texts: What evolutionary advantages does a longer muzzle have against a shorter muzzle and vice versa

texts:
Basically I'm curious as to why when it comes to mammalian predators that some like say bears and canines tend to have longer muzzles than those like big cats.

aside from their ancestors/evolutionary line and such, what advantages or disadvantages do short muzzles and long muzzles have against each other and which is better?


texts: Do COVID-19 vaccines produce more spike protein than natural infection?

texts:
The SARS-CoV-2 spike protein has been shown to be harmful on its own.
However, a news article quoted an "expert" as saying

The spike protein components of the vaccine are not produced in the same amounts as a normal viral infection (probably a million times less)

On the other hand, I've also read that

Antibody levels induced by mRNA COVID-19 vaccines are much higher than those induced by natural infection

These statements seem contradictory: I'd expect higher antibody levels in response to larger amounts of the spike protein.
So do COVID-19 vaccines produce more spike protein than natural infection?

There is also an argument that the spike proteins produced by the vaccines are localized in the muscle. I think this issue is orthogonal to the question of how much protein is produced.
It should also be noted that the Pfizer, Moderna and J&J (unlike AstraZeneca and Sputnik V) vaccines encode a defective spike protein, which may help with their safety.

Edit: The variation from person to person is a red herring. Here is why:
Let's take a person who has not had Covid or vaccine. Give him the vaccine and count the number of spike protein molecules he produces and call it x. Now, in a different scenario, take the same unvaccinated person and give him Covid. Count the number of spike protein molecules he produces and call it y.
The above claims are, respectively:
y = 1000000 x

and
y < x

We don't even compare x from one person to y from another. We could also understand them as statements about average values. There would still be a contradiction.


texts: During the autologous transplantation of stems cells from bone marrow to produce new blood cells why all the other stem cells other than the one obtained are destroyed?


texts: Phylogenetic Independent Contrasts with discrete traits

texts:
I understand that PICs are normally only used for continuous traits. However, on this how-to site (https://www.r-phylo.org/wiki/HowTo/Phylogenetic_Independent_Contrasts) there is mention of "Discrete traits can be coded as continuous variables (see ?contr.treatment) and analysed as usual, if they are independent (explanatory) variables."

However, I'm having trouble understanding the commands described in ?contr.treatment and how they relate at all to using discrete traits in PICs. I assume it is a way to transform discrete into continuous data (or at least the appearance of cont. data) so as to perform the PIC, but I don't know how to get there from that hint.

This would very much help analyze my data, which includes both continuous and discrete data. I've already performed a phylogenetic logistic regression, but I feel that PICs could help cement my case if possible to perform.


texts: Why are local field potentials generally band-pass filtered?

texts:
I was wondering what the rationale was behind low-pass or band-pass filtering in local field potential measurements?

It seems to me that we could potentially filter out potentially valuable information by filtering procedures.

Is there a physical limitation for this that would not allow to measure, say, the responses in a frequency range of 0 to 5 kHz?


texts: Acetylcholine and muscles- excitatory or inhibitory? (muscle atonia and myasthenia gravis)

texts:
I have heard that acetylcholine can be excitatory or inhibitory, but I am confused as to which it is when it comes to muscles. On the one hand, I believe that muscle atonia during REM sleep is associated with an abundance of acetylcholine in the brain stem, suggesting it has an inhibitory response on the motor neurons. On the other hand I know that the illness myasthenia gravis is caused by antibodies blocking acetylcholine receptors, which suggests to me that acetylcholine is excitatory. Could it be that with myasthenia gravis, the effect occurs at the neuromuscular junction where acetylcholine is excitatory, but it has an inhibitory effect on the motor neurons in the brain stem?

Thank you in advance.


texts: Identification of an insect found in Edmonton, Alberta, Canada.

texts: It's 8.5mm long found in front yard. Unusual wing shape. Sorry about the images: the insect is so small my camera was struggling.


texts: If left glossopharyngeal nerve and right vagus nerve are intact, but there is a lesion at left vagus nerve, would stimulating the left side of pharynx elicit a gag reflex?


texts: How do kidney cells excrete their own wastes?

texts:
The kidney is composed of tissues, and those tissues are made up of numerous cells - so how do these cells excrete their wastes?

Lastly, are there any wastes in the venous blood (renal vein), what makes the renal artery and vein different? - what substances do they each carry?


texts: How didn't large, highly active dinosaurs overheat?

texts:
The cube-square law seems to be the deciding factor when it comes to biological heat management. Small organisms with large surface areas relative to their volumes, like mice, need fast heartbeats and huge energy consumption relative to their size to keep themselves warm. Large organisms like elephants with small surface areas relative to their volumes need slow metabolisms and fairly little energy consumption relative to their size to keep from overheating.

But, dinosaurs. Most research seems to indicate they were basically warm-blooded (yes, that wording really bothers me too, but research as recent as 2015 states that they seem to lean decidedly toward warm-bloodedness, though they are technically somewhere in between). Modern-day creatures of that size tend to divide neatly depending on whether they live on land or in water, with the former being fairly inactive and herbivorous and the latter sometimes able to support the metabolic needs of predation by having water to help disperse the heat.

Dinosaurs, though, are an exception. Many of the fiercer predators were large, highly-active land-dwellers, three conditions that are mutually exclusive in modern organisms. How was this possible?


texts:
What product of cellular respiration creates an acid when in solution with water?

Topic question really, haven't been able to find a direct answer.


texts: Why doesn't the polar side of the plasma membrane block nonpolar diffusion?

texts:
It is often stated that small molecules or nonpolar molecules can diffuse through the plasma membrane because they can pass through the middle nonpolar bit, but why don't the polar sides block these nonpolar molecules. Estrogen is nonpolar and can diffuse across the membrane right? Why don't the polar heads of the phospholipids block it? Or look at H+. H+ can't diffuse across the membrane because it's charged (it's not like nonpolar molecule have a repulsive force against it, neutral objects don't repel charged ones as far as I am aware, I don't get why we say polar and nonpolar repel each other, as I understand they just stick to themselves better than each other). Regardless, H+ a small charged molecule would be able to get past the hydrophilic heads right? Estrogen wouldn't be. Where am I going wrong here?
Thanks!


texts: Why doesn't patients with chronic acne's body lower sebum production itself?

texts:
Background
My cousin has had nodular acne for at least 9 years. Her sebum plugs usually causes bumps on, and inflame, the skin, before the sebum emerges or can be extracted with a comedo extractor. Occasioanlly, this happens without inflammation.
Dermatologist's Feedback
He said that topical retinoids open pores to help expel the trapped sebum, but only oral treinoin (E.g. accutane) can dwindle sebum production.
Question
We forgot to ask him why the body (on its own) doesn't slack sebum production ? We're assuming the body's ability to detect the inflammation and acne nodes, and to adjust sebum production?


texts:
Why should you use an annealing temperature about 5°C below the Tm of your primers?

According to my current research, I think it has something to do with the other reactents in the PCR, but I am not sure.


texts: What causes feeling of feet falling asleep to be delayed?

texts:
This answer explains the sensation of extremities "falling asleep" as a result of sustained pressure on a nerve. The answer links to an external web page that says that the feeling "quickly goes away once the pressure is relieved."

In my experience, however, it doesn't usually go exactly like this.  For me at least, usually what happens is I will start feeling a tingling sensation in my feet after sitting in an awkward position for an extended period of time. If I ignore the sensation for long enough, it continues to get worse until I finally do stand up.  But after I stand up, rather than the sensation quickly disappearing, I find that usually it suddenly gets much worse for a period of time.  What started as an annoying tingling when I was sitting quickly turns into something quite uncomfortable upon standing up, even to the point where I am not able to walk around properly until the sensation passes a few minutes later.

But once I am standing up, the nerve shouldn't be pinched anymore, so why does the sensation of my foot being "asleep" remain for a few minutes after standing up, and why does it actually seem to briefly get worse after I have already stood up and "unpinched" the nerve?


texts:
I found a few of these walking in the middle of the night (about 3 AM) on a wall in my room near the floor. They are at most a few millimetres long (no more than 2 I would say). I am living in Poland, in a block of flats.

EDIT:  Since I first wrote, I have seen few more - very small - less then 1 millimetre long. They seemed to be coming from behind the baseboard. This time I've seen them during daytime.


texts:
I know that BRCA2 interacts with RAD51 to repair DNA damage.

But how exactly does it function ? What are the other proteins that interact with it ?


texts:
Why do most fishes have a "vertical" body shape instead of a "flat" one ?
Here "vertical" means that the body(from a front view) is roughly orthogonal to the horizontal plane, and a "flat" body shape means something like a frog's or a bird's with spreading wings.

PS: This question was raised when I was thinking how I can swim faster.


texts: Why does an increased heart rate mean increased blood pressure?

texts: Say a person starts exercising. If their cardiac volume remains the same but their heart rate increases so that the overall result is an increase in cardiac output, will their blood pressure increase during the exercise ? If it does, why ?


texts: How much does 10g of glucose raise the blood glucose level?

texts:
If you would calculate it:
~5 liters of blood = 50 deciliters
10g glucose = 10000 milligram

so the glucose level raises by 10000mg/50dl = 200mg/dl

However, it is known that ingesting 10g glucose only raises the blood glucose level by ~40mg/dl

Why?


texts:
This answer to How does the “heat vision” of some snakes work? explains the basic idea and there are several linked sources within that go into greater detail on the sensing mechanisms on a physical and a molecular level.
But searching these sources for terms like "spatial" or "angular" in an attempt to understand how they get direction information (specifically for striking a  pray) turned up nothing.
Some snakes have multiple pit organs that point in somewhat different directions, and I suppose it's possible that the heat-sensitive nerves across the pit membrane could have spatial resolution and the whole thing act like a pinhole camera, but so far I've found no actual explanation of how they obtain direction information from their pit organs.
Question: How do snakes determine the direction of prey from their thermal infrared sensing pit organs?


texts: Why is oxygen needed for the electron transfer phosphorylation?

texts:
I understand that oxygen is the acceptor of electrons and hydrogen ions during the electron transfer phosphorylation, the last step off the ATP-producing aerobic respiration.

But why?

Aren't there any other alternatives for this acceptor? Oxygen is already recognized to have several harmful effects to cells - wouldn't another molecule be a better choice?

Why does it even require an "acceptor" to accept the electrons and hydrogen ions? What would happen if they were left alone?

I apologize if my question was due to my ignorance in basic chemistry or biology, but do please point it out and explain it to me. Thanks!


texts:
When a biologist is talking about a genetically engineered mouse strain which is a "tool strain", what does that mean? What is the exact definition of a tool strain? What is the difference between a tool strain and any other mouse strain?

Also, how are tool strains connected to recombinase techniques? Does using a recombinase automatically create a tool strain? Or are the properties "tool strain" and "recombinase containing strain" independent from each other?

If it is important, the context is mouse (and possibly other animal) strains used in cancer research.

It would help if you could keep the explanation high-level. I only have high-school biology knowledge and I am trying to make sense of the requirements for a software application for use by biologists.


texts:
I am interested in knowing how our Circadian Clock responds (and if there are resultant changes) when we travel across Time Zones?

UPDATE 24th April

I am reopening this question as the statement in the answer "When you travel to different time zones, your circadian clock will be off" has further confused me. If it's the case, then I am looking to get a better explanation than that (with solid references). Thanks


texts: Let's say I drink some Kefir Milk, what happens to the lactic acid in the Kefir Milk that has entered my digestive system?


texts: To understand Second messenger signalling in I/c and E/c

texts:
I found this picture in my study materials.
I think it is too schematic and ignores the big pictures.

I think the thing connected to the hormone is receptor.
The second messanger is then connected to the receptor which stimulates the effector cell in the cytosol.
The cell then response both to cytosol and to extracellular space.
How do you understand this picture?

Do you know any similar pictures which present the same thing but clearer and more exactly?


texts: Is this description of etiology of celiac disease correct?

texts:
There is a detailed and, to my inexpert eyes, plausible description of the etiology of celiac disease and other autoimmune disorders posted here: http://no-gluten.org/CeliacDisease.htm

Is it is at all accurate? If any of it is speculative or incorrect, which parts are those? Red flags to me are that it cites no sources and is much more detailed than any other description of celiac that I've seen. But, again, it does coincide with what little I do know of human immune biology.


texts: JMol "calculate HBONDS": which atom is the donor/acceptor?

texts:
JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS".  By outputting the state of the network, we can obtain a lisdt of H-bonds.

Here's one line from an example output (PDB ID number 1a1x):

74    540    4096    0.001    -2.507   hbond;

I believe the correct interpretation of the first two numbers is that atom 74 is H-bonded to atom 540.  (I'm not really sure what the other numbers mean.)

  Question: How can we determine which atom is the donor and which is the acceptor?

In the above example, atom 74 is a Nitrogen atom and atom 540 is a Carbon atom, so presumably the Nitrogen atom is the donor.  But, how can we tell in general?


texts: Why mutations in genes involved in general processes like DNA repair increase the risk of developing specific types of cancer?

texts:
For example, mutation in MHS2, which encodes a protein involved in the repair of mismatches that occur during DNA replication, dramatically increases the risk of developing colon cancer.
(There are many other examples, like the RB gene which encodes a tumor supressor protein and is correlated to retinoblastoma, thus its name)

My question is: how a gene like MHS2 which participates in a general mechanism of DNA repair increases the risk of a specific type of cancer? Why doesn't it increase the risk of developing cancer in other tissues as well?


texts: what is the name of this small plant with yellow flower?

texts:
Can someone please help me find the name of this flower. The close I got to is maybe some kind of diasy?.

Location: Hyderabad, India


texts: Most textbooks seems to restrict pathogens to the domains bacteria and eukarya. Are there any pathogenic archaeans?


texts: Time taken for species to become endemic

texts:
Is it known how long species take to become endemic? I know from examples such as Canada which have no endemics following the end of glaciation that the process must take at least 10 thousand years, but this merely demonstrates endemism must take a longer time. Has any technique been developed that provides some measure of the time needed for species to become endemic?

I am especially interested in the rate of endemism on a small and extremely isolated island such as St Helena.


texts: Questions regarding serial passage of virus through animals arising from the paper The proximal origin of SARS-CoV-2

texts:
In this answer on bioinformatics.stackexchange.com to the question inquiring about the validity of the paper Kristian G. Andersen et al, The proximal origin of SARS-CoV-2, the author asserts the following two points, which I do not understand.

Serial passage of a virus through either animals will always attenuate the virulence, say the affinity to the ACE2 receptor, of the virus. My question: Could people artificially select for thus increase the virulence of the virus?
We can always tell whether a virus is artificially serially passed because we know the mutational patterns of other serially passed viruses. My question: How does this distinguish artificial from natural passage?


texts:
According to this video (sorry for the poor reference but it represents my level of understanding in physiology), muscle grow as a consequence of repairing micro-lesions.

How are these micro-lesions sensed in order to activate protein synthesis? What are the key molecules that trigger myosin synthesis and muscle growth?


texts: What is this insect in Southern California?

texts: I saw this insect flying around in Southern California, USA during the summer. It is about 1.25 cm in length. When it flies, it opens up its wings like a ladybug's.  What is this?


texts: Can plants produce oxygen at night (without light)?

texts:
I accidentally clicked on a "Top n X's that Y" result in google and found Top 9 Plants that gives (sic) off Oxygen at night as well (best for indoors).
In this helpful answer I've found a nice, concise description that I'm just going to reproduce here:

Photosynthesis consists of two general steps, one that requires light and one that does not. The first step occurs in the thylakoid membrane, and splits water into oxygen, hydrogen ions, and energy. The second step is the carbon fixation step, which occurs in the chloroplasts and uses energy to convert the carbon dioxide into carbohydrates.
Step 1: $\ce{2 H2O + light → 2 H+ + O2 + energy}$
Step 2: $\ce{3 CO2 + 6 H+ + energy → C3H6O3-P + 3 H2O}$

In general, the oxygen released from plants comes from water splitting which is driven (in a multi-step process) by photons. From what I remember, the oxygen molecules ($\ce{O2}$) are usually produced and released to the air within seconds, and certainly within minutes after all of the necessary photons for it have been absorbed.
So I am asking; are there plants that really make meaningful, or even just measurable amounts of oxygen without light?
(Or is the idea here that you leave your lights on at night and so actually any plant can make oxygen at night?)


texts: ATP yield of fermentation: study to cite?

texts:
Everywhere I find the ATP yields of respiratory and fermentative metabolism of glycolysis. While that of oxidative phosphorilation I could find in Stryer to cite one study where this was addressed (Hinkle 1991 observed 30 ATP/glucose) I cannot find a study where the 2 ATP/glucose was observed and the textbooks I've searched do not provide a citation.

Can anyone please provide a link or citation to a paper where the ATP yield of fermentation (regardless of process) was quantified/estimated?

Thanks


texts: How can I normalize mRNA samples for sequencing?

texts:
Is there an easy, inexpensive, not too labor intensive way to normalise mRNA samples so that even though one loses information of gene expression levels, each of the transcripts in the transcriptome is equally represented in the sample for sequencing? This is to say, one has a uniform distribution of transcripts, so that the lowly-expressed transcripts still have a good chance of being sequenced.

I have seen a few papers mentioning protocols for mRNA normalization, but I can't tell if any of them are practical in real life wet lab situations.


texts: "synapses grow closer together in order to decrease the distance", is it true?

texts:
Is there a source?

That synapses get physically get close as their interaction increases.

I have also read that where neurons crosses each other they create new neuron, is that true?


texts: How does LDL leave the circulatory system and enter the interstitial fluid to deliver cholesterol to cells?

texts:
I have read that small molecules like oxygen and carbon dioxide diffuse through the capillaries, but larger structures can't fit through.

This answer indicates that some proteins go through via transcytosis.

The wikipedia article on capillaries shows that there are 3 types of capillaries, and it looks like LDL could fit through fenestrated or sinusoid, but sinusoid seem to only be found in certain organs, and if it did go through the holes in fenestrated capillaries, how would the LDL get to cells that are nearby only continuous capillaries? Would fenestrated capillaries be regularly dispersed so one is always nearby, or would the LDL just diffuse through the interstitial fluid originating wherever the fenestrations are?


texts: Humans genetic/phylogenetic "next relative" in central Europe?

texts: What species in central Europe in the phylogenetic tree shows the closest difference in time to the most recent common ancestor with Homo sapiens?


texts: Why does the membrane of a neuron not stay at its depolarized state?

texts:
When an action potential is transmitted along the axon, the membrane reaches its depolarized state by opening Na+ channels. Both K+ (potassium) and Na+ (sodium) are now on both sides with close to equal concentration-ratios. It is the next step that confuses me: the K+ rushing out of the cell, thus repolarizing the membrane.

Wouldn't the two substances balance themselves out according to the Electric-/Substance-Concentration-Gradient once the Na+/K+ channels are open? I don't understand where that energy comes from, the energy that not only mediates polarization, but also the subsequent re-polarization.


texts: Why do mutations not take place in mRNA of higher eukaryotes?

texts: Is it because it is too short-lived to be mutated? Both DNA and RNA are nucleic acids so how is mRNA protected? RNA viruses undergo mutations to evolve so I guess it is not immune to mutations


texts: What do Illumina HiSeq/MiSeq paired end reads look like?

texts:
My understanding is that paired end reads from the Illumina HiSeq/MiSeq platforms looks something like this:

R1:
    AAAAAACCCCCC
R2:
    GGGGGGTTTTTT

Where the reads found in R2 are the reverse complement of those found in R1. This does not appear to be the case however, for my sequencing data. If it helps I have a read pair from one of my MiSeq runs below.

R1:
@M01814:86:000000000-A6MU9:1:1101:15397:1339 1:N:0:2
TACTCGCACCTATCCGGCACAGCAACACCATCTGGGGCTGAATCGCAATAGCATCTCTCACTTCCTCCATATCAGATTGCTCAAGGCAAGCACTACGCTGCAGTGCCCTCCACTCCCAATTCCCTGATGCTGGTCGTAACTTGCCACACCA
+
>>AA?BBBBBFFGGG2EEEGFBGHHHGA2FGHBGHF2EE?GHGHHFFEEHDGHEFGF5FEEFBGHGBCB5FHHH5F553@434FF31G11??233B1/1/?333B?3FB?/B24B2/2B2?44?3?23333B223<>@0CB22@2@F0/?/

R2:
@M01814:86:000000000-A6MU9:1:1101:15397:1339 2:N:0:2
TAAGGGGCCTAGAACAGGCACCATACATTCAATTGGCTGTGGCAAGTAACAACCAGCATCAGGGAATGTGGAGTGGAGGGCACTGCAGCGAATTGCTTGCCTTGAACAATCTTATATGGGGGAAGTAGACGAACCAATGTGGAGTCAGCCC
+
>AA>>>ADDAFFGGGGG4FGGGFHFHFHHHFHHHB3B32EFBGGE25FGHHHHACEGG533BAGFFF355331BG1@1>EF1E23F333/>//134B43?F34B3334B334444?443B?/<C/23333////<0/<11111/?01?G0?

For reference, this is the reverse complement of R2:

GGGCTGACTCCACATTGGTTCGTCTACTTCCCCCATATAAGATTGTTCAAGGCAAGCAATTCGCTGCAGTGCCCTCCACTCCACATTCCCTGATGCTGGTTGTTACTTGCCACAGCCAATTGAATGTATGGTGCCTGTTCTAGGCCCCTTA

This is the alignment (with BLAST; alignment shown only for the HSP):

                                                           60                                                                                148
                                                           |                                                                                |
TACTCGCACCTATCCGGCACAGCAACACCATCTGGGGCTGAATCGCAATAGCATCTCTCACTTCCTCCATATCAGATTGCTCAAGGCAAGCACTACGCTGCAGTGCCCTCCACTCCCAATTCCCTGATGCTGGTCGTAACTTGCCACACCA
                                                           |||||| |||||| |||||| |||||||||||| | |||||||||||||||||||||  |||||||||||||||| || ||||||||||
                                  GGGCTGACTCCACATTGGTTCGTCTACTTCCCCCATATAAGATTGTTCAAGGCAAGCAATTCGCTGCAGTGCCCTCCACTCCACATTCCCTGATGCTGGTTGTTACTTGCCACAGCCAATTGAATGTATGGTGCCTGTTCTAGGCCCCTTA
                                                           |                                                                                |
                                                           126                                                                                38


texts: What is the difference between average sperm epimutations and intersection sperm epimutations, in the context of the attached article?

texts:
The paper of interest is Manikkam et al. (2014).

In research for a school Year 10 Science project, I came upon this article and the following two graphics. I don’t quite understand the difference between the two graphics in the context of the article: what is the difference between average and insertion epimutations? Also, what do the Mb’s along the x-axis mean? Is it in a reference to genetic information size, like megabytes? And how does it refer to the loci of the epigenetic changes? I want to be able to interpret and explain this graph, so could someone provide an analysis and explanation of these graphics.


texts: Why is there sperm mitochondrial suicide?

texts:
The mitochondria in the sperm are digested upon entry into the egg, making mDNA inheritance exclusively female. What is the advantage of this? Wouldn't some male mDNA be beneficial because of the advantages of (at least a little) sexual reproduction?

Reference:
"Postfertilization autophagy of sperm organelles prevents paternal mitochondrial DNA transmission" (behind paywall, here's a ScienceDaily article discussing the results).

Edit:

Both answers seem valid but it is hard to quantify the relative costs.


texts: How do cis-regulatory elements and trans-regulatory elements behave differently?

texts:
Suppose you are working with an operon in a diploid organism.

I'm looking for either a biochemical or genetic explanation.

What I'm having trouble with mainly is understanding how something would only be able to regulate a gene on one chromosome but not the other. I was thinking cis would be favored because the gene is close by, but everything is just floating around randomly in the cell so it should favor cis either way and level out if you waited long enough.


texts: SPINAL CORD: Do the axons from white matter synapse with the cell bodies in grey matter?

texts:
After wading through a sea of information, I understand the main differences between the white matter and grey matter of the spinal cord.

I know that white matter contains myelinated axons in the ascending and descending nerve tracts from the brain to the spinal cord. I know that grey matter contains somata which contribute to sensory and motor functions from and to the peripheral nerve fibers.

With the differences in mind, I am confused about the relationship between the two.

The main question being: What signaling, if any, takes place between the myelinated axons of white matter and the somata of grey matter? More pointedly, do the myelinated axons from the nerve tracts in white matter ever synapse with dendrites from somata in grey matter?

My guess is yes, that this is a key aspect in how the brain and the spinal cord communicate. But I haven’t yet found any definitive source that addresses this question directly.


texts: Why would stablising selection ever happen?

texts: If the aim of evolution is to allow an organism to better compete against rivals, why would stabilizing selection ever happen? If you're not selecting the most highly adapted competitors at either end of the spectrum then how would a species progress?


texts: If blood loss necessitates immediate cell division to replace lost cells, does the increase in cell division correlate to shortening of telomeres? Does it further cause the Hayflick Limit to be reached sooner? Does blood loss accelerate apoptosis?


texts:
Consider a population of two altruist with coefficient of relatedness
$r$. The average inclusive fitness of this population will be
$w_{0} + br -c$. Like in this example, assignment of inclusive fitness
I've seen in books and articles follow the rule that you should
not count changes in inclusive fitness that result from the
action of your neighbor. For instance, in our example, the calculation
of average inclusive fitness include the increase in indirect fitness
to the actor (i.e., $br$), the costs (i.e., $c$), but do not include
the effects of the altruist behavior of the neighbor (i.e., $b$). That
is, the average inclusive fitness is not $(w_{0} + br -c) + b$.

My question is: why is it that, in inclusive fitness models, you do
not count changes in inclusive fitness that result from the
action of your neighbor? Wouldn't it make the model more accurate to
take into account the effects of your neighbor's behavior? In other
words, in our example, why isn't $(w_{0} + br -c) + b$ a better value
for the average inclusive fitness than simply $(w_{0} + br -c)$?

Note:

As @Corvus pointed out, if we include changes in inclusive fitness that result from the action of your neighbor, we will double-count benefits. Consider the example mentioned above once again of a population of two altruists with a coefficient of relatedness $r$:

If we write $w_1 = w_2= (w_{0} + br -c) + b$, the help of 1 on 2 appears as $rb$ in $w_1$ and as $b$ in $w_2$. If we write the fitness in the right way, $w_1 = w_2= (w_{0} + br -c)$, the help of 1 on 2 is only counted once (i.e., $br$ in $w_1$). However, I cannot help but ask "Why not count the help of 1 on 2 twice?" We are counting the help of 1 on 2 twice, but each time we are assigning it to different individuals, 1 and 2.


texts: I found this picture online claiming it was a grass cell. Clearly it is a cross section image but I was hoping you could tell me if this is actually grass, or something else if anything.


texts: Why don't anti-viral drugs like "Acyclovir" work against coronaviruses?

texts:
I've always used Acyclovir to treat cold sores, why doesn't it work on other viruses?

How do coronaviruses differ from herpesviruses?


texts: What percentage of human body's cells are contained in blood?

texts: What percentage of human body's cells are contained in blood vs. the rest of the body?


texts: Consider a plant like Aloe Vera that grows up in a toxic environment where the concentration of pesticides, and materials like lead, mercury, cadmium, arsenic etc is very high(e.g. Marshland dumping yard ). Would that mean that the extract from these plants would contain all these toxic elements.


texts: This is a house plant I have that I love but I don’t know what it’s called. I’d love to research it and even buy more but it’s name is a mystery. Picture taken in Ontario, Canada.


texts: Which processes are included in the process called cells eating themselves?

texts:
I am reading about atrophy and I am thinking to which processes the phrase cells eating themselves refer to.

  Cells need something to survive these difficult times. To decrease
  protein synthesis to survive. If insufficient, cells start
  to eat themselves. Then, ubiquitine-proteosome pathway and autophagy
  pathway.

I am not sure if it is only apoptosis.
It can refer here to longer cascade.
I think it can at least refer to autophagy where one cell degrades its components.

Which processes does the phrase cells eating themselves include?


texts: Suppose the mimicry of a voice is very accurate. Will it  have similar spectogram as the original voice?


texts: Autotrophic and heterotrophic organisms in anaerobic condition

texts: Can both heterotrophic and autotrophic organism survive in anaerobic conditions? If an autotrophic organism does not produce carbon dioxide but requires oxygen, it should not be present in anaerobic conditions, instead the heterotrophic organism can develop. Is this correct?


texts: Receptors for red and far-red light in plants: Shade avoidance

texts:
Franklin (2009) describes how plants use the ratio of the red wavelength (660-670nm) over the far-red wavelength (725-735nm) (R:FR) in order to avoid shading.

My question is: which receptor is stimulated by the red and which receptor is stimulated by the far-red?

In his paragraph on Phytochromes (3rd page, right column), K. Franklin seems to say that PhyB is responsible for measuring this ratio but I am not sure.


texts: What are the universal laws of Nature concerning animals' behaviour?

texts:
I'm looking for very old (centuries) treaty or recent (20 & 21th century) research that state what some of the laws of Nature are, particularly concerning wild animals' behaviour. Such as; every animal does this, no animal does that, etc.

Laws that could be then used to simulate or reproduce natural behaviours or check against unnatural ones.

Added: I'm looking for more simple laws, such as "no (wild) animal eats cooked food". Assuming it's true then humans broke that law of Nature. It's the relation to Nature that interests me. I used the word behaviour in the large sense, as in, what are the laws that animals seem to follow (dos  and don'ts) in the world. I suppose that by looking at what the human is the only one to do we can find lots of those laws.


texts: The smaller the cell the greater its surface-to-volume ratio?

texts:
I read in a book that the smaller the cell the greater its surface-to-volume ratio (the surface area of a cell compared to its volume).

And larger cells have limited surface area compared to its volume.

How is this possible? I don't understand.


texts: Strange Cordeyceps-looking Mushroom in Australia

texts:
In the past few weeks, after the rain started up I noticed these mushrooms around my local area. I'd never seen them previously out of the 20 years I've lived here (a town in Queensland, Australia).

Sometimes they have a net-like section, and they sometimes have 10+ flies around a mushroom cluster.

What are these mushrooms? Are they common in Australia?


texts: Do whales ever just hang out on the surface breathing?

texts: You only ever hear of whales surfacing for a brief second to exhale/inhale before they dive back down. But do they ever just stay at surface level, laying there with their blow hole up in the air, continuously breathing for a while? One would think that might be a relaxing experience for them?


texts: Is there a genetic reason explaining the difference of the height of male and female?

texts:
The male and female height difference seems to be around 1.08 if all cultures are counted from these stats: https://en.wikipedia.org/wiki/Human_height

Can this ratio, 27/25, be explained by genetics and is there any research to explain how genes affect the growth of a man and woman? I assume there are a lot of factors that affect height and it might be very difficult to say if environmental and selective reasons or genetics are behind this factor.

ADDED:

GIANT study reveals a giant number of genes linked to height (October 6th, 2014)

  “Height is almost completely determined by genetics, but our earlier studies were only able to explain about 10 percent of this genetic influence.”

https://www.broadinstitute.org/news/6119


texts: How are the vitreous humour and aqueous humour of the eye, connected?

texts:
My question is regarding the biological nature of the separation between the vitreous humour and aqueous humour of the human (or mammal) eye. What connects the two in terms of the passive transport of proteins between the two? Is there a single membrane?

If so what is the name of this membrane and is it the only thing separating the aqueous from the vitreous? What is the anatomical difference between the aqueous and the vitreous?

Apologies, I am far from a biologist.

Specifically what sort of transport is arrow 9 in the figure below representing? And is backward transport (from the aqueous to the vitreous) possible?

Any links to papers detailing this mechanism would be highly appreciated, I can only find references to experimental readings of concentrations, but nothing about the transport process itself.


texts: Looking for dataset of proteotypic and non-proteotypic peptide

texts:
I doing experimentation for peptide prediction using machine learning. I need some data for testing. My background is Computer Science.

Any advice how to find proteotypic and non-proteotypic peptides. I already got one dataset "Y.pestis". However, I'm looking for another dataset (for verification). For example, S.typhimurium or S.oneidensis, but any other peptides will be OK.

I tried PRIDE archive, but I couldn't figure out how to get two datasets; one for proteotypic and another for non-proteotypic

Any advice is appreciated!

Thanks!


texts:
If I'm not mistaken the only time homologous pairs of chromosomes need to find each other is during gamete formation in preparation for crossover recombination.
How do they find each other?


texts: Average dimensions of the human back (anthropometry)

texts:
I am wondering if anyone can point me to (a scientific source that provides) the estimates of the dimensions (length x width) of the human back?

I am specifically interested in the dimensions (length * width, or surface) of the lower back of the average adult, and in specific the region between the 7th thoracic and 4th lumbar vertebra - i.e., the region between T7 - L4 in the image below:

Ideally a distinction is made between males and females and perhaps kids as well. The area of research dealing with this matter is anthropometry.

Please mention the source to any information provided. I have access to some not-scientifically based sources (clothing companies for example). Although additional such sources are welcomed, scientifically-based answers are preferred.


texts: Why Egg shell is not called a cell wall?

texts:
Egg is a single cell and has a outer hard covering outside inside which there is a cell membrane. Then why isn't the egg shell a cell wall?
Is it because no exchange of materials take place through it?


texts: Na+ / K+ ATPase: How does it restore resting membrane potential?

texts: Could not find any sources talking about this (in a clear manner). If the Na+ / K+ ATPase pumps 3 Na+ out for every 2 K+ it pumps in, thus making the cell more negative, why is the Na+ / K+ ATPase used to restore resting membrane potential following hyperpolarization? Wouldn't that must make the cell more negative, which is the opposite of what we want?


texts: What are good databases for RNA-binding motifs?

texts:
I am asking this question because it is hard to prove non-existence (of better data):
I am searching for a good RNA-binding motif database that is as up-dated as possible and covers motifs for as many proteins (RBPs) as possible.
I am mostly interested in motifs that are derived from RNAcompete (i.e. data from this paper) and SELEX, CLIP motifs would also be nice.
After some research I found that ATtRACT looks like the best source. According to my analysis, it covers 77 proteins from RNAcompete- data and 27 proteins from SELEX-data.
Background:
I am not interested in a single protein, I need as many different proteins as possible.
I am asking this question to make sure I don't have to repeat my analysis, if reviewers say my sources are too old.


texts: How does the blood of the veins in the legs get to the heart?

texts: Does it have something to do with the valves? Thanks in advance!


texts: Can someone tell me if the example I wrote below is one possible answer?

texts:
Here is an imaginary mRNA sequence:
5’- THE BIG BOY SAW THE CAT EAT THE HOT DOG – 3’
Each 3 letter-word is equivalent to the codons in real mRNA.

What would the imaginary mRNA sequence look like if there was a deletion of two bases near the 5’ end of the mRNA? Write out the example above with the two-base deletion and 3-letter “codons” to explain your answer. Label the ends of your imaginary RNA and clearly show the mutation.

I used this: 5’- TBI GBO YSA WTH ECA TEA TTH EHO TDO G-3’. However I am not sure if writing in this form answers the question, can someone tell me whether this is correct and if not how should I change it?


texts: Bug identification: rectangular green and copper creature

texts:
I've found a very strange-looking creature on the street of a local park (Russia, Urals). It was 2-3 cm long,  almost rectangular, with green and copper colors, running somewhere with low speed. I've never seen anything like it before. Here's a picture (sorry for the quality):

Does anybody know what this is?


texts: Fruiting of trees — environmental stimuli and biochemical cascades

texts:
My question concerns fruiting of trees in general.  However, I live in a
tropical country (Philippines) where mango trees are ubiquitous, so I'll use it
in stating my question.

The question is about >>seasonal<< trees — trees that produce flowers and fruit
in season, i.e., they produce flowers and fruits at specific months of the year
and never in the other months.

The main question is:

 What is/are the environmental stimulus(es) which trigger the flowering of
 seasonal trees.

During summers here, one can't help but notice the fruiting of mango trees
everywhere.  On closer observation, the process really starts late in the year
when the trees start producing flowers.  It takes a few months for the fruits to
develop, grow, and ripen.  The fruits are ready for picking during the second
quarter of the following year.

Has anybody figured out for certain the environmental stimuli that trigger the
production of flowers in seasonal trees?

I have several guesses:

 (1) The annual fluctuation in daily average temperatures;  if this is the
 case, then the trees' biochemical makeup must have an amazing sensitivity
 to temperature as stimulus because annual variations in daily average
 temperature here does not exceed about 10°C (20°F).

 (2) The annual fluctuations of the level of the water table under the
 ground.  During the months (november or december) when the flowers start to
 appear in mango trees, the rainy season is nearing its end, so the water
 table must be near highest during these months.  But this is complicated by
 the el niño / la niña cycles, which alter the length of the rainy season
 and the amount of precipitation received by the ground, which must have an
 effect on the height of the water tables.  Nevertheless, the flowering and
 fruiting seasons seem to have no noticeable change:  they still occur at
 the same months of the year!

 (3) The annual variations in the solar irradiation received by the trees.
 If this is the case, then, like in guess # 1, then the trees' biochemical
 makeup must have an amazing sensitivity to irradiation as stimulus because
 the annual variation in the solar irradiation is only about 25% (at 14°N
 latitude, with the earth's tilt at 23.5°).

At any rate, I would also like to get a glimpse of the biochemical cascades involved, the
hormones, signalling pathways, proteins, etc.


texts: I consistently read in non-scientific resources that I have to put my rosemary to low temperature (about 10°C) in winter (unless I don't want it to freeze). I googled, but I fail to find a scientific resource about why room temperature is not good for it. Do you have any explanation (with scientific references ofc.)?


texts: What is this species of angiosperm? It's got succulent stems and leaves that do not produce latex. Photographed in spring.


texts: Do person with strong immune system have less chance of surviving SARS-COV-2 attack?

texts:
In most of the cases dealing with SARS-COV-2 disease, the major mortality cause is due to cytokine storm in response to Corona-virus that also attack healthy organs causing multiple organ failure.

  leading to inflammation and fluid buildup in the lungs.(7) Certain kinds of cytokines trigger cell death. When you have many cells doing this at the same time, a lot of tissue can die. In COVID-19, that tissue is mostly in the lung.(5)

    Among the many mysteries of Covid-19 is why relatively healthy young people suddenly become critically ill — or die.Many otherwise robust patients were experiencing cytokine storms. One key sign of that was the body’s levels of ferritin, a protein in the body that binds to iron. This massive over-reaction, known as a cytokine storm, is believed to be a major reason that a growing number of exceedingly fit people find themselves fighting for their lives.(7)

Assuming healthy people having a strong immune system have greater cytokine storm against SARS-COV-2, isn't coronavirus naturally selecting people with "weaker" immune response?

However an interesting case has been observed within Haemodialytic patient(not-healthy):

  HD patients with COVID-19 even displayed more remarkable reduction of serum inflammatory cytokines than other COVID-19 patients. Epidemiological, clinical, and immunological features of a cluster of COVID-19 contracted hemodialysis patients

References:

https://scroll.in/article/962574/what-is-a-cytokine-storm-and-why-is-its-prevention-key-to-treating-covid-19
https://www.sciencedaily.com/releases/2020/05/200521165706.htm
https://www.sciencedirect.com/science/article/pii/S1359610120300927
The cytokine storm in COVID-19: An overview of the involvement of the chemokine/chemokine-receptor system
Cytokine Storms May Be Fueling Some COVID Deaths
Why Some COVID-19 Patients Crash: The Body's Immune System Might Be To Blame
He ran marathons and was fit. So why did Covid-19 almost kill him?


texts: When an animal eats something, it obtains matter and energy right? But, what are the 3 possible fates of the matter and 3 possible fates energy. I don't understand what they are even asking. What would be the 3 possible fates of each.


texts: Identify this insect (looks like part of a tree)?

texts:
I found this insect and thought it was part of a tree at first, then it moved and so I knew it was an insect. I've never seen it before though so I am posting here hoping someone knows what it is.

The location is North East US, during the day, in a tennis court surrounded by trees. The insect was clinging to the cover seen above (which covers the tennis court fence).

Any idea what this insect is called?


texts:
I have been trying to learn some basic DNA sequencing techniques and have been using BLAST as a reference. I thought that I was starting to get it, but then I cam across this:

It looks like it's saying that the match starts at 10835 and ends at a smaller index (10714).
I tried clicking the link to view the full sequence, and I couldn't find the highlighted portion anywhere (not at 10835 or at 10776).

My question is: Where (in NR_046235.1) can I find the highlighted sequence?
And what does it mean to say that the Sbjct starts at 10835 and ends at a lower index?

I can post my query if necessary.
Thanks.


texts: Which extinction event killed the highest proportion of organisms?

texts:
The P-T extinction (a.k.a. the Great Dying) tends to be considered the worst - for example, Wikipedia states:

  It is the Earth's most severe known extinction event, with up to 96% of all marine species and 70% of terrestrial vertebrate species becoming extinct. It is the only known mass extinction of insects. Some 57% of all families and 83% of all genera became extinct. Because so much biodiversity was lost, the recovery of life on Earth took significantly longer than after any other extinction event, possibly up to 10 million years.

Presumably the "96% of all marine species" (which references two books, neither of which I have) is in terms of multicellular marine species or some similar subcategory that's easier to observe in the fossil record (I could be wrong).

My question is this: Would the Great Oxygenation Event not have killed a higher proportion of organisms (taking into account all organisms)?

I know that we don't have any records that can tell us how many died in the GOE and hence this question is necessarily speculative, but surely nearly all organisms pre-GOE would have been obligate anaerobes (and therefore found oxygen to be toxic)?

What I'm unsure about is how single-celled organisms fared in more recent (Phanerozoic) extinctions, as most discussion seems to be in terms of opisthokonts (i.e. animals + fungi) and archaeplastidans (i.e. plants + algae).


texts: Where is ethanol detoxified? peroxisomes or smooth ER? Or both?

texts:
I am reading the textbook Biology (Campbell et al, 2005), and I am confused.

In Chapter 6.4, on page 104, it says that "In the smooth ER,  other enzymes help detoxify drugs <...>", and alcohol is mentioned later.

In Chapter 6.5, on page 111, it says "Peroxisomes in the liver detoxify alcohol <...>"

Googling the question also brought me mixed results.

As I understand it, alcohol detoxification happens in two stages, first oxidising ethanol to the also toxic ethanal, and then oxidising ethanal to acetic acid.

Do these processes happen in different organelles? Is that the reason that both of them are mentioned? Or do they both detoxify alcohol completely, but do it in different circumstances?


texts: I've often pondered the fact that we only pass on the DNA of our youth. Any mutations to our DNA that occur after having children, that may help us to respond to getting older, are not inherited. Do older parents pass on a different, perhaps more learned "quality" of DNA? Anyone know the answer to this?


texts: Why is gene finding in Eukaryotes such a difficult task?

texts: Why is gene prediction in eukaryotes such a difficult task? Every gene starts with a codon and the non coding regions in between a coding region also has some specific base sequence(which are used by enzymes to recognize non coding regions during splicing). A computer program could simply search for start codon and then for stop codon. In between it could also search for those non coding regions since they start with specific base sequences. Why does gene finding need such complex things such as HMM?


texts: Does the fact cordyceps mostly affect insects have something to do with chitin being polysaccharide?

texts:
This is just a conjecture of mine based on those observations:

Fungus seems to be very good at attacking tough chains of sugars like cellulose and starch.
insects are covered by Chitin, a polysaccharide.
cordyceps only attacks arthropods and in rare instances other fungus. Both arthropods and fungus have chitin in their body.


texts: İrreversible dopamine antagonist vs. Dopamine agonist

texts: Can a dopamine agonist reverse the effects of an irreversible dopamine antagonist?


texts: Is there such a thing as an autotroph that doesn't use photosynthesis?

texts: I've heard of photoautotrophs, which are just autotrophs that use photosynthesis. What I'm wondering is if there's any other way for an organism to make its own food that doesn't involve it using photosynthesis?


texts: What happens to the umblical cord inside the mother?

texts:
After giving birth to a child, the umblical cord is cut (and stored if they want). The end connected to the child's navel will fell off eventually but what happens to the end inside the mother?

Will it be removed right after birth by doctors or what happens?


texts: At what point is a picked flower considered dead?

texts:
Let a flower be picked from the ground such that its stem is cut and the flower is separated from the root system (as in figure).

Questions:
1a. At what point is it considered dead?

Does the flower and attached bit of stem continue to live for some time before dying?

Is this like asking when an limb that has been chopped off an animal dies - should we considered not the flower, but the root system?

1b. How does one define death for an organism without a nervous system?


texts: How does aminoacyl-tRNA synthetase recognize different tRNAs?

texts:
There are about 20 aminoacyl-tRNA synthetases, one for each amino acid. Each aminoacyl-tRNA synthetase has a binding site that recognizes a specific amino acid, and other binding areas that recognize a particular tRNA through unique identity sites at the acceptor stem and/or anticodon loop of the tRNA.

When there are different tRNAs for the same amino acid, the aminoacyl-tRNA synthetase that recognizes a specific amino acid must also recognize the set of tRNAs that can be charged with that amino acid. Given that all tRNAs have different anticodons, how does the enzyme achieve the aforementioned task?


texts: Can you find the mass of drug X remaining in the body after an oral dose with only bioavailability and half-life?

texts:
I'm reviewing this question and think you can't find the answer with the information given.

A patient receives 1g of drug X as a single oral dose. Drug X has a
half-life of 12 hours and an oral bioavailability of 40%. What mass
(in milligrams) of drug X will still be present in the body 24 hours
after a 1g dose?

I think the fact that it is an oral dose means the question is more complicated, involving absorption and distribution of the drug, meaning more factors are needed which are provided in the question.
Is it as easy as:
$1000mg \times 0.4 \times 0.5 \times 0.5 = 100mg$
Or there is is more it than that as I suspect? Many thanks!


texts: What is the relationship between the e value reported by HMMER and BLAST? (Are they equivalent?)

texts: Both HMMER and BLAST report an e value for alignments.  Is it calculated in the same way and - assuming that default settings are used - can they be compared directly (are the equivalent)?  If not equivalent, what settings can be changed to make them equivalent?


texts: Can two hammerhead ribozymes simultaneously cleave each other?

texts: I am working on a project in which an XOR gate is being built by having two hammerhead ribozymes simultaneously cleave each other when both are expressed, but have these ribozymes cleave a target transcript when expressed alone. Has it ever been shown in the literature that a hammerhead ribozyme was able to cleave the flanking arms of another ribozyme?


texts: Looking for hard cell segmentation problem

texts: I am a physicist working on a new image segmentation technique, and I would like to test it by segmenting some images with low-refined cells on a noisy background... Do you know where I could find such images? Thanks!


texts: Sugars which are Carbohydrates and vice-versa?

texts:
Is it right that are all sugars are carbohydrates but not all carbohydrates are sugars?

If so, which carbohydrates are sugars and which aren't and why all sugars are carbohydrates?

If I had to answer I'd say there are carbohydrates of three kinds: sugars, starch, fiber and from which we can deduce that "not all carbohydrates are sugars".


texts:
I'm working on a piece of software that computes melting temperatures for nucleic acid duplexes, and I'm about to add support for 5-methylcytosine as a nucleotide base.  At the moment, the bases accepted by the program are adenine, cytosine, guanine, thymine and uracil, with their standard letters A,C,G,T,U.  Is there a standard letter for 5-methylcytosine?  The only example I've found is this paper, which uses an italic C for 5mc, but I want a distinct letter.  The three candidates I've thought of are:

5 - for '5-methylcytosine'
M - for 'methyl'
B - Since methylation of U gives you T, which is one place earlier in the alphabet, so methylation of C gives B.


texts: Survival of E. coli on agar plate at -20 degree C without glycerol stock

texts: If I kept E. coli transformed with plasmid at -20˚C without making glycerol stock, will it survive? Actually I have kept it this way for 18 hours. What will happen with it? Will it grow in fresh media?


texts:
I 'm using STRINGdb package from biconductor to manipulate String database of ppi
I'm newbie and I don't find the documentation of the package useful for me .
I wanna extract the associated network of cancer fo example ,
I tried to used this function s <- string_db$get_term_proteins(terms_id,string_ids =NULL , enableIEA =TRUE )
and I don't know  what that terms_id attribute stand for .

second , is there a simpler way to get the full network using R interface  given in the url as an example

https://string-db.org/cgi/network.pl?taskId=2hQuabKoXe02


texts: What is the difference between Totipotent cells and Pluripotent cells?

texts:
I read the Wikipedia article about Cell Potency
(Article on Cell Potency)

  Totipotency is the ability of a single cell to divide and produce all of the differentiated cells in an organism.

while pluripotency means

  a stem cell that has the potential to differentiate into any of the three germ layers: endoderm, mesoderm, or ectoderm.

I don't quite understand the difference, then, between a totipotent and a pluripotent cell.


texts: In C. elegans, why does knock-down of cco-1 in some tissues increase lifespan, and knock-down of cco-1 in other tissues decrease lifespan?

texts:
Full question: In C. elegans, why does knock-down of cco-1 via RNA interference in specific tissues like body wall muscle decreases life span, whereas knock-down in the nervous system and intestine increases life-span?

http://www.wormbase.org/db/gene/gene?name=WBGene00000371;class=Gene

Also from paper 'The Cell-Non-Autonomous Nature of Electron Transport Chain-Mediated Longevity'

Supposedly, it's through hormesis. But why is there a differential effect from tissue to tissue?


texts: Amount of carbon captured in photosynthesis by a plant

texts: Is it more proportional to the mass or the volume of the plant? I thought it might be helpful to think on the cellular level here. Even a reference to an external explanation would be useful.


texts: Why are minor introns bounded by nucleotides AT-AC, where T is not normally in RNA?

texts: Major intron boundary nucleotides are GU-AG. Minor intron boundary nucleotides are AT-AC. Why does the former use RNA Uracil and the latter use DNA thymine? Since introns are in the primary RNA transcript, shouldn't both be RNA and use U rather than T?


texts: How do plants 'tell time' for circadian rhythms based on a ~24 cycle?

texts:
I've read that many plants have some sort of circadian rhythm where they perform a certain action on a cycle of about 24 hours, like the mimosa plant opening and closing its leaves. Obviously, this is done in order to synchronize with the sun, but many such plants continue to perform these actions even when left in constant darkness or light. It follows that this is the result of some sort of biochemical pathway, but whatever internal 'clock' is used is also independent of temperature.
How can these plants perform certain actions every 24 hours at different temperatures when the chemical reactions most biochemical pathways use are temperature dependent?
It would seem like the length of the cycle should vary widely according to the temperature as it affected the reactions involved, but instead it stays at a very constant length very close to 24 hours. How can this be?
(This is in my textbook, but unfortunately the book doesn't cite any studies. I would greatly appreciate it if anyone could help me find one to link to so I can improve the  question. :)


texts: How do you accurately measure anguiliform (eel) locomotion?

texts:
In one of my courses, we were discussing a paper by Muller and van Leeuwen (2006) which made a lot of comparisons the differences between carangiform (mullet) and anguilliform (eel) locomotion. While reading the text, one of the passages stood out to me:

When comparing the estimates of vortex ring height with those of ring width, mullet and mackerel shed approximately round vortex rings, whereas eel vortex ring are almost twice as wide as they are tall. Such distorted rings are less likely to form and once formed, they are more likely to break up, all of which results in a different vortex pattern in the wake.
The time-resolved flow fields of eels indeed support the notion that the vortices in its wake break up: two independent studies, visualizing horizontal cross-sections through the eel’s wake, observed that individual vortex cores elongate and split into two (Muller et al. 2001; Tytell 2004a). We can therefore conclude that the shape of the propeller, and hence implicitly the propulsion mechanism, might affect wake shape. This observation also implies that a propeller shape that promotes the formation of a suboptimal wake is less efficient, and therefore the absence or presence of a wake that is predicted to maximize efficiency is a valuable indicator for the hydrodynamic efficiency of a fish’s swimming design.

So, essentially during carangiform locomotion the body of the fish moves 1/2 wavelength whereas anguiliform swimmers make 1 wavelength. My questions are how can they make such a statement when particle image velocimetry (PIV) does not adequately measure the movements of anguiliform swimmers, let alone their efficiency, when they are essentially swimming through their own vortexes? Are there any studies that address this issue in anguiliforms?


texts: What are some examples of evolving networks in biology?

texts:
I'm a master student working on networks analysis in general. A network is something that has nodes and there are links between the nodes. Nodes and links could have attributes. An evolving network is one that changes overtime (new nodes and links are added..etc). An example of that is Facebook. Nodes are users and links represent the friendship relationship. Users have attributes (gender, age, etc.). A Facebook network as you know is an example of a social network.

The issue is that so many people studied traditional evolving networks like social networks, the web, or transportation networks. Currently I'm looking for novel examples of evolving networks to study them. So I thought there might be some examples in biology that could represent some kind of an evolving network.

So my question: Can you give me examples in biology for evolving networks? I'm aware of metabolic networks, but that is also heavily studied, I need something else.


texts:
In lectures, we have discussed Michaelis Menten enzyme kinetics, but from lectures it was clear that this was not the only type of kinetics.

After looking into this, I have found enzymes that give a sigmoid curve relating initial rate of reaction to substrate concentration.

So so far I have:

Michaelis Menten Kinetics

For which I think the only conditions are that the enzyme reaction follows

and the enzyme does not bind more than one substrate molecule (isn't allosterically binding)

'sigmoidal' kinetics

Where the enzyme is an allosteric enzyme and binding of more substrate to the enzyme increases the enzyme's affinity for the substrate.

Are these the only two main types of enzyme kinetics?


texts:
Reading Okasha's "Evolution and the levels of selection" he talks about "the levels of selection problem." There is a bit of a problem with this opening chapter because, while he talks about why the levels of selection problem is a problem, he doesn't define what the levels of selection problem is.

The opening line from the book..

  "The levels of selection problem is one of the most fundamental in
  evolutionary biology, for it arises directly from the underlying logic
  of Darwinism. The problem can be seen as the upshot of three
  factors..."

I think what he means by the "levels of selection problem" is that selection acts on many levels, and what is adaptive at one level may be maladaptive at another. Therefore we can not define selection as acting at one single level, and studying it as such is likely to lead to incorrect conclusions - studying selection is not a simple process. Can anyone provide a firm definition of what Okasha, and the general community on the matter, mean by the "levels of selection problem"?

(Note: The factors are the abstract nature of the principles of selection, the hierarchical nature of biological organisation, and the process of adaptation via natural selection).


texts: How does DNA still work after recombination?

texts:
If you take two computer programs and randomly swapped pieces from each of them. The result is not going to work. It will just be garbage. If you take two novels and randomly swapped chapters the result will be garbage too.

How is it than DNA (which is infinitely more complicated) can be combined, some from the father and some from the mother and yet it still somehow works?

Can you give a simple example?


texts: One flybase gene number (FBgn), many Affymetrix Id's

texts:
I am trying to convert a set of Affymetrix ID's, like this one 143053_at_3745, to Flybase Gene Numbers (FBgn) like this one FBgn0000015. I have downloaded the Flybase file required to do so (as described here) but I have noticed that most of the FBgn's have more than one associated Affy id.

My question is, how do I know which to assign to my data? From the list of affy-ids that I have, how do I label each one with the appropriate FBgn? I am using data from the Ayroles et al 2009 (DGRP) which has a column of AffyID which look similar to the ones in the Flybase file but shorter (1638273_at). Perhaps I don't grasp why there would be more than one.

Some have one affy id which is repeated across 15 columns in the file, whereas some seem to have several affy id's associated with them.

Some questions this problem raises:

Why does a singular FBgn identifier have more than one associated affy identifier?

Why do some datasets, such as the dataset I have, have shorter versions of the affy identifier?

Where can I find an up to date and appropriate list matching these Affy id's the FBgn identifiers correctly?


texts: How to distinguish those flowers in outskirts: hawkweeds (Hieracium), hawksbeard (Crepis) and hawkbits (Leontodon)?

texts:
How to distinguish those flowers of the forest outskirts: hawkweeds (Hieracium), hawksbeard (Crepis) and hawkbits (Leontodon)?

I am not asking about concrete species it should be extremely hard since they have hundreds forms, but what are observable differences between genus?

I have read wikis articles but still not sure that I could distinct those flowers in the field right way.

http://en.wikipedia.org/wiki/Leontodon
http://en.wikipedia.org/wiki/Hieracium
http://en.wikipedia.org/wiki/Crepis


texts: Why is only one primer used for DNA sequencing instead of two?

texts:
I understand that PCR uses two primers that anneal to the two ssDNA's in order to exponentially amplify a DNA and that Sanger sequencing uses only one primer because a sequence can be determined with only using one primer and one single-strand with ddNTPs. However I've read this:

"Sequencing uses one primer, while PCR utilizes two. If we try to sequence with two primers present, you'll get the two sequences back, superimposed on each other and completely unreadable."

I'm struggling to visualize why using two would be an issue though, how will that make the DNA unreadable?

Thanks in advance!


texts: On the definition of gDCW (gram dry cell weight)

texts:
I need some clarification on the concept of gram dry cell weight.

The unit acronym gDCW stands for gram dry cell weight. My interpretation is that 1 gDCW is equivalent to 1 gram of dry cells, but I am not sure. Is this accurate?

For example, the dry cell weight of mouse cells is roughly 300 pico grams. Therefore, in this case, one gram of dry mouse cells contains $10^{12}/300$ mouse cells (1 picogram $=10^{-12}$ grams). And if one says that there are 0.6 mmol of alanine per gDCW of mouse cells, this means that the total alanine content of $10^{12}/300$ mouse cells is 0.6 mmol. Is this accurate?


texts: What is a good minimal medium for Pseudomonas bacteria? Do I need different media for different Pseudomonas species?


texts: Breeder's equation and equivalent expressions for narrow-sense heritability

texts:
I am trying to model the phenotype of a trait as $X = G + E$, where $G$ and $E$ are the genetic and environmental effects. (I'll ignore the distinction between broad-sense and narrow-sense heritability in this question.) Wikipedia tells me that $$h^2 = \frac{\mathrm{Var}(G)}{\mathrm{Var}(X)}$$ The same page also gives the breeder's equation $R = h^2S$ but also says "Note that heritability in the [breeder's equation] is equal to the ratio [${\mathrm  {Var}}(G)/{\mathrm  {Var}}(X)$] only if the genotype and the environmental noise follow Gaussian distributions." So let $G \sim N(0, \sigma_G^2)$ and $E \sim N(0, \sigma_E^2)$ be distributed according to normal distributions. Then $X \sim N(0, \sigma_G^2 + \sigma_E^2)$ so $$h^2 = \frac{\mathrm{Var}(G)}{\mathrm{Var}(X)} = \frac{\sigma_G^2}{\sigma_G^2 + \sigma_E^2}$$

Now I want to perform a selection, choosing a parent with $X=a$. We can expect the child to have the trait $\mathbb E[G \mid X=a] + E'$ where $E' \sim N(0, \sigma_E^2)$ is some other environmental effect. (I don't want to bother with recombination and multiple parents, so we can just think of it as cloning the parent: given that $X=a$, we expect the parent's genetic part to have been $\mathbb E[G \mid X=a]$.)

To find $\mathbb E[G \mid X=a]$, note that $\mathbb E[X \mid X=a] = a$ and by linearity of expectation, $\mathbb E[X \mid X=a] = \mathbb E[G \mid X=a] + \mathbb E[E \mid X=a]$. To get the terms to cancel, we want to write $E$ as $\alpha E$ where $\alpha E$ has the same distribution as $G$. Since $\alpha E \sim N(0, \alpha^2 \sigma_E^2)$, we want $\alpha^2 \sigma_E^2 = \sigma_G^2$, so $\alpha = \sigma_G/\sigma_E$. Thus we have $$\begin{align}a &= \mathbb E[G \mid X=a] + \frac1\alpha\mathbb E[\alpha E \mid X=a] \\ &= \mathbb E[G \mid X=a] + \frac1\alpha\mathbb E[G \mid X=a] \\ &= \left(1+\frac1\alpha\right)\mathbb E[G \mid X=a]\end{align}$$ Hence $$\mathbb E[G \mid X=a] = \frac{a}{1+\frac1\alpha} = \frac{a}{1+\frac{\sigma_E}{\sigma_G}}$$

Since the parent was selected at $X=a$ and the child has mean $\frac{a}{1+\frac{\sigma_E}{\sigma_G}}$, we have $$h^2=\frac{R}{S} = \frac{1}{1+\frac{\sigma_E}{\sigma_G}} = \frac{\sigma_G}{\sigma_G+\sigma_E}$$

Now my problem is that the two expressions for $h^2$ don't match. They look pretty similar, but one of them has all the terms squared while the other one doesn't. What's going on/where did I go wrong?

ETA: To give a concrete example, suppose 80% of variance in the trait is explained by genes. Then the breeder's equation predicts the child to have $0.8a$. But computing $\mathbb E[G \mid X=a]$ gives $a/(1 + \sqrt{0.8^{-1} - 1}) = (2/3)a$. So the two approaches predict different things (although if it was 50% they would give the same prediction).


texts: Does mixing alcoholic drinks really make you more drunk?

texts:
There is plenty of anecdotal evidence ("beer after wine and you'll feel fine, wine after beer will make you feel queer") that mixing alcoholic drink types leads to a stronger effect, but I can't find any true studies.

In fact the only studies I found are looking at mixing energy drinks and alcohol (mixing with energy drinks increases motivation for more alcohol (in college students) [1]), and discussed mixing caffeinated beverages with alcoholic ones [2].

Are there any studies specifically looking at mixing alcoholic drinks? They would have to compare people drinking the same amount of alcohol, but some people mixing, others drinking the same thing. Maybe even a cross-over study design? Same people do both, one after the other? The only way to get an unclouded answer!

I am also interested in the follow-up why question: Why does mixing some drinks make you more drunk? Presumably it is something in wine (for example) that interacts badly with something in beer at the chemical level (the metabolites maybe)?

Marczinski CA, et al, (2012). Mixing an Energy Drink with an Alcoholic Beverage Increases Motivation for More Alcohol in College Students. Alcohol Clin Exp Res, epub. doi: 10.1111/j.1530-0277.2012.01868.x
Touyz LZ, (2011). Mixing drinks and concocting troubles. Curr Oncology, 18(6):262-3. PubMed; FullText.


texts: Can you please identify this species of beetle? It was about 2 cm (or 0,8 inches) in size. Photo is from Greece, Europe.


texts: Plant identification: San Francisco, USA

texts:
I am taking a biology lab class and I need to identify all these plants which are from the San Francisco area.

My question is how can I find the right keyword to find their names on internet? Or can you recommend any book that I can find in library?


texts: How can neurons divide without centrioles?

texts: I have read in my studies that neurons lack centrioles. If that is so, then how is it possible that new neurons are added to our brain? Does this have anything to do with memory loss?


texts:
I found this bug in my kitchen, in front of my oven.
It has wings and moves quite slowly on the ground.

I can provide additional pictures if required.

Can somebody tell me what it is?

I have found an article on a local website that seems to say this is a carpet beetle even though it's written bedbug right bellow it.

http://www.exterminationmontrealbedbugs.com/insects/


texts: What is called the "area size that an animal usually lives in"?

texts: What is called the "area size that an animal usually lives in" or "needs for a normal life"? Is there any specific term?


texts: I'm trying to observe the behavior of simple viruses in different environments. I'm just looking for simple viruses like the common cold and the flu virus nothing major. Is there a way to obtain them?


texts: Biological meaning/interpretation of clustering coefficience

texts:
I have been looking for some time to find an answer to the following question. I would be grateful for any help/advice or directions.

I work very frequently with large number of proteins and assess their importance in a biological network. Traditionally there are two methods used to visualise proteins in a network and withdraw conclusions purely on network architecture bases, before one looks at the top hits in details using databases. One is degree and the other is clustering coefficience.

Degree refers to a node being connected to edges. The higher the degree, the more nodes are connected to a given node. Traditionally people interpret nodes with high degree as being biologically important, so called hubs. Since hubs are so highly connected it means that a failure of a biological hub has catastrophic consequences since the functions of many proteins are related/dependent on hubs.

However what confuses me is the biological meaning of clustering coefficient of a node in a given network. I’m aware that clustering coefficience refers to the tendency of a nodes neighbours to connect to each other; however, I was unsure as to what it means biologically and whether that means a node with a high clustering coefficience is more “important” than a node with low clustering coefficience. This just seems unlikely to me because hub proteins, are considered important proteins; however, hubs usually have low clustering coefficience but that doesn’t mean they are less important since they are highly connected (high degree). Therefore to put it in plain english, why do people use clustering coeffience in biological networks and what biological information is it providing them?

So I would appreciate any explanation/advice and references you could provide that would help me understand the biological meaning/interpretation of clustering coefficience.


texts:
I have been following documentaries about crocodiles and amazingly, crocodiles and hippos apparently seem to live happily in the same pond together without attacking each other.

Why is it so? Like no matter how strong hippo is, its soft skin is no match to the brutal jaws of a crocodile?


texts: Why is there a difference in the rotation of the tail fin in fish compared to marine mammals?

texts:
I've been thinking about this one, but I can't seem to find what causes this difference.

All fishes that I've seen have their tail fin positioned vertical:

But all the marine mammals I know have their tail positioned horizontal:

Why is there this difference? Is it because it's mammals compared to fish? Or could fish as well have horizontal tail fins?


texts: Of people who develop Alzheimer disease, are those people genetically predisposed to it?

texts:
I have read a lot lately about microbiological pathogens that are found in blood vessels in the brain of patient's with Alzheimer disease (positive association).
So, I am confused whether there are genetic markers and testing of susceptibility to this disease, or whether there is some other type of disease process occurring here (given the microbiological pathogens association). Is that widely discussed in the popular press?


texts:
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)?


texts: Why does agrose gel runs horizontally, and SDS-PAGE gel runs vertically?

texts: It seems in electrophoresis, agrose gel always runs horizontally, and SDS-PAGE gel always runs vertically, why?


texts: Is it possible to graft plants from different families?

texts: For example, I have some Eastern Hemlock rootstock (Pinaceae), and want to graft a scion from Dawn Redwood (Cupressaceae) onto it. Is this possible? Is anything like this possible?


texts: What could independent investigators learn from the first (known) copies of the virus from Wuhan, if they had (physical?) access to these samples?

texts:
RFI reports:

"You have to remember -- these labs are still open inside of China these labs that contain complex pathogens that were being studied. It's not just the Wuhan Institute of Virology," Pompeo told reporters.
"It's important that those materials are being handled in a safe and secure way such that there isn't accidental release," Pompeo told reporters.
Pompeo cited the example of nuclear facilities, pointing to the rigorous global inspections to ensure safety.
He renewed concerns that China has not shared a sample of the initially detected virus, known scientifically as SARS-CoV-2.
"We still do not have a sample of the virus, nor has the world had access to the facilities or other locations where this virus may have originally originated inside of Wuhan," Pompeo said.

(China has now rejected this US call as being "politically motivated" but they weren't terribly specific beyond that.)
Would China [physically] sharing "a sample of the initially detected virus" (which of course begets the question which sample is that precisely--but let's assume they share all 40 or so initial samples they reported/discovered back in Jan) have any scientific value? E.g. is [physically] sharing those samples (more broadly) likely to shed any additional light on the virus' origins? (In that regard, have Western scientists asked for those [physical] samples, or said they are important for China to [physically] share them, independently/before the US political leadership's involvement in the matter?)
For more context, a Yale med page from January says:

Two weeks ago, we didn't even know what the nCOV2019 virus was. Today, thanks to China’s quick public release of the initial nCOV2019 virus genome [...] To go from unknown pathogen to diagnostic tests so quickly is incredible! The scientists at the Fudan University, China CDC, Chinese Academy of Medical Sciences, Chinese Academy of Sciences, Zhejiang Provincial CDC, and the Thai National Institute of Health should be highly praised for making their data rapidly available to the public.

A bit later, Chinese researchers published a paper on 10 genomes from the initial outbreak in Wuhan. The (FASTA) data for those seems publicly available, although behind a registration page.
So, per comments below, if Pompeo means something else by "sample of the virus" (not physical sample[s]), what is that?


texts: What causes adenosine build up in the brain when awake?

texts:
Adenosine is an important hormone in sleep regulation.  It is postulated that when a person is awake, there is a build up of adenosine in the brain, which inhibits the neurons in the brain, and produces tiredness.  (See answer for more information:  What causes humans to be sleepy?)

However, I am wondering what specifically causes this adenosine build up.  I understand ATP (adenosine tri-phosphate) is broken down to ADP in the brain to produce energy.  I thought this ADP would then be used to re-generate ATP again etc, so I'm not sure how adenosine is built up in the brain over a day.

Basically I am unsure how Adenosine itself, as opposed to ATP or ADP, is produced during the waking state?

My theory is that during the high demand waking state there is insufficient energy to convert ADP back to ATP, and the excess ADP is broken down to adenosine somehow.

I would appreciate an explanation of how this build up occurs, and also an explanation of how this in turn how it induces sleepiness would be a plus.


texts:
I am working on building a real time PCR machine. Is there any chemistry set that I can purchase online to:

Identify if PCR amplification was successfully done.
Test fluorescence dyes that could be used to validate if the fluorescence detector optics worked; i.e. something I could excite with a specific wavelength and monitor for fluorescence.

I am looking for something that is not dangerous and only serves the single purpose of validating the real time PCR machine.

Mods please advise if I need to move to Chemistry StackExchange


texts:
Why does infection and scarring occurs at poles in Vesicoureteric reflux but not in Obstructive pyelonephritis?

It is said in Robbins that, it is due to polar papillae being flattened or concave unlike convex lateral papillae, but why is it not the case in obstructive pyelonephritis?

Also why polar papillae are not convex?


texts: Why are compost worms sensitive to light?

texts: I read that compost worms dislike light. But I'd say they don't have eyes and I couldn't imagine their skin is sensitive to light in general, is it? And if so, then why?


texts: Why do mushrooms grow in rings (sometimes called "Fairy Rings")?

texts: Mushrooms disperse their spore in all direction. Then why is there a formation of fairy rings? Why do they grow in one shape and not randomly?


texts:
I read several different articles about virology, including the Wikipedia article on viruses and none of them explain how a virus is isolated. Some talk of injecting a virus into a chicken egg, but this does not isolate the virus, it just reproduces it.

If a researcher filters the particles in a serum to get those of a particular size, it proves nothing, because every creature has many thousands of different viruses in their blood, so any sample filtered by size will potentially have hundreds of different viruses in it, all the same size range. How can they possibly be separated?


texts: Can any organisms see non-electromagnetic radiation?

texts:
Some examples would be cosmic rays, neutron radiation, alpha radiation, beta radiation, muon radiation, and antimatter radiation.

Some related questions: How is non-electromagnetic radiation detected, and would it ever be evolutionarily beneficial?


texts: What happen if we inject restriction enzyme into the blood

texts:
Just a curious question, if we extract restriction enzyme and inject it to our body, what happen?

Does antibody recognize and block it?
Can restriction enzyme pass over cell membrane and destroy the DNA of a living cell ?


texts: Osmosis vs protein-binding in preserving foods through salting

texts: I had assumed that the preservative function of covering foods with NaCl or brine was due to osmosis killing the microorganisms on the food by dehydration.  However, I am now wondering to what extent denaturing of bacterial protein through interaction with salt ions could be responsible for killing the microorganisms.  And what evidence suggests a dominant role for one or the other mechanism.  I hope someone can clarify this matter for me.  Thanks in advance.


texts:
I need to convert all of my microRNA names e.g. hsa-miR-30e-5p to e.g. entrez gene IDs, ensemble IDs or another ID. Does anyone know a good ID conversion tool for microRNAs?

(I managed to convert it to miRBase ID e.g. MIMAT0000692, but David does not recognise them apparently)


texts: Solubility of lithium carbonate in blood

texts:
When a person with Bipolar Disorder ingests a pill of $\ce{Li_2CO_3}$ and it enters the stomach the pill cap is dissolved in the hydrochloric acid; however, when it gets absorbed in the blood how does it dissociate?  Does it dissociation is there an enzyme, is that enzyme Carbamoyl phosphate, or is it the blood that separate them. Thank you.  I have also been reading biochemistry books, and would be willing to cite the information that lead me to guess.

Reference:

Data for Biochemical Research
Third Edition

Rex M.C. Dawson, Dophne C Elliot

The book notes that the enzyme does 100 percent hydrolysis of $\ce{Li_2}$ salt in 2 min. at 100 degrees Celsius, 50 percent in 2 hours at 30 degrees Celsius.

This confused me because lithium carbonate is a salt. So I was confused.  Thanks again.


texts: What is the purpose of two cell divisions in meiosis?

texts: At the moment, my thoughts are that the two cell divisions are necessary for recombination to occur, although I am not sure. I cannot really see why technically, the chromosome from each parent cannot just recombine with the other chromsome when each is a single DNA strand and not in the form of two sister chromatids joined at the centromere. Something tells me that there are several reasons why there are two cell divisions. Perhaps the S phase of interphase triiggers some further stages of cell division such as cytokinesis, and the splitting of the cell will not occur unless some DNA replication has taken place? However in meiosis 2 there is no further DNA replication, so this can't quite be right...


texts: (How) Does the human digestive system process petroleum jelly, aka petrolatum?

texts: Does the human digestive system processes petroleum jelly? In other words, does it pass through the digestive system without any interaction, or is it absorbed and/or metabolized?


texts: Can someone explain the color-changing unit (CCU) to me?

texts:
I've been physically carrying out serial  tenfold dilutions on samples of Ureaplasma to work out the color-changing units (CCU).

As a definition, the CCU is the highest dilution at which there is a color change.

If the highest dilution is 10^3, apparently that means that there are 10^3 cells per ml in the original sample. But this is what I do not understand. How are we sure of this?

I feel like there is a lot that I am missing.

Any help would be greatly appreciated.


texts: In a human, what non-germline cells have the highest/lowest mass?

texts: I'm just curious which cells are largest/smallest in the human body other than sperm/ova.


texts: How do geneticists compute the percentage of DNA shared between species?

texts: It's not exactly clear to me what is meant when people say that humans and bananas share 50% of their DNA.


texts: I was telling the theory of evolution to my friends. But they asked me for the proof. They said, we are not seeing any such transition species at present. Neither we have such evidence for evolution. What should I do? I saw many proofs like archaeoptaryx, but now it has been proved that it is fully functional bird and others are also not supporting the theory of evolution given by Darwin!


texts: Problems with SDS-PAGE, no separation - what could be the problem?

texts:
I work in a lab were we have a common stock of 30% Acrylamide, TEMED, TRIS-HCl (pH6.8 and pH 8.8.) and a 10% (w/v) SDS solution pH 7.2.

We use the recipe for loading buffer (which we of course mix with BME before use):

3.15 mL MilliQ water
1.25 mL 0.5M Tris-HCl
2.9 mL 85% Glycerol
2 mL 10% SDS
0.4 mL 0.5% (w/v) bromophenol blue

Our problem is that there is no separation.

I have tried making 2 gels because I though I might have mixed the separating and the stacking gel, but I made sure i did not do this the second time. Then I asked someone else to make the gel, and it did not work for them either (nothing on the gel, no samples no ladder).

Then I remade the 10% SDS solution and both the TRIS buffers, but again something strange is going on as we get nothing on the gel.

The gels are obviously polymerized as its a solid gel when you take out to stain and destain, and I dont understand how the loading buffer can do this even if you mess it up (because you should see something on the gel as long as your sample in the well, even without denaturing). We obviously remade the loading dye and tried again, but this does not work.

I know there is protein in the samples, as I am putting cell pellet and purified protein (which I have tested the catalytic activity of) on the same gel.

Does anyone have a rational explanation for this, or suggestions of what can typically be wrong.

Bellow is a picture of the gel as it looks when its almost done running at 200V (80mAmp) for approx 40min. When we stain and destain there is nothing on the gel. Also I think the color (bromophenol blue) looks as if its running a bit strange on the gel, not as it normally should, see picture below, but perhaps I'm getting a bit paranoid.


texts: What is the biological advantage of bilaterity?

texts:
I was wondering why there were so many bilateral species (under the bilateria clade) in comparison with the cnidaria clade. I have two or so questions:

Am I (or are we) unaware of the diversity and population of the cnidaria clade, so I can't say that bilaterity seems to be prefered by the natural selection?
Is bilaterity an advantage only on earth and not in water (where I think most of the cnidaria clade is (jellyfishes)).
If the answer to the last question is true, why is bilaterity an advantage on earth and less an advantage in water, and why is the contrary true for "unilaterality" (I don't know what is the word to describes the cnidaria clade).

Thanks!


texts: What are the upper and lower limits for chromosome length? Are these limits different in different species or kingdoms? If there is any limit, which cellular or molecular factors are reasons?


texts: Can epigenetic changes affect reproductive success?

texts:
This is prompted by niallhaslam's answer to this question [Since Darwinian times, has there been any striking/notable effects of evolution on humans?]. A comment by Alan Boyd asks whether epigenetic changes count as evolution.

Transgenerational epigenetic inheritance can occur, and does increase the natural variation of a species (although this review is more about plants, this does apply to animals too) [1]. Based on this alone I'm inclined to say that epigenetics can affect the fitness of a species, and thus could contribute to evolution.

I am interested to know if, in practise, this does occur, and whether epigenetics have been shown to affect the reproductive success of a species? Because the changes are not permanent I could imagine that they actually have very little impact "species-wide", as environmental effects (infections, toxic exposures) also affect epigenetics. So, is there any evidence for epigenetics affecting the reproductive success of a species? This also includes whether epigenetics can influence traits enough to create a new sub-species.

Becker, C., & Weigel, D. (2012). Epigenetic variation: origin and transgenerational inheritance. Current opinion in plant biology. doi:10.1016/j.pbi.2012.08.004.


texts: Whole Genome Sequencing vs Whole Exome Sequencing

texts:
I am working on a project where I want to discover causative genes for a certain disease I may have. I was wondering whether to get WGS or WES to perform this experiment:-

I am looking at SNP's and CNV's of my genes and I want to compare my data with that of normal and diseased individuals. For a gene I calculate the document distance for each group (normal and diseased) using this algorithm (https://math.stackexchange.com/questions/1080377/how-close-apart-are-two-message-document-distance-algorithm) as this will allow me to determine which genes I have that are abnormal or are "close" to being classified as abnormal and which genes are normal or "close" to being called normal per the algorithm and the data obtained from the two groups.

To perform this experiment I need to sequence my genome AND identify databases that would allow me to conduct my analysis. I wanted to know which is better for my experiment WGS or WES as publicly available data might also influence the decision.

Also, I believe alternative splicing adds a layer of complexity and wanted to know why WES is performed anyways.

Thanks in advance for your replies. Please do answer whatever you can. Thanks once again!


texts: Coincidence that navel is near the womb?

texts: The attachment point of the umbilical cord in a baby girl is very close to where her own baby would develop. Is there something in the evolutionary history of mammals that explains this, or some anatomical constraint? Or is it just a coincidence?


texts: Which DNA polymerase can use a nick as priming site?

texts:
Which DNA polymerase (commercially available) can initiate polymerization at nicks, without a standard primer?

My goal is to perform rolling circle amplification starting at a nick.


texts: Bird brain-eating Mantis - how does it crack the skull?

texts:
The New York Times' Science article Birds Beware: The Praying
Mantis Wants Your Brain is a good read and is well researched. Apparently the larger Mantises have been documented to occasionally kill and eat (parts of) birds on six continents.

The mantis was clinging with its back legs to the rim of the feeder, holding its feathered catch in its powerful, seemingly reverent front legs, and methodically chewing through the hummingbird’s skull to get at the nutritious brain tissue within.
“It was staring at me as it fed,” Mr. Vaughan said. “Of course, I took a picture of it.” Startled by the clicking shutter, the mantis dropped its partially decapitated meal, crawled under the feeder — and began menacing two hummingbirds on the other side.

The article continues:

James V. Remsen of the Museum of Natural Science at Louisiana State University and his colleagues documented 147 cases of mantis-on-bird predation in 13 countries representing all continents but Antarctica — not surprising, Dr. Remsen said in an interview, since there are no mantises on Antarctica.
Hummingbirds were the most common target, but mantises also went after warblers, sunbirds, honeyeaters, flycatchers, vireos and European robins. Large species like the Chinese mantis, which grows to four inches in length, were the most avid avivores, and females were responsible for virtually all the bird-killing observed worldwide.
In two reported cases, females feasted on birds while copulating with males. Sometimes the mantises would tuck in through the bird’s breastbone, but more often they went for the head, Dr. Remsen said.
“They bite in and eat the brains,” he said, “which might imply this is something they’re professionals at.” (emphasis added)

Question: How does the mantis break through the skull? I'm guessing it is smooth and much larger than the insects mouthparts, so it can't crush it. Does it cut through somehow? Or maybe go in through the ear? (Yuck!) What "tools" does the mantis have at its disposal to break through a bird's skull?
note: The link is to Bird Predation By Praying Mantises: A Global Perspective, Martin Nyffeler, Michael R. Maxwell, and J. V. Remsen, Jr., The Wilson Journal of Ornithology 129(2):331-344. 2017, https://doi.org/10.1676/16-100.1

below: "An unlucky hummingbird caught by a mantis at a feeder in Colorado." From here. Credit Tom Vaughan/FeVa Fotos


texts: How does the placement of it's motor domain affect the directionality of a motor protein?

texts:
I'm going over some of my notes, and I have written down that motor proteins with + cytoskeletal directionality have a reversed schematic representation relative to - directed motor proteins. Then I have this sort of image drawn. I just want to clarify it, since I don't remember this part of lecture at all.

Schematic representations

Kinesin: N terminal - |Head||Coils||Tail| - C terminal
Dynein: N terminal - |Tail||Coils||Head|| - C terminal

Does this look right?


texts: Is there a glossary about which infrared (IR) colors which body parts reflect?

texts:
I am doing medical research and I'm trying to find parts of the body that look about the same to the human eye, but reflect different "colors" in IR, so that using a light source and a camera of that frequency helps to distinguish between them. Thus I was wondering if there is a glossary out there that lists all the colors (visible or invisible to the human eye) for all body parts (cells, bacteria, organs etc.) that get reflected.

I'd also be interested in literature on that topic, but it's sort of difficult to feed the right words into search engines without getting tons of unrelated results.