text:
Digestion Enzymes in Carbohydrate Metabolism?
Digestion of carbohydrates is ending in small intestine with mainly disaccharidases. Isomaltose is broken down to 2 molecules of glucose by the enzyme called alpha dextrinase(oligo-1,6 glucosidase or isomaltase) which hydrloyze 1,6 linkage of isomaltose. In the case of glycogen metabolism there is debranching enzymes that are transferase and alpha 1,6 glucosidase. According to this informations can we say that alpha dextrinase (isomaltase) and alpha 1,6glucosidase are the same enzyme ?

The answer depends on what you mean by "same enzyme". Some people say "same enzyme" when they mean "same enzymatic activity" (as opposed to same protein). For example, the EC system often is said to classify enzymes, when it really classifies reactions. It's confusing :-/

1,6-glucosidases are a class of enzymes and not just one enzyme. It does not mean that all the members of this class are the same enzymes. They catalyse the same kind of reactions but their properties and substrate specificities differ. Check BRENDA for details.
BTW, dextrin-1,6-glucosidase is a synonym for amylo-alpha-1,6-glucosidase. Other 1,6-glucosidases are different enzymes with different EC numbers.


text:
Can bacteria or other microorganisms be killed by applying pressure?
Can you smash a bacteria (or any microorganism) and kill it?
Let's say there is millions of microorganisms on a table. When you put your finger on the table, will or can you kill at least some of them ?

I'm voting to close this question as off-topic because it is just too silly.

Yes, you can kill bacteria using pressure. The devised used is called a French press
https://en.wikipedia.org/wiki/French_pressure_cell_press
http://www.glenmills.com/cell-disruption/high-pressure-homogenizer/french-press-gm/
However the pressure use is about 40k psi.... which is a lot higher pressure than anything a human body can generate.
Other methods to kill bacteria include,
heat, gamma radiation, oxidative chemicals, antibiotics, dehydration, salt, oxygen exclusion, freezing.
However bacteria are a very diverse group, so it might take one or more methods in combination to kill all bacteria (and their spores) in a sample.

I'm probably being overly pedantic here, but a human can certainly easily generate 40,000 psi, if merely by standing on something pointy (a surface of up to a few sq mm, depending on your mass). Of course, clearly not as OP is suggesting by pushing your finger on a table without the aid of something like a pin.

Well if you get a 70kg person to stand and balance his complete weight on a pin (2 mm2),... then yes, 40k psi can be achieved by a human body. But if we start factoring aids, a human can do a lot of things.

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Can humans ever directly see a few photons at a time? Can a human see a single photon?
I am not asking the following question: Can humans ever see a photon in the same way we see a chair?
My question is: Can a human retina respond to a single photon? If so, how does this happen and why is the retina able to "sense" (detect) a single photon?

Related Quora question

A single molecule of rhodopsin (actually the cis-retinal bound to it) can and actually does react to one photon (Purves et al. Chapter: Phototransduction in Neuroscience).

It has been estimated that a single light-activated rhodopsin molecule
  can activate 800 transducin molecules, roughly eight percent of the
  molecules on the disk surface. Although each transducin molecule
  activates only one phosphodiesterase molecule, each of these is in
  turn capable of catalyzing the breakdown of as many as six cGMP
  molecules. As a result, the absorption of a single photon by a
  rhodopsin molecule results in the closure of approximately 200 ion
  channels, or about 2% of the number of channels in each rod that are
  open in the dark. This number of channel closures causes a net change
  in the membrane potential of about 1 mV.

Photoreceptor cells continuously secrete the neurotransmitter glutamate in dark; with light exposure glutamate release would reduce. This leads to activation of the next line of cells (bipolar, horizontal cells and retinal ganglion cells).

 Modelled relationship between glutamate release and rod membrane potential.  From Witkovsky et al. (1997).

From this model (Witkovsky et al. 1997) it appears that for a change in glutamate release rate, a larger change in membrane potential is needed. Moreover, the depolarization of the photoreceptors has to be sustained for a while so that downstream cells can react (light absorption is much much faster than biochemical processes). The lifetime of an activated rhodopsin molecule is ~40ms in mice (Gross and Burns, 2010) and ~400ms in salamanders (Lyubarsky et al., 1996). We can assume that human eye is more similar to that of mice. There are approximately 40,000,000 molecules of rhodopsin in a rod cell (BioNumbers). The most sensitive of retinal ganglion cells need ~0.04% of rhodopsin molecules per rod cell to be activated (Takeshita et al., 2017).

(b) Absolute threshold of On and Off retinal ganglion cells
Both On and Off RGCs carry rich information about the weakest light
  signals. Off cells are somewhat more sensitive than On cells but have
  a higher error rate in their gap-based coding. The absolute threshold
  for primate On and Off parasol cells in a two-alternative
  forced-choice task is extremely close to the limits posed by the
  quantal nature of light: On parasols reach 75% correct choices at a
  light level corresponding to approximately 0.0008 R* per rod per flash
  (mean, n = 6) and Off parasols at a light level corresponding to
  approximately 0.0004 R* per rod per flash (mean, n = 5).

A single activated rhodopsin molecule would be 0.0000025% of the total. This would be insufficient to activate an RGC.
So, I can make a reliable guess that you cannot actually "see" a photon although one of the retinal photoreceptor cells can sense it. However, I'm still looking for a solid reference that says how many photons are needed (and for how long) to produce a visual response.

A single photon is sufficient to elicit a somewhat reliable response (whether this counts as "seeing" is open to debate, but seems to fit the OP's criterion): https://www.nature.com/articles/ncomms12172#discussion

Another thing to add would be that if our eyes were good enough to reliably grab single photons, we'd have great night vision. Your cats might stand a better chance, though it's much harder to determine if they have actually "seen" anything or not. Moreover, if our eyes were good enough in that regard, we might even have discovered photons and quantum mechanics earlier than we did in our actual history, by trying to figure out why that very dim light gets "staticky".

I've been looking for a reference on how many photons are need for threshold perception, for a while. For some reason the number seven to ten photons knocks around physics teaching circles, but I have no idea where it comes from.

The numbers I remember having heard are 10 photons per second sustained exposure or 100 photons in a single burst

A recent study published in Nature by Tinsley et al. Direct detection of a single photon by humans found that it is possible for dark-adapted humans to respond to a single-photon stimulus, but only rarely. They used a source which created pairs of photons, and used one of the pair to determine whether the subject may have been exposed to a single photon. The subjects were asked to respond whether they had seen a single photon after an event, and to rate their confidence in their response on a scale of 1-3. Of the highest confidence trials, $60\% \pm 0.3 \% \space (P=0.001)$ of responses were correct. Not exactly reliable, but strong evidence that it is possible.
They also interestingly found that the detection efficiency was highly increased if another single photon was emitted in the previous ~3.5 seconds.
As far as mechanisms, I'm no biologist or biochemist so I'll suggest reading section III from Rieke & Baylor (1998) Single-photon detection by rod cells of the retina, which covers it in detail.

Interesting. I just skimmed through the article. The concept does not sound very convincing to me but I'll read it more carefully and check if there have been any replies to this finding.

Neither P=0.001 nor 60% of correct responses sound like proof beyond reasonable doubt.

@DmitryGrigoryev very hard to believe without a molecular explanation.

@WYSIWYG It's definitely open to bias as any psychophysics experiment is, but the paper gives me the impression that it was very carefully undertaken. The concept seems to be essentially the same one that's been used for decades, just with a much better source

@NicHartley they state somewhere in there or the supplementals that they didn't have good enough individual-subject statistics to do that convincingly, but that people took a few sessions to get good at it

@DmitryGrigoryev a lot of biology uses p<0.05. At 0.001, its fairly strong evidence that people are better than a coin flip (but still pretty bad!) at detecting single photons.

@mbrig Or perhaps people are good at detecting something correlated with the photon emission (like noise), but not everyone figured that out.

@DmitryGrigoryev they both minimised (sound damping foam, fibre to couple light into room a distance from source) and tested for that. The efficiency of the single photon source is low, because if you crank it up you get significant numbers of multiphoton events. Most trials (92%) actually had no photons, although they would have had every other possible signal that would bias a subject. "in these trials the probability of correct response was not different from the baseline for both the combined and the high-confidence responses (0.505±0.003, P=0.08 and 0.507±0.01, P=0.3, respectively)"

I haven't read the paper but I wouldn't be surprised if the better than chance performance is an example of stochastic resonance.

Technically, we can sense the individual photons. Here is an quote from a cellular biology textbook:
"Absorption of a single photon of light induces a conformational
change in the rhodopsin molecule, which transmits a signal to a heterotrimeric G protein (called transducin ), which activates a coupled
effector." (Karp's Cell and Molecular Biology 8e, 603).
However, we have neural filters (part of evolution/adaptation) that only "see" light if somewhere around 5-9 photons are detected within a 100 ms period. Here is a source for this.
According to that source, this neural filter is actually an evolutionary advantage, as it will prevent unnecessary visual data from being processed (which would add a lot of noise to the "images" we see).
However, something interesting is that frogs can actually detect and see single photons of light. I remember watching a video some time back where it was explained as follows: If a frog is launched to the outer edges of our solar system (where photon density from the sun is very little), time-to-time a single photon will enter the frog's eye, and the frog will see flashes of this light, while seeing darkness when photons aren't entering. You can Google more about these frogs, or read a summary of it on The seeing power of frogs: Frogs can detect single photons of light.
Edit: As WYSIWYG pointed out, frogs aren't so special after all! There are more than one organisms that can "see" (not just sense) these individual photons.
Hope this helps!

@WYSIWYG Hi, I read it from this source for my class last year: http://math.ucr.edu/home/baez/physics/Quantum/see_a_photon.html

@F16Falcon I just found that the lifetime of activated rhodopsin is longer in salamander than in mouse. Not sure about frogs but photoreceptors of different organisms can have different sensitivities.

@WYSIWYG Yes they can, and the frog was just an example that I wanted to give because it was fascinating to me. I didn't know about other organisms that did this, so thanks for sharing! Also, that is the original document I read (I didn't read the full research papers); Vaxquis is correct.

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How to derive rate of product formation for an allosterically inhibited enzyme?
I'm working through Mathematical Modelling in Systems Biology: An Introduction by Brian Ingalls, and in Chapter 3 there's an example of a simple allosterically inhibited enzyme with reaction scheme shown here:
$$\ce{S + E<=>[k_1][k_{-1}] ES->[k_2] E + P}\\[2em]
\ce{I + E<=>[k_3][k_{-3}] EI}\\[2em]
\ce{I + ES<=>[k_3][k_{-3}] ESI}\\[2em]
\ce{S + EI<=>[k_1][k_{-1}] ESI}
$$
where E is the free enzyme, I is the allosteric inhibitor, S is the substrate, P is the product, and ES, ESI, EI etc. are the various complexes between them. The book goes on to state that the rate of formation of P is
$$\frac{V_{max}}{1+I/K_I}\frac{S}{K_M +S}$$
where
$V_\text{max}$ is the maximal rate of reaction ($k_2$ * Total enzyme concentration), $K_I$ is the dissociation constant of the inhibitor $k_{-3}/k_3$ and $K_M$ is $(k_{-1}+k_2)/k_1$
No proof for this is shown, although the book says the solution is assuming a quasi-steady state of the complexes ES, EI and ESI. I've attempted to work it out, and arrived at almost, the same equation, except I have I/Ki * (k-1+k3)/k1 instead of I/Ki * KM. I have no idea how to get to the equation present by the book. Can someone explain how their equation was derived?

If you apply quasi-steady state approximation for the complexes then you will get three equations for each of the complexes. Then you have to use the conservation law for enzyme to obtain the equation with respect to just substrate and inhibitor. If you try solving these algebraic equations, it gets very complex and difficult to solve by hand. However, in this system of chemical reactions, you can notice one thing: the binding of the inhibitor is not affected by the binding of substrate. In other words, the amount of enzyme inhibited will not depend on the amount of substrate present. So, in the absence of substrate:
$$\frac{d}{dt}(EI)=k_3I.E - k_{-3}EI = 0$$
So the total uninhibited enzyme ($E_u$) would be:
$$E_u=\frac{E_0}{1+\frac{I}{K_I}}$$
When the substrate is present, the amount of total enzyme available for catalysis would be $E_u$. Now, apply the Michaelis-Menten equation for uninhibited enzyme but substitute total enzyme ($E_0$) with total available enzyme ($E_u$):
$$V=\frac{k_2S\left(\frac{E_0}{1+\frac{I}{K_I}}\right)}{K_M+S}$$
From here you can get the equation given in the book.
The above logic works only if the rate of inhibitor binding is much faster than that of substrate binding. If not, the dynamics of product formation will depend on the different reaction rates and this simplistic equation would not be valid.

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Are there any half-evolved animals alive today?
I know that there are animals that are "simpler" than other animals but are there any that are half-evolved? Are there any animals with half-evolved functions, like arms, legs, etc?
This was part of the original question, but it was incorrect.

Saying that every species on the planet is "transitional" is an unacceptable answer because it only works on the assumption that macro-evolution is true.
Saying that all the transitional animals just died off also doesn't seem quite right. If all the previous transitional  animals just went extinct, then wouldn't we just have a few specialized species alive today? This wouldn't allow for the diversity we see today.

Evolution is a process which has no defined intermediate states and no endpoint. We are all constantly evolving...

Where and how do you define "half"?  Certainly you can find groups of species (e.g. ring species) in which neighboring species grade almost insensibly into one another and interbreed, but widely-separated ones are distinct, and don't interbreed.

If there were any living "half ape half humans" then you'd be asking why there aren't any "half that half humans".

I don't think this question should be closed. It's a legitimate question that simply comes from lack of knowledge in the field of evolution. I'm sure many people (wrongly) think about evolution in the same way. The question is otherwise fairly well written and to the point, and an answer that builds on the current comments will help inform the OP.

@Bryce Could you please clarify what you mean in your second paragraph? I don't follow how "no ultimate or final species" implies "macro-evolution is true".

Humans are half-ape / half-whatever-we'll-be-in-a-few-hundred-thousand-years. What does "half-evolved" mean? We only label things "transitional" (a relative term) as a convenience because they're partway between the origin and our current reference point. In the far future we'll just be identifying current species alive today as "transitional" as well.

Although the question displays some misunderstanding of evolution, it might be possible to reframe and instead think "Have we ever observed speciation in animals?" It's not really right to say "half-evolved" but the answer to that is yes, we have observed speciation, for example see this previous question/answer.

Take a look at the Monotremata that albeit being mammals show some sauropsid ("reptiles" + birds) features, the most characteristic perhaps that they lay eggs. They are most basal in the mammal tree and are thought to have been widespread but now comprise only three species.

I've heard one fairly well-known species described as half-ape, half-angel... :)

@theforestecologist you are actually correct. I am somewhat ignorant when it comes to evolution.

@Bryce and please know that I did not mean that in a negative or accusing way. You just can't know something until you learn it. Kudos to you for trying to learn :).

You can say that some thing is just half the way when you have a standard for it.  Like "the beaker is half filled" you can say this when you know the volume of the beaker and the volume of the water that you poured has just reached half the limit.  But in case of evolution we do not have any standard limit. It is not standardized that any given animal would evolve 'this much' or 'that much'  nor it is written that all animals should evolve into a standard super-animal. So thus we cannot say that something has just half evolved, while others are fully evolved.

I know that there are animals that are "simpler" than other animals but are there any that are half-evolved? Why aren't there living half ape and half humans?

Oh come on. You know if Australopithecines or Homo habilis still existed you would be asking "Why aren't there living half Homo habilis and half humans"? And when the other Great Apes go extinct you'll be wondering why there are no transitional forms between humans and monkeys. The answer to that question is, humans are apes; chimpanzees and we are pretty much as close as two species can be; we could have closer forms that survived but we could also have a much bigger gap between us and our closest relatives than we currently do. In other words, any ape is a valid example of something "half-human half-ape". It's like asking for a vehicle that's half-car, half-volvo.

Are there animals that are just starting to evolve arms and legs?

You mean, modifying fins into limbs in a general movement from water-living to land-living, like the first tetrapods are thought to have done? I like mudskippers.

Saying that every species on the planet is "transitional" because there are no ultimate or final species is an unacceptable answer because it only works on the assumption that macro-evolution is true.

Not quite, it is an explanation of what "macro-evolution" is and what things it predicts.
There are two aspects to the theory of evolution that are often confused; one is how it works to generate diversity and change in living organisms, and the other is how it works to adapt living organisms to their environment and create what we humans see as "design", "function". Both things are results of evolution, but the latter is much less important than we'd think, which leads people who explain evolution to de-emphasize it, which then leads people to be confused as to how it can happen at all.
The thing is, both "design" and "goals/purposes" are concepts that are meaningful in considering evolution, it's just that the words are dangerous because they imply an conscious intention that isn't there. You could replace "design" with "optimization"; random mutation combined with natural selection can form an optimizing process, i.e. a process that will over time generate forms that have specific properties. In the case of life, whatever properties promote the spread of the organism we're looking at.
As for "goal", that's just the physical fact of the world that some arrangements of matter have different effects from other arrangements of matter; meaning that if some arrangements of matter will lead organisms to reproduce better, the optimizing process of evolution will predictably lead to organisms having that arrangement of matter. So we can talk about, say, eyes being "designed" by evolution "for seeing"; the difference between that and a rock "being designed" "for having its shape" is that "seeing" (i.e. that organisms ancestors surviving and reproducing based on how well they interpreted light signals) had a causal influence on the organism's eye's structure.
So in that sense we can think there are "goals" in evolution; seeing, flying, swimming, breathing... and many lineages can be retrospectively seen as evolving "in the direction" of those goals. But the important thing is that those "goals" are completely dependent on the environment; as long as there's selective pressure for improved sight a lineage will evolve to have better eyes, but the second the selective pressure disappears or reverses, the lineage will evolve to maintain its current eyes or to lose them. And of course different lineages may have different selective pressures on them and "evolve in different directions". That's why there isn't a single overriding goal in evolution, just millions of lineages under different selective pressures that might change tomorrow.
That's why we can say every species is "transitional" (because they'll all be something different tomorrow, or not) and at the same time not be able to say transitional towards what (because the environment is complicated and we usually can't tell under what sustained selective pressure a given organism is under, and even if we could we couldn't be sure it remained the same over the next thousand or million years).
Having said that, when our human brains say "half-evolved" we often have specific goals and images in mind - like "halfway towards flight", "halfway towards eyes", "halfway towards limbs", "halfway towards dolphinhood". And there are plenty of "transitionals" by that definition - I brought up the mudskipper; there are also plenty of gliding animals, a plethora of eyes (or "eyes") at every point on the "good at seeing" continuum (more of a state space than a continuum really), aquatic mammals that may remind one of what the ancestors of cetaceans were like and might evolve to be more aquatic in the future...

Saying that all the transitional animals just died off also doesn't seem quite right. If all the previous transitional animals just went extinct, then wouldn't we just have a few specialized species alive today? This wouldn't allow for the diversity we see today.

Ah, but what diversity do we see today? What we observe in the fossil record is the constant extinction of some forms and diversification of others, that nevertheless remain more like each other in important ways than they were to their earlier aunts and uncles - meaning while at some point you might have forms A, B, and C, a million years later you have A1, A2, A3 and A4. To illustrate, the earliest tetrapods had a wide variety of number of digits on their limbs. Of course they all basically looked like fish. Most of those early tetrapods went extinct; the only line that survived had five digits. And millions of years later we have a stunning variety of organisms descended from that lineage, most of which look nothing like fish or each other, yet they all follow the same basic skeletal plan, down to the five digits. So which is more diverse?
Basically your question accurately describes the biosphere as the fossil record shows it, you just missed one thing: diversification. Meaning the "few specialized species" are actually a "few specialized families/orders/classes/phyla that themselves contain many species".
When thinking of evolutionary change it's better not to think of a line from A to B, but something like self-spawning fireworks. One group expands, a lot of its elements fizzling out but some of them spawning their own subgroups that expand in turn while still being recognizably part of the original group, and so on so forth with the fizzling of the most and spawning of the few, at some point the older groups might be so large and full of different subgroups that they start losing their definition, and basically at some point you realize the whole big mass of elements that now cover the sky includes both A and B, meaning if you roll back the tape you can certainly track how something that looked like A changed over time into something that looked like B, but it's really a very small part of the whole show.

Re "...animals that are just starting to evolve arms and legs", you might consider otters and seals as partly-evolved whales.  That is, they're at different points along the evolutionary path from a terrestrial animal with legs to a fully aquatic animal with fins.

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text:
Is this a stag beetle?
Just saw this beetle on my window.
The coin is an American dime.
Location is Shenandoah Valley,
in central Virginia, U.S.A.

This is indeed a Stag Beetle (Family Lucanidae); in particular a member of the genus Lucanus.  Looking at the bugguide.net page for the genus here your specimen is most likely Lucanus capreolus, though Lucanus placidus also looks possible -- the two species are very close in appearance, though the former does seem more likely based on distribution.  Consulting The Generic Guide to New World Scarab Beetles here confirms that L. capreolus is featured here -- the femora (the first long segment in the leg, and the first we can see -- look at the right front leg) are bicolored (darker at the tips) -- the femora of L. placidus would be solid dark brown to black.


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What is this small tree?
I found a dozen of these small trees in a local park that is just an overgrown homestead.  The leaves look something like an elder but the flower clusters surrounded by white, four petaled false flowers are completely unknown to me. What species is this?

Location:  Shenandoah valley in central Virginia, U.S.A.

Sandy soil on inside of a sharp curve of the South River,
just above the flood plain.
This area has been occupied by people, for a couple hundred years,
so this could very well be a cultivated plant.

Please add your location. Most species IDs require knowledge of the general location(e.g., country, region, state, etc.) and preferably info about the surrounding habitat. Thanks.

The location is the Shenandoah valley in central Virginia, U.S.A., sandy soil in side a sharp curve of the South River, just above the flood plain.  This area has been occupied by people, for a couple hundred years, so this could very well be an escaped garden plant.

This is very likely some species of Viburnum.
Viburnum is a genus of about 150–175 species of shrubs in the Adoxaceae family that are primarilly native throughout the temperate Northern Hemisphere.
All species of viburnum (as far as I know) have opposite leaves, as does the specimen in the picture.
Many species of Viburnums bloom in white in the last part of April through early May, and typically you have to pay attention to flower shape and often, more importantly, the leaf shape to differentiate species.
Without location information, an exact species ID is not guaranteed, but your specimen looks very similar to:
Doublefile Viburnum (Viburnum plicatum)

 Source: Dave's Garden

 Source: Missouri Botanical Garden
This species produces two rows of white flower clusters, with both small and large flowers, along the stem.
According to Wikipedia: Viburnum plicatum is a popular ornamental plant, both in its native area and in various temperate regions.
Based on the "double" flower types of your specimen, it's likely V. plicatum f. tomentosum:

Cultivars with wild-type flowerhead structure are sometimes described as a separate botanical form V. plicatum f. tomentosum. They include 'Cascade', 'Lanarth' and 'Rowallane'.2[3] Two cultivars in this group, 'Mariesii'[5] and 'Pink Beauty',[6] have gained the Royal Horticultural Society's Award of Garden Merit.

Habit: A deciduous, multi-stemmed medium-sized shrub that typically reaches 2.5 3 m tall. [Source].
Leaf: ovate, 5-10 cm long, up to 5 cm wide; pointed apex and rounded leaf base; serrated leaf margin; 8 to 12 pairs of veins; pubescent underside; dark green leaf color. [Source].
Flowers: individual flowers form a large (up to 10 cm diameter) flat-topped cyme composed of showy infertile flowers surrounding unshowy fertile flowers. Blooms in May. [Source].

Viburnum is absolutely right. Without location, species will be difficult. And as it is a park, it is probably a cultivar anyway.

@RHA Right. Which is why I picked a common cultivar as the best guess :p. Of course it couldn't be easy and just be one of the ones i know well (rafinesquianum, acerfolium, prunifolium, rufidulum, etc), but for doing a 5 min search without location info, I'd say this is a pretty good guess at species!

It also isn't any European species I know. I am guessing this is an American/Canadian location.


text:
Does anyone know what this living creature is?
There are two different things I am trying to identify. I live in Lexington, Kentucky. The first one I started seeing was a small white larvae looking worm thing. They would very in size but never bigger than a few centimeters long and very thin.  I started seeing these around my house about two months ago.  I had not seen them before.  It seemed like they showed up all of a sudden.  They were in the floor and on the furniture.  I never would see them move. When I would try and pick them up or investigate, at the slightest touch they would turn to liquid almost like water, clear.  Just disappear.  The other form I am seeing is a bit bigger I don't know if they are both the same species just in various stages or if they are 2 separate species.  The second ones I seen were almost an off white with rings vertically around its body. With hair all over them.  Some were hairier than others and they were not all the exact same color.  It seemed to me that they used their hair as a weapon or defense not sure how that was intended.  They started showing up on my hanging cloths in my closet as well.  Shortly after we started noticing small holes in our cloths.  I call them creatures since I am not sure what they are.  They then started burrowing into us. I never seen the darker one with hair burrow but for sure the small white larvae looking one.  But only me.  Not my kids or husband.  The doctors can't tell me what they are.  The darker one in the picture came out of my leg.  When I got it out it was still alive.  They seem to prefer my nose and sinus's.  I spent hundred on exterminator and have not seen anymore.  The pest control company said they had never seen them before.  The one picture of the white larva is one that I had to download.  I accidently lost all of my pictures on a phone before they were downloaded to my computer.  That picture is identical to what I have found.  I may have more pictures.  I will go thru all of them in the morning and try to add some here.
Hairy:

White in colour:

Welcome to Biology.SE! Could you please edit your post and give the location of where you took the pictures?

Do you have better pictures? Give the size? Is there a reason one of the pictures is 5 years old?

I have lost some of my pictures due to a phone issue.  I will go thru all pictures I have in the morning and get some more added.  I had to download that picture, but it is identical to the ones in my house.


text:
How are the correct tRNAs transported to the ribosome?
I have been trying to understand how the tRNA transporting the correct amino acid required by the ribosome reaches the ribosome. The only way I can imagine this happening is that all types of tRNA+amino acid reach the ribosome, bombard the ribosome, and the ribosome will 'accept' only the one that matches what it is waiting for.
I can not imagine any other mechanism in the cell's cytoplasm that will somehow filter or push the correct tRNA+amino acid and move it towards the ribosome that needs it.
How do we explain this mystery?

The only way I can imagine this happening is that all types of tRNA+amino acid reach the ribosome, bombarding the ribosome, and the ribosome will 'accept' only the one that matches what it is waiting for.

Yup, basically.  This is an extremely cool figure showing the process. There are various elongation factors that aid the process, such as EF-Tu, which essentially waits until there is a good codon-anticodon match before hydrolyzing GTP and allowing the tRNA/amino acid to enter the ribosome.
This process can be particularly salient when you look at a concept such as codon-usage bias.  Certain tRNAs are more common in the cell, so if a given mRNA uses codons to match those tRNA instead of matching other degenerate but less common anti-codons, translation will occur faster.  This is more obvious in organisms such as E. coli where growth is paramount.

Apart from random movement, are there any other factors which move the tRNA near the ribosome, where the ones you mentioned take effect?


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On average how many genes / alleles do people share?
I am curious about how much more a child can be alike to one parent than the other. If a child were to inherit all the alleles that are shared between both parents from one parent, but inherit all alleles from the other parent which the first parent doesn't possess, wouldn't this make the child genetically more uniquely similar to the second parent?
This question would be aided by understanding of how many alleles on average a person already shares with another person. Taking into account regional areas probably yield more similar people, I would imagine the average couple would share more than two randomly chosen people on the planet.

I will attempt to answer the question. Allele is defined, in simple terms, variation of a given gene, e.g. through deletions, SNPs etc. Humans are diploid organisms, meaning we have two sets of chromosomes, one from mother and one from father. Now since we have two sister chromosome, we can only have (share) two alleles of a given gene (one from mother and one from father) unless there are multiple copies of a gene or chromosome, which is mostly observed in disease conditions but that's not what we are talking about. Now since every humans have SNPs at roughly 1 every 1000 base pair, there are genetic variations between sequences of genes between humans, although there are some hot spots, which are more varied and some genes are very highly conserved due to their critical function such as cytochrome C. This just means that parents of the child you are describing (if not related to each other) are not likely to share the exact same, sequence wise, genetic code for a given gene selected at random.
The inheritance of a given allele of a gene on a chromosome happens through independent assortment (a process which happens maternally and paternally), meaning a child (offspring/zygote) would get one copy of a gene/allele (from the possible two that each parent themselves have) from maternal and one copy from paternal side at random. This is one source of genetic variation in a zygote. The other source of genetic variation is gene cross-over (through homologous recombination) meaning bits of the maternal or paternal chromosomes swap at gamete stage before the gametes are fused together to form a zygote, which makes the offspring unique and no offspring alike (except MZ twins but thats another discussion). This overall means that you can inherit a maximum of two alleles of a given gene (assuming again the parents of the child are not closely related) and even then the sequence of the offspring genes are not likely to be exactly the same as their parents, which makes every human unique. But saying that, you have a much higher gene sequence match to your parents than any other non-related human selected at random.
One thing worth noting here is that mitochondrial genes, are inherited exclusively from you mother (through the egg) and males inherit the Y chromosomes paternally so there are circumstances I guess you could say you inherit certain gene/alleles paternally or maternally.
What I speculate you might be thinking about is how many homologues (similar versions) of a given genes humans have and I think the average in the human genome is 3 but do check this! Flies (Drosophila) tends to have one, which is why its such a great model organism to study genetics and genetic interactions with as you do not tend to get redundancies.
I hope this answers your question

This certainly adds to my knowledge, but isn't a wholly satisfying answer. I found this helpful and interesting: "during miosis you get gene cross-over meaning bits of the maternal or paternal chromosomes swap, which makes the offspring unique and not just half versions of its parent"

There appear to be a couple spelling errors, and a few run on sentences that I find hard to follow. Maybe you or someone with knowledge can properly edit this answer?

made an edit to my original answer. Hope this is more helpful and any further edits are welcomed!


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Omnivore vs Carnivore territory size
Edit: Large carnivores require lots of territory. What about bears? They're omnivores. How much does that count?
Is there anywhere I could find weight/territory ratios for mammals, depending on diet? Does necessary territory matter so much depending on the diet of a large mammal?
Thanks

Bears (depending on species) are omnivorous

Yep. Realized I was wrong. But the territory size is still something I'd like to find an answer for, if possible

Also consider that elephants, giraffes, rhinos etc. Are large herbivores and have large territory/ranges

Any answer is going to vary quite a bit, depending on the productivity of the land in question.  It would take much less area to support a bear in say the lush forest/stream environment of southwest Alaska, than in the near-desert eastern Sierra.


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Can this image be the result of a Western Blot?
I am currently researching image manipulation in the life sciences and stumbled upon a Western Blot looking very similar to the image below.
For creating the image I have cut out the blot using the Fuzzy Select Tool of GIMP and then greatly adjusted the local contrast of the blot as well as the background. By using the Fuzzy Select Tool some pixels of the original background are also captured. That is why the blot shown has a brighter background around the edges. I normally would not expect to see bright edges around a blot.
While I know how Western Blots look when they are captured with a digital camera, I do not know about techniques like Chemiluminescent Blotting (I am an undergraduate student in Computer Science). Maybe there is a blotting technique that results in an image like the one i created.
Is it possible to get a Western Blot result like this without inappropriate modification of the image?

Can you explain a bit more?  I'm still confused by what that image is, in particular why it's colored the way it is.

this looks like a normal band in a gel, with the image manipulated to replace every pixel above a certain cutoff to black.  could be manipulation or it could be an accidental data issue

@Amory I have edited the question and provided some more details. Hope this helps.

Yeah I'm with @shigeta on this.  Do you have the unaltered image?  I can post an example of one of my chemiluminescent blots if you like.

I have the unaltered image but i am not sure if it helps as the image posted is altered to imitate another image from an actual publication. The image i stumbled upon is from an actual publication and i can't post it here due to legal risks (but it looks almost exactly like the one i posted). I would appreciate to see an example of a chemiluminescent blot.

How was the initial image aquired? Could just be a result of the compression algorithm used for the original image...

The initial image was retrieved from the supplementary figures from a database for medical publications and is a compressed JPEG image. The original image shows multiple blot regions of different experiments and not all of these regions show this behaviour. The publication states that the displayed regions are Western Blots.

@RalfThaenert Are you implying that the original image came from a publication?  If it's from the same institution you go to, you might try and see if you can get your hands on the original file if it's not in a standard image format.  Most image systems can save images in a format that has a lot more information than a standard image. They are harder to modify, and might give a hint. Not every lab keeps them, however (I always insist on it for these reasons).

@RalfThaenert Can't you post a link to the actual publication? This will make it much easier to know exactly what you are talking about, and to evaluate possible reasons problems/errors.

The original publication comes from a different institution and is a publication gathered from Pubmed Central. I'm sorry but i won't provide the original publication because of legal issues (the authors of various blogs about image manipulation faced legal threats, like science-fraud.org). But i will report the finding to the author of the publication. Thank you all for your help.

I do not think that a publication quality blot should have such an artifact, but I was able to find something similar by purposely over blotting (not the same as over exposing) a gel.  If you use too much primary, secondary, or developing reagent, you can get your HRP signal to "burn in" a membrane where you get a distinct "negative band."
By negative band I mean a region that is more clear/white than background. This happens mostly when you have way too much secondary antibody.  Normally when this happens, the CENTER of the band burns in first so you would see a white center with dark edges.  And that's only when you are imaging the membrane as it is burning in.  Often the whole band is white.
After going through the westerns of grad-student who is working with me, I found this image:

It came with the clear notation that it was burned in and disregarded (said student was learning how to do Westerns at the time).  It's a GAPDH blot for those that care.  When this does happen, it's obvious because you can then see the band with your naked eye on the membrane.  Again this would be a reason to not publish the blot.
The image could have non-maliciously been edit via compression, screens, filters, etc as mentioned by others in the comments.  This is the only way I can think of to experimentally have a similar image.  Ether way I don't think the image should be reported as is.

Thank you, that's close to the image i posted. Still the white area is bigger and does not have sharp edges as the one posted. Assuming that one will not publish damaged blots the remaining option is that the image is edited inappropriately (with or without malicious intent).

@RalfThaenert as I mentioned it's similar, and I think as close as you can get to your image experimentally.  I could imagine that if you, by immense chance, got an image just as the outer edge was fading you could get tighter, but it seems improbable. As scientists we are not prone to saying something is impossible, but rather that certain things are likely, especially compared to others. So yes, I think everyone thinks the simplest way to your image is digital editing (intended or not).

Here's an example of a chemiluminescent blot:

For those who care, the first column on the left is the weight standard, the next two are pooled pellets, and the rest are increasing fractions of purified HIV using a mouse monoclonal anti-p24 (capsid) antibody.
This blot is pretty clean (although for my work it was pretty disappointing...) but here's one that looks less-than-ideal, and perhaps more like your example:

These are lysates and pelleted supernatant from Jurkat uninfected (left) and HIVIIIB-infected (right) cultures, detected with a mouse monoclonal anti-tsg101 antibody.
I agree with shigeta's comment that your image might not be exactly what I would expect, but that doesn't necessarily mean it was done maliciously; as you can see, there can be a fair amount of variation in how blots turn out depending on the equipment used, the type of membrane, the protein itself, and so on.  I try to be pretty conservative with image filters but there's a lot you can do with those guys that can be shady but falls short of Photoshop.

Thanks for the images. The images do not show such a behaviour around the blot regions. So there is no Western Blot technique which shows this behaviour by default? Of course such an image can be the result of compression, filtering and beautification and is not necessarily an intended manipulation.


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Why aren't complex-stabilizing proteins like transcription factors considered catalysts/enzymes?
I'm not asking the question on a superficial level. Obviously, (most) transcription factors are not acting directly on a substrate to produce a chemical change. I pose the above question as more of a philosophical inquiry.
First, a definition: A catalyst is a substance that increases the rate of a chemical reaction and is not consumed in the reaction. As every biochemistry class emphasizes, catalysts do not change the equilibrium constant of a reaction, only the rate.
So for example, if we take the following example of transcribing a gene of length $n$ ($G$) into a transcript of length $n$ ($M$).
$$
\ce{RNAP + G + nNTP <=>> RNAP + G + M} \mbox{    (Reaction I)}
$$
The hydrolysis of the NTP's bonds drives the reaction forward (source). The Gibbs free energy has decreased. Obviously, there is some probability that the NTPs in solution would spontaneously polymerize into the length-n transcript, this possibility is unfathomably infinitesimal though.
The RNA polymerase is acting as an enzyme here, since it's 1) increasing the rate of an otherwise slow reaction and 2) not being consumed in the reaction. Our nomenclature is consistent as we usually reserve "-ase" suffix reserved for enzymes.
Transcription factors bind elsewhere on the DNA and facilitate (or impede) the formation of RNA polymerase complex from its constituent subunits ($mS$). Assume we have an activating transcription factor $TF$. We can model this as:
$$\ce{TF + mS <=> TF + RNAP} \mbox{    (Reaction II)}$$
Putting these reactions $I$ and $II$ together, you might have:
$$\ce{TF + mS + nNTP <=> TF + RNAP + M}$$
From our understanding of activating transcription factors, we know that this will increase the rate of the transcription reaction. The TF is not being consumed in the reaction. So, what am I missing here? Why isn't this transcription factor considered a catalyst for helping to stabilize the initiation complex?

TFs are a big group and at least some are considered catalysts - e.g. histone deactylases/acetylases. Because they aren't part of the reaction; your supposition about the reactions II and III are incorrect. In chemistry the TF would go over the arrows!

If this is a question about philosophy you are on the wrong site. If you are using this as a platform to make an argument, you are misusing the site. If this is a question about historical linguistics, SE English Language and Usage might be more appropriate. And, paradoxically, your definition of an enzyme in naïve historical terms, although used in chemistry and taught to undergraduate biochemists, does not conform to what we know or think about enzymes. You must be aware that biochemists regard enzymes as macromolecules that participate in chemical reactions to increase their rate.

I think the rewording of this question is devious. It sets up a straw horse because of the weakness of his original question. Biochemical classes talk about the properties of enzymes, not catalysts, and we do not talk about "factors and catalysts". If you want to ask a question about catalysts, ask it on SE Chemistry. It also suggests he is not interested in knowing why biochemists describe proteins the way the do, but is indulging in what our Help terms a "rant". Using the site as a soap box for his jesuitical casuistry.

I’m voting to close this question because it is an attempt to start a discussion regarding a point of view rather than a question seeking an answer.

Because the TFs DO NOT PARTICIPATE in the catalyzing reaction themselves, and that reaction involves breaking of chemical bonds in the substance that's being catalyzed and forming temporary chemical bonds between it and the enzyme, which is not the case with the TFs.

Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers in the help center.

Do you mean TFs (transcription factors) instead of TTs? Please [edit] your post and clarify.


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Determine acidification of milk (no-probe/contact/destruction)
For a project, I am trying to figure out if it is possible to determine the acidification of milk without probing, touching, destroying or opening the sample, thus leaving the sample inside the plastic, transparent sample container. I am fairly experienced with machine vision and sensors, but not even a little in biology. I read somewhere that "Milk spoils when bacteria convert the lactose into glucose and galactose, producing lactic acid." I was wondering if there is any way of detecting any of these changes using a special camera or special lighting. Any advice or help will be much appreciated.

The easiest way would be to use a colored indicator in the milk that changes color with acidity.

Thank you for your suggestion, but I am looking for a no-probe/contact/destruction way to achieve this goal. I will edit my question to clarify this better.

Thanks for the edit, but are we supposed to correct spelling in a quote?

Supposed is probably said too much. I would have suspected a typo and corrected it as well.

If you're going to be using (I assume) a flow cell to do spectroscopy, why not just have a pH meter in the flow?

@MattDMo Thank you for your suggestion, unfortunately there is no flow, there are only samples in containers, I edited my question to clarify this.

Speculation here.
The viscosity may slightly change. Perhaps detectable by vibrating the sample and checking the pattern of standing waves on the surface.
Note that acidification due to lactobacilli may well happen after spoilage due to other bacteria.


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Can RNases/DNases survive in strong acid/base solutions of around 10M?
This might be a very stupid question, but I am worried about RNase/DNase contamination of my samples. Since I use 37% HCl and 10M NaOH to pH almost all my buffers, this is a potential source.
I have read however, that both NaOH and HCl should hydrolyze the peptide bonds in amino acids at high concentrations. For HCl, however, I have read that a heating step is required to facilitate the protein hydrolysis, so am a bit confused. Perhaps someone with a better background in chemistry could help?
Thanks a lot!

I could just guess it could be safe, because I have not seen the data suggesting it is OK. NaOH or KOH is used to wash glass ware because it has excellent cleaning effect. You could wash away even if you have some RNase in NaHO. But you might miss something making more trouble than that. How about the electrode of pH meter. So, it is good idea to make efforts to remove RNase activities after making buffer. If you really want to RNase free reagents, check if any companies are selling Nuclease free products.

RNAse-A is a very stable protein and tolerant to alkaline conditions. It  is used in alkaline lysis and remains unaffected by moderately high pH (0.2N NaOH- Solution II). It even survives GTC and GnCl treatment (refolds when the denaturant is removed). I think 10M NaOH is a very high concentration and the acid/alkali stocks are certainly not a source of RNAse contamination. Pipette tips are one place to look for contamination.

You are safe here.
RNase is much more stable than DNase (of any flavor). Extreme pH would destroy even RNase, especially considering time (it has to sit in the bottle with all that acid/base..)
Also, consider this: it is highly unlikely that high-tonnage chemicals like HCL or NaOH could be contaminated with organic enzymes.
If you have a problem with RNase/DNase contamination I would look elsewhere for the source of it.

Treatment with NaOH is one of the methods used to prepare equipment that needs to be RNAse free. DEPC is preferred in my experience, but NaOH certainly works as well. Highly concentrated NaOH like in your case will certainly destroy any RNAses present.
I'd assume the same for concentrated HCl. RNAse is very stable for a protein, but concentrated HCl is not something I'd expect it to survive.

RNAse-A at least survives 0.1N NaOH (in solution-I of alkaline lysis 1:1 with solution-II containing 0.2N NaOH)

@WYSIWYG Interesting. There are quite a few protocols I've seen that use relatively low NaOH concentrations over night to remove RNases, though the one I used myself used 2M NaOH and worked for me.


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Why does the inhibition of translation initiation cause the accumulation of 80S ribosomal monosomes?
As I have read in (1), inhibition of translation initiation will increase the number of 80S ribosomes while decreasing the fraction of polysomes due to the polysome-runoff. The net effect is to decrease the polysome/monosome (P/M) ratio and we observe it for example by inducing ER stress by tunicamycin in (2).
I understand the reduction in polysomes - since we don't interefere with elongation, polysomes work as normal, fallling of eventually, but new monosomes cannot proceed to polysomal stage due to inhibited initation.
However, why do the 80S ribosomes accumulate? I have always thought that 80S ribosome is always bound to mRNA, otherwise it dissociates as separate 40S and 60S subunits. Does this effect therefore mean that the accumulated 80S fraction is mRNA-free and therefore "vacant 80S ribosomes", as decribed in (1), can exist?
Thanks a lot!

https://books.google.co.uk/books?id=6sEq1xLu_hcC&pg=PA130&lpg=PA130&dq=polysome+translation+initiation&source=bl&ots=Un6JjImBJX&sig=ln9mn0KoJDJaVOGK8LbrEmMz9XE&hl=cs&sa=X&ei=x2JiVci8N4jX7Ab02YLgBQ&ved=0CGQQ6AEwCw#v=onepage&q=polysome%20translation%20initiation&f=false
http://jcs.biologists.org/content/115/11/2443/F4.large.jpg

It will depend on the drug you are using. There is a pathway that forms the translational initiation complex that starts with binding the mRNA's cap, the small subunit scans to find the AUG, then the large subunit binds, and so on. The 80 S peaks on the density gradients are not vacant, they are poised on mRNAs waiting to initiate (if you removed the inhibitor).


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Good place to ask health based questions?
I like the development of biology.stackexchange.com, but it is still in an early stage and far from perfection. While we develop it further, could you guys help me finding places to ask questions related to health and biochemistry in general?

Since this question is more about the Q&A site rather than an actual question on the topic, I think this belongs on meta.

Health: ask your doctor.
Biochemistry: ask here, there are already >100 biochemistry questions.

Thanks, but what if I want to ask health questions from a student - not pacient - viewpoint? That is, I want to find papers, data and literature about certain topics. Do you/someone here know?

In that case you're still the closest to on-topic here. I don't think we have any professionals for medicine here yet but as a fellow medical student I might be able to help. Plus there are people with extensive knowledge on human biology, which tends to cover a lot of health topics.


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Does anaerobic glycolysis produce lactate or lactic acid?
I am not properly educated in biochemistry so I apologize if my question makes incorrect assumptions or uses bad definitions.
I am confused about the seemingly interchangeable usage of "lactate" and "lactic acid" when talking about anaerobic glycolysis. I'm aware of a similar question on chemistry stackexchange, but I don't fully understand the answers.
I think I understand that practically, at physiological pH, lactic acid will deprotonate which results in lactate and a hydrogen ion. However, this seems meaningfully different to me than just lactate being produced. If lactic acid is produced and immediately depronated, then wouldn't the solution still be more acidic than before due to the hydrogen ion? On the other hand, if just lactate is produced, then wouldn't the solution be slightly more basic?
This question is motivated by what seems like a debate about the role of cellular acidosis in fatigue. Historically, "lactic acid" was blamed, but it seems like more recent opinions are that "lactate" actually helps buffer the ions and is thus not a cause of acidosis or fatigue directly - instead the ions are blamed. I'm confused since the ions and lactate seem to come from the same source anyway.

Welcome to StackExchange! The article Robergs, R. A. Lactate, not Lactic Acid, is Produced by Cellular Cytosolic Energy Catabolism might be of use to answering your question.

@Donen If you give the poster a link rather than providing an answer one assumes that you think the question is off-topic, perhaps as "homework" being easily answered by the online source. Glancing at it, I would think it of sufficient length and complexity that a condensed description of the argument would be helpful to the poster and others interested in the topic in relation to acidosis and exercise physiology (not my field). I would urge you to provide an answer yourself.

What I did not – and I should – mention to the poster is that the question is – like many others – underdeveloped as it does not show enough of prior research. Instead, I provided some suitable reference which could be read and included in the question if there are any additional subquestions. Furthermore, this could also help someone else to write a comprehensive and well-written answer, for which I currently don't have time to do.

What is the actual question here? there are several questions in this.

Thank you @Domen for the link. This article seems to answer my question, so I'll try to summarize my understanding of it here for anyone else that stumbles upon this. Warning that I am just a layman so I may very well get things wrong and will definitely oversimplify (but hopefully Cunningham's Law will hold).
The article criticizes a separate review that gave a history of cellular lactate production for using the term "lactic acid" instead of "lactate" and for associating this production with cellular acidosis.
To explain why the discrepancy seems to exist at all, the article points out that "lactic acid" was first discovered before there was an understanding of acid-base chemistry, so presumably they did not have the proper tools to appreciate and observe the difference between lactate and lactic acid at the time.
The article acknowledges that "lactic acid" production is correlated with acidosis, but emphasizes that correlation does not imply causation.
My first confusion was, well, if lactic acid is produced, how does it not cause things to be more acidic?
The article argues that lactic acid is not produced at all. Not that it disassociates immediately, but that it is not produced to begin with. (I'll summarize their explanation, but not just yet)
The article continues by acknowledging that anaerobic metabolism does contribute to acidosis. The crux of the question then is, where does the H+ come from?
They go into some detail on the chemistry involved here that I won't summarize because frankly I don't understand it all that well. But in short, they claim that ATP hydrolysis is what releases the H+. Since ATP is hydrolyzed during earlier steps of glycolysis, this means it is the earlier steps of glycolysis that lead to acidosis.
Interestingly, the article highlights that as pH decreases, glycolysis releases more H+:

Note, as pH decreases, there is increased fractional H+ addition to HPi for H2Pi, which accounts for the increasing fractional H+ release during the production of 1,3-bis-phosphoglycerate

The article also explains that after 3-phosphoglycerate is produced with an unprotonated carboxylic group, every intermediate afterwards also has an unprotonated caroxlylic group. This is how they explain that lactic acid is never produced to begin with it at all; instead lactate is produced:

The first carboxylic functional group intermediate of glycolysis is produced in the sixth reaction where 1,3-bisphosphoglycerate is converted to 3-phosphoglycerate (see Ref.9, Fig. 5, p. R507). This is a phosphate transfer reaction, adding the phosphate to ADP forming ATP, with the co-production of 3-phosphoglycerate having an ionized (unprotonated) carboxylic functional group at carbon-3. This is key to understanding the H+ load of glycolysis and H+ metabolic buffering from lactate production. Each glycolytic intermediate following this reaction remains in an ionic form.There is never a glycolytic production of a carboxylic acid since they are all carboxylic ions.

So in short it appears that lactate is produced and that it acts as a buffer against H+. "Lactic acid" has been the go-to term due to the history of its discovery, but it's actually lactate and it does have meaningfully different implications as the production of lactate does serve to consume H+. The earlier steps of glycolysis do lead to acidosis, presumably through ATP hydrolysis. After 3-phosphoglycerate is produced, every intermediate following is also a carboxylate (as opposed to carboxylic acid).

(+1) That indeed in an interesting link! But one sentence is very  unusual, and is surely an error: " For example, the work and achievements of Haldane in acid-base chemistry did not occur until the1940s (11), ... "  J. S. Haldane (the father of JBS Haldane and Naomi Mitchison) died in 1936

Unfortunately you cannot understand the paper or acidosis in general if you do not understand the chemistry of weak acids and bases and the significance of the acid dissociation constant (and the related pKa) on their ionization. If you did you would realize that as lactic acid has a pKa of approx. 3.7 lactate cannot possibly be a physiological buffer. In order for it act as a buffer a significant amount of lactic acid would have to be formed by lactate combining with hydrogen ions at cellular or blood pH. It does not. That is why we refer to it as lactate, as the Chemistry SE answers explain.

Hi @David thank you for the response and context. I apologize if  I misunderstood what “buffer” means, but I believe the paper claims that lactate production consumes H+. Does “buffer” mean something else? Please let me know if I’m misunderstanding both you and the paper, but it sounds like you disagree with this claim of the article?

My reluctance to answer this question relates to your motivation — and the concern of the quoted paper — acidosis and fatigue resulting from exercise. I am a biochemist not a physiologist and cannot express any opinion on that. I would only say that I find a letter that is so critical of the terminology of others should not use the word cytosol (an artificial fraction of broken cells) instead of cytoplasm. The term "consumed" is also unscientific and "coefficient of H+ exchange" is unknown to me. What I do know is a buffer works best ±0.5 pH units from the pKa of its acid: 3.8 for lactic acid.

"but I believe the paper claims that lactate production consumes H+" This, I think, has nothing to do with the buffering effect of lactate (or ionization of carboxylate group of lactate in any sense) but to the fact that a proton is consumed in the LDH reaction (pyruvate + NADH + H+ = lactate + NAD(+)). Have a look at the later papers of R.A. Alberty (or Physical Chemistry by Alberty and Silby)

Furthermore, the pKa values of the carboxylate groups of pyruvate and lactate will be about the same

@David It appears Robergs et. al have netted quite a bit of criticism as well -- see https://journals.physiology.org/doi/full/10.1152/ajpregu.00662.2005 and https://journals.physiology.org/doi/full/10.1152/ajpregu.00069.2005.

Regardless, basic stoichiometry and electroneutrality always dictate $$\ce{C6H12O6\text{(glucose)} -> 2C3H5O3^-\text{(lactate)} + 2H^+}$$ hence lactate production is always "accompanied by" (one way or another) proton production in a 1:1 ratio. Of course, what "happens" to those protons (any buffering / transport / etc) is a different question, and so the topic of discussion in those exchanges...

...which seemed to have gotten somewhat heated actually ---> "...Readers will judge for themselves whether ad hominem comments (16) are appropriate to scholarly debate..."


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How can Nematodes be the most numerous animal species when their habitat is smaller than that of other species
Wikipedia says Nematodes represent no less than 80% of the animals on earth.
I don't know anything about biology, but I've had this thought: isn't their habitat much smaller (in terms of volume) than the one of other species (for example: fishes) ?
Indeed, the volume of Nematodes' habitat is about $10m × S$ where $S$ denotes the surface of the earth, whereas the volume of fishes habitat is about $3 700m × S$. (considering $3700 << \sqrt S$).
So, how come Nematodes be the most numerous species on earth ?

If only the universal language was my mother tongue...!

Where are you getting your numbers for habitat volume for each? Seems likely there are some unfounded assumptions in there. Also fish are really big.

I took the average depth of oceans (I Googled it but don't remember the link) and for Nematodes I've just guessed the number. However, I just asked chatGPT (the artificial intelligence) the depth at which Nematodes can live: it answered me $15$ to $20cm$.

Never ever ever take information from chatGPT like that. ChatGPT does not "know" anything. It cannot check or understand information it gives. It has no concept of "correct" or any concept of concepts at all.

Fish don't live at all depths of ocean, certainly not with uniform abundance. Nematodes live in aquatic environments as well as soil. The Wikipedia page you started your question with talks about nematodes living very deep. Did you read the page that you yourself linked here?

"They are found in every part of the earth's lithosphere,[16] even at great depths, 0.9–3.6 km (3,000–12,000 ft)". Yes, I should have noticed this part of the Wiki page, I did read rapidly the page but I think I skipped this part.

For future reference, the exact Wikipedia quote is: "Their numerical dominance, often exceeding a million individuals per square meter and accounting for about 80% of all individual animals on earth, their diversity of lifecycles, and their presence at various trophic levels point to an important role in many ecosystems."
I could not look at a free online copy of either source, but I have a guess where the 80% figure comes from. Imagine giving every living individual animal a number and then holding a lottery where every number you gave out has an equal chance of being picked. What I believe this quote is saying is that there is an 80% chance that the winner of the lottery will be a nematode.
The reason so many individual can live is so small a space is because most species are extremely small. This site offers data on the average weight of individuals in each nematode families and the largest was steinernematidae at less than 115 micrograms. Wolfram Alpha says that is less than half the mass of a grain of sand.

Half the mass of a grain of sand seems to me a bit small. Actually this picture from Wikimedia let me think they have a length of a few ( more than 5) centimeters. It's also possible that I'm not reading correctly the ruler next to the Nematode's picture

@niobium indeed that is one of the larger species - Females of this species are up to 35 cm I think.

Nematodes can actually get quite a bit larger. The largest species (according to my first link) can be up to 13 meters long and is a parasite of sperm whales. However, these species are the exceptions, not the general rule. It's like ostriches are birds, but that does not mean the most birds weight over 200 lbs. Those nematodes species are a few centimeters big, but the vast majority are microscopic.


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Plant identification?
Can anyone identify the plant below? It's in a backyard in Pennsylvania, and the photo was taken today.

It would help if you provided more photos, such as a detail of the flower (where petals and other structural elements can be counted), the stem, the leaves, etc.

This question appears to be off-topic because it is about plant identification. These questions are usually asked on Gardening and Landscaping Stack Exchange. This topic is not found in the following appropriate topics listing in the Help center: 1) General questions about biological concepts 2) Questions about the biological mechanisms behind medical conditions 3) Questions about techniques in a biological or biochemical laboratory

Those flowers don't come from the same plant as that big leaf in the front do they?  Cant help you with the leaves, but the flower looks like a daylily. source: I know nothing about plants, but happen to have a mom who got a degree in horticulture :)

And the big leaf could come from some kind of zucchini. Source: grandmas garden.

The flower is a Hemerocallis fulva (Hemerocallidaceae).
The leaf seems to be a Cucurbitaceae, as said above, the same family as the zucchini


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How does a thymidine block halt DNA synthesis?
The best I've been able to find is that there's a feedback mechanism, but what is this feedback, and how does the mechanism work? If it's just that the concentration of thymidine is too high, why won't excess quantities of other nucleotides do the same thing? (Or do they, and I don't know about it?)

Excess thymidine in a mitotic cell generates negative feedback on the production of deoxycytidine triphosphate from cytidine-5'-phosphate. Excess quantities of deoxyadenosine and deoxyguanosine also block progression through S-phase. However, as a reagent for the control of replication timing, thymidine has been found to work best as its blocking activity can be applied and reversed more consistently.
Xeros N. (1962) Deoxyriboside Control and Synchronization of Mitosis. Nature 194: 682-683.


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What's the difference between a free chromosome fragment and an extrachromosomal array?
This is reference to a review on C. elegans mosaic analysis by Yochem and Herman, in which the authors make a distinction between free chromosome fragments and extrachromosomal arrays.
For the former, they reference Herman 1984.
For the latter, they reference Lackner et al 1994 and Miller et al 1996, but these are studies that use extrachromosomal arrays, not papers defining them as a technique, per se.
I am curious to know what the distinction is - I am under the impression that extrachromosomal arrays are fragments with many copies of the gene of interest + a marker.

I added an answer below, but please supply better answers if you have them!

I asked my professor, and the answer appears to be differences in both the generation and the final product.
Free chromosome fragments are created through irradiation/other damage of the germline in one animal.  Through a series of crosses, it is possible to introduce individual fragments (containing a duplication of your gene of interest, as well as a marker) into a mutant background.  The extrachromosomal fragment will be lost during mitosis at various points in development, and in a mosaic analysis, you can look for the loss of your marker (and therefore the loss of the wildtype allele), and see if yfg product is required in certain cell types for a wildtype phenotype.
Extrachromosomal arrays are created by cloning, and you typically have many copies of both the gene and marker.  It's the same principle as free chromosomal fragments in terms of mosaic analysis, but it's very powerful, as you can easily clone individual genes (versus irradiating and hoping to discover yfg on a fragment) and markers (and now you can use non-endogenous markers like GFP).
Even though extrachromosomal arrays are comparatively easier to generate, the problem is that you end up with many copies of the gene, which leads to non-endogenous dosage levels. Even if this doesn't cause a completely different mutant phenotype in the cells, it is possible that enough of these proteins could segregate at mitosis into the daughter cells, such that even if the fragment is lost, you could still have your gene product around in the daughter cells (if your marker protein didn't also segregate like this, you might draw erroneous conclusions about the necessity of yfg product in those particular cells).


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Manipulation of gene expression using VP16 fusion and engrailed fusion to a transcription factor?
Today, a presenter briefly mentioned that gene expression in sea urchins during development might be manipulated using VP16 and engrailed fusions.
On a slide, it said that expression might be increased by mRNA injection or "VP16 fusion to binding domain of TF" and decreased by antisense morpholinos or "engrailed fusion to binding domain of TF".
I understand mRNA injection and antisense morpholinos, but I am unclear about the roles of VP16 and engrailed in this context. Can anyone clarify?

VP16-activation domain fusion to a DBD can make the  hybrid protein get strongly and easily activatable. Check this paper out.. quite an old one

@WYSIWYG: thanks, that addressed the first part of the question.  Apparently, genetic manipulation in sea urchin embryos is quite tricky, so I'm not surprised to see a rather old paper as a reference for a technique.

And I found the answer to the second part: http://nar.oxfordjournals.org/content/30/21/4709.abstract. @WYSIWG, if you want to write your part as an answer, I can add this part and mark the whole question as answered.

sure..no problem..

VP16 is a herpesvirus derived protein transcription factor, which activates the early genes of the viral infection cycle. The activation domain (AD) which is formed by the 78-amino acids from the C-terminal, can be fused to DNA binding domain of other protein transcription factors, such as GAL4, to make a hybrid protein that constitutively and strongly activates transcription, without the requirement of any ligands. VP16-AD interacts with TBP, TFIID, SAGA histone acetyltransferase complex, and PC4 (transcriptional coactivator positive cofactor 4) to drive transcription.
The engrailed gene, from Drosophila, is a transcriptional repressor.  When the repressor domain is fused to transcription factors, the fusion results in trans-dominant negative functions of the transcription factor (phenocopying loss of function mutations in the target genes).


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How might gene clusters like the lac operon evolve?
The obvious answer for a gene cluster is gene duplication and mutation of one or both genes. But the genes in the lac operon seem not be so functionally/structurally similar (as compared to the Hox gene cluster, for example), so I was curious as to how they ended up physically associated in the first place.

Operons, often but not always, contain clusters of genes (under the control of an operator region) which are involved in the same metabolic pathway. There have been several theories for how these groups of genes have arisen but the current feeling seems to be based around the regulation of the genes in question 1. To facilitate co-ordinated gene regulation there may have been strong selection for physical clustering of genes involved in a particular process. By being physically clustered this also means that all the genes within a given operon are probably subject to the same chromatin remodelling and will then be more easily switched on and off under the appropriate conditions i.e. all turned on when they are needed and switched off when they are not.
Operons with similarly arranged genes have been found in different micro-organisms, leading to the thought that the operon was an ancient and evolutionarily conserved arrangement [2]. The figure below from Fani et al. 2005 presents two possible ways of generating the current state of genome organisation for present day proteobacteria.

If the operon is an ancient arrangement we would predict high gene conservation within operons; but genome analysis of different micro-organisms shows this not to be the case (i.e. gene conservation is low and operons are pretty unstable). Accordingly, another author suggests that due to the lack of conservation, operon structure is pretty plastic and can change readily during evolution [3]. Indeed, Fari et al conclude in their paper that the histidine biosynthesis operon has been a construction or re-construction event from scattered genes and not from the descent of an ancient arrangement:

Our model suggests that the his gene organization in the extant proteobacteria arose from a gene scattering in the genome of the proteobacterial ancestor. The model also predicts that all or most of the his genes (except for hisD) were monofunctional and that they underwent a progressive clustering and compacting which occurred together with gene overlapping and fusion events

They found, as you suggested, evidence for several gene modifications which included elongation, duplication and gene fusions. As for what caused the progressive clustering, see reference 1 again.
Obviously different operons are probably going to have formed in different ways in different organisms and I don't think we can rule out the 'ancient arrangement' argument completely. It's a pretty broad and confusing topic and there's a lot of literature, I hope the examples I picked and have listed are useful!
1 Osbourn, A. and Field, B. Operons. Cell. Mol. Life Sci. (2009) 66:3755–3775
[2] Fani et al. The Origin and Evolution of Operons: The Piecewise Building of theProteobacterial Histidine Operon. J Mol Evol (2005) 60:378–390
[3] Itoh et al. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol (1999) 16(3):332–346


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How does a pinched nerve cause pain (at the molecular level)?
Is this due to pressure differentials in the surrounding tissue? (Is it possible to have a pinched nerve without compression of the surrounding tissues, and does this cause pain?)
What are the molecules/cell types involved in this process? Is the pain dependent on the compression of axons from mechanosensitive or nociceptive neurons?

Typically nerve compression or a "pinched" nerve is due to inflammation in the tissue through which a nerve passes. The gap is already quite narrow so any inflammation is quite potent. Inflammation causes you to feel things as more painful (hyperalgesia). In a similar way to how of you burn your hand then poke it, it hurts, when cells are damaged the receptors surrounding them are sensitised to be more reactive. Binding of many ligands involved in inflammation leads to higher than normal sodium influxes which means you feel pain as this impulse is sent. I could be a lot more detailed but not sure what level you want, however for much more detail see this review.

I thought it might be that! Thanks for the review.

As AndroidPenguin described the nociceptive pathways are activated by inflammation or noxious chemicals.
Sometimes pain can arise independent of active nociceptive pathways. Most evident in cases of Neuralgia and perhaps in case of Pseudoneuromas.
In certain cases the injured nerve causes disinhibition of the pain pathways arising from the dorsal horn of spinal cord. This disinhibition is because of loss of the nerve function.
Sometimes increased nociceptor drive can activate dorsal horn of spinal cord which will now respond to normal mechanosensation also [1].
Phenotypic switching is also possible [2].
PS: Both these articles are inaccessible to me at this moment. Refer them for more details.


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Which kind of inflorescence(s) does Sonchus oleraceus have?
Many capitulum inflorescences, several corymb inflorescences with capitulum inflorescences as the end nodes of each corymb inflorescence, or one compound corymb inflorescence with capitulum inflorescences as the end nodes?

A picture would be of great help here.

@Darlingtonia picture uploaded. Thanks.

Thank you. I'm a little concerned this is a homework question. What have you found about capitula (capitulums?) and corymbs that might help with the question?

@Darlingtonia I read some materials that say Sonchus oleraceus's capitulums are arranged as corymbs or raceme at the end of stem. I'm confused what on earth the inflorescence of Sonchus oleraceus is. Isn't the inflorescence of a plant fixed?

A flowering plant's inflorescence is the grouping of flower clusters on the plant. Inflorescences are categorized based on the architecture of the arrangement of flowers within them.
As members of the sunflower or daisy family, Asteraceae, Sonchus has it's flowers compressed into tight heads called capitula. A sunflower might casually appear to be a single flower, but close examination will reveal that it is made of many (dozens in the case of Sonchus) smaller flowers. In the photo above, each yellow petal, including those in the interior of the disc, originates from a separate flower. As such, the inflorescence of Sonchus is a capitulum.
However, Asteraceae is an extremely diverse family, and the arrangement of capitula can be an important character in classifying and identifying these plants. Because of this, the same inflorescence terms applied to a group of flowers can also be applied to a group of capitula. In Sonchus one can (often) call the arrangement of capitula a corymb*. One definition of corymb is "a flat-topped or round-topped inflorescence, racemose, but with the lower pedicels longer than the upper".
So, strictly, the inflorescence of Sonchus olearaceus is a capitulum, and the capitula are arranged in (approximate) corymbs.

*The first resource I found listed Sochus as "corymbiform to subumbelliform" which means, roughly, ranging from a corymb (but maybe not exactly) to not-quite-an-umbel.

Thank you for your analysis. I think there exists a difference between an inflorescence and a sub-inflorescence in an inflorescence. For example, a sub-inflorescence of a compound corymb is also a corymb. As to Sonchus olearaceus, the capitulum seems a sub-inflorescence, not an independent inflorescence, but I did not find the name of this type of compound inflorescence. All the named compound inflorescences I find have sub-inflorescence the same inflorescence type as the  compound inflorescence itself such as compound umbel, compound corymb, and  compound racemose.


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Help me identify this wasp-like insect
I've never seen wasps with long legs like that.
It's not big, about 1-2cm in length (not counting legs).
Could you identify this?
UPD: location is central Ukraine

The details of the insect are listed below:
Common Name: Craneflies
Zoological Name: Ctenophora flaveolata
Location(mostly found at): Eastern Europe
Here is the Biological Identification,
Kingdom: Animilia
Phylum: Arthropoda
Class: Insecta
Order: Diptera
Family: Tipulidae
Genus: Ctenophora Meigen
Features: The species are large (about 20 mm long, with 25-mm wingspans), shiny black craneflies with large yellow, orange, or red markings to mimic wasps. Males have comb-like antennae. The larvae are saproxylic. The species are confined to old deciduous forests, orchards, and other habitats with continuity of the presence of dying and fallen trees. Ctenophora species are important bioindicators.
Source: Ctenophora (fly)

This is mostly a copy from Wikipedia. You have to mention your sources when you copy stuff. On the SE network, however, it is discouraged to copy-paste anything ad verbatim as it can be plagiarism, especially when sources are not mentioned.

Sorry, I forgot to mention the source. Thanks for the comment.


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Role of Fbx15 in ES cells and its use in assaying for iPS cells (Yamanaka paper and others)?
I am trying to understand the assay for iPS cells in the Takahashi & Yamanaka 2006 paper.
They inserted a beta-geo cassette, which contains the neomycin resistance gene, into the Fbx15 gene.  The idea is that the beta-geo cassette will be expressed when Fbx15 will be expressed, thus conferring G418 resistance to only those cells expressing Fbx15.
They say that "Although specifically expressed in mouse ES cells and early embryos, Fbx15 is dispensable for the maintenance of pluripotency and mouse development."  Does this mean that Fbx15 will be expressed in induced pluripotent stem cells, and won't be expressed upon differentiation? (What is special about Fbx15 that will distinguish iPS cells from somatic cells, including those that might derive from iPS cells, as when pluripotency is not maintained?)

Another paper from Yamanaka's group explains Fbx15.
It says:

Inactivation of Oct3/4 in ES cells led to rapid extinction of Fbx15 expression.
Fbx15-null ES cells were normal in morphology, proliferation, and differentiation. These data demonstrate that Fbx15 is a novel target of Oct3/4 but is dispensable for ES cell self-renewal, development, and fertility.

So Fbx15 wont be expressed in Oct4⁻ cells.
I haven't seen any paper describing the function of this gene but in the case of cassette insertions the locus would prove useful in expressing the inserts specifically in Oct3/4⁺ cells

So, Fbx15 is a nonessential marker of iPS cells? As in, it's expressed only in iPS cells, but disrupting the gene with a cassette isn't expected to have any effect on the iPS cell?

Seemingly. [as per the paper]

Ok thanks. I don't think it's going to get much clearer than this.

there are only 9 reports on this gene in pubmed. Only one tries to attribute some function. It is in cancer cells, though: FBXO15 regulates P-glycoprotein/ABCB1 expression through the ubiquitin-proteasome pathway in cancer cells

@dd3 I don't know if Fbx15 is so much a marker of iPS cells as it is just a target of the Oct4 transcription factor, meaning its expression will be active in Oct4+ cells, providing a convenient way of driving exogenous (and then endogenous) expression of the Yamanaka factors long-term.

@MattDMo.. Yamanaka factors :P


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Why are there so few organisms that are both photosynthetic and eat for energy?
Carnivorous plants don't count as they don't use their prey for energy. Photoheterotrophs don't seem to fit based on a quick read as they use light and carbon in the same reaction. I'm looking for something that both eats for energy and does photosynthesis for energy. A select few animals that are symbiotic with algae barely fit. But is there a reason why 99.9999999% of organisms choose one or the other?
As an example, why couldn't some seaweed evolve to catch plankton like an anemone?

Welcome to Biology StackExchange! You seem to somehow mix up the terminology. Auto- and heterotrophy relates to the source of carbon (inorganic vs organic), not the source of energy. I suggest reading the article about Primary Nutritional Groups on Wikipedia which also have several examples of different groups.

Carnivorous plants don't count as they don't use their prey for energy. Of course they do. Why else would they eat them if not for the energy they provide?

@MattDMo As a source of nitrogen and other nutrients? Maybe there are exceptions but I thought that was the primary impetus for evolving carnivory in plants.

@MattDMo carnivorous plants normally grow in nutrient poor environments, typically nitrogen and/or phosphorus limited, such as in acidic bogs or as epiphytic plants, though other environments exist too. The consume the animals as a nitrogen source. It's all energy when you come down to it, just one particular form of energy in this case!

@bob1 that's kind of what I was referring to. Thanks for clarifying it!

@MattDMo I'm sorry what? Technically all matter is energy but nitrogen is always referred to as a nutrient, not energy. It's used to construct proteins and other molecules, not ATP.

@AlexanderWu yes, nitrogen is a nutrient, but the prey of carnivorous plants contain more than just nitrogen compounds. In addition, energy is released during the metabolism of polypeptides, which the plants can then use. My point was it's simplistic to just think of the prey as a nitrogen source with zero energy. I could have worded it better, though.

@MattDMo But is the energy in the prey used, and if so does it make up for the additional energy expended to create the trap and digest the prey? Do you have a source in that?

It is because there is no need for developing such as a system like this.
Some recent research depict that some organelles were independent organisms in ancestors. If we assume that consuming energy from other organisms, and gain energy through photosynthesis are two different paths of evolution, they separated in history. Possibly, two different branches of gaining energy formed.
Obviously, having two systems of obtaining energy would be brilliant, but it may bring a lower efficiency in the body. <<#i am not sure>>

Welcome. Please cite relevant literature that support your claims; if you are not sure as you write, then refrain from posting. Maybes, perhapses, academic guesses and guesstimated numbers are OK, but only when supported by appropriate and credible sources.


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How long does it take for a creature to adapt for a different diet?
For the sake of the question, let's say that a population of piscivorous birds are put in a Europe-sized box. Half of the box is sea, populated with their diet of fish and crabs and cephalopods, and the other half is open steppe filled with grasses, bushes and small insects.
Assuming there is nothing else to compete for the open terrestrial niches, how long would it take for these birds to diversify into insectivores, seed-eaters and herbivores respectively? I imagine it'd take very little time for them to become insectivorous, but I don't have a general frame of reference for how long it'd take for herbivory to develop.

Although it may not appear so immediately, I think this is likely a duplicate of: https://biology.stackexchange.com/questions/35532/why-do-some-bad-traits-evolve-and-good-ones-dont

Have a look at the first sentence in the Modern Research section on Darwin's Finches and read the linked article from there...


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Does anybody know what kind of creepy-crawly this is?
My son found this caterpillar in our garden in the UK. Have asked multiple people with more knowledge in this area who have been unable to identify it. looking for any help?
Having looked online the closest I have found are moth caterpillars, but not found anything like this one. I hope you can see from the images it has 'whiskers' around its head and around 1/4 of its body but no further, a yellow squishy looking head and quite muted green and black body.
It's the 'whiskers' (not sure of the proper term for them) not extending to its full length that I think is the most identifiable feature and that is what I have been unable to find when looking online.

Have you identified the plant it was found on, if possible?

We think it was a persicaria, it seems to be eating those leaves in the tank anyway.

It looks to my eye like some variety of tent caterpillar (though I've never seen that exact pattern before), have you noticed any silky structures in any nearby trees or shrubs? Also, if you still have it can we get a picture of its lovely face?


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How is magnet based bead capture used for indexing-first ChIP-seq?
The context for this question can be found in this paper by Lara-Astiaso et al. Here, to study H3K4 trimethylation in various cell types, they

sort cells
sonicate chromatin
immobilize chromatin on Dynabeads with anti-H3 antibody
index chromatin (barcode)
pool samples
perform H3K4me3 ChIP
sequence

I am interested in the purpose of step 3 and how that contributes to step 4. What could be the purpose of essentially adding another IP step?
The Supplementary Materials (where all the methodology is described) mentions that "magnet based bead capture was used to efficiently add, wash and remove the different master mixes used in the indexing process." I'm somewhat confused as to how this adds efficiency, as I thought barcoding prior to sequencing is typically performed as a ligation step without selection (they perform the H3K4me3 ChIP after the indexing step anyway, so why select for histone H3 chromatin first?).

The anti-H3 antibody will precipitate all chromatin. They could have used an antibody against any histone monomer; that they initially used anti-H3 and then later used anti-H3K4me3 is coincidental. The idea behind the first immunoprecipitation is to immobilize the chromatin on the beads to allow easy recovery of pure chromatin after each step of the indexing process. These steps are seen in the supplementary material (4. Chromatin Indexing). For example, after immobilization, they perform end repair using specific buffers and T4 polymerase and polynucleotide kinase. These enzymes must be removed and the buffer exchanged before the subsequent indexing. The beads facilitate this process.


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EasyHLA HLA Upgrade Tool Website does not work
I'm trying to use Easy HLA, HLA Upgrade (https://hla.univ-nantes.fr/recherche/recherche.php) to impute my low resolution typings into high resolution ones but I have this error when I upload my file:

Has anyone ever used this tool? I wanted to use it because it is said to be better than HaploStats (couldn't find a reliable source though) but I couldn't make it work so I cannot even compare them.

This isn't really the kind of question we welcome here, though I can understand your desire for an answer and the logic to posting it on Biology.SE. I'm a technophobe, so when I'm frustrated by a product (if I paid for it), I call their customer or tech support. If it's a popular product, it may have its own forum for problem solving. No disrespect intended, just trying to help (with the full realization that help isn't likely to come from a technophobe!)

Oh I'm sorry, I was hoping someone might have been using it on a regular basis.

I’m voting to close this question because this is not about a problem in biology.

Not a problem at all; as I mentioned, it was a logical place to post. Please don't take the closure personally; it's a site issue. I forgot to say welcome. Welcome! I hope we can help you in some other way(s). :)

A 504 error is a server error caused by lack of response of an upstream server. The website owners are the only people who can fix it. You might be able to contact a webmaster for the page indicated (try going to the homepage and see if there is a webmaster contact).

I have used it in the past and you typically have to wait several hours between the moment where you upload the file and the moment you can download the result. The website will not be accessible in the meantime.
About a source proving it's better, there is a github repository I found a few weeks ago that benchmarks different imputation tools and does find better results for HLA Upgrade compared to HaploStats as you mentioned. However, it seems HaploSFHI yields better results overall. It's only one random github repository though, I wouldn't trust it blindly.

Oh yes you're right, my file went through!! Thank you

You can also contact them at easy-hla@univ-nantes.fr, it's hard to find but it''s written at the bottom of the page ;)

Huzzah! An answer!