Plant Anatomy - Science topic

Really interesting Q and A !

Would love to read about progress in further elucidation of the phenomenon...Thanks also to Lora Benoit for posting the link to litearture.

Best regards, WHM.

The folllowing articles can give you a clue on the issue you raised, Thank you!

Thanks for this interesting thoughts

Every body will agree that "transverse" is OK.

Strictly speaking the 2 other plans which are necessary for a 3D description are the "longitudinal radial" and the "longitudinal tangential" ones.

The "longitudinal radial" section is determined by the longitudinal axis and any radius. OK, it's clear.

The "longitudinal tangential" section is determined by the longitudinal axis and any plan perpendicular to a radius. Such plan is tangential to the growth rings, hence its name.

A plan tangential to the organ (supposedly cylindrical) will not intersect the organ, obviously. Thus a "tangential section" is necessarily an oxymoron, unless admitted that it has to be understood as "an almost tangential section". A nuance that is perhaps insufficient to justify a revolution, which has hardly bothered generations of users and could only make learning more difficult.

Thanks again for this occasion to think to that

marc

Alistair Leverett Var St. Jeor Sabine Dürr Thanks so much for your suggestions! I actually cut the succulent leaves into 2-3mm sections before the dehydration and embedding in resin, to make sure that the resin will penetrate the tissues. So most of the surface is already exposed mesophyll, so that reasin can penetrate. When looking at the sections, the appearance inside the tissues seems homogenous, which leads me to believe that the resin penetrates properly. It is only the cuticle itself which sometimes detaches from the resin and tears the epidermis in the process. I will reassess the protocol that I'm using, maybe I can make some adjustments following your suggestions. Thanks again :)

hello

Abbas-Azimi, R., Jalili, A., Bakhshi-Khaniki, G., Sobhanian, H., & Matinizadeh, M. (2020). EFFECT OF LATITUDE AND LONGITUDE ON QUANTITATIVE CHANGES OF SOME ANATOMICAL AND MORPHOLOGICAL FEATURES OF ALNUS SUBCORDATA CA MEY. LEAVES IN HYRCANIAN FORESTS. The Iranian Journal of Botany, 26(1), 75-90.

يمكنك مراجعة المختصين في هذا المجال

شكرا لكم

Seems that the images I found have a water mark, or have strong restrictions, so the best way to go is to generate my own images, which is not that bad. It requires more time. The issue here is that images I need will be used for a book , and although I am not expecting to get rich very likely the publishing company will get its share. So the images will be used for commercial purposes. That is the little but important detail that makes this issue tricky. Thank you all for your interest.

Hi

I am doing, the effects of the nanoparticles on plant anatomy (used spray and siol methods)

Without flowers impossible to identify in most cases...

Impatiens omeiana should have underground stolons.

Please have a look at this useful link.

Dear researcher, A research work is based on ones own interest or it can be a work suggested by your guide provided you are confident enough to undertake it. Almost all areas that you have suggested is interesting. Kindly do literature review so that its easy for you to understand what type of research work you would like. Research is neither a work to be done under pressure nor should be hectic. It has to be an enjoyable job which makes you curious to find more...Best wishes..

One of the simplest methods is to make manual cuts from the plant tissue and observe all types of phloem cells under the microscope. Electron microscopy can be useful.

Jose M. Rojas , did you try embedding into resins? Instead of paraffin you may use hard resins such a epon hard, durcupan, araldite or LR White hard. They are used for electron microscopy but when you cut semithin sections (500-1000um), you can observe them in light microscope as well.

The sample need to be properly infiltrated with resin.

Lenka

Dear Ibrahim Abd El Khalek Abd El Mola,

Please also have a look at these useful ResearchGate links.

...

Good luck!

Dr Yeung’s 1998 book might help. Chapter 9 with sectioning techniques is available online:

Please see below the reference:

Daloso, D. M., Williams, T. C., Antunes, W. C., Pinheiro, D. P., Müller, C., Loureiro, M. E., & Fernie, A. R. (2016). Guard cell‐specific upregulation of sucrose synthase 3 reveals that the role of sucrose in stomatal function is primarily energetic. New Phytologist, 209(4), 1470-1483.

There is an exhaustive chapter that listed cuticle properties for plant species. The fine structure of the plant cuticle. In: Riederer M, Mu¨ller C,

But I found contradictions when collecting data from the bibliography..

We are also using image J. The limiting fact is to prepare good slides to have good resolution. The method to mesure is of a minor importance then.

Hi,

For the kind of work you want to perform and being ethanol a soft fixative, you can go for hand cut sections and/or paraffin embeded sections. Yo can also try resin embeded protocols for semithin sections in case you need more resolution.

For hand cut sections (or vibratome sections, if you have one available), you will need practice, so be sure you take useless material and perform several cuts before going with the important samples. You can stain xylem with Toluidine blue O (TBO) or with Phloroglucinol. Here youi can find some info and pictures about what you should get: http://www1.biologie.uni-hamburg.de/b-online/library/webb/BOT410/410Labs/LabsHTML-99/Xylem/Labxyphlo99.html

For TBO, try 0.05% TBO in PO4 buffer (pH 5.5). You will need to adjust time, but start with 5-10 minutes. Then wash with distilled water and mount for microscope observation.

Phloroglucinol: put some drops of 0.1 g Phloroglucinol + 16 ml HCl(37%-12M) + 100 ml etanol 95% on the sample and incubate about 30 minutes (again, check and test time for your samples). Be very careful, because you are using HCl at high concentration! And keep in mind that you must make the observations quickly and take pictures, because the acid will disolve the tissues.

This book can be useful for you to find protocols and techniques, so try to check it: Ruzin, S.E. (1999) Plant Microtechnique and microscopy. Oxford University Press, New York.

For paraffin embeding, you can check internet for general protocols. I have a general description in this paper: https://academic.oup.com/aob/article/95/6/935/189223/Interaction-between-Orobanche-crenata-and-its-Host

I hope this will be helpful for your work.

Cheers.

Have a look at this useful researchgate link also.

You can use Syros et al (2004) methodology for lignin quantification.

Hi, I used for 100mL:

formaldehyde (37%) - 10mL 

Ethanol  (96%) - 50mL

Distilled water - 35mL 

Acetic acid - 5mL 

However,  I don't recommend storing tissues in FAA because it's aggressive and may cause the hardening and fracture of the samples. I recommend wash the samples with water after fixation and storing in ethanol 70%.

Hi Melissa,

measuring vessel length in roots in quite similar as measuring it in shoots.

Tyree has revisited this topic recently. See for instance: 

Pan, R., Geng, J., Cai, J., & Tyree, M. T. (2015). A comparison of two methods for measuring vessel length in woody plants. Plant, cell & environment, 38(12), 2519-2526.

Depending on what you are trying to do, you might want to try looking into a Safranine/Alcian blue combination. Lignified tissue will stain red while the remainder will stain blue.

nice photos...thx steve

Thanks for answering @ Urszula Zajączkowska. But there is a lot  of difference between trichomes & stomata counts in leaf sample. So the above link wont provide me enough help.

I recomend hystoresin embedding kit. Woody structures are hard to cut, and the parafin embedding is not good for this purpose. I'm not sure if cryosectioning is a good technique for woody fruits.

Hystoresin is expensive, but is very good for both woody and non woody fruits. I have had good results with it. The sections can be very thin.

The protocol is detailed with the product.

You will need a rotative microtome.

The classical literature about plant anatomy methods is in:

Johansen, D.A. 1940. Plant microtechnique. New York: Mc Graw-Hill Book.

I recommend this book too, because it has succinct protocols:

Kraus, J.E.; Arduin, M. 1997. Manual básico de técnicas em Anatomia Vegetal. Rio de Janeiro: Edur.

Dear Elham Maghsoodi 

Leaf life span and plant phenology are central elements in strategies for plant carbon gain and nutrient conservation. Although few studies have found that leaf life span correlate with the patterns of leaf dynamics and reproductive output, but there have not been sufficient conclusive tests for relationships between leaf life span and plant phenological traits, the forms and strengths of such relationships are poorly understood. This study was conducted with 49 herb and shrub species collected from the eastern portion of the Tibetan Plateau and grown together in a common garden setting. We investigated leaf life span, the periods of leaf production and death, the time lag between leaf production and death, and the period of plant reproduction (i.e., flowering and fruiting). Interspecific relationships of leaf life span with leaf dynamics and reproduction period were determined. Leaf production period was far longer than leaf death period and largely reflected the interspecific variation of leaf life span. Moreover, leaf life span was positively correlated with the length of reproduction (i.e., flowering and fruiting) period. These relationships were generally consistent across different subgroups of species (herbs vs. shrubs) and indicate potentially widely applicable relationships betweenLLS and aboveground phenology. We concluded that leaf life span is associated not simply with the dynamics of the leaf itself but with reproduction period. The results demonstrate a plant trade‐off in resource allocation between production and reproduction and a coordinated arrangement of leaves, flowers, and fruits in their time investmen

Juliano and Hanan are right! The question is not correct. But you may put these stems and roots in a  polietilene bag and then - in a refrigerator at + 4 degree of Centigrade.

At a gross level, mechanical strength is a function of dry matter/length of the stem.  This indirectly also accounts for the diameter.  Within the dry matter, proportion of cellulose is main determinant of strength.  Although not separately published, it is described in brief in the attached documents.

Fig. 8 in the attached patent contains valuable information on contribution of different maize stalk parts to mechanical strength.

Dear Fatemeh Babaei, after your kind personal message via RG I understand now better. If my "extempore" really / in fact was helpful I shall be glad and again should state that there is no "general fixative" for most of the problems in Natural or Life Sciences we have to solve.. (:-)). But, hopefuly, you'd be willing to state some more detail...? Best wishes and regards, Wolfgang

Dear Sayed,

The description should not only be based on the holotype but all other specimens cited in the protologue i.e.  isotypes and paratypes as well.

Let me explain you the situation. Suppose someone  has designated a flowering specimen as the holotype and its duplicate as isotype. A months later he collected a fruiting specimen and cited it as the paratype in the protologue. It is logical that the  description of the fruiting specimen will also be included in the protologue.

Hope this helps.

Subir.

I  tried to measure chlorophyll content in stems using SPAD, it was unsuccessful because of high stem thickness. Stem chlorophyll content can be measured through colorimetry but need to express on weight basis.

Cellulose is an insoluble substance which is the main constituent of cell walls and of vegetable fibres. Chemically it is a polysaccharide consisting of chains of glucose monomers. Lignin on the other hand side is an organic substance binding the cells fibres and vessels which constitute wood. Lignin is an adaptation to terrestrial habit. Cellulose and lignin are the most abundant renewable carbon sources on Earth. Lignin is highly resistant to decomposition.

Fourier shape analysis is quite common in fisheries studies where fish can be classified into groups by the shape of the otolith (ear bone). Momocs is a really neat package in R for this and the user guide should give you some good ideas on how to start.

regards,

james 

The most common metabolic pathway for photosynthesis is C3. C4 and CAM metabolisms are thought to be an evolution of the C3 pathway.

You may choose your species according to the environment you live. In certain environments C4 are more efficient than C3 or CAM. For instance, the water use efficiency (i.e. amount of carbohydrates produced per unit of water) is definitely higher in CAM plants compared to C4 and C3, respectively. This means that you would probably choose CAM plants in arid environments.

Wild species did not change their photosynthetic pathway due to a direct connection with domestication. They were likely to change their metabolism because of a change in their original environment, which could have been due to domestication or to other factors (e.g. colonization).

I hope I was helpful.

Sapindaceae?

PAS and you can review the book 

Pearse AGE. 1985. Histochemistry: Theoretical and Applied. Vol. 2: Analytical Technology. Edinburgh: Churchill-Livingstone. 1055 p.

Dear Ekaterina,

The suggested 3D effect is a good idea. Many flowers are darker in the center than in the periphery.

I don't know whether humans like spiral shape. If so it may have to do with the so-called golden ratio of picture composition. But this is just an idea.

Hi Lars,

Thank you for your answer!

Following the method of Murakami and colleagues (2006), the principle of this method is the driving of a dye solution in a shoot-to-root direction by increasing the water potential of the shoot (supplying a dye solution) and decreasing the water potential of the soil through desiccation. Thus, the dye percolates downwards trough the root. After staining, the soil is heated (to prevent discoloration of the roots during cleaning) and roots are washed or a soil core is taken. In this case, staining is performed to distinguish the roots of different plant individuals.

Janneke

You can use the equation given by Montgomery (1911) to calculate leaf area of maize from leaf length and width measurements:

LA =  L* W * A

 where LA, L, W, and A are leaf area, leaf length, leaf maximum width and a constant , respectively.  The value of the constant (A) is 0.75.  Once you calculate the total leaf area of all plants in a given area, you can calculate the LAI as the ratio of total leaf area  to the total land area available to the plants.  For tropical maize you can refer to Elings (2000).  You can also refer to the following sources for more information.

Mokhtarpour, Teh,H.C.B.S., Saleh, G., Selamat, A.B, Asadi, M.E., Kamkar, B., 2010. Non-destructive estimation of maize leaf area, fresh weight, and dry weight using leaf length and leaf width. Communications in Biometry and Crop Science 5 (1):  19–26.

Dwyer, L.M., Stewart, D.W. (1986). Leaf area development in field-grown maize. Agronomy Journal 78, 334–343.

Elings, A. (2000). Estimation of leaf area in tropical maize. Agronomy Journal 92, 436–444.

McKee, G.W. (1964). A coefficient for computing leaf area in hybrid corn. Agronomy Journal 56, 240–241.

Montgomery E. G. 1911. Correlation studies in corn. Nebraska Agr. Exp. Sta. Annu. Rep. 24:108-159.

Pearce, R.B., Mock, J.H., Bailey, T.B. (1975). Rapid method for estimating leaf area per plant in maize. Crop Science 15, 691–694.

The second photo is Blepharis maderaspatensis (L.) B.Heyne ex Roth (Acanthaceae) and third Photo looks like a Cyphostemma setosum (Roxb.) Alston (vitaceae)

If the gradient is strong enough in your system, you should be able to find a zonation of some plant functional and anatomical traits. In that case, I would look for different growth rates, contrasting production and/or presence of fleshy tissues and leaf-structures, contrasting production of below-ground structures, presence of water storage structures.. However, independently of whatever you may find, you will have to have in mind conducting experiments to determine whether the correlation between soil characteristics and plant traits have a cause-effect association. Correlation does not imply causation per se. So, the finding of a given pattern won´t "explain" the causes that regulate the establishment of the species you find; it only will give you a clue about it. It will help you to design a better experiment.

Good luck!

Morphometrics is more complex than length, but an optimal sample size is corresponding to the number of replicates that shows the minimal standard deviation. A plot of standard deviation  versus number of replicates is an empirical way for selecting the correct number. Light is a morphogen as well leaf age and sampling should keep these factors under control. a ref for shape analysis is http://www.fc.up.pt/dmat/engmat/2012/seminario/artigos2012/PedroSilva/Plant%20species%20identification%20using%20digital%20morphometrics:%20A%20review.pdf

Yes, you can wash the proteins with NaCl and get rid fo the dye !

According to my microscopic  observation, the vasculars of the maize midrib  have no Kranz structure. The vascular is like those in the stem. Not only in maize, the vascular bundles of the rice midrib are like those in the stem, and  unlike those in lateral veins.Of course, Rice is not a Kranz type plant.

Dear Almeera, 

I found in "Comparative embryology of flowering plants", Leningrad, 1985, for Medinilla mannii  one layed anther wall at maturity, with exothecium only (it have thick walls), without endothecium, (p.94, fig. 5), no fibrous thickening, tapetum is secretory, one-nuclear, middle layers ephemeral. Before opening, two camera of a theca unite (for all species). If it will be useful for you, I can make a copy from a book pages with citations, studied species and figure.

Dear Michaela,

Following points could be studied:

1. Type of Plant-Ant association and specificity/preference

2. Types of biochemicals secreted by both the partners and their response upon each other

3. Synergistic effect of this interaction upon other organisms and vice versa

4. Evolutionary significance (structural and functional)

5. Co-evolutionary mechanisms

etc.

Best Wishes,

P

interesting, I would like to see these images !!, I've worked with plant fibers in TEM

DEar Tanja, according to photo of leaves it is  Acer pseudoplatanus. Maybe the content , shown in long cells represent  some kind of mucilage, which is very common excret of roots  of many plants. However, i have to check the monography of maples what I promissed but  forgotten.

Hi, I can give you some advice coming from my experience. Good sampling is very important; I assume the plant is herbaceous? It is crucial to collect individuals growing in the similar environmental condition and take leaves from the same part of the plant. In our studies we sample 10 leaves per individual and 30 individuals per population (so 25 should be OK). If you need inter-individual variation, you should analize at least 10 leaves - and if you expect differences between vegetative and flowering shoots, you would need 10 leaves od each type of shoots (5 should be enough if you have many samples). This is important to choose leaves from the same part of a shoot - the middle is the best usually, with fully developed leaves. One measurement of each trait from every leaf. You can find examples in the papers (you will see there statistical methods also):

Boratyńska K., Jasińska A.K., Ciepłuch E. 2008. Effect of tree age on needle morphology and anatomy of Pinus uliginosa and Pinus silvestris – species-specific character separation during ontogenesis. Flora - Morphology Distribution Functional Ecology of Plants 11/2008; 203(8-203):617-626. DOI:10.1016/j.flora.2007.10.004

Boratyńska K., Boratyński A. 2007. Taxonomic differences among closely related pines Pinus sylvestris, P. mugo, P. uncinata, P. rotundata and P. uliginosa as revealed in needle sclerenchyma cells. Flora - Morphology Distribution Functional Ecology of Plants 09/2007; 202(7):555-569. DOI:10.1016/j.flora.2006.11.004 ·

Marcysiak K. 2012. Variation of leaf shape of Salix herbacea in Europe. Plant Systematic and Evolution 298: 1597-1607.

Yes I have the article! I was able to download it through my school's journal network. I've attached pictures of a 10 micron thick section where I removed the paraffin first and then stained for 2 minutes, with and without fluorescence. It is a scleriferous evergreen leaf that is thick and fibrous. The second set of pictures are thin deciduous leaves from the same batch. Thank you for the input, I really appreciate it! 

Carnoy's fixative is not suitable for any delicate tissue or organ, usually it is recommended for probes intended for staining of chromatin or chromosomes. Root is built of strongly vacuolated cells that shrink easily at any disturbance of osmotic pressure - try some fixative used for ultrastructure and dehydrate the probes gradually

good luck :-)

post-embedding staining of epoxy sections is difficult, most protocols do not work

standard staining is methylene blue + azure A mixed on a slide put on a hot plate, lignified walls are green, protein-rich parts are blue, and if the probe is OsO4-postfixed, tannin-like compounds are black

there is also a very nice staining with safranin, but it starts at probe dehydratation and does not work well with osmificated probes: add a few drops per vial of stock safranin while in etOH 70%, leave probes for a few days in closed vials, complete the protocol, additionally stain sections - and carefully - with VERY DILUTED methylene blue + azure A; lignified walls + phenolics in vacuoles are brightly red, everything else is blue or blue-green

the safranin idea is from: Baroni Fornasiero R, Bianchi A, Pinetti A. 1998. Anatomical and  ultrastructural observations in Hypericum perforatum L. leaves. Journal of Herbs, Spices and Medicinal Plants 5: 21–33 and my results you can see in Botanical Journal of the Linnean Society, 2010, 163, 70–86.

Good luck :-)

Roots are used to uptake water (among other things) from the soil, therefore the closer proximity to the exterior by the xylem provides a more efficient means of transporting water through the epidermis and into the vascular tissue.

There is link to follow publication:

Tomoda, M., Gonda, R., Shimizu, N, Nakanishi, S., Hikino, H. 1987. A mucilage from Hibiscus moscheutos leaves. //Phytochemistry. Vol. 26. P.2297-2300

http://www.sciencedirect.com/science/article/pii/S0031942200847056 

I hope it will be helpful for you.

Best regards,

Anatoliy Khapugin

Is Lagunaria petersonia!!!

North-east Queensland, Lord Howe Island and Norfolk Island.

Hello,

You would surely find some answers to your questions in this recent review: 

Assessing the response of plant flavonoids to UV radiation: an overview of appropriate techniques

Julkunen-Tiitto et al. Phytochem Rev (2015) 14:273–297

DOI 10.1007/s11101-014-9362-4

Francoise

Hi Victoria,

You should find the answers to all your questions in Sack et al. 2014 Plant Phys. LVD is NOT scale dependent as Price et al suggest (their results are due to artifacts from theLeafGUI software which gives highly inaccurate results; this is explained in depth by Sack et al 2014). You need high enough resolution to actually see all the veins (to measure minor VLA you will need microscope images). For major veins, scanner is fine (for most species). In all cases your leaves have to be chemically cleared. There is a protocol online in Prometheus that explains how to clear leaves, and images veins. (Quantifying leaf vein traits, by Scoffoni&Sack; an updated version of this with more detail should come out soon on the wiki).  We use ImageJ to trace/measure VLA.

Best,

Christine

Hi,

yes the vaccuum extraction method work fine for species with medium size vessels (not for conifers, not for ring porous). 

A good and easy alternative is the 'sap displacement' method: perfuse your segment with a colored solution (like Phloxine or eosine, but NOT Safranine !!!) under low pressure (10 kPa) and collect the sap flowing out of the distal segment. The colored solution will displace the xylem sap. Stop collecting when you see the colored solution flowing out.

Hope you enjoy your Xyl'em apparatus ;-) 

Hervé

Hi Nick Fi,

Please try Dynamic Time Warping((DTW)  for image similarity index. Its a wonderful similarity technique.

Regards:

Ashish

There are two likely explanations that immediately come to mind with this question. Firstly, seedings and saplings of forest tree species are at a competitive disadvantage in terms of light harvesting in the understorey. While the leaves of some species are simply larger during the early phases of development, other species may increase the surface area of the leaf by producing compound forms to increase photosynthetic efficiency. Secondly, compound leaves can be beneficial to a sapling if the plant is attacked by insect predators. If a simple leaf is being eaten, it is likely the whole leaf will be lost before the plant can stimulate production of secondary compounds in defense. In compound leaves, insect attack on a single leaflet can stimulate defense mechanisms which might allow the remaining leaflets on the leaf blade to be protected. This is important in terms of conserving energy.

I do  agree  with Riccardo

One file more

You can use Laser Microdissection Microscope (see http://www.leica-microsystems.com/products/light-microscopes/life-science-research/laser-microdissection/ or http://www.olympusamerica.com/seg_section/product.asp?product=1111&p=410&sub=2&c=0  or http://www.zeiss.com/microscopy/en_de/products/laser-microdissection.html) for single cell isolation.

Hello, Kindly go through enclosed articles fully.All the best.

HÉRAIL (Joseph), BONNET (Valère) - Manipulations de botanique médicale et pharmaceutique - Iconographie histologique des plantes médicinales. Paris : Librairie J.B. Baillière et Fils 1891 320 p, 36 pl describes the rhizome of Acorus calamus

Hello, I read one article related to your query that is,

         "The high concentration of GA3 increased the size of the midrib and its vascular bundle numbers. Both low and high concentrations of 2,4-D inhibited the formation of the midrib. 2,4-D in both low and high concentrations decreased the number of vessels in both protoxylem and metaxylem and also decreased their diameters, where as GA3 in low and high concentrations have less effect on the number of vessels and its diameters."

Go through the attached articles that may very useful to you.

Frank provided a great explanation for easy and accurate LAI measurement.

However, if you want discrete leaf area using imagej, you have to use a plane image of a leaf (using a flat scanner for example), knowing your image scale (you can draw a linear segment of 5 cm next to the leaf). 

Using the straight line tool you can outline the scale, then click Analyze > Set scale... This box will help you to tell imagej how long in cm your straight line is. Then you just have to threshold your image and do a particular analysis to know the area in cm2. I attach a small tutorial (in french language) I had made for interns, hope it helps!

Regards,

Alexandre

Oh, thank you all so much!

Believe, you all helped me in different ways.

My best regards,

Letícia.

E.g. WinRhizo software can be very useful...

Anyway, check whether the roots or root segments in question have developed root hairs, it can change dramatically the real root surface...