one that works with your data type.
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Rice husk is known to be rich in silica. Apart from this, is there any plant known to be rich in Silica?
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Bamboo is also rich in silica content
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Total nitrogen estimation in the plant is preffered.
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The protocol is as follows.By this you can estimate protein as well as non protein (soluble nitrogen).
Crush desired amount (50 mg) of plant material with 5.0ml distilled water.Take 2.0 ml from this and add 3.0 ml 10% cold TCA and centrifuge.Supernatant and residue are used for non protein and protein nitrogen respectively.Digest supernatant and residue separately with 2.0 ml conc.sulphuric acid and a pinch of catalyst (CuSO4 :K2SO4:SeO2 :: 1:8:1).Appearance of apple green colour confifms digestion.Make the volume of the digest to 15 ml with distilled water.This will act as stock solution.
Now,take 1.0 ml of stock solution and to this add 14 ml distilled water and 2.0 ml of 6 N NaOH and keep in an ice bath for 30 minutes.After 30 minutes add freshly
prepared Nessler reagent and read the O D at 490 nm with help of spectrophotometer.
Caliberate the nitrogen content against standard curve. Prepare the standard curve for nitrogen by dissolving 66.0 mg of Ammonium sulphate in 100.0 ml water.
Preparation of Nessler reagent -----
Dissolve 100 g mercuric iodide and 70 g potassium iodide in about 400 ml water (solution A) .A separate solution of NaOH is prepared by dissolving 100 g in about 300 ml water (solution B).Now mix solution A and B and make the volume
to 1000 ml.When the small amount of brownish red ppt. settles down,pour of the
supernatant and use.
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Inulin is a group of naturally occurring polysaccharide produced by many types of plants
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DMSO
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Hi. I am making a research work in a course on my master degree in biotechnology (not a thesis). The assay is about finding new plants with antimicrobial activity. Plants without any kind of investigation in this area.
I prepared extracts of different plants (10 grams dry plant to 200 mL of solvent) in 99,5% ethanol and I just tested them with the Bauer method (disks). 
I now have ethanol extracts of 7 different plants wich already proved to be efficient in some ways against Gram + and Gram - bacteria. But I need to quantify my phenolics.
I never used Folin-C. reagent, neither anything like it so my experience is really zero on this. I read some articles and even the SIngleton et al. paper about this and I can't seem to figure it out how to apply it to my study.
I can't change my solvent due to time and working limitations on the lab, so is it possible to make the FC quantification test for the TPC with ethanol as a solvent?
Can someone please tell me the steps I need, considering I have the FC reagent avaiable and gallic acid as a standard (and I don't know how to use it).
Thank you so much
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Hello all,
I want to design specific primers to amplify a gene using qPCR. I already have many sequences geted by Blast method.
I used Primer3Plus to design primers, then to verify specificity of these primers I blasted each primers with genome of species on which I will work after. But when I blast these primers, they are hybrided in a multiple locations in the genome.
My questions are:
I can consider these primers as specific?
If not, is there a method to specify these primers?
Can you help me to resolve this problem..many thanks.
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Please see below shared information.>>>>>the link: https://bitesizebio.com/10041/designing-qpcr-primers/
A Step-by-Step Guide to Designing qPCR Primers
Primer design is a critical step when setting up your qPCR or reverse transcription-qPCR assay (RT-qPCR). qPCR primers that anneal poorly or to more than one sequence during amplification can significantly impact the quality and reliability of your results. Also, if you are performing a one-step RT-qPCR, the reverse transcriptase will use the reverse primer to prime the transcription reaction. In this scenario, a poor primer would result in both inefficient reverse transcription and inefficient amplification – a lose-lose situation.
Considering the above, it’s well worth spending the time necessary to design good qPCR primers. This article will tell you exactly how to do that!
The good news is that primers are cheap, so you can easily test several different pairs to choose the best ones for your experiment. The bad news is that primer testing requires time and patience, so the sooner you get a pair of primers working, the better.
The NCBI tool Primer BLAST is widely used for qPCR primer design. There are many other primer design tools available online, including primer3, and PCR suppliers often offer their own design programs free of charge.
Below are the main steps involved in designing primers using the NCBI tool Primer BLAST. The design steps will be similar if you use other primer design programs, and the information below should give you an idea of the parameters to watch out for.
Getting Started
Go to the Pubmed gene database and search for your gene of interest. You can filter by species in the right-hand corner of the screen. Click on your gene of interest and scroll down until you find the NCBI Reference Sequence (RefSeq) for your gene (e.g., “NM_203483”). Click there and in the next screen you will see a link to “Pick primers” in the right corner of the screen.
Parameters for qPCR Primers
Set the following primer parameters:
  • PCR product/amplicon size: For efficient amplification, design the primers so that the amplicon is between 70 and 200 bp long.
  • Number of primers to return: This is up to you, depending on how many options you want to choose from. It won’t take long for the program to design ten primer pairs, and this should give you a reasonable chance of finding a suitable pair.
  • Melting temperature: As a rule, aim for a minimum of 60°C and a maximum of 63°C; the ideal melting temperature is 60°C (with a maximum difference of 3°C in the melting temperatures, Tm, of the two primers). You can use a Tm calculator to determine these temperatures.
Exon/Intron Selection
To avoid amplification of contaminating genomic DNA, design primers so that one half of the primer hybridizes to the 3′ end of one exon, and the other half to the 5′ end of the adjacent exon. To do this, simply select “Primer must span an exon-exon junction.” You don’t need to change the other settings.
Primer pair specificity checking parameters: Use the default settings. The program will use the RefSeq mRNA sequence from the organism you selected to design the primers.
Checking the Output Screen
Take a look at the options the program returned and pay special attention to the following:
  • Make sure the 3′ end of the primer contains a C or G residue, because T and A residues bind more easily to DNA in a non-specific way.
  • Aim for a GC content of around 40-60% to ensure maximum product stability.
  • Avoid self complementarity to decrease the possibility of primer-dimer formation. Ideally, the primer should have a near random mix of nucleotides.
Now, pick the best two or three primers and test them. Good luck!
Originally published in 2013. Updated and republished in 2017.
Image Credit: Ulf LiljankoskiBy New England Biolabs
I hope that this will help.
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I'm currently looking for protocols for measuring reducing sugars content in seeds from Passiflora crops. In my review, I have found that the dinitrosalicylic acid assay (DNS) and Nelson and Somogyi methods are repeatedly recommended. And even though I've read some papers comparing these two methods, the comparisons these papers have dealt with are regarding the measurement of enzymatic activity rather than reducing sugars content.
I would appreciate if you can provide me with any references or insights regarding the pros/cons of each method for the measurement of this variable.
Thanks in advance,
Carlos A. Ordóñez-Parra
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Dear Carlos,
Stanley Benedict was an American chemist that discovered a solution to detect the presence of reducing sugar. This reagent (Benedict's reagent) is a complex mixture of sodium carbonate, sodium citrate, and Copper (2) Sulfate. I attached Benedict's original paper for your reference.
Another method for this purpose is the Nelson-Somogyi method that is performing by a mixture of sodium sulfate, potassium sodium tartrate, sodium carbonate, copper (2) sulfate, and sodium bicarbonate that I attached Michal Kaczmarek's handout for you.
Use of dinitrosalicylic acid reagent in another method for determination of reducing sugar that I shared the protocol of this method with you.
I hope that the papers will be useful to you.
Kind regards, Homayoon.
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α -tocopherol is the major vitamin E present in green plant tissues, more specifically in the membranes of chloroplasts and thylakoids.
I performed many protocols to detect and quantify α -tocopherol in Arabidopsis thaliana, tomato, tobacco and grape vine extracts using HPLC (C18 reverse-phase column, methanol as eluent, UV detection 292 nm). The problem is that only one protocol has worked and only on Arabidopsis extract !!! (De vasconcelos et al. 2010. Evaluating the potential of chestnut (Castanea sativa Mill.) fruit pericarp and integument as a source of tocopherols, pigments and polyphenols).
Any suggestion??
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Try a 'spike and recovery' experiment using your standard and extracted sample. This will demonstrate your HPLC is capable of the analysis. In the case were you have a 'high' %Recovery the tocopherol may be below your detection and quantitation limit (LOD and LOQ)(ng?). This may not be surprising since some plants only make tocopherol for their own use which may be very low in concentration. Remember, only a few plants make Vitamin C (Ascorbic Acid) at high levels like lemons that prevent the disease 'scurvy' in humans.
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More and more of world's landscape is getting degraded as a consequence of environmentally detrimental anthropocentric activities. During the 21st Century, when life support system is getting increasingly scarce, humanity's preoccupation must be to restore earth's degraded landscapes. Can mycorrhizae assist in this?
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Dear Birhanu Kagnew, I agree with your statement, but I would advise against
inoculating with mycorrhizal products, derived from other environments. That can have consequences like mutations, that are not always desirable.
If instead, we support the local ones, even if in minimal amounts, the results are much better. Altering the micro equilibrium with "foreign" organisms, is not wise.
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what is the best method to extract and evalute the antimicrobien activity for calotropis procera, like antibacterien & antioxidant activity
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we are try to comparing total cellular content like chlrophyll ,carotenoid ,anthocyanin, proline ,sugar ,antioxidant enzymes of medicinal plant at different altitude level of Himalayas , know about the plant response to abiotic stresses . Will it show any significant result. what else we can do to make our project more informative ?
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Dear Shubhan
The alterations in the leaf structural elements (leaf morphological, anatomical, ultrastructural, morphometrical and photosynthetic parameters) and genome-wide investigation of molecular mechanisms for high-altitude adaptation have attracted great attention in the last few years.
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Hello,
I am looking for a protocol by which I can detect the Ion-leakage in the anthers of my Arabidopsis Mutants.
I want to know the detailed protocol mentioning the tissue amount (anther numbers) and steps to be followed.
TIN
Cheers,
Dharmesh
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Dear Dharmesh, have a look to the attached file!
Regards
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Which one is more suitable to measure heavy metal uptake by aquatic plants.
Can anybody provide me these 2 equations with references? 
Regards
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Bioconcentration factor (BCF) can be expressed as the ratio of the concentration of a chemical in an organism to the concentration of the chemical in the surrounding environment. BCF is expressed in units of liter per kilogram (ratio of mg of chemical per kg of organism to mg of chemical per liter of water).
National Bioaccumulation Factors - EPA
BAF=Cshoot/Csoil; Cshoot and Csoil are metals concentration in the plant shoot (mg/kg-1) and soil (mg/kg-1), respectively. BAF was categorized further as hyperaccumulators, accumulator and excluder to those samples which accumulated metals>1 mg/ kg-1, and < 1, respectively
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The culture is 4 months old and I have used activated charcoal (1%) and citrate (1%) to avoid browning of the PKB's and Seedlings.
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Hello
The PLBs treated with VW medium containing 20% tomato extract did not turn brown during the culture period, and well-developed and healthy PLBs with improved proliferation rates could be harvested
after 12 weeks of culture
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does plant need more light as they grow? what factors in plants to validate that they need more light.
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Jaime , as plant moves through different developmental stages , the plants ability to trap light for photosynthesis undergo huge reorientation over time , within the same light intensity and photoperiod in a given geographic area...
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It seems there's a number of brands and companies to choose from, and no one I know has performed this test.  Abcam's kit seems to be the most widely used from the literature.  Do you have any brands to recommend or any secret tips to share?
Thanks!
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Hell, I am working with this subject and am to use Abcam's kit . I want to know what you used finally, and can you offer me your protocol .
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I want to measure oxalic acid from spinach plant so at the first I need to extract that, but I can't find any protocol about it. Can you help me?
Thanks
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Dear Mahboubeh
Please following this Elsevier paper
Best wishesh
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Does anyone know dubois (1951) formula for calculation of sugar in plant extract? I have already calculated soluble sugar content in the sample using the standard graph developed using pure glucose.
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Biochemical calculations
CALCULATIONS for many biochemical like protein, sugars, free amino acids with appropriate standard.
Amount of test sample taken = 0.5g
Total volume of the supernatant = 10ml
Volume of the sample taken for experiment = 1.0ml
Test sample Absorbance of 1.0ml =____OD units
Find out standard absorbance (OD) units and Standard absorbance value (micro gram) through standard graph.
Calculations
Test sample absorbance x STD. Absorbance Value (micro g) / STD absorbance units = ------- micro gram
micro g/1000 = -------mg
i.e., 1.0ml sample contains = ____mg
10ml supernatant contain ____mg x 10 = _____mg
I.e. 0.5g test sample contain = -----mg
1g of test sample contain = ---mg x 2 = -------mg / gram test sample
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 The net photosynthetic rates of  plantlets  grown in-vitro decreased with
increasing sugar concentration in the medium. 
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I know that cells under tissue culture conditions are different from those in vivo in many ways, but what exactly could trigger antioxidant enzymes such as POX, SOD and CAT in tissue culture media?
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Greetings Abdulla
The main sources for oxidative stress in cell culture is dimolecular oxygen O2 which necessary for cells to grow in culture this source is more pronounced in serum and proteins free culture media where serum and proteins are a good contributor to antioxidants and keep oxidants/antioxidants status in balance in normal animal cells while this balance is disrupted in cell culture due to removal of serum and proteins as well as addition of some various compounds and regulators known to disrupt such balance such as ethanol.
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Dear Colleagues,
Is There a simple method to prepare the extract of leaf, stem and root in order to estimate Na, K, Ca, Mg, Mn, Zn, Fe.
Thank you for your contributions
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Thank you all of you
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Dear colleagues,
Is there any simple method to estimate tannin leaf?
Thank you
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Thank you all of you
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How can I identify fatty acid salts from a plant sample?
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GC-MS is usually the preferred method of analysing fatty acids, but there are many problems with simply extracting the plant material and analysing it.  The fatty acids may be free fatty acids in the plant; more often most of the fatty acid is bound into acylglycerols or phospholipids and these cannot be analysed easily by GC-MS as the molecules are too big.  Then you have two choices.  You could extract the organic material from the plant and break up the complex molecules to release free fatty acids, in which case you will then need to derivatise the fatty acids to analyse by GC-MS.  On the other hand you could aim to analyse the complex molecules by another method (LC-MS or HPLC-MS would be options).  In addition hexane may not be the best solvent for extraction and plant tissue will contain many other compounds besides fatty acids.  The extract may need to be separated by preparative chromatography, depending on how complex the composition is, before analysis.
There is some good information at the link below.  Read some papers about measuring fatty acids in plants as well as they will give methods you could use.
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Recently I have gone through a discussion where they showed that under nitrogen deficient conditions the total carbohydrate content of microalgae increases significantly. as per my knowledge it is not possible if we provide the nitrogen deficient conditions simultaneously we have to provide the other carbon source like glucose, sucrose etc then only we can expect the increase in the total carbohydrate content in the algal biomass.  
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 @togarcheti sarat chandra @vinayak sir  actually I got confused with these two studies no.1 http://ac.els-cdn.com/S0960852413019494/1-s2.0-S0960852413019494-main.pdf?_tid=3d1dbcae-9eb7-11e7-80a3 00000aacb360&acdnat=1505989730_5c0c502257c07cb40400dbcc822b8824
I have some ideas about study 1, if somebody have explanation for the study 2 regarding increased yield of carbohydrate contents can share there ideas.  
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I have visited many historical botanical gardens, but I think that the situation is not one of the best, what are the most serious concerns that face the existence of these botanical gardens? how could the experience of a very expert curator help new botanical gardens to survive?
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Lack of adequate fundings, manpower & proper management and lack of awareness amongst some of the visitors are the major causes for deterioration of the existing historical botanical gardens.
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In rice, under low light condition, the height of the plant increases in comparison to the plants in the normal light environment. Under low light stress, the rate of photosynthesis(P) decreases. As the height of the plant is more so the food the plant produces is utilized for sustenance, instead of grain filling. So if the flag leaf is isolated at the flowering stage for the estimation of total soluble sugar(TSS) then (P) will be always positively (significantly)correlated with TSS. But as the TSS not promptly converted to starch under low light condition, there will be a non-significant correlation between the (P) and starch in the grain. However, under the normal light, the (P) will be positively correlated with TSS in the leaves at flowering stage and starch in the grain. 
IS THIS ANALYSIS CORRECT?
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This question is related to carbohydrate partitioning and sink-source relationship in plant, so you may want to search on those topics. Generally speaking, it depends on whether the plant is annual or perennial. Rice is an annual plant, therefore it has the tendency to give everything it gets to the seeds. Under low light condition, you will notice that seed weight is reduced much less than vegetative part as compared to normal light condition. As such, the correlation between seed weight (mostly starch of course) and PPF in low light condition in rice will be weak. Perennial plants, on the other hand, will sacrifice the fruits or seeds under low light condition to ensure the survival of the plants to wait for another, more favorable year. Therefore in these plants, there is strong correlation between PPF and fruit/seed yield. Under too low light condition, you may not even have any fruit/seed at all.
The correlation between leaf sugar and PPF is another story. This usually depends on the nature of each plant species to buffer its leaf sugar content. In many plants such as tomato, the leaf sugar content is buffered by leaf transitory starch, and as PPF varies, the transitory starch content will vary accordingly, but leaf sugar content will change at a much lesser extent. Other plants such as lettuce, and I believe rice also, do not emphasize on this buffer mechanism, and as such you will see a much clearer correlation between PPF and leaf sugar.
So, in short for your question, for rice, PPF to leaf sugar: yes, PPF to grain starch: not so.
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I am working on protein profiling and I need information on how to collect and preserve leaf samples.
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Thank you.. saidi  for raising the useful question. Thank you for all the answers. I have a doubt for the storage duration. After cold storage, how long we can store the leaf for protein isolation. 
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 iam searching for the protocol to isolate auxin from seaweeds. 
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Hello every on, 
Pease I need the  protocol for the Dark treatments of seedlings of Arabidopsis. If anyine know how can I do that please help me .
Thank you
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I would like to add a general point to the above mentioned protocols.
For germination and subsequent growth experiments it is essential that the developmental programm of the seeds is insync. To acchieve this, I usually put the prepared plates (already wrapped in aluminium foil) for at least 48h to 4°C. Then, at the start of the experiment, I always put the plates for 4 hours to light (best in a light chamber for even light quality), wrap them again afterwards and put them to the growth chamber. The light pulse of 4 hours starts the germination program in all vernalized seeds at the same time. With this you minimize biological variation what results in smaller error bars.
Good luck with your experiments!
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We try to make determination total polyphenol and chlorophyll from younger leaf until mature leaves (from first leaf until 4th leaf). is there any correlation between total polyphenol and chlorophyll in leaf, actually betwen young leaf or mature leaf?
Thanks
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Normally it has been reported that chlorophyll content is directly correlated with antioxidant capacity. For instance, see the following references:
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How can calculate hydrogen peroxide   and MDA content in plant leaves
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 calculated using the extinction coefficient (155 mM-1cm-1). for MDA and (0.28 mM-1cm-1) for H2O2 the calculate  (A532-A600)/ 155 or (A532-A600)*155 and Also for H2O2 
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according to various research paper many researcher prefer soxhlet method for extraction of palnt material. i need some more information about this method. 
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Soxhlet apparatus allows isolation of desired oil even if it has limited solubility in the solvent & when other substances or impurities are insoluble in that solvent. What happens is a nonstop extraction of the oil by continuous contact with the solvent.
Of course,  Soxhlet extraction requires a volume of solvent which reaches the siphon level & time until nearly all the oil is separated. Some may consider this as a disadvantage but this operation is more efficient than extraction by a separatory funnel.
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Ammonium nitrate is banned at present. So it is urgent to find the alternatives to carry  on tissue culture. 
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As for the amounts of KNO3 to be used in the nutrient solution, as mentioned, balances should be made with respect to the initial concentrations of N and K in the basic solution. Meanwhile, KNO3, will have the twice conc. of NH4NO3 subtracted, since it has half the molarity of N. Then, depending on the potassium form already present in the solution, of course it is necessary to make appropriate adjustments not to increase too much the potassium concentration. For example, if you have just K in the form of  KNO3, you could compensate (to reduce) the addition with NH4H2PO4. Obviously, the result must be not to alter (or keep as unaltered as possible) the concentrations of the various micro- and macronutrients of the base solution, of which you know the exact composition. Good job,
Daniela
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Many articles suggest that these compounds are abiotic elicitors but they are synthesized in plants! Pls suggest
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thanx all..
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Hello! I would love to know about the production of secondary compounds, especially about phenolic compounds which are produced in the process of culturing plant tissue. It is supposed to be negative effects for the plant tissues, isnt it? Can anyone help me to explain more about this, and can we eliminate this phenominon? And, it would be better if you can give me the links or references as well. Thanks a lot!
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I think that you are talking about the 'browning' effect, which has a negative impact on the explants and affect regeneration during plant tissue culture.
When the cut explants are placed on tissue-culture medium, in some plant species, brown phenolic exudation around the cut edges of the explants can be seen and even diffuse into the surrounding agar. They have detrimental effect on the explants and even lethal to them. Researchers are adding some substances into the medium to remove or reduce browning. Such substances are, for example, PVP, activated charcoal, antioxidant mixture (ex. ascorbic acid and citric acid) .......
If you use 'browning' and 'plant tissue culture' as keywords for online search, you will find plenty of info regarding this topic. Attached is one review paper for you, which focus on activated charcoal.
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I'm doing isolation of endophytic PGP from plant root and I've read about journal that use bromothymol blue (BTB) as indicator, is there any other option other than using BTB?
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@all, what about growing a potential nitrogen fixer on Glucose nitrogen-free medium (GNFM) and BTB as an indicator for nitrogen-fixation?
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Please colleagues, I need to know how to convert the measure of enzyme activities in plants (Ascorbate peroxidase and Glutathione reductase) from the SI unit of U/L to umol/L. I found that most literature did not report in the SI unit, so I want to convert to make the results comparable to other studies. Kindly assist.
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@Shapiro, thank you for the contribution. I appreciate so much!!!!!!!!!!
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I have tried to separate using Kraay et al 1992 methods using ODS UG 5 HPLC column, however the chlorophyll c1 and c2 cannot separate properly. 
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Please find some links...
Separation of chlorophyll c1 and c2 by reversed-phase high ...
Separation of chlorophyll c1 and c2 by reversed-phase high-performance liquid chromatography on ... of chlorophylls in a typical brown seaweed was ..
Separation, identification and quantification of photosynthetic pigments from three Red Sea seaweeds using reversed-phase high-performance liquid chromatography by Muhammad MI Hegazi
Abstract : Thirty one photosynthetic pigments (chlorophylls, carotenoids and degradation products) from the seaweeds, Codium dwarkense, (Chlorophyta), , Laurencia obtusa , (Rhodophyta) and , Lobophora variegata, (Phaeophyta), were separated in a single-step procedure by reversed phase high-performance liquid chromatography. An elution gradient of methanol, acetone and ammonium acetate solution, and a program time of 65 min, was used to obtain high resolution peaks. Eighteen photosynthetic pigments were separated from C. dwarkense, sixteen from L. obtusa and fourteen from L. variegata. Chlorophyll b, micronone, microxanthin, neoxanthin, siphonein and siphonoxanthin were the most typical and characteristic pigments of C. dwarkense, while chlorophyll c1, c2, fucoxanthin, fucoxanthol, flavoxanthin, diatoxanthin were the most typical pigments in L. variegata. In L. obtusa, chlorophyll d, α-cryptoxanthin, β-cryptoxanthin and fucoxanthin were the most abundant pigments. Source ; Egyptian Journal of Biology Vol.4 2002: 1-6
Preparation and some properties of crystalline chlorophyll c1and c2 from marine algae ,Biochimica et Biophysica Acta (BBA) - General Subjects
Volume 279, Issue 1, 18 August 1972, Pages 15-33
Abstract
1. Chlorophylls c1 and c2 have been purified and crystallized from brown algae, diatom cultures and symbiotic dinoflagellates. The methods involve cellulose chromatography to obtain the first crude chlorophyll c fraction, precipitation of the chlorophyll c at low temperatures from petroleum ether solution, and crystallization from pyridine-acetone. Chlorophylls c1 and c2 were separated by polyethylene chromatography, and crystallized from pyridine-acetone as rhombic platelets (chlorophyll c1) of fine needles (chlorophyll c2).
2. Absorption spectra and extinction coefficients were recorded in pyridine, tetrahydrofuran and dioxane, since crystalline preparations of chlorophylls c1 and c2are not fully soluble in the common solvents diethyl ether and acetone. Extinction coefficients (Band I) of chlorophylls c1 and c2 were 35.0 aand 31.81·g−1·cm−1, respectively, in pyridine solution.
3. Of all algae tested, dinoflagellates contained the highest proportion of chlorophyll c, with a:c ratios on a molecular basis ranging from 1.2:1–2.3:1. In brown seaweeds, diatoms and chrysomonads the a:c ratio varied from 2:1–5.5:1. The content of chlorophyll c1 was equal to chlorophyll c2 in most algae tested. However, exceptions where chlorophyll c1 was greater than chlorophyll c2 and where chlorophyll c2 was greater than chlorophyll c1 were found in several common diatoms. Only chlorophyll c2 was present in dinoflagellates and cryptomonads.
4. Fluorescence spectra of chlorophylls c1 and c2 extended well into the region of chlorophyll a absorbance, with maxima in acetone of 633 and 694 nm and 635 and 696 nm for chlorophyll c1 and chlorophyll c2 respectively. Quantum efficiencies of 0.16 for chlorophyll c1 and 0.15 for chlorophyll c2 were obtained under conditions where values for chlorophylls a and b were 0.24 and 0.09.
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Phytoremediatiion.
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Lead (Pb) accumulates both in roots and leaves of plants, but the concentration is greater in roots than leaves. Please go through the PDF attachments.
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Heavy metal in plant tissue.
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Please check attached link for detail procedure.
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I have grown Arabidopsis in liquid MS for 10 days then I transferred them into 5 micromolar coelenterazine for overnight and I add Jasmonic acid isoleucine for 10 mins. now I want to rescue this plant... so tried to transfer them back to same liquid media, MS agar plates also on the soil. but every time these plants don't grow.. I am fed up of trying to rescue them.. can anyone suggest me something to rescue them??
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 Arabidopsis seeds germinate very well in soil. Even seeds grow on agar plates and plantlets with true leaves are later transplated into soil in pots taking care they remain under high humdity by covering them with polythene bags initially.  It would be interesting to know why you need to grow these plants in liquid medium.
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we are working on improving salinity tolerance in plants  using various strategies. one of the biochemical  indicators of salinity tolerance in plants is the synthesis of the amino acid proline.
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Proline detoxifies the excess reactive oxygen species, improves osmotic adjustment, lends protection to biological membranes, and stabilizes enzymes/proteins. Thus, as expected, proline content in plant leaves increased substantially with the increase in salinity stress. The increase in proline content due to salt stress, as observed in numerous crop plants, is correlative to plant tolerance to salinity. However, we have examined in few plants that foliar application salicylic acid markedly reduced this enhanced proline production. The reduced proline level in salicylic acid treated plants, is indicative of the stress-mitigating role of salicylic acid that might boost plant growth under stress. Reports are also available on up-regulation of proline-biosynthesis enzymes (such as pyrroline-5-carboxylate reductase and γ-glutamyl kinase) and down-regulation of proline oxidase activity resulted in the increased proline level, which helped maintain cell turgor under salinity stress.
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In response to senescence, silver is quite popular in blocking ethylene receptors (by displacing copper). I'm just wondering if it's effect extends beyond ethylene receptors to cytokinin especially in the spirit of cross-talk between these two PGRs
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Thanks Bekele and Petr. From the paper Bekele shared I propably would speculate some silver triggers CK autocatalysis. Probably not by interacting with a CK receptor but as a consequence blocking perception of ethylene. Maybe plant uses CK as substitute?
I can't help notice CK quantities declining at very  high concentrations of AgNPs (if I understood results in fig 4 and 5).
I've seen an old paper by Andrew J. Cary suggesting CK acts upstream of ethylene signalling...I'll think some more about this.
Thanks Petr for your reply. I'll look out for you colleague's paper. Maybe connecting what is known about CK and Auxin with what your colleague would share about Auxin and Ag (seems really cool, I'm expecting to see lots of connection with ethylene - hope I don't get disappointed!) might help me make some sense of CK-Ag relationship (if any) and slowly put a certain observation in cassava into context.
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Root biomass composition like amino acids, fatty acid, sugar, nuc etc composition in mg or in mmol.
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Thank you.
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hi
im studing salt stress. i need to determine cl concentration in roots and leaves.
please help me to know a correct method.
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thanks a lot for your answers.
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Can anyone tell me any cost effective method for extraction of phytohormones especially IAA, Gibberellic acid and cytokinins.  
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Thanks a lot Akila
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I have been told that I should sample only between 11h and 15h. Is it a raisonnable recommendation? Do you have any litterature supporting it?
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Photosynthesis is indeed affected by photoperiod. However, you should note that plants do not use clock. They don't perceive time as human being. Rather than standardize your measuring time from "11 h to 15 h", you should standardize as "5 - 9 hours after sunrise". It is also preferable to measure at times with little change in day length (at high latitude day length may change after 1 month), as well as choosing days that are forecasted to have clear weather with no cloud for stable PPF.
For weather condition, it is good practice to note the condition each time you measure, as suggested by Sam Amsbury. However, you don't need to worry too much because the LI-6400 will set the condition inside the measuring chamber to standard (temp. 25oC, CO2 400 ppm), and as long as the outside condition stays within normal range for the plants, small change in weather (except PPF) would not cause change in photosynthesis of the leaf area inside the chamber.
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I am attempting western blots on Arabidopsis seedlings (7 to 10d old). We have working anti-bodies and western blot conditions, but we are unable to find any signal. I suspect this protein is not very abundant. In addition, this protein may be rapidly degraded. What protein extraction buffers and conditions would be best for this type of assay?
I typically grind liquid nitrogen frozen tissue and then incubate on ice for 30 minutes in an extraction buffer that contains salt, protease inhibitors, triton, EDTA, and DTT in tris buffer. Any help would be greatly appreciated.
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I can typically get 40 ug per well. We know where this protein is expressed, and in seedlings it appears to have a wide pattern based on microarray and GUS data.
Thank you for your suggestions, I will take a look at that publication.
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I am trying to measure free phosphate (Pi) concentration in tomato leaf using molypdenum blue method (ammonium molypdate + ascorbic acid). I followed several published papers to extract Pi from tomato leaf with HClO4 10% (Bozzo et al., 2006, Plant, Cell and Environment 29, 303-313) and TCA 10% (Wilcox et al., 2000, Crop Sci., 1601-1605). Strangely enough, both methods caused serious precipitations with the molypdenum blue reagent, which interfered with OD reading. Increasing ascorbic acid up to 8% in the reagent solution and reducing extraction:reagent ratio to 1:10 (v/v) did not help. You can view the demonstration in the attached files.
Recently I tested the extraction with acetic acid 1%. The result was surprisingly good. There was no precipitation with molypdenum reagent and the color was strong. However, I couldn't find any reference using acetic acid to extract Pi from plant, which seems strange. My question is whether acetic acid 1% is capable of fully extracting Pi from leaf cell, as well as killing cell enzymes which might change Pi concentration upon extraction, and whether it hydrolizes any organic phosphate compound and change the free phosphate content. Any suggestion about the problem with perchloric acid and TCA or a better extraction solvent for this assay is also welcomed.
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In my study I want to measure free phosphate (orthophosphate) in leaf only, therefore I do not perform ashing step, and I also cannot use any extracting solvent that may hydrolize organic phosphate compounds. Free phosphate level in tomato leaf, according to Bozzo et al. (2006), is only around 10 ppm FW (probably around 100 ppm DW), so I think molypdenum blue method which has higher sensitivity would be better.
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working on flower bud formation mechanisms of blueberry, I need to know about previous works on effect of CPPU, and auxin inhibitors on flower bud production in blueberries.  
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Hi Daniel, thank you very much, I saw this paper, it contains very valuable findings.
How about CPPU affect on flowering regulation of blueberry?
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Does canopy diffusive conductance refer to canopy stomatal conductance, canopy transpiration, or canopy evapotranspriation? Or is it something else entirely? 
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Prof. Erik H. Murchie has a lot of papers regarding canopy photosynthesis. You can search of it!
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I am working with hydroalcoholic extract!
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Olá Daniel,
com o HPLC-DAD você conseguirá apenas identificar os componentes presentes na sua amostras. Não recomendo utilizar o GC para identificação de compostos fenólicos. Para determinação da actividade antioxidante tem de utilizar outros ensaios como ABTS, DPPH etc, não sendo possível atraveés das duas técnicas mencionadas anteriormente.
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DNA extraction from a plant leaves rich in phenolic compounds.
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I have a similar protocol for extraction of DNA from plant leaves.  If this protocol doesn't work, you may add PVP to the initial grinding step.
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I am using a protocol from Dhindsa et al., 1981 for SOD, taking OD 560 nm. How do I calculate the SOD activity?
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e.g. SOD activity 45.5 U/ml  and the same samle has protein concentration 2mg/ml it means:
(45.5 U/ml)/(2mg/ml) = 22.7 U/mg protein
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I want to extract total RNA from apple skin. can i use trizol or alternative method should I use?
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Hi mr Alabboud and Yeu Yau 
Thanks so much for your response
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Such as germination, photomorphogenesis, photosynthesis etc.
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As a strong reductant, DTT could disrupt redox homeostasis in many important processes as photosynthesis and respiration.
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I need to prepare substrate with concentrations of arsenic from 0.0 to 10 ppm. Which could be the best substate and preparation for this? I work with seedlings of a tree species.
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