texts: How do we know the presence of light when our eyes are closed?

texts:
Last night I laid on my bed and tried to go to sleep with the light off.
I closed my eyes (but hadn't gone to sleep). My younger brother touched the wireless mouse (which had laser) for the laptop.  He wiggled the mouse and it's laser contacted my closed eye . I knew some light was thrown on my face, and it's color was red. The laser on the mouse was actually red. So my question is, when my eyes are not functioning (not seeing, closed) how did I come to know that there was a light aimed at my eyes, and it was red?


texts: Are there differences between the activation proteins of Eukaryotes and those of Prokaryotes

texts:
I'm in BIO 203 (for reference to my skill level), and I noticed the textbook makes a whole section out of transcriptional activator proteins, their function and applications in eukaryotes, but in prokaryotes the term "activator protein" is used only once when mentioning the lac operon.

Are they the same type of activator proteins? Do they employ the same mechanisms?


texts: Fraction of naive T-cells in CD4+ T-cells isolated from whole blood?

texts:
Many papers isolate CD4+ T-cells from whole blood.
I am wondering approximately what proportion of naive T-cells there will be from such a sample? Are these predominately naive T-cells or are there more memory and effector cells?


texts: I have no background in biology but in the context of other research I am wondering if there is an organism, however simple it is, whose functions and structure is fully understood by biology or biochemistry. This would mean that all the functions and roles of all its genes are documented and all its internal procceses also. In other words is there an organism that can be fully analyzed in terms of its chemical processes and its RNA/DNA?


texts: On which date did the official name change of Lactobacillus sanfranciscensis change?

texts: When did the change of official name from Lactobacillus sanfrancisco to Lactobacillus sanfranciscensis happen? An answer ((to the exact day OR within a few days) AND the name of the conference at which it happened) would be appreciated.


texts: Cleanliness of cast iron never cleaned between meals

texts:
Cast iron cookware has unique benefits. One difference between cast iron and most other cookware is that many people advocate for not cleaning it with any soap between uses, because the soap can degrade the seasoning which protects it. I wonder, how hygienic is that?

The way I understand it, the seasoning on cast iron cookware is a smoothed layer of polymers that prevents food (and bacteria) from contacting and sticking in the iron cookware. Simply scraping it clean, maybe rinsing with some hot water briefly and drying off immediately after, is generally considered enough to 'clean' the cookware.

How is it that bacterial growth on the cookware is never a problem, given they are not washed with soap for long periods of time? I'm under the impression that most kitchenware - pots, pans, dishes, utensils - are susceptible to bacterial growth that could make you sick or transfer illness if you eat with them and don't properly wash off all the food, oils, etc. that gets on them. Does the layer of polymer on cast iron protect it from such growth? The main question here is: Does other cookware really need soap any more or less than cast iron to be used hygienically, and why or why not?


texts: Does every ovule undergo fertilization at the same time?

texts: After fertilization ovary becomes the fruit and  ovules develop into seeds. Does this mean that all the ovules undergo fertilization at the same time?


texts: Is there any evidence that genes which are associated with physically adjacent structures are located near each other within the genome?

texts: I am not sure if there are individual genes for, say, fingers and if so, would such genes be near the genes that affect hand growth? If not "near" in the Euclidean sense, could there be a different metric where genes for associated structures could be considered near?


texts: What is mold detection threshold in humans?

texts:
I managed to find primary taste detection thresholds, e.g. for sweetness it's 1 part in 200 of sucrose in solution.

Recently I've noticed that I can detect mold smell/taste even if there are no signs of product getting spoiled.

What is the mold detection threshold in humans, and is that a dangerous amount?


texts: (Updated question) Problem with Fold-change mean compared to absolute data (in qPCR)

texts:
For the problem below I am aware of the statistics involved but just can't get my finger around the following:

In biology we use qPCR to measure gene expression or basically number of mRNA copies. It does this by counting how many cycles of amplification (2^) it needs to reach a threshold. So to simplify everything lets assume that 1024 copies would require 10 cycles (2^10). If there are more copies it would take less cycles to reach the threshold, therefore 2024 copies would take 9 cycles, 512 copies 11 cycles etc.. Now imagine the following scenario:

We have the following samples:

Sample 1. 1024 copies of gene A and 4096 copies of gene B
Sample 2. 1024 copies of gene A and 16384 copies of gene B

Now we want to compare sample 2 to 1, with gene B in relation to gene A:

In absolute numbers this would be:

Sample 1. 4096 / 1024 = 4x more B
Sample 2. 16384 / 1024 = 16x more B
The average amount more B = (16 + 4) / 2 = 10x more B

Now with qPCR the same samples from above would look like the following:

Sample 1. Gene A 10 cycles, Gene B 8 cycles.
Sample 2. Gene A 10 cycles, Gene B 6 cycles.

Now using the methods standard used for qPCR data we first take the difference between Gene B and A. Followed by the mean of the difference and this is taken 2^.

Sample 1. 10 - 8 = 2 cycles
Sample 2. 10 - 6 = 4 cycles
The average amount more B = 2^((2 + 4)/2) = 8x more B

All publications / software tools etc will compute an average of 8x more B. And I am aware this originated from a log2 scale, however why does this statistically correct method differ in outcome from absolute numbers?

Update
I oversimplified my question therefore below some more details of my "problem".

Condition 1 biorep 1. 1024 copies of ref and 1024 copies of gene X
Condition 1 biorep 2. 1024 copies of ref and 1024 copies of gene X
Condition 2 biorep 1. 1024 copies of ref and 4096 copies of gene X
Condition 2 biorep 2. 1024 copies of ref and 16384 copies of gene X

So to compute in absolute numbers the average amount more of gene X in condition 2 versus 1:

We can forget the reference gene here as cDNA amounts are the same, therefore:
Condition 1 biorep 1 & 2: average (1024 + 1024) / 2 = 1024 copies
Condition 2 biorep 1 & 2: average (4096 + 16384) / 2 = 10240 copies
Condition 2 vs 1: average 10240 / 1024 = 10x more gene X in condition 2 vs 1

Now with qPCR CT values based on the numbers above:

Condition 1 biorep 1. Ref_CT 10 and GeneX_CT 10
Condition 1 biorep 2. Ref_CT 10 and GeneX_CT 10
Condition 2 biorep 1. Ref_CT 10 and GeneX_CT 8
Condition 2 biorep 1. Ref_CT 10 and GeneX_CT 6

Now using the official qPCR calculations:

Condition 1, Ref_CT mean (10 + 10) / 2 = 10
Condition 2, Ref_CT mean (10 + 10) / 2 = 10
Condition 1, GeneX_CT mean (10 + 10) / 2 = 10
Condition 2, GeneX_CT mean (8 + 6) / 2 = 7

Ref_deltaCT (10 - 10) = 0
GeneX_deltaCT (10 - 7) = 3

delta_deltaCT (3 - 0) = 3
Difference Condition 2 vs 1 = (2^3) = 8x

This equates to 8x more of Gene X on average in condition 2 compare to condition 1. Here now is the difference of 8x vs 10x. Also any program you will use to fill in these CT values it will result in a ratio of 8 compared to 10.

Is this perhaps as this method equating to 8 should only be used for technical replicates, and bioreps should use a different equation resulting into 10?


texts: What does the concept of information mean in biology?

texts: We use a lot of borrowed analogies from other sciences; linguistics, computational sciences but what do we really mean, mean with information in living systems?


texts: Why are children and adults so different?

texts:
In many animal species, juveniles aren't just smaller versions of adults. In mammals, the contrast is not as spectacular as in species that undergo metamorphosis, but still quite noticeable.

For example, puppies have shorter limbs and flatter faces than adult dogs. Fawns are coloured differently than adult deer, and males do not start growing antlers until they reach sexual maturity. There are behavioural differences as well: habituation is much stronger and faster in juveniles. In humans, children have different proportions than adults and lack secondary sexual characteristics. But why? Wouldn't it be simpler to form a small version of the adult and grow linearly?

Why delay sexual maturity in the first place?
Why tie sexual maturity to a host of other changes? For example, why aren't babies born with adult hair patterns? (Yes, because hair growth responds to sexual hormones, but the response could be different.)
Why the different body proportions?
Why lose play behaviour and learning ability as adults?

I'm interested in mammals in general and humans in particular.


texts: Mass Spectrometry (proteomics): How isotopes can be used to to determine charge of the peaks?

texts:
I'm trying to understand how isotopes can tell me something about the charge of the different peaks. This pdf file mentioned the following about isotopes in correlation with the charge of the peaks:

  Isotopes
  If the mass spectrometer you are working with has sufficient resolution look at the isotopes, a singly charged ion will show isotopic peaks that differ by 1 mass unit, a doubly charged ion will show peaks that differ by 0.5 mass units and so on. This is another way to deduce the charge state of a peak and thus the mass.

So let's suppose the spectrometer has a sufficient resolution to look at the different isotopes. It's not really clear for me at which peak I have to start. So to summarize my questions realted to this topic:

Which peak do I have to look at when determining the charge based on the isotope distribution?
Why would the peaks differ 0.5 mass units (see above)?

update

source: http://mascot.proteomix.org/help/mass_accuracy_help.html

When looking at the above graph, there is a difference of 1 amu between the different peaks.

What do the isotopes have to do with the charge?
What does this charge (and isotope distribution) tells us about the peak on which we zoomed in to create the above graph?


texts: Are omeprazole and other members estrogenic and/or antiandrenergic?

texts:
As of 2020, omeprazole is a widely used OTC medicine for various types of acute heartburn and some other gastrointestinal disorders.

Almost every time I read about it I read that one of the possible side effects is gynecomastia, which Wikipedia defines as "noncancerous increase in the size of male breast tissue".

As a non chemist (let alone biochemist), it is unknown to me why should it at least theoretically cause gynecomastia.

Are omeprazole and other (chemical family) members estrogenic and/or antiandrenergic?


texts:
I am interested in a gene which is null lethal but I need to temporary induce diminished capacity. If a cell is homozygous is it possible to induce heterozygous phenotypes or a partial knockout from WT with siRNA or other molecular methods without virus vectors? I'm not interested in a medillian solution but an inducible molecular way.
Thank you

I would like to generate a heterozygous Sod2+/- like they do in this paper in mice and possibly human:
http://physiolgenomics.physiology.org/content/16/1/29.full.pdf+html


texts: How do I prepare a Basal medium for autotrophic mutant creation

texts:
Minimal medium (MM) was prepared by adding 2.0 g sodium nitrate (NaNO3) to 1 L of basal medium (BM) fol- lowing Correll et al. (1987). Chlorate resistant sectors (CRSs) were generated on two media i.e. MM and PDA containing 2.5% chlorate (KClO3), represented as MMC and PDC, respectively. The chlorate served as a toxic ana- logue of nitrite (Corell et al. 1987). Four phenotyping me- dia (Correll et al. 1987) were used i.e., i) sodium nitrate (NaNO3); ii) sodium nitrite (NaNO2), 0.5 g of NaNO2 was added to 1l BM; iii) hypoxanthine (HX-), 0.2 g of HX- was added to 1l BM; iv) ammonium tartrate (NH4+), 1.0 g NH4+ was added to 1l BM. MM was also used in pairing of the complementary nit mutants

I’ve tried using the procedure on above but the minimal media is not solidifying


texts: What are the trajectories of flying insects?

texts:
Many flying insects tend to have very jagged trajectories. For moves of a fruit fly looks like a random walk.

Is there any research on the properties of trajectories (e.g. their fractal dimension or mathematical models producing similar behaviour)?

Besides the path of a single insect, I am also interested in the interaction of a small number of insects (e.g. 2 or 3).

I am aware of the research in flocking and swarming (e.g. Tamas Vicsek, Anna Zafiris, Collective motion 2010) and of techniques of obtaining such trajectories (e.g. Danping Zou, Yan Qiu Chen, Acquiring 3D motion trajectories of large numbers of swarming animals or an open access pdf, 2009). However, I haven't found within them an answer to my particular question.


texts:
Why aren't there any competing biologies on Earth? I read sci-books about life based on silicon and I've read an article that said that other structures than DNA can encode genetic information.
So does physics allow for many competing biologies? What makes DNA-based biology the dominant biology on earth according to known laws of physics?


texts:
After revising some evolutionary concepts, I stumbled on the "big five" of evolution (e.g., mutation, selection, mating, genetic drift, gene flow). I wanted to understand if mating as in "bacterial mating" or gene transfer using a pilus could be thought as assortative or disassortative mating.
Perhaps it could be thought only as gene flow if introduced in novel populations, but I was intrigued by the fact that if 2 bacteria are dissimilar in their plasmid, and they exchange DNA, then they would be disassortatively mating.
Perhaps, the definition of assortative mating (on wikipedia) is not including bacteria when saying:

[It] is a mating pattern and form of sexual selection in which individuals with
similar phenotypes mate with one another more frequently than would be
expected under a random mating pattern.


texts: Does the Enzyme Monoamine Oxidase, Isoenzyme A have an allosteric modulatory site?

texts: Does the Enzyme Monoamine Oxidase, Isoenzyme A (MAO-A) have an allosteric modulatory site? I ask because I would like to know if it is possible, in theory at least, for a positive allosteric modulator of MAO-A to be developed.


texts: How to Calculate how many times an enzyme would cut a plasmid

texts:
I'm a little confused as to how to figure out the formula needed to figure this out.

I have a plasmid that is 7.3Kb and am told that it is cut with an enzyme of 4bp. For some reason I thought that the formula needed to figure this out is:

(1/4)^4 x 7300

But it gives me such a low number that I don't think it's right so I'm just a little confused.


texts: How to take precise/low number of cells from cell lysate?

texts:
I would like to know that how can we take low or precise number of cells from a cell lysate? (without using any protein quantification assay).

Let say,
If I have a cell line having cell density 5x10^5 cells/mL (and its avg amount of protein concentration is 0.1ng/cell)

If I lyse these cells at the concentration of 5x10^5 cell/mL with buffer (eg., 0.1% rapigest + 10mM DTT). After achieving cell lysate, how can I take precise cell numbers from this lysate for further sample processing (e.g, alkylation, digestion etc)?

For eg., if I want to have 100cells/5ul or 1000cells/50ul , then how can I take it from cell lysate?

I know I'll have to dilute my lysate, but I'm bit confused how to achieve that based on cell concentration? how much lysis buffer and dilution would be appropriate?

Note: In my case I can't use any protein quantification assay for measuring protein concentration.

I would highly appreciate if anyone can help please.

Looking forward to hear soon.

Sincerely,


texts: Hypotonic or Hypertonic solution and why?

texts:
A doctor needed to administer 5% albumin to a patient. Albumin is normally administered dissolved in 0.9% saline solution. Since the physician did not have any 5% albumin solution, he diluted 25% albumin with water and administered this to the patient. Describe what you think happened to the blood cells of the patient as a result?

So this is what I think:

If the doctor dilutes the 25% albumin, that will make the solution have a lower concentration of solute, creating a hypotonic solution. Therefore the water will move into the cells, causing them to swell, lyse or burst.

Is this correct?


texts: Effect of toxin-producing phytoplankton on zooplankton?

texts:
I've been searching for quite a while without really finding an answer to this question, so I decided to try it here.

Some phytoplankton species produce toxins as a defense strategy. But what exactly happens to the predator, e.g., to zooplankton?
I've read that they may have a decreased reproductivity. But is there a faster effect acting as a defense mechanism such as phytoplankton sensing zooplankton, then producing toxins and zooplankton sensing the toxins and avoiding the area or similar? Otherwise, it would be quite a long-time defense.. If anybody knows something about this, please answer and give me a reference.

Thanks a lot!


texts:
what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other
and how does one go on to prove this
many thanks


texts: What is official term for contraction induced muscle "vibration"?

texts:
I can activate my tensor tympani muscles at will, it makes me hear rumbling bass sound becose the muscles "shiver / "vibrate" when contracted. Also when I put cleched fist to my ear I can hear it too. I read all muscles make makes this rumbling low frequency sound when contracted.

I wanted to study this thing but I run into the problem becose I dont know how is this muscle vibration officialy called. I dont know what words should I type to get relevant search results. I dont want anything about shivers, tremors or other stuff, I just want to know how is the normal muscle "rumble" called.


texts: What does it mean when a patient suffering from malignant tumor (cancer) has been declared cured?

texts:
Comment by Anongoodnurse, has made me curious as to what a doctor means when (s)he says "The cancer is cured" to a patient.

My idea up till this point (based on what I read and what I learned in my classes from my professors) was that the prognosis was declared based on the survival rates and that cancers could never be declared cured as no one could be sure that every single malignant cell has been eradicated.

However Anongoodnurse commented:

  Curable cancers are not few and far between.

So I would like to know what it means when it is said "Cancer is cured"

Though the answer by Anongoodnurse has been accepted, I would like to have other answers too, please feel free to contribute


texts: Why are centrioles aligned at 90 degree with each other?

texts: The centrioles are aligned at 90 degree with each other. What is the function of this?


texts:
Some mammals can have a black, pink or spotted skin, depending on race - see for example humans or pigs. But I recently learned that this is not the case with mice. Even black furred mice have pink skin, and there is a rare mutation which produces black skinned mice.

I was talking with a friend about cats and we got to wonder if (domestic) cats are the type of animal which can have dark skin, like pigs, or the type which doesn't, like mice. The tons of cat related sites on the Internet seem to all talk about black furred cats only, or about diseases presenting with skin discoloration, but they don't mention the skin color. So, which type of animal are cats?


texts: Are mitochondrial genes decoded in the same way as nuclear genes?

texts:
Mammalian mitochondrial genomes contain only 22 tRNA-coding genes, which is an insufficient number to decode mRNAs under the standard wobble rules.

How is translation of mitochondrial mRNAs achieved with this number of tRNAs?

The possibilities that occur to me are that certain genes encode multiple tRNAs (but this appears unlikely as each gene has its own promoter) or that mitochondrial tRNAs can adopt alternative three-dimensional structures, each with a different anticodon loop and hence a different anticodon.


texts: Can juice have a higher sugar content after packaging?

texts:
It seems like the orange juice thats been sitting in the fridge for awhile always tastes sweeter than the juice just brought from the grocery store.

Can juice ripen in the container ? By that I mean, the concentration of fructose and other sugars increases.

I remember learning in Bio class that fruit releases a chemical that causes nearby fruit to also ripen faster. I'm not sure of the source of this chemical but my question leads me to believe that it is in the juice itself.


texts: Vo2 of the brain is 21% of Q=13% or of the entire blood?

texts: I am reading now the book which states that the Q (blood flow per unit of time) of the brain is 13% while the Vo2 (relative Oxygen used per unit of time) is 21%. Now my question is if the Vo2 of the brain (21%) is taken from the entire blood or from the part the brain gets (Q=13%)?  It is not clear on the book. I've attached the picture with the explanations.


texts: What does the spectrum of Chlorophyll fluorescence look like?

texts:
I've just posted the question Which spacecraft can see plants "glow" during photosynthesis during the day, and what wavelength does it use? in a different SE site. I can't remember the details of which spacecraft this was or how exactly it worked.

My question here is simply about light produced by vegetation during photosynthesis. In this question I've shown a hodgepodge of absorption or sensitivity spectra of photosynthesis, but what I'm looking for is an emission spectrum and some details about where in the process this light is produced.

The Wikipedia article Chlorophyll_fluorescence covers the topic in general and mentions 735nm but I'd like to be able to see a fairly accurate spectrum in order to compare it against absorption lines in the Sun's spectrum.

NASA's OCO-3: Watching Plants Grow and Glow: https://youtu.be/_x-VzdEeq0c


texts: What does the "Psi" in "Psi broth" stand for?

texts: When making competent cells I've been using a medium called "Psi broth", which per liter consists of 20 g tryptone, 5 g yeast extract and 5 g MgSO4. Today I got curious about why it's called "psi". Is it an acronym like SOC and LB?


texts:
I am trying to find out which species these are.  Someone claimed they were Aloe Vera, but I am skeptical as I have never seen Aloe Vera with that kind of growth. These look more like Aloe Juvenna to me.

What do you think?


texts:
I came across this idea while reading an excerpt of my textbook $-$

  Muscles move eye lid , tongue, beat the heart, popel food through gut, discharge wastes, squeeze out secretion from the glands etc.

But I don't understand how this happen ? Does glands really squeeze out hormones?


texts: Why my protein transferred but ladder did not (western blot)?

texts:
My protein of interest is about 200Kd, I ran the gel for 35 min at 95V, the protein transferred but the ladder did not, I used dual color ladder(Precision Plus Protein™ Dual Color Standards, 500 µl #1610374), I tried 10 ul and 15 ul, but neither showed. The gel was 4-20% Mini-PROTEAN TGXtm Precast Protein Gels.
Any input?


texts: Species Identification - small insect: is this a bed bug?

texts: I found this bug in my apartment in Chicago.  We had bed bugs in our house the previous year (but we thought we got rid of them).  This bug was very small - maybe 2 millimeters in length.  These photos are all of the very same bug (just different lighting).


texts: How did the first sexual animal come to exist?

texts:
I am more or less familiar with the evolution theory based on mutations.

Now, starting with a nonsexual being, how did the first organism that reproduces sexually come to exist.


texts: What network motifs or other mechanisms can make the expression of a gene invariable to the environment?

texts: Next to double positive feedback loops and chromatin modification, which other mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another?


texts: Why does vacuum sealing of foods prevent spoilage from anaerobic bacteria?

texts:
I have noted that many purchased food items in containers only require refrigeration after they have been opened, thus eliminating the vacuum seal.  Air contains bacteria and fungus spores that enter the food container and if not refrigerated, the aerobic micro-organisms will proliferate, thus altering and rotting the food.  The air also allows any dormant micro-organisms that survived the factory sterilization process already in the food to come back to life and proliferate.
However I do not understand why anaerobic bacteria, that don't require and cannot survive in air, do not proliferate and thrive in the vacuum sealed food containers.  That plus the fact that we can leave already opened food items such as honey, jams, and peanut butter out of the refrigerator for weeks but they do not spoil.


texts:
The following image is from Campbell Biology, 12th edition

It says, "Each gametophyte develops sperm-producing organs called antheridia and egg-producing organs called archegonia". This seems to suggest gametophytes are either always hermaphrodites or most of the times hermaphrodites.
I have done a little bit of searching and now am convinced that they are not always hermaphrodites.

"Most ferns, on the other hand, are homosporous; they produce a single
type of spore. After germination, each fern spore has the potential to
develop into a male, female, or hermaphrodite gametophyte."

https://science.sciencemag.org/content/346/6208/423.summary#:~:text=Most%20ferns%2C%20on%20the%20other,%2C%20female%2C%20or%20hermaphrodite%20gametophyte.
Are they most of the time hermaphrodites? How common are unisexual gametophytes?


texts: Do "scars" in humans replace all the skin layers or only some layers?

texts: When someone has a cut or surgical incision that results in a "scar", is the scar tissue replacing all 3 layers of the skin (epidermis, dermis, hypodermis)? Or only the first one or two of them?


texts: Why does ESR have to be waited for one hour?

texts: It is said that the length of the column of clear plasma in a narrow tube left by erythrocytes which gradually sediments after one hour is the measure of ESR(erythrocyte sedimentation rate). Its normal values are found to be 3-5 mm after 1st hour for male and 4-7mm after 1st hour for female. What I want to know is why "1 hour" has been chosen. Why not 30min, 2hr, 3hr etc?


texts: How do I efficiently develop a plant cultivar?

texts:
Or, perhaps: how do I develop a cultivar at all?

First off, my knowledge and experience on the subject is close to nil. I've got a decent enough knowledge of gardening concepts, but have done precious little plant breeding, and nearly everything I know about genetics comes from the reptile hobby and the breeding of various morphs (also haven't done any of that).

But I wanted to try my hand at plant breeding - at least, get started somewhere.

I've decided to go for something simple - a dandelion. Hardy, easy to grow, flowers quick and I know will definitely reproduce for me. Contamination from external sources might be an issue but there's several easy fixes for that. I could probably wait around and inbreed them until some funny traits pop up but for now I want to try some obvious changes - wider leaves, bigger flower, maybe both.

All I (think I) know is that I'll have to keep track of my individuals and their ancestry and select for traits based on their current expression and genetic pedigree. On the surface that sounds pretty simple but I don't know the details of the execution. Is there a specific way plant breeders do it? Software that would make the management easier?

I tried looking this up, but Google isn't very extensive on this subject. Any advice or resources that can get me started would be greatly appreciated.


texts:
This skull was found in Greece, about 40 years ago, possibly in the island of Euboea (there is uncertainty about the area it was found).

The length from nose to the end of horns is 67 cm. The skull's length without the horns is 42 cm. Just for reference, the floor tiles in the pictures have a side of 33cm.

What could this animal be? It does not have to be native to Greece, even though a native animal would be more probable.

Update:
The size of the skull points to an animal larger than a goat. It looks more like an antelope, a gazelle, or even a deer.  Only deers are native to Greece, however the horns look nothing like deer.

I believe the horns are the key to unlock this mystery.


texts: How is the Concept of Simple Diffusion Possible

texts: How can a substance pass through a lipid membrane in a cell through simple diffusion? In order for something to be able to go through the membrane, in simple diffusion, it must be hydrophobic, or non polar. The reason for this is that in order for it to easily interact and pass the fatty acid part of the lipid membrane, which is hydrophobic or non polar, it must also be hydrophobic and non polar. But in order for this substance to pass the phosphate part of the membrane, which is hydrophilic, or polar, doesn't it also need to be polar and hydrophilic?


texts: Why doesn't Clopyralid damage cool season lawn grasses?

texts:
I use Clopyralid (3,6-dichloro-2-pyridinecarboxilic acid) to kill broad leaved weeds in lawns. From my understanding, it works by mimicking an auxin which affects plant growth. Naturally this pulls the chemical to the growing points (stems, roots) of the plant and disrupts the growth, killing the plant.

My question is: Why doesn't this affect cool season lawn grasses (Winter rye, fescues, bluegrass)? It is also considered safe to use on some warm season grasses, but in my experience the results are not always good.


texts: Relationship between action potentials and EEG recordings

texts:
It is possible that I am overthinking this but I have difficulties relating the neural activation to the amplitude and frequency of EEG recordings.
For example; if at the EEG location P3/P4 we observe alpha waves at 10Herts, what will that tell us about the action potentials and membrane polarisation within the population of neurons generating the wave at this frequency?
Also, high amplitude within alpha frequency may indicate attention deficits, but how is the high amplitude related to or explained in terms of electrochemical activity within a neuron?
Informed replies are very much appreciated!
Many thanks


texts: Which biological kingdom comprises the greatest biomass on Earth?

texts:
Which of the five biological kingdoms - animalia, protista, plantera, monera, or fungi - has the largest biomass?

To clarify, if the biomass of every species in each of these kingdoms was added up, which kingdom would have the greatest sum?


texts: Why do I still see a bright light after looking directly at it?

texts:
When you look directly at a bright light, maybe accidentally when looking at the sun, the shape of the image may persistently be perceived even after you look away.

Does this image persistence have something to do with the light hitting the back of the eye and leaving an imprint, or is something else going on?


texts:
I read online that they have found around 10 million single nucleotide polymorphisms (SNPs) across individuals in the human genome [1]. However, this number includes all SNPs found in all people who have been sampled and does not tell us much about SNPs in any single person.

I was wondering instead how many SNPs there are in a single person on average. I had trouble finding trustworthy evidence about this question.


texts: Are there any ways to force DNA-origami to create a geometric shape from non-nucleotides (not from DNA)?

texts: I mean, can we create with the help of DNA-origami figures that would not consist of DNA, but, for example, carbon? Is it even possible?


texts: what if there is a door for which our immune system has no key?

texts:
And as a B cell matures, it develops the ability to determine friend from foe, developing both
  immunocompetence -- or how to recognize and bind to a particular antigen -- as well as
  self-tolerance, or knowing how to NOT attack your body’s own cells.
  Once it’s fully mature, a B lymphocyte displays at least 10,000 special protein receptors
  on its surface -- these are its membrane-bound antibodies.
  All B lymphocytes have them, but the cool thing is, every individual lymphocyte has
  its own unique antibodies, each of which is ready to identify and bind to a particular kind of antigen.
  That means that, with all of your B lymphocytes together, it’s like having 2 billion keys
  on your immune system’s keychain, each of which can only open one door.

This is what Hank said in Crash course. So the b cells, each are having several unique antibodies and I also saw that this is true for T cells too and the dendritic cells  look for a helper T cell that can bind the parts of the intruders which the dendritic cell has presented on its membrane.

my question is

What if there is no antibody in any cell against an antigen?

Does the immune system has antibodies against all antigens in the world?

What happens if an antigen came into our body which has no antibody matching for it?


texts: How is deviated nasal septum related to cold

texts: I have a deviated  nasal septum and I always suffer from  common cold I was just wondering how a deviated nasal septum can be the cause for chronic common cold


texts: Why do electrocardiogram waves go  P, Q, R, S, T and not like A, B, C, D? Is there any specific reason behind this?


texts: What purpose do the opening(s) serve in diapsid and synapsid skulls?

texts:
Did synapsid skulls evolve from diapsid skulls or vice versa?

Aditionally, do birds have diapsid skulls? The research I have done has yielded some mixed results.


texts:
I read that proteins that have been highly conserved are non-immunogenic.

Why is it so ? What is the special thing that makes it non immunogenic(antibodies against them are hard to make) ?


texts: What is this mushroom that only grows next to my tomato seedlings?

texts:
So far something like ten out of fifty seedlings (20%) have had this mushroom grow right next to a tomato seedling and nowhere else in the planters.
The black gooey caps are between a peppercorn and a small pea in size. They only seem to grow at night and collapse within a couple of hours after
I have removed the glass jar cover in the morning. The jars are used to keep out the slugs at night. What type of mushroom is this and is this a symbiotic relationship?


texts: How does a frog separate blood in its ventricle?

texts:
Since a frog has two atria and one ventricle, how does it separate oxygenated blood from deoxygenated blood when both are mixed in the ventricle? Or does a frog simply pump a mixture of both to the heart and the lungs? I checked a few videos and sites for this, but was unable to find an answer.
https://www.youtube.com/watch?v=MhOCzvA4KhM&ab_channel=iWorxSystems%2CInc.
My best guess, based on the above linked simulation, is that it has to do with a difference in densities of oxygenated and deoxygenated blood, but I am not sure.


texts: Why is the DNA codon table "equal" to the RNA codon table

texts:
Before anything else please pay attention of the double quotes on the "equal" in the title - I know they are not equal, but you will understand in a bit.
If I look at the DNA codon table here or in wikipedia, and at the RNA codon table here or in wikipedia, their only difference is that the former has thymine (T) whereas the latter has uridine (U). But I am not understanding how all other nucleotides are the same. Bear in mind that transcription reads DNA from 3'->5' and translation reads mRNA from 5'->3'.
Look at this example, focusing on the 3'-TAC-5' of the antisense strand.

The 3'-TAC-5' codes for Tyrosine according to the DNA codon table. However, it transcribes and translates  3'-TAC-5' -> 5'-AUG-3' -> Methionine.
Now focus on the corresponding codon in the sense strand, 5'-ATG-3', which codes for Valine according to the DNA table (it is read from 3' to 5'). This codon transcribes and translates 3'-GTA-5' -> 5'-CAU-3' -> Histidine, not Valine and not Methionine.
So my questions are:

Why do DNA codon tables show the correspondence between codons and amino acids in the sense strands (5'-ATG-3'), if the only way to go from ATG to Met as in the figure is to consider the antisense strand?
I can see that the AUG codon translates to Methionine, and it is translated by reading the 3'-TAC-5' codon in antisense strand, whose corresponding codon in sense strand is 5'-ATG-3'. But this last one is read from 3'->5', so it reads 3'-GTA-5' -> 5'-CAU-3' -> His.

I am guessing I'm getting many things wrongly in this... Maybe on the way that I'm reading  the tables: I always take into account that transcription is read 3'->5' and this is the order I take to read DNA tables.
Thank you and sorry if I was confusing.


texts: Is warmth/temperature sensed linearly or on a different scale?

texts: I understand that the atmospheric temperature is sensed relative to external body temperature. However, is the sensation of warmth registered linearly, or is it on a logarithmic scale, similar to sound that works on the Decibel scale? Or is it on another scale entirely?


texts: Why is facial symmetry of the opposite sex attractive?

texts: Why do we give so much importance to the symmetry of face in the opposite sex? Why do we yearn to reproduce with a person with a beautiful face? How is it important for survival, if at all? Is there a biological explanation for this?


texts:
I found this picture of a fox in a news article about arctic foxes in Sweden (source), but I'm not sure whether it is actually an arctic fox.

On the one hand, it has white fur, which is the correct winter coat for an arctic fox. On the other hand, the fox's ears do not have the distinctive shape of arctic fox ears, but ears that look more like red fox ears.

The image credit given by the article is just "iStock", so I searched iStock to see if I could find more information about the photo. I found another photo of the same fox here, also labeled as an arctic fox, but not really any further information.

What species is this fox?


texts:
So I find these flies every year in my mulch, and I've never seen them anywhere else. The mulch becomes full of their larvae, which I feed to my toad and lizards. There are so many that you can hear them moving. The adults are black, look like a wasp or hornet, and have a curious green patch on the underside of their abdomen, which is a clear patch showing some kind of liquid. The larvae are brown and have a little hair on them.

It's about one inch I think maybe a little less. I hope the quality is good enough, because I used my iPod for the picture and you can't do macro with it. Also, I live in Hillsboro Oregon. I am near a small forest and in the suburbs.


texts:
i couldn't take a picture because i get rid from it as soon as posible. Because i thought maybe it was a bad parasite.

But i draw a picture of it at my computer. But my picture not very accurate because it was very tiny to see what it actually look like. and i cant remember all of the characteristics of it.

It is very tiny about 5 mm in length. and maybe almost 0.1 mm thick. I assume that yellow thing is head, because of movement directions is towards that way. To move, he elongates its own body then holds to surface with its own head, then let free its other ends grasp from the surface simultaneously shrinks to shorter length maybe half of its elongated length. than repeats whole process.

It was shrinks and elongates to move

it was moving like its got very soft body. and it was becoming significantly thinner when elongates.

Sometimes looks like checking surrounding surface with his head. Seem like it tries to navigate.

finally I must describe how my picture could inaccurate: it was very tiny i cant see his body parts exactly. i guess i see a tiny structures appears like his 2 pair back leg and 1 structure ball like thing attached to end. But this structures possible thickness are micrometers so i also thought that structures could be attached dust particles. And i also saw structures like this at the front end, but it was so tiny, i cant even drew because i see just barely but cant figured what was it like.

only im sure about its head and white-ish neck.

it is elongated at the picture.

So picture is representing what i see. but not %100 accurate. due to reasons i described.

i hope my questions description is enough and isn't improper.


texts: The new DNA study showing that we have two DNA codes and not only one unique code

texts:
I am looking for a study that i read maybe 2-3 years ago that i cant find at the moment.

Scientist has always believed that humans only have one unique DNA code that makes us who we are, but a couple of years ago scientist found that we actually have two DNA codes, something that the scientists called mysterious and that this changed what we always have belived regarding humans uniqe DNA code that makes us who we are, now this was not true anymore with this new finding, since we have two codes which means that who we are could be more complex and not only be information stored in one DNA code. I cant find this study when i look for it on google, do you know which study i am speaking of? i would like to find it again, so that i can see if there is any updates by the scientists, and i also think it is extremely interesting and don't want it to get lost, i forgot to save it in favorites before.


texts: How close are we to having phages take over the role of infection control from antibiotics? What developments need to occur?

texts: The discovery of, and research in, the field of phages was overshadowed by the discovery and implementation of antibiotic treatments for infectious disease control.  With the rising concern of antibiotic-resistant microbes, is there a serious effort to refocus research and development to master the science and technology of phages?


texts: Why do endotherms need more food than ectotherms?

texts:
I have a rough idea: endotherms need more food to keep their temperature stable whilst ectotherms use less of their food in respiration.

but that's just me parroting the textbook I don't really understand it.

Could someone help out? Thank you.


texts: Is there a complete connectome of a cortical minicolumn?

texts:
I know that there are projects that try to map brain connectivity. Given that a cortical microcolumn has only around a hundred neurons I wonder whether there is a dataset available with the complete connectivity of just a single minicolumn of the neocortex. Doesn't have to be human.

I posed this question on cognitive science stackexchange already, but it doesn't seem to be happening.


texts: Do pregnancy and breast feeding increase basal metabolic rate?

texts:
Since pregnant or breastfeeding women have extra nutritional needs, does that mean they have a higher BMR?

Why I thought the conclusion would be sensible: Since BMR is the energy needed to perform body functions (breathing, respiration, homeostasis, digestion, etc), pregnant woman or breastfeeding women, because of their extra 'activity' (due to the presence of the fetus) will have a higher BMR.


texts: Which Receptors are Involved in the antidepressant effects of SSRIs?

texts:
From what I've read the major receptor subtypes involved in the antidepressant effects of SSRIs are:

5-HT1A
5-HT2C
5-HT3
5-HT6

Please cite journal articles to back up your claims, I don't want any piece of information to be unverifiable.


texts: What stops messenger RNA from binding to itself?

texts: Since mRNA is single-stranded, and (mostly) floats freely within the cytosol, what stops it from folding onto itself (like DNA) and preventing transcription?


texts: Do housekeeping genes vary between tissues

texts: I am working on an RNA-Seq project, and I am aware that some researchers use housekeeping genes as a method of normalization.  My project has several different tissues, and I was wondering if housekeeping gene expression is generally invariant across tissue type?


texts: What is difference between several mRNA RefSeq for one gene?

texts: I'm looking for mRNA RefSeq sequences for a given gene in the UCSC genome browser by searching gene name "HLA-F" in human (scroll to Refseq genes section). There are several RefSeq mRNA for the gene, what is difference between these RefSeq sequences and which one of them is what I want?


texts: I know that salt is used as preservative as it dehydrates microbes. Is there any other advantage like - altering pH or inactivating microbial enzymes ?


texts: How can the pressure during contraction vary between the left and right ventricles?

texts:
After reading this passage from my physiology textbook (Vanders Physiology p. 384), I'm confused about how exactly the right and left ventricle can create markedly different pressures as they pump blood even if they have the same stroke volume, i.e. they push out the same amount of blood.

Typical pulmonary arterial
systolic and diastolic pressures are 25 and 10 mmHg,
respectively, compared to systemic arterial pressures of 120
and 80 mmHg. Therefore, the pulmonary circulation is a
low-pressure system, for reasons to be described later. This
difference is clearly reflected in the ventricular anatomy—
the right ventricular wall is much thinner than the left.
Despite the difference in pressure during contraction, however,
the stroke volumes of the two ventricles are the same.

How can two ventricles push the same amount of blood but at different pressures? I always assumed that pressure was created by a change in volume of the ventricles, and so I expected that if both ventricles have the same "change in volume" as they contract, they should also push out blood at the same pressures. Why is this not the case?


texts:
I just got my finger burnt (first degree burn $\Rightarrow$ I didn't even bother to bear the wound). It didn't hurt much, even when I pressed the wound.
However, when exposed to heat (hot water, but not so hot to hurt undamaged skin), the pain became at least nasty.

Is it an evolutionary adaptation to avoid hot objects not to get burnt again?


texts: What are negative and positive after potentials?

texts:
After depolarization: is the slow repolarization phase which follows a rapid fall in spike potential and extends up to attainment of the RMP level. It is called phase of negative after potential and lasts for about 4 ms.
After reaching the resting level (–70 mV) the potential further falls and becomes more negative (–72 mV).This phase is called after hyperpolarization or phase of positive after potential.

What is the reason for naming them as negative and positive after potentials?
My attempt: I think we are naming them based on the direction
of current, i.e. during after depolarisation membrane potential is going further negative , so the name negative after potential, and during after hyper polarisation, membrane potential is going from hyper polarised state to resting state, so its named as positive after potential.
Am I correct?

Source:Textbook of physiology


texts: Although skeletal muscle fatigues fairly rapidly, clams have a protein called paramyosin that allows them to sustain contractions for up to a month. What might be the role of paramyosin at the molecular or cellular level, which results in this peculiarity?


texts: Is it dangerous to combine MAOIs with stimulants? According to wikpedia, Parnate, for example, "leads to an increase in the availability of monoamines, such as serotonin, norepinephrine, and dopamine, as well as a marked increase in the availability of trace amines, such as tryptamine, octopamine, and phenethylamine." A stimulant like Vyvanse, for example releases dopamine but doesn't act significantly on serotonin. So would combining the two be dangerous?


texts: What is the signal that indicates which neurons Schwann cells should myelinate versus which should remain unmyelinated?

texts:
Schwann cells are neuroglial cells that produce myelin in the peripheral nervous system.

However, not all axons are myelinated - some will remain unmyelinated.

There must be some signal that indicates which cells are to be myelinated - what is it?


texts: Statistically, why is the number of mutated genes in eggs treated with chemical mutagenesis one?

texts:
Excerpted from the Guide to Research Techniques in Neuroscience [1]:

  In chemical mutagenesis, a scientist applies a mutagenizing chemical, such as ethyl methane sulfonate (EMS) or N-ethyl-N-nitrosourea (ENU), to thousands of eggs/larvae, which statistically creates lines of ani- mals with mutations in a single gene in the genome.

My hypothesis is that the discrete probability distribution of the number of mutated genes can be approximated by a normal distribution with mean=1, thus it is said statistically the number of mutated genes is one. But how can the scientists know which organism or cells contains only one mutated gene, or for that matter one mutated gene that is caused only by chemical mutagenesis?

[1] Carter, Matt, and Jennifer C. Shieh. Guide to Research Techniques in Neuroscience. Academic Press, 2015. ISBN: 978-0-12-374849-2


texts: What are these stars in my microscopic image?

texts:
I see this very curious patterns on the sun-facing side of a jasmine (probably) leaf - visible with a makeshift microscope (about 50x)

What are them? Pores? Are there other plants with similar textures?

The microscope is made out of a webcam, as described here


texts: effect of amino acid limitation in CHO cells

texts:
I would like to know the effect of individual amino acid and their role in CHO cell growth and their effects on their metabolic pathway if any.
And also if there is an amino acid which has an effect on the cells what will be the condition of the CHO cells is there any drastic drop in the viability or is there any reduction in the product quality.
Im working with a recombinant CHO cell line for the production of recombinant antibodies.


texts: List of the biggest companies that work in selective breeding

texts:
Looking at this question, I've been wondering, What are the biggest private companies which work in both animal and non-animal selective breeding?

Let me know if Biology.SE is not appropriate for this kind of question.

Thank you


texts: Why do oncogenes show genetic dominance?

texts: As we know that tumor suppressor gene causes cancer only when both the alleles are recessive in nature.But in case of oncogenes if only one allele is dominant it can cause cancer.Why in case of oncogenes to become a cause of cancer both allele aren't recessive?


texts: Why do parasitic amoeba lack a contractile vacuole?

texts: Compared to the other amoeba, most parasitic amoeba lack contractile vacuole. I could not get the correct answer as to why these parasitic amoeba lack contractile vacuole.


texts: Books about famous experiments in biology - 'methods of investigation'

texts:
I'll explain briefly what I need (hoping to find something) :

I wanted to know if someone knew about a book that in a way or another talked about the greatest experiments in biology (Griffith, Avery-MacLeod-MacCarty, Hershey-Chase) or methods normally used to study  certain phenomena  for example, and explaining or talking about the paradigm used in biology research in such cases.

I know it might sound too vague, but I will have a kind of 'exam' essay, in which in addition to the biologic phenomena asked in terms of "notions" one will also have to suggest a 'method of investigation' to study it.

And my main problem is that in school just the theory is normally taught and not the practical approach to such topics, so I really lack knowledge in this.

So what I'm asking is whether there is a certain book or even a suggested approach that I might start using that might help me in learning what I explained above.

Thank you for your help!


texts: What is the meaning of conservation site in miRNA-mRNA pairing context?

texts:
I am not biologist and just work in Bioinformatics field.
Does anyone know what is the meaning of conservation in the context of miRNAs and their pairings to mRNAs?

Example:

Each of these duplexes has a region called the “seed”, a site located at 5’ part of miRNA (positions 2-7) which is characterized by a strict or almost strict Watson-Crick pairing between miRNA and its target site and shows the best conservation among the miRNA sequence.

(from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182075/)


texts: What percent of the population has some form of synesthesia?

texts:
Data I am trying to get my hands on:

What types of synesthesia (e.g. Grapheme-color synesthesia,  Chromesthesia, etc.) are most common across the population?
What percent of population has that type of synesthesia?

It would also be great if there's geographical (genealogical) data on what types of synesthesia are more common to what areas.

What percent of the population has what type of synesthesia?


texts: How could a species be engineered to go extinct?

texts:
Non-biology background here.

I read this very interesting article: https://www.wired.com/story/crispr-eradicate-invasive-species/

However I am having a hard time wrapping my head around something:

From my basic understanding of natural selection, a gene/trait will spread if it gives the group a relatively higher chance of having children, who will pass on the trait, etc.

However in this example, the trait is infertility! Doesn't it go completely against natural selection? How could this spread??


texts: What's the difference between a simple and 1-foliolate (unifoliolate) leaf?

texts: How is a 1-foliolate leaf (e.g., Hardenbergia) different from a simple leaf?


texts: Genes where both a disabling mutation and copy number amplification cause different genetic diseases

texts: I'm trying to make a list of such  genes, because they must be tightly regulated. MeCP2 is one - it causes Rett Syndrome with a disabling mutation, but causes MeCP2 duplication syndrome if its copy number has been increased. Anyone know of any others?


texts:
The human brain consists of neurons that transmit impulses like wires that conduct electricity.I am confused about where are our thoughts stored and what really are thoughts? For example if I think about space, what is actually happening in my brain, and in what form is my memory that there are black holes in space, stored?

After doing a little bit of research I somehow came to the conclusion that thoughts are nothing but the electro-chemical reactions that are triggered by external stimuli and Hippocampus is responsible for storing long term memory. But I was unable to understand what the following paragraph means:

  "The hippocampus helps to solidify the pattern of connections that form a memory but the memory itself depends on the solidification of connections between the individual brain cells".

Please explain it. Am I correct so far? Please help.


texts:
I must calculate the incidence values for Watermelon Mosaic Virus in different seasons within of habitat factor.
This incidence data comes from infection detection of some plant sampled in different habitats (Oakwoods, Wastelands, Edges, Crops).
The plant sampled in these habitats were sampling in different seasons (Summer, Spring, Autumn)
The Crop habitat was sampled only in Summer, and the host sampled in Crops was in majority Cucumis melo species.
This virus have a preferred against Crop habitat, Cucumis melo hosts.
I calculated the incidence, and then I calculated the significant difference between them.
Fisher test, showed that the incidence is higher in summer and in Cucumis melo host.
Is it possible to separate the effects of Crop and Cucumis abundance (the unbalanced sampling of seasons across habitats) of my conclusion of significant seasonal variation?
I know that my conclusions are not really a seasonal effect. Because I sampled 10,000 melon plants for a short period in summer, and that is the preferred host.
How can I separate the abundance of the incidence results?
What statistical analysis may I perform?
Thanks in advance


texts: Why are there no multicellular prokaryotes

texts: Why don't complex multicellular prokaryotes exist and also what makes eukaryotes multicellular?


texts: Taking a look in internet you can find photos of mutated mammals with 6 legs. Some cows with legs in unnatural positions were shown in website versions of widely known newspapers (you can easily guess here that if the animal gets his additional legs in the back or another unuseful position why a mutation like that wont spread, but the point here it's 2 additional legs in mammals do appear occasionally) . Also there are some dubious photos of sheeps with appparently functional 6 legs, these ones are dubious and hard to confirm if real, some clearly fake but the dubious ones are there and make you wonder. Insects have 6 legs, there are confirmed mutations of mammals with 6 legs, then why did it never appear a mammal species with 6 legs. Is there any known reason why 6 leg mammals are only found in mutations? (how about size and enviroment, is there any reason in those for them not to get 6 legs?)


texts: What type of insect is this? Is it ant or something else?

texts:
I was sitting under morning sunshine when I saw this:

At first, I thought that it is a common Indian black ant. But it was moving much faster. Also, it seemed to have 2 (or probably more) eyes (sorry, couldn't take images as 'twas too fast). The most surprising part was when it leapt over the chair WITH A WEB! (just like a spider). Also, its mandibles(?) are much bigger than an ant's. Is it some kind of hybrid of ant and spider. I recently read that in some caves new varieties of spiders, which look like beetles (or maybe opposite) have been discovered. Is this related to them?

Details: I found it in Northern Plains, India. Its length is almost 1 cm (maybe bigger) and breadth is about 0.5 cm (actually slightly smaller than that).


texts: Alternatives to NCBI BLAST during US government shutdowns?

texts:
Many molecular biologists are used to going to NCBI BLAST for quick, hassle-free BLAST searches of their genetic or protein sequences.

However, during the last American government shutdown in 2013, BLAST was rendered unusable due to lack of funding.

The incumbent president is also threatening to shutdown the government if funding for the Mexican border wall is not approved by the Democrats.

What are some alternatives for NCBI BLAST that are reasonably fast, easy to use, and would not be rendered unusable in the event of American government shutdowns? Ideally, the tools should encompass all of the standard BLAST sub-functions (pblast, PSI-blast, etc).


texts: Alignment tools on desktop for peptide alignment sequence and how to make annotations on alignments look presentable?

texts:
I have 10 transcripts where I need to do 5 peptide sequence alignments (2 transcripts per alignment). I need to do this in order to indicate which amino acids lead to which domains.
My questions are two:

Is there a tool I can use from my laptop that aligns peptide sequences? Because clustal omega peptide alignments only last two weeks and is not ideal for replicability in a paper.

The ultimate aim is to use those alignments and domain classifications to a project I am writing and I am trying to make it as presentable and scientific as possible. Any suggestions on how to make peptide alignments and annotations on peptide alignments (which indicate protein domains) look presentable for a paper or if a paper has already shown peptide alignments in a presentable way that would be highly appreciated.


texts:
I've a question about ORF and translation into protein. Say I have an RNA transcript that contains two ORFs, one in phase 1 ; one in phase2 ; as:

ORF number 1 in reading frame 1 on the direct strand extends from base 529 to base 759.
ORF number 2 in reading frame 3 on the direct strand extends from base 849 to base 1223.

So ORF number 1 comes earlier in the transcript, but ORF number 3 is longer ..
Is it always the first ORF that is translated ?
Edit >

It's in an eukaryoytic organism and same gene (it's the same transcript)

I use ORF finder (http://www.bioinformatics.org/sms2/orf_find.html) on my transcript sequence and it gives me two potential ORFs (ORF 1 and ORF 2 within two different frames)

Thanks


texts:
Since the new queens-to-be have wings, it means that ants either evolved from insects that can fly, or insects that can fly evolved from ants, or that we have a case of parallel evolution (which is unlikely).

Now, what evolutionary benefit is there to not have wings?


texts: Feeding behavior of organisms that prey on microorganisms

texts: Is there a specific term for organisms that feed on micro-organisms?


texts: Beetle identification - Kakadu NP, NT, Australia

texts:
I am trying to ID this beetle;

Size: not too big - approximately 2 cm (3/4 inch)
Where: Litchfield National Park, Northern Territory, Australia;
When: Southern hemisphere's spring, early September; the end of the dry season;
Time of day: night.

To my untrained eye, it looks like a cockschafer, but from the linked wiki page I understand they are a species confined to Europe. I tried a reverse Google image search and sifted through the site of Parks Australia and related pages, but to no avail.


texts: How does Iota-Carrageenan achieve an antiviral effect?

texts:
"Cold Defence" nasal sprays are recommended to be taken either preventatively or in the early stages of a cold.  The active ingredient in these sprays is Carrageenan.  After some research, the active compound is Iota-Carrageenan (ι-Carrageenan).

This study by Eccles et al[1] shows that this drug is clinically effective.  The study was only designed to test efficacy rather than to explain the mechanism, however. A fleeting mention is provided in the discussion section:

  The above results suggest that the treatment with Iota-Carrageenan reduces the viral replication. Consequently fewer cells are infected, the immune reaction against the viruses is less pronounced and fewer symptoms occur.

How does ι-Carrageenan produce an anti-viral effect?

Eccles R, Meier C, Jawad M, Weinmüllner R, Grassauer A, Prieschl-Grassauer E. 2010. Efficacy and safety of an antiviral Iota-Carrageenan nasal spray: a randomized, double-blind, placebo-controlled exploratory study in volunteers with early symptoms of the common cold. Respiratory Research, 11:108, doi:10.1186/1465-9921-11-108.


texts:
So I understand that tRNA bonds to a codon (with an anticodon) in the translation process. I read in my biology textbook that the ribosomes "read" the mRNA strand.

Why do the ribosomes need to read the mRNA strand? Are the ribosomes able to intepret the message and bring the correct anticodon to it? Or is the main function of the ribosomes just to join amino acids to make polypeptides? I'm just confused why the ribosomes read the mRNA strand when it seems like there is no need to.


texts: What is the motivation behind fluorinated pharmaceuticals?

texts:
From what little research I've done, it appears that a significant portion of modern psychoactive drugs are fluorinated in one way or another (for example, Buproprion, Fluvoxamine, or any number of other antidepressants).

What is the motivation behind the addition of these groups? My initial guess would be that it either increases blood-brain barrier clearance or reduces the drug's metabolism, but I've been unable to find papers supporting either idea (or papers on the subject at all, for that matter). Any books/papers illuminating the subject would be greatly appreciated.


texts: Each cell in our body contains identical dna. And, yet some cells become liver cells, some become brain cells etc. How this happens , when all of them has same dna? Is it because of epigenetic control of gene expression?


texts: N-methylcocaine cation (pictured) is a cocaine analog that blocks HERG intracellularly, if somehow it were able to get into a cell.  A review of tropane alkaloids in Erythroxylum does not include it, or any N,N-dimethyl derivative, but this might be attributed to the issue that a quaternary ammonium salt, though it might be technically considered an alkaloid, would not be isolated (or removed from a soft drink flavoring?) by acid-base extraction.  But before we let paranoia overtake us ... is there any indication the compound exists as a natural product?  (You don't need to look beyond Erythroxylum.  An answer just for E. coca or E. novogranatense would be welcome.)


texts: What is the distance between the sciatic nerve and the colon at the closest point?

texts: Is it possible that a full colon impinges on the sciatic nerve? Is there anything that physically separates the sciatic nerve from the colon?


texts: in order to align genome multi-fasta files, do you ignore the chromosome sections?

texts:
I want to test my implementation of Needleman-Wunsch on two fasta files downloaded from https://hgdownload.soe.ucsc.edu/.
However, fasta files on this site are multi-fasta and therefore are split into sections each one belonging to a chromosome.
If I want to align the entire genomes in these files:

do I just ignore the chromosomal separation inside these files? thus do I stitch the chromosomes of each file into one big chunk?
or do I align combinations of these chromosomes?


texts: The advantages of using a strand specific cDNA in RNA-Seq?

texts: May I ask what are the advantages of using a strand specific cDNA library in an RNA-seq experiment? as far as I know it can make us able to read the code region but what about other advantages?


texts:
GTP gamma S is routinely used in studies of G proteins to stably activate the G protein. Comparing the structures of GTP gamma S and GTP, the Sulphur atom replaces the Oxygen attached to the leaving Phosphate group. However, this is not the bond that is hydrolyzed (dashed line). What makes it non-hydrolyzable then?

GTP:                    GTPgS:


texts:
I am trying to learn about basic cell biology, and have what is probably an extremely simple question.

So this is how I understand it so far:
Proteins are made from amino acids. This process is called protein biosynthesis, which is carried out by the ribosomes. So proteins are made by the ribosomes in every single cell.

So are the proteins made by the ribosomes to stay in the cell? Or can a protein move to other cells, and if so, what's the reason behind it?


texts: The reproduction patterns of fungi: what’s the difference between them?

texts:
I am going to take TOEFL, and am getting perplexed by the difference between cell division and budding and fragmentation of fungi.

Those three terms seem like all the same all to me, so could anyone teach me fundamentally how they differ from each other?


texts: What inhibits linkage between actin and myosin filaments

texts:
What is the mechanism behind the inhibition for cross-bridge linkage between actin and myosin filaments in the binding-tilting cycle? There are 2 possible ways that are in my mind:
a.  Tn-I (tropnin-I), binding to F-actin: when [Ca2+] falls below the threshold, Tn-C are inactivated. Therefore, Tn-I relocates and SOMEHOW this causes the cross-bridge to break (ref)
b.  ATP rebinds to the myosin head, forming ATP-myosin complex. This has a relatively low affinity towards binding the myosin-binding sites on F-actin (than myosin-ADP-Pi complex). Therefore, the cross-bridge break.
From my understanding, (a) is strange: when Tn-C is inactivated, it should cause Tn-T to change conformation so that tropomyosin covers the binding sites again. But I think I am wrong as otherwise, Tn-I is useless, but I really don't know how Tn-I exerts its inhibitory effect.
Thank you.


texts: Why do some fruits have a much wider range of acceptable sizes than others?

texts: Some fruits such as pumpkins can grow to be 100 lbs. Under different conditions, the same variety of pumpkin can produce a 15 lb. fruit. Both plants are healthy, and look the same except for their size difference. If I took two red apple trees and planted them in extreme opposite conditions, the fruit size would be nearly the same. The fruit quantity would be lowered in the tree grown under poor conditions. Why do fruits have such a variable range of acceptable sizes?


texts: In mitochondria, what is the mechanism by which electrons are transferred between different cytochromes?

texts: And how is the energy gained from the lowering of the "energy level" of the electron used to generate the chemiosmotic gradient?


texts: Why doesn't the cytosol dissolve the polar structures?

texts: we know that cytoplasm of cells are filled with water molecules and other hydrophilic molecules so my question is why the water of cytosol doesn't dissolve the ionic part of the lipid bilayer or why it doesn't dissolve the proteins and enzymes which are most polar and ionic and they still form structures,organelle and function and suspended in water?


texts:
I sometimes wonder how many different individual musical scales could be perceived by human ears. I define a musical scale as a collection of notes that relate to some fundamental frequency by specific ratios. For instance

do $2^{0}f$
re $2^{\frac{1}{6}}f$
mi $2^{\frac{1}{3}}f$
fa $2^{\frac{5}{12}}f$
sol $2^{\frac{7}{12}}f$
la $2^{\frac{9}{12}}f$
ti $2^{\frac{11}{12}}f$
do $2^{1}f$

I once did an experiment where I took various sine waves at different frequencies and multiplied them by the appropriate ratios. I found for the ones I tried that I did indeed heard the major scale. But a mathematician will look at the positive real numbers $\Bbb{R}^+$ and say there are an infinite, uncountable number of possible frequencies. However, Biologically I cannot imagine the human ear is capable of distinguishing between an infinite number of frequencies.

What is the biological limit on hearing resolution? Is there a way to estimate how many different major scales one can hear? In other words, how many different frequencies can be heard?


texts: What is the surface area of the vitreous humour in contact with aqueous humour?

texts:
This is a question regarding the anatomy of the human eye, however for my purposes medium sized mammals should do. I am interested in estimating the surface area of the hyaloid membrane of the vitreous humour which has contact with the aqueous humour circulating in the posterior and anterior chamber of a typical human eye.

The surface area in question is highlighted in red in this schematic of the cross section of the human eye.


texts: TRANSFAC Matrix.dat retrieve count matrix using BA or CC field

texts:
In the TRANSFAC Matrix.dat most of the motifs are given in the form of count matrix, but a few of them are given as some kind of frequency matrix. Those aren't ordinary PWMs because rows don't sum to 1, but these sums are more or less stable across rows.

I would like to have a raw count matrix in all cases, so I trying to retrieve the count matrix from those several "fractional" cases.

At first I thought that the field BA (Basis - statistical basis of the matrix) MANDATORILY starts with a number of sequences actually used in the matrix, so I would be able to simply multiply:

$$
\frac{\text{nucleotide value}}{\text{row sum}} \times
\text{number of sequences from BA}
$$

Moreover, sometimes in CC field there's information like: core from: 11

Unfortunately, the results are not very close to integer value, so this cannot be explained by rounding errors.

For example, in a certain row we have (btw, the row sum is $10.73$ from rounding errors):

3.99   4.07   0.87    1.8

BA  17 compiled ... sequences; total weight of sequences: 10.74

CC  core from: 11, length: 6

$$
\frac{4.07}{10.74} \times 17 = 6.4423
$$

$$
\frac{4.07}{10.74} \times 11 = 4.1685
$$

In my opinion these values $0.44$ or $0.16$ couldn't be explained by rounding errors. There's no description (link to article) enclosed to this motif. That aren't log-odds because all of them are non-negative values.

In this particular case, if I use the formula $count(x) = round( (\frac{x}{10.74}) \times 11 )$, the resulting counts will sum up to $11$, so it's fine.
This method with value $11$ replaced by $17$ doesn't result in set of values summing to $17$, but $16$.

The problem is that in another example I have

BA  17 compiled binding sequences; total weight of equences: 12.86

CC  core from: 1, length: 4
In this case I should rather multiply by $17$ not $1$ to get the sum of $17$.
As you see, I cannot stick to either BA or CC for all such motifs.

How would you retrieve the raw count matrix in a such case and what could be the problem in my approach? (jumping between BA and CC values)

Could anyone explain how those values in matrix have been derived, is it some kind of log-odds?


texts: How long does it take for dopamine to reach normal levels after a significant drop?

texts:
The building block sequence for is: Phenylalanine << Tyrosine << L-Dopa << Dopamine. It’s produced in only a few, very specific regions: Substantia Nigra and the Ventral Tegmental Area. Although, on average does this take minutes, hours, days, weeks? And does releasing it between synapses or something else for normal activity affect the time?

Ultimately, I am trying to find a graph of the average anergia level after sex. Or similarly, dopamine levels after orgasm. Most of the research I have come across is about disorders or is too general. Also, there are informal articles and graphs of dopamine levels, but they very widely and are not sourced.


texts: Does terminology for changes in membrane potential refer to additive or multiplicative change?

texts:
Is the membrane potential just the number of mV, or is it to what extent it differs from 0?

For example: If the mV goes from -40 to -60, can you say that:

The membrane potential decreases, because the number of mV decreases (from -40 to -60)
or
The membrane potential increases, because the difference to 0 increases (from 40 to 60)?


texts:
I found this fossil near a beach in Victoria, Australia. Can anyone identify it?

It is roughly the size of an Australian 20 cent piece (~30 mm). I think it might have been washed down from an eroding cliff.

I found another similar sized but less detailed fossil near by, which might be the same thing.


texts: Do humans have a huge impact on the ecosystem ? is it possible for other animals to live without us ?


texts: Why is Lamarck's evolutionary theory considered incorrect?

texts:
Many sources postulate without much argumentation that Lamarck's evolutionary theory is "obviously incorrect". A classic example provided in such sources is the one with giraffes, in which Lamarck argued that the necks of these animals became long as a result of continually stretching to reach high foliage. This mechanism for adaptive change in response to the environment is considered wrong.

Now the counterargument to Lamarck's ideas comprises modern findings in genetics. So it is stated that organisms pass down traits through predetermined genetic information, not based on environmental adaptations during their lifetime. Furthermore, genetic research shows that living organisms cannot alter their genetic material as needed.

Doesn't the latter contradict the evolutionary theory itself, which states that nature (i.e. environment) shapes species through natural selection in the environmental milieu? If it is not the environmental/natural factor that is responsible for genetic evolution, then what is?
If genetic material were to be unchangeable, then how would adaptation to the environment and consequent evolutionary change would ever be possible? The genotype (following this logic) would remain the same.
And lastly, maybe giraffes do not develop long necks at such a rapid pace (as Lamarck probably thought) by simply stretching their necks in one generation; however, what, if not neck stretching, is responsible for their consistently longer necks throughout thousands or millions of years? Hadn't the environment gradually shaped their genotype? Similarly, if I run more often, maybe my children will not become more fit, but isn't it just a matter of time (thousands of years) that if all of us consistently run a lot, then our offspring will eventually become more fit? Wouldn't our voluntary efforts eventually enhance our genetics? I do not see any problem with Lamarck's logic at all, except probably the time frame.


texts: Why prefer $MgSO_4$ over $MgCl_2$ in recipies

texts: Many molecular biology recipes use MgSO4 (and not MgCl2). Is there indeed a preference? If so, why?


texts: Why is the Tm defined as the temperature at which 50% of dsDNA has changed into ssDNA?

texts: In molecular biology, Tm is defined as the temperature at which 50% of dsDNA is converted to its single stranded form. Intuitively it would seem that the melting temperature should have been defined as the temperature at which the entirety(100%) of the dsDNA converts into ssDNA. What is the basis of using this ratio, i.e, 50% in the definition of Tm?


texts: Difference between protein channels, protein carriers and protein pumps?

texts:
I'm revising for my biology exam and I don't fully comprehend the difference between protein channels, carriers and pumps. I know that:

Protein channels do not require ATP (passive transport)
The difference between passive and active transport

My questions are:

Are protein carriers and pumps the same?
I read that protein carriers can perform both active and passive transport, is this true?
But protein pumps always require ATP?


texts:
I can get goosebumps at will, regardless of the environment. Its mostly visible on my arms, and I can feel it on my head. It requires some level of concentration to achieve this.

My questions are : what biological mechanisms are involved in doing this ? Is it common ? Is it useful ?


texts: Processing of speech/non-speech sounds in the human brain

texts:
I have a ""which came first: the chicken or the egg?"-kind of question regarding the processing and understanding of speech / non-speech sounds in the human brain.
I'm wondering whether speech and generic non-speech sound processing in the human brain are somehow related and whether one of the two is used as a "basis" mathematically speaking or a reference to understand the other.

Most people use "His voice/It sounds like .." to describe sounds/human voices, besides, we are able to tune out and block any non-speech acoustic activity surrounding us if we are not in a conversation which suggests that we have a special sensibility for hearing speech (or maybe our language or just our names if someone is calling us).

I've read an article which states that :

  Knowledge of our mother tongue acts as a sort of auditory "template" that influences the way we perceive the sounds of other languages (scientists call this "native listening").

Hearing other languages differently than its native speakers is easy to grasp but is there any research that studies the difference in brain activity when speech / other sounds are heard and whether there is something special about hearing speech in particular.


texts: I keep seeing these bugs on a wall in my house in Istanbul (Turkey) walking up and down generally during evening and night. They are about 1 mm long and have a brownish color. I see more of them through late hours. Does anyone know what they are called?


texts: aspartame in relation to generating methanol

texts: So I posted another question with respects to methanol and aspartame in metabolism with respects to toxicity.  So another question I have is "Why is aspartame used as a dietary component to generate methanol following metabolism?"  This is a topic of discussion in my thermonuclear pharmaceuticals class at my institution, and more or less it's also part of an active assignment that we're expected to cover for a weekly discussion which is no graded; otherwise I wouldn't seek free advice on this.  As much as I read in my book it does not go into detail and I am curious if anyone out there has any advice on this or perhaps you could point me towards relevant articles?


texts: Why are plasmid genes not already incorporated into bacterial chromosomes if necessary for stressful situations?

texts: If plasmids are important for bacteria to express specific genes under stressful conditions, why are these genes not already incorporated into their chromosome to begin with? What is the evolutionary significance for this?


texts: How do I use BEAST for divergence time estimation in this case?

texts: I am interested in using BEAST to find the divergence time estimates of species separations within a genus of frogs. The genus separated from a outgroup taxon I have chosen around 80 million years ago. That is all the information I have. Is it possible for me to do a divergence analysis using BEAST and set an informative prior based on the information I have ?


texts:
The title says it all, what makes eye defects so common in the world? Whereas defects of any other body part is quite uncommon, I searched online and one of the articles said that 6 out of 10 people wear glasses, I think that is a big percentage of people with eye defects, BTW I'm myopic and I wear glasses too. Are all body parts defective to a certain degree, but It seems more pronounced in the case of eyes?

P.S

I know nothing about biology, I appreciate if someone could explain it with preferably less technical terms, this is my first question on BSE, let me know how I can make the post better.


texts: I wish to calculate how much CO2 would a sq m of moss fixes to glucose in one day, taking about 20 degrees C average temperature, 55% humidity and a regular 8 hour day. Water and nutrients are at optimal amounts. Is there a formula I could use? I can't seem to find anything online.


texts: What is the practical difference between SC, SD and CSM?

texts:
Is there some logic to how SC, SD and CSM yeast dropout media differ from each other? I have encountered these three formulations in Sunrise Science Products' catalog, and it appears that the composition differs quite a bit, but I couldn't find any information on what the purpose of these media is.

Obviously, any nutrients that are "dropped out" (e.g. -Ura) will select yeast cells on the basis of that marker. However, what about SD-Ura, SC-Ura and CSM-Ura?


texts:
For presynaptic inhibition, I am aware of these:

Ca²+ influx (into the presynaptic nerve terminal) is decreased. And this in turn reduces the probability of releasing synaptic vesicles from the presynaptic neuron.

The influx of Ca²+ is under the influence of voltage-gated Ca²+ channels.

My questions:

What inhibitor(s) can be involved in this inhibition?

What is the ionic basis of this inhibition? (By this, I want to know how the movement of ions affects the voltage-gated Ca²+ channels)

Does the reaction cascade intitiated by the inhibitor in any way affect the amplitude of the AP generated upstream when it reaches the presynaptic nerve terminal?


texts: How do disulphide bonds in hair cause curling?

texts:
I understand that there are several characteristics of curly hair which differ from straight hair (such as an asymmetrical distribution of disulphide bonds in curly hair), but really am struggling to understand the root cause of inherent curl on the macroscopic level.

My current understanding of the hair structure is based mostly upon this website

The most relevant part of the hair for our discussion is the cortex, which is made up of many axially aligned macrofibrils, or macroscopic keratin fibers, which are in some filler essentially of lipids/proteins. Inside these macrofibrils are microfibrils. These are also aligned axially and in some filler of lipids/ proteins. Inside the microfibrils are the protofibrils, even smaller fibers which are twisted around each other like a yarn. These protofibrils are made up of 4 keratin chains which are essentially twisted together and connected by disulphide bonds and hydrogen bonds. While hydrogen bonds are easily broken, the disulphide bonds are not. In curled hair, the macrofibril isn't symmetrical but I am unsure as to how this, or what other effects, actually lead to the curling.

I had previously assumed that the reason for curling is that in an asymmetrical configuration of the hair(IE not cylindrical but more oval in cross section), some residual stresses are formed by the disulphide bonds between the keratin, If this is true, it would lead me to believe that it would cause increased buckling of the protofibrils. But, even with straight hair and more symmetrical disulphide bonds, you already have some curling and buckling of the protofibrils, but the hair doesn't curl on a macroscopic level.

As such, it doesnt seem like this buckling due to asymetrical disulphide bonds would necessarily lead to a curled or organized structure on the macroscale, with the macrofibrils. This leads me to believe I am missing something.


texts: Can a sound frequency 'not' within human hearing (20 Hz - 20 kHz) damage hearing when it is of high volume?

texts: We can't hear sounds outside the range of  20 Hz - 20 kHz. However, if an inaudible sound is played at high volume, will one's hearing be affected?


texts: Could Junk DNA be used as a Turing Machine by nature?

texts:
In what ways has DNA been studied to see if there a "programmable" aspect to it?

Has nature produced anything resembling a Turing machine within the cell, perhaps using the "junk DNA" as its code? I expect nature's way would probably be very round-about and not compact.

NOTE: I am not asking about building DNA computers, as this question had recently been contorted to become.


texts: How can binaural beats change mental state?

texts: Can anyone tell me how binaural beats of 10 Hz can cause a person to calm down and one of 40 Hz to cause someone to heighten their attention. All I know is that they work on the principal of Brainwave Entrainment. I am confused as to how can a 10-Hz difference in 2 sounds cause the brain to change its state of mind! A detailed but simple explanation would be great.


texts: How are horses and donkeys able to interbreed and produce a mule. Don't their genetypic variation or chromosomal difference prevent them from doing so? If not, then why not?


texts: Can IVF decrease the probability of trisomy in the fetuses of older mothers?

texts:
Is trisomy mostly due to complications with fertilization?

If so, does in vitro fertilization reduce the probability of trisomy for the fetuses of older mothers?

If not, can zygotes be screened before in vitro fertilization?


texts:
Suppose a plant sprouted when $t=0$ and died when $t=T$. Let $t_*$ be the time when the plant shifts the resources usage to maximize its reproductive organ. In the case of nitrogen shortage during plant growth, it is known that $t_*$ becomes earlier. Would someone please explain this phenomenon by relating to Rubisco?

Here are some of my findings:

It was shown that the decrease in the amount of Rubisco during leaf
senescence is higher compared to plants grown under suboptimal
N‐feeding conditions (Tercé‐Laforgue et al., 2004).
Rubisco is also considered as one of the most important Nitrogen
source that can potentially be remobilized and translocated to growing
or storage organs.

Currently, I understand how the nitrogen shortage is related to Rubisco, but I still do not how to relate this to the prioritization of reproductive organ. This might be a mere uneducated guess, but does this have something to do with survival of the plant? Say, it senses that Rubisco itself cannot replace the needed amount of nitrogen, then it is wiser for the plant to reproduce rather than growing.


texts: Can one type of bacteria cause several diseases?

texts:
If yes.
Does it change its shape in every disease, or does it remain in the same shape and cause several diseases?


texts: How do I measure bacterial growth in agar dishes (either by cell mass or by cell count)?

texts: I am doing an experiment in which I am growing S. mutans in agar dishes, and I am not sure how I would measure the growth of the S. mutans. I am also not sure if I would do this by measuring cell mass or by cell count. Any ideas?


texts:
I was under the impression that both ends of a muscle contract. For instance, the fibers of the biceps run parallel to the humerus so I thought they pulled toward the middle.

But now I'm confused because it sounds like the contraction of the fibers doesn't necessarily have to parallel the motion of the muscle itself. In other words, just because the fibers contract doesn't mean that the muscle lengthens or shortens in a particular direction.

Can someone clarify if muscles contract in both directions?

Or perhaps a better question is do muscle contract in a particular direction and is this the same direction that the fibers contract or does the muscle as a whole move in a different direction in comparison to the direction the fibers are contracting?


texts: Has an ectopic pregnancy's blastocyst ever been made to implant?

texts: Has an ectopic pregnancy's blastocyst ever been successfully extracted from the Fallopian tube and made to implant in the uterus?


texts: Why is the neuronal plasma membrane more permeable to potassium ions than sodium ions?

texts:
From what I understand, the greater permeability of the neuronal plasma membrane to K+ ions (which diffuse out) than Na+ ions (which diffuse in) helps to maintain the -60 mV resting membrane potential. However, I am not sure why. After all, K+ ions are larger so should the membrane not be less permeable to them? Could it be to do with the greater charge density of Na+ ions or is there another reason altogether? Does it have something to do with the 'leakiness' of ion channels?

Also, why is it that the resting potential is maintained and does not become increasingly more negative? Should it not be that because 3 Na+ ions are pumped out and 2 K+ are pumped in continuously, and more K+ ions are diffusing out than Na+ is diffusing in, that the potential is becoming increasingly negative? Is movement of other ions also involved in maintaining this potential?


texts: Is there any bank of animations for Embryology?

texts:
I am trying to find animations which can anonymous or generalised for Embryology.
However, I have not find any single good source.

Is there any bank of animations for generalised embryos?


texts: What is the role of pyrophosphatase in RNA polymerization?

texts:
In Molecular Cell Biology (8th edition) there's a fragment in chapter 5.2 that says:

The energetics of the polymerization reaction strongly favor the addition of ribonucleotides to the growing RNA chain because the high-energy bond between the α and β phosphates of rNTP monomers is replaced by the lower-energy phosphodiester bond between nucleotides. The equilibrium for the reaction is driven further toward chain elongation by pyrophosphatase, an enzyme that catalyzes cleavage of the released PPi into two molecules of inorganic phosphate.

How does the pyrophosphatase make the reaction more favorable? Does it make "harder" for triphosphates to form back again (now you have to attach phosphates one by one, not two at once)? If so, isn't one additional phosphate just as bad as two? To remove either you have to break one bond (between the first phosphate and the second), and you have a specialized enzyme to remove two of them (the RNA polymerase). Isn't forming a diphosphate (which needs to form in order to later make triphosphate) actually worse? Or maybe it somehow "reuses" energy stored in the bond between the two phosphates left?
Sorry if I didn't use the proper vocabulary, I'm new to biology.


texts: Are mosquitoes actually louder than similar flying insects, or have we evolved to hear them?

texts:
I've come across many flying insects smaller than the common housefly, but (anecdotally) the only such species that I can hear from an appreciable distance away is the mosquito, with its distinctive buzzing whine. It may just be luck that the loudest small flying insect (in my everyday experience), and therefore the easiest to detect and avoid, is also by far the most annoying. On the other hand, mosquitoes are the single deadliest animal for humans and were probably common on the African savannah in which we evolved, so maybe this apparent loudness is actually an auditory illusion, and similar-sized insects are equally loud but at frequences that we haven't evolved to hear or focus on. Are mosquitoes objectively louder than similar-sized flying insects, or might we have evolved to be particularly sensitive to their emitted frequencies?

(This question is the flip side of this one, which focuses on the mosquito's evolution rather than the human's.)


texts: Lampreys and the origin of certain brain structures

texts:
I'm not sure why, but I'd been under the impression that things like the optic tectum and basal ganglia developed post-2R (the double duplication of the genome ~1/2 Ga).

Lampreys (as far as I'm aware), also have these brain structures. The problem is that TimeTree seems to indicate that - unless the outlier of Otsuka et al is correct - lampreys diverged before then:

While trying to figure out which bit of my thinking is wrong, I came across this article that suggests lampreys had whole genome duplications, but completely separately to those in our lineage.

Does this mean that their structures evolved convergently? (Perhaps they're "obvious" things to evolve post-WGDs?) Or is my initial assumption wrong, and the structures are much older than 2R and pre-divergence from lampreys?

Or something else entirely? I'm confused, and I'm sure I'm missing something: I just don't know what.


texts:
The wikipedia page on surrogacy highlights two main forms of surrogacy: Traditional Surrogacy and Gestational Surrogacy. Traditional surrogacy inseminates the surrogate mother with sperm, while gestational surrogacy uses in vitro fertilization to form an embryo from egg and sperm, which is then transferred into the surrogate mother.

It does not discuss whether surrogacy is possible after a natural fertilization has already taken place, such as if a woman becomes pregnant and then wishes, for whatever reason, to have a surrogate take the baby to term. Is this biologically possible? If it is possible, what is the mechanism? Also, if possible, is heightened risk a major reason it is not more common?


texts: Why are the sex chromosomes called X and Y?

texts: Is there a specific reason that the letter Y is used as the symbol for the male chromosome and X is used for the female chromosome?


texts: Structure and reactions of the cofactors of oxidoreductases such as ferredoxin

texts:
I have seen the word flavoprotein being used in place of ferredoxin in few places and vice-versa. I have not found any source that mentions them both together and explains the relation between them.
Examples I have found are:
FAD-Flavin Adenine Dinucleotide/Ferrodoxin Adenine Dinucleotide
FNR-Flavo protein NADP Reductase/ Ferredoxin NADP reductase
Is there any relation between the two? Are they the same or do they serve the same purpose?


texts: Do somatic cells alter their own nucleotide sequence?

texts: I seem to remember reading that embryonic cells will frequently replicate the section of their genome containing rDNA by splicing in duplicate genes. The cells use this to produce ribosomes at a rate which would be impossible with the DNA present in cells from full-grown organisms. Is this real? Are there other examples of cells altering their their own nucleotide sequence?


texts: When you have your gallbladder removed, how does it affect bile flow into your small intestine?

texts:
Cholecystectomy, or surgical removal of the gallbladder, is an extremely common operation around the world. The gallbladder is typically viewed as a storage organ for bile produced by the liver, but is not necessary for life.

The classical teaching from digestive physiology is that bile is stored in the gallbladder and then released in a pulsatile fashion from the gallbladder in response to nutrients/hormones in the intestine during a meal. The major function of bile for digestion is to solubilize dietary fat so it can be digested by digestive enzymes in the small bowel.

When you don't have a gallbladder and there is no storage of bile, how does that affect bile flow into the intestines? Has anyone ever examined the effects of gallbladder removal on the release of bile from the liver? Is bile continuously released by the liver or is there still pulsatile release in response to intestinal nutrients?


texts: Are the cytosol and extracellular fluids electrically neutral?

texts:
I've found several sources that state that overall, the cytosol of a cell is electrically neutral. The extracellular fluid is also purportedly electrically neutral. How can that be when we have membrane potentials?

Also in that regard, how do the ion transporters that set up the membrane potential know when to stop pumping ions to get a certain potential set up?