Plant Morphology - Science topic

Hi, the answer provided by Prof. Janak Trivedi is pretty comprehensive, agree with that. The ideal approach would be to capture equal number of slices for each stack, but I guess some samples have the signal spread over a greater depth (axially) so you don't want to miss out that signal. Also, you mentioned you make "a maximum intensity profile of Z- stack". So I suggest you average out and also make a montage of your stacks (ImageJ options) and then compare the intensity profiles. Additionally. check out this article:

Hope it helps.

Please also see this useful video.

, Thanks dear Ozodbek,

The blow research article has been conducted from this work, and another paper under editing.

"A novel horizontal subsurface flow constructed wetland planted with Typha angustifolia for treatment of polluted water".

Thanks again

Without flowers impossible to identify in most cases...

Impatiens omeiana should have underground stolons.

It is an Aquenie

Have you checked the ploidy level? In other dicot species haploids show this phenotype...

Alternatively, you can break your directions into a north-south and an east-west aspect component.You require assignation of angles or compass directions in degrees. Depending on your study system, one of these slope aspect components might be of greatest interest (for example if working at a temperate latitude, most likely you would expect the degree of N-S orientation to matter more biologically, due to the difference in solar incidences). If you take the cos (angle) this will give you the N-S component as a numeric form ranging from 1 to -1, with 1 being N (0 or 360 degrees) and -1 being S (180), zero indicates a compete east or west exposition. The Sin(angle) is the E-W component, again ranging from 1 (East) to -1 (West). Then you can run correlations and linear regressions with your data.

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.

Hi Geonyzl,

Is everything going well with the organization of the plant morphology book?

I would love to collaborate. Thanks for the invitation.

My best,

M. Athaydes

This question certainly requires specification. The answers depend heavily on what you are actually want to now.

(1) Morphological evidence considered in total evidence studies; A wide range and the selection depends mostly on the morphological disparity of the lineage inferred. Thus, the answer depends on the lineage of taxa inferred.

(2) Morphological evidence considered in the discussion of studies employing molecular phylogenetic: Again, the answer depends on the organisms studied.

(3) Material used to extract DNA for molecular phylogenetic studies: Again, the answer depends on the organisms studied and the question asked.

The hypothetical answers has one thing in common: it depends very much on the organisms studied.

Have a look at this useful researchgate link also.

Thank you for the answers. 

Thank you, Prof. Munivenkatappa Sanjappa ji, for motivating the budding botanists to consult local floras and become familiar with the native plants. This will surely increase their taxonomic knowledge.

Alternately, photographs of plants can be posted on efloraofindia (many Indian Taxonomists are associated with this google group) or Plant Wealth of India (FB page)  for identification.

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 Dipti,

By seeing the image, its looks like spider web or mite’s web. Insects will form a white sticky thread like structures to protect themselves from the enemies, catching the preys, and to lay eggs. Kindly check any insects or tiny bugs associated with the plant.

Thanks

See this publication it will give you many ideas: http://www.tandfonline.com/doi/pdf/10.1080/01140671.1991.10421787

The tamarillo, Cyphomandra betacea (Cav.) Sendt. (Solanaceae), is a minor fruit crop grown in New Zealand and in subtropical climates elsewhere around the world. There is little genetic variation in the cultigen, but characters of commercial importance have been observed in related wild species. Cyphomandra betacea was crossed with nine other Cyphomandra species. Generally, fruit set was poor and no viable seed was set in the crosses attempted. The use of polyploid forms of C. betacea in some species crosses did not enhance the success of interspecific hybridisation. Various stages of cross failure were identified, most of which were post-zygotic. The data would suggest that incongruity, rather than the S locus, is governing interspecific compatibility in this genus. Suggestions are made for the future genetic improvement of the tamarillo by interspecific hybridisation.

Scenedesmus is not a filamentous form, it is colony of 4,8 and 16 rarely 32 cells.while Spirulina is considered as SCP but recent studies revelas that it may be filamentous rather than unicellualar.

tnx

Ahmed:

Have a look at this link for useful insights:

Best

Syed

Depends a bit how your database was build. If you imported RDE files from different institutes and used the matching options to add duplicates to exisitng records it is possible there are multiple "current dets" within one collection record. You can trace these using the option in the collection file: tools-> determinations->check current det against det history file.

If you added duplicates manually, there will be only one current det, but you can still see if other herbaria have other dets (if you entered so at least) by comparing the records in the dethistory file (botanical records-> view /edit determinations) or when you use an extract, in the "all determination records" extract. In an extract you can first tag all records that are identical for brahms number and identification and remove the duplicates, then tag all double brahms numbers: those should be different dets for the same brahms number. If you only want to compare the most recent dets: first remove the older dets. If you have a slightly different question you can adapt this method to tag records that do satisfy your needs.

Critical Point Dry the petals first otherwise you will observe massive shrinkage and distortion.

I am also agree with expert comments that it is Mucuna pruriens

Mycetia longifolia (Wall.) Kuntze is correct answer by Dr. Arvind. In  Mycetia javanica (Blume) Reinw. ex Korth. the size of peduncle and pedicel is less. 

 I agree totally withnDr, Weston Testo's suggestions

Dr. Srinathrao 

Dear Giulia Arsuffi 

please look into the resources related to your topic

regards

aob.oxfordjournals.org › ... › Annals of Botany › Advance Access

I suggest you to try ImageJ.

Besides reason (1) stated by Dilip Kumar, there coul be an attack of rice blast at panicle neck node. Regards.

Dear Natalie

You should be able to get the PPsystems TPS manual at

It has a lot of useful information.

A relative CO2 calibration can be achieved using the system and a source of very fresh air but of course an absolute calibration would be better using a standard gas as Dr Bongi says, but the manual is very clear – DO NOT USE A WATER TRAP as he suggests as there is real danger of water being sucked back into the IRGA which is very damaging.  The manual gives the correct method. As for the LED – it should not really need calibration but in the absence of a photo flux meter full sunlight can be used  as the upper value. Simple filters based on old darkened photographic negatives can be used to give relative values of PFD for measurements.

Hope this helps

Best wishes

David Lawlor

Mathematics, computer programs, &c., while certainly very useful in many situations, have - like any other "rigorous" methodology - two immanent Achilles' heels. First is what computer specialists often formulate as "garbage in, garbage out": to start a procedure we must put some data in, and if these data are wrong, wrongly interpreted or wrongly selected, then the results would have usually rather little in common with the truth; selection, formulation and interpretation of the data to be put in must be done based on the observable "external" (ecological, geographical, or any, but in taxonomy most frequently morphological) evidence, so our morphological knowledge and intuition is in most cases primarily responsible for the "input" not being "garbage". Second is the fact that complicated (and sometimes even relatively simple) mathematical or computerized procedures are almost invariably (at least for the "average": not specially trained in mathematics and/or computer programming) biologist something like a "black box": we put something (garbage or not) in and receive something out, but typically are not able to check (and understand!) step-by-step what happens in between, so we cannot easily (if at all) discover potential "bugs" (e.g. analogical to those on which the popular mathematical or logical "tricks" - "proofs" that 3 is less than 2, that swift-footed Achilles would never overcome a turtle, &c. - are based, or resulting from the application of the procedure in a situation where the preconditions of its reliable functioning are not met); such pitfalls are not always easy to see, and formalized procedures are typically not "self-verifying": they will not by themselves warn us if the result is wrong, here again the help of observable facts are needed. So, even if we recourse (as we must frequently do) to mathematics or computer-program, the external, directly observable (typically morphological) evidence remains the "alpha and omega" of our study: this assures that input is not "garbage", and this enables us to check whether the output makes biological (ecological, geographical, and especially morphological) sense. Only in this way we can avoid acceptation of such "rigorously derived" results as those obtained by Giribet & Ribera [2000. A review of arthropod phylogeny: new data based on ribosomal DNA sequences and direct character optimization. Cladistics 16: 204-23] where any of the 7 versions of molecular-phylogenetic reconstruction consistently placed e.g. Daphnia among Myriapods or Onychophora, or in BUHAY’s (2009. “COI-like” sequences are becoming problematic in molecular systematic and DNA barcoding studies. J. Crust. Biol. 29, 1: 96-110) somewhat surrealistic but highly symptomatic experiment “I used a subset of” a dataset from a published phylogenetic analysis “and added my favourite recipe for pumpkin pie (imagine it is a numt sequence or junk DNA) to the nexus file ... executed the file and”... “demonstrated” (with 100% bootstrap support!) that her pumpkin pie belongs to the genus Orconectes (Crustacea: Decapoda: Cambaridae) and is the sister species of O. burri! [that, of course, neither Buhay nor Giribet & Ribera have accepted the result of "rigorously performed analyses", was just because the morphological control ["The polyphyletic status of hexapods is certainly unacceptable from a morphological point of view, although it has been repeatedly obtained in molecular analyses of ribosomal sequence data ... [Giribet & Ribera: 222]"]. Not only taxonomy, but science in general, is - as it was for Goethe and Saint-Hilaire - "art and science at the same time", and it must remain so if we do not wish to reduce it to a kind of formal game in which (to use the famous mathematician, Kornél Lánczos words) "interesting is not what the world is, but what it should be" - I am biologist, not mathematician, for me interesting is what the world is, not what it (according to somebody or some rigorous formula) "should" be!

I have been using a little program called imagej it's free to download and simple to use, if you can't figure it out, there are many tutorials on YouTube, but it I s very simple and accurate, just scan your image with a known measurement and you are all set 

Thank you very much for your help,

I found the information needed for my publication. I hope to share it on Research Gate as soon as possible.

Best regards,

Rita

 Thank you for your answer. Then, how about in monocot plants?

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 

Utiliza el método convencional de embebido en parafina (Paraplas plus), fija con FAA en frio (24 horas) en el refrigerador a 6 grados para evitar daños a los tejidos, deshidrata en series de alcoholes o si tienes usa 2,2 dimetoxipropano, corta entre 5-7micrometros y colorea con Safranina y azul de alcian

Dear Tagelsir,

What come across my mind when one talks about cultivars is

Why is it created? ... to get a better juicier or sweeter fruit or keeping the plant at a certain height or having a much better texture or even creating fruits that could be harvested without much pest diseases or even for ornamental

In the above case, there will likely be some differences on the fruits itself, size of seed, colour and thickness of pulp, degree of sweetness and perhaps amount of fibres on the fruit, skin colour and surface, fruit shape and size. Normally, we could guess that a cultivar will have smaller seed compared to wild ones. The descriptions of the fruits and its range can help to differentiate cultivar in the market. I'm sure it has been very much used on cash crops such as apple. Bioversity International (formerly known as IPGRI) had created some plant descriptors and its descriptions regarding this matter as guidelines.

Leaves characteristics such as shape and colour or certain modification feature can be used if you are able to note the differences with your naked eye among the varieties. One that I stumbled upon is in the case of papaya cultivars where the lobes of the leaves can be slightly different when you scrutinized closely among several known cultivars. Together with its fruit and flower characteristics will make it more stronger supported.

 Hope this information will find you useful.

I'm not familiar with RMorphand a cursory online search only brings up references to that book.

I've had success with the R Package Geomorph which may be of help to you; it's designed to handle general landmark geometric morphometrics in 2 and 3 dimensions.

kigelia species 

Dear Eugene

Thank you for your  interesting answer but i am asking for that  for use in field purposes only to give a rough before taking samples for Lab. calculations.

Best Regards

Ali Alhayany

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

You detect QTL through interval mapping and fix it through marker assisted selection.

You can find several striking examples of heterophylly in Marcgraviaceae (Ericales) and in some arboreal Proteaceae of the genus Roupala.

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.

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 :-)

We sequenced the transcriptome last year

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

thanks

This is a cultivar. There are a few varieties of Rosa rugosa but only on the basis of the photo is difficult to say.

TDZ  has a high carry over effect, as pointed out by Yasser. Residual TDZ causes stunting of shoots and inhibits rooting. Subculturing  the explants/plants to a medium containing another cytokinin either alone or in combination with low levels of the auxin IAA or NAA may solve the problem. I faced a similar problem with the tree  Melia volkensii (Meliaceae) and found 1/2 MS  with 0.1 mg/l BAP + 0.01 mg/l IAA  quite effective in restoration of elongation capacity in shoots regenerated on MS or  1/2 MS  using 0.05 to 4mg/l TDZ.

You may also look at the following reference which I found useful in my study.

Hi Sayed, try to read this paper ...

 www.eflora.cn/foc/pdf/Asclepiadaceae.pdf

it may be helpful for you...

 It is Poikilospermum suaveolens, but the  picture is not a fruit, but only flower buds.

I am planning to use a Traditional Morphometric Analysis to determine the quantitative measurement of morphological parts. If I already get a morphometric data, is it applicable to undergo a phylogenetic analysis to determine the evolutionary relationship of a different cultivars of Cassava?

After you characterize based on the result, try to identify the best sesame cultivar for climate change adaptation.

Dear Andres,

I'm from Brazil at São Paulo State University. Here we have one specialist in underground system. Her name Is Professor Beatriz Appezzato da Glória. You can contact her : bagloria@usp.br

She is a specialist in savannas from Cerrado biome  and studied morphological and anatomical aspects of underground systems.

Don't know during which plant developmental stage you observed these mixed leaf structures. But, as Biswapriya suggested, probably you need to wait and check the fully-matured leaves, as the young leaves are still growing and the remaining lobes have not formed yet.

Also, Mohamed raised a good point, what if a plant organ phenotype is decided by allelic genetic segregation results, how would a Plant Taxonomist document it? Especially a QTL trait.

thank you very much for your comments!

Dear  Eustaquio - Is there any alternative to euparal?

Thanks.

I think the first step is to make careful hand sections.  With practice you can get excellent sections of living material.  Put a piece of leaf on a slide in a drop of water and then lay another slide across the first at 90 degrees.  Hold down the upper slide so that it does not move.  Using a sharp razor-blade (I like the "Pal" single-edge carbon steel blades) make a single cut holding the blade against the edge of the upper slide, then a second cut with the blade angled in slightly.  With practice you can get sections almost as good as paraffin sections.  After getting a good look at your material that way then you can decide which embedment to use.

 You can give it a try with agarose imprints (that, besides, shouldn't damage the tissue).

Check this paper: Hensel LL, Nelson MA, Richmond TA, Bleecker AB. The fate of inflorescence meristems is controlled by developing fruits in Arabidopsis. Plant Phys 1994 vol. 106 (3) pp. 863-76

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...

I know that Nathan Kraft (http://life.umd.edu/biology/kraftlab/Home.html) from the University of Maryland works on that subject in Amazonian Ecuador and may have data. I also know two researchers from my university who might have data or guide you to others who do: Renato Valencia (https://www.researchgate.net/profile/Renato_Valencia) and Rafael Cárdenas (recardenasm@yahoo.com). Hope this helps.

Am I missing something here? All I can see is a horizontal rhizome (not a root, but a subterranean stem) from which arise the pinkish developing aerial shoots that will eventually produce leaves and become photosynthetic. There are also some dark-brown remains of the previous year's leaves. All in all, perfectly normal vegetative structures.

It depends on whether it's local flora or alien taxa. I suppose you mean unexpected plant for your area, which you don't have any idea about it.

In this case, a good starting point could be to find the genera with google images if we have some idea about the family. We can keep trying with family, flower color, leaf shape, etc. It's very possible to find some suitable genera and their distribution.

Once we have a short list of possibilities, we could search in local floras available in internet, with good and solid information.

You can find two different examples in links below:

efloras.org: with Flora of China, of Chile, of Misouri, of North America, etc.:

Muestras Neotropicales de Herbario, a visual herbarium of Neotropical countries:

Regards.

Fascinating idea but I am not aware of any such comprehensive code, either.

Concerning birds (as you mentioned them explicitly), there is a standardized age code usually used (at least in Europe) in bird banding/ringing, e.g. 1=nestling, 2=age unknown, 3=first calendar year, etc. (see e.g. http://www.ifv-vogelwarte.de/files/Richtlinien/Handbuch%202-5.pdf - in German). There are also different codes for plumages or moult stages when dealing with field observations.

There are also codes for different breeding records (e.g. whether a nest was found or courtship behaviour was observed. (in Austria: http://www.ornitho.at/index.php?m_id=41; other abbrevations in Germany: http://ornitho.de/index.php?m_id=41 ).

I admit that this far away from a comprehensive code like the one you suggested and it does not concentrate directly on phenology – let alone that it does not include a broader taxon range – but I hope it helps a bit.

Best regards

Darius

This paper is the original description of Sceptronema orientale.

Hmmm. Noticed my counting went wrong in my last answer. I can count up to five -- honestly :-)

It may be worth you reading the paper by Redecker et al. 2013 (Redecker, D., Schüßler, A., Stockinger, H., Stürmer, S. L., Morton, J. B., & Walker, C. (2013). An evidence-based consensus for the classification of arbuscular mycorrhizal fungi (Glomeromycota). Mycorrhiza, 23(7), 515–31. doi:10.1007/s00572-013-0486-y). Can't put it on ResGate for copyright reasons. But this does deal mostly with higher level classifications. Look also at our website amf-phylogeny.com where many original species descriptions can be found as pdf files. You will, I am afraid, notice that several files are not available as the authors and/or journals would not give us permission to add them. The nomenclature is not quite up to date there, but we will try to do it as soon as possible (neither Arthur Schuessler nor myself have any funding for this work).

I fear very much that relating old and new literature will prove very difficult indeed. Few researchers keep voucher specimens, even of cultures, let alone of 'species' they identify from field collections. Lists of species are published without any evidence of the veracity of identification. Careful and detailed re-descriptions and definitions of individual species are difficult or impossible to publish in high-quality journals (not of interest to the general reader, or so it seems). But I must not go on as I am accused by some of my peers of 'ranting' ... (I am indeed old and very cranky).

Hi Anna,

We are using the imprinting technique as well. Before the nail polish stage we attach a dental resin (light-bodied vinylpolysiloxane dental resin (Heraeus-Kulzer, Hanau, Germany) directly to the leaf and removing it as soon as it dries (1min). The resin is the epidermal imprint. The resin is than covered with nail-polish so you'll get a mirror image of the resin imprint. You can look at our article for more details (Hexokinase mediates stomatal closure).

Gilor

Hi,

To compare growth of genotypes, you can use thermal time after sowing or after emergence rather than days which gives a time scale independant of the growing temperature (especially if you did not grow the plants under the same conditions and during the same lenght of time). For this purpose and to be precise, you'll need the base temperature (for germination or for emergence).

I think that the number of leaves, days after sowing and days after emergence are all relevant for comparing DM. To me, it depends on the lenght of the period you compare the hybrids:

-number of leaves: refers to PAR interception and hence biomass accumulation, relevant for studying the vegetative phase and later

-days after sowing: refers to seed reserves (heterotrophic growth) and its impact on early growth and biomass accumulation

-days after emergence: refers to autotrophic growth and hence the capacity to photosynthetise during early phases

Do the hybrids have similar shoot morphology? If not, instead of leaves number, leaf area?

Hope it helps,

Regards

Thanks Dhiraj Singh, it will be a good character to correlate, can you suggest seed boldness range to be resistant to shattering.