texts: Location of male and female reproductive organs in fern (prothallus)

texts:
I can't seem to find an authoritative answer to this anywhere else online.

Basically, my school text-book says the antheridium (male organ) is located on the lower surface of the fern prothallus and the archegonium (female organ) is located on the upper surface of the fern prothallus.

Another (somewhat unreliable) book mentions that both the antheridum and archegonium are located on the "ventral side". With regard to plants, I'm not quite sure what "ventral" is...is it the side that's in contact with the soil/substratum (i.e- the "lower" surface)?

Besides, which source is right? Or are they both wrong?


texts: Why are cells in blood smears undetectable after absorbing moisture?

texts:
I'm a student learning how to prepare blood films and today I was curious about something, so I performed an experiment.
After preparing a thin blood smear and drying it (no staining), I took a look under the microscope (at a total magnification of about 200X... I have a cheap microscope). Even though it was zoomed out, the red blood cells were easy to distinguish. The cells were clear but they had dark edges.
Then, I blew some hot air onto the same slide, causing the dry smear to absorb some moisture. Then I let it dry once again.
I observed the same slide under the microscope once more, but this time, I could barely make out the red blood cells. They were certainly still there, but their features/borders were extremely hard to make out and distinguish.
I'm wondering what causes this. Are the cells absorbing moisture and thus changing their morphology? I couldn't find any answers online, so I thought I'd ask here.


texts: Why do mammals in the wild retain the "trait" of menstruating with blood?

texts: This question intrigued me a lot since if animals in the wild did have menstruation with blood flow, wouldn't all that blood be attracting every other predator in the vicinity?


texts:
How does natural selection affects seasonal polyphenism in animals?
In this Wikipedia article there is a following statement:

Since these animals in widely separated groups have evolved
separately, the similarity of coloration is due to convergent
evolution, on the presumption that natural selection favours a
particular coloration in a particular environment.

By looking at e.g. snowshoe rabbits, how can it be that natural selection "favors" a particular coloration during winter and summer? Is not the environment causes coloration without any "benefit" for these animals? How can it be proved, that these animals change their coloration because it is useful for them?


texts: Would a human survive eating only living ants?

texts: After reading an admittedly foolish question about 1 googol ants vs. 1000 humans, I had a question. Could a human survive solely on eating ants (common ants, not the stinging kind, or leafcutters etc.)


texts: What is the lifespan of a human skeletal muscle cell (such as in the biceps)?

texts: I have read that most human skeletal muscles (such as those in the biceps) cannot multiply after development (except for exceptional situations of severe damage that involve satellite cells) and that human adults generally have the same number of muscle cells as they did in their childhood or teen years. However, I have also read that skeletal muscle cells have an average lifespan of 10-15 years. If both facts are true, wouldn't that suggest that humans would lose most of their muscle cells by 10-15 years of age? If only the first fact is true, it would seem that the lifespan of skeletal muscle cells is approximately the same as the lifespan of the individual owner.


texts: Where does the lactate produced by tumors go?

texts:
Tumors are known to burn glucose and secrete lactate (this is known as the Warburg effect).  Where does this lactate go?

Does it steadily accumulate in the neighborhood of the tumor? This doesn't seem likely. I mean, eventually an equilibrium concentration of lactate in the neighborhood of the tumor must be reached that is balanced by some process taking lactate away from the tumor. The nature of this lactate drain is what I am asking about.

Does it enter the circulation system and is degraded somewhere else in the body (as a part of the Cori cycle)?

Is it consumed by neighboring non-malignant cells?

A combination of all of the above?

Something else?


texts: Pectoralis muscles as push muscles vs pull muscles

texts:
Pectoralis muscles are the adductors, flexors of arm in addition to medial rotators  of arm. How does this action translate in to acting as helping in push ups or in bench press?
I am having trouble visualizing the primary actions helping in these compound movements.
I also have trouble understanding why this muscle being a powerful adductor does not work in pull up exercise?


texts:
There's a relatively big scare in local news about the Heracleum sosnowskyi plant, considering how dangerous it can be.

I was strolling through the park when I noticed these plants - the ones I photographed were rather small, but there have been a lot bigger examples in the park as well. For reference, I live in Poznań, Poland.

I have a feeling this isn't Heracleum sosnowskyi, but the only reason I'm thinking this is because it was in a local park where there are a lot of people / kids, and if there were any dangerous plants there there would be an uproar... but I'd rather be sure, thus I'm posting this question.

Is this Heracleum sosnowskyi?


texts: What is this ornamental, yellow flower that looks like a smooth pineapple skin?

texts: My mom got this in her Mother's Day arrangement and we have no idea what it is.


texts: Is differential equation modelling in molecular genetics useful?

texts:
I graduated last year with a degree in Applied Mathematics and just this month I started a PhD in molecular genetics. I was accepted into a program specifically for individuals with a quantitative background, though the differences between my program and the general graduate program seems fairly minimal.

The department is fantastic and I'm enjoying learning the experimentation, but I haven't had the opportunity yet to use my actual skills.

The more talks I attend, the more I realize that much of the "computational" side of molecular genetics seems to be split between machine learning, bioinformatics and statistics or some combination of the three. In my undergrad I studied topics such as differential equations (partial and ordinary, extensively), dynamical systems, vector calculus (though I never took any fluids courses, I was more of a systems guy), computational mathematics, control theory and some computer science (about 5 courses).

I've talked to a few of the faculty so far and when I mention the possibility of differential equation modeling, they don't seem comfortable giving me guidance. In addition, I read a review paper today that seems to suggest this kind of modeling is fairly uncommon.

So, my questions are these: Are differential equation models useful to geneticists and biologists? Why are they not done more often? How difficult would it be to create my own project that involves differential equation modeling coupled with experimental parameter finding and model verification?

Nobody seems to be able to give me an answer, so I hope the Stack Exchange community has some insight.

Thanks in advance!


texts: Does estrogen have a more potent neural pruning effect in adolescence than testosterone?

texts: I have read a study here which finds that female rats with their oestrogen inhibited had more neurones in a region of the visual cortex than intact female rats. To me, this suggests that estrogen may have a more potent neural pruning effect than testosterone, and that this may explain why female brains are on average slightly smaller than male ones. However, this study is A) not on humans and B) not on the whole brain. Further, the difference between average brain weight extends into childhood when sex hormones are low (but not non-existent. So, I wanted to know whether there was any consensus on the difference between testosterone-controlled neural pruning and estrogen-controlled neural pruning, and whether my conjecture is reflected by any evidence.


texts: Is "muscular attachment" synonymous to tendon? (when talking about the insertion of glutei medius and minimus to greater trochanter of the femur)

texts:
I have read the following two terms in an MRI report (both points refer to the insertion of gluteus  medius/minimus to greater trochanter of the femur):

mild degeneration of the muscular attachment of the left gluteus medius
mild tendinosis of the left gluteus minimus

Is muscular attachment (to a bone) synonymous to tendon? Or does the muscular attachment designate the muscle part that attaches to the tendon? Or something else?


texts: What is the difference between myopia and hyperopia?

texts:
In myopia the lens is bending the light too much even in the most relaxed state. Thus the image is produced in front of the retina. If the object comes closer  the lens just adjusts a bit less than a healthy eye and the myopic subject is able to see clearly.

Why is the hyperopic eye not able to do that? If the object is far away, could the lens not just bend a bit more to elicit normal vision? So, why is the Myopic eye able to adjust its focus, but the Hyperopic not?


texts: Is every neurotransmitter receptor an ion channel?

texts:
This is a rudimentary question--perhaps the answer is well known to biologists, but is every neurotransmitter receptor also an ion channel?

For example, NMDAR is a glutamate receptor and cation channel and GABA_A receptors are gated ion channels.  Is this true generally?  If not, is there a classification of neurotransmitter receptors according to abstract function (e.g. all gated ion channels would form one class, then perhaps there are others)?

Thank you in advance!  I am a mathematician just getting interested in some biology problems and trying to organize the basic knowledge in this area.  I appreciate any insights here!


texts: Oil absorbed into human skin -- where does it go?

texts:
For example, I apply petrolatum to my dry hands twice a day as in winter I am usually in a 20-30% RH environment.  Within an hour, the petrolatum seems entirely absorbed.

According to [1], petrolatum and the other oils tested there "do not reach the viable cells of epidermis, saturating only the uppermost horny layers of the skin."

So my question is: Where does the oil go?   I do not believe I am shedding unseen skin layers fast enough nor transferring the oil to other objects fast enough that I can repeat and apply twice a day, without the oil going deeper than "uppermost horny layers" and being excreted internally. (Via lymph? blood?)  Also, I rarely wash my hands with soap.

[1] Confocal Raman microscopy for investigating the penetration of various oils into the human skin in vivo.
Choe C, Lademann J, Darvin ME.
J Dermatol Sci. 2015 Aug.
https://atlasofscience.org/oil-penetration-into-the-human-skin/
Accessed 2/8/2019


texts: Why there is replication of DNA before meiosis?

texts: It seems to me that, even without replication of DNA before meiosis, the homologous pairs can still do crossover, and then be pulled to opposite poles, directly forming 2 haploid gametes.


texts: Why does radiation sickness cause hair to fall out?

texts: As I understand it, radiation poisoning (acute radiation syndrome) is fatal because the radiation kills cells. However, why do victims experience hair loss at such an early stage in the process?


texts: What happens to eyelids when we feel sleepy?

texts:
Why is that whenever we feel sleepy, our eyelids start to feel heavier.

It is not like we can any time close our eyes and will immediately fall asleep. But, when we feel sleepy our eyelids automatically become heavy.

What causes heaviness of eyelids? Is it because of sleep hormone or something?


texts: What does a wing shake in crickets indicate?

texts: What does it mean when a male cricket (Acheta domesticus) shakes its wings towards another male cricket? Is this an act of aggressiveness?


texts: Evolution of Upside Down Catfish (Synodontis nigriventris)

texts:
My Biology teacher asked us to write 3 texts, explaining the evolution of the Upside Down Catfish Synodontis nigriventris, each one according to Lamarckism, Darwinism and Neodawrinism theories. She asked the same thing for other species but I'm having trouble with this one, since the other ones are simple to explain (like giraffes' necks or flamingo's legs).

She gave us a sheet in which there is some information:
They swim upside down, and their colors are inverted, because their backs are light and their bellies are dark (unlike the general fish). Their predators usually swim below them and it is harder for predators to find fish if their belly is light, because of the sun rays.

Well, all of this suggests that this fish swims upside down so that he can avoid predators, but how could he do this according to Lamarckism and Darwinism?
Also, how does he have inverted colors, and did he get them because of evolution?
I believe that the things which cause the evolution are the predators and the environment, but which characteristic is the first one and which is the one who appears because of the evolution? Also, both of them could be a product of evolution, right?

So how can I really explain this according to the theories of evolution?


texts: Why is erythropoietin produced in the kidney?

texts:
Erythropoietin is a hormone produced in the kidney to stimulate the generation of more red blood cell. It is triggered by low oxygen via HIF transcription factors. Makes sense. Oops, oxygen is low, let's make more erythrocytes to carry more oxygen from the lung to consuming cells.

What doesn't make sense is why evolution would locate the production of EPO in the kidneys. These are organs tasked with excretion via the urine - pump and retrieve. They have very little to do with red blood cell gas exchange (lungs), generation (bone marrow), or removal (spleen).

Can somebody think of a good reason why you would locate the synthesis and release of the primary hormone to trigger red blood cell generation in a seemingly unrelated organ like the kidneys?


texts: Found lots of these insects on my study desk today. What are these?

texts:
I came home today, switched on the lights and saw many of these running around my study desk. Any help in identifying these little insects? The picture is zoomed in so it doesn't really do justice to how tiny it is.
Approximate Size: 1mm
Location: Mumbai, India
What are these insects ? How do I get rid of them ?

Additional Images:
Additional Image 1
Additional Image 2
Additional Image 3
Additional Image 4
Video 1
Video 2
Any help in identifying these is really appreciated. We are freaking out crossing our fingers that it is not bedbugs. What are the chances these are baby bed bugs?


texts: Taq Polymerase's stability at high temperature

texts:
I was asked a question as to what is so special with Taq Polymerase that makes it quite stable at high temperatures though its functioning is the same as other DNA polymerases like that of mesophiles.

I just think it's the adaptation of that particular bacteria in that high-temperature environment. But I want to know if there is any strong reason for this stability.


texts: What is the difference between second and third generation sequencing

texts:
I am writing the section about history of DNA sequencing in the introduction chapter and after reading quite a few research papers, I am still confused about them. Here I compile some questions to make sure that I understand it correctly.

Is second generation sequencing the same as next generation sequencing?
Is Sanger sequencing the first generation?
As of today, is there any commercial 3rd generation sequencing technology in use (or is it still in development)?

If there is any paper reference that could explain all of the above then it would be really great.


texts: How does amiodarone act as an alpha and beta blocker?

texts:
Amiodarone is potassium channel blocker but also voltage-gated Na+ channel blocker according to Pubchem. However, upon reading my notes I discovered

  Amiodarone blocks potassium channels and block alpha and beta channels.

I think it must be alpha and beta receptors here, instead of channel. Pubchem proposes that there may beta-blocker-like properties in amiodarone.
However, its alpha-like properties are obscure to me as I cannot find any sources. How is amiodarone working as alpha and beta blocker?


texts: How to prevent blobs under the microscope?

texts:
My task is to take photographs of fungus spores under a microscope at x100 using oil immersion.

My problem is that I get all these little blobs. How do I prevent the blobs?

So, I have been instructed to first put the spores on the glass slide, then add a teensy drop of water to it (I use a syringe so I have exact control over the droplet) and then put the coverslip on top of that.  Then I tap the coverslip down with the eraser-end of a pencil to force the excess water out from under the coverslip.  The immersion oil goes on top of that and then I can view the spores and take the photos.

This is what I mean:

All those little blobs aren't supposed to be there.  I can't tell what are spores and what aren't, or if these spores have ornaments or not.  However, I happen know this spore does have ornaments (rhodotus palmatus).


texts:
I am in the process of creating biological key software tool for use on android devices. I would like to know if there are any established file formats for storing biological key data.

Thanks


texts: How is it that the WI-38 cell line isolated by Hayflick in 1962 is still very much around and not affected by the 'Hayflick Limit'?

texts:
I have searched the net and I have not been able to come up with an clear answer.

Edit: Here is the para quoted from Nature http://www.nature.com/news/medical-research-cell-division-1.13273
"So began WI-38, a strain of cells that has arguably helped to save more lives than any other created by researchers. Many of the experimental cell lines available at that time, such as the famous HeLa line, had been grown from cancers or were otherwise genetically abnormal. *WI-38 cells became the first 'normal' human cells available in virtually unlimited quantities to scientists and to industry and, as a result, have become the most extensively described and studied normal human cells available to this day".*


texts: How do inward rectifier potassium channels work in the heart?

texts:
Apparently in cardiomyocytes, there is an inward rectifying potassium channel that operates during phase 4 of the cardiomyocyte action potential.  I have heard that despite this potassium channel being referred to as an inward rectifying channel, that in vitro the channel in fact still transports potassium from the inside to the outside of the cell.  It appears that Wikipedia seems to suggest otherwise (?).

Can someone please explain what the inward rectifier potassium channel does and its role in phase 4 of the myocyte action potential?


texts: Could a virus produce prions, leading to prion disease?

texts:
Viruses can make cells produce proteins that are not a part of the new viruses themselves, but are used to help with replication. However in the case of rotavirus, one of these proteins (NSP4) is actually a toxin that causes diarrhoea. Prion diseases like Creutzfeldt–Jakob disease are caused by misfolded proteins that make normal versions of the protein also misfold, causing a chain reaction.

While this might not actually have been observed in real life, is there a biological basis for a virus containing genetic code for producing a prion, that after infecting an organism will cause the production of prions inside of infected cells (or perhaps proteins that cause the production of prions in the body), leading to a prion disease - in a similar way to how rotavirus causes the production the the NSP4 toxin? Since these prion diseases often have 100% fatality, would this mean a virus like the common cold could arise, that spreads quickly and non-fatally, but then triggers a fatal neurodegenerative disease in its victims by causing the production of prions in the host?


texts:
I'm trying to identify the white flowers in this photo. Location is in the Pyrenees mountains near Luz-Saint-Saveur in France. The image was shot in early September of this year. Any help is greatly appreciated!
Robert


texts: Does age affect the frequency of flatus?

texts: Is there any relation between age and the frequency of flatus? I often have this feeling that older people f*** more often than younger ones. Is this feeling scientifically correct?


texts: effect of arterial vasocontriction on the pressure in arteries

texts:
if experimentally one induces smooth muscle contraction on an artery and cause it to constrict, keeping the cardiac output same and also the arteriolar resistance(total peripheral resistance) the same
will the pressure in the artery increase or decrease?


texts:
I'm really new to RT-qPCR and probably I've just a minor problem than I think.

So, what's my problem about.

I want to quantify a virus by a specific area within a gene on its genome. I've specific primer which are working fine with the extracted virus rna from my samples. But now I need a template for a dilution series to quantify this virus. And there's my little problem. And maybe you can help me.

So I know that the genome of my virus is a negative sense single stranded RNA, so -ssRNA, and moreover I know the virus strain and the gene, which RNA I want to synthesize for the quantification. So I looked it up on ncib and I found the sequence of the gene, but it is listed as the complete cds of the gene and not the RNA sequence. And as I'm right the cds is the same sequence as the positive sense RNA, with Us instead of the Ts?!? So is it right for synthesizing, that I have to translate the cds first in +ssRNA and then in -ssRNA and this -ssRNA sequence I have to synthesize to get a standard?

If the cds would be: ATG , the +ssRNA would be: AUG and therefore the -ssRNA would be: UAC and this UAC , I would have to synthesize? Sorry for this stupid question but I am a lil bit confused at the moment with the difference of - and + ssRNA regardind the RT-qPCR. Another question would be, whether the Reverse transcriptase with Random hexamer primer is specific for -ssRNA or +ssRNA. It isn't ? So my quantification would also work with the AUG as a template for a standard curve?

Thanks a lot!

dan


texts:
How do the B-cells and T-cells recognize or distinguish a body cell from a foreign particle?

I suspect something to do with this causes Auto Immune Disorders.


texts: Are Restriction Enzymes obsolete with CRISPR?


texts: Does the human abdominal cavity use pressure to maintain posture?

texts:
Several of my PT friends have referenced a physical therapist p who has studied breathing named Mary Massery. In her articles, she has referenced the idea of "intra-abdominal pressure"

http://www.masserypt.com/images/pdfs/Massery.%20Seating%20Symposium.%20Vancouver%202010.pdf

See page 2

If I am understanding her correctly, she is basically saying that

an unopened soda can is sealed and hard because of the pressure inside the canister
the human trunk tries to support itself upright. In this sense it is rigid. Therefore, it too must be using an internal pressure to create the rigidify necessary for uprightness. This is what she calls "intra-abdominal pressure."

My Question

Given what is known about the mechanics of human breathing, do the pressures of the abdominal cavity actually behave this way? Does the abdominal cavity rigidity itself using some sort of pressure? If so, how does this pressure mechanism relate to the mechanisms used during respiration?

If I am understanding her model correctly, I am extremely skeptical. A soda can is really not similar at all physically to the abdominal cavity.


texts: What is responsible for soft rot of organic matter?

texts: In soft foods, for example, why is there a limited amount of time before consumption is no longer safe due to soft rotting of material.


texts:
I was told a human should drink a small glass (0,3 liter) of mineral water per day to get the minerals. What is the rationale behind this? What is the difference between tap water and mineral water in terms of nutrition facts and effects on human health?

Values for tap water in my area:

How good are the values regarding nutrition facts?


texts: What's the mechanism of action of Levomepromazine's analgesic effects?

texts: I have absolutely no idea as to how Levomepromazine elicits its analgesic effects so please do direct me to journal articles and other credible sources with you, the answerer, making a summary of Levomepromazine's mechanism of action in your answer.


texts: For humans, what's the difference between an edible leaf like lettuce, and a non-edible (in the sense of null nutritional value) leaf like grass?


texts: Is Parthenogenesis known as Sexual reproduction or Asexual reproduction?

texts:
I have seen that in some books refer to Parthenogenesis as sexual and in others as asexual.
The ones that say it's a form of sexual reproduction,they focus on the fact that meios has happened in the process and also,we are using a sexual reproduction system in that animal to produce the offspring.
The ones saying it is a from of asexual reproduction focus on the fact that although meios is involved,we only have one parent in the reproduction process and we cannot have any new alleles in the offspring than the ones the parent has.(unless we have mutation)

so how can we conclude in the end?which is it ?

and also,what is the evolutionary explanation for this phenomenon(parthenogenesis)?


texts:
In an experiment by Pollard, T.D. and R.R. Weihing, amoeba cells injected with  Cytochalasin B were inhibited of movement, while the control group amoeba cells did move. A hypothesis was made that Cytochalasin B blocked polymerization of actin monomers into actin filaments, thus preventing the cell from moving. To validate this hypothesis the experiments were made again with cycloheximide (inhibits new protein synthesis), and dinitrophenol (inhibits new ATP formation), and colchicine (inhibits polymerization of microtubules Here are the results:$\\$

$\begin
Condition:                                  % of cells that didn't move
No drug                                      3
Cycochalasin B                            95
Colchicine                                   4
Cycloheximide                             3
Cycloheximide + Cycochalasin B    94
Dinitrophenol                               5
Dinitrophenol + Cycochalasin B      85$
$\\$

Question: Why were these control important? How did they help validate the hypothesis?
Note: this is for self-study.


texts: How does the descending branch of the loop of Henle equilibrate concentration?

texts:
I'm learning physiology and I have a hard time figuring out how the cortico-papillary gradient is created.

Most explanations go as follow:
1) Sodium is pumped out the ascending branch into the interstitium until a 200 mOsm/L gradient is established between the tubular fluid and the interstitium.
2) Water passively flows from the descending branch into the interstitium to equilibrate osmolarity between the tubular fluid and the interstitum.
3) The tubular fluid flows, moving everything towards the ascending branch.
1 bis) Sodium is again pumped out until the 200 mOsm/L gradient is established
Reapeating this steps over and over again creates the vertical gradient.

This is illustrated here

Ok, so far, so good; here comes my question :
In step 2, how comes the final concentrations in the interstitium and the tubular fluid in the descending branch are equal to the initial concentration in the interstitium?
I would expect the final concentration to be the mean of the two. In the examples above, starting from 400 mOsm/L in the interstitium and 300 mOsm/L in the descending branch, I would expect 350 mOsm/L at the end, not 400 mOsm/L.

How is that possible? Is this because at every moment, when water flows into the interstitium diluting its content, the ascending branch keeps pumping sodium to maintain the 200 mOsm/L gradient?

Thanks a million to whoever will answer this question!


texts: Fetal development, gastrulation and embryonic disc

texts:
I am completely confused by the images circulating on the internet of human gastrulation.

First, lets see how it happens in deuterostomes. This image depicts the process:

(image is from Wikipedia)

From here we can conclude that blastula becomes gastrula when some of the ectoderm beecomes endoderm, the place where it goes inside becomes anus and then mesoderm is formed.

Ectoderm here is the outermost level and gastrula already has anus.

However, in this image of human gastrulatuion we see completely different things:

(image source)

The mesoderm here is the outermost layer, ectoderm is inside and the gut cavity is formed by the separation of a part of the yolk sac. There is no anus and the posterior end of the gut is blind. Also other similar images suggest that a twins may be separated already after the mesoderm was formed (thus uniplacental twins).

The lack of agreement between the images disturbs me.

Just to point out some of the differences in the depicted processes:

In first image mesoderm forms after gastrulation, on the second it forms far before gastrulation
In the first image anus forms in the process of gastrulation, in the second image anus remains blind
In the first image ectoderm is the outermost layer, while in the second picture mesodem is the outermost level that encloses all, including ectoderm.


texts:
I'm a second year bachelor electrical engineering student and self-taught programmer. I've always had a interest for biology, but never got into it (besides two year biology in secondary school and some basic biochemistry in chemistry class).

I'm especially fascinated by the interplay between computer science and biology, both computer science used for biology and computer science concepts inspired by biology. Think of things like the human genome project, genetic algorithms, deep learning, protein structure prediction etc etc. I think many of this things (the computer science used for biology things) are - as far as I know - part of bioinformatics.

I've done challenges on Rosalind and although they are nice, it feels more like training/reinventing the wheel. Althrough it may be too much to ask, I'm want to do something "real" which could actually be used. Not that I want to start straight away without learning, but I don't have a picture in mind of what I can do after learning some theory.

I'm looking for an overview of the field of bioinformatics and some guide on how to get started. Some examples on what I can work on. Maybe there are some power intensive algorithm I can start designing chips (ASICs) for, in order to speed up the process. This just one example.

I hope you can help me, thanks in advance.


texts: Chemical inhibition of fertilization in plants

texts:
Are there any chemical compounds that inhibit fertilization in plants after gametogenesis? Simply put, I am talking about spermicide or emergency contraception for plants.

Specifically, I am searching for a compound that will inhibit fertilization of an ovum when a pollen grain has already contacted the stigma. This compound may be effective before or after the pollen tube has formed, but ideally before zygogenesis. Although, I am also interested in compounds that prevent maturation of the zygote (basically an abortive action).

The compound is effective when applied externally to the plant (via a liquid spray, for example). Alternatively, it could be absorbed via roots or some other route.

The compound may be a small-molecule or macro-molecule.


texts: Minichromosome maintenance protein structure and function

texts:
I am having difficulty answering three homework questions which relate directly to Chong et al. (2000).
Questions

The authors have determined that MtMCM is able to bind both ssDNA and dsDNA (see Figure 1). However, they don’t mention whether it is the same or a different site on the protein that is involved in binding the two forms of DNA.
Question #1: Propose an experiment that would help to distinguish between these two possibilities and what result would you expect?
Question #2: If ssDNA and dsDNA do share the same MtMCM binding site, what part of the DNA do you suppose is involved in stimulating the ATPase activity? In a helicase assay, the authors show that MtMCM can displace large ssDNA fragments (up to 500 bases) from a circular substrate (p. 1533).
Question #3: Explain why this is, or is not, a suitable assay for MtMCM processivity?

My Answers
Question 1:
One possible method to determine whether the MtMCM complex uses two different sites to bind ssDNA and dsDNA is through the identification and blockage (i.e. by using a ligand) of a single specific binding site on the MtMCM. If the blockage of this site prevents the binding of MtMCM to both ssDNA and dsDNA, this would suggest that the same site is used for both. The research paper suggests that ssDNA and dsDNA do share the same binding site because chelation of magnesium ions prevented the protein from binding to DNA.
Question 2:
No ATP hydrolysis was detected in reaction mixtures containing the K341E or delta-N mutant proteins, however, both wt and K341E protein still formed complexes with the DNA. If ssDNA and dsDNA do share the same MtMCM binding site, then perhaps it’s the delta-N portion of the DNA that is involved in stimulating ATPase activity.
Question 3:
I found it hard to start this question. This is what I have so far: This is a suitable assay for MtMCM processivity because a population of substrates possessing displaceable strands of increasing length was used. This allowed the researchers to compare the displacement of the different strands and quantify the processivity of the MCM complex.
Let me know if I should provide more information. Any help or guidance would be greaetly appreciated!


texts: How can I resuspend a cell pellet without harming the bacteria?

texts:
When using a preculture with Ampicillin in my protein expression, I have to get rid of the preculture medium to avoid carrying over too much beta-lactamases that will destroy the ampicillin in the main culture. To do this I pellet the cells and resuspend.

Which methods of resuspension are best suited if you need the bacteria alive afterwards? I'm not sure how much force I can apply without harming the bacteria, and resuspending very gently takes a very, very long time.

Which methods can be used to resuspend bacteria alive, and which ones are the fastest?


texts: Reproduction number of a SIR model with mortality

texts:
We know that reproduction number $\mathcal{R}_0$ is $\frac{\alpha}{\beta}$ for the following system, such that if $\mathcal{R}_0>1$, there is an epidemic in the population.

Now, assume the system below with mortality rate of $\delta$:

I'm wondering which one of options below represents ${R}_0$?

${R}_0 = \frac{\alpha}{\beta + \delta}$
${R}_0 = \frac{\alpha}{\beta \delta}$
${R}_0 = \frac{\alpha}{\beta}+\frac{\alpha}{\delta}$

Could you mark the right option with its justification?

Thanks


texts: Significance of upper-case, lower-case and Ns in UCSC DNA files

texts:
I have downloaded human chromosome's data from UCSC FTP. Some part is in small alphabets and some is in large alphabets. Does it show the coding and non-coding region?

Here is an example from the file I just downloaded:

gagaatcccttgaacccgggaggcggagcttgctgtgagccgagatcgca
ccactgcactccagcctgggtgacagagccagactccgtctcaaaataaa
taaataaataaataaataaaAAAGAAAAAGGTTAATACAACATTAAAGAA
CAAGAATTAATATAGCtttttttttttttttttttttttgagacctagtc
tcactctgttgcccaggctggagggcagtggcatgatctcagctcactgc
aacctccgcctcccgggttcaggcgattctcctgcctcagcctcccgaat
aggtgggattacaggcgtgcaccaccatgcctactttttgtatttttagt
agagacggggtttcactatgttggccaggctggtgtcgaactcttgacct
caagtgatctgcctgccttggcctcccaaagtgctgggatgacaggtgtg
agccactgcacctggccTAATATAGCTTTAATAGAAAAGGAGCTAATACA
AGCTTAGAATAATAAACTTTATGCAGACTTACTGAAACAAACAGTCAATG
CAACCTTAACCAAACAGGAATTGATAACAGTTTAATAAAAAAGCTAATAC
CACTTGAATAGAATATATCTTACTACAACCTTCATAAGAAAAACAACTAA
TAcactttgggagaccgaggcaggcagatcacgaggtcaggagatcgaga
ccatggtgaaaccccgcctctactaaaaatacaaaaaaattagcctggca

Second strange thing is to see it beginning with sequence like NNNN. Like here it is:

>chrX
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
ctaaccctaaccctaaccctaaccctaaccctaaccctCTGaaagtggac
ctatcagcaggatgtgggtgggagcagattagagaataaaagcagactgc

So the question is two fold:

What is the difference between upper and lower case in nucleotide fasta sequences?
What are the repeating N characters denoting?


texts: Is the strength of presynaptic stimulus on the postsynaptic neuron affected more by the dendrites, or the cell body?

texts:
Is the strength of presynaptic stimulus on the postsynaptic neuron affected more by the properties of the dendrites & axon terminals, or the cell body & axon?

Two years ago I asked a question here and learned that neurons do have a bias, and that various factors affect that bias, and now I'm trying to learn more specifically, how much of the strength of the the strength of a synapse, i.e. the size of the effect of a presynaptic stimulus on the postsynaptic neuron is dependent on the properties of each individual axon terminal / dendrite terminal, vs how much is dependent on the properties of the axon or cell body.

And do the properties of each individual axon terminal / dendrite ending vary diversely, even among dendrites of the same neuron, or do individual dendrites and axon terminals of the same neurons typically have similar properties?


texts: Regional circulation and Cardiac output?

texts:
I am reading my study materials and think what is the systemic POV here

  Regional circulation Blood flow within the tissue/organs based on the functional demands of the tissue.
      E.g. The blood flow to the brain should remain relatively constant from a systemic POV (13% of CO at rest).

What is the POV here?

Extension to the question and explanation.
The last part is just 13% of maximal cardiac output.


texts:
We are looking at modifying the signal peptide of a receptor in a common immortalized human cell line.  The cell line already expresses an unusually high amount of the protein, but much of it is not surface expressed.

When we compared the sequence of the signal peptide in the cell line (in this specific case the first 19AA), we found 2 mutations vs the wild type (WT) sequence.  One obvious idea, which we will do, is to restore the peptide to the WT version.

But I've been curious about options that increase trafficking to the plasma membrane over WT.  When I've looked up groups that have actually done this, it's normally been with large screens against every possible mutation in the signal peptide.

Are there targeted approaches to choosing a small number of signal peptides to increase surface expression?

I'm playing around with swapping it out some viral peptides that are totally unrelated to see if we can get increased expression with a receptor that's still (semi) functional.


texts:
Today I saw this curious colorful spider on its web near a sapota tree in my garden.
I have never seen any spider like this,its around 2cm or a little less.
The most curious part is this part of its exoskeleton which looks like when a moth rests.Like a cape.

here's the underside and the yellow patterned legs.

But the spider was bothered by my presence and was trying to crawl away,and I took this angled shot:

I live in South India.
So what is this spider ?
Is there any advantage of the wing like part?
Links to websites with details of the spider are also appreciated.


texts: Is it true that some organs "sleep" at certain times of the day and does this affect dieting or when to take medicine?

texts: Is it true that some organs (such as the liver or the intestines) are less active at certain times of the day, regardless of whether the individual is awake or not?


texts: What is the name of this insect? It is from Punjab, India.


texts: Why is the origin (patient zero) required to cure a virus?

texts: I'm not sure if it's just a movies thing but I always notice that the original strain of a virus is required to cure a virus, why is this? is this even true?


texts:
Why do the guard cells of the stomata close when they come in contact with salt water?

I recognize it has something to do with osmosis and the fact that osmosis makes the water drain in some sort, following this distilled water has the opposite effect.. why?


texts: Is there a taxon that "adaptively" radiates faster?

texts:
It seems that there are some taxa that have a greater potential to radiate through adaptations. Off my head, I can think of birds:

Darwin's finches
Hawaiian honeycreepers
House finches (Carpodacus mexicanus)
Manakin (or other passerine birds)

Also, there are some fish:

Cichlid fish (Lake Victoria in east Africa)
Threespine Stickelback

Plants:

Hawaiian silverswords
Erythranthe lewisii (Lewis' monkeyflower, great purple monkeyflower)

Lizard(s):

Anolis lizards

Insects:

Heliconius butterflies
Drosophila (Hawaiian Drosophila particularly)
Spider (Maybe peacock spider)
Leaf beetle

Generally:

Angiosperm plants
Dinosaurs
Marsupial mammals
etc.

So, is there a group of organisms (taxa could be any level: family, gender, species...) that is consistently radiating more than other?

By radiation I take the points that Grant defines here:

  These examples have the following in common: (1) they comprise
  several to many species, (2) the species vary morphologically in
  conspicuous ways, and relatedly, (3) they occupy a diversity of
  ecological niches. Most of the species were (4) derived from a single
  ancestor in their current environment, and (5) most diverged
  relatively rapidly.


texts: how can a pseudo coelomate like ascaris lay 200k eggs in a single day

texts:
as per this site the dimensions of eggs of ascaris lumbricoides are 78-105 microns and as it is shown in the pic down here only half of the body cavity would be used for storage of all the stages of different sizes of eggs

and as we all know pseudo coelomates have very minute width of their body cavity
and rest of the body cavity is filled with mesoglea

so my question is how can a round worm accomodate $2$x$10^6$ eggs in its womb before its release


texts: How can a plant resist glyphosate (Roundup) herbicide?

texts:
In my area, the most common weeds that strongly resists (N-(phosphonomethyl)glycine) (glyphosate) are the horseweed, or mare's tail, Conyza canadensis, and Canada thistle, Cirsium arvense There are several other weeds with similar resistance. I use the brand Roundup on jobs where a complete kill is necessary. However, I sometimes have to go through again, with glufosinate, to control these weeds. I'd prefer not to, as the glufosinate lingers much longer in the soil.

Glyphosate inhibits an enzyme used in the synthesis of the aromatic amino acids tryptophan, tyrosine,  and phenylalanine. It is taken in by the stomata in the leaves, and is moved throughout the plant to all the points of growth, acting fastest on those plants which are undergoing fastest growth.

I can't seem to find an article on how the weeds mentioned can tolerate this treatment. How do these weeds resist the glyphosate?


texts:
Imagine you swallow something up and not everything gets out of the windpipe (this is possible right?).

Would it be possible for the lung to handle with the rest implying that it is organic? Would it slowing absorb it?


texts: Null hypothesis of Chi-square test for independence

texts:
My understanding of null and alternate hypotheses :

The null hypothesis is a hypothesis whose plausibility is being tested by a test statstic and is denoted by H0. It assumes that observed data follows a standard scientific theory (and the variation/deviation is due to
chance).1 Alternative hypothesis is a hypothesis that contradicts null hypothesis. It assumes that the variation in the observed data is real, not due to chance.It is usually the hypothesis that a scientist is trying to establish.
(Source: Biostatistics by Lee & Forthofer & Statistics by David Freedman)

This1 holds good for Goodness-of-fit test but not chi-square test for independence as there is no theoretical data to compare the observed data with.

So my question is in a given problem of chi-square test for independence how to determine what the null should be?

When what the scientist is trying to establish is mentioned:

Q : In a study of effectiveness of an antipsychotic drug, patients are treated with the drug and were compared to those receiving a placebo. 698 of 1068 patients were released after taking the placebo while 639 out of 2,127 relapsed after taking the antipsychotic drug.
Test the prediction that the antipsychotic drug is significantly more effective in preventing relapse than placebo.

A:  Ho : Edrug = Eplacebo  Ha : Edrug > Eplacebo

(Reasoning: Ha is the hypothesis the scientist is trying to establish and so Ho should be something that opposes the Ha that he has to disprove.)
When what the scientist is trying to establish is not mentioned (at least not clearly):

Q: Among 60 males and 50 females, 25 males and 20 females were with attached ear lobes. Statistically prove whether or not the attached pinna has any relation with sex.

Not sure what the scientist wants to establish so unable to assume a null.


texts: What is the expected relative RNA concentration level using T-REx Flp-In?

texts:
I need to understand the level of RNA over-expression that is normally reached with HEK293 T-REx Flp-In cells. This over-expression system is widely used in PAR-CLIP experiments, which is why I want to understand it. I asked some gene-expression experts, but so far nobody give an estimate. Here I would like to ask for a reputable source, while "gut-feeling" estimated would be helpful as well.
Additionally, to give an idea how I tried to approach this question, here I found a data-series that could finally reveal the answer:
https://www.ncbi.nlm.nih.gov/gds/?term=GSE44616%5BAccession%5D

Expression of FLAG/HA-LIN28A or FLAG/HA-LIN28B was induced by addition
of 250 ng/ml doxycycline 15 to 20 h before crosslinking.

This contains 2 replicates of RNA-seq with and without induction of LIN28A or LIN28B. So the idea is to ascertain the expression level of LIN28A/B with or without induction, relative to the whole transcriptome. However, the file uses read identifiers like "213084_x_at" instead of transcript/gene names/IDs, and I don't know how to map them to genes automatically.
Similar to this idea, has anyone maybe read any other papers where HEK293 T-REx Flp-In overexpression is performed, that measure the RNA levels?


texts:
The answer to this question, saying that Down Syndrome - a trisomy of human chromosome 21 - is caused by de novo mutation (rather than resulting from standing variation) made me think about polymorphisms in the number of autosomes (not so much for sex chromosomes because of dosage compensation). The reason for this question is that I would never have thought that an aneuploidy, in theory, could be a segregating trait because of meiotic barriers.

I found evidence of ploidy polymorphisms in plants (especially their hybrids) that occurs when plants with different karyotypes hybridise [see, for example, Vandenhout et al. (1995) and Husband (2014)]. Additionally, I also found that this also applies to some aquatic vertebrates, however, 'fish' are also known for karyotype diversity (see Zhou et al. (2007) and Zhao et al. (2016)).

In rather sharp contrast to that, mammals are (almost) strictly diploid and most mammal species are characterised by fixed chromosome numbers, even though exceptions exist, i.e in mice and other rodents that exhibit intraspecific variation in diploid numbers - these are created by Robertsonian translovations [Graphodatsky et al. (2011)].

However, all of these are diploid and variation always needs to be expressed as a chromosome number of the form $2n$ because of meiosis. The karyotype of a human with trisomie 21 cannot be expressed in that form as this person has $2n +1$ chromosomes. All cases of aneuploidiy in autosomes I am aware of cause disease. My (related) questions now are:

(1) Are there described cases of non-deleterious aneuploidies in autosomes?

Those cannot be segregating in the populations as aneuploidies are not inherited to children, so more importantly:

(2) Are there indirectly segregating aneuploidies in autosomes (i.e. some sort of heritable trisomy that e.g. result from a trisomy followed by chromosomal rearrangement)?

If so, do any of these also exist in mammals, particularly in humans?


texts: Wash adsorbed protein without destroying Biotin-Avidin-Mechanism

texts:
I am looking for reliable protocols to wash protein (e.g. Fibronectin) adsorbed onto glass surfaces. According to Protein immobilization literature, people usually use 1% SDS and some incubation time. For me this did not work.

Furthermore, the removal step should not destroy an existing avidin-biotin-mechanism.

Does anyone have experience with that? Or is there some kind of standard protocol, which I am missing?

More detailed process:
I have a quartz coverslip with covalently bound Biotin on some surface area. First I add Avidin (Sigma, 10µg/ml), then biotinylated human plasma Fibronectin (Sigma, 10µg/ml). Now I want to wash adsorbed Avidin/Fibronectin, so I have free "glass" area. This is important for me.

For some reason changing the system is not an option for me.


texts: found this flying ant like insect in pune, help me identify it?

texts:
Is it species of wasp or ant or fly? I found it in Pune/India. I need its common name at least.

Here is another photo I managed to take...Found at same place as previous one.


texts: Can elephants smell when they have water in their trunks?

texts: For humans, humans cannot smell when they have water stuck in their noses. However, I am wondering if elephants can smell scents when they have water in their trunks, as they are designed to hold water.


texts: Does hydrolysis of carbohydrates, proteins, and fats occur in the small intestine?

texts:
Does the hydrolysis of carbohydrates, proteins, and fats occur in the small intestine? I have researched this and just cannot seem to get a clear-cut answer. Perhaps I am misunderstanding something?
Any help and/or links to resources are appreciated! I just want to make sure that I understand this concept before moving on with other biology topics that I am learning.


texts:
I was reading how plants make use of sunlight, CO2 and some other stuff to make energy. So why can't we create artificially engineered bio solar panels which will take sunlight, C02, water and other things and give us energy (maybe electricity or heat etc). So basically instead of solar panels which are made of silicon or something we can have bio panels made of organic materials. Then we need to supply it with water and it will convert sunlight into electricity.

I googled this on the internet and I don't find anything relevant in this regard. So I am assuming there must be a very good reason we are not trying to do this. I want to know if there is any research going on in this regard and if not why this idea is not feasible.


texts: Does caffeine increase the speed at which sperm travels?

texts:
I'm not even sure if this claim is true, but...

This source states that

  Caffeine gives both types of sperm a boost, but the Y-sperm would get a little more of a boost.

This article reinforces the quote. In fact, this "tip" can be seen all over the internet to preferentially conceive a male rather than a female.

My question is how. What is happening at the molecular to increase the overall mobility of sperm? It clearly wouldn't work as a neurotransmitter (as it "normally" works).


texts: Why are sight and sound prerequisites for intelligence?

texts:
Edward O. Wilson, in The Diversity of Life wrote (emphasis mine):

Ninety-nine percent of the animals find their way by chemical trails.  […]
Animals are masters of this chemical channel, where we are
idiots. But we are geniuses of the audiovisual channel, equaled in
this modality only by a few odd groups (whales, monkeys, birds). So we
wait for dawn, while they wait for the fall of darkness; and because
sight and sound are the evolutionary prerequisites of intelligence, we
alone have come to reflect on such matters […]

I'm getting this from an anthology (Dawkins' "Modern Science Writing") so I don't see how Wilson supports this statement, and my google-fu is bringin up nothing relevant-seeming.
My question is: why are sight and sound prerequisites for a species to evolve intelligence?


texts: Why do people feel extreme cold at different temperatures compared to other people of same body structure?

texts:
I have seen some people shivering in the room temperature of 18°C while others of similar body structure do not feel that much amount of cold.

Of course the clothing of both people is similar if not same.

What can be the cause of such different body reactions?


texts: Rationale behind Most Recent Common Ancestor (MRCA)?

texts:
My main question is this -
I heard Richard Dawkins say in a video that after 1000s of years, any given individual alive today will be either an ancestor to ALL of the humans (in that future time) or none of them. What is the rationale behind this?
I'm unable to find the link to that video. I'll keep searching and add it once I find it.

But my fundamental question is perhaps this - is it necessary that a given species must have at least one common ancestor? I understand that there are multiple common ancestors to humans, the most recent one being MCRA. But could it have been otherwise? I think there's some underlying logic that I'm missing.

I'd appreciate it if someone could answer in a non-technical manner since I know very little about genetics and how all this works.

Update:

Consider the following example. Here's there's heavy inbreeding and as you can see no matter how many generations pass, the population are never going to share a common ancestor from current generation or later. (They could still have a common ancestor from before). But this case violates Dawkins' statement.

But this is an unrealistic example with no mixing and cross breeding. Let's consider another example as shown below. I want to see how the individual A from current generation can be related to all the population in future. As shown in the diagram, although A is related to everyone in some future generation, he is not a common ancestor to all of them. The actual common ancestor belongs to some earlier generation.

For any given no. of generations, theoretically, I could conceive similar lineages by which someone from current generation need not necessarily be a common ancestor to all of the future population (or none). So I don't understand how Dawkins' statement is inevitable.


texts: Is H antigen considered as an agglutinogen?

texts: A and B antigens which have the potential to cause agglutination in certain cases are called agglutinogens. But, as far as I know, H antigen cannot give rise to agglutination. So can it be said that H antigen also is an agglutinogen?


texts: Tryptophan side-chain structure, how should it be orientated?

texts:
I would like some clarification on whether it matters where the NH and double bond are placed in these two structures of tryptophan (W) that I drew. I marked the right side as correct and the left side as the incorrect one, but suddenly I am thinking that where you place the double bond and NH don't matter as long its placed in either orientation of the structure it should be tryptophan right?
Simply put, I took my chemistry classes a few years ago and don't remember if this changes the structure if I changed the position of the NH and double bonds, that is all, and would some clarification on it.

EDIT / UPDATE:
I noticed a mistake and re-drew the structure, but am still not clear about the so called "trivial" rotation mentioned. Does the new picture reflect whether or orientation not mattering? I am still confused if I drew it correct.


texts:
After a day at the beach, my skin tans due to Melanin.

But I also observe the black hairs on my arm turn a blond colour.

My question is What is the chemical process involved in human hairs changing colour after sun exposure?


texts: Can virus and bacteria move on the surface?

texts:
Do viruses/bacteria have some motive mechanism? I mean if the virus/bacteria reach some surface by touching, can it move on that surface?

Life example: suppose the cooler is not so clean and has some viruses on his surface. My cup came into contact with the cooler in some little area, so virus migrated to that little area of my cup. Can the virus eventually move to another area of my cup's surface? Or can I be sure that it remained at the point of contact? If yes, is this also true for bacteria?

P.S. obviously parasites can move, but I can't figure out are the viruses and bacteria can..


texts: Can we predict a person's tolerance to cold exposure during excercise?

texts:
Being an amateur athlete and student of anatomy I've always wanted to know if there is a formula for determining an unconditioned body's tolerance to cold temperatures while exercising.

I know the factors of age,weight, gender, humid versus dry weather etc. are going to make it tough to determine.

Has there been any research into formulaicly describing a persons cold temperature tolerance?


texts: Are there any good reviews on the mouse and human conservation in coding and gene regulatory module regions?

texts: I was looking for reviews that deal with conservation between mouse and human of proteins, noncoding RNAs, gene regulatory module (such as promoters and enhancers), gene regulatory networks post the mouse genome sequencing era


texts: Basic behaviour patterns of animals for a modeling project?

texts:
I am working on a project (a tool) for my GIS class that models natural habitat of an animal based on landcovers, distance to the nearest watersource and distance from developed area in Kansas, USA. I need these numerical values for at least a couple of animal species (larger herbivores that can occur in Kansas) so the user can enter these values and visualize the natural habitat.

Now, I know it is very difficult to determine such values (and modeling natural habitat is much much more complex than this) but these values don't need to be very accurate as it aims at showing the capabilities of the GIS software rather then producing real-world output (again, its a school project).

I've contacted a professor at the Department of Biology but she only provided me with tons of over-detailed information and links to scientific research which are of no use for me.

For example: a deer goes to drink water twice a day and doesn't move more than 10 miles a day -> it is most likely to occur within 5 miles from a water source. I know it is a crude simplification but it really doesn't matter in this case.

Is there a source of such information?


texts:
I ran across this paper recently.

http://www.ncbi.nlm.nih.gov/pubmed/21151122

I am confused on their use of Western blotting. Their unmodified protein (no PTM group) has a band and their modified protein (succinylation of Lys) has no band, yet they use this as evidence of successful identification of the PTM. Can anyone see what they are doing here?


texts: Can viruses protect themselves against restriction enzymes?

texts: Restriction enzymes cut the DNA of bacteriophages. Have bacteriophages evolved any mechanism to protect themselves from it ?


texts: Which fruit compounds affect the speed of fructose absorption?

texts:
Blood fructose levels are not regulated by insulin in the human body. This means that the body absorbs pure fructose very fast, and it raises the blood fructose levels rapidly.

Do fruits/ vegetation contain compounds, which help the digestive system to regulate the absorption of fructose? If so, what are they?


texts: Why ketoacidosis is less common in patients of Noninsulin Dependent Diabetes Mellitus?

texts:
The other day my teacher said ketone bodies are mostly formed when insulin is less and NIDDM type diabetes mellitus has less chances to grow ketosis. https://medlineplus.gov/ency/article/000320.htm
P. S. I had read the difference between the type 1 and type 2 diabetes.


texts: Where does the inverse seconds unit come from in the association constant?

texts: I'm working to determine Kd(s) kinetically by generating association and disassociation curves.  Kon (association constant, or on-rate) is in inverse seconds multiplied by inverse molar.  I get that the molar comes from concentration, but where do the seconds come from?


texts: Inability of vultures to digest diclofenac

texts: The population of Indian vultures has been rapidly declining since 2003. This is attributed to the diclofenac present in the carcasses which the vultures eat. Vultures seem to digest all sorts of food items but why can't they digest diclofenac? What is the mechanism which causes this?


texts: Recommended applications for commercial antibodies

texts:
Commercial suppliers of primary antibodies for given protein targets typically list recommended applications, for which the antibody has presumably been shown to work. I am usually looking to use them for immunofluorescence, and my impression (which admittedly may be based on an unrepresentative sample) is that most antibodies are recommended only for use with Western Blotting.

Why is this? Is WB the most common application? The most general? Is it easier to test for than IF?

And, perhaps more to the point, how seriously should one take these recommendations? If an antibody is not recommended for IF, does that mean that it probably won't work? Or that it may well but no-one's bothered to check? Or that it almost certainly will?


texts: What are the effect of microtubule or microfilament inhibition on yeast expression profile?

texts: I was wondering whether anyone has looked at what are the expression changes in yeast when the microtubule or the microfilament polymerization is inhibited? Have there been whole-genome studies?


texts: 4DGenome or another comprehensive database of chromatin interactions

texts:
I'm searching for the most comprehensive source of chromatin interactions to support enhancer targets (data such like Hi-C, ChIA-PET, IM-PET, 5C, 4C, 3C, etc.) and my question according that could be split into two following parts:

On page http://epigenie.com/epigenetic-tools-and-databases/ I've found out links to two databases, but the reference to 4D Genome doesn't work. Does anybody know whether this database
http://4dgenome.int-med.uiowa.edu was moved somewhere else or maybe its only internally available for U Iowa community? (I'm asking about probably exclusive access, because on Tan's lab page http://www.healthcare.uiowa.edu/labs/tan/software.html only the 4DGenome has the trailing part of the link int-med.uiowa.edu (presumably this int-med strands for internal/general medicine or maybe in the sense of internal/intranet access), whereas all other services like IM-PET has its link starting with http://www.healthcare.uiowa.edu/labs/tan/.
Maybe you know even better database for chromatin interactions covering as much as possible cell lines/tissue types for GRCh38 assembly or any other whose coordinates could be easily converted, e.g. by liftOver? I need data only for human and mouse, but I would be grateful also for solely human data.

Thank you in advance for your answer.


texts: How dissimilar are the fingerprints of identical twins?

texts:
It is a very well-known fact, stated multiple times even in this Stack Exchange, that identical twins have different fingerprints. However, to what specific extents, and in what specific ways, do the sets of fingerprints of identical twins typically differ? Are the differences usually very minor (e.g., just a few stray loops and whorls here and there)? Are they perceptibly different but still fairly similar, with the similarities most likely stemming from heredity and/or cultural ties? Or does the determination of fingerprint patterns behave similarly to a uniformly weighted random number generator, with the fingerprint sets of twins being just as different as those of two people born on opposite sides of the world?

Obviously, due to the random/probabilistic nature of this feature, there may be no single answer to this question — there may be cases where one pair of twins has fingerprints that are more similar than those of another pair. But does anyone know what typical similarities and differences are present between the fingerprint sets of identical twins, and, if possible, the biological causes of such similarities and differences?


texts: Can ingestion of B6 cause gastrointestinal disturbance?

texts: Can the ingestion of vitamin B6 upset the stomach, and if so by what mechanism?


texts:
Birds and humans have a four chambered heart. All animals having 4-chambered hearts are warm-blooded.
Why are crocodiles an exception? Why are they cold-blooded even though they have a 4-chambered heart?


texts: Difference in frame rates of normal and peripheral vision

texts:
I recently encountered an incident in my laboratory. It was evening and the sunlight entered the lab through a window with exhaust fans. So the ray kept flickering at fixed intervals.

I noticed that the flickering was more noticeable when it was viewed through the side of my eyes.

Is it a fact that the frame rates of the two visions are different?


texts: What is the relationship of stimulants to hair loss?

texts:
I've noticed several topical hair loss products (ex: minoxidilmax) add caffeine to their recipes with the claim that "caffeine stimulates blood flow to the scalp" thereby improving hair quality/hair growth.
I find this strange because I had read elsewhere that stimulants such as caffeine and nictoine constrict blood vessels when drank/smoked.
So the question:

Is it that being applied topically is different than being consumed as a liquid? What would be the biochemical explanation behind this? Or is there no basis at all for the claims that caffeine stimulate hair growth

If caffeine indeed does stimulate hair growth, could it be possible that other stimulants such as nicotine if applied topically, would help as well?


texts: Wikibooks claim that it is difficult to find two texts that agree on the definition of an animal

texts:
In this entry of Wikibooks we find the claim

  It is surprisingly difficult to find two texts that agree on a precise definition of an animal.

Is this true?

[I know nothing about biology, but I find this claim perplexing.]


texts: Differences between neurotransmitters and neuromodulators

texts:
According to the Wikipedia article on neuromodulation

  a neuromodulator can be conceptualized as a neurotransmitter that is
  not reabsorbed by the pre-synaptic neuron or broken down into a
  metabolite.

In another Biology SE answer I read that

  neurotransmitters can be considered neuromodulators when their action
  is on channels outside of the synaptic cleft.

Trying to bring these two conceptualizations together I come up with the following more specific differences between neurotransmitters and neuromodulators:

Neurotransmitters have typical short delay times (until they reach a receptor). Neurohormones may have arbitrary long delay times (the time they need to diffuse through the extracellular fluid). As a slogan: "Neurotransmitters work at once, neurohormones with a distance-dependent delay."
Neurotransmitters have specific target neurons (via the receptors of the synapse where they are released). The number of target neurons of a neuron (affected by the neurotransmitters it releases at its synapses) is rather well-defined (and goes into the thousands). The number of target neurons affected by the neurohormones a neuron releases is not so well-defined (and I'm missing an idea of the order of magnitude).
Neurotransmitters are effective only once and for a short time (due to fast reabsorption or break down into metabolites). Neurohormones can be effective for a long period of time.
This is due to different biochemical mechanisms by which specific neurotransmitters and neuromodulators affect specific receptors.

I wonder if this list is somehow correct and complete. (This is my question.)

Next to this list a list of commonalities would be interesting:

The same molecules can be neurotransmitters and neuromodulators.
Both are stored in and released from vesicles by similar mechanisms.
Both get effective by interacting with receptors and affect if a ligand-gated ion channel opens or not.


texts: Why do the hormones FSH and LH decrease when the follicle is maturing and does size of follicle change during menstruation phase

texts: There are three phases in menstrual cycle. In follicular phase of menstrual cycle, the level of FSH and LH would rise because they would stimulate ovarian follicle to mature. However, when I check with diagram of menstrual cycle, I find FSH and LH hormones do actually decrease during day 4-14. Is that because of increase of oestrogen? However, by the time when FSH decreases, the follicle hasn't fully matured. Also, will follicle grow during menstruation, because in diagram, the size of follicle actually changes during Day 0-4, and FSH and LH hormones increases.


texts:
Sound waves move human eardrum back and forth, like the peak to peak excursion of speaker driver, how much is it though? Ofcourse this movement depends on sound pressure, frequency and even location on eardrum, the edge moves less than center just like rubber surround around driver diaphragm.

I am interested in center of eardrum, the part of it that moves the furthest. The SPL is 100db at the eardrum and I would like to know how far it moves at 20 Hz and 20 KHz. I know this is hard question without specific answer becose every person have different eardrum but I believe there must be some rough average, some decent estimation about how much is it.

Is it micrometers? Is it nanometers? Or does it exceed 1 milimeter?


texts: What is the nature of action potentials in autonomic nervous system?

texts:
My conjecture is that the natures of sympathetic and parasympathetic action potentials are different.
My findings propose me that

sympathetic action potential is little longer lasting than parasympathetic

there may be another mechanism in sympathetic action potential - some sort of plateau phase which does not exist in parasympathetic action potential
however, I have not managed to gather any convincing evidence on this claim

parasympathetic action potential has greater energy per one time instance, while the energy of sympathetic AP is distributed along wider time space

My hypothesis is that the energy of parasympathetic and sympathetic action potentials is equal.
This would suggest me that the action potentials of the autonomic nervous system are coming from the same source.
Their nature is just different.
What can this source be exactly?

I have read the recent Physiology and Pathophysiology books where this topic was not covered rigorously.
I did not manage to find any good publication about the topic, probably, I missed something.

What is the nature of autonomic nervous system action potentials?
You can select what ever condition you want and see if you can get some findings as I have got.


texts: Why does it hurt when you take sweets, if you have cavities in your teeth?

texts: When you have cavities in your teeth taking any sweetend drinks or food causes sensitivity or pain. What could be the reason?


texts: Sugars is a common component in diet of mammals. Why then their teeth did not develop resistence to sugar decay?


texts: What are the differences in the two possible methods to calculate the Hardy-Weinberg Equation?

texts:
I am more than flabbergasted by calculations of Hardy-Weinberg equilibria. The formula's theory assumes a binomal distribution of allele frequencies in a population, and hence allows the comparison of observed phenotype frequencies to an ideal model distribution.

$$
p^2 + 2pq + q^2 = 1
$$

with

$p^2$ = Frequency of homozygous phenotype PP

$2pq$ = Frequency of heterozygous phenotype PQ

$q^2$ = Frequency of homozygous phenotype QQ

There are two different methods of working with the HW equation that I have come across, and they do not seem to be compatible; used on the same data sets they yield wildly different results. I feel like I'm not seeing the forest for the trees, to be honest.

Is either of these methods (technically) wrong? How do I decide which one to use for each data set (i.e. is it valid to use method #1 on 3-allele-data sets)? Or do I just use whatever method is easiest? Doesn't this lead to discrepancies in the results? This seems like a big thing, especially when comparing real-world observation data to assumed HW distributions.

Example data set (EST/California) and results of HW calculations. I'm using observed phenotype in the place of the original data's observed genotype.

Phenotype     n  |   HW1   HW2p   HW2q
PP           37  |  33.9   37.1   28.8
PQ           20  |  25.0   23.0   28.2
QQ            7  |   4.5    3.8    7.0

Calculation method #1

As suggested by above-linked data set source and Beebee/Rowe's Introduction to Molecular Ecology, alleles are simply added up to get values for p and q respectively:

Phenotype    n  |   P    Q
PP          37  |  74    0   (37 * PP = 74 P)
PQ          20  |  20   20   (20 * PQ = 20 P + 20 Q)
QQ          7   |   0   14   ( 7 * QQ = 14 Q)
Sums        64  |  94   34

From this we can directly infer p/q: $p = 94/(94+34) =0.73$ and $q = 34/(94+34) = 0.27$; with the condition $p + q = 1$ remaining true.

Using these values for p and q in the HW equation yields:
$$
p^2 + 2pq + q^2 = 1
\\
(0.73)^2 + 2(0.73)(0.27) + (0.27)^2 = 1
$$
And a population-wide phenotype distribution of

Phenotype      n
PP         33.92    p^2 * 64
PQ         24.96    2pq * 64
QQ          4.48    q^2 * 64

Calculation method #2

The second method of utilising the HW equation is a lot more direct, and just about every text book I could find uses this method to solve 3+ allele problems (as, for example, blood types); Wikipedia commends its usefulness in calculating heterozygote frequencies of genetic diseases in large populations.
In this calculation frequencies are directly inferred as per the definition of the HW equation. This means $p^2$ is equal to the frequency of the phenotype PP (see above).
$$
p^2 = \frac{37}{64} \\
p = {\sqrt 0.578} \\
p \approx 0.76
$$
$$
q = 1 - p = 0.24
$$
Leading to a HW distribution of
$$
(0.76)^2 + 2(0.76)(0.24) + (0.24)^2 = 1
$$

With a new ideal phenotype distribution:

Phenotype      n
PP          37.1    p^2 * 64
PQ          23.0    2pq * 64
QQ           3.8    q^2 * 64

Inverting the calculation by starting with $q^2 = 7/64$ leads to even more diverging results:

Phenotype      n
PP          28.8    p^2 * 64
PQ          28.2    2pq * 64
QQ           7.0    q^2 * 64

Using both $p^2$ and $q^2$ inevitably violates the condition $(p+q)^2 = 1$.


texts:
Many plant tissue types end in the affix -enchyma.

Etymology: enkhyma "infusion," from en- "in" + khein "to pour"

Examples are parenchyma, collenchyma, and sclerenchyma.

(meaning "to pour beside," "glue infusion," and "hard infusion.")

My question: Where did this usage of -enchyma meaning "infusion" for plant tissues come from?

I'm curious from a biological more so than a historical perspective. I.e., why was this word choice chosen for plant tissues?

The best explanation I've found is from Plant Systematics by Michael Simpson:

Para, beside + en-chein, to pour; in reference to the analogy that parenchyma is poured beside other tissues to fill up space.

So far I haven't been able to corroborate this or expand upon it...


texts: Why do I have a lot in common with my mother?

texts: I have not spoken to my mother in 15 years but recently connected with her and her side of the family. I was primarily raised in a different sub-culture after the age of 4. As it turns out I "accidentally" have a lot in common with my maternal relatives. We like and dislike many of the same things. Is there some dominate trait in our nature which affects our psychology to cause us to agree on everything from TV, food and lifestyle?


texts:
I saw a dozen or more clusters of what I think are insect eggs attached to a few vertical sticks protruding from a small pond, and a few more to stalks of grass nearby. Location is in Hsinchu County, Taiwan, end of March, fairly good weather these days in the neighborhood of 15-22 C.

Each cluster consist of a group of roughly 150 spherical hot pink colored eggs stuck to a surface, each about 2.5 to 3 mm in diameter. One group was deposited almost completely around a stalk of grass on land next to the pond, and several others were deposited on the side of a stick from a fallen branch sticking out of the water.

Questions:

Is it possible to identify what kind of insect produces such clusters of eggs?
Is there any explanation possible for the "hot pink" color? I suppose it could be a general "don't eat me" signal like these big juicy red bugs but it's such an artificial looking color, I've never seen it anywhere in nature, at least that I can remember.

click images below for full size:

update: This answer suggests that snails are the likely culprits, and so I returned to the scene of the crime today and caught them red-handed, or in this case "pink-footed".

Click for full size; the larger snail is about 5 centimeters in diameter.

 caught red-handed, or in this case "pink-footed"


texts: How exactly do birds get drunk eating fruit? Fermentation should be anaerobic

texts:
The Washington Post article Drunk birds are causing havoc in a Minnesota town. Police say they’ll sober up soon. describes birds becoming intoxicated after eating berries:

“The Gilbert Police Department has received several reports of birds that appear to be ‘under the influence’ flying into windows, cars and acting confused,” Police Chief Ty Techar wrote in a statement Tuesday. An early frost meant that berries had fermented earlier than usual, he explained, and birds were eating them and getting drunk.
Incidents around town involving intoxicated birds appear to be more prevalent than in past years, Techar added, because many have not yet migrated south. “It appears that some birds are getting a little more ‘tipsy’ than normal,” he wrote. “Generally, younger birds’ livers cannot handle the toxins as efficiently as more mature birds.”

A few supporting videos:

ABC TV: Drunk birds are flying into windows, cars
TIME: Drunk Birds Are Flying High In Gilbert, Minnesota | TIME

Is the fermentation happening to the berries while on the tree or on the ground as the police suggest, or is it really after being ingested by the birds? How is an anaerobic environment produced for fermentation into alcohol but not subsequent conversion to vinegar?
Humans are a clever species, on par with some birds. They are known to collect the berries and ferment them first before ingesting, and will forage for a trap to let gas escape but keep the oxygen out. Have birds found a better way?
 Source


texts: How many plants arise from a polyembryonic seed?

texts: When I asked this question to my teacher she said that she doesn't know. So I wanted to know? Is there any use of polyembrony in plants?


texts: Wim Hof Method claims Alkaline Blood is Good. Contradictions? Counterproof?

texts:
The Wim Hof Method claims, that it is beneficial to have alkaline blood.

On the other site there is the medical claim that if the pH-value is not within the
range of 7.36 – 7.42, enzyms are not functioning properly and their 3D structure could be broken (denaturation). The correct pH-value is also invaluable for exchange of gases/O2/CO2, proper function of muscle contraction and
nerve conductivity.

So: What is this all about and how can this method be so good? After all, they also have conducted medical studies, so there must be some truth in it?! Thanks!


texts: Why are dietary recommendations for methionine consumption combined with cysteine?

texts:
I want to understand the amino acids missing in certain vegetables. I looked up the US recommendations for amino acids
(source: wikipedia).
I don’t understand why they pair

Methionine + Cysteine: 25 mg/g protein
Phenylalanine + Tyrosine: 47 mg/g protein

I searched for a justification but I cannot find one. While I acknowledge the chemical and structural similarities between them, they are separate amino acids. If these pairs could simply be transformed from one to another, then why bother considering methionine and phenylalanine to be essential? If you could easily convert cysteine to methionine, then methionine could be manufactured by the body. Similarly, so could phenylalanine. But it is commonly assumed this does not occur. Thus, an answer based on the idea that they can be "easily transformed into one another", if true, needs to address these issues.
Here are references for methionine:

The intimate relation between amino acids and protein and nitrogen requirements is well recognized. Nutrition research has focused on the capacity of food to meet the need for nitrogen and indispensable amino acids (IAA) and led to the conclusion that the quality, not just the quantity, of protein is critical. This is especially relevant in regard to the sulfur amino acids (SAA) methionine and cysteine because of the increased understanding of their relation to chronic diseases (e.g., cardiovascular disease, dementia, cirrhosis), immunomodulation, DNA transcription, and RNA translation. Considerable effort has been expended to determine whether and to what extent cysteine can spare the requirement for the IAA methionine. In vivo studies in humans generally concur that the dietary requirement of the SAA ranges between 13 and 16 mg/kg/d, but how much can be met by cysteine relative to methionine remains controversial.
Using the indicator amino acid oxidation (IAAO) approach to further examine this issue, Di Buono et al. (9–11) confirmed the mean requirement for methionine as 12.6 mg/kg/d in the absence of exogenous cysteine but noted that a safe level of intake of total SAA for the population was substantially higher at 21 mg/kg/d.

Naomi K. Fukagawa; Sparing of Methionine Requirements: Evaluation of Human Data Takes Sulfur Amino Acids Beyond Protein, The Journal of Nutrition, Volume 136, Issue 6, 1 June 2006, Pages 1676S–1681S
...and phenylalanine:

Conclusion: On the basis of the 24-h IAAO and 24-h IAAB methods, a mean phenylalanine requirement of 38 mg/kg/d is proposed for healthy well-nourished Indian adults in the absence of tyrosine intake. This finding is similar to that in Western adults.

Anura V Kurpad, Meredith M Regan, Tony DS Raj, Vidya N Rao, Justin Gnanou, Vernon R Young; The daily phenylalanine requirement of healthy Indian adults, The American Journal of Clinical Nutrition, Volume 83, Issue 6, 1 June 2006, Pages 1331–1336
Questions:

Why would amino acid requirements be grouped together?
If methionine is considered an essential amino acid, wouldn't grouping it with cysteine allow a food high in cysteine to appear as though it is satisfying your methionine requirement?
Suppose I consume 12.6 mg/kg/d of methionine, would this affect my ability to consume cysteine?
If the recommended level of methionine and cysteine is 19 mg/kg/d and this article proposes 12.6 mg/kg/d, then is it logical to consume approximately 6.4mg/kg/d of cysteine?
If true, would the same logic apply to phenylalanine and tyrosine?


texts: Genotoxic agent and their metabolic pathway

texts:
What are the mechanics (set of biochemical reactions) allowing a given genotoxic agent

to modify the mutation rate at a given spot?
to induce only a given type of mutation (from Gs to Cs for example)?
some other consequence of the kind that you think is worth talking about!

I am not necessarily seeking for a very detailed explanation of the biochemical pathway but rather some kind of understanding of how such things are possible (not evolutionary speaking but in terms of physiology and cytology).

This question comes in reaction to this post.


texts:
Unlike non-enveloped viruses, enveloped viruses can be killed with soap, alcohol, etc. Why?

Why does just having an envelope make it susceptible to soap and alcohol?


texts: Will genetically modified food affect our health?

texts: It's a popular public sentiment that - GM foods like tomatoes (flavr savr) will affect our health.. Is there any logical scientific explanation behind this?


texts: Pretty much this. I've been wondering if any of the yogourt and other "health" foods containing living probiotic cultures survive digestion to populate our intestines? If so, is there peer-reviewed evidence you could point me to?


texts: What is the word for a group of genes inherited together?

texts:
I know the words haplotype and haplogroup, as well as genetic linkage, but...
I recently came across a new phrase describing genes which tend to be inherited as a group, and wrote it down, but now cannot find it...
Also, is there a word or phrase for genes which are expressed together?


texts: Why do zoologists classify sponges as animals rather than plants?

texts: Sponges are fixed, do not move settle at one place, do not have a reproductive apparatus, respiratory apparatus, or organs, and live in marine environments. Why then zoologists consider that sponges are animals? In the past, zoologists considered them as plants and then considered them animals. What is the principe that zoologists have adopted to classify sponges are animals rather than plants?


texts: Why X-chromosome linked diseases happen due to recessive gene?

texts:
All the X -chromosome linked genetic disease I have studied (Color-blindness, Haemophilia, Muscular dystrophy) happen due to a recessive gene.

At first, I thought it was because there could be a 'good' copy of that gene on the other X chromosome (in case of females). So that's why these genes are recessive. But this is a bogus reasoning, I soon realised.

So, why X-linked genetic diseases happen due to a recessive gene? Maybe not all. But why some are recessive?


texts: Choosing a book to gain general knowledge about biology

texts: I will be first year undergraduate at Physics department next year and last year I was at the Medicine faculty. I want do double major in the second year of faculty with Molecular Biology and Genetics. The intersection of biology and physics is my interest. I have two books about biology, first one is What is Life?-Mind and Matter by Erwin Schrödinger and the second one is This is Biology by Ernst Mayr. Which one should I read to acquire general knowledge about Biology?


texts: When we humans look around, we pan smoothly from one side to the other. Birds on the other hand seem to point their head in one direction for a while, then abruptly point their head in another direction and stay in the new position for a while. Then they continue with the abrupt movement. Why is that?


texts: Is the masking effect of sound related to action potentials or to mechanical aspects of hearing?

texts:
I am an applied mathematics / signal processing engineer who wants to learn more and I have a question that has been bugging me for some time. It is known in audio coding circles that human hearing is masked both in the frequency and temporal domain. This means that when two sounds of almost the same frequency are presented, the loudest will overshadow the weakest for short periods of time.

I was thinking that maybe here on Biology.SE I can get some explanation of this phenomenon. Is this masking effect caused by properties of human neurons, or is it mediated by processes earlier than the neurons, i.e.., due to the mechanical aspects of hearing while the sound is entering the ear and hitting the eardrum, or one of the tools behind the drum?


texts:
Having watched a lot of olympians the last few weeks, I was struck by how many of them have actually spent their wholes lives/careers training for their one event (be in running a marathon, or throwing a javelin). This is of course unsurprising - a lot of people take their sport very seriously - but I wondered to what degree these athletes are predisposed to becoming atheletes, and to what degree they just 'happened' to end up doing it.

I've had a bit of a search around, but have been unable to find any studies (although there is an awful lot of media attention to the topic) that actually study the interaction between nature (genetics) and nurture (environment/training etc) in the context of top-end athletes.

It is quite clear to me that the answer is of course 'both', but to what degree? Have any common genetic variants/loci been identified, or is 'athleticism' a far too complex trait for this? Thanks.


texts: centiMorgan distribution among human chromosomes

texts:
Using the rough estimate of 7,000 centiMorgans in a human... Is there an estimate that breaks down this total by chromosome (including the sex chromosomes)?  E.g., in the human karyotype, do chromosome pair 1a and 1b have n1 cM, 2a and 2b have n2 cM, etc. so that n1 + n2 +...+ n22 + sex chromosomes = 7,000?

If you understand what I'm getting at and can re-phrase my question to clarify it, please do so.


texts: Are there biological ratchet cycles that are small in number?

texts:
I recently came across the strange factoid that all animals that can jump do so to roughly the same height (within an order of magnitude).  The argument was that the work done by muscles in a single contraction is proportional to their mass, and the amount of energy required to jump is also proportional to their mass.  The secondary issue of power could be solved by an approach like the click-beetle uses, where they store the energy in their shell slowly, then release it quickly.

I'm an engineer, so my first thought is that a ratchet could be used to circumvent this sort of limit.  If I could cycle a muscle 2-3 times and use a ratchet to store that energy, I could release 3x more energy and jump higher.  As an engineer, it seems like a no-brainer.

But I can't seem to find any biological example of such a ratchet.  The closest I could find was the muscle proteins that cause contraction in the first place.  But that didn't fit the image of the structure I cared about because it was literally millions of these ratchets and the result felt "too smooth" for the concept I was searching for.

So my question is whether biology has a structure that operates like:

Powered by a muscle that gets to contract multiple times (or another chemical process which cycles a small number of times. 2-10 is fine, 10 million is not)
Stores the energy of each contraction
Releases that energy in one burst.

Mentally I'm thinking of a ratchet that I could crank down with 3-4 pulls of a lever, and then release all that energy at once, but I'm open to other biological structures which meet the above requirements.


texts: How to do a whole genome analysis of Multidrug-resistant Mycobacterium tuberculosis

texts: I'm looking for tutorials and software that can help me study whole genome sequence data is and genome wide associations. I have Matlab and Bioconductor R so anything involving those packages would be preferable.


texts: I've heard of anorexia nervosa being a severe loss of appetite. I'm wondering what causes such disease in humans?


texts: Why does the DNA of Bacillus subtilis not contain DNA families of 20-37 members?

texts:
I am reading the book "Molecular biology of the Cell, 6th edition" and in chapter one page 18 the following figure is included

I am presuming this figure represents all genes within the Bacillus subtilis, which makes me wonder: why are there no families with 20-37 genes? There is a group for 4-19, and one for 38-77. What happened to all sizes in between?


texts:
I live in Santiago, Chile, and I see this Araucaria frequently:

For what I have read, it seems to be a female A. angustifolia individual (leaves are 2-3 cm long and a few mm wide, with a very sharp point; it gives round-ish cones with nuts, about 15 cm in diameter). Am I right?

Two days ago I found a nut in the ground, which I took without thinking about it too much. It was laying superficially and it took me no effort. Only when I had it in my hand I realized that it was a sprout, and become interested in knowing more.

Only then I learned Araucarias reproduced sexually, and understood the unlikeliness of my finding. It is possible that the sprout is A. angustifolia x A. araucana, since there are individuals of both species in the vicinity. (not very close, though!)

Considering the IUCN status of both species, I'm interested in raising it. I put it in a pot.

Q: How can I identify the child? Can I save it? How should I care for it? (especially, watering, temperature, lighting, and the like)


texts: What does the Gini index mean in a biochemical context?

texts:
What is the meaning of the Gini index, as specificed in this link, which describes the Gini index of beta-glucopyranose bound to hexokinase?

Is this true that if Gini index has a very low value that means it doesn't interact much? If Gini index is high for a compound, it will interact?


texts: Can Magnesium be absorbed through the skin? Some athletes believe that Homeopathic magnesium lotions can reduce muscle pain. I've tried this and it doesn't work nor can I see how it can.


texts:
Lymphatic drainage occurs from many portions of the body:

To venous angle:

head
axillary lymph nodes

hands
abdomen

legs (I think legs' drainage goes through abdomen)

The speed of the lymph drainage is different in each part of the body depending on the situation at hand.

Assume you have tense muscles in the hand (biceps and trieps).
The lymphatic drainage there can be lowered and be the limiting factor in the system.

I think lowered lymphatic drainage in one part of the body causes more lymph goes to other parts of the body.

What are the negative results of too high lymphatic drainage in an organ?
My intuition

edema
hypertrophy in some cases (excess of nutrients)
hypertension

Negative results of too slow lymphatic drainage are the prolonged intoxication times of

biological,
chemical and
physical factors.

I am trying to find any studies about the effective speed of lymphatic drainage.
I have an intuition that the lowest drainage of one section is the limiting factor in the whole system.
Is there any studies about how to quantify the speed of lymphatic drainage from one part of the body?

Heart pumps (blood) and sucks (lymph).
So probably some cardiovascular study relates the pumping to the lymphatic drainage.


texts: Is C. elegans always observed with precisely 302 neurons? Are there ever individual viable exceptions?

texts:
This answer mentions that the C. elegans hermaphrodite has exactly 302 distinct neurons. This has made it a very effective model for a variety of types of biological research, including neurology and cell differentiation. It is also currently the only organism with a completely mapped connectome.

But the word "always" made me wonder - has a viable specimen ever been verified to naturally have a number of neurons other than 302? Not as a result of an experiment, just naturally?


texts:
I m looking for universal primers M13. I found different version. For instance :

M13 (-21) Forward TGTAAAACGACGGCCAGT
M13 (-40) GTTTTCCCAGTCACGAC

What's the meaning of (-21) and (-40 )


texts: How do I prepare a solution? (Calculation)

texts: I have to make 100mL of 400mM NaOH. How do I go about calculating what I need to prepare this?


texts:
How can we move our lips even though they don't have any bones?

We can move everything if it is attached to the bones. Example: Legs & Arms.

otherwise we can't move it.


texts: Is it appropriate to say "selection of" or "selection for" an allele that evolves by genetic hitchhiking?

texts: In terms of Sober's selection of/selection for distinction, is it appropriate to say that there was selection of or selection for an allele that evolved by hitchhiking?  I am inclined to say selection of.  Is that correct?


texts: Why shouldn't I clean microscope slides with a paper towel?

texts:
I've recently bought a microscope and been looking at a lot of bacteria and such, and have quickly run out of clean slides. I've seen videos and articles saying how you shouldn't clean microscope slides with a paper towel and to use an ultrasonic cleaner instead. I don't have access to an ultrasonic cleaner, so I am wondering what is wrong with cleaning them with a paper towel?

Also if anyone knows of any good liquid solutions for cleaning slides that information would much be appreciated.


texts: Why doesn't nitrogen diffuse into blood?

texts:
In school, I have learnt that the deoxygenated blood brought in to the Alveoli by Pulmonary Arteries contains Carbon Dioxide. And that Carbon Dioxide present in the blood diffuses into the Alveoli and squeezed out with the help of Diaphragm.

Then, why doesn't the Nitrogen present in the Alveoli gets diffused to the blood? My guess was that the blood vessels don't allow anything other than CO2 and O2 to pass through.

But I recently saw a video on KhanAcademy where Sal said that some amount of Nitrogen does get mixed with blood. Is Sal right? If yes, then why doesn't the whole Nitrogen present in the Alveoli gets diffused from there (where it is present in high concentration) to blood (where it is present in low concentration)?

To summarize,

Why doesn't the inhaled-Nitrogen present in the Alveoli diffuses into the blood present in Pulmonary Veins, similar to how CO2 present in blood gets diffused out to the Alveoli?


texts: Is Hypericum Perforatum (St. John's wort) a C3 or C4 plant?

texts: I've been curious as to which photosynthetic cycle St. John's wort uses to synthesise glucose and more complex carbohydrates. I know it probably won't be the crassulacean acid metabolism (CAM) cycle seeing how that applies mostly to plants that require a limited amount of water as opposed to St. John's wort which tends to prefer moisture. I suspect the answer to my question will be C3 seeing how they dominate in the plant kingdom and I know that St. John's wort requires relatively cool climates to grow successfully -- a trait characteristic of C3 plants seeing how high temperatures tend to cause excessive and wasteful photorespiration.