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Growth on raspberry cane: What is it?
I have raspberries growing in my garden.
One of the raspberry canes has some sort of growth on it.

Size: Approximately 2 inches long
Location: Zone 5; east of Toronto, Ontario, Canada
Date: April 4, 2019.

What is the growth? Is it insects, fungus, bacteria, a defect, or something else?

Not sure, but possibly the raspberry cane midge, Resselialla theobaldi? Or some other cane midge?

A botanist at a local university says it is most definitely Crown Gall.

He didn't provide any other information than that, so all I can do is quote Wikipedia:

Agrobacterium tumefaciens (updated scientific name Rhizobium radiobacter, synonym Agrobacterium radiobacter) is the causal
  agent of crown gall disease (the formation of tumours) in over 140
  species of eudicots.

https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens


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How is chewing gum processed?
There is the common belief that

Chewing gum takes 7 years to digest

But is this actually true? Does it really stick to your intestines for 7 years, or is it processed like all foods, except it isn't broken down and is excreted soon after digestion?

I think this question fits much better to skeptics.se.

Agreed with Chris that it doesn't belong here, but it is probably too simple for skeptics.se - you probably can't find a sufficient "notable claim" that this is true. Rather, if you just search for "chewing gum digestion myth" you will find many reputable sources that make it clear that, no, gum doesn't stick in your intestines for 7 years.

If I changed to 'how are indegestible foods like chewing gum processed?' wold that be on topic?

Close voter - how is this primarily opinion-based? It's not like we choose whether or not it takes 7 years

@BeastlyGerbil we can't answer unless you provide a breakdown of the composition of the specific type of chewing gum you are thinking about. We're biologists, not industrial chemists and have no idea what chewing gum is made of. And are they all made of the same thing? That said, I very much doubt anything takes years to digest, but this is another question.

Although I agree that this could go on Skeptics.SE, this question is relevant on Bio.SE b/c the OP is asking a straightforward question about how non-digestible food is digested. @terdon, I think you're being  unfair as those details are really irrelevant and could even be addressed further in a biologically-focused answer. (Also, a quick google search will inform you about general ingredients of chewing gum). Beastly Gerbil, edit a bit more and provide a bit of evidence demonstrating your own research and people should leave you alone.

Purportedly White House Spokesman Sean Spicer consumes (chews and swallows) at least 35 pieces of gum every day.
Mastication breaks down the components and carbs, oils and alcohols are digested accordingly, but the rubber is pushed through by your intestinal muscles. You might enjoy this article which goes into detail about the breakdown and digestion of "gum" constituents. For the most part tho the rubber in gum passes through like corn, peanuts and such.
So, no - no "seven years" to digest. I remember hearing that as a kid. I think it is the kind of thing kids are told to discourage them from swallowing outright instead of chewing gum.

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sort: votes


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How to calculate the geometric mean titer (GMT) of titers from a haemagglutination assay (influenza)?
I got a list of Influenza-specific antibody titers from a hemagglutination inhibition assay.
They look like this:

40
640
160
<10

One site says: “The swine influenza HI scale is geometric: 20, 40, 80, 160, 320, 640 (successive values increase by a factor of 2). The geometric scale is logarithmic. It is best to express an average influenza HI titer as a geometric mean. A geometric mean is calculated by averaging the logarithms of the test values and then converting the mean to a real number. This prevents a few obviously high positive values from making the mean unrealistically large.”
What does that mean for my sample? How do I deal with <10 in this calculation? This is surely not rocket science, but honestly I don’t get it right now.

Typically "<10" is converted to a number that is below the limit of detection; often "9".  After that simply following the instructions you have yields a GMT of 77.9.  If you are using spreadsheet apps such as Excel or Google Sheets, they almost certainly offer "GEOMEAN" functions which will give the number directly.

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What purpose does the wax coating on blueberries serve?
What purpose does the wax coating on blueberries serve? Is it some sort of protective layer?
A search on the web reveals that it is called "bloom". But the source is not a credible, scientific source. And it doesn't explain in detail what the coating does.

My uneducated guess is that the wax is called Epicuticular wax.

The main functions of the epicuticular wax are to decrease surface
  wetting and moisture loss. Other functions include reflection of
  ultraviolet light, assisting in the formation of an ultrahydrophobic
  and self-cleaning surface and acting as an anti-climb surface.

Years ago my wife and I made  grape juice that turned to wine. This happened because the bloom on the grapes harbors yeast cells. The same situation occurs with other berries including blueberries.  Organisms living on the surface of other organisms are usually symbionts


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Why do Arctic predators accumulate vitamin A?
Top predators in the Arctic are known to accumulate vitamin A, often to levels that are toxic for human consumption.  A 2012 study by Senoo, Imai, et al. found that the livers of several predator species in the Arctic showed much higher levels of vitamin A than other Arctic species or closely related continental species, with no symptoms of hypervitaminosis A.
Why is it that these species accumulate vitamin A?  Does this have something to do with the food sources available in the Arctic as opposed to the mainland?  Or are there physiological reasons why Arctic predators would tend to accumulate vitamin A rather than breaking it down or otherwise eliminating it?
References:

Senoo, Haruki; Imai, Katsuyuki; Mezaki, Yoshihiro; Miura, Mitsutaka; Morii, Mayako; Fujiwara, Mutsunori; Blomhoff, Rune (2012). "Accumulation of vitamin A in the hepatic stellate cell of arctic top predators". Anatomical Record 295 (10): 1660–8. doi:10.1002/ar.22555. PMID 22907891.

This study seems to be the only research on this particular topic, so no one will be able to provide you a definite answer. The authors suggest the following explanation: "Without huge capacity of storage ofvitamin A in HSCs in the arctic top predators, these ani-mals may suffer from hypervitaminosis A after intake ofthe large amount of vitamin A through the food chain,and cannot stay in the top of the food web there."

@Hav0k That "explanation" fails to account for why non-Arctic predators do not store vitamin A at such levels.

It doesn't explicitly state it but the implication is that non-Arctic predators don't have high vitamin A content in their food chain.  Many saltwater fish carry high levels of vitamin A.  So if this is the primary food source, e.g. seals eat fish, bears eat seals, then you need high tolerance for it.  Land animals have less vitamin A, so their predators don't need the tolerance.  I can't find any evidence of it but I thought vitamin A helped animals survived the cold, but there are also high concentrations in tuna liver, which are typically temperate or tropical.

The phytoplankton at the bottom of the food chain have high levels of vitamin A and precursors like beta-carotene.  At each step up the chain, vitamin A bioaccumulates.  Top predators in the Arctic deal with this by storing the vitamin A in the liver (bears, cetaceans) or blubber (pinnipeds).
This is the same mechanism that causes accumulation of pesticides like DDT in animals.  https://en.wikipedia.org/wiki/Bioaccumulation
Carotenoids are part of the photosynthetic system, and also protect the organism from sunlight.  Phytoplankton are unicellular, so each cell needs protection.  Therefore land plants contain much less carotenoids, since most of the cells are interior and protected from the sun.  For example, grains, roots, and wood have very low levels of carotenoids.
This occurs in polar regions due to up-welling nutrient-rich waters supporting high productivity.  Temperate and tropical deep ocean regions are typically deserts due to low nutrient levels, particularly iron and fixed nitrogen.

This answer does not answer the question on the difference between top predators of the arctic area and those of the mainland (or the oceans) closer to the equator, and the question why they do not suffer symptoms of hypervitaminosis A. Regarding the first question, does the phytoplankton in the Arctic area have higher concentration of vitamin A and precursors like beta-carotene?


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At which point does a cell switch its function?
In a multi cellular organisms there are many cells of different functions. How / when does a cell change its function compared to its parent?
Is it done by influence of other cells after its has been created?

Yes, as opposed to what? Cells respond to signals, both within themselves and from other cells/tissues/organs, to differentiate. Sometimes a parent cells differentiates, then divides, and other times a parent (stem) cell divides and one of its daughter cells differentiates. Since the mechanisms and reasons are as varied as there are types of cells, I'm voting to close this question as too broad.

Ok so the cell changes after mitosis not during mitosis. There is no mechanism during mitosis to change the function of a cell. Its all done by influences after the cell has been created.

That is not necessarily the case, as although it's rather unlikely that differentiation would begin during mitosis, there's no rule that says it can't. Like I said, this is a very broad question, as each differentiation event is slightly different.

As MattDMo suggested there are so much possibilities. I would recommend to take a look at this information:

Cellular differentiation wiki
The Cell: A Molecular Approach. 2nd edition (NCBI)

I will summarize some points, however note that this will not include every aspect.
Every cell contains the same genome (same DNA), so what can make these cells to differ so much form each other (e.g. neurons vs muscle cells). As noted in the Wikipedia article:

Since each cell, regardless of cell type, possesses the same genome,
  determination of cell type must occur at the level of gene expression

I added this figure just to give a representation of the hierarchy.
However probably you already knew this because you were asking about the mechanism of how these cells can become different from their parent cells.
I will provide two important examples (again notice that this is just a simple summary):

first let's talk about Cytoplasmic determinants

Cytoplasmic determinants are special molecules which play a very
  important role during oocyte maturation, in the female's ovary (wiki)

the cytoplasmic determinants are molecules such as mRNA or proteins which are e.g. unequally distributed in the egg cell, which means that if this cell devides one half will get other proteins(e.g. transcription factors(TF)) and mRNA than the other half. Different TFs --> different gene expression --> different proteins --> different cells.
Secondly we have induction which is really important in cell differentiation:

frequently we find that cells become different from one another as a
  result of inductive signals coming either from other cells or from
  their external environment (source)

These two (induction and Cytoplasmic determinants) are important to determine the fates of cells(we also have gastrulation, HOX genes, etc). But how does the induction and the cytoplasmic determinants cause a change in gene expression? The same is true for this, there are a lot of different ways how this can happen (see gene silencing):

Genomic Imprinting
Paramutation
Transposon silencing (or Histone Modifications)
Transgene silencing
Position effect
RNA-directed DNA methylation

I can write pages of Cellular differentiation because this question is really broad. So I will advice you to read the following articles:

Differential gene expression and development
The process of differentiation
Cellular differentiation


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Do sea sponge cells transfer nutrients to each other?
Does a sea sponge cell transfer nutrients or energy to their neighboring cells or is their only symbiotic relationship that they are connected to each other forming a structure?
The sea sponges that I'm talking about are the ones that can be broken apart and naturally reassemble themselves.
YouTube of the sea sponge I'm talking about.

yes choanocytes handle the bulk of sponges digestion and transfer nutrients to other cells. in some species Amebocytes also perform a similar function.


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Looking for research related to burising sensitivity and rate of heeling
Are there studies/data on the potential correlation between how quickly a body heals itself and how prone to bruising the body is?
I've been reading that oxygen is needed in the healing:

Wounds need oxygen to heal properly. Exposing a wound to 100% oxygen may speed healing. Hyperbaric oxygen therapy can be done in a number of ways. It can be given in a special type of room called a hyperbaric oxygen chamber. -Hyperbaric Oxygen Therapy for Wound Healing

And that bruising essentially is the pooling of blood from damaged blood vessels.

Bruises occur when blood vessels break, due to some kind of force, and leak blood into areas under the skin. -Mount Sinai: Bruise Information

This has led me to hypothesize "On average a person with a higher sensitivity to bruising will heal faster than a person with low sensitivity.". This hypothesis was created out of the idea that due to the increased concentration of oxygen found at the wound location (caused by the trapped/pooling of red blood cells), the damaged cells will be able to utilize this increase to heal quicker.
I'd like to do some research to determine if this hypothesis is true, plausible, unlikely, false or unknown.
If the hypothesis is true then some blood vessels might be more prone to leak blood when damaged. This trait would have been selected for, because it would help the initial healing process by increasing the oxygen concentration at the wound location.
This is just my hypothesis and I'm looking for information to guide my research.

Why do you think that the blood at a bruise site has more O2 than elsewhere in the tissue? Read up on responses to bruising by the body...

I do not believe that the blood at the site has more O2 than blood anywhere else in the body. I believe that a higher concentration of blood forming in a location normally without blood will increase the density of O2 in the area.

If you think about the biological processes that go on - why does a bruise appear? Why does it not disappear in a short time-frame (as it should if blood flow happens...) What happens to the O2 in the blood cells? What happens if the blood flow is stopped (tied in to q 1 and 2 above) - where does the O2 go and is it replenished? BTW use the format @ followed by username to notify someone you've made a response to a comment e.g. @Tolure will notify you of a comment.

@bob1 the red blood cells get trapped after the body heals the damaged blood vessel. The red bloods cells give the bruise its redish colour. After the red blood cells break down the oxygen is released to the area and the bruise changes colour. Now I will accept that there might not be a mechanism to allow for a damaged cell to take advantage of this. If so please draft an answer stating as such.

No this is homework for you - I think your understanding of the timing of events is off. Blood gets trapped almost immediately. The body uses up the O2 (normal cellular respiration) and changes colour (that's not due to respiration, rather degradation of the RBCs) - so why would there be more O2 at the bruise than elsewhere?

@bob1 would you agree that a volume of oxygen-rich hemoglobin has a higher concentration of O2 than the same volume of tissue? If so why would the concentration of O2 in an area not change when the ratio of tissue to hemoglobin changes due to the pooling of blood caused by bruising?

@Tolure You need constant circulation of blood for it to stay oxygenated. Blood just sitting there isn't resupplied with new oxygen.

Agreed but I'm only looking at the initial state. Where the hemoglobin still had oxygen. Once the hemoglobin have released their oxygen then yes I agree the hemoglobin wouldn't help in the healing. Now when the trapped hemoglobin release their oxygen that they already had prior to being trapped could it help the healing?

@Tolure How fast do you think the O2 from the pooled blood will be gone? How fast do you think healing processes are?

@bob1 O2 Used up: Very quick and Healing: very slow.
I also know that sometimes just a little benefit now can have compounded benefits later on.

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How to isolate two plasmids from E. Coli strand?
I have an E. coli cell line I use to express a protein using a two plasmid system. One confers AmpR and one KanR.
For mutagenesis I would like to separate the plasmids to increase efficiency of the mutagenic PCR reaction. I was able to cure the cells of the KanR plasmid because it is low copy whereas the AmpR is high copy so I could easily grow the cells in ampicillin only and I ended up with only the AmpR plasmid. However I was unable to do the same to isolate the KanR plasmid.
My next idea was to run the plasmids through a gel and do an extraction. Since I didn't do a digest it was very hard to differentiate the bands and I ended up getting a negligible yield. I believe the plasmids were simply smeared through the gel due to tertiary structures.
My final hope is to perform a digest on the plasmids using a restriction enzyme that cuts each plasmid once. My concern is that I will not be able to get the stoichiometry correct due to the plasmids both being simulatenously present in vastly different concentrations.
Does anyone have any tips on how else I could isolate the plasmids? Or maybe does anyone have experience running a digest on plasmids with unknown concentrations? I really need help doing this. The mutagenesis project has been going on for months and this isn't even a molecular biology lab... so it's detracting time from main research goals!

Couldn't you digest with a restriction enzyme that cuts the Amp plasmid one (or preferably many) time(s) but does not cut the Kan plasmid? Then you could gel purify and transform the result, and presumably it would be nearly all Kan

@Luigi I guess my question would still be how would stoichiometry work? If I have anywhere from 10-50x more of one plasmid than another, would that be a major issue? I suppose I could do a serial dilution...

I don't really why stoichiometry matters here..? You have an excess of the Amp plasmid, but if you cut it all, you'll be left with only Kan. Unless I misunderstand your question

@Luigi I just mean when setting up a digestion or any reaction you prepare the reactants in certain concentrations. For example for digestions they say one 'unit' of enzyme per microgram of DNA.

In my experience as long as you're within an order of magnitude with restriction enzymes you're probably okay. Since Amp is in excess, you could probably operate using the overall DNA concentration and be just fine. It'd be harder to figure out how much to use to digest the Kan, but I'm not really sure why you want to in the first place

The gel solution is a good idea, to avoid smearing try heating up the miniprep for 30 min at 70 degrees centigrade before running it on a gel.

A retransformation should get you a pure plasmid. Transform the plasmid mix into empty E.coli (don't use too much DNA), plate on Kan / Amp depending on what you need. The probability that one cell took up both plasmids is extremely low, and you could check with colony PCR just to be sure.
Otherwise: ask around, there must be (old) stocks of the single plasmids around, or glycerol stocks of E.coli containing only one of the plasmids.
Third option: take a look at your mutagenesis method. For your needs there might be techniques around that'll work on a mixture of plasmids. If you just need one variant or a single site saturation library you could use Quikchange for example. I don't see a reason why this wouldn't work on a mix of plasmids.


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How is oxytocin produced?
Is oxytocin (or other peptide hormones) produced from a gene through translation, or is it made some other way?

seems like a straightforward question...all proteins are translated from mRNA that is transcribed from DNA - that's the central dogma of molecular biology - is there a reason you think that it could be made another way?

Peptides like oxytocin (I think it is only 9 AAs long) seem small enough that maybe a cell would synthesize them using proteins rather than by a ribosome translating a gene for them.

Some peptides are synthesized via nonribosomal peptide synthetases, so the question seems legit.

Oxytocin is produced by cleavage of the protein of the oxytocin/neurophysin I prepropeptide gene. The precursor peptide is cleaved by Proprotein-Convertase 1
. Mice lacking the gene which encodes for this enzyme have reduced levels of oxytocin. The final step in the biosynthesis of oxytocin is carried out by Peptidyl glycine alpha-amidating mono-oxygenase.


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Is it possible to make a cancer cell that doesn’t encode any neoantigens?
The cell still has mutations, but those mutations only occur in the noncoding sequences, such as promoters, which drives over expression of proto-oncogenes and downregulation of tumor suppressor genes. So the cell will proliferate uncontrollably, but won’t express any neoantigens.
Will such cell be invisible to our immune system?

Immunosurveillance of cancer cells is predicated upon multiple "signals" derived from the cancerous cells and their microenvironment.
I should point out tumor mutational load (Figure 1). A sort of take-home point here is that certain indications have less mutations and thus less neoantigens than others. You also have to take into consideration the stage of the tumor, though. Stage IV tumors have amassed more mutations than stage I/II.

Figure 1. Mutational prevalence by indication. A higher prevalence predicts a higher neoantigen frequency or mutational load for that cancer histology. (1, 2)
It's interesting to point out the bottom part of figure 1 where the authors of a separate review note for us where it's believed the disconnect between traditional checkpoint blockade immunotherapy and CAR-T immunotherapy exists. Just to educate a bit on the subject, checkpoint blockade targets T cells, the drivers of antigen-dependent cell killing. T cells naturally infiltrate the tumor as it develops and attempt to mount an attack. One of the methods tumors use to evade T cell killing is through persistent antigen, expression of inhibitory receptors and secretion of inhibitory molecules. Checkpoint blockade immunotherapy uses antibodies against the inhibitory receptors such as PD-1 (Opdivo, Keytruda), it's ligand PD-L1, CTLA-4 (Yervoy), Tim3, Lag3, and so forth. This attempts to lift the dampening effect these receptors have on T cells so that they may resume killing. The T-antigen-dependent paradigm is also supported by such publications which look at checkpoint blockade in the setting of clonal T cell diversity and confirm that (1) a diverse repertoire of T cell clones result in successful checkpoint blockade, and (2) enrichment of certain clonotypes within the repertoire, presumably the antigen-specific clonotypes, further indicates a response (3).
So below that are indications circled in red, notably the histologies with a low neoantigen frequency. The idea behind CAR T cells is that I can take advantage of T cell biology, notably that T cells recognize antigen with a receptor and kill the target cell. So just backing up to checkpoint blockade immunotherapy real quick, say a patient has melanoma which can consist of 1000s of mutations and 100s of neoantigens. There is a greater chance that an infiltrated T cell has specificity for any particular antigen. So how about a glioblastoma patient? They may have 10-20 neoantigens, or as you said they may have no neoantigens, at least none that their T cells are specific against. So checkpoint blockade may not be so effective. CAR stands for chimeric antigen receptor. It's essentially a monoclonal antibody against one target connected to a linker connected to the intracellular domain of a T cell receptor. Hematologic malignancies such as NHL like diffuse large B-cell lymphoma are commonly targeted for a B cell receptor known as CD19. So all you have to do is make your CAR CD19 specific and transfect the T cells with it in place of their own T cell receptor or TCR. So the basic process behind CAR is I isolate your T cells as with leukapheresis, lentivirally transfect with my anti-CD19 CAR, expand, and infuse. There are two CD19 CAR T products with great response rates on the market (Kymriah, YESCARTA). The whole reason these are good is because we can direct them to whatever antigen we want (of course be careful about self-antigens, see autoimmunity).

Figure 2. Schematic of CAR T cell therapy. (4)
The CAR T approach is in fact because the neoantigen load is low or non-existent, which is problematic for un-modified T cells, and thus problematic for standard-of-care treatments like checkpoint blockade.
As such, there are other ways, and other cells that can handle some of the abnormalities presented by tumors as a whole. This includes the presence of danger/damage-associated molecular patterns (DAMPs) and the regulation of surface receptors, for example, NK receptor ligands such as MIC.
The way DAMPs work is that a milieu of molecules are secreted by cells that are damaged or transformed, signaling cells of the innate immune system. One of the issues is that the DAMPs promote an inflammatory environment. This means that yes, you get immune cells checking out the situation, but that some of these are good immune cells and some are "bad" (myeloid-derived suppressor cells (MDSC), tumor-associated M2 macrophages (TAM), or T-regulatory cells (Treg)). These dampen the immune response both through inhibitory cytokine release like IL-10, and expression of inhibitory receptors like PD-L1.

Figure 5. The molecules secreted by the inflammatory tumor microenvironment both help and hurt the immune response. (5).
And then the idea behind NKR ligands is pretty straightforward: Natural killer (NK) cells patrol your body routinely for abnormalities and are licensed to kill cells that are abnormal. For example, all nucleated cells express class I major histocompatibility complex (MHC-I) on their surface. Some receptors like MIC are also present on the cell surface that engage receptors on the NK cells like NKG2D in distress. So what do cancers do? They sometimes express truncated and thus inactive MIC, express no MHC but also express inhibitory receptors to NK cells, and so forth.
Everything is summed nicely in the following figure on cancer immunoediting (Figure 7). Note that while things are working normally, the immune system can handle the tumor load. As the scales tip, and this could be for example, your T cell response edits out an immunoantigen but doesn't take care of the whole tumor, resulting in growth that those T cells no longer respond to. As this happens, the cancer becomes increasingly invasive.

Figure 7. Cancer immunoediting. (7).
So just to clarify at the end, there probably isn't a case where the immune system isn't responding at all unless you had chemotherapy that destroyed your immune system. Inflammatory environments alone are sufficient for your immune cells to at least check out the tumor. In fact, and I cant find the paper now but I'll try, investigators even found naïve T cells in the tumor microenvironment simply due to the inflammation. We could also get into "hot" and "cold" tumors, but that's out of scope here (take-home point, cold tumors aren't inflamed and are known to contain less immune infiltrate). I used immunotherapy as a vehicle to get my point across, note that this answer isn't about immunotherapy but rather about immune escape and mutational load theory.

Let me know if something doesn't make sense. There are a lot of caveats to the system that were cut out for brevity, like a formal definition for T cell repertoire diversity, for example.


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What Ontario mammals hibernate?
What mammal species are known to hibernate in Ontario, Canada? (native and non-native)
From memory:

American black bear
Deer mouse
White-footed mouse
Eastern chipmunk
Red squirrel

Are there others?

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text:
Do strawberry seeds have different DNA within the same fruit?
It is my understanding that a strawberry is composed of many small fruits clustered together.
Does that mean each seed within a given strawberry has different DNA? Or are all the seeds in a strawberry clones?

Strawberry seeds will all have different DNA.
It is standard for seeds to have different DNA, even those contained in the same fruit. Normally, the egg cells held in the ovule ultimately come from meiosis, and this process occurs separately in each ovule. Similarly, the sperm cells held within pollen grains were produced from a meiosis event. So, just as human gametes all contain different DNA, even gametes from one person, so do plant gametes.
Your question also touches on the seed/fruit arrangement of strawberries. A strawberry can be termed both an aggregate fruit and an accessory fruit:

An aggregate fruit is where multiple separate ovaries are held together on a single flower. In case of the strawberry, each "seed" on the red flesh developed from an ovary, and a true seed is held within each one. A raspberry is another example of an aggregate fruit, where each fleshy ball developed from a separate ovary.*
An accessory fruit is one where the "fruity" part of the fruit has developed from some tissue that's outside of the ovary. The red flesh of the strawberry has developed from the receptacle, which is the tissue that all the ovaries were attached to. A raspberry is not an accessory fruit because in that case the ovaries themselves have become fruity.

However, none of that seed/fruit arrangement makes any difference to the fertilization processes of the strawberry, which mirrors other seed plants.

*In some strict definitions, each of these developed ovaries could be considered a separate fruit. However, it is also common and useful to apply the term to the unit overall.

The challenge in understanding (flowering/angiosperm) plant reproduction is that there is such a variation in flower types and structures.
Gynoecium ('female part') > pistil(s) > carpel(s) > ovary(ies) > ovule(s)
For any flower with female parts (as some species may be dioecious), it may contain one or more pistils, comprising one or more ovaries that can contain multiple ovules.
The key here is that the ovule is the basic unit of fertilisation. The pollen tube may enter the ovule, allowing for double fertilisation to occur. Of course, as with everything in nature, not all ovules may become successfully fertilised within a given flower. As a rule of thumb, one ovule gives rise to one seed (if successfully fertilised).
The number of ovules per plant varies, e.g. for tomato this is in the region of up to 300-400 ovules (ref1). In the case of an apple, this comprises five carpels, each containing two ovules. So there is a theoretical maximum of 10 seeds per fruit (ref2). And fruits such as apricots (and other drupes from Prunus spp.) contain two ovules, but, confusingly, one of the two regresses, so only one seed is produced (ref3).
From a genetic standpoint, each ovule is an independent site for sexual reproduction. The (female and male) gametes are produced via meiosis (so they are genetically distinct, even if originating from the same individual). Therefore, each ovule will contain slightly different egg cell, fertilised by a slightly different sperm cell, giving rise to genetically different seeds. So each seed within a tomato fruit is different; conceptually they are all siblings (rather than twins/clones).
As a side note, there is a special case of self-fertilisation - where pollen originates from the same plant as the ovule it fertilises. In this case, the genetic diversity is reduced, but the overall principles hold (as each gamete is generated by meiosis).
And coming back to the strawberries, the fruit type (whether is simple,like a tomato, or aggregate, like a strawberry) does not fundamentally change the genetic make-up of the individual seeds (as they are independently generated, even in simple fruits).


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White oak germination in autumn — Leaves or just roots?
I collected fallen acorns from a white oak tree in Toronto, Ontario, in mid-September 2023. The acorns were germinating at the time, so I planted them (in a cage to protect them from rodents).
So far, only roots have grown, no leaves. Is it normal for only roots to grow in this case, saving leaf growth for the spring?

All seeds start by putting down roots, which allow the first set of leaves to absorb water/swell, splitting the seed capsule. How much time this takes depends on conditions, but it's weeks for acorns, not months.

@anongoodnurse It's Nov 13 and still no leaves: https://i.sstatic.net/CUxic.jpg

Clearly they have germinated, so that's good. Is it very cold? is there sufficient moisture? I don't know how many weeks, but if you like, you can google the time span for the Toronto area. Maybe (maybe) it's different up there?

@anongoodnurse You might find Falko's answer interesting. And my comment on that answer to.

Nice to know. Thanks!

Nice that you started observing so early, so I can complete this here while learning something. I usually only get aware of the new oaks when stem and leaves are sprouting in the lawn, and, yes, that's in spring. I always asked myself why they already have such a large root. This makes it clear.

I brought the pot of acorns into the house a couple of months ago. To be honest, I forget why; maybe to protect from freezing temps. I dug up one of the acorns just now to see how much roots it had. And I removed the acorn's shell to see how it looked inside. Here's a photo. https://i.sstatic.net/nxZqj.jpg It's hard to tell, but the main root actually broke off when I dug it up. So it was likely a few inches longer. Also, here's a photo of my pot/cage setup: https://i.sstatic.net/bID5L.jpg. I screw the wire waste basket onto the bucket to protect the actorns from mice, squirrels, etc.

A friend took some of the acorns at exactly the same time/place. But he planted his indoors right away. Here's a photo from Oct 14, 2023: https://i.sstatic.net/OXHVn.jpg. His leafed out, I guess due to the warm conditions.

@User1974 - Oooo, nice little oak there!

I wonder. Generally it seems that acorns, as chestnuts, don't survive a dry out. So these are seeds that work differently than, say, peas or corn. I don't know any general distinction of plant groups along this difference. Yet :-)

@anongoodnurse and Falko: The acorns/roots now have leaves (indoors): https://i.sstatic.net/5A6Yv.jpg


text:
Yellow fruit with calyx, long leaves
What species of plant is this?

Location: Greece
Date: April 30, 2024
Description: Yellow fruit with calyx, long leaves

This is the Loquat (Eriobotrya japonica). Loqat, as the scientific name suggests are an asiatic plant propagated for their edible fruit. They are a large shrub to small tree form and have long, tough, rough-textured, dark green leaves.
Fruit, which are 2-5 cm (~1-2 in) across, grow in clusters off a spike-like shape. There is a large brown stone/seed inside the fruit and the fruit will be yellow or orange when ripe.

Addition of a figure and confirmation of the distribution of the plant can help a lot; the pic is from Greece and your ID is an Asian one; of course it can be imported, but with the limited info available in the Q, it does add uncertainty to your ID imo

Definitely Loquat; the leaves are a giveaway.  Also, it s a hardy plant, widely domesticated, including in Greece, and if you're lucky enough to find a good breed, delicious.


text:
How much current various kind of body tissues can tolerate without any serious damage?
Human body can tolerate some amount of current. How much current (and duration) various kind of body tissues can tolerate without any serious damage?

Welcome to Biology.SE! What research have you done before asking it here?

@another 'Homo sapien' I hope you're not asking him to electrocute someone are you?

@PrittBalagopal haha of course I don't mean a practical ;)

Regarding this, if the O.P has access to organs from a hospital or any source (preferably a rejected one for grafts), the O.P could do an experiment to find out. I invite @wgc to answer his own question after doing some research. It would be great for us to learn new stuff (not for electrocuting people of course).


text:
Why aren't nucleic acids on Nutrition labels?
All the other macromolecules are listed on the Nutrition labels and nucleic acids do have some caloric value, why aren't they on the nutrition facts?

Please remember to provide reasons for a down vote so the OP can make appropriate edits to this and future questions.

nucleic acids are in nearly all foods, with the only exception being certain condiments. that alone could be the reason no one bothers labeling them.

They're probably counted as carbohydrates. Ribose and deoxyribose are carbohydrates after all.

Despite the question being interesting, I am voting to close. I am voting to close because it is clearly a public policy / food security question and not a biology question.

This FAO report can tell you all about food analysis and why things are and aren't on the label: http://www.fao.org/docrep/006/y5022e/y5022e03.htm#TopOfPage

First, not all nitrogen in foods is found in proteins: it is also contained in variable quantities of other compounds, such as free amino acids, nucleotides, creatine and choline, where it is referred to as non-protein nitrogen (NPN). Only a small part of NPN is available for the synthesis of (non-essential) amino acids.

The DNA in food would contribute to the nitrogen content. Then (using a food-specific "Jones" factor) total nitrogen content is converted to protein content. So in a way it's already there.
Listing DNA separately would require extra testing, and also the difference in daily use would be negligible. There's not that much DNA in food anyway and, like protein, DNA can be converted into new protein and energy. The Jones factor already accounts for this.


text:
Maximum biologically possible age for a human being?
Today, most of people die because of some kind of illness that we do not yet have a cure for. However, if that was not the case, how long can human body possibly live for? Is there a theoretical maximum at which our brain will simply refuse to function due to age alone, or can we remain conscious forever if we could simply swap our brains into new bodies without any risk?

technically we mostly die becasue the body systems start failing as we age this makes us susceptible to disease. Its kinda like AIDS, if you have it it is an infection that will kill you but really AIDS is the reason you got the infection in the first place. Technically the infection killed you but ultimately it was having AIDS that did it.

@John - Body systems failing is directly fatal disease. Does kidney failure predispose you to other causes of death? What about congestive heart failure, or straight up myocardial infarction? The only common examples of killer infectious diseases in the elderly I can think of are UTI's and pneumonia.   Can you be more precise perhaps?

Yes sorry that is a bit confusing the way I worded it. My point was that if we have a cure for all illnesses then you have a cure for aging. The current theory of senescence "detrimental aging" is that it is a product of our own genes not be proof test by evolution for how they interact much beyond our reproductive age combined with them not producing structures that last forever. It is difficult to cure age related illness  becasue they are a product of a "healthy" body acting as it naturally would. If you can "cure" this then you can make people live as long as you want.

Even in perfect environmental conditions we would age. Living is associated with a myriad of deleterious processes, both random and deterministic, which are caused by imperfectness, exhibit cumulative properties, and represent the indirect effects of biological functions at all levels, from simple molecules to systems. Here is a good read on this topic https://www.ncbi.nlm.nih.gov/pubmed/27060562
Even if nothing else was wrong (which is not the case) the accumulation of intracellular and extracellular junk which our systems are unable to dispose of (lipofuscin, amyloid beta, etc) would eventually kill us. https://en.wikipedia.org/wiki/Senile_plaques
As for the maximum age - nobody we know of made it past 125 years yet. https://en.wikipedia.org/wiki/List_of_the_verified_oldest_people


text:
What am I looking at in Franklin's Photo 51 of DNA?
Here's Rosalind Franklin's famous Photo 51, the X-ray diffraction image of DNA from which Watson and Crick deduced its structure:

My understanding is that it depicts a short segment of DNA shown from the side (so the axis that the strands wind around would run up and down through the center of the photo). Like this double-helix diagram from Watson and Crick's paper:

I have a lot of trouble connecting the photo to the diagram.
What am I actually seeing in the photo? There are dark blobs at the top and bottom. A diamond shape of dark lines. A concentric circle (or rounded diamond) inside the outer diamond. An X formed from two intersecting rows of 7ish mostly horizontal short lines or blobs. Which of these features correspond to what parts of the DNA molecule?

@another'Homosapien' Just Wikipedia and Google. There's a smorgasbord of info about the structure of DNA and about the history of the photo, but I was unable to find anything directly labeling the structures shown in the photo and relating them to the diagram. Forgive me if I missed something obvious.

The interpretation of this image is not as easy as you think, but it took me less than a minute to find this.

@another'Homosapien' I also found that and read it, but unfortunately I don't understand it. It says that the large dark patches at top and bottom "represent DNA’s ‘bases’", but then goes refers to the smaller "ten blobs" as "ten bases", so it left me a bit confused. I was hoping for something more definite and specific.

I just gave an example link. It was just to tell that its not very difficult to find such papers, seeing that @GerardoFurtado has found a couple more links ;)

@GerardoFurtado Yes thank you that is exactly what I was looking for!

@GerardoFurtado Do you want to make this into a real answer? Would be great...

@GerardoFurtado Why? You digged out the relevant paper, so I think you deserve the credit for this.

Your opening statement is incorrect - "Here's Rosalind Franklin's famous Photo 51, the X-ray diffraction image of DNA from which Watson and Crick deduced its structure" - Watson and Crick did not deduce the structure from the picture alone. They were able to do so because they already had a host of information about the structure and had been working on the problem for some time. If it were a matter of simply looking at the picture, Franklin - who was far more skilled at this kind of crystallography - would doubtless have rapidly identified the structure.

Like Gerardo, I thought this was down the long axis - I also did some re-reading into the issue thanks to this question and discovered the photo was actually Ray Gosling's, not Rosalind Franklin's. I can't even confirm whether she was (formally) his supervisor; it sounds from another source (with better references than Wikipedia) that she wasn't officially eligible to supervise students because of the position she held at the time. I'll probably put together a proper question about this later when I have time.

Separate question now posted: https://biology.stackexchange.com/questions/59015/was-raymond-gosling-supervised-by-rosalind-franklin


text:
Measuring depolarizations over the membrane
Measuring the rest potential of a membrane is relatively easy and straight forward: put one electrode inside the neuron, the other one (the "counter electrode") outside the neuron.
Because everything is at equilibrium (steady state), it's not important where exactly inside the neuron you place the first electrode, and even less important where outside the neuron you place the counter electrode: in the extracellular fluid next to the neuron or inside a container filled with extracellular fluid placed anywhere. One may even connect the other electrode to the ground (a lightning rod), if one does it consistently (over all measurements).
But now consider you want to measure the spread of depolarization along the membrane by measuring the membrane potential at two different locations of the membrane: You place one electrode underneath the membrane at point $p_1$ (and its counter electrode to the ground). And you place another electrode underneath the membrane at point $p_2$ (and its counter electrode to the ground).
Now it seems possibly important where exactly inside the neuron you place the two electrodes: the distance from the membrane might make a significant difference. (But maybe not.)
What probably would make a significant difference: Since the ionic compositions of the extracellular fluid in the vicinity of $p_1$ and $p_2$ will differ, it might be important to connect the counter electrodes not to the ground (or to some volume of normal extracellular fluid) but to corresponding points $p_1'$, $p_2'$ directly opposite to $p_1$, $p_2$ on the other side of the membrane.
I emphasized might be important because in practice it may be not important. That's what my question is for:

Is it OK, even for the measurement of the dynamics of depolarizations,
  to connect the counter electrodes to the ground (if only
  consistently). What would be the difference in the measured voltages,
  and can these be determinstically be cancelled out?

It is extremely important where you put your electrode when measuring such delicate structures as dendrites (which is when you want to compare voltage changes between two parts of a neuron). That is why you put your electrode inside the dendrite. Each recording electrode has its own ground that goes inside the bath, i.e. outside the neural tissue. Alternatively, you can observe fluorescence changes of a calcium or voltage dependent indicator that you have introduced inside them.
https://www.janelia.org/sites/default/files/Labs/Spruston%20Lab/Stuart_Spruston_2015.pdf

That's what I presumed: I put two electrodes inside the dendrite. But where to put their respective "counter electrodes"? Or do I use only two electrodes (both inside the dendrite), the second being the counter electrode of the first? But how to take measurements at three, four, many points on the membrane?

The ground goes inside the bath, i.e. outside the tissue. I am not sure I've seen any paper with more than three recording electrodes, but of course I cannot exclude that it exists. A 'usual' setup is having one electrode in the soma and one or two more electrodes on the dendrite. Needless to say, these are very challenging recordings and very few labs in the world are able to perform them. That is why fluorescence imaging of activity is becoming more popular, despite its limitations.

I've edited my answer to address your comment.

Llinás in  his "I of the vortex", p.9 evoked the following picture: "[The membrane voltage] may oscillate in a manner similar to the traveling, sinusoidal waves that we see as gentle ripples in calm water, and are weakly chaotic." What you say ("no paper with more than three recording electrodes") means - not surprisingly - that we will probably never see these ripples measured - but only simulated. (Do you know a reference for such a simulation?)

(I already asked this here: https://biology.stackexchange.com/questions/65550/visual-maps-of-the-neuronal-membrane - without explicitly mentioning membrane potentials, being another kind of "item").

@HansStricker Llinas is almost certainly referring to temporal oscillations (since that's what his whole book is about), i.e. plotting voltage versus time. The analogy to ripples is just that, an analogy.


text:
Why half of the protein is saturated when [L] =Kd
let's suppose the following reaction:

At equilibrium we can calculate the Kd (Dissociation constant) using the following formula:
Kd = [P][L] / [PL]  or kd / ka
We can then use the Hill equation to calculate the fraction of binding sites which are occupied:
occupied binding sites = [L] / [L] + Kd

When [L] euals Kd, half of the ligand binding sites are occupied (Lehninger principles of biochemistry)

Why is this true? This would mean that at equilibrium half of the binding sites are occupied?

As the other answer says, it is true for a simplified model. The model you describe has only one ligand binding site per protein, which makes it the most simple model there is.
It doesn't mean that this is the case at equilibrium as you asked. This is because Kd is not necessarily equal to [L] at equilibrium.  Hopefully this simple derivation will help:
As you said, we know the formula for the dissociation constant: Kd = [P][L]/[PL]
Suppose [L] = Kd. If we plug back into the equation above we get: [L] = [P][L]/[PL]
Doing some algebra we can derive: [P] = [PL]
Therefore, at equilibrium, when [L] = Kd, the
amount of free protein ([P]) and the amount of ligand-bound protein ([PL]) are equal. In other words, half of the protein is bound to ligand, which is exactly what you were asking about.
But now let's suppose that [L] =/= Kd. The reaction will still come to equilibrium, finding concentrations of [P] and [PL] that satisfy the equation Kd = [P][L]/[PL]. However, these values will not be equal. Either more or less than half of the protein will be bound to ligand.
Only in the specific case of [L] = Kd will half of the protein be bound to ligand when equilibrium is reached.

The Hill equation in that link uses the simplifying assumption that all ligands bind simultaneously and that the binding sites are identical. The reaction is then P + nL = PL,
and Kd = ( [P][L]^n )/[PL]
Then by rearranging you get the expression in the link.
The equation "fraction occupied binding sites = [L] / [L] + Kd" Is not the Hill equation. It is called the binding isotherm. You can see that if Kd = [L] then the fraction of occupied binding sites (let's call it theta) = 1/2. Thus half of the binding sites are occupied.

It is the Hill equation where the Hill coefficient is 1, which kind of defeats the purpose of using the Hill equation.


text:
MS/MS for complex samples
I saw this figure in this atricle:

It's a really nice representation of what happens when using MS/MS. However I was wondering how this works when there are more proteins present in the gel spot. How would you be able to select the parent ion(because there are multiple of them)?

Liquid chromatography (LC) allows the peptides from a complex sample to be fed into the mass spectrometer over time. The bottom half of the image shows an MS spectrum from a single precursor scan and the machine is programmed to select the three most intense peaks (parent ions or precursor ions) from this scan for MS/MS (MS2).

This process is repeated throughout the LC-MS/MS run and programs usually include exclusion criteria where a parent ion is ignored for 30 - 90 seconds once it has been scanned 1 - 2 times. Usually the machine will also ignore singly charged parent ions as many of these ions will be inorganic contaminants and you want the machine to be busy with peptides.
Efficient use of machine time is critical to getting good coverage of the proteins in the sample. Proteins that are small create fewer peptides that are amenable to sequencing so these can be missed. Also those proteins that are less abundant may produce peptides that stay below the selection criteria. Good chromatography and efficient use of machine time are critical to getting good results and even in good conditions most peptides will not be subjected to MS2 sequencing. This estimates that of 100 000 peptides with only 16% were 'sequenced'. This explains why proteomics labs are speed freaks, and has driven the development of faster machines. The ~ 1 hour yeast proteome paper demonstrates the 'work' that the newer machines can get through;

Over a 1.3 h chromatographic method .... collected an average of 13,447 MS1 and 80,460 MS2 scans (per run) to produce 43,400 peptide spectral matches and 34,255 peptides with unique amino acid sequences (1% false discovery rate (FDR)).

Thankyou! One thing isn't clear for me, from the MS spectra 3 peaks were selected(for peptide fragmentation). But how are the parent peaks detected? e.g. how could the program "know" if a peak is a parent ion peak or not? Because in the spectra (bottom right) all the peaks (from three peptides) are mixed up.

Precursors are selected for MS2 based on their intensity, the three in the image are the three tallest (most intense) peaks. The machine switches between MS1 where the precursors are screened and MS2 where mass filters close to the source (entrance to machine) only allow precursors within the precursor window to continue to the fragmentation and measurement sections of the machine.

So the precursors are selected based on their intensity and if they "match" the mass of the input (which makes sense to me because they only differ by one H atom)? @Michael_A

I'm not able to find information about the determination of the input mass you mentioned. Can you please add some information about the determination of these parent ion peaks, that would be great!

No shotgun sequencing relies on collecting the most abundant precursors that are in the machine at any given time. This bit is not true for shotgun sequencing; and if they "match" the mass of the input (which makes sense to me because they only differ by one H atom)? The bracketed portion is only true of singly-charged precursor ions. I said mass filters in my previous comment but it is really an m/z filter. If you can quote where I mention "determination of the input mass" as I can't see where you got that from but I clearly need to improve my answer so it's clearer.

Sorry I didn't meant you said that specifically it was about "mass filters close to the source (entrance to machine)" However it would be great indeed if you improve your answer on how the three precursors ions are selected @Michael_A

The precursors are selected for MS2 because they are the most intense, this is a programmatic consideration. I assume you have understood this so it's not the how that you mean? The question of "How do MS allow molecules of a specific m/z to pass to the next part of the machine?" is physics which doesn't belong in SE biology. If you don't understand the physics you need to accept that the machine can do what we say it does. This guy does a great job explaining how quadripoles select a specific m/z window.

Thankyou for the link! What I mean is I see one large peak (the middle precursor peak), in my opinion the left precursor peak could just be a fragment of that middle precursor peak? @Michael_A

No, that is an MS1 scan. There is no fragmentation occurring.

I understand, I mean there are 4 proteins in the beginning --> which are digested --> peptides --> MS. So in this spectrum we got the peptides of ALL 4 proteins. But you don't know how many proteins there are at the beginning so the peak on the left could be just a peptide of the same protein as where the middle came from e.g? Sorry for all these questions but I can't get it clear

Let us continue this discussion in chat.


text:
Which nucleotide as start point for maximum parsimony?
Background
Maximum parsimony is used to build an evolutionary tree by choosing the "simplest" one. I see a lot of examples about how this should be done. For example:

Question
However it's not clear for me WHICH nucleotide should be used as starting point?
Let's consider the first tree(from the figure above):

Nucleotide G was chosen as starting point resulting in one mutation, however if we choose T we would have two mutations and if we choose A we would have three. So what determines the nucleotide which should be used to start with?

Both the text on your diagram and the WP link explain this don't they? The chosen ancestral residue is the one which, in order to fit the tree, needs the fewest total changes. If this doesn't answer your question then maybe you need to rephrase it.

For every tree the number of mutation should be counted to determine the simplest tree rigth? So let's say we have 4 sequences --> 3 unrooted trees --> write every tree down --> for every (informative) position fill in the nucleotides and count the number of mutation needed. But to count them you need to know the "ancesteral nucleotide". So as you suggest you should make the trees as simple as possible (by selecting the best fitting nucleotide as ancestor) and than from these trees againg select the simplest one (the one with the fewest mutations)?@AlanBoyd

Yes, so you need to try the tree with each possible ancestral nucleotide in order to find which gives maximum parsimony (lowest number of substitutions).

Hmm so actually you can make 3x4 trees in the case of 4 sequences? and than select the simplest? @AlanBoyd

The "starting point", or ancestral state, is chosen so as to obtain the most parsimonious tree.
Parsimony is used both for choosing the topology and for choosing the ancestral states for a given topology:
1) The parsimony score for a given topology is computed for the set of ancestral states minimizing the number of transformations.
2) Then, the topology minimizing this minimized number of transformations is chosen as the most parsimonious tree.

Do you have any references for that? I would like to read more about this @bli

@RickBeeloo In terms of algorithms, the process may not necessarily be implemented the way I describe it, but by definition, the most parsimonious tree needs to have its internal nodes states optimized for minimizing the number of transformations, otherwise, we might end up with the wrong topology.

See for instance definition 11.18.1 in https://ab.inf.uni-tuebingen.de/teaching/ws06/albi1/script/phylogeny_31Jan2007.pdf: "where the minimum is taken over all possible labelings λ of the internal nodes of T"


text:
Does GC content determine codon bias or does codon bias determine GC content
I was wondering if someone knows the answer to this quenstion, because I can't find a clear answer, maybe there isn't a clear answer :).
question
Which of these two is right? or maybe both influence each other

GC% determines codon bias
codon bias determines GC%

Thankyou,

Think about it this way, the G-C content is averaged over the entire genome, and varies between different species.  Whether you are dealing with prokaryotes, with relatively compact genomes, or with eukaryotes, with lots of non-coding regions, the open reading frames will, in general, be influenced by the average G-C content across the genome. Therefore we would predict that in species with lower G-C their open reading frames would be biased to using the codons in the genetic code that are higher in A-T. N.B. this also means that their tRNAs should also favour anticodons higher in A-T. In contrast, we would predict that in species with high G-C content, the open reading frames would be biased, in general, to using codons that are higher in G-C.
That is all G-C bias in codons is; for some amino acids like Met and Trp, there is only a single codon, but for other amino acids there can be up to six codons that can each encode the same amino acid side chain. It is in these ones with a higher number of degenerate codons that you are going to see the effect of codon bias.

Thankyou for the answers, it cleared up a lott, but there is one thing I still don't get: I thought the GC bias is determined by the availibility of tRNA, so if a gene needs to be transcribed and translated to a protein very often like ribosomes, it prefers codons of which al lot of tRNA availible for, what am i missing here? @mdperry

This may be debatable (the cause of GC bias). If the abundance, or cellular concentration, of individual tRNAs is fixed, or pre-determined, then over many generations the individuals in the population who use more of the corresponding codons would be able to replicate faster, and over time, the G+C% of the species would appear to change. However, it is difficult for me to imagine a mechanism that would fix, or pre-determine, the concentrations of individual tRNAs in the cell. The concentrations are a combination of the rate of synthesis and the rate of decay. There is probably feedback.

Maybe the codon bias is determined by the GC% of the whole genome, so favoring the most GC rich codons. Futher, de codon usage is maybe determined by the availibility of tRNA, It's just what I think? @mdperry


text:
why is the cleavage in frogs holoblastic and not meroblastic?
background information
The cleavage of the frog embryo during the embryo development is holoblastic (complete cleavage). However when we look at yolk-rich eggs we see a cleavage pattern which is meroblastic (partial cleavage).
Question
But the frog eggs are also yolk rich right? So why do frog embryo's use holoblastic cleavage?

Because:

Frog eggs are not yolk-rich. They are mesolecithal, they have an intermediate amount of yolk.
Yolk is concentrated within vegetal pole of the egg. That is why yolk-packed macromeres divide much slower than micromeres on the vegetal pole, which barely contain any yolk.

My sources:

https://kjcscientific.wordpress.com/project-excalibur/
Gilbert's Developmental Biology (2009)


text:
How to interpret the relationships of PTMs from BioGRID's data
On BioGRID Database, PTMREL is a file that describes relationships of the PTMs (Post Translation Modification) tabulated in a PTMTAB file.
I have several issues with this file.

Foremost, I am not sure how to interpret the 'relationships'.

There are two columns 'Relationship' and 'Identity' that supposedly describe the relationships of PTMs.
    Relationship. A plain text descriptor of the type of relation represented. (Unique values: ['-', 'kinase', 'phosphatase'])
    Identity. A plain text descriptor of additional identity details if available. (Unique values: ['catalytic', 'regulatory', 'PTM'])

Lets say, a gene has a relationship (in in PTMTAB file, column 'Has relationship' is True) and in PTMREL file it is 'kinase' (in PTMREL file column 'Relationship'), does that mean that the gene is kinase or it is phoshorylated by a kinase?
Also what does it mean if the gene is additionally 'catalytic', 'regulatory' or a 'PTM' (in PTMREL file column 'Identity')?
Here's BioGRID's wiki page describing (but not detailing) the file format of PTMREL file.
https://wiki.thebiogrid.org/doku.php/biogrid_ptmtab_ptmrel.

If PTMREL contains data associated with PTMTAB file, why not simply combine it with PTMTAB file? Without knowing how to interpret the relationships of the PTMS, the users too, can not combine the two files.

Additionally, there are PTMs included in 'BioGRID TAB 2.0' too, and the number of PTMs (for a species) in that file are not the same as in PTMTAB file(!).

I understand that BioGRID provide this data 'WITHOUT ANY WARRANTY'. But still, since BioGRID is the most unified and constantly updated resource of gene interaction networks, users should know about basic usage of the data.
UPDATE:
After some data explorations, I could guess the meanings of the data.
If Relationship is '-' -> Identity is always 'PTM'. So, these are the PTMs that do not have known relationships.
If Relationship is 'kinase' or 'phosphatase' -> Identity is 'catalytic' or 'regulatory'. Now, here, I am not sure what do 'catalytic' or 'regulatory' mean.


text:
Frequency of dominant phenotype (Hardy-Weinberg)
The question is:
The frequency of a recessive allele a is 0.6. If a population is in Hardy-Weinberg equilibrium, what is the frequency of the dominant phenotype?
This question is a bit confusing to me. I'm not sure how to use my knowledge about Hardy-Weinberg in this problem. I know that when q = 0.6, p = 1 - 0.6 = 0.4. But when they are asking for the dominant phenotype, should it be p^2 or the squareroot of p? I have watched several YT-videos about this, but I still can't get the hang of it. There's not much help in my teacher or books. I would be really grateful if someone could clear up my confusions!

I was about to recommend the post Solving Hardy Weinberg problems but then realized that you are the OP and that you have accepted the question suggesting that the answer did not help much. The difficulty of this problem is to remember what genotype have the dominant phenotype and then sum their frequencies, just like Alan Boyd did (+1).

Hi! If you are referring to your answer in my previous post - it did help a lot, but these problems still get me confused. You suggested opening a new post with my question, so I did after a while. If you are referring to the answer I got here - also helped, but I'm afraid that when I'm coming across another problem phrased slightly different than this I won't know how to break it down. Anyways I'll check back later

Yep. I did not ask for justification. It is all good :) Glad the other post helped.  Good luck @Thomas

Ok! Aha - I read the last bit of your comment just now, thanks for the tip. Are you some kind of moderator? Can you think of any good sources to clear up on my confusions about this? My examdate is getting closer and closer

p = p(a) = 0.6
q = p(A) = 0.4
Frequency of homozygous recessive, aa = p2 = 0.36
All other genotypes have dominant phenotype therefore the frequency of the dominant phenotype is 1-0.36 = 0.64
(Frequency of homozygous AA = q2 = 0.16
Frequency of heterozygous Aa = 2pq = 0.48)
And if you want a deeper explanation you really should study this answer by Remi.b

Since the frequency of the dominant allele is 0.4, or 40%, the chance of each allele being the dominant allele is 0.4. Since you are asking what is the probability of BOTH alleles being dominant we use the multiplication rule of probability, 0.4*0.4 = .16.
This is similar to the probability of flipping two coins and having them both be heads. Each coin has a 50% chance, therefore the probability of both being heads is 0.5*0.5 = 0.25.
That is the logic behind the Hardy Weinberg formula, p^2 + 2pq + q^2 = 1.

“Since you are asking what is the probability of BOTH alleles being dominant” — No. The question is asking after the frequency of the dominant phenotype. That is, any one dominant allele is sufficient. See the other reply for the correct answer.


text:
Pyrimidine bases + genetic variation
I don't understand this question, hoping someone can help!
One of the following bases does not belong among pyrimidine bases:
 - Uracil
 -  Adenine
 - Cytosine
 - Thymine
I thought that everyone was bases, expect that uracil is in RNA, and that in DNA it is replaced by guanine.
Also one more question:
Which of the processes would never contribute to genetic variation within a bacterial population?
 - Transformation
 - Meiosis
 - Mutation
- Transduction
I have a hunch that the right answer is mutation, but I don't know why. If you know the answer, it would be very helpfull if you could explain why :-)

Welcome to Biology.SE. A post should never contain more than one question. As such, the post should be closed as too broad. Also, homework question requires that the OP shows its effort at answering the question. Typically, for the first question, it really is just a matter of googling pyrimidine. You can have a look at our policy about homework questions here.

I'm really sorry for breaking your policy! I thought that by asking more than one question I was being efficient for both myself and the ones answering. You're absolutely right about the first question - but stress can be paralyzing. I will follow the rules from here on.

No worries. It takes a few posts to get used to the SE policies, formatting and things. After that, it is in my opinion a fantastic tool to be using during your studies.

You are correct - they are all bases. However there are two types of bases. Purines and pyrimidine bases. Purines have two ring systems, while pyrimidines have only one. With this hint, I think you will be able to find the answer to your first question.
As for your second question. Can you give me a definition for what a mutation is? I think if you are able to define this word you will know why that answer is incorrect.
Also, bacteria are incapable of performing one of the four processes that you have listed - and that particular process, is therefore the correct answer to your second question.

Thank you for your detailed and very pedagogic answer. Forgive me for being a total newbie, but as far as I can see both guanine and adenine are pyrines?
Mutation are permanent changes in the DNA. So it could contribute to genetic variation.... but bacterias are incapable of meiosis, of course!

Yes, guanine and adenine are purines. And bacteria are incapable of meiosis. Well done.
But, one last thing, it is actually thiamine that is replaced by uracil in RNA; and not guanine as you stated in your question.

So the correct answer to the first question is adenine (I mixed up guanine as one of the alternatives, as you may have guessed ;-). Thank you for clearing up my RNA mix-up as well.


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How can a powernap boost memeroy and cheerfulness?
Background

A power nap is a short sleep which terminates before the occurrence of
  deep sleep or slow-wave sleep (SWS), intended to quickly revitalize
  the subject. (wiki)

The results of powernapping are described in An ultra short episode of sleep is sufficient to promote declarative memory performance

In the first experiment we assessed free recall of a list of 30 words
  after a 60 min retention interval that was either filled with daytime
  napping or waking activity. Memory performance was significantly
  enhanced after napping as opposed to waking but was not correlated
  with time spent in slow wave sleep or total sleep time within the
  napping condition. The second experiment was designed to clarify the
  role of total sleep time and therefore included an additional third
  group, which was allowed to nap for no longer than 6 min on average.
  In comparing word recall after conditions of no napping (waking),
  short napping, and long napping, we found superior recall for both nap
  conditions in contrast to waking as well as for long naps in contrast
  to short naps. These results demonstrate that even an ultra short
  period of sleep is sufficient to enhance memory processing

Question
I'm wondering how it's possible that such a short napping period can boost cheerfulness and memory (thus in a biological sense).

Perhaps better asked on CogSci?


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Which parts of the cerebral cortex don't belong to the neocortex?
In the Wikipedia article on the cerebral cortex one reads:

»Most of the cerebral cortex consists of the six-layered neocortex.«

Accordingly, in the Wikipedia list of regions in the human brain, one finds "cerebral cortex" and "neocortex" as almost synonyms.
But assuming that they are not perfect synonyms – but that there are some parts of the cerebral cortex that are not part of the neocortex – I wonder which parts this might specifically be.
To make my question specific, I list here all parts of the cerebral cortex as listed at Wikipedia:
Cerebral cortex (neocortex)
Frontal lobe
    Primary motor cortex
    Supplementary motor cortex
    Premotor cortex
    Prefrontal cortex
    Orbitofrontal cortex
    Dorsolateral prefrontal cortex
    Superior frontal gyrus
    Middle frontal gyrus
    Inf. frontal gyrus
    Brodmann areas
Parietal lobe
    Primary somatosensory cortex (S1)
    Secondary somatosensory cortex (S2)
    Posterior parietal cortex
    Postcentral gyrus (Primary somesthetic area)
    Precuneus
    Brodmann areas
Occipital lobe
    Primary visual cortex (V1)
    V2
    V3
    V4
    V5/MT
    Lateral occipital gyrus
    Cuneus
    Brodmann areas
Temporal lobe
    Primary auditory cortex (A1)
    secondary auditory cortex (A2)
    Inf. temporal cortex
    Posterior Inf. temporal cortex
    Superior temporal gyrus
    Middle temporal gyrus
    Inf. temporal gyrus
    Entorhinal cortex
    Perirhinal cortex
    Parahippocampal gyrus
    Fusiform gyrus
    Brodmann areas
    Medial superior temporal area (MST)
Insular cortex
Cingulate cortex
    Anterior cingulate
    Posterior cingulate
    Retrosplenial cortex
    Indusium griseum
    Subgenual area 25
    Brodmann areas

If there are parts of the cerebral cortex missing here, a hint would be welcome!

The hippocampus is considered archicortex rather than neocortex. Sometimes hippocampus is considered "sub-cortical" but I think this is only really fair if you really mean "sub-neocortical"; it's common for "cortical" to be used as a shorthand for neocortex in human neurobiology. Writers will be more specific when necessary.
The piriform cortex and related olfactory structures are considered paleocortex.
Some also delineate an in-between periallocortex that includes entorhinal cortex and limbic structures around the hippocampus.
Neocortex is mostly a six-layered structure and found only in mammals. The other, non-neocortical types of cortex have fewer layers, and are shared by an older common ancestor that includes other vertebrates.


text:
Distribution of synapses of CA1 neurons
In the Wikipedia article on dendritic spikes I read:

In the hippocampus, the CA1 neurons contain two distinctive regions
  that receive excitatory synaptic inputs: the perforant path (PP)
  through the apical dendritic tuft (500-750 μm from soma) and the
  Schaffer-collateral (SC) through the basal and apical dendrites
  (250-500 μm from soma).

I wonder how the distinctiveness of these two regions does appear when plotting the number of synapses as a function of the distance to the soma:

More like the gray, or more like the red, or more like the green curve? Or which other?

One source for this estimate is Megias et al. 2001, an electron microscopy study in CA1 of the rat hippocampus.
I plot their data from Table 3 in the following graph.

The X-axis is not in micrometers. Rather it represents dendritic subclasses. $Ori$ stands for Stratum Oriens, $Rad$ for S. Radiatum, $L-M$ for Lacunosum-Moleculare, $T$ for thick dendrites, $t$ for thin dendrites, $prox/med/dist$ for proximal, medial, and distal, respectively. Stratum Oriens represents basal dendrites that are close to the cell body, stratum Radiatum apical trunks, and stratum Lacunosum-Moleculare the apical tufts. The approximate locations of the layers in reference to the cell body are (in micrometers): $Ori = (-100, 0)$, $Rad = (100, 350)$, $L-M = (350,550)$. The Y-axis represents the total number of synapses, both excitatory and inhibitory.

Isn't it possible to attach rough distances to the dendritic subclasses? Since distance to the soma is important.

What does a  negative distance mean?

If we assign the cell body, or more precisely the stratum pyramidale, at $0$, then stratum oriens is to its dorsal side and stratum radiatum on its ventral side. I've arbitrarily assigned dorsal $\rightarrow$ ventral as the positive direction.

But the effective (physical) distance is still positive, isn't it?

How could the soma distinguish between dorsal and ventral?

I have included direction to help the reader realize where the cell body would lie in the above bar graph, nothing more.


text:
Are ion channels/resistancies in Rall's model voltage-independent or not?
In the description of the electrical circuit that models a piece of membrane

in Rall's Scholarpedia article on Ralls model, I read:

"[...] this conductance [$G_e$] is zero under resting conditions, but
  is turned on by an excitatory synaptic input. [...] this conductance
  is [$G_i$] zero under resting conditions, but is turned on by
  inhibitory synaptic input."

Does this mean, Rall is assuming voltage-dependent ion channels? Or why does he stress, that the conductances can (or even must) be turned on and off?
From an electrical point of you, I would guess, that the three resistancy-battery pairs can be replaced by one such pair that would not be voltage-dependent, and maybe even the battery is not needed, as in cable theory:

Or would Rall's model not work anymore, then? This doesn't get clear to me, and would not have been stressed by the author. (Later in his article, Rall doesn't mention $G_r$, $G_e$, $G_i$ anymore, but talks only about membrane resistance $r_m$.)

Is it clear for you that the switch for those conductances turning on or off is synaptic transmission? Channels at the synapse will only conduct ions when a neurotransmitter binds on them. $G_e$ and $G_i$ could be replaced by a single element, except we know that excitatory and inhibitory synapses exist and may be active at different times and in different places of the cell. So you need them there if you try to describe further attributes in more complicated models (timing, localization). $G_r$ I guess cannot be fused with the other conductances as it is always on.

Yes, this is clear for me, but I didn't want to think of the initial creation of the potentials but only how the travel and spread (driven and controlled by membrane capitance and resistance). The conductances then will not be turned on and off by neurotransmitters but by the traveling potentials themselves. This means: I am only interested in voltage-gated but not in ligand-gated ion channels. (The initial potentials at time t=0 may just be "given".)

Then Rall's model is not appropriate for your purposes. Once $G_e$ and $G_i$ are turned on there is no additional voltage modulation - synaptic transmission is their only purpose. His is a 'passive' model, as we call it, and you seem to be interested in 'active' models.

@vkehayas: In this question I actually was interested in passive transport. Thanks to your explanations I now understand: that travel and spread of EPSPs - once initiated - is controlled solely by $C_m$, $G_r$, and $E_r$ - the other conductances are just off. And they are not voltage- but ligand-gated channels, so won't be influenced by passing-by potentials, right?

Mostly correct. The passive diffusion is described by the cable equation $$\frac{1}{r_l}\frac{\partial^2 V}{\partial X^2} = c_m\frac{\partial V}{\partial T}+\frac{V}{r_m}$$ Each compartment like the one you showed is assumed to be connected to its neighbours with $r_l$.

If you are interested in passive diffusion and not just membrane potential generation in a dendritic compartment, then you need to look at the cable equation:
$$\frac{1}{r_l}\frac{\partial^2 V}{\partial X^2} = c_m\frac{\partial V}{\partial T}+\frac{V}{r_m}$$
Here, every compartment is connected in series with resistances $r_l$.
We define the length constant as
$$ \lambda = \sqrt{\frac{r_m}{r_l}}  $$
and the time constant as
$$ \tau = r_mc_m$$
Then the equation can be re-written as:
$$\lambda^2\frac{\partial^2 V}{\partial X^2} = \tau\frac{\partial V}{\partial T}+V$$
The reason $G_e, G_i$ are not mentioned when talking about diffusion along the dendrite is that they are only involved in the generation of voltage $V$ in the compartment.

I added the corrections based on your comments.

I deleted the comments.

Final remark: the ion channels that are responsible for $G_r$, resp. $r_m$ are the leak channels, right?

Not quite. The diameter of the process comes into play: https://en.wikipedia.org/wiki/Cable_theory#Deriving_the_cable_equation

OK, $G_r$, resp. $R_m$ depend solely on physical properties of the leak channels, but $r_m = R_m/2\pi a$ also depends on the diameter $a$. Now I got the picture!

Wouldn't a natural refinement of Rall's model be simply to consider the voltage-gated (dendritic spike generating) ion channels during (otherwise passive) transport, instead of just neglecting them or switching them off (like the ligand-gated channels, that are described by $G_e$ and $G_i$)?

They simply were not known to exist and/or be implicated in dendritic processing when Rall's model was first formulated. For the rest, you may want to ask a new question.


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What is this animal? Reminds me of a crab because of the way it crawls but it looks like a plant.
Crablike animal however it looks like a plant. Doesn't seem that fast when it comes to speed.

Welcome to Biology.SE. Can you please indicate where (broad scale and finer scale) and when you took this picture. Was the picture taken underwater? Also what do you mean exactly by "not so fast"? Feel free to add any other information that may help.

It looks like a clump of seaweed to me. But I can pick out pairs of legs.
It is a species of "seaweed crab" or "decorator crab": a crab that camouflages itself with bits of seaweed it picks up, so its appearance can vary depending on its surroundings. Here's a video, and as you say, in the speed department, it's a bit lacking.
It is identified as Naxia tumida as opposed to the larger decorator crabs. The cephalothorax is that round brown bump in the middle, and in front of it (in the middle below the long axis) are the pincer legs. The second and third pairs of legs have quite a lot of seaweed attached (making up what I've described as the 'long axis'.)
Here is a screenshot from the video of a Naxia tumida.


text:
Why does lactate build up prevent a further increase in the speed of an athlete?
This question was triggered by an exam question that I was doing on the following paper (Q2 part (b)(i)):
http://qualifications.pearson.com/content/dam/pdf/A%20Level/Biology/2013/Exam%20materials/6BI05_01_que_20120307.pdf
Here is the markscheme:
http://qualifications.pearson.com/content/dam/pdf/A%20Level/Biology/2013/Exam%20materials/6BI05_01_msc_20120215.pdf
I do not understand why the decrease in pH results in the lack of of increase in speed, despite hours of research. Here are my best attempts:
The build up of lactate will have to keep the power output of the muscles, as a whole, constant, rather than allowing it to continue increasing. Therefore, there must be a link between the increased acidity of the muscle cells and the limiting of the power output. Now, if the markscheme is correct and the increase in acidity causes a decrease in the ATP production, this means that the ATP concentration within the cell decreases. However, the decrease in ATP concentration should decrease the power output rather than limit it, because less myosin heads will be able to contribute to the pulling of the actin filaments during the contraction of a sarcomere. Am I correct, or is there more to this? If so, why is there a limiting of the power output of the muscles rather than a decrease in it?

There is not complete shift to anaerobic respiration.

@JM97 may you please elaborate? How does that ansswer my questions? Moreover, what are your comments on my deductions? What am I missing?

During sprinting the runner maintains constant output not only just because of anaerobic respiration but also aerobic respiration, limited supply of oxygen limits the output.


text:
Where do the antibodies that trigger the specific immune response come from?
In A level Biology, we are taught that in order to trigger the specific immune response of the body, antibodies must first attach to the pathogen. The macrophages contain antibody receptors, and this allows them to attach to the antibody carrying pathogen and subsequently engulf them by phagocytosis. This then triggers a certain pathway that involves T helper cells activation, which release cytokines to cause differentiation of B helper cells into plasma cells, and THESE release the antibodies.
The question is: where do the antibodies that start off the whole process even come from?

First: What your teacher says about the free floating antibodies is not correct. The first contact with a new antigen to generate specific immunity is done by naive B cells which have a membrane bound B cell receptor and their effector T cells. This contact can either happen directly or by the presentation of the antigen to the cell by antigen presenting cells (APC).
Short answer:
These naive B cells are present in our body without antigen contact, but are not highly specific.
Long answer:
Our body has the possibility to express a vast variety of different antibodies - estimations go up to 10 billion different antibodies which the human body can produce, each of them capable of binding a different antigen (see reference 1).
To begin with, naive B cells express antibodies as a membrane-bound version, the so called B cell receptor. The antigen specificity of these receptors is random and occurs before the individual had contact with the antigen. These receptors bind a wide variety of different antigens, more or less good. This is the so-called affinity of the receptor (or the antibody) against an antigen.
Upon binding of an antigen, the B cells get activated (if the receive a co-stimulatory signal from a T cell). When activated, the cells starts to proliferate and to differentiate, as shown in the figure below (from here).

Basically, the cells start to re-arrange the genes which are responsible for generation of the variable region of the antibody (the part which does the actual binding of the antigen) to generate highly specific high affinity antibodies to the antigen and then mature into relatively short lived plasma cells, which produce big amounts of antibodies and long lived memory cells. The later are dormant in the body and get reactivated, when the body is challenged by the same antigen, against which it already produced highly specific antibodies.
When re-exposed to an antigen, the antibodies in the blood stream bind to the antigen and mark it for phagocytosis. The phagocytes will then take up the antibody bound antigen, process it and present parts of it on their surface to B/T cells. This either starts the process of selection and clonal expansion as described above or if there are specific memory cells, these cells will proliferate and differentiate into antibody producing plasma cells.
The initial process of adaptive immunity takes about two weeks until highly specific antibodies are available, if you only have to "wake up" the cells from the memory pool, this will take a few days. This is also how vaccinations work.
See also the Wikipedia page on Antibodies for much more details.
References:

Development of the immunoglobulin repertoire.

@iayork I changed my answer to adress this more clear.

To address your question about antibodies, produced by antigen-specific B cells or plasma cells, I'm first going to address how you activate a B cell.
Naive B cells are produced in the bone marrow with antigen specificity encoded in it's B cell receptor (BCR), a product of VDJ recombination. Each B cell has a specificity toward a single antigen through it's BCR, much like T cells have a single-antigen specificity through their T cell receptor (TCR).
The ways that B cells are activated differ and I think you can get an idea here in 9.1 and 9.2. The take home point is there are T cell dependent and T cell independent pathways, but typically multiple cells are involved.
So to be certain, however, antibodies come at the late stage of infection, they do not start the process. As a matter of first response, you typically have the innate immune cells and the complement system responding. B cells have complement binding proteins that can link innate and adaptive immunity, like CD21.
Also, In the case of allergic reaction, it's different because it requires a priming stage by an initial contact with an allergen, and then the IgE antibodies present on mast cells during the second encounter cause the reaction, but here we'll focus on pathogens.
The entire process of antibody production takes place generally at the B cell receptor locus. The B cell receptor is expressed as two insoluble isotypes in a naive, circulating B cell: IgM and sometimes IgD. Keep in mind that secreted IgM and membrane IgM are structurally different. BCR IgM is monomeric, not pentameric like its secreted counterpart. The significance of IgD is also under investigation, but some research shows it's indispensible for responding to large multi-valent antigen when the B cell is already anergic (ref).
Whether the antibody is membrane-bound or secreted depends on post-translational modification, and these are affected by the activation state of the B cell (I like this reference). So when the B cell activates as it does in the above reference, either T-dependent or T-independent, two things are necessary: The antigen stimulation, and specific cytokines. Take a look at the B cell receptor locus:

You get an immunoglobulin by taking the variable region produced by VDJ recombination and attaching it to a constant region. The Ig locus has multiple constant regions: Cµ, Cy, Cα, Cδ, and Cε. When it wants to produces IgM and IgD, it transcribes a long mRNA V-Cµ-Cδ and then the cell edits the mRNA into V-Cδ or V-Cµ. The mu and delta C regions are spatially separated so that they are co-transcribed but the other C regions are not. Then it translates and modifies the protein to get a secreted or membranous Ig. B cells that secrete antibody are activated and a referred to as plasma cells.
But, if you're being stimulated by interferon-y at the same time, B cells can class switch to IgG by editing the gene locus so that the mRNA produced is V-Cy. If the cell is receiving Th2 cytokines like IL-4, it can make IgE by editing the gene so that the mRNA is V-Cε. The B cell actually deletes the other C regions in the DNA so it never reverts back. I go over class switching here.
Does that make sense? The antibody requires a concerted effort of other cells, and intracellular splicing and protein-modification machinery. See my favorite text, cellular and molecular immunology, 8th ed. for a powerful reference.

"In order to trigger the specific immune response of the body, antibodies must first attach to the pathogen" - This is wrong. Either you misunderstood, or the teacher was mistaken.  Specific immunity is triggered with no need for antibodies to bind to the pathogen.  Very simplistically, the earliest stages in specific immune responses require T cells and antigen-presenting cells.  The non-specific immune response is also very important in setting up a milieu in which specific immunity can efficiently start and progress.
From Immunobiology: The Immune System in Health and Disease. 5th edition.:

10-4. An adaptive immune response is initiated when circulating T cells encounter their corresponding antigen in draining lymphoid tissues and become activated
As described in Chapter 8, immature dendritic cells in tissues take up antigens and are stimulated by infection to migrate to draining lymph nodes. Antigens introduced directly into the bloodstream are picked up by antigen-presenting cells in the spleen, and lymphocytes are activated in the splenic white pulp (see Fig. 1.9). The trapping of antigen by antigen-presenting cells that migrate to these lymphoid tissues, and the continuous recirculation of naive T cells through these tissues, ensure that rare antigen-specific T cells will encounter their specific antigen on an antigen-presenting cell surface.


text:
What is the mechanism by which passive immunity works?
My idea is that passive immunity can be used to cure an individual who is infected with a certain disease. For example, for someone infected by clostridium tetani, you would inject them with an antiserum. The antibodies give protection against bacteria, until the active immune response takes action. In this link (http://pmt.physicsandmathstutor.com/download/Biology/A-level/Notes/Edexcel-IAL/Unit-4/6-Infection-Immunity-and-Forensics/Set-A/Vaccines.pdf), page 3, the graph shows that the level of antibodies in the blood actually rises after injection! To me, this naturally begs the question, what is the mechanism by which passive immunity operates (because I want to know why the level of antibodies rise in order to understand the situation dynamically)?
[Note: would I be correct in saying that a short answer would be that the level of antibodies rises because the active immune system is stimulated due to the enhancement of phagocytosis by macrophages when the antibodies attach to the antigens? My book states that release of antibodies (by B-cells) that bind to the antigen is required to allow the macrophages to engulf the pathogen with the specific surface antigen.]

You seem to be overlooking the obvious answer, which is also spelled out in the linked document: "Sometimes actual antibodies are injected into people to give instant, short term, passive immunity." If you inject antibodies then yes, the level of antibodies in the blood rises immediately because that is what you injected.

No, that's not what the graph shows. The graph shows that after an initial injection you continue getting a rise over the subsequent weeks. I did not overlook the obvious answer. The sentence that you stated answers the question 'why use passive immunity'?

Yes, apologies, I understand now what is concerning you - I've posted an answer.

I'm voting to close this question as off-topic because it is not a question in the terms of SE Biology. SE Biology is a question and answer site, not a discussion site. Furthermore your titles seem to be an attempt to disguise the fact that your are not asking a question. I have already explained this in detail in relation to another of your questions I have voted to close, so will not repeat chapter and verse here.

Mr. David, I am not disguising not asking a question in this case. I see where you were coming from in the other case though. Apologies.

I commented on this question, but the OP's response prompted me to think again. Here is the graph from the document that the OP linked to:

Clearly what is confusing is that the parameter referred to as 'antibody level' rises quickly, but not as a step. In terms of the x-axis, vaguely labelled as weeks, it looks as if the level of antibody continues to rise over several days at least. The OP attempts to read into this an effect whereby the injected antibodies somehow stimulate the immune response in the recipient.
My knowledge of immunology isn't extensive enough to rule that out completely, but I don't think that is what this sketch graph is illustrating since the levels of these antibodies is shown as falling to zero due to destruction and excretion. This indicates that what is being graphed is just the injected antibodies.
In the absence of some real data for the time-course, my explanation for the rising phase illustrated is that this is showing levels of antibodies in the blood. However the prophylactic use of injected antibodies will often involve an intramuscular injection near the site of an injury. Here for example is a quotation from a recent review on the use of recombinant immunoglobulins (RIG) against rabies:

Because vaccination needs time to induce a humoral response, application of RIG immediately after exposure is important to inhibit viral spread, even when accelerated vaccination schedules are applied. As much of the RIG dose as anatomically feasible should be injected into the area around the wound, and the remaining volume then given intramuscularly at a site distant from rabies vaccine inoculation. Isotope-labelled HRIG, injected around simulated bite wounds, diffused readily into surrounding tissue and about 25% was still detectable around the injection site 24 h later.

Thus the level of antibodies in the blood will continue to rise as they slowly enter the circulation from the site of injection.

As Alan Boyd says, the relatively slow rise is due to gradual uptake of the injected antibody.
If you deliver the antibodies by intravenous injection or another mode that allows rapid uptake (I use intraperitoneal injection in mice) then the antibody levels peak rapidly, less than a day and probably a couple hours, and then drop off; there is no continued rise as shown in the chart, which shows that there's no effect on production of new antibodies.
If you deliver the antibodies via intramuscular injection, which is probably the most common mode in humans, they'll enter the circulation much less rapidly. According to Uptake and elimination of hepatitis B immunoglobulins after intramuscular application in man, following intramuscular injection of antibodies, most people showed peak serum antibody concentrations between 3 and 7 days after injection, and they note

The passive immunization via the intramuscular route does not accomplish an instantaneously available, maximum anti-HBs titer. There seems to be a great range of variation in uptake and elimination of the immunoglobulins in man.

The antibody levels go up, because you're adding more antibodies. The increase in antibodies isn't from the patient, it's from the injection of antiserum.
The half life of IgG (the most common antibody) is around 20 days. IgM and IgA last for 5-8 days.  Reference. So as you can see, the antibody levels increase due to the injection of antibodies into the patient.
The comment by Alan Boyd gave the answer I was just typing out, but I'll still put it as an answer.

Please see my reply. I disagree. This does not address my question.

I've edited my response. The injected antibodies survive for long and the injection of antibodies causes the subsequent increase.