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Does a breastfed infant gain immunoprotection due to intramuscular vaccination of the breastfeeder?
There is a claim that infants gain immunoprotection from breastfeeding.  I am especially interested in specific protection against pathogens the breastfeeder (not necessarily the mother) has been vaccinated against intramuscularly.
While I know, that IgA and IgM may be present in breast milk and provide passive protection against foodborne pathogens, it is unclear to me, whether there would be any synthesis (and transport to breast milk) of those antibodies without contact between the pathogen and a mucosal membrane of the breastfeeder.  Answer to my previous question suggest that there would be no IgA production as signals received by B-cells in a muscle will lead mostly to IgG synthesis.
I am not asking about the transplacental transport of IgG, only about breastfeeding.

Vaccinating the mother or a breastfeeder to provide immunization for the baby through breastfeeding is not proven nor recommended by health authorities.
If a mother is vaccinated intramuscularly or any other route, it will anyway pass IgA and IgM, and to a much lesser extent IgG antibodies to the baby through breastmilk but it is not proven to confer specific immunity against all pathogens.
And as per your other question, a child from a mother who hasn't had any infection/vaccination with Hepatitis A and hasn't passed any IgG through the placenta will not be conferred immunity against Hepatitis A even if it is breastfed from a woman who had the infection or was vaccinated against Hepatitis A.
There are other ways a mother's breastmilk can induce immunity (cell immunity) this is currently under research and it has been proven to confer immunity in animal models in recent studies but is still not a medical recommendation in humans (studies in pups regarding passing immunity through foster breastmilk for candida albicans , tuberculosis and helminth infections).
What is already proven is that breasfeeding and vaccination of the baby does provide with a more robust vaccination response so that is why breastfeeding and vaccination to the baby at the same time are encouraged.
Maternal Milk T Cells Drive Development of Transgenerational Th1 Immunity in Offspring Thymus
Pre-conception maternal helminth infection transfers via nursing long-lasting cellular immunity against helminths to offspring

May you point me to the source of the claim that intramuscular immunization leads to transport of specific IgA/IgM to breastmilk? The answer I linked in the question suggests there is no synthesis of specific IgA.


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Is there alternation of generations in animals other than cnidarians?
Are there other animals besides cnidarians that exhibit alternation of generations (having distinct sexual and asexual life stages)? If so, what are these animals? Further, why do so few animals have this kind of life cycle? What are the evolutionary advantages of such a life cycle, and why are cnidarians emphasized in zoology?

Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, each question should be posted separately — this improves the chances that you will get answers for each question and makes the answers more accessible for future users. ——— We also encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). Thanks!

Also note that you are using alternation of generations differently from any usage I have ever encountered. I encourage you to change this to avoid confusion.

According to Wikiwand the heterogamy occurs also in:

some aphids
several rotifer species
Daphnia (freshwater crustacean)

source: Stack Exchange

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Identify this black dragonfly with a bright bluish-white band around its body
I took these photos around noon in late July in Hsinchu county Taiwan. This particular stick in this particular pond is visited by many dragonfly species. This one was very high energy and nervous but taking my time and waiting for it to return each time I spooked it I eventually got almost (but not quite) close enough to take a decent photo with my phone.
Its body is about 5 cm long and mostly jet-black. However it has a bright, solid white or blue-white band about 1 cm long behind the fat part of it's body along the long "tail section".
I'm showing the two best photos below, for the darker one I lowered the brightness of the photo on my phone before taking it so that the band wouldn't be saturated but it is still extremely bright. It may in fact be slightly blue-hued or that could be an effect of the phone's camera.
Is it possible to identify this particular species of dragonfly?

update: A week later on August 7th I revisited the same pond and it's drangonfly stick and photographed what appears to be the same species, but this time it was perched at a different angle and I was able to photograph the "white forehead" more clearly. The first one is overexposed, so I set the exposure on my cellphone camera lower and took the second image. It's remarkable just how bright white these markings are in bright daylight!

@Alex's answer found a very close match with Pseudothemis jorina but as pointed out there that species is generally found in Southeast Asia, not Taiwan or Mainland China.
Pasting Pseudothemis jorina in the species search box in https://www.inaturalist.org/observations (found in this answer to Identify this large, beige or pine cone-colored squareish beetle and/or the pine cone it's on?) it is recognized and the alternative name "Banded skimmer" is also displayed. I show a screen shot of the map of reported sightings below, and it confirms that the range is SE Asia from northern Laos to Singapore. This is not likely the right species, but it seems close.
I remembered another site for Taiwanese insects that was cited in this answer to Identify this insect with a big “face” pattern on its brown fuzzy wings. The site is in Chinese and I can't read it, but I could use google to search the main page http://gaga.biodiv.tw/ for Pseudothemis and we may have a winner!
黃紉蜻蜓 (Huáng rèn dragonfly) Pseudothemis zonata (Burmeister, 1839 )!
inaturalist.org calls this a "Pied Skimmer" and shows sightings from Myanmar in the west to Davao in the southern Philippines up to to South Korea and southern Japan, and even a reported sighting in northern California!
Like Pseudothemis jorina, this species is also reported to have a "white forehead" (per Google translate). I can almost see it in one of the images in the question, I'll be walking past that pond again today so I'll see if one is there and if it has this feature.
I notices in the second image below that there is also a slight bluish hue to the white band on the lower dragonfly. This could also be a photographic artifact and not real, but it's worth noting at least.

The closest match I can find is Pseudothemis jorina:

It's very similar to your pictures in regards of body shape and the light distinct band, although I'm not sure it would normally be found in Taiwan. It's more common further south like Thailand and Malaysia.

Yes I see what you mean, this looks quite close! More images here; but I also see what you mean that it seems a long way from home https://www.inaturalist.org/taxa/149689-Pseudothemis-jorina (I think I'm going to have to get a real camera very soon)

aha! in one of my other species identification questions I've also had links to  http://gaga.biodiv.tw how about this one? http://gaga.biodiv.tw/new23/s3-64.htm

@uhoh Yeah, that looks even closer and also have the black wingtips. I think you have found it, make that an answer.

Oh for Biology SE it's difficult for me to write answers; in this case I'd appreciate it if you just incorporate this into your answer if you don't mind, it's the same genus after all, I just searched the gaga.biodiv.tw site for Pseudothemis. Thanks!

@uhoh I think that you should write an answer and get credit for your research, but I might do as you suggest if this isn't resolved otherwise.

I just checked and my answer to question ratio in Bio SE is 3/89 which seems a little low, so okay I'll write this up. Thank you for your encouragement!

I checked and my answer to question ratio in Bio SE is 3/89 which seems very low, so okay I've written up an answer. Have a look and please feel free to edit if it needs work. Thank you for your encouragement!

Looks like this species is Orthetrum triangulare commonly known as blue-tailed forest hawk.
It is an Asian fresh water dragon fly species.
As you mentioned that the dragonfly had a bluish hue, it became clear.

Since a similar type of this, called Orthetrum albistylum commonly known as black-tailed skimmer is found in Central and South Europe to China and Japan.
However it has got a black color.

Well this is an interesting situation, because these images look very much (but not exactly) some pics I took 20 minutes later at a different pond! https://i.sstatic.net/ldszK.jpg and https://i.sstatic.net/arDJx.jpg This one was much more approachable and I could get quite close. The band on the dragonfly in my original posted image looks much more abrupt and contrasty than your images or these I've put in this comment. I wonder if I should post them in the question instead of the one that's there, and then post that one separately? What do you think? Are both the same species?

I don't think this is right. The distinct white band in OPs pictures ends right after the second wing pair, quite different from this. Also, it has black tips on the end of the wings, while this has black markings slightly in front of the tips.

@uhoh are you sure the images which you have given in the comment section are of the same dragonfly which you had seen earlier?

@Alex yes but the op had mentioned about the blue color instead of black. That changed my answer

@Ojasvi no I think they are different, and the images in my comment are a better match to your answer than my question. Why don't I post those two as a new and separate question and you can copy/paste this answer there as well?

@uhoh I think my images do not match your pic in the comment. Since it is not much clear in the pics can you recall whether it's tail had a uniform color or had straps ?  I am talking about the one you have posted in the comment

I don't recall at all, the only thing I have is these and a few more photos very similar to them. The photos are taken from much closer to the insect than my eyes were, I definitely didn't see this level of detail until later when reviewing the photos.

And yes, you should make those two images into a new question!

@Ojasvi okay I'll get to it today, thanks!

@Ojasvi well not quite the same day, but I've finally gotten to it! I’ve now just asked: Identify this black dragonfly with bluish coloration along its flat top, yellow on it's mid-body and green on its head

@uhoh Thanks for letting me know. However I think I agree with Andrew's answer

@Perhaps it's one of these? Identify these two big, beautiful dragonflies in Taiwan?

@uhoh Thanks! You seem to have a great interest in dragonflies!! :)

I grew up in a cold climate with limited flora and fauna. I've been living here a long time now but I'm always seeing something I've never seen before; it's very exciting for me :-)

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A strand of my hair has a grey section in the middle, how is this possible? And why does it happen?
My hair is usually brown and black, I haven't dyed my hair for two years and if I had this would be strange. A strand of hair went from black(roots) grey (middle) then light brown(bottom).
How does hair change color along its length? And why does this happen?

I am curious about this too! I am naturally blonde, and on some of the strands of my hair I have random sections of red, then it goes back to blonde.

Your hair gets its color from a compound known as melanin, produced by special cells called melanocytes. There are two versions of melanin - one that produces dark pigmentation and the other that produces light pigmentation. If your natural hair color is brown/black, then it normally has a specific amount of dark vs light pigment. The middle section of this hair is grey because there was an absence of melanin production when the hair was still growing. There could be multiple factors (including stress , as described on the library of congress site), but it's nothing to worry about. Your melanocytes started to normally produce melanin again, which is why the newest hair growth (closest to the roots) is dark in color (dark brown/black).

Hi, @Kate. This is a good answer, thanks. I've often heard about the stress link with grey hair. Could you provide a citation to it? Could you provide a citation about the temporary lack of melanin production. I know some people produce a grey hair once in a while, but I thought the whole hair would be grey, not a section. Generally, on this site citations are useful for good answers.

Sorry - new here, didn't know! Here's a useful link:
https://www.loc.gov/rr/scitech/mysteries/grayhair.html

Welcome to Bio.SE :). I added the link into your answer. I have a feeling that this question will be closed though since it might be medical related.

It has recently been found that hair greying can be reversible in humans.
https://elifesciences.org/articles/67437

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What species is this marine invertebrate sighted 2m below the surface near Halifax, NS?
This image was taken at ~2m depth, with a small ROV in Halifax, NS in May. We're in the Northwest Atlantic Ocean and as far as I know, don't have gooseneck barnacles.
Considering that it may be a polychaete worm as several other species were sighted during same dive (Tomopteris ?, Chaetopterus) and the fan appears to have more than 10 appendages. Possibly a sabellid or goblin worm?
Sizing is difficult to estimate but ~5cm in length.

Adjusted, enlarged version:


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Help identifying small snake in southern India
I found a baby snake near a hill in Karnataka, Southern part of India.
It's monsoon season here.
Approximate length - 15 cm


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Giant insects growing question
During the dinosaurs time 100-200 million years ago there were giant insects like 1 meter long. An example is here. One of the theories why they could grow this big is that oxygen level was much higher than now. Now we have like 20% oxygen in the air and that time it was 30 or 40.
The question:
If I make a tank/aquarium with 40% oxygen and all the equipment to make this oxygen concentration constant. I put there modern insects, dragon fly, worms, slugs, etc. Will they grow to much bigger size than normal from the 1-2 generations, or I will need to have 100 or 1000 generations before they will be bigger?

This has been done in insects at least: https://jvandenbrooks.wordpress.com/research/

You would need some sort of factor that selects for a larger size.  This isn't impossible, since humans do selective breeding for size in animals (e.g. St. Bernards and Chihuahuas) and in plants.  I don't know of any selective breeding of insects (maybe honeybees?), but I'm sure it could be done.

that sounds like a fun experiment!  But unfortunately you are right, the size difference is shaped by genetics as well as an environmental condition that might be hard to pin down.
For the genetics, It would indeed take millions of years (or at least 100,000s) for the genetic adaptation to kick in to create that change.
As for the environmental conditions, another source of gigantism is being on an island.  As the small number of species expand to fill out all the niches in the tank, they may get larger simply because the environment allows it with no predators.
The tank would have to be enormous to get those niches I think. This paper describes an archipelago of islands and shows that you tend to get smaller animals more easily with smaller islands, and larger species need larger islands.  Large here is millions of square meters.
Both of these processes take many generations. This is not my field but this paper studied 200 generations of plants and showed only migration and lifespan changes.  Size adaptations that come with changing ecological roles might have to take 1000s of generations. We'd have to freeze ourselves to see the giant slugs.  I'm sure there's a better answer out there, but this is what i found so far.

was richard nixon frozen in time?


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Is this aquatic plant duckweed or something else?

This plant has been growing in my pond for quite a time now. It multiplies in large numbers rapidly.
 Some told me it is duckweed or is it something else?

Can you please [edit] to add additional information as specified in the "species-identification" tag (hover over or click the tag to see details). In particular, measurements of the leaf diameter might be very helpful. Thanks!

That looks very much like a duckweed.
The multiple roots rule out most genera within this group and so this is probably a Spirodela.
The apparently relatively large size and red undersides are consistent with this being Spirodela polyrhiza.

Picture by Christian Fischer available under Creative Commons Attribution-Share Alike 3.0 Unported.

Not duck weed. It is Salvinia species very easy to grow ( invasive). I believe it is illegal to introduce in some US states. Koi /carp will eat duck weed.There are a few similar species of salvinia , unfortunately references will give the same name for different plants. My book ( Aquarium Plants ; Barry Jones, Tetra press) calls it auriculata which I believe is wrong. Auriculata is also called giant salvinia and looks different ( see comments @ tyersome ). I have grown Auriculata but not the salvinia that you have.

This is not correct — Salvinia species look completely different, for example they have hairs on the leaf surface and their "roots" look completely different — see for example here: https://www.cabi.org/isc/datasheet/48444.

I have edited to what I believe is correct.


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In Griffith's experiment, if both S and R strains are added, can the R strain be isolated from the blood of the mice?
In Griffith's experiment on transformation, when both the S strain and the R strain were injected into the blood of the mice, could the R strain be isolated from the blood of the dead mice?
I think it's not possible as R strains are deactivated by the immune system of the mouse, but Wikipedia says both R and S strains were isolated from the dead mice.

What is your question?

whether live r strain can be isolated from blood of the dead mice in griffith's experiment when injected with both virulent s strain and non virulent r strain

It would be nice if you could start sentences with a capital letter, and also use capital letters for people’s surnames. Question marks are needed after questions. If you did this it would show that you had made an effort in constructing your question and encourage us to answer it.

I have a suggestion if possible read the Griffith's experiment from Benjamin Peirce..

S starin have capsule and cause infection.
R starin have no capsule and not cause infection.
According to griffith experiment S strain was killed by heat but R starin remain active, because S strain provide genatic information R strain. Then R strain use information to complete own structrure and reproduce itself.


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What parasites would be easiest to examine using a compound microscope?
I want to find some parasites that are easy to examine under the microscope.
I'm a beginner but I have an olympus microscope with total magnification up to 400x (also 200x, 100x and 10x).
I would like to choose parasites that are safe for me as an amateur to work with and would like to have one that parasitizes people.
I prefer lets say:
Helminths, mycose (Candida alba) or something that can make people sick and is safe to work for someone who is an amateur.

You don't need microscopes to observe some parasites (for e.g. leech). So you should clarify what kind of parasites you are interested in.

You should also specify how you plan on getting ahold of parasites that can make people sick because that likely limits your options.

I suggested an edit to your question that includes changing "Helmits" to Helminths — if that isn't what you meant can you clarify what Helmits are?  Also I'm not sure that a microscopic human parasite is ever going to be "safe" for an amateur to work with — can you add something to your question to clarify why you want to do this?

Yes safity is very important. So I dont want anything that is dangerous. So I want to examine them under the microscope.

Lets say mycose and to choose candida alba, how to grow them cultivate and examine under microscope? So first question is then how to cultivate it (grow), control it and then as last step examine them undet microscope? Or should I start with beer mycose, that is safer and after that to start with othes spicies?


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Specificity in MAPK/ERK pathway and PC12 Cells
Background
PC12 Cell stimulation leads to distinct outcomes upon stimulation with either EGF or NGF (epidermal and nerve growth factors). The outputs are transmitted through the MAPK/ERK signaling pathway; stimulation with EGF causes transient activation of the ERK, via a negative feedback loop, leading to cell proliferation whereas stimulation with NGF leads to sustained activation of ERK, via a positive feedback loop, leading to differentiation.
Question
How does the signaling pathway know which kind of feedback loop to initiate at the ERK level from upstream stimulation by EGF or NGF?
Helpful Image to explain question
To reiterate: I want to figure out how EGF binding at the membrane level triggers negative feedback downstream, and NGF binding triggers positive feedback?
A link to the image is (http://www.nature.com/nrm/journal/v12/n2/fig_tab/nrm3048_F4.html)

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Freezing after restriction digest
Brief question:
I have performed a double digest with heat inactivated restriction enzymes with no star activity. I usually purify the DNA (PCR inserts and linearised vector) using a kit or gel electrophoresis but today I don't have time for it.
Is it okay to freeze (-20*C) the PCR inserts and linearised vector following heat inactivation of the enzymes? After a week, I will thaw, purify and perform ligation on these products.
Thanks!

From my experience I would say that it is no problem to freeze the digested DNA, when the enzyme is inactivated (even when not, for this time period I wouldn't expect much damage).
However, if possible, I would rather opt to freeze the PCR product and make the digest fresh, since the overhanging ends are kind of sensitive to hydrolytic degradation. I have also frozen linearized vectors without problems.


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How do the connections from V1 to V2 form during early development of the human brain?
I am wondering how corticocortical efferents from layer I and II in V1 develop to forward visual information to layer IV in V2. Is there topology preservation in these connections from the beginning on or does it only emerge later?


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How long does a spiking signal last?
It is surprisingly hard to find information about the timing of neurons, in particular how long an action potential can contribute to the summation of a neuron. Is it on the order of milliseconds or rather seconds, i.e. for a neuron to fire, do many of the presynaptic neurons fire about at the same time?

I can answer the first part but I don't quite understand how your second part "do many of the presynaptic neurons fire about at the same time?" relate to it. Can you elaborate or clarify?

My thought was that if the falloff of the activation is very quick, then it would matter than many neurons have to fire within a brief time window to surpass the activation threshold.

Effective integration time of a typical neuron is in the order of 10-100 ms. You might want to look into this classic paper (read it with a critical mindset):

Shadlen, M. N. and Newsome, W. T. (1994). Noise, neural codes and cortical organization. Curr. Opin. Neurobiol., 4:569-579.

Or some biophysics book like:

Biophysics of Computation by Christof Koch

What is effective integration time? and what is a typical neuron? Do you mean a physical one or a modeled one?

@nico good questions. I should expand this answer at some point...

The length of an action potential (or spike) varies depending on several factors: refractory period, type of cell (interneurons tend to be faster) and where in the brain you are recording (in cortex both area and layer are important). Wikipedia page says something about 1ms for sodium based and 100ms for calcium based spikes.I never saw a 100ms AP, usually I record from cortex where I find AP in the range of ~1 to ~5ms.
The length of the integration however depends on too many factors, length of the dendritic tree, spatial location of the synapses, number of those synapses, strength, spine clustering, affinity and time constant of receptors, amount of Calcium, etc... the Shadlen and Newsome paper @Memming referred to is a good start. In general I'm always weary of magical numbers, if its a measurable phenomenon it's just what it is if not everithing comes with a lot of assumptions...

Thanks for this answers. Since you know about neuronal measurements in the cortex, you might perhaps also know an answer on this question on neural firing rates. Thanks again!


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Biological implementation of convolutional neural networks
In computer science, 'convolutional neural networks' are used, that are meant to be inspired by biological network structures like found in the human brain visual cortex.
In the computer implementation, the 'convolution' means that any neuron of a certain 'layer' is linked with several spatial adjacent neurons in the previous layer. When those networks are trained, the 'weights', which are analog to synaptic strength, of all neurons of one layer have an equivalent local topology, and thus can be mapped between the neurons, and finally unified. This way, only one 'weight' is trained for all equivalent synapses on all neurons of an layer.
Is there any biological mechanism found that may sport this feature? My guess would be that the vision cortex is partly organised by self structuring not depending on neural activation to achieve low level vision processing. Otherwise, all neurons in one 'layer' would need a way to exchange information to synchronize their synaptic structure.
However, I guess that the human brain would have some mechanism of this kind, as it would provide for example the ability to learn the detection of certain visual patterns or events independent of their retinal position, without learning the detection individually for every image location.
Is any such mechanism known or how could it work?

As you already said, there are several parts of the brain that have this kind of mechanism. I am not clear about what you are asking.

The usual model of neurons and plastic synapses does not explain this feature, as large numbers of physically unconnected synapses would need to have some magic remote communication to equalize their transmission strength. So my question is if there are any mechanisms known in neural tissue which may implement this feature.

I believe CNNs were inspired on the fact that the visual cortex has neurons that have a fairly small "visual field" and they overlap each other. Not necessarily that they are tied together.

The eye might provide alone an example of a convolution neural network (as made popular for image classification tasks).
The cell types and synaptic connections in the retina are even organized in layers (laminae) to make the parallel clearer, as seen here:

source: http://webvision.med.utah.edu/book/part-vi-development-of-cell-types-and-synaptic-connections-in-the-retina/development-of-cell-types-and-synaptic-connections-in-the-retina/
The topology of the network is in a sense self-structured but a relatively slow process as the blueprint is a product of Evolution and the practical implementation (actual cells and connections) takes place during the development of the organ. "Weight tying" can then be seen as a result of having different cells types in the network.

I would agree that this is a data processing convulutional structure. But shared wheights (maybe encoded by cell types) would be a genetical feature then, and they can not be trained in a shared fashion in the living organism. Simply said, if the circuit learns by weight adaption how to detect an eye projectet to part of the retina, that doesn't mean other parts of the visual field would detect this eye as well.
This feature however holds for CNNs by sharing the weights on all convolutional subunits in one layer and speeds up learning by orders of magnitude.
So can brain do this?

I believe it is important to create a distinction in terms of what level of visual system you are referring to; i.e. retina vs higher level cortical visual areas. Also, if I remember correctly, the weights are represented by the strength of synaptic connections, which are modified adaptively during the process of learning and not hard-coded by genetics. You might find it useful to take a look at http://goo.gl/ygP6nF

One could hypothesize that "learning" takes place at two levels: one is evolutionary and one is within an organism's lifespan. Cell (neuron) types are "trained through evolution (may be not the idea you had of speed though but the same advantage, presumably). Regarding the amount of visual "processing" performed down by the retina (not everything is down in the cortex), there is a relatively short read on wikipedia: https://en.wikipedia.org/wiki/Receptive_field


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Ant trail behaviour
I observed an ant trail through a house for some years. I wonder why the ants established that trail.
The ants are small ants of common type for middle europe, found almost everywhere in this region.
The very small trail (about one ant per second) enters the house through gaps near the front door, travel the entire house almost hidden except some short parts where they need to cross nacked floor and exit the house through gaps on the other side. They pass the kitchen, but do not enter it, missing the easy chance of picking food there.  Before and after the house, the place is sealed (eg. asphalt or stone plates).
Ants are passing the trail in both directions.
The trail is almost impossible to fight. If cleaned up (using alcohol to remove the traces) it reestablishes in about one day. If holes are blocked, new ones are made (even through silicone or soft concrete) in some days. If hidden gaps are sealed, they tend to use visible trails for some days, but work hard to repoen the hidden gaps.
If all ants on the trail are killed or collected over some time, it doesn't seem to have a long term effect at all.
I've never seen any of the ants visibly carrying anything, if the carry something it must be in their stomach.
So why are the ants so eagerly establishing this trail?

Interesting question. BTW: do you know the species? Lasius niger?

Most likely it's Lasius Niger. But I am no expert in this.


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What happens when a genome is shorter than the other?
Say there were 2 creatures of the same species. Creature 1 has a longer genome than creature 2, it may be just a few base pairs, but what would happen when the genes were crossed to create creature 3 (via Sexual Reproduction)? Do the genes know where to match up or are there genes that end up being corrupted during this process?
Thanks in advance

there wont be a third species when you cross two organims of the same species with one which has a mutation in some areas of its genome. All of us have some mutation or the other and our genomes are never identical. So when humans have kids, you can expect some mutations in the child but never another species. Unless you are talking about evolution over millions of years or a case where there is crossbreeding between species like a horse and a donkey

@TheLastWord a second or third species was never mentioned. OP talks about Creatures 1, 2, and 3, but they are all the same species. The question seems pretty clear to me - What happens when homologous sequences of DNA have short insertions or deletions on one chromosome but not the other?

What type of "matching up" and possible "corruption" (during recombination?) are you referring to? Mitosis in creature 3, meiosis in creature 3 or normal gene expression during the life of creature 3?


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What is the top speed of muscle contraction?
Currently I am looking into what muscles groups are most used during a football kick. I have a hypothesis that the quadriceps are not as used as most people think because the momentum the swing creates makes the knee extend to fast for the quadriceps to contract.
To prove this I need to know the speed the knee extends during a football kick and the time it takes for the quadriceps to contract. I know how fast the knee extends through my own research.
Does anyone have any information on the speed of muscle contraction?
Quadriceps contraction time would be optimal, but any information relevant would be very helpful

Your question is a good one. The velocity of muscle contraction depends on the:

Initial length of the muscle
The Load on the muscle

Source: Medical Physiology : a cellular and molecular approach by Walter F. Boron, Emile L. Boulpaep - 2nd ed. Page 248

From the above picture we can see that:

The velocity of muscle contraction is not constant. Initially it is zero and then it accelerates to reach a peak
The maximum velocity of muscle contraction is constant at any different initial muscle length
The lower the load the steeper the rise of velocity

So the velocity of muscle contraction should be calculated on a case by case basis.
What can be calculated
What can be calculated is the displacement and frequency of actin myosin cross-bridging.
Under microscopically isotonic conditions, the quantal displacement of a single cross-bridge is ~11 nm.
The frequency of actin-myosin cross-bridging depends on atleast:

ATP concentration
Temperature

At an ATP concentration of 1 µM the frequency is 3.8 ± 0.4 M-1s-1
At 170C the mean time for single displacement was 15±20 ms. While at 250C the mean was 6.4±3.6 ms.

Source: Characterization of Single Actin-Myosin Interactions by Jeffrey T. Finer, Amit D. Mehta and James A. Spudich.
Biophysical Journal, Volume 68, April 1995, p.291s-297s

Concerning your actual question regarding the quadriceps velocity and the velocity of the swing, you should keep the following in mind while calculating:

Quadriceps acts over a second order lever: The Knee is the fulcrum, the effort is put over the tibial tuberosity where the quadriceps is inserted and the load is the foot and whatever it hits/lifts...
The contraction of the quadriceps is calculated as linear velocity while the kicking action is circular - so what you actually observe is the angular velocity. So appropriate angular velocity to linear velocity conversion should be made.

All the best!


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How did evolution support sports, fun, entertainment etc
We know that many animals entertain themselves by playing games. But sports actually increases risks of death,or at least accidents. So why did evolution choose it? And why did evolution decide to make us look for entertainment every now and then?

not moving and sitting behind a desk all day probably poses more risks.

Evolution didn't "make" us do anything, it created a brain which can choose to do or not do them.  As for games and participant sports, think of them as practice for the various challenges of life - the old "use it or lose it", with a rider that if you lose it, you're lunch for something.  The existence of pectator sports, though, leaves me completely baffled :-)

I would advise that you read up some basics of evolution. Evolution does not decide; it is stochastic. Most sports are basically a kind of simulation of war, hunting or other essential physical activities that ensure fitness of the individual or the community.

@WYSIWYG. Talking about evolution as 'deciding' is a cruder way to describe evolution than describing it as 'stochastic', but it isn't strictly wrong in so far as it describes what evolution produces as contingent on the relevant facts of the world - just as what an agent decides to do is contingent on the relevant facts.

If you're asking about entertainment generally, I think music and dancing are pretty obviously related to reproductive fitness. The evidence says so anyway. In fact, there's a pretty strong correlation between the amount of the right sex hormones in a person (i.e. testosterone in men, estrogen in women), fertility, physical sexiness, and singing and dancing ability. In short - we find fertile people hot, and signs of fertility are found in physical appearance, singing, and dancing. Kind of neat.

@Hal but an agent can still decide in long term. Evolutionary process does not "think" long term. It is Markovian and not a decision process.

@WYSIWYG Fair enough. I don't regard 'decide' as entailing (or precluding) long term planning. E.g. When given two appealing options, sometimes my dog just reacts to one instead of the other. Sometimes he seems to think about it. However, I don't think he ever thinks long term, it's always an immediate response to what's happening. in any case, I don't mean to defend the analogy. It's far from perfect. I just mean to say that it's not dead wrong.

@WYSIWYG What are your thoughts on the use of game theory (the study of multi-move - i.e. long term - decision) in modeling evolution. From what I've heard, it often models evolution well. Although, I really don't know.

@Hal though it may not be dead wrong, it instills a doubt and as such most people do not understand evolution properly. Therefore it is always good to be explicitly clear. Game theory also just predicts long term consequences (simulation of steady state) and ignores any possibility of an event that may cause a change of scenario. It is possible to model and predict the outcome of stochastic processes.

@WYSIWYG Thanks for the info.
"It is always good to be explicitly clear" +1

This answer can be from many different perspectives! I'll try to blend them all together as much as possible.
First of all evolution did not choose to make us love sports. Evolution made us social animals. And sports is just one of the tools we use for that purpose. Think about it, because if evolution gave us sports, then you will play sports, your kids will inherit that bit of experience from you and they would be that much better than you. But no, we all start from level 0 when we try to play any games or sports. This is because, sports is primarily a motor memory
So why are we social?
This study back in 2014 was one of the first to suggest that memory can be heritable. It generated a lot of attention and the authors themselves suggested that their findings were standing on a very capricious footing and required further validation.
This point is valid because evolutionary forces require mechanisms by which features/mechanism which bestow advantages towards the survival of the species are positively reinforced. In this case social behaviour is the function.
Do not go googling the word Social behaviour, for some reason the wiki article looks only at dogs and cats. That is unpragmatic, because we also have the same function.
I will broadly breakdown social behaviour into

Accommodation of non-aggressive behaviour from individuals in neutral territory.
A means to communicate

But, you may ask how does social behaviour benefit you? Well the answer is simple, increased survival capacity, and better chances of propagation.
Such studies exist in crows, which have studied social behaviour. Indeed, if you start to consider studies in behavioural biology, you would find that there are instances where female mosquitoes do not just mate with any male mosquitoes, even in this case you can call it a very rudimentary form of socialising.
So in your case sports is a tool which allows us to accommodate and communicate with others in neutral territory.
You can take a look at this which better explains the social aspects of sports

You should avoid usage of statements like So why did evolution choose to make us social? .. Evolution does not decide.


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Can birds touch their wing tips together either in front or behind (not above and below)?
Can the tips of a birds wings touch so that it would form a ring if view from above or below? I suspect it might be a bird of prey and at the moment it is picking something up from the ground but I can't find a good photo.

Please [edit] to clarify your question. Are you asking if it's possible for a bird to touch its wings together, or are you asking for an identification of a species that you see doing this??

Black herons (Egretta ardesiaca) can overlap their wing tips in front of them while doing what is known as canopy feeding.

Oooo, just saw this! Great example!

Thanks! I think I knew some herons must do this because of "canopy feeding" by the Reddish Egret — happy new year!

Cool, I never knew that. Happy New Year to you, too!


text:
What is this soft cased worm-like creature?
Found this creature in the bathroom
Features which ought to help for identification:

Size = 1 cm
Soft casing
Can emerge from either end of its case and thus reverse the direction it crawls.
Many tiny legs.
Can walk pretty fast.

Found in the middle east

Welcome to Biology.SE!  Interesting creature, can you add more information about the local environment and specify where in the middle east you found this?  Also, what do you mean by "soft shell" — do you mean that the (sandy?) casing is flexible?

Looks like a plaster bagworm (https://en.wikipedia.org/wiki/Phereoeca_uterella)


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Problem with joining the gene of interest into the open plasmid when their lengths are not the same
Before the recombinant plasmid is obtained in recombinant DNA, the gene of interest is inserted into a linearized plasmid by DNA ligase.
What happens if the length of the gene of interest is not the same as that of the gap in the open plasmid? (e.g. far longer) Can the gene still be connected with the gap or are other processes needed before the recombinant plasmid can be put back into the bacteria?

From your question I suspect that you are thinking of DNA as being a very rigid molecule — it isn't.
Double stranded DNA is reasonably flexible and a useful mental model would be to think of this as being like tying the ends of two pieces of thin wire together to make a circle.
Double stranded DNA can make a closed circles smaller than 250 bp long1,2 and I don't think there is any known upper limit — for example there is a known circular bacterial chromosome 14,782,125 bp in length3.
A typical plasmid can accommodate inserts of any size up to total size of around 50 kb, but plasmids that are more than 20 kb are very difficult to work with and may require special transformation techniques.
References:
1: Thibault, Thomas et al. “Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity.” Nucleic acids research vol. 45,5 (2017): e26. doi:10.1093/nar/gkw1034
2: Shore, David, Jorg Langowski, and Robert L. Baldwin. "DNA flexibility studied by covalent closure of short fragments into circles." Proceedings of the National Academy of Sciences 78.8 (1981): 4833-4837
3: Land, Miriam et al. “Insights from 20 years of bacterial genome sequencing.” Functional & integrative genomics vol. 15,2 (2015): 141-61. doi:10.1007/s10142-015-0433-4


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What is disease risk?
I would like to find an accurate definition of disease risk for virus ecology.
I am searching in articles and in none of them this term is defined, they only mention it.
Schematic of the relationship between habitat heterogeneity and disease risk.
Disease is greatest in fully cultivated plants, intermediate in wild plants
that are tended by humans in anthropic habitats, and lowest in fully wild plants.
On the other hand, biodiversity is highest in the habitats of wild plants, and
lowest in those of cultivated plants.

Roossinck, M. J., & García-Arenal, F. (2015). Ecosystem simplification, biodiversity loss and plant virus emergence. Current opinion in virology, 10, 56-62.
I have defined it as the probability of a host to develop a disease. However, I have the feeling that this definition is somewhat lax.

To my knowledge disease risk is not a generally acepted epidemiological term. You may want to look at the incidence rate or prevalence and follow the suggestions from the "See also" section.

Thank you @Vadim for your answer. However as you see in many papers disease risk is introduced as a term:  The ecology of infectious disease: effects of host diversity and community composition on Lyme disease risk. Proceedings of the National Academy of Sciences, 100(2), 567-571.  I defined it as the probability of a host to develop a disease, I have the feeling that this definition is somewhat lax

Perhaps you should edit your question to make it more specific: pointing that you are discussing ecology (rather than epidemiology), and perhaps giving examples of the articles.

I have changed it. Thank you for your support


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What kind of snake is this? Seen in Peru along the Inca Trail
I have been searching so much to find out what kind of snake this is. It looked black with white stripes. We found it on the Inca Trail to Machu Picchu in Peru. It was about 2500 m above sea level.


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What type of wasp is this?
I've been trying to match this wasp to photos, but it seems like every species has something that doesn't quite match up. I killed it in my home in Indiana, USA. My best guess is a Northern Paper Wasp (Polistes fuscatus). Does that seem right? I read they can sometimes be dark in color like this one.

It is hard to tell from the image, but using this species key for Polistes wasps, it is reasonable to conclude that your wasp is either P. metricus or P. fuscatus.
If you look at this image of a P. metricus female, you can see the dull reddish markings on the abdomen:

On your image, you can see the same markings on the abdomen, at a different angle:

Based on these markings, your wasp is most likely Polistes metricus. You can read more about this insect here and here.
Here is a link to the image I modified.


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How to find the amino acid in the DNA protein
    3' A T A G T A C C G C A T G T A C G G G C G A G A C A T T C G A G C A T T C A T 5'

This a Template DNA.
How to find the number of amino acids amino acids in the protein encoded by the above gene?
The answer is $7$.
My Try:
First I converted the above DNA to RNA and got
   5' U A U C A U G G C G U A C A U G C C C G C U C U G U A A G C U C G U A A G U A 3'

Then I found the start codon which is A U G
5' U A U C |A U G| G C G U A C A U G C C C G C U C U G U A A G C U C G U A A G U A 3'

From here I am not understanding how to proceed.
Can anyone please explain how to solve this?

Short question: How does RNA translate into protein?

Then you just have to read the codon until you reach a stop codon. There are three stop codon UAA, UGA and UAG. So, in your example..
             Start                                                   Stop
5' U A U C | A U G | G C G | U A C | A U G | C C C | G C U | C U G | U A A | G C U C G U A A G U A 3'

Your protein is therefore 7 amino acids long (incuding the starting methionine). The genetic code is

Therefore the 7 amino acids are
Met Ala Tyr Met Pro Ala Leu

In case you are confused about having an AUG codon in the middle of an open reading frame, then you should have a look at the post Effect of a doubling of the start codon in a gene.
Of course, I assumed that the region is indeed transcribed and that the first AUG is indeed the start codon and not just a methionine in the middle of an open reading frame.

Good answer, though perhaps you should include the first methionine as the N-terminus since it is not always cleaved and the answer given in the OP is 7.

@canadianer Thank you! Edited. I did not know the methionine of the start codon was sometimes (often, usually?!) kept.

Each protein-coding gene consists of coding and non-coding regions. Coding region, a.k.a CDS (see: Coding region and Open Reading Frame), is spanned between translation initiation site (TIS), and one of stop codons. Non-coding regions include introns and non translated regions (5'UTR or 3'UTR) in the exons.
You need to know first, if (and where) your DNA template contains the information about amino acids sequence. Does your DNA template is the protein-coding region only or do you have some non-coding parts (eg. introns).
(Short remark: Methionine can be also found within the amino acids chain, not only at TIS = not every methionine is a TIS)


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Is Klebsiella pneumoniae found in the throat of healthy people?
Is Klebsiella pneumoniae found in the throat of healthy people?

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). For example, reading and linking to the relevant Wikipedia article and (if this is true) indicating that you were specifically interested in the throat and why knowing it is in the normal oral microbiome isn't sufficient. Thanks!

Klebsiella species, including pneumoniae, are normal members of the healthy human oral microbiome.
Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota
Saliva microbiomes from 6 healthy adults were analyzed by 16S sequencing over a starvation timecourse, where oral microbes were cultured in minimal medium (PBS or 1:1 PBS:cell-free saliva).  Figure 1 shows that the genus Klebsiella is initially low abundance in the healthy oral microbiome, but the proportion of Klebsiella increases over the starvation timecourse in the two media tested.  An excerpt from the results:

At day 1, several species of Streptococcus were recovered, as were Gamella sanguinis, Klebsiella pneumoniae, and Klebsiella oxytoca. At day 20, K. pneumoniae, K. oxytoca, Enterobacter homaechei, and Providencia alcalifaciens were the only recoverable species. Finally, at day 84 and day 100, only K. pneumoniae and P. alcalifaciens were recoverable under the conditions tested

Given the proximity of the mouth to the throat, I think it's fair to say that K. pneumoniae is likely a member of the healthy human throat.
If that's not convincing, you can check the supplemental data from this paper, which looked at 16S data associated with throat tissue samples from 29 patients with laryngeal carcinoma and 31 control patients with vocal cord polyps.  Looking at the relative abundance of different phyla, they found that Proteobacteria (the phylum containing the genus Klebsiella) accounts for 11% of the recovered 16S reads on average for all patients (range 0–67.1%).  The authors claim to have recovered 218 genera and >3000 unique OTUs at 97% similarity, though they only report the ~30 most abundant genera in their differential abundance analyses, and it doesn't look like they included the full dataset in this publication.

Proteobacteria being "considered the predominant phylum within the realm of bacteria", isn't that an argument of how efficient our mucosa is in eliminating them, if only 11% prevalence in throat culture?

The reason is called K.pneumoniae is because is known to cause pheumonia in the lungs. Another K. is formerly known as Enterobacter aerogenes, for being an intestinal pathogen. I muse that having it in the throat feels too close to both lungs and esophagus to be comfortable


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Are the social-distancing measures implemented against SARS-CoV-2 also suppressing the spread of other viruses?
With social-distancing measures being implemented in many countries I would expect other viruses, like the ones that cause seasonal flus, to have also a hard time propagating in these circumstances. Are there any estimates or research (epidemiological models) I can check, about the possibility we are winning by accident a war against many other less alarming viruses?

relevant XKCD

@Dirigible full page (so you can read the hover text as well)

Of course there's an xkcd. How couldn't there be?

Anoter relevant XKCD

I think "killing" is the wrong therm here. Social-distancing is reducing the spread of viruses.

Not enough reputation for an answer, but this is the respiratory infection rate in Germany: https://grippeweb.rki.de/Diagrams/2019_2020/2020-22-01.png It’s at ~2% compared to the usual ~5% for this time of the year. I think this even includes COVID19.

Not enough rep to answer. Norovirus in Sweden  https://imgs.aftonbladet-cdn.se/v2/images/65de546d-9803-4977-9e51-ba8d44636c6d?fit=crop&h=720&q=50&w=960&s=2d38e1da546acb07b726e76334a900f34c5cbfab

It seems that at least for pneumonia in the US the lower numbers could be entirely caused by incomplete data. https://skeptics.stackexchange.com/questions/47265/has-the-number-of-pneumonia-deaths-in-the-us-dramatically-dropped-in-2020

Yes, this helps as well with other infectious diseases. A good example is the flu, which season was measurably shorter this year than in other years on record. See the figure from the reference 1 for comparision:

Reference 2 shows that this is also true for other respiratory diseases (figure 2):

This shows very well that the isolation measures and the social distancing work very well to control such transmissable diseases.
References:

How coronavirus lockdowns stopped flu in its tracks
Monitoring respiratory infections in covid-19 epidemics

The flatline of on that second chart is absolutely remarkable compared to previous years.  I wonder if these effects will last a significant period of time or if spread of common viruses will be back to normal next year.

Of course there are possible reasons for that flatline in addition to limiting the spread.  For instance, people who otherwise might have made a doctor visit for the flu may have decided to skip it this year.

@jamesqf That graphic is as a percentage of analysed specimens, so those people staying home are not part of the sample at all. Additionally, "there may be other contributing factors, such as people choosing not to go to a place where sick people often congregate" is really killing two birds with one stone in this specific case.

Looks like the flu season was off to an unfortunately strong start before social-distancing guidelines and lock-downs were put in-place, then presumably the safety procedures helped drive the curve down.  But for reference, is there some simple way to qualitatively describe when lock-down procedures kicked in?

The second chart makes it seem like there was a single case of covid-19 and then all diseases dropped.  Given it became a global pandemic, I'd expect at least one line to shoot up before the drop.

@DavidStarkey The chart does not include COVID-19, since it is not an influenza. As you said, once the pandemic was declared everywhere people started to apply precautions (whether imposed by the government or not) and thus all other deaseses started to drop pretty quickly.

@DavidStarkey, if you look into the reference, that chart only applies to Hong Kong. Given their proximity to mainland China, they started taking aggressive precautions before COVID showed up, as I recall.

In addition to Chris' answer above, the effect is even more pronounced in Southern Hemisphere countries where flu season started during the pandemic.  The New Zealand lockdown and health response dramatically lowered the prevalence of reported flu-like symptoms.

Reference:
  Flu Tracking reports - New Zealand – week ending 31-May-2020

NZ's winter is only just beginning, and their lockdown is over.

@curiousdannii flu season =/= winter, flu season lasts a lot longer

I don't have points to write my own answer, but this is a great account of Lab confirmed flu cases in Australia over the past few years and early 2020 (updated 15 June). https://www.immunisationcoalition.org.au/wp-content/uploads/2020/03/15Jun-Aust-Flu-Stats-2020.pdf


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Evolutionary reasons why you cannot tickle yourself but you can masturbate
There are obviously good reasons that explain why you cannot tickle yourself (see e.g. here). This got me thinking why it is possible to masturbate...
Wouldn't it make more sense to not be able to do that so that you are more inclined to have real sex. Individuals who were not able to relieve themselves in this manner should have been more actively producing offspring. And the tickling example shows that self-produced sensations can be inhibited.
Does this make sense? I know that it is always hard to reconstruct evolutionary processes but are there reasons that explain this?

I am sure I saw a paper that suggested masturbation can enhance fitness via ejaculate quality

I guess tickling has an element of surprise.

When you watch porn you trick your brain to think you are actually having sex, so the brain doesn't think of it as self-produced stimuli. It's that simple... (If you don't have any porn you'll find it's much harder to trick the brain)

@Downvoter: Please give us a reason as is good practice here. How can I improve the question? Thank you.

I can tickle myself. (No pun intended.)

You don't need porn, though. People have been using their imagination for millenia.

Access to females is something regulated by an alpha male in chimps social groups. Most of males have to wait to be very old to have a chance to become alpha, and before that, mating will occure by chance on very rare occasions. Male chimps do masturbate. Regular ejaculation is said to avoid some cancers (prostate essentially) and masturbation is the most straitforward way to avoid those cancer in absence of mating oportunity.
This, of course, regards chimps but may tell us something about our ancestors and our evolution timeline.

As it is human males differ from animal by the fact that their organ is always outside the body. Could this be related to evolution from monkeys doing that since hundred thousands years ago ?

Is there any evidence that masturbating discourages (young) men from having sex? If not then there is no evolutionary reason to stop it.

I think there is a bit of a logical leap here (or at least in the title).
The simple answer is that there are many biological phenomena for which there is no logically satisfactory explanation. For instance: why do people have wisdom teeth? We come up with some hand-wavy explanations about ancestral diets, but at the end of the day we just have wisdom teeth (or at least most of us do) and there isn't a great immediate causal pathway that tells us why this rather inconvenient thing exists in modern humans and hasn't been lost.
Getting back to the question at hand, there are a number of assumptions that seem to come along with this question:

Most importantly, why is it assumed that there must be an evolutionary "reason" for a biological phenomenon? In many/most cases there is no such reason. Most (molecular) evolution is neutral and random.
Why is it assumed that there is an equivalence between tickling and sexual stimulation? (then again, a cursory google search suggests there is a relationship...)

Both tickling and masturbation are phenomena that seem to occur in primates. However, this does not require that there be a link between them even if they appear to be similar superficially. Furthermore, it is not logically required that either of them satisfy any particular purpose, even if we can imagine a possible purpose (as some of the commenters have).
Of course, there are lots of reasons why these things exist if you're willing to drop the evolutionary mumbo-jumbo. For instance: both of these things can be fun and God loves us and wants us to be happy. This is the same as the platitude from Ben Franklin on why booze exists. Substitute your favorite demiurge.
These arguments are not much different from arguing that constant ejaculation leads to better sperm on evolutionary time scales. There is equally good (better?) evidence that having to produce more sperm leads to a higher prevalence of birth defects and other disorders. So maybe masturbation is bad from one reasonable point of view, and is in fact a deleterious vestigium like wisdom teeth. The "scientific" answer depends a bit on which literature you pay attention to.
Evolutionary answers of this type tend to be this kind of just-so stories. They give an air of precision and authority with uncertain logical backing, and they don't even have the folksy philosophy as a consolation.
This may not be an answer in the fashion the OP intended, but hopefully it does at least give a perspective on thinking about these kinds of questions.


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Monohybrid Recombinant Frequency? (three point Gene Linkage)
I am curious to know if it is completely impossible calculate recombinant frequency for monohybrids ( three point link, gene map etc.)
Here is an example:
Marker 1

xx= 25
xy=100
yy= 20

Marker 2

xx=30
yx= 89
yy= 20

Marker 3

xx= 100
yx=50
yy= 100

This is what I think it would be like for x:x Marker 1 to 3
grand total = 534
So from Marker 1 to Marker 2 it would be 25+30/534 = 0.1029
Marker 2 to Marker 3 : 30 +100/534= 0.2429
Marker 1 to Marker 3: 125/534= 0.2340
Am I on the right track --- if not can you please show how it would be done for this example?

Can you please clarify what xx, xy and yy are as well as the genotypes of the parents? What are the two loci and the alleles at each locus?

xx and yy are the parents (genotype), the alleles are either x or y

How about the other locus, then? You can only talk about recombinants if you consider at least 2 loci.

This information is from a sample SNP call data indicating the to total calls for those genotypes. That's all the information I have is there no way to calculate RF ?

No, you can't calculate a recombination rate between two loci with only information about a single locus. If your question is a homework question, please use the homework tag

Oh I understand what you are saying ( this is not hw , it a "what if" question) Let give some more hypothetical information--- the information above is for Marker 1 I I will a bit more to my question

Homework questions are off-topic unless you have shown your attempt at an answer. Can you please show your attempt? You can have a look at this Khan Academy article that very nicely explain how to compute genetic distances.

Hi -- My attempt above for x:x


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Is there a single protostomate common ancestor that has pseudocoelomate structure?
I think about 15 years ago I saw a new classification system that placed Plathyhelminthes worms with Annelids and Mollusks into a superphylum (or other systematic clade) Lophotrochozoa,  while Nematode worms were grouped with Arthropods into a clade Ecdysozoa.  This would suggest that Arthropods and Annelids did not have a common coelomate or pseudocoelomate ancestor (in the past believed to be a nematode), or that if they did, then flatworms evolved FROM the pseudocoelomate ancestor.  What are the current views of the characteristics of the Protostomate progenitor?  It looks like Roundworms may have diverged from a flatworm like ancestor, and then given rise to current roundworms and Arthropods, while Annelids and Mollusks may have arisen independently from a flatworm ancestor.  It would violate something I was taught in evolution (as a loose rule) that you don't usually call features like a coelem "homlogous" if they arose independently which would be the case for the Mollusk/Annelid Coelem and the Arthropod coelem.  Of course, it is possible since the genetic changes that allowed both coelom may have existed for some other purpose prior to divergence, but been activated by other similar evolutionary phenomenon, or if a gene became deactivate (for example, if a gene were deactivated in mammals making scales for instead of hair those scales would still bear homology with reptile scales.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614230/

https://www.cell.com/current-biology/comments/S0960-9822(17)31033-3


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Can ELISA be used to detect a plant enzyme? Creating assay for a new enzyme
If the goal is to generate a rapid assay for an enzyme of plant source what are the typical options?
i.e. Could one do something like: Generate an antibody to the enzyme and then use it to create an ELISA? Would animal-injection be the way to generate the specific antibody needed?
If not, what is typically done in such cases. How does one go about creating an assay for a new enzyme of plant source. Are there alternative approaches that avoid the antibody creation?

I want to add something on top of Chris answer.
The production of an antibody it is usually a quite slow (and expensive) process, an alternative that worth to consider is phage display (https://en.wikipedia.org/wiki/Phage_display). Once you find the phage that effectively bind your protein of interest, you can use it instead of an antibody in what is called a Phage-ELISA assay.
However, mind that the ELISA (or Phage-ELISA) will give you information about the presence and the concentration of the enzyme, it will not give you any hint about its activity.

Thank you. I did not know about this. Sounds like this could be what I need.

Feel free to contact me for more info. I got quite a lot of experience with phage display.

you can send me an email at alec_djinn-at-yahoo.com

I think the most promising routes use antibodies. You could either develop an ELISA or do western blot analysis of plant material - both need a good and specific antibody. To generate these, the protein of interest (or at least parts of it) are injected into animals (typically mice or rabbit) and then antibodies are pourified from the blood of these animals. These antibodies are polyclonal, but this approach is rather fast and can be done in a few weeks.
If you want to use a more sustainable source of antibodies, the antibody producing cells from these animals are isolated, immortalized and characterized as single clones to get monoclonal antibodies.
Since you are using an enzyme, you could also think about activity assays. So either a chromogenic or fluorogenic substrate is metabolized, or you could use coupled reactions where your enzyme uses a substrate which is refilled by another reaction - classical examples here are coupled reactions which use NADH or ATP.
It is also possible to measure the metabolic rate if the substrate or the product of your enzyme shows fluorescence. Then you can either measure the decrease of your substrate or the increase of your product.

Thanks Chris! Can you elaborate more about the chromogenic / flurogenic substrate part? The enzyme I'm interested in converts FPP (Farnesyl Diphosphate) to a specific terpenoid.

Since I don't really know your enzyme, I can't tell you about this. But reactions like this are widely used.

In paragraph 2 you talk about the production of monoclonal antibodies, but isn't the process more like that mAb antibodies are antibodies which are derived from a B cell clone, then an animal is injected with the antigen which thus produces plasma cells, those are hybridised with tumour cells (because of endless divisions), and the resulting hybridoma is then synthesising large quantities of specific antibodies, or am I misunderstanding something?

@JordiZambrino I am not sure if I get your question completely. Monoclonal antibodies are made from animals where the animal is vaccinated with the antigen of choice, then the spleen is removed and from it lymphocytes are isolated. These are then grown into single clones and the secreted antibodies are characterized. These are then fused to make hybridoma cells which produce large amounts of antibodies.

Thank you for the explanation. The characterisation of antibodies could be seen as a structural specialisation, right? Where the composition and sequence of AA are determined?

@JordiZambrino if you have specific questions about antibodies, please ask, as the topic is quite broad. Sequencing is not necessarily a part of monoclonal antibody characterization, unless you are planning on producing it recombinantly. Plenty of mouse monoclonal antibodies out there for research use are grown in ascites where all you need is a healthy hybridoma culture. I used to work for an antibody company producing research reagents, so I have some experience :)

@JordiZambrino or, you can always ping me in chat.

@MattDMo what you said is really interesting and helps my understanding a lot. Also, thank you very much for your offer :)


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Enzyme Activity under High Pressure
Wikipedia has this image titled "Pressure Chamber to measure Enzyme Activity under High Pressure"
Made me wonder why do we need to measure Enzyme Activity under high pressure?
Are there enzymes in nature that must work under variable pressure conditions? My impression from my knowledge of conventional chemical kinetics was that in the liquid phase the effect of pressure on chemical kinetics was typically very low simply because of incompressiblity of liquids. Unless Pressures were very very high. Is this not so with enzyme activity? Or are there enzymes that must work under very high pressures?
https://en.wikipedia.org/wiki/Enzyme_assay

Not sure what this device is, but I would guess pressure is important mostly for enzymatic reactions that involve dissolved gases (O2, CO2, etc). Increasing the gas pressure above the liquid would serve to raise concentrations of dissolved gas.

At least one group who have published on the effect of pressure on enzyme activity (Cho and Northrop) are not interested in it from a practical point of view, i.e. they are not subjecting enzymic reactions to pressures that they think they encounter naturally. Instead they are using the effects of pressure to test the kinetic and thermodynamic predictions of different models of enzyme catalysis. In particular they believe that pressure effects provide a means of testing the idea, first suggested by Linus Pauling, that an enzyme has a greater affinity for the transition state, rather than for the substrate.
This is explained in a paper on yeast alcohol dehydrogenase, but only the abstract is freely available. They claim to have evidence against Pauling’s idea, but I am not sure the extent to which this is generally accepted.

Paper can be found here.

Legally? I don't read Russian.

Sci-hub is quite a lot, but it is surely not legal.


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How to put a gene under the control of a regulable promoter?
Suppose I have a hetrologous (eukaryotic, plant) gene sequence that I want to express in E Coli under the control of a regulable promoter (say the lac promoter induced by IPTG) how exactly does one add the promoter sequence upstream of the gene?
Are there any tools to do this?
e.g. Say this is the gene itself, what sequence modification is needed to put it under the control of the lac promoter? The goal is to induce overexpression of the protein coded for by the gene on addition of IPTG to the medium (if I understand the strategy correctly)
atggctaccg ataatgacag ctctgaaaac cgtcgtatgg gtaattacaa gccgtccatc       60

tggaactacg acttcctgca gtccctggct acccgccaca atatcatgga agagcgccac      120

ttgaaactgg cggagaaact gaaaggccag gtgaagttta tgtttggtgc cccgatggag      180
.................................................................
gagccgttcg tgacgttcaa cctgaacagc gttcgtggtt cccatttctt ttacgagttt     1560

ggtgacggtt tcggtgtgac gaatagctgg accaaggttg acatgaagag cgtcctgatt     1620

gatccgattc cactggatga agaataatga                                      1650

If you're expressing the gene in E. coli, then you're almost certain to be using a plasmid or other ectopic gene vector. There are a wide variety of plasmids available, with many different promoters. With a commercial plasmid, you're not adding in the promoter sequence, but the gene sequence. You pick the promoter you want and then clone your gene sequence into the plasmid's multiple cloning site, which is designed to lie downstream the promoter.
There are a variety of tools to design and order plasmids. A common plasmid repository is addgene and my favorite tool for designing plasmids prior to ordering is APE.
Design the plasmid with APE or another tool, to be sure that everything looks good, then you can order the appropriate plasmid vector and enzyme cut site-flanked gene sequence and go to town cloning.

I have asked a follow up question here & it would be great if you can help with any comments / advice: http://biology.stackexchange.com/questions/48451/how-to-specify-a-promoter-in-de-novo-gene-synthesis-service

I believe that @March Ho's comment to your follow-up question provides the best answer. I've never seen a 'promoter menu' offered. Rather, promoter sequences are generally specified within a given cloning vector and can otherwise be found using tools such as GenBank. Hope that helps.


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Transgenic Plant-Gene source for introduction into host organism
Let's say the plant-gene itself is known, i.e. the exact neucleotide sequence is available in a gene bank (originally sequenced from a tree sample extracted RNA). Previous work has already successfuly inserted & expressed the gene in a host bacterium, say, E Coli.
My question is: Does subsequent work on inserting the gene into other host organisms also have to start from tree samples as source of the RNA & hence DNA?
Or is there a more direct route to convert a Neucleotide sequence from a gene database into actual DNA that can be inserted into hosts?
e.g. Are there machines that can take a sequence & synthesize the correct DNA molecules? Or not yet?

If you've access or someone else does and wants to answer, there's a good article through nature current to Dec. 2013 here.
The process is known as de novo synthesis.

@Kendall Thanks for the pointer. Googling up the term is getting me lots of info.

@Kendall Would it be fair to say that in cases like the one I described e.g. a tree gene as of today extracting the RNA & then purifying it & converting it into cDNA & cutting out the gene needed is a lot simpler / cheaper than de novo synthesis?

I guess what I am asking is when does one typically choose de novo synthesis over extraction from natural source material?


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Computer Models of E Coli / Saccharomyces cerevisiae metabolite pathways
Are there mathematical models one can use to predict the expression levels of a foreign gene inserted into a well studied host organism like  E Coli or S cerevisiae?
I'm not, obviously, looking for some magical, accurate in silicio model; but even an approximate heuristic. e.g. Before starting a cloning experiment to estimate levels of a secondary metabolite expression in different organisms that both contain the substrate natively but may have it in different levels.
Alternatively, can the math models help in estimating which other competing pathways may be draining away a precursor of interest so that a rational attempt can be made to block such pathways to promote selective expression of the metabolite of interest.
Of course, the cloning experiment is the gold standard but are there ways to simulate a part of this and reduce the dead ends of experiments. Is there standard software I ought to be looking at?

Yes there are Flux Balance models but you would have to incorporate your gene into the metabolic network..

@WYSIWYG Thanks! Can you offer any pointers on where  / what software to start with? What sort of parameters would one need to introduce an ad hoc gene into an existing flux balance model?

I don't actually know a great deal about this but you would have to introduce new reactions in your metabolic network which might consume some primary metabolites and produce your desired secondary metabolite and by-products. You can then calculate the flux balance that can maximize the secondary metabolite production. This is basically a linear programming problem. There are some optimized programs for this but I don't have much idea. You can start by reading some basic books on flux balance analysis.


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Fertilization of the human egg- where does our centrosome come from?
Is there a centrosome in a human egg cell? Is the reason why the egg cell remains paused before meiosis 2 because there isn't a centrosome, and it only divides when the sperm fertilizes it thus it can have a centrosome? If this is so, then how did oogenesis happen? ?

To answer the first part of your question. The sperm actually introduces two centrosomes. The centrosome then nucleates the new microtubule assembly to form the sperm aster — a step essential for successful fertilization. You can visit these sites Simerly, et al as well as Paweltz, et al

Could you provide a more recent reference? (The ones you provided are from 1995 and 1987). I ask because From Zero to Many: Control of Centriole Number in Development and Disease (2009) says: "Notably, oocytes and spermatozoa lose parts of the centrosome in a complementary manner. Centrioles, but not centrosome proteins, are lost in the oocyte. On the other hand, in sperm, the PCM material is lost, but not the centriole/basal body, which is necessary for flagella formation.  ...

...  Fertilization brings together the basal body from the sperm, which becomes a centriole within the zygote, and the PCM from the egg."


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When the sister chromatids are joined in the centromere, why is it stated that the number of chromosomes is 46 and not 72?
Before the DNA is replicated in a human somatic cell, the cell has 46 chromosomes. Also, after the sister chromatids are separated during Anaphase, the chromosome number in the cell doubles to 72, so when the sister chromatids are joined, why isn't the chromosome number also 72? On the internet, some sources say that one chromosome in a cell that hasn't replicated its DNA is equal to one chromatid. Is this correct, or are chromosomes and chromatids structurally different?

When I was learning genetics for the first time I have also found naming the two chromatids joined at centromere as chromosome a little bit strange. The number of DNA molecules and their behaviour in cell cycle seemed to me more important for understanding of genetics.
What you need to understand.is the term chromosome predates knowledge of DNA structure. The name literally means colored (chromo) body (soma). It is an object visible under the microscope when using specific dye. In metaphase two chromatids joined at centromere look like a single object - a chromosome. Sometimes the two chromatids of one chromosome are so close together it is difficult to tell them apart. In anaphase the chromatids separate and one object (two-chromatid chromosome) visibly splits to two objects (single-chromatid chromosomes of daughter cells)


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Calvin cycle- combining three "turns"
In the common Calvin cycle diagram, it is commonly stated that "three cycles are combined to show the production of 1 molecule of G3P".
How does the G3P molecule escape from this cycle in one of these turns?
Is one carbon atom "released" from this cycle at each turn and the G3P forms in another reaction?
Or alternatively,
is the G3P released at the end of the three "turns"? If this is the case, then shouldn't this diagram represent only one "cycle" of the Calvin cycle?
[1]: https://i.sstatic.net/mzizw.jpg

Your question is unintelligible without reference to a diagram. Please revise your question accordingly, and phrase it so that it addresses a biological problem, rather than the interpretation of a particular mode of presentation in a specific text.

Not quite sure I understand what you are asking; the cycle is clearly not closed, there is a reactant entering and a product leaving, as well as interactions with other cycling molecules as ATP/ADP and NADPH/NADP+.

This is a great question - the secret in a nutshell is that five three-carbon G3Ps are turned into three five-carbon RuBPs at the left.  This involves a lot of making change with sugars - see the Wikipedia article section on the regeneration step.  You might also compare the pentose phosphate pathway.  I should submit an answer but I'm not feeling energetic enough to write out all those steps right now ... which is presumably how this textbook author felt!


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Can fermentation and aerobic respiration occur at the same time?
In muscle cells during exercise, does lactic acid fermentation and aeorobic respiration occur at the same time, and does this mean the cell makes more or less ATP during this time?
The cell can't completely lack oxygen, which means that some of pyruvate will move into the mitochondrion, however, lactic acid is also produced which means that anaerobic respiration occurs. Is this reasoning correct or is there some other mechanism that I am skipping that doesn't allow these processes to simultaneously occur?
Also, the NAD+ used for glycolysis is regenerated and net 2 ATP is releaseD in glycolysis, but the NADH doesn't move into the mitochondrion, so if pyruvate moves into the mitochondrion at the end of glycolysis, then there will be less NADH in the mitochondrion, which makes sense because there is too little oxygen and too many electrons in the ETC.

You keep posting questions in which you provide no support for your statements, no context to your qustions and do not respond to requests for clarification. Please sort out the questions you have already asked before posting any more.

@David In this case I believe the question is self evident and clear to understand, what part of it do you need more information about?

By posting one is asking others to spend time and effort providing an answer which will be of value to the "library of detailed answers" that this site aims to build. The poster therefore has a duty to write a good question, one that shows research (including previous questions here), is specific and explains the context in which the question is asked. If clarification is requested it should be provided. One should only "answer well-asked" questions. Until you respond to the queries to your ΔG question, I see no reason to consider others.

What happens at rest is that the muscle relies on blood glucose for energy supply. This involves glycolysis, Krebs' cycle and the ETC. In short, glucose is split into two trioses. The two trioses are then completely oxidatively decarboxylated. This produces reduced coenzymes, carbon dioxide and ATP. The reduced coenzymes are reoxidised by the ETC which takes the hydrogens, splits them into protons, that leave into the matrix, and electrons that jump between electron carriers, the last of which is oxygen which unites with protons too to form water. The jumping of electrons generates energy. The energy is used to pump protons from the matrix to the intermembrane space to a certain level. Once this level is reached, electron transport and proton pumping are stopped by ATP synthase and the already pumped protons diffuse through ATP synthase to the matrix. The energy that was used to pump the protons is then used to make ATP.
What happens during excercise is that energy consumption is faster so we need to generate energy faster. We use three mechanisms to do so.

Phosphagen system
Aerobic system
Glycogen-lactic-acid system

The phosphagen system is the one we use first. It relies on the phosphocreatine store. Phosphocreatine can donate its phosphate radical to ADP forming ATP and creatine. This system is short-lived.
When the excercise becomes prolonged, we rely on the aerobic system to maintain higher energy supply than at rest. It's essentially the same as what we do at rest with the exception that we start breaking down glycogen stores to free more glucose. The aerobic system can operate indefinitely; as long as there are enough oxygen and glucose.
If we need more energy than what the aerobic system can provide (more than oxygen supply allows), we start employing the glycogen-lactic-acid system. This system involves glycogen breakdown and glucose splitting into the trioses with no net oxidation and no decarboxylation. This is because the trioses that glucose is split to are oxidised producing reduced coenzymes, but the coenzymes can't be reoxidized by the ETC because there's not enough oxygen supply, so the trioses take back the hydrogens so the coenzymes can be used for another cycle. ATP is only produced at the substrate level. The resulting non-oxidised trioses are lactic acid molecules. Lactic acid, being an acid, causes fatigue, which is gradual reduction in the ability of the muscle to do work.
So to answer your question, yes they happen at the same time.
You can also check this answer for a more in-depth explanation.


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When two amoeba cells form from one amoeba, does spindle fibers form?
When two amoeba cells form from one amoeba, does spindle fibers form? Some sources say that spindle fibers do not form while an amoeba cell is undergoing cell division. If spindle formation does not occur, than how are the chromosomes pulled apart? Which intracellular transport mechanisms are used?

Amoebas undergo binary fission, which is a much more simplistic process than mitosis. In binary fission, the duplicated chromosomes simply separate as the cells is pulled apart. There are no spindle fibers used in this method of cell division.
Ok - so some of my references were a bit older, and I went through and looked through the literature a bit further - and found this great newer (ish) reference that actually used optical imaging to document the process of cell division: https://link.springer.com/content/pdf/10.1134/S1990519X16010041.pdf   Demin, S. Y., Berdieva, M. A., Podlipaeva, Y. I., Yudin, A. L., & Goodkov, A. V. (2016). Optical tomography analysis of Amoeba proteus chromatin organization at various cell cycle stages. Cell and Tissue Biology, 10(1), 84-94.
The process by which they undergo chromosomal separation is  a bit different in that there is no clearly identified kinetichore, but it looks as if microtubule spindles are involved. My error!  The process of DNA replication and other stages are quite different in this process that in typical mitosis.


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Struggling to make sense of Km
So I have two substrates for one enzyme and I measured the product formation-> michaelis menten kinetics. The Vmax for both substrates is the same, the Km however is higher on substrate number 2.  What can I conclude from this in terms of enzyme-substrate interaction?

Homework questions are discouraged on here.

The situation you described is entirely normal. $V_{max}$ is the same, so when described with a graph of initial reaction rate vs. substrate concentration, both curves will asymptotically approach the same maximum level. $K_M$ is higher in one than the other, so the exact shape of the curve as it goes from 0 to $V_{max}$ is different. As you may know, you can interpret $K_M$ as the substrate concentration that causes the initial reaction rate to be half of $V_{max}$. This means the substrate with the higher $K_M$ will have a shallower first half of the curve.
You can read more about these parameters and initial enzyme kinetics in Berg biochemistry or at khanacademy.

This does not answer my question of enzyme-substrate interaction though :), thank you for the effort nonetheless.

@Flip you'll have to clarify your question then.

@DeNovo : Seems like the question of OP is to describe the enzyme substrate interaction when Vmax is same and Km is different.

@user237650 that still needs clarification. As I understand the words of that question, this answers it (the difference between the way those two substrates interact with the enzyme is that the initial reaction rate increases more gradually for the second substrate) but there must be something else the OP is looking for.


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Troubleshooting agarose gel electrophoresis - Loading dye and DNA samples moving in opposite directions
The students of my Genetics class and I (instructor) are experiencing a systematic issue with our agarose gel electrophoreses which we cannot explain. We are looking for ideas that could explain our observations, so that we can resolve this issue (or these issues, in case multiple overlapping issues are present).
We are conducting our agarose gel elctrophoreses under the following conditions:

Agarose gel: 1% agarose gel (made with agarose I and fresh 1X TAE buffer of pH=8)
Sample-loading dye-ethidium bromide mixture: 5 uL of DNA sample (DNA quantity > 100ng/uL as confirmed via NanoDrop) + 2 uL loading dye + 2 uL ethidium bromide (1:10 dilution)
Gel rig: negative electrode (black cable) connected to top of rig, positive electrode (red cable) connected to bottom of rig (see image); filled with 1X TAE buffer; agarose gel positioned such that gel wells near top of rig
Run conditions: 30 minutes at 80 V, then visualization under UV light
IMPORTANT: The first lane of the gel is loaded with a gene ruler-loading dye-ethidium bromide mixture: 3 uL of 'GeneRuler 100bp' + 2 uL loading dye + 2 uL ethidium bromide (1:10 dilution)

We have run these conditions on different gel rigs and varied the run time (20-40 min.), the buffer (either TAE or TBE buffer), and the DNA intercalating substance (either ethidium bromide or SYBRsafe), yet the result is always one of the following unsatisfactory results:

no bands whatsoever
bands that are "stuck" in the gel well (i.e., only the gel wells are illuminated by the ethidium bromide under UV light)
bands that run in the "wrong" direction (towards the negative electrode!; see image)

Two important observations:

In all attempts, the loading dye has always moved in the expected direction (i.e., toward the positive electrode), whereas the DNA fragments (if present) have not

Please note that a low DNA concentration in the sample cannot be the reason for missing bands, as none of the commercial DNA ladder (Gene Ruler 100bp) bands are visible either.

Loaded samples: The lanes in the following images represent (from left to right):

Gene Ruler 100bp
DNA sample (fresh PCR product; expected lane at 219 bp)
DNA sample (fresh PCR product; expected lanes at 175 bp and 44 bp)
empty
empty
DNA sample (fresh PCR product; expected lane at 219 bp)
empty
empty

Edit 1: A potential clue to resolving this issue may reside in the fact that the filled wells of the agarose gels still "light up" under UV light within the first 10 minutes of running the gel, as displayed below (for a different sample). However, after another 10-20 minutes, any indication of these bands are either gone or represent blobs that migrated into the "wrong" direction.

Edit 2 (Nov-07-2024): My students and I followed the advice given to us in the comments sections and prepared an agarose gel electrophoresis with entirely fresh materials: fresh PCR product, fresh agarose gel, fresh SYBRsafe, and fresh TAE buffer in dish-washer clean glassware. The SYBRsafe was added when making the agarose gel at a concentration of 10 ug SYBRsafe per mL molten agarose. The result of that electrophoresis is just as before: the DNA ladder migrates the "wrong" direction (towards the negative electrode; see lane 1), whereas the PCR product is "stuck" in the gel well (lane 7).

How did you prepare the sample, and what is its expected size? The fact that you can't see the ladder (in either direction) indicates that there's something wrong with your set-up. I would suspect that the blobs at the top are not DNA. I'd suspect DNA degradation first off.

@bob1 I have added the relevant details to the post. What do you mean by "DNA degradation"? Lane 1 represents a fresh commercial DNA ladder, lanes 2, 3, and 6 fresh PCR products. Why would any of those be degraded, not least in multiple attempts spread out over multiple days?

First of all: Are you absolutely sure that your PCR worked? When you measure the reaction, unincorporated oligos will give you a signal. I would at least clean up one reaction. Are there residual salts in your chamber? These can disturb. Have you tried either staining the gel afterwards or adding the EtBr to the gel mix? I never mixed it into the sample.

@Chris Yes, I am certain that the PCRs worked. Not only have we been conducting very different sets of PCR amplifications (sometimes targeting smaller amplicons, sometimes longer amplicons), we also see clear changes in the DNA concentrations before and after the PCRs using both the NanoDrop (not precise in these cases) and the Qubit 4.0 (better in these cases). And even in the off-chance that all our PCRs failed, we should at least see the commercial DNA ladder after gel electrophoresis. Yet we don't!

@Chris Yes, we tried adding either the ethidium bromide or the SYBRsafe into the liquid agarose (once it cooled down but before it hardened) or into the sample that was loaded onto the gel. It did not change the outcome of a lack of bands.

@MichaelGruenstaeudl By degradation I mean that your gel component(s) might have become contaminated with DNase somehow. Often this is from bacterial residues in unclean glassware or even in your pipettes. It might be in your loading dye. In your last gel photo (the one with the wells lighting up) is it the same sample order as in the other photos? Also, the movement of the samples in that photo indicates them going in the right direction....

@bob1 If DNase contamination were the case, it must have occurred in very different pipettes, gel rigs, and loading dye samples; the likelihood of that is very, very low.  While samples of the photo posted under "Edit1" are not the same as the ones posted before, they illustrate a common observation among our unsuccessful gels: that the gel wells almost always "light up" upon being loaded, at least initially. However, after 20-40 min electrophoresis runtime, the anticipated bands are nowhere to be seen.

Try including EtBr in the gel and running buffer. Alternatively, soak the gel in EtBr/TAE after the run. EtBr is positively charged and migrates in the opposite direction of DNA if not intercalated. It also binds DNA with a relatively low affinity, so EtBr added in the loading buffer only could be stripped off during the run.

Try running a higher percentage gel - 1% is too low to resolve those sizes properly, Aim for closer to 2%. Not that you shouldn't see bands, just that bands will be indistinct at those sizes, which make them harder to see. The upper bands on the ladder will be OK at 1%. The GeneRuler documentation recommends 1.7%. Degradation of samples and ladders is a common effect in labs. Don't rule it out! Get a new un-opened ladder, make a fresh gel with fresh TAE etc. Load old ladder and new. Run the gel.

In my experience (and they are something I set up regularly), taught labs are all set up from stocks - students are given aliquots of that stock. If one stock is contaminated/off, then that can cause a lab-wide issue. It might not be the pipettes (though I have seen it on autoclaved batches of tips - autoclave had been used for a wasteload of a DNase producing bacteria immediately beforehand), but it could be the glassware used to prepare the TAE stock, or the agarose, or even the EtBr or loading dye. Talk to the tech who set it up and ask for new stocks of everything, and test systematically.

@bob1 Thank you for your suggestions. Since I do not have a lab tech (small teaching college), I have my students make their own buffers fresh at the beginning of every semester. If DNase-contaminated buffer were the reason for our problems, then it must have occurred in the Tris-base powder or the EDTA powder, as multiple independent students experience the same contamination. I consider this unlikely. Similarly, glassware is washed in the dishwasher (using LabConoco's LabSolutions non-foaming power detergent as detergent) and pipette tips autoclaved (or re-autoclaved) before every lab.

@bob1 We have already tested gels with slight deviations from an 1% agarose content (e.g., a 2% agarose gel), yet those gels result in exactly the same problem: neither the samples nor the DNA ladder are visible after 10 minutes of electrophoresis runtime. It all circles back to the same question: What happens at the beginning of or during the gel electrophoresis? Something at that moment either degrades the DNA or removes the EtBr/SYBRsafe from the DNA.

@bob1 I will say, however, that all pipettes themselves are routinely shared with the microbiology students (who do numerous experiments on live bacteria). The insides of those pipettes have not been cleaned in recent memory. Whatever is growing inside of these pipettes is anybody's guess.

@MichaelGruenstaeudl Try loading intact genomic DNA or plasmid of known concentration. Should get a high MW smear (genomic) or band(s) for plasmid. If you load enough you should be able to see if this migrates out of the well and/or degrades over time or if it gets stuck; monitor every 5 min or so. Add EtBr to the running buffer or gel to prevent EtBr shadow; I think those blobs in your first gel are EtBr. Load your mix alone to confirm. I don't think it'll take the DNA with it. I use EtBr at 10 ug/ml (1:1000) in gel or buffer - is that similar to your 1:10?

@bob1 My students and I followed your suggestions, yet received the same weird pattern: the DNA ladder migrates the "wrong" direction (towards the negative electrode), whereas the PCR product is "stuck" in the gel well (lane 7). Please see the gel image under 'Edit 2 (Nov-07-2024)' above.

@Chris My students and I followed your suggestion and mixed the SYBRsafe into the agarose gel when preparing it, yet our results were as always: the DNA ladder migrates the "wrong" direction (towards the negative electrode), whereas the PCR product is "stuck" in the gel well (lane 7). Please see the gel image under 'Edit 2 (Nov-07-2024)' above.

@MichaelGruenstaeudl Wow, never seen both directions before. Ionic problems would be my first thought. pH of 8 as in your question is ~correct, so it shouldn't be that. You sometimes see these sorts of effects if there is a problem in the amount of ions in one of the solutions added - e.g. added MgCl2 instead of H2O in PCR. I'd guess that with longer run time, the PCR product would start to migrate in the wrong direction too, currently balanced by the ions in the reaction. Is the ladder in the same loading dye as the samples?

@MichaelGruenstaeudl That's really weird and something I have never seen (and having teached undergrad molecular biology courses I have seen a lot of errors). It would mean for some reasons that your marker is charged wrongly. Do you have the chance to get another marker which is known to have run in the right direction in the past?