Frogs - Science topic

Erythrocytes of lower animals have phagocytic abilities.

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8792903/

2.

...

Never worked with that kind of samples but when working with bacteria, the sample after heating with laemli buffer gets slimy because of the DNA in the sample. This problem is avoided when DNAseI is used during the protein extraction step (we use 5ug/ml DNAseI final concentration).

You have to find out which frog makes which noise and just train yourself to know :)

KitKat

Favor

Hello Dmitry,

Yes you are right, the M-H equation is same as that of wave equation. Taflov (3rd Ed.) discusses that equation in 2nd chapter. Problem is that book does not discuss TFSF and how to implement it on wave equation.

The problem I was working on required on SF and therefore I was trying to figure out how to implement TFSF in wave equation.

Don't underestimate the strength of the conventional wisdom. The conventional wisdom can explain some parts, but probably not all of a phenomenon. However, in order for others to see that, they have to acknowledge your form of testing to elicit the problem parts. Way too much personal energy and investment in points of view are involved. Much easier to hold to the conventional wisdom and see heads nod when you speak that conventional wisdom. By holding to the conventional wisdom, they retain their positions as "experts." That sounded a little negative, didn't it?

You can obtain eDNA?

Unfortunately, systems that were innocent, such as education, can become doctrinal or ideological elements in the hands of certain governments.

Why is the lysis so long? It should take 10 min.

AudioMoths - https://www.openacousticdevices.info/audiomoth - great sound quality, relatively inexpensive. Depending on the recording duty schedule and the size of the memory card, they can be left out for a few weeks. Unfortunately, they are very difficult to find right now because of chip shortages.

The best program I used to record the sounds of different types of amphibians is Avisoft-SASLab Pro

Interesting question

(The trematode Troglotrema acutum and nematodes of the genus Skrjabingylus are parasitic helminths infecting nasal sinuses of mustelids. Despite different infection routes of these parasites, their occurrence becomes evident due to their destructive lesions of the bone structure of the head).. cited from: Evidence of Troglotrema acutum and Skrjabingylus sp coinfection in a polecat from Lower Austria... DOI: 10.1515/HELMIN-2015-0011

Best regards

Hi there Lachlan,

I don't think you want to do ANOVA or similar linear models since you're using time-dependent data (the number of calls at one hour depends on the number of calls the previous hour). I think your approach of averaging throughout the days is good, but maybe there's no need to average within the hour. Why not have 48 points instead of 24?

Regarding the analysis, you need to do something called time-series analysis, which can get quite complicated (https://stats.stackexchange.com/questions/30640/a-list-of-common-time-series-tests). Instead of going deep into time-series statistics, I propose you perform pair-wise t-tests for each step (0 vs. 0.5, 0.5 vs 1, etc.). There will be significant differences if the frogs start/stop singing. Looking at your graph, that'll be significant at four different times (18-19; 20-21; 5-6 and 7-8). If the difference is (t1 - t0) is positive, the frogs singing more, if it's negative, they're singing less. Using the significance and differences you'll be able to describe their singing behaviour.

Just a note, you might want to consider plotting the counts in a circle plot (polar coordinates), since the end and beggining of the plot are the same hour (24/0). Here you can see some examples in R. http://rstudio-pubs-static.s3.amazonaws.com/3369_998f8b2d788e4a0384ae565c4280aa47.html

Good luck!

Dear Valbona Aliko

As far as I understood correctly from the description of this case. We see an erythrocyte that has frozen - it has a white lumen in its cell, the ice has violated the integrity of the cell. And normal red blood cells that did not have time to freeze.

Regards, Sergey

Thank you for your answers!

, I expected that the RNA would be degraded due to thawing the samples (ubiquitous RNAses) while the DNA (usually considered less prone to degradation) would still be viable, so I was wondering what would be the cause for seeing the exact opposite.

As I am more interested in extracting the DNA for methylation analysis, I was wondering if it could be something related with the extraction kit that I used, so if I use another method, maybe I could still save the DNA from those samples.

But I was not able to formulate a reasonable technical or biological hypothesis for this.

interesting. I did not know. Keep going!

Dear Dalia, Kindly follow the references, although I think you need more papers for comparing the contamination and pollutions, by the way , you can ask me to send other articles for your discussion part!

Anyway, hope they would be helpful:

1- Distribution and Accumulation of Heavy Metals in Surface Sediment of Lake Junín National Reserve, Peru; Available online:

and it is in research gate !

2- The heavy metal contamination of Lake Junín National Reserve, Peru: An unintended consequence of the juxtaposition of hydroelectricity and mining

Available on : https://www.geosociety.org/gsatoday/archive/24/8/article/i1052-5173-24-8-4.htm

3- The History of Mining in Cerro de Pasco and Heavy Metal Deposition in Lake Junin Peru ( it related in 2012 and I attached it)

4- Protected Area Profile Perú Junín National Reserve ( It has been attached)!

Chytridiomycosis is an emerging infectious disease of amphibians caused by an aquatic fungal pathogen, Batrachochytrium dendrobatidis (Bd). You can refer the link given below for more information about Chytridomycosis and its causes, how many species are infected by it, where it is found and how it is spreading etc.

Hello,

besides the previous answers, and integrating some of them, I list some survey techniques used for amphibians and most terrestrial reptiles, inclusive of skinks, in tropical forests, but also in more general contexts.

· Visual detection along fixed transects (not the best in tropical environments, but applicable in some context)

· Visual detection without fixed transect, freely scouting a specific area

· Acoustic encounter along fixed transects (amphibians)

· Acoustic encounter scouting a specific area (amphibians)

· Sporadical-opportunistic observations and acoustic records

· Hand-capture

· Dip-nets

· Hand-capture

· Grabber

· Noose

The use of binoculars can be applied in some environmental contexts and cameras are often essential, as photographs of detected or captured animals are an evidence for verifying species identifications.

Obviously, a general knowledge of the potential presence of some species in the investigated area must lead to examine the zone keeping into consideration the general ecology of each taxon:

- specific forest type (e.g., zones where small areas of primary-secondary dry forest, transitional dry to moist, moist forest, human altered forest are close to each other)

- specific habitat (e.g., trees, poles, tree holes, small rivers, and waterfalls, breeding sites)

- best season

Naturally, each point should be examined regardless of the knowledge of the potential presence of some species in the investigated area (hiding places for some amphibians and skinks, poles for tadpoles, etc.).

Other similar, obvious considerations are as follows.

In all cases, the above mentioned techniques are employed in different ways based on:

- forest type

- season and/or the weather conditions

- hour of the day

(e.g., clearly, for amphibians these techniques aren’t employed in tropical dry forests, during the dry season and in full daylight).

To maximize the success of a survey, some artificial environmentscan be used, such as:

· Artificial covers (amphibians)

· Shelters (amphibians and skinks)

· Basking substrates (skinks)

If the transect techniques is used, each transect can be settled basing on the presence of one of these artificial environments.

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· Pitfall traps (eventually with drift nets)

· Funnel traps

· Bottle traps

· Artificial cover traps

· Microphones (vocalizations ;-)

· Camera-traps (very rarely)

· Pit-fall traps

· Pipe-trap

· Camera-traps (very rarely)

Here again cameras are essential, as photos of captured animals are an evidence for verifying species identifications.

A general, again obvious, remark is to record the location, date, time, and micro-habitat of each record.

A conclusive short remark is as follows.

There aren’t fixed rules to plan a survey, even though sometimes it’s recommended to involve, if possible, 3 to 6 people for 3-5 days in each survey. The number of surveys and their temporal distance depending on the specificity of the study.

Finally, op­portunistic records of various species encountered by local people are useful to create a more exhaustive checklist of the species of an area.

Bennett, D. (1999). Expedition Field Techniques - Reptiles and Amphibians. Geography Outdoors.

Heyer, W. R., M. A. Donnelly, R. W. McDiarmid, L.-A. C. Hayek, and M. S. Foster (1994). Measuring and monitoring biological diversity. Standard methods for amphibians. Smithsonian Institution Press, Washington DC.

Rödel, M.O, Ernst, R. (2004). Measuring and monitoring amphibian diver­sity in tropical forests. I. An evaluation of methods with recommen­dations for standardization. Ecotropica 10: 1–14.

Wilkinson, J. W. (2015). Amphibian Survey and Monitoring Handbook. Pelagic Publishing, Exeter.

Costa-Campos CE, Freire EMX (2019). Richness and composition of anuran assemblages from an Amazonian savanna. ZooKeys 843: 149–169. https://doi.org/10.3897/zookeys.843.33365

Mira-Mendes CB, Ruas DS, Oliveira RM, Castro IM, Dias IR, Baumgarten JE, Juncá FA, Solé M (2018). Amphibians of the Reserva Ecológica Michelin: a high diversity site in the lowland Atlantic Forest of southern Bahia, Brazil. ZooKeys 753: 1–21. https://doi.org/10.3897/zookeys.753.21438

Rödel MO, Glos J (2019). Herpetological surveys in two proposed protected areas in Liberia, West Africa. Zoosyst. Evol. 95: 15-35. https://doi.org/10.3897/zse.95.31726

I agree with Ghassen Kmira. Another benefit is that they are advertising for reproduction as they can afford to be colorful. You could turn it around and ask why aren't all frogs extremely colorful? Most frogs depend on camouflage to avoid predators. Poisonous frogs don't need to hide from most predators. Now I'm wondering if poisonous frogs are as loud as other frogs, since their coloring makes it easier for potential mates to find them. Also most poisonous frogs live in rain forests, where the flora around them is also very colorful.

Selection of appropriate statistical method depends on the following three things: Aim and objective of the study, Type and distribution of the data used, and Nature of the observations (paired/unpaired). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639881/

Agree with the views of Dr Zaal Kikvidze and Dr David Dawson

Hello Zuania,

In your case, I think it would be interesting to build a chamber that can measure respiration both in water and in air. You can check papers on mudskipper or crabs which studied bimodal respiration, you may find advices for chamber design.

I don't work on this but someone in my department does. She said that it varies among species. There are several gene expression studies concerning this topic. Check out Eskew et al., 2018 and Rosenbum et al. 2008

Maybe you could use Partitionfinder (https://www.robertlanfear.com/partitionfinder/) to test if it's ok to run your analysis as a unique sequence or if it would be better to partition it based on different substitution rates. Some algorithms (like the one on RAxML) can construct a tree based on partitioned data with reliable results.

The algorithm should generate the initial population in the search space

Hi Davi Lee,

Fascinating stuff!

I always thought that glass frogs would be good candidates for ultrasound production.

What kind of recorder are you using, Davi Lee? With a sampling rate of 44 kHz, you will necessarily be limited to 22 kHz upper limit in your recordings, as you point out. We are using a 2-channel digital recorder from Sound Devices (model 722) and a GRAS ultrasonic microphone. The recorder has adjustable sample rates up to 192 kHz. I like this recorder very much. It can record directly onto its compact flash card and then the data can be stored on the internal 40 GByte hard drive. The recorder is small and lightweight, but a bit expensive; the microphone is also high-priced. If you can borrow one for your work, this would be a good plan. Hope this helps.

Peter

You somehow seem to confuse homoscedasticity with the fitted values. Clusters of the fitted values only mean that not all fitted values are equally frequent. This happens when the model function has segments that are more "horizontal" (parallel to the predictor dimensions) then other segments. For these "flat" segments, all fitted values are very similar, leading to a cluster in the fittes vs. residual plot (in your case it should be the interaction of continuous predictors allowing for such a "flat" region in the response surface). Homosecdasticity is a feature of the residuals. The variance of the residuals should be similar, independent of anything else, including the fitted values. This means that the scattering in the vertical direction in the residuals vs. fitted plot should be similar along the horizontal direction. It is irrelevant if and where the values on the horizontal direction cluster.

In your plot I don't see a severe violation of the assumption of homoscedasticity.

The QQ plot shows that there is in fact some more or less considerable information in the data that your model is not aware of. Hard to say if this unused information is relevant to your problem.

I would make (many different) plots of the fitted function together with the observed data to get an impression how the model looks like, if it is reasonable and where it has problems to describe the data well. Added variable plots can also be helpful here.

Possible remedies are: i) adding interactions, ii) modelling non-linear relationships.

i) You could try to fit a model with at least all pair-wise interactions

~ (bout_progress + bout_length + WAMP_t + numbr_chucks)^2

or even with all triple-interactions

~ (bout_progress + bout_length + WAMP_t + numbr_chucks)^3

to see if this may be due to a missed interaction.

ii) If variables are included "just" to adjust the effects of other variables, you may consider to use splines rather than linear relationships for these variables (include package splines, then use ... + ns(x, df=3) + ... to include a nonlinear relationship of the variable x in your model. "df" is the number of degrees of freedom of the spline and has a similar meaning like the order of a polynomial (like poly(x,3)), but splines are more flexible (e.g. a spline with 3 d.f. does not need to be symmetric, but a cubic polynomial must be symmetric).

Please see some of the papers we developed at gps-test-site.uga.edu/.

In general, a recreation grade GPS (inexpensive GPS, watch, or phone) has an average accuracy of 6-10 m. A better GPS ($1000-5000) should have an average accuracy of 2-3 m. None of these are "sub-meter" accurate on average.

Hi Vineeth,

In the paper

Narins PM (1995) Temperature dependence of auditory function in the frog. In: Advances in Hearing Research (GA Manley, GM Klump, C Köppl, H Fastl, H Oeckinghaus eds.) World Scientific Publishers, Singapore 198-206, the authors present examples of how temperature afects frog call parameters. The following is one example from this paper of how to calculate the effect of a 10 degree C temperature change (the thermal Q10) for a frequency shift of s octaves:

Hi Umilaela Arifin .

Three methods of DNA extraction from FFPE samples (for each method) were tested: salting-out; Phenol-chlorophorm methods and EasyPure® commercial kit. Two common methods have been used to measure quality and quantity, DNA purity / concentration is measured for quantity using a spectrophotometer (absorbance) and quantity using an agarose gel analysis.

The best concentrations and purity of DNA were obtained by salting-out method and Phenol-chlorophorm . The BCL-2 gene was amplified by PCR to evaluate the equality of extracted DNA. There was no amplification for salting-out and phenol chlorophorm methods. Instead, the BCL-2 gene was amplified only in 2 of 18 samples extracted by EasyPure ® FFPE kit.

Size: We used the same size of tissue for the three protocols, 10µm.

Is frog a model organism for metal toxicity assay? How much heavy metal-containing meals do frogs consume? What does the literature say about effect of heavy metals on frogs? How many people consume frog meat? People in terms of cultures. These are some of the areas of your research that you must tidy up. My answer is Yes! you can. However, your ecotoxicological model will be localized.

Use RNAaes step in the DNA extraction protocol

Hi Nikola,

This is a very interesting topic. I first noticed this phenomenon when on a field trip to Thailand in June, 1995 with my then graduate student Thom Ludwig and my then post-doc, Jakob Christensen-Dalsgaard. We saw several females of Polypedates leucomystax toe tapping on the dense vegetation on which they were perched. We reported this in several publications, including these:

Narins PM (1995) Comparative aspects of interactive communication. In: Active Hearing (Å Flock, D Ottoson, M Ulfendahl eds.) Elsevier Science Ltd, Oxford, UK 363-372.

Narins PM (1995) Frog Communication. Scientific American 273: 78-83.

Narins PM (2001) Vibration communication in vertebrates. In: Ecology of Sensing (F Barth, A Schmidt eds.) Springer-Verlag, Berlin 127-148.

Christensen-Dalsgaard J, Ludwig TA and Narins PM (2002) Call diversity in an Old World treefrog: Level dependence and latency of acoustic responses. Bioacoustics 13: 21-35.

Narins PM (2019) Seismic communication in the Amphibia with special emphases on the anura. In: Biotremology- Studying Vibrational Behavior II (PSM Hill, R Lakes-Harlan, V Mazzoni, PM Narins, M Virant-Doberlet, A Wessel eds.) Springer-Verlag, Heidelberg pp 277-292.

Hope this helps!

Peter

Just a word of caution when recording with a hydrophone in a closed (20L) container. Any vocalizations by the frog will reach the hydrophone via the direct path and via various paths after reflections from the tank. The hydrophone will measure the sum of the sound arriving via all the paths. Ideally, you would want to measure the sound pressure level via the direct path only. There are at least two ways to make the correct measurement. 1.Measure the frog vocalizations in a natural pond (without glass surfaces) to minimize reflections. 2. Measure during a discrete time window that includes the earliest arriving wave (the direct wave) and then stop the measurement before any of the reflected waves arrive. The larger the tank, the easier this is to do. I hope this helps.

how to isolate proteins from spittlebug's foams

many thanks Orlando Grabiel Toledano López for your contribution

Thank you very much for your contribution Orlando Grabiel Toledano López

Dear Dr. Crawford, are you sure that two VERY will be enough?

Xenopus Express

Your welcome!

@ Teguh Muslim

Please have a look at the following references regarding occurrence of Rhacophorus harrissoni in the East Kalimantan province of Indonesia.

https://www.cifor.org/mla/download/publication/amphibian.pdf

Well i dont have exact idea about hatching period of south american toad but it takes about 3 to 14 days and temperature could be in between 17 to 28°c, i hope this little information will be helpful to you. You can refer to this link http://dougwechsler.com/toad/toad_life_cycle.php @

Re Stephen M Levin: Wouldn't an auxetic muscle decrease in volume when it shortens? In any case, it's actual measurements I'm after. Thanks for your interest.

Do you have any information regarding the historic forest composition of the site or region? You could also compare your site to Hyla versicolor sites in Maine, USA. Since H. versicolor has such an extensive range spanning multiple biogeographic regions of the US, it inhabits a wide range of forest types and isn't likely associated with any particular species of tree, but may be more associated with deciduous trees in general. I would try to research the predominating tree species in sites as close as possible to your site and think about forest composition further south using the biogeography of H. versicolor as a guide.

See the ecoregions of New England here: ftp://newftp.epa.gov/EPADataCommons/ORD/Ecoregions/ma/new_eng_eco_pg.pdf

Christopher James Evelyn I am thinking about both of them but mainly focusing on the positional status. Thanks for advices, i got them.

Hi Tokouaho,

It sounds like you should generate a diversity measure for each site (eg. such as the Shannon or Simpson index, or Bray–Curtis dissimilarity), then plot these metrics against time to look for trends. The non-parametric Kruskal–Wallis ANOVA test can be used to test for differences in species richness and relative abundance across sites. Non-metric multidimensional scaling (NMDS) plots would be useful to visualize species-richness patterns among sites based on species composition. There are other ways of getting at these type of questions, but these methods should be a good starting point.

Good luck!

Danny

ps. check out the attached files for more details on assessing temporal changes (Magurran et al. 2010) and spatial differences (Ndriantosa et al. 2017).

Hi,

I am including a reference to an article which I think might be useful. Kindly have a look.

Thank you.

You need to follow standard procedure, such as this one:

Thank you, Rainer and Alexandre, for sharing this information. Interesting! I have also seen Trigona bees feeding on carcasses of different animals. In the upcoming months, I will share our observation of Trigona bees preying upon frog eggs ( in a short manuscript currently in review).

Thanks all for your valuable input! I got the FLIR E8 and will do several tests while in the field.

I have found an answer to this problem. Using galaxy the mpileup option lets you generate a file showing variants in vcf format. Viewing the data in galaxy will show you the raw read depth per base (DP). The output file will be in vcf or bcf format but it can be converted into tabular. I loaded the tabular file in R and created a .xslx file as an output. The raw read depth per base can then be accessed via excel file.

Hello --

If you just want to check spatial and temporal overlap of two beams, all you need is a crystal supporting sum frequency generation (SFG) of the two input beams. You can search online for the correct crystal and phase matching angle for these wavelengths, or you could calculate them yourself very easily using some free software like SNLO's Qmix function. In any case, oftentimes the required crystal cut isn't too different than one you might use for SHG (like in your FROG), so you can often use a crystal you already have (e.g. BBO or KDP) and just tilt/rotate it a little bit to get the desired angle. (Be sure to pay attention to your desired polarization to know if you should be targeting type-I or type-II phase matching! Also, if you reuse a crystal, be aware that some crystals might be coated specifically for use with certain wavelengths, so be aware you might incur some extra losses by using unintended wavelengths.)

Once you've got the right crystal set at the desired angle, align both beams to the crystal using your favorite IR card/viewer in order to ensure spatial overlap. For the beampaths themselves, measure out as carefully as possible the propagation distance of your 800nm and 1040nm beams to get their lengths starting as close as possible to each other. (It would also be wise to use a photodiode and an oscilloscope to directly view the arrival time of your two different pulses, which should easily let you get them overlapped to well within a foot/nanosecond of each other if you've got a diode and scope with halfway decent bandwidth.) In one beam, incorporate a roof mirror on a delay stage so you can easily add and subtract propagation distance without changing the pointing (and therefore the spatial overlap); this will allow you the fine tuning needed to achieve temporal overlap at the fs level (imagine that, for a 200 fs pulse, your path length needs to be accurate to within a few tens of microns (200fs * c (0.3um/fs)) at the very most). To find the temporal overlap at first, adjust the micrometer of the delay stage to the end of its range, and then manually push the stage back and forth, quickly scanning multiple times across the full range while looking at the output for flashes of blue/violet (the sum frequency should generate ~450nm light). If you see the flash, eyeball the position of the stage where you get this temporal overlap, and adjust the micrometer to the position until you can fine tune the temporal overlap with your delay stage, and you're done!

(If you don't see the blue flashes, any number of things could've gone wrong: Do you still have spatial overlap? Do you have the right crystal and polarization? Are the path lengths still too mismatched? Are the intensities of your beams too low to generate the nonlinearity? Is there an underlying synchronization problem? Is the individual jitter in timing/pointing/path length/etc. too large to overcome?)

(All of this assumes that your two beams share a common source/are mutually coherent; if not, none of this will work under normal circumstances.)

(An SHG-FROG is usually designed to accept a single input of a pre-designed wavelength and pulse duration, so the purpose of the device is not specifically to look at overlap of two different beams.)

Good luck!

~Eric

I believe what you have circled is, as Oualid pointed out, genomic DNA, not pcr product. When you start out with a large sample amount you often end up with a large quantity of starting material and, if not diluted, often shows up as a high MW smear on the gel.

I would rule out Batrachochytrium dendrobatidis as temperatures in that brackish waterbody are probably way above the temperatures Bd can handle. But as I am already mentioning temperature: Salinity looks obvious but if that happened during a very hot summer temperatures could have suprassed the CTMax of the species, especially because adult and subadult frogs have lower thermal tolerances than tadpoles. Here is some lit:

Dear Zhang professor,

About missing the protein coding gene, I have concluded in my previous paper in scientific report. I focus on this aspect in discussion. Please check my paper, The mitochondrial genome of booklouse,Liposcelis sculptilis(Psocoptera: Liposcelididae) and the evolutionary timescale of Liposcelis.

Thanks!

Parasite colonization inside the host and way of life would vary according to their feature.

Thank you very much, Max! I will try Oriana first, hoping it is straight forwards!

Amael

Hello,

It's Kaloula pulchra and it's an interesting observation because the species is not often found on trees. Other species within the genus (K. borealis) also climbs trees in fall, for unknown reasons (see link below), and other species preferentially live on trees ( Blackburn et al. 2013. Evolution 67:2631–2646). If it's a (natural) recurrent observation it could be interesting to think about a natural history note to report the behaviour.

Best,

Amael

Hi, you can use the 4th generation Song Meter SM4 which is a compact, weatherproof, dual-channel acoustic recorder capable of capturing large amounts of data from wildlife such as birds, frogs and aquatic life.

Hope this link useful https://www.wildlifeacoustics.com/

Thanks Dr Bakwo for your contribution. i will contact them and give you feeback

looks like Pelobates cultripes (western spadefoot or Iberian spadefoot)

Best regards

Alfonso

Dear Gregor ,

what is the estimated size of the tree frog?