texts: Have researchers discovered how epigenetic information is passed down during cell division?

texts:
For example, how are histone code patterns passed down?

This question was asked a few years ago in this thread:

How are epigenetic marks transmitted during cell division?

However, it has been a few years now, and I'd like to know if researchers have made any progress.

Clarification:
I'm specifically interested in figuring out how chromatin modifications are epigenetically inherited. There seems to be some evidence that it can be inherited, but there doesn't seem to be a full explanation as to how.

A good source for what I'm talking about is a article published in 2010 called: "Epigenetics and the Origins of Paternal Effects", which goes into detail on experiments done on rats that show epigenetic traits being inherited across offspring. However, the article ended on a note saying that the evidence is speculative, and further research needs to be done.  Here's the link:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975825/


texts: Why is some scat in the form of little pellets?

texts: The scat I most often encounter when out and about is from coyotes, black bears, deers and rodents. The deer and rodent droppings I find are in little pellets, what is different about their digestive system or their food choices that produces these perfectly uniform little balls?


texts: Why isn't the p16-INK4a gene involved in apoptosis expressed in heart or liver tissues?

texts:
New York Times article explains how killing p16-INK4a positive senescent cells can help keep the surrounding cells vigorous.

So here's my question: why is p16-INK4a expressed in most cells other than heart and liver cells? What would happen if we knocked it out everywhere?


texts:
What can stop the body from being able to process or break down palmitic acid?  The acid stays in the stomach and burns causing a similar reaction as heart burn when the volume is high.  Heart burn medication makes the issue worse. In smaller doses it causes the esophagus to swell causing a asthma type reaction and wheezing when breathing through the mouth but leaves the nasal passages unaffected.  The symptoms appear several hours after consumption.  The reactions have been noted in any food containing the acid natural or additive usually in the form of palm or peanut oil.  Once such natural example is a Pizza with Mushrooms, several hours after eating nausea will occur along with the burning sensation.  Expelling of the contents reveals acidic liquid and the mushrooms only.

Is there any recourse for neutralizing the acid safely or supplementing the body with the missing function to process the acid.


texts: I believe she is either Lasius or Formica, but I am an amateur so thanks for any help. This queen is completely black and gray, with a gaster that kind of looks like the stone Tiger Eye but gray. There is no red or brown on her. She’s approximately 1.5 cm long and I found her in central Minnesota. She laid eggs overnight after being caught. I know the photo is terrible thanks to my phone but it was the best one I got of her.


texts: Are there any de-novo genome assembly programs for HADOOP?

texts: I have access to a small (approx 20 nodes) cluster that has HADOOP running on it, and I need to do some de-novo genome assembly. I'd like to ask is anyone knows of any program that can do this on a HADOOP cluster. Cloud based stuff is not an option right now, unfortunately, so I need something that I can deploy on our cluster locally. Thx in advance.


texts: Is it possible to perform selection of plants without seeds?

texts:
When a plant spread using roots or branches I believe new plants keep same genome.

Many plants don't have fertile seeds. How it is possible to improve quality of genome (perform selection) for such plants?

Should we wait for natural mutation to spread across entire plant?

Strawberry is a good example of such plant and we know large verity among this species. How was it achieved?


texts: How would i describe a Cladogram as paragraph?

texts:
I have this paragraph that i have halfway finished, but i do not know what to put in the spaces.

A Cladogram is a branching diagram that represents the proposed phylogeny or evolution of a species or a group. The groups used in Cladograms are called clades.. To construct a cladogram, two characters are defined. Then the outgroup of various species are identified based on the sequencing or closeness of the derived characters in the clades. In making a cladogram, ______ assume that groups that _____ more derived characters have a more close common ancestor.

The letters that are italicized are words that i think are correct. This paragraph is needed for part of a recite that i have to do in front of my class. The prof. gave me a page like this. And  I don't know what those spaces are. Can someone help me.. please?


texts: Why does a distraction cause a longer reaction time?

texts: Does it have something to do do with the fact that the individual isn't concentrating on reacting to the stimulus, so it takes longer for it to be processed? How can this be out in terms of neurones and neurological pathways? what is happening for there to be a delayed reaction time?


texts: Do I need to serially dilute E. coli cultures for optical density measures?

texts: I am expected to track cell growth by measuring the incubating culture's cell concentration every 30 minutes or so. So my questions are: Why do I need to do serial dilution (assuming that I do)? Why can't I just fill up a cuvette with the cuvette's volume's worth of incubating culture and measure that against the blank every 30 minutes? And if I do need to dilute, how far should I dilute (1:100, 1:1000, etc)? This is for a culture filled with E. coli.


texts: Would the number of specialised cells in a leaf decrease if the plant was located in a shadier area? I thought it would decrease as there would be no need to store as much food in the plant and that the plants usually take nutrients from the surrounding environment. However, I don't know if this is correct; it would be nice if someone could provide a better/correct deduction or explanation defining the difference in the number of specialised cells in the leaf in shadier areas.


texts: What kind of larvae are these. Lots of them in the basement in the summer, crawling around on the floor and the walls

texts: larvae crawl on basement floor.  Some are also found on the first floor of the house.  Lots of legs--I also thought they became "rolly polys"  but never knew for sure what they were either.


texts:
What is the main difference between a precursor miRNA and a mature miRNA?

It is often the case that we have more than one precursor miRNA but only one mature miRNA.  The miRNA-seq data contains only precursor miRNAs, so I was wondering if we could use the expression of the precursor miRNA as the expression of the mature product or not?


texts: Can proteins/peptides pass through the intestine?

texts:
I've heard somewhere said that :

  Stomach cells do not absorb anything larger than single amino acids.

Is that wrong?
How do biological toxins (peptides/proteins) from mushroom or bacteria like Botulinum come to our blood and affect our body after we eat them?

Update: In fact, i want to know if we drink milk, is there anyway IGF-1 protein from milk can pass through the intestine and affect our body. Because I see some arguments/debates about the IGF protein in milk can cause acne.


texts: Why was the precipitation-streamflow correlation greater in the intact catchment at Hubbard BrookI

texts:
I gave an assignment and ran a class on this data last year.

https://lifediscoveryed.org/r290/hubbard_brook_streamflow_response_to_deforestation

Its a classic small watershed experiment where streamflows and precipitation are compared for two catchment areas, one with intact tree cover, the other deforested.

Streamflow and precipitation are, unsurprisingly correlated, but this correlation is apparently much greater for intact (0.91) than deforested (0.72) watershed.

I had no explanation to offer students for this, (I'd expect the opposite) which is OK, but if I run it again I'd like to have one up my sleave.


texts: Do any cells change in size or mass as mammals grow?

texts: That is to say, are there cells that, between infancy and adulthood, get larger?  Or is all growth done entirely via cell division?  I'm wondering if it is safe to assume that the approximate number of cells per unit mass in a mammal will remain fairly constant throughout its lifespan.


texts: Method of figuring out how much of a certain mRNA is present in a bacterium

texts:
I am trying to develop a method for figuring out how much of a certain mRNA is present in a bacterium. This is what I have so far:

Perform a mRNA extraction
Using Electrophoresis, to isolate the wanted mRNA strain (based off of size)

Now, I am not sure how I would quantify the amount of mRNA. I was thinking of using nano drop to test concentration, but I am not sure if that will give a good enough answer. What other methods could I use to quantify the amount of mRNA in my sample?


texts: what are the best books for the IIT-JAM biological sciences exam?

texts:
I'm from India and i'm preparing for a competitive exam called the Joint Admissions Test for a Masters admission.

I need help in finding books to read from for these chapters:

General Biology: Taxonomy and physiology, Pro-and eukaryotic organism; cell organelles and their function; multicellular Organization; energy transformations; internal transport systems of plants; respiration; regulation of body fluids and excretory mechanisms; cellular reproduction; Mendelian genetics and heredity; biology and populations and communities; evolution; genesis and diversity of organism; animal behaviour, plant and animal diseases.

Basics of Biochemistry, Biophysics, Molecular Biology: Buffers; trace elements in biological systems; enzymes and proteins; vitamins; biological oxidations, carbohydrates and lipids and their metabolisms; digestion and absorption; detoxifying mechanisms; plant and animal hormones and their action, nervous system, nucleic acids, nature of gene and its function, Genetic code, synthesis of nucleic acids and proteins. Enzyme mechanisms and kinetics, nucleic acid metabolism, photo synthesis.

Structure of Biomolecules: intra and intermolecular forces; thermodynamics and kinetics of biological systems, principles of x-ray diffraction, IR and UV spectroscopy and hydrodynamic techniques.

Microbiology, Cell Biology and Immunology: Classes of micro-organisms and their characterization, nutrient requirement for growth; laboratory techniques in microbiology, pathogenic micro-organisms and disease; applied microbiology; viruses, Microbial genetics. Innate and adaptive immunity, antigen antibodies.Cell theory; Cell architecture; methods of cell fractionation; cell division; types of chromosome structure; biochemical genetics- inborn errors of metabolisms; viruses and fungi; principles of processes of development.

PS. I've studied biology only until high school.


texts:
From this article,  second paragraph of the second page

  A classic theoretical result is that the mean of a character controlled by a single locus i with two alleles Ai1 and Ai2 is only affected by the value of f if there is some degree of dominance.

where f is the Wright's inbreeding coefficient.

The authors then add:

  Assume that the trait is scaled such that the values for the genotypes Ai1Ai1, Ai1Ai2, and Ai2Ai2 are -ai, di, and ai respectively. The quantities ai and di measure the effect of the locus on the character and the degree of dominance of the locus, respectively. With two alleles, there is a linear decline in the mean of a trait
  with increasing f either with overdominance (di > ai) or if the allele associated with an increased value of the trait is dominant or partially dominant (ai ≥ di > 0). With additive joint effects of different loci on the trait, this conclusion can be extended to a polygenic character; inbreeding decline occurs if the average value of di over all i is positive.

I don't understand why "[..] there is a linear decline in the mean of a trait
with increasing f either with overdominance (di > ai) or if the allele associated with an increased value of the trait is dominant or partially dominant (ai ≥ di > 0)"

Can you please explain why the mean of a character controlled by a single locus is only affected by the value of "f" if there is some degree of dominance.


texts: What limits our ability to grow enamel rods?

texts:
From what I've understood from what I've read (which might be wrong), enamel rods extend away from the dentin in our teeth. As young people grow, the rods are thickened.

What are the technical limitations and/or problems/challenges of trying to extend/grow the rods/crystals while the teeth are in the mouth?

One issue I guess could be that the enamel is porous, and so chemicals could affect the other parts of the teeth.

But one example of trying to improve the quality of tooth enamel is Novamin, which some manufacturers have claimed creates a glass on the tooth. But I don't understand what that means.


texts: Which function do nicotinic receptors have in the periphery?

texts:
I came across this question today, it says:

  Nicotinic receptors stimulation is directly responsible for …....

I should fill the spaces by one of the following choices:

Increasing the excitability of sympathetic postganglionic neurons.
increasing the the force of stomach contraction.
delaying the emptying of liquids from the stomach.
decreasing the excitability of sympathetic postganglionic neurons.

The only article speaking about the nicotinic receptors in my physiology book says that they are cholinergic receptors found in the autonomic ganglia, i.e., they are found on the postganglionic neurons.

So when I tried to solve the question, I thought the upper three answers are correct. Specifically, because stimulating the receptors on the postganglionic neurons will increase their excitability, option 1 seems to make sense.

But if that postganglionic cell happen to be sympathetic it may provoke the emptying of the liquids from stomach to be delayed (choice 3)?

And, if it was parasympathetic the force of stomach contraction would also increase (choice 2)?

I am confused as all three answers 1) 2) and 3) seem to be correct and the question asks specifically for one correct answer. Could someone help me find the correct answer, but put simply please, as I'm just a first-year dental student.


texts:
About 75 cm long. Thin tail. Camping site near Grado, Italy, northern Adriatic sea.
It climbed a tree in the rough bark and i followed it to take these photos.


texts:
There's some theory around that orgasm will cause a dopamine surge and drop, and that this can lead to a period of low mood or depression. A come down.

Is this true, does orgasm have a negative psychological consequence ?


texts:
Cell's organelles give us evidence that they might have been independent organisms on their own.

Are there any single-cell microorganisms known to have gone so to say this way back as well, i.e. having some evidence to have their past as part of a larger organism?


texts: How to recognise the type of allele by pedigree analysis diagrams?

texts:
It was said that this interference pattern is due to dominant allele. I fail to see that.
In general how to recognise the type of allele by pedigree analysis diagrams?


texts: Human sleep cycles and dream times, what influences the timing and intensity? Sleep history included

texts:
I'm doing sleep and dreams research and have developed an iPhone application to help me track my bedtime, rise time, sleep onset and also mark dreams. The app also monitors overall activity overnight as an Actigraph, recording periods of elevated motion and inactivity.

I have a lot of sleep cycle data that I have trouble analyzing.

I know that circadian rhythm is at play with 90-110 minute sleep cycles ehxibited over the course of the night, each one is a progression of various sleep stages, from NREM to REM. REM is more likely to result in a dream reported if awakened during REM.

What I'm seeing is a bunch of orderly patterns, and a lot of chaotic behavior that I cannot explain. Particularly the times of going to sleep and awakening, while dreams exhibit more orderly behavior, with dreams reported at similar times on subsequent days.

I'm also interested in any insight as to what's causing me to wake up at certain times and report dreams. What could be involved in this kind of behavior? I saw research about deuretic hormones not being suppressed for the night, causing the urge to urinate to awaken the dreamer.

Right now I have 90 days of sleep onset and dream data that looks like this:

Complete 90 day sleep history

In this case, each black marker indicates the sleep onset time for
the night
The orange marker indicates the time of getting out of bed
The green markers are dreams that I report upon awakening from a
dream, so dreams occur prior to the marker's location.
Each green
    marker's brightness indicates more clear dream content remembered
    and    recorded.
Cyan markers are lucid dreams, where I was aware
    that I was    dreaming within a dream.
Cyan color of a marker
    indicates that I    could control the dream's content from within a
    dream.
Red markers    are periods of insomnia.
The cyan line is
    number of hours after    bedtime
The purple line is sleep cycle
    approximation (90 minutes).

The data is stacked with each row being a day of data. You will notice that your eyes start to automatically seek patterns within the vertical arrangement of markers. Because each marker is a dream reported upon awakening, they roughly trace the sleep cycles over the course of the night.

I'm interested in learning what influences the desire to go to bed at a particular time?
What influences the getting out of bed times?
is there some sort of analysis I can perform to understand the pattern within the sleep cycles as it evolves over multiple nights?

Any input is appreciated!


texts: How do infants get their very first gut bacteria?

texts:
First of all, I'm a complete layman in Biology. Recently I read "The evidence for evolution" by Richard Dawkins. Pondering about this matter, I wondered about the origin of human gut bacteria (could be more generalized to mammal gut bacteria).

Generally, I see two possibilities:

These bacteria are

acquired later on through the environment (probably after birth) or
they are produced by the organism itself

The former option seems to me a little bit too vulnerable to be true (different food, different bacteria due to geographical location, etc.)

The latter option seems baffling to me. Bacteria are, as far as I know, independent lifeforms. Is it possible, that our DNA contains the information for other lifeforms as well?


texts: EM field in living organisms and tissue resonance frequency

texts:
I have two questions which I can't find enough information about, and I would be very grateful if someone could give me a lid to the answer:

As far as I know, if we accelerate charged particle it will radiate EM radiation. In many processes occurring in our body charged particles move from place to place, and they accelerate in the processes (For example when a voltage-gated ion channel is opened). does it mean that our body creates small EM fields all the time? or did I missed something?

Does every tissue in our body has a resonance frequency? It sounds logical that there should be since all tissue are made of fundamental chemical elements. If so, in case I insert this type of tissue into a magnetic\electric field which makes the particles in the tissue to resonate in the tissue's resonance frequency, is there any danger for the tissues to be torn apart?
e.g. if the resonance frequency of the particles which constitute the epidermis is 1 hz and I stand next to a source of radiation which makes the particles which constitute the epidermis to resonate in 1 hz, could it cause a rapture of the cell membrane?

I hope I my questions are not too messy.
Thank you for your time and attention!


texts: It was hovering and in between it was very fast and hard to photograph. I'm not even sure if it is an insect? Photographed in Germany.


texts: What is the developmental and health outcome of an XY individual with an SRY addition on their X chromosome?

texts:
I know that "XX male" syndrome occurs through various means, including the addition of an SRY gene in one of the X chromosomes. The developmental and health outcomes of such individuals can be problematic. But what about a person with an X chromosome with an SRY addition, along with a Y chromosome?

It seems that it would be similar to XYY syndrome, but without the over-expression of anything but the SRY gene. Would it even be obvious, from a visual point of view or fertility point of view, that a person has the extra SRY gene?

I know that rodents aren't humans, but it does appear that there are species that have naturally acquired multiple copies of the SRY gene.


texts: How does a ribosome gather tRNAs at a fast enough rate for Translation?

texts:
There are many animations of the ribosome in action, and all I have seen show the correct tRNA neatly entering the ribosome and its amino acid being added to the growing protein chain. My question is this: is it really possible that mere brownian motion and diffusion are responsible for getting the right tRNA out of 20 possible types to that point? Presumably that would require tRNAs of every type arriving and most being rejected until the right one meets its codon and is used. Not only that, you would expect orders of magnitude more tRNAs to be arriving at almost the right place but being the wrong way round or hitting the wrong place on the ribosome.
Has anyone in the field ever done any calculations using dynamics equations, along with the known volume of cytoplasm and tRNAs to see if this is even feasible?


texts: Genomic DNA extraction protocol by salting out with NaCl, how to improve yield

texts:
In these papers

A rapid non-enzymatic method for the preparation of HMW DNA from blood for RFLP studies
A simple salting out procedure for extracting DNA from human nucleated cells
Modified salting-out method: high-yield, high-quality genomic DNA extraction from whole blood using laundry detergent.

In brief, red blood cells are first reduced/removed. Nucleated cells are lysed in the presence of SDS and genomic DNA are released. The resultant lysate are gooey. Addition of NaCl results in protein precipitation which is then removed by centrifugation. The genomic DNA is believed to not be precipitated by salt and thus remain in the supernatant which is recovered by ethanol/propanol precipitation.

Typically, ~30 µg of DNA is obtained per mL of blood.

I tried the salting out method recently and the yield is quite low (~ 10 µg per mL of blood), so no where near the published figure. In comparison, I obtained ~ 30 µg using phenol/chloroform from the same blood sample. I have tried using NH4Cl and still get a low DNA yield. I believe one of the reasons is that a lot of genomic DNA get trapped in the protein precipitates after addition of salt.

What can be done to prevent or minimise genomic DNA being trapped with the protein precipitate?


texts: How much does donating blood affect the amount of oxygen in your blood stream at high altitude?

texts:
I am a regular blood donor and I am also a skydiver.  We normally go to around 13,000 feet AGL (above ground level).  Depending on how high above sea level the ground is, altitudes could be as high as 15,000 MSL (mean sea level) before a jumper is required to use supplemental oxygen.

At those altitudes hemoglobin is less effective at carrying oxygen, which is why hypoxia is a risk.

The following chart taken from this article about aviation and the body shows how oxygen levels decrease as altitude increases:

What I would like to know is if there is any research into the effect blood donation has on the blood stream's oxygen capacity?  Is it possible to say that x days after a donation, due to reduced hemoglobin levels, operating at 15,000 MSL would be equivalent to operating at 15,000 + x MSL without donation?


texts: Healing rate of cut while suffering from a cold

texts:
I recently cut my finger fairly deeply with a box cutter and had to have it stitched. During the healing process I contracted a strong cold/mild flu (a sore throat and runny nose with a high fever, aches and shivering). I doubt the two have anything to do with one another apart from happening to occur at the same time.

But they did occur at the same time. So I'm wondering: what is my body going to do?

If I recall my junior high biology, a cut is healed by platelets and [other stuff I can't recall], whereas a virus is fought with antibodies. Presumably in both cases it's a bit more complicated than just that. I'm also not sure if there is any crossover - are antibodies, for example, needed to protect the open wound from bacterial infection? Regardless, my question is:

Since the resources in the human body are finite, would having to fight off the cold have a detrimental effect on the healing of the cut?

If certain resources are needed for both tasks, would the body divide its resources or give one precedence over the other?

I'm guessing this is not something that is easy to measure, since it would be difficult to conduct a control experiment given the insane amount of variables. But presumably there is a consensus in the biological community on whether there would be an effect, even if it is not possible to determine the degree of said effect.

I should mention in closing that I am not remotely worried about any of this; it just piqued my curiosity.


texts: Why are aminoglycoside antibiotics particularly effective for aerobic gram negative bacteria?

texts: Aminoglycosides are short chains of sugar molecules with some -OH groups substituted with amine groups. As far as I understand they function by causing bacterial ribosomes to misread RNA and create non-functioning proteins. These proteins both stop providing essential functions of the cell and increase permeability of the cell to aminoglycosides, eventually leading to the death of the cell. What I don't understand is why this mechanism is specific to aerobic, gram-negative bacteria. Surely membrane permeability would be roughly the same for both classes? And also ribosome structure? Any help would be much appreciated.


texts: What kind of spjder is this? It was found in nova Scotia


texts:
I need some biological data for many types of trees, but I can not find good source of this on internet.
Where can I find following type of biological data of any tree:

Biological Profile
Taxonomy
Distribution
Cultivation
Edible Medicinal Parts
Phenology


texts: Are platyhellmintes and annelids segmented?

texts:
Are the organisms of platyhelminthes unsegmented worms or segment? And what about those belonging to annelida?

I guess Platyhelminthes are unsegmented and annelida are segmented but i am not sure about it?


texts: Over what range do Thyroid Stimulating Hormone (TSH) levels tend to fluctuate over the course of a day?

texts:
I understand that the majority of doctors consider the TSH test "the gold standard" for measuring thyroid function (examples stating that literally are here and here).

The reference range for what is a healthy TSH is under debate, but no matter what range is considered there tends to be a proportionately large difference between the top and bottom (eg 0.3 to 3.0 μIU/mL).

However I've never seen anything indicating over what range TSH varies over the course of a day, or a few days. It's also unclear as to how much error there tends to be with a test result, even if tested from the same sample.

How much fluctuation in a TSH result is normal over the course of a day?


texts:
I am looking for an algorithm that shows the exact coefficients some variables that have on a hospital patient's chronological age versus their biological age.

I understand a lot of the variables that go into determining ones biological age (i.e. Blood pressure, diet, family history of disease, obesity etc.) but not the amount of impact that it has on the actual scoring of their age.

I have found many sites that will calculate it, however I need the actual variable coefficients and influence in order to produce a proper score for thousands of patient records.

Thanks in advance for your input!


texts: If I shone a UVC lamp (11W) on something (say for example a plastic phone case) for an hour, would that kill off a noticeable amount of bacteria? That is, if I were to go over the case with a cotton swab before the hour and swipe the cotton swab over a petri dish with nutrients and if I were to do the same after the hour with a different cotton swab and a different petri dish. Do you think that after a week there would be a noticeable difference in bacterial growth between the dishes? I think it should, since some filters for ponds work the same way, but I'm not sure, since in my case, the light needs to penetrate about 10 inches of air first and the environment isn't as closed off. What are your ideas on this?


texts: Where does the mass come from when you grow plants in water?

texts:
How do plants like green onions seem to grow forever when put in jar of water?  I understand that plants get a lot of their carbon from the air (as per this question) but surely they need more than just carbon to grow new leaves.

The answer in the linked question mentions that plants in general get their mass from sources like water and nutrients like nitrogen and phosphorous, and ions.

However, if a plant is growing directly in [distilled] water where will it get those nutrients (like phosphorous and the ions) from?

Where does that extra mass come from?


texts: What is this 2-3cm insect found in South-Eastern Brazil?

texts:
Noted in South-Eastern Brazil rainforest at low level - about 2-3 cm from head to tail.

Maybe a Cassadine Beetle?


texts: How does Isoxaben kill newly germinating seeds, with almost no effects on established ones?

texts:
Isoxaben (N-[3-(1-ethyl-1-methylpropyl)-1,2-oxazol-5-yl]-2,6-dimethoxybenzamide) is a pre-emergent herbicide used in landscape beds before the application of mulch (my use for it, anyway). It kills the weeds as they germinate, while not harming most established plants.

Here's the mode of action, as stated by Dow AgroSciences:

  Isoxaben belongs to the Benzamide family of herbicides and inhibits cellulose biosynthesis in the cell walls of susceptible
  weeds (WSSA group 21). This means that cells cannot divide during the reproductive cycle; therefore, they cannot grow,
  causing death. While cell division does not occur, this mode of action should not be confused with mitotic inhibition that
  occurs with dinitroaniline herbicides.

How does this only affect germinating weeds, while not noticeably affecting weeds that have emerged from the soil (I have to hit those with another herbicide)?


texts: Why can't dopamine cross the blood brain barrier but l-dopa can?

texts: Levodopa can cross the BBB and is less lipid soluble then dopamine, so dopamine should be able to cross the BBB more easily then l-dopa, but for some reason dopamine cant cross the BBB. Both dl-methamphetamine and levomethamphetamine can cross the blood brain barrier, but why not dl-dopamine?


texts: Why don't we feel hungry after waking up?

texts:
Yesterday, I was fasting (drinking only water until I had dinner at 9 pm). After dinner, I went back to my lab (I am a Master's student) and worked till 1:30 AM. By 1 o' clock, I was feeling quite hungry, probably because I hadn't eaten anything all day and only had a light meal for dinner. However, I didn't eat anything then and just slept. Today morning I wake up (around 9 AM) and I don't feel hungry! I could surely eat something if I wanted, but I am not feeling the acute hunger that I was feeling last night!

More generally, what could be the reason for the behavior that a human experiences acute hunger, but after sleeping for an extended period of time, he/she may no longer have the hunger. Since a passage of time has passed, one would expect the hunger to increase, which would have certainly happened if the person had not slept. Is it the case that sleeping somehow affects the overall hunger/glucose demands of the body?

I suspect that it is possible that the body's food needs could be majorly affected by the circadian clock, but I wanted an explanation to contrast the situation when one is not hungry and when one is very hungry before sleep. How can the difference between both the situations be easily trumped by the circadian rhythm's effect? (if it is the explanation!)


texts:
I recognized that there is some controversy about the average mass of amino acid masses in different online sources.
Expasy and Wikipedia report the same masses, but UWPR and Mascot report different ones. However, the monoisotopic masses are always the same.
Does anyone know where these differences come from or where to find a definite source for the masses?
In the end, the question boils down to the average masses of single atoms. The UWPR names UniMod as a source for their calculation. What different ways of calculation for average mass exist and who defined them?


texts: Would you please explain to me what GST RhoA fusion protein means and how it differs from RhoA protein? I am a kind of doing an experiment using this protein.


texts: Why is therapeutic index a ratio instead of an interval?

texts:
The therapeutic index of a drug is defined as its toxic dose ($TD_{50}$) divided by its effective dose ($ED_{50}$).  Why is it defined as a ratio rather than the difference $TD_{50} - ED_{50}$?

For example, if drug A has an effective dose of 1 ml and a toxic dose of 2 ml, and drug B has an effective dose of 50 ml and a toxic dose of 100 ml, then they both have the same therapeutic index (2), but intuitively, I would say drug A is much more dangerous, which is reflected if we take the difference instead.


texts:
It seems that a human bite can be very dangerous, because of the myriads of bacterial species found in saliva.  This leads to several questions that, perhaps, may have the same single answer.  But, I'll boil it down to a single question per the comment.

Is there a mechanism by which the body "tames" their own oral bacteria that could otherwise be dangerous pathogens, so that the bacteria don't cause pathology but also don't arouse a typical immune response or inflammation?

No doubt this question has been explored often, but I haven't been able to find a clear answer.


texts: Why do provitamins-A do not cause Vitamin-A toxicity?

texts: Why do beta-carotene and other provitamins like alpha-carotene not cause vitamin-A toxicity but rather carotenosis (Orange skin) whereas retinal, retinol, and retinoic acid cause vitamin A toxicity with dosage as low as 4000 IU?


texts:
I am writing an article where I describe real-time PCR experiments. My collaborator, after reviewing the article, consistently replaced the word "parallels" with "replicates". Are they not synonymous?

I prefer the word parallel, because, in the context of PCR, it implies that these three identical experiments were performed in the same real-time PCR run (and not consecutively).


texts: Problem with phosphorylated and total forms of antibodies

texts: Antibodies are available that can detect both phosphorylated and total endogeneous levels of the given protein. I have a question here, why is it necessary to have equal amounts of total protein? This is a common assumption that variations come in phosphorylation status but since total detects levels of both phosphorylated and non-phosphorylated forms, it is supposed to be equal. Not necessarily! Depending on the requirement of cells, phosphorylation status may change. And so does the expression of the total protein itself specially if the non-phosphorylated form is acting as a transcription factor.This is what I find in my studies as well. But the literature suggests the opposite. Why?


texts: Can the theory of natural selection distinguish between two correlated phenotypic traits?

texts:
Consider the following two situations:

A species X has trait $T_1$ that is gradually selected for by some characteristic $E_1$ in some ecological niche but it turns out that the genes for $T_1$ also "turn on" genes for trait $T_2$ so that eventually species X with trait $T_1$ also have $T_2$. Then it turns out that $T_2$ is evolutionarily advantageous i.e it does help in increasing fitness because of some characteristic $E_2$ in that same ecological niche.
A species X has $T_1$ that is selected for by some characteristic $E_1$ in some ecological niche, this ecological niche also has characteristic $E_2$ that separately selects for $T_2$.

Both of these cases have as the end product $T_1$ and $T_2$ being advantageous for survival but in one case $T_2$ was selected for and in the other it's usefulness was accidental. What in the theory of natural selection distinguishes these two cases? To put things more bluntly, you are an evolutionary biologist and you are telling the standard story that corresponds to situation 2, how do you know (from the theory of natural selection) that we can discount situation 1?

I did a research project for my undergraduate research where I simulated mutations of cells in a petri dish and I know that mathematically these two cases can be disentangled because they lead to two different cluster size distributions with different scaling laws. As a physicist I know what to do but does a evolutionary biologist using theory of natural selection know what to do.

Update: The point is that in case 1 $E_1$ and $E_2$ could act at different times so that only $T_1$ is responsible for survival and $E_2$ while acting $T_2$ was completely useless for it's survival i.e other species disappeared not because they didn't have $T_2$ but because they didn't have $T_1$. Then a naive biologist could tell separate evolutionary stories assuming that $T_1$ and $T_2$ were selected for separately because when the biologist is observing the situation both $E_1$ and $E_2$ are present and $T_1$ and $T_2$ are present.  In other words, he or she would assume case 2 occured. In this case, random mutations and natural selection as told in science classes is completely useless because of $\textit{dynamics}$ in the environment and $\textit{correlations}$ that prevent mutations from being just random.

Why does this bother me? Well, because I hear evolutionary accounts that span hundreds of millions of years and it would seem simply applying the Darwinian story naively could make wrong predictions all over the place. I haven't seen people worry about this as they give evolutionary accounts for everything. From sexual behaviors to marketing.


texts: How does heredity work with Endogenous retrovirus?

texts:
Q1: If someone in a species gets infected with an endogenous retrovirus, does that mean that absolutely all of their children will have that endogenous retrovirus? Or is it based on chance?

Q2: is there such a thing as an allele for the virus being there, and for it not being there? How does it work?

Q3: how can an endogenous retrovirus disappear from a species? And when it cannot disappear?


texts:
Wikipedia states that “Severe coeliac disease leads to the characteristic symptoms of pale, loose and greasy stool (steatorrhoea)”. However thumbing through the causes and the pathophysiology it did not become clear to me what leads to this key symptom.

By what mechanism does coeliac disease cause excess fat in the feces?


texts: What is these mushrooms in my indoor pot?

texts:
I am living in Japan and in summer, it's very hot and humid even inside my room.
Today, I've found two mushrooms in the pot of a plant.

What is this species? It's very surprising than within one day they grew like this.


texts: Correlation between genetic distance and birth defects

texts:
It is folk knowledge that in-breeding causes birth defects due to similarity of genetics between parents. Consequently, is there a similar correlation between genetic distance of parents and probability of birth defects?

The best reference I can find of this is this handout by the Australian Centre for Genetics Education which says:

  If parents are unrelated, their chance of having a child with a birth
  defect or disability is between 2% and 3%.

  If parents are first cousins, the chance is a little higher at 5% to
  6%. This is due to the increased chance that they will both carry the
  same autosomal recessive mutation, passed down through the family.

However this doesn't talk about genetic distance in particular.

This question is really just a more specific version focused on a single metric (genetic distance) and outcome (birth defects) of two previously answered questions:

Genetic pros or consequences of children born to parents of mixed nationalities?
Does it make sense to classify all humans in a single species?


texts: Amino acid characteristics that determine their chemical properties?

texts: What chemical aspect of amino acids results in their having different properties such that the chemical and physical properties of polypeptides vary with both amino acid content and amino acid order?


texts:
Why are lactate level high in diabetes? For example, type II diabetes are resistant to insulin. If those patients are insulin resistant their gluconeogenesis should be working at a high rate and, because of that, lactate uptake by the liver should be removing lactate from the blood.

Alternatively, type I diabetics don't produce insulin, so the ratio insulin/glucagon would always be very low and gluconeogenesis should be stimulated... So I don't understand why lactate levels are high in diabetes... Can someone help me?

PS. This question came up after doing an experiment in school, with diabetic rats and normal rats. Diabetic rats had higher levels of lactate and my professor said that it was because the diabetic rats don't perform gluconeogenesis and so, lactate accumulates in the plasma. But it doesn't make sense for me.


texts: Explain to a layperson how cigarettes smoke might cause cancer

texts:
I have a very intelligent friend who is a light smoker, and also a Biology layperson.
I wondered whether understanding exactly how cigarettes smoke can cause cancer, might encourage him to smoke less (or quit entirely).

So how would you explain to a Biology layperson how cigarettes smoke might cause cancer?

To clarify, I am looking for a detailed explanation for a layperson, that makes the cause-and-effect much more vivid for them, and thus makes it much more likely that the intelligent layperson would internalize the risks of smoking.

Online resources that I found either gave a too simple answer or concentrated on statistics (which are usually hard for humans to internalize, if I understand correctly).
(Nothing wrong with such explanations, they are just not what I am looking for.)


texts: Are there health benefits to donating blood?

texts:
Donating blood is typically thought of as a commensal act, benefiting the recipient at no cost beyond time and inconvenience to the donor. Some even view it as a parasitic act, wherein the recipient benefits at some health cost to the donor. But it seems reasonable to posit the opposite.

Iron has been suggested as the reason why women have notably lower incidence of cardiac events than men, until menopause that is. Why? Because some blood loss every 28 days helps to reduce iron levels in the blood. Similar logic holds with metabolic syndrome and type 2 diabetes.

Additionally, treatment-resistant high blood pressure responds — unsurprisingly — quite well to blood loss, as a bit less blood means, all other things being equal, proportionately lower pressure.

But this is speculation. Is there any legitimate evidence of the health benefits of blood donation?


texts: Species Identification: large shiny black beetle, Detroit USA

texts: What sort of beetle is this? I live in a suburb of Detroit and found a whole bunch of these living under my lawn when I was replacing a section of it. I'm assuming these are also the source of the grubs I found as well. Are these harmful?


texts:
I harvested some lentivirus from 293T cells and want to titre the result. I infected 293T cells on a well plate with 400,000 cells per well which I infected with virus stock, and 1 in 10, 100 and 1000 dilutions (as well as a few uninfected wells). After 72h incubation I trypsinised the cells and used FACS to titre first, but 293T do not express the promoter under which GFP is located in some samples and hence these do not appear on FACS. As an alternative, I extracted the genomic DNA from all samples using a QIAGEN DNeasy kit (also the samples which I was able to titre by FACS already) and then performed qPCR on them.

I used the ABI PRISM 7000 SDS: http://www.cgenetool.com/products/abi_prism_7000.shtml

Included on the PCR plate were:

Number standards: 1000, 10k, 100k, 1m copies
Samples in triplicate
No-template controls as well as untransduced controls

Each of those was doubled, once with primers and probe for WPRE (an element specific for the lentivirus) and once with primers and probe for beta-actin (a housekeeping gene present in all cells).

The results returned by the machine include for each well the cycle at which the threshold fluorescence was crossed - along with the automatically calculated quantity of copies (which the software calculates from the standards I assume).

Since I named the triplicate samples identically, it also automatically calculated the mean quantitiy among each triplicate (practical, eh?). I checked if there were any outliers which should have been excluded from the means but everything was fine.

So now for example I have a result of 700k for the quantity of WPRE in sample A. The quantity of beta-actin in sample A was 6.82 x 106. The transfection was 400,000 cells per well, sample A was transfected with 10uL of viral stock diluted 1:100.

How do I calculate the virus titre per mL from this?

I have been given the formula: WPRE Qty / (b-act Qty*0.5) * cells in well (400k) * dilution factor (100), but am struggling to figure out a) why b-act Qty is divided by 2, b) whether the result would be virus titre per uL or per 10uL (transfection volume) and c) how beta-actin can have almost 107 copy numbers consistently across all samples when there were only supposed to be about 105 cells...


texts: Did Darwin ever reach the conclusion that selection will remove variation?

texts:
According to simple models of selection the genetic variance in a population should be reduced by selection. (Fisher's fundamental theorem states that the rate at which a population can evolve is limited by its variance). If we select the next generation from one population we will only ever capture as much, and probably only a subset of, the variation that exists in a the first generation.

Did Darwin ever discuss this loss of variation? What did he conclude?

(For now lets ignore the potential roles of sexual antagonism, pleiotropy and such)

A little clarification on my question:

Darwin saw variation in phenotypes, and variation in fitness dependent on phenotype - an effect he called selection. He also saw that this variation was heritable (but did not know how). This is the basic concept of evolution, and is mathematically speaking, the breeders equation:

$r = h^2 s$

He also would have realized that life must therefore have started out as a simple unit, and new variance in traits (and whole new traits) must have arisen over time, i.e. that some kind of changes (mutations) were going on in the heritable information (genes). However, what I'm asking is, did he realize that selection would act to reduce the variation in a population? This would reduce the rate at which evolution can occur over time (Fisher's fundamental theorem - assuming no influx of variance or potential for pleiotropy to maintain variation). Or was it Fisher that first formally discussed the concept of lost phenotypic/genetic variance?


texts:
I noticed this plant growing on the Azores islands. It has a surprisingly perfect distribution of branches, which gives it the appearance of a fake decorative plant. Does anybody know what type of tree this is?

I apologise for the image, I could not find any better ones.

Edit: here is another image I found:


texts: Introns are sections of noncoding DNA that separate exons within a gene locus. However, between different gene loci, I also would assume there to be noncoding regions of DNA. What are these regions called? (And if my assumption is wrong, then please correct me.)


texts:
The TL;DR is in the subject line.

The back story is as follows:

I am combating ants in my high-rise apartment unit.  One piece of online advice was to vacuum regularly, and pay attention to edges of the floor.  I'm considering taping up the vacuum bag opening so that I'm not tossing out a nearly empty bag every day (almost $10 each, and terrible for the environment).

I had initial concern that an ant might get out, so I also double bagged the vacuum bag.  This is making it inconvenient to use, meaning that I'll vacuum less.  Exactly the opposite of the online advice.

I think that the chances of an ant getting out is low, and even if escape was possible, it probably wouldn't be more than one or two.  I can accept that, if they don't go start generating more ants.

I haven't found anything online about workers being able to transform into queens once they are foraging.  What I have read is that it has to do with genetics and extra nutrition during the formative stages.

Is it safe to assume that foraging workers will not be able to turn into queens?

After note: It just occurred to me, if ants can chew through wood, then there's nothing to prevent them from chewing through a vacuum bag over the course of a day or more.  They can even chew through the plastic bag in which the vacuum bag is sealed.  Is this a valid concern, or is their ability to chew limited to wood?


texts: How to isolate host cell RNA (tRNA,mRNA,rRNA) from viral RNA?

texts: A retrovirus with RNA genome infected a host cell. You would like to isolate the host cell’s RNA (rRNA, tRNA, and mRNA) from the virus RNA. What properties can you rely on to determine the three types of host cell RNA- for example, in terms of their size, complexity, GC content, or abundance in the cell? The undetermined RNA can be identified as the virus RNA.


texts: What is the sequence of pPROLar.A plasmid?

texts:
I've been looking for the sequence of pPROLar.A122 plasmid but I haven't found it. Where could I find the sequence?

The first link (addgene) on googling reports a plasmid which is reported to have the pPROLar.A backbone. However, this is a modified version with Ampicillin and LuxR. I'm trying to reconstruct it from it and another plasmid.

The plasmid map looks like this:

Thanks!


texts:
I shipped 10 µL of my vector miniprep to a collaborator in a 1.5 mL eppendorf parafilmed shut and stuffed into a 50 mL conical with some paper-towel padding.  However, something happened on the way and there was nothing (no liquid) in the tube when it arrived.  They didn't make any comments about the microcentrifuge tube popping open or broken parafilm, so nothing crazy happened but something did.

What's the most reliable way to ship plasmids?


texts: Can a second mass extinction by microbes happen?

texts:
Science Daily reports that the mass extinction at the end of Permian period happened by the Methanosarcina archaea wiping out 90% of species:

Methane-producing microbes may be responsible for the largest mass extinction in Earth's history. Fossil remains show that sometime around 252 million years ago, about 90 percent of all species on Earth were suddenly wiped out […]. It turns out that Methanosarcina had acquired a particularly fast means of making methane, and the team's detailed mapping of the organism's history now shows that this transfer happened at about the time of the end-Permian extinction.

Is it possible by the global warming and all the spores of bacteria come out from melting glacier or anywhere else and mass extinction occur?


texts: What am I looking at in Franklin's Photo 51 of DNA?

texts:
Here's Rosalind Franklin's famous Photo 51, the X-ray diffraction image of DNA from which Watson and Crick deduced its structure:

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

I have a lot of trouble connecting the photo to the diagram.

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


texts: Is there a chemical compound, element or something else that could color the eye lens in purple?

texts: I hope this is a right place to ask this question. I'm writing scifi book, and looking for information whether it is possible for any element, chemical compound, radiation or something else to color the human eye lens (and or freckles) to purple.


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

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

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


texts:
If I want to make sure that a ZFN cuts at only a certain position in a genome, how many subunits would I need to ensure this?

If the human genome is roughly 3 billion base pairs, we need a sequence that is 16 base pairs because 4^16 exceeds 3 billion (if my thoughts are correct). But then I don't quite understand how the subunits of the ZFN come into this.


texts: Surface Plasmon Resonance (SPR) Predicting Molecular Weight Limit?

texts:
Just asking, can we predict how low molecular weight (LMW) analyte our SPR system can detect based on our LOD (limit of detection) and our sensitivity on another protein detection? So right now our developed system can detect alpha-synuclein (14 kDa) with LOD around 5fg/ml. Can we predict how LMW can we detect? Is there any reference paper or something. Because as far as my knowledge we can get the change of RII based on the experiments first. But right now my case is I want to test the limit of our SPR devices to detect LMW (I'm choosing what LMW analytes to buy right now)
Thank you! any discussion or comments are very appreciated


texts: What mechanism is responsible for germinating in the right direction (root towards gravity)?

texts: Regardless of the initial seed orientation, the root always grows/sprouts/germinates "towards gravity" (see picture), sometimes curving around in sharp 180°. What is the mechanism responsible for the gravity sensing and for the growth adjustment?


texts: Is there a simple test that can differentiate menstrual blood " period blood" from spotting blood?

texts:
I have a simple question: If I give two samples of blood; one from a the menstrual period and one from spotting, is there a simple way to know which one is from the period and which one is from spotting " normal, non uterus " blood?
Thanks


texts: What are the blood groups for human beings?

texts:
Human blood groups are of 4 types with negative and positive of each types (Wikipedia). But according to this forum thread there are some other types too:

  A+,A-,B+,B-,O+,O-,AB+,AB-,A1+,A1-,A2+,A2-,A1B+,A1B-,A2B+,A2B-

I'm going to make software for blood donation, where I need to put a dropdown list of actual blood types. I had intended to use:

[ Select Blood Group V ]
[ O Negative           ]
[ O Positive           ]
[ A Negative           ]
[ A Positive           ]
[ B Negative           ]
[ B Positive           ]
[ AB Negative          ]
[ AB Positive          ]

But now I am uncertain whether this is appropriate. What is the most suitable list of blood types for donors?


texts: How can I get the yield of my purified immunoglobulins?

texts:
In order to get the yield of IgY through a set of purification steps, what method can I use?

Thanks in advice!


texts:
While I was reading about "Neural Control and Coordination" I came across this
"Association areas in the forebrain are responsible for complex functions like intersensory associations, ....."

What are "intersensory associations"? I have searched the net but could not find anything useful.


texts: Is there a certain environment where all cellular functions (or at least some) increase their rate?

texts: Is there a certain environment in which all the functions (or some) inside a cell increase in their rate? Would the increased rate cause any damage to the cell?


texts:
Does anyone know of any research/examples on Hopeful Monsters in Plants?

I define Hopeful Monsters as organisms of a species that have macroevolutions to prompt new speciations. These macroevolutions being themselves, prompted by smaller gradual microevolutions in the species. See this paper for more details. I'm interested in a plant based example, or any good recent example, if plants can not suffice. Ideally research that is easily read and recent, and useful for arguing the existence of themselves?


texts: Brain centers vs areas (and how they relate to nuclei)

texts:
I'm looking for a reputable source that can provide succinct definitions differentiating the following terms in the central nervous system (CNS; particularly in the brain):

Area

Center

Nucleus

Examples include Wernicke's area, piriform area, deglutition center,  olivary nuclei, vestibular nuclei, etc.
Really, I'm trying to corroborate my experiences having seen many examples of each but never having seen official definitions of either centers or areas. I know well that a nucleus is a cluster of cell bodies in the CNS [ex: source]. I also feel as though areas are regions with functionally-related roles, and that they tend to be associated with the cerebral cortex. Centers seem to be deeper functional regions.
What I'm not clear on is what the official differences between an area and a center are, whether (or to what degree) either term is inclusive vs exclusive of nuclei, and to what degree the relationship of all three words overlap either structurally or functionally.

I do know that Tortora & Derrickson (15th ed, 2017) indicate explicitly that certain centers are nuclei, but I'm not sure whether this more broadly describes all centers or is simply indicates a narrow example of a center.

Examples of nuclei in the medulla ...include the cardiovascular center and medullary rhythmicity center.

Motivation: trying to find a reputable source to provide a simple definition for my students. I usually just run with broad explanations based on repeated exposure of each, but I think my students would appreciate a cited, specific definition of each term.


texts: Why is Cannabis Sativa considered a distinct form of Cannabis?

texts:
My understanding is that the word Sativa is Latin and means "cultivated." See here: https://en.wikipedia.org/wiki/Sativum

Since all cannabis consumed by people is cultivated and grown from seed, shouldn't all Cannabis be called Cannabis Sativa? And so isn't Cannabis Indica also Cannabis Sativa? If taking a cutting of a plant grown from seed and rooting it means that "clone" isn't considered to have been grown from seed then maybe those plants shouldn't be called Sativa, although this would still seem to qualify as cultivation. But either way I fail to see what bearing it has on phenotype or alkaloid profile. How has it come to mean having thin leaves and high THC content?


texts: Circulation through the liver in light of drug metabolism

texts:
I have a lingering question which stems from an answer that I gave to What hydrolyses aspirin within the digestive tract and blood stream?

When a drug or any other substance is absorbed into the bloodstream in the stomach or small intestine, it ultimately passes through the hepatic portal vein and into the liver sinusoids, where it is processed by hepatocytes and introduced into the general circulation via the vena cava.  In terms of metabolism, this is what causes a "first-pass" effect for drugs that are ingested.

For drugs that are delivered either by intravenous, intramuscular, or sub-lingually (as in the other Biology.SE question), this first-pass effect is avoided, and the drug is introduced into the general circulation without being metabolized by the liver first.

Even though the first pass is avoided, the blood in the body still makes its way back through the liver eventually via the hepatic artery, which is a branch off of the celiac artery.

The issue I still have is, does the incoming blood from the hepatic artery merge with the blood from the hepatic portal vein?  If not, does the blood from the hepatic artery still interact with the hepatocytes in some way? (it makes sense that it does, and I have also read that one of the main functions of the hepatic artery was to deliver blood supply for the liver's metabolic needs)  If this is not the case, where in the body would these drugs that were introduced via IV, etc., be metabolized?


texts: What is this part of blastula called and how is endoderm formed?

texts:
Could you tell me what the yellow mass within the blastocoel is called ?
I know that blastocoel is a fluid filled cavity, so are the yellow coloured cells the inner part of blastoderm or are they some other cells ?

If they are the part of blastoderm itself, why is it not in the same colour of light-orange as the blastoderm, or is it the mesoderm, or the inner cell mass  ?

And is it the blastoderm that forms ectoderm , and endoderm pinches  off the ectoderm during gastrula phase? And could you also explain how the orange mesoderm formed ?


texts: Nature vs Nurture in Rooster mating dance: Are roosters lame dancers because they never learned any better?

texts:
I've seen, read about, or heard several avian courtship dances, flights, songs, and other rituals. They are general very impressive, fancy, and beautiful. Roosters, by comparison, are quite lame. The link is a pretty good example of the sort of best effort I've seen or read about from a rooster. A lot of them seem to do quite a bit less than that.

Some time ago, I remember hearing about the various distinct finch calls, and the fact that these songs seem to be largely a learned behavior. In a modern factory style farm, chicks are usually hatched in an incubator and raised by humans in a brood of similar aged chicks. Some chicks, on more traditional farms perhaps, are raised in more natural settings with a mother hen present, and perhaps a rooster too, but even when a rooster grows up observing his father's behavior frequently, I wonder how often such a parent child example extends beyond just a few generations. In other words, I doubt that any chicken benefits from a long lineage of fine courtiers like their wild finch cousins.

My question then is primarily whether there is potentially a learned component of roosters' dancing, and secondarily whether a lack of sustained parental lineage stunts the development of proper dancing in a rooster. They certainly have some sort of instinct driving them, and they're beautiful birds, but their mojo falls flat compared with more wild relatives, like this pheasant. To avoid soliciting opinion-based answers, I want to focus this question on specific verifiable knowledge. For example:

Are there any actual studies on this topic with roosters or close relatives? Or is there any husbandry knowledge on the subject? For example are specific steps recommended to preserve the beautiful mating behavior of pheasants or pea fowl in captivity?
Is there any evidence of learned avian  mating behavior other than song?
Are there any notable recorded differences between the mating dance of an orphan rooster compared with roosters that have grow up with fathers?

Don't feel like you need to address every point for a good answer. I'm just trying to provide a framework for avoiding opinion-based answers.


texts: I am trying to identify this medium arching shrub growing to about 1.5m high x 2m wide in the subtropical climate of the Mt Coot-tha Botanic Gardens in Brisbane, Australia. Unfortunately there was no label with it. The inflorescence is about 3cm across, a greenish yellow, and made up of many tentacle-like florets.  I don't think it is an Australian native plant.


texts: Stability of the chromosomes of thermophilic bacteria

texts: We know thermophiles — generally archaebacteria — can survive high temperature, but their genomic DNA also contains hydrogen-bonded nitrogen bases. Why don't they collapse like ordinary hydrogen bonds?


texts: Is there empty space left in the skull after the second set of human teeth grow out? What happens to it?

texts:
Reading about teeth on this website, I came across this link and picture of a human child skull, where we can see how both sets of teeth are placed.
It made me wonder: after the second set of teeth move into the mouth (do they actually move?), what happens to the space they occupied before, while they were hidden?
Or do they not actually move, but stay in place and the mouth/skull/bone grows in size to expose them? I'm not sure which way it is.
https://io9.gizmodo.com/the-mouth-of-a-child-is-a-terrifying-thing-to-behold-5910844


texts: What's the amount of blood passing through heart every second at Max Heart Rate?

texts:
How many mL of blood passes through the heart every second at maximum heart rate?

Is there any formula to calculate the amount of blood flowing through the heart per sec at say for example 70% of the max heart rate?

I didn't ask
Let's assume that the person in question is a fit 23 yo Caucasian male(if there are differences for various ethnicities)


texts:
What is the mechanism of insulin stimulation in the human body?

Is leptin release stimulated by circulating insulin directly? Which other factors are involved in the level of insulin release? My goal is to identify nutrients that aid/trigger leptin production and release without causing undue inflammation or body-fat storage.


texts:
Given the obvious importance for global health, I've found it easy to track down lists from Google of the top lifestyle related causes of death (like heart disease, lung cancer etc), but as a consequence it proven difficult to find a source of the opposite, the leading causes of death which have no (or very little) relation to lifestyle choices (like smoking, obesity etc).

What I'm interested in is those chronic and generally quite fatal disease which just happen for either genetic or spontaneous reasons, or perhaps due to environmental causes which are so ubiquitous as to be unavoidable.

I'm not looking for an exhaustive, or even very large list, the top five to ten would do, and I understand that there's no clear distinction between lifestyle and genetic factors, but obviously health organisations make some estimate of what is mainly the cause otherwise lists like these would not be possible. I just want the opposite list.

To clarify in the light of some answers, I'm looking for diseases which one might contract in adulthood (this could include pathogens) which could in a normal healthy person living within reach of modern medicine still present a more than 50% chance of being fatal. Basically I'm after a risk figure (my field of research) which would act as a baseline presuming a safe, healthy life.


texts: Beautiful blue enigmatic insect (mantid?) in Kenya

texts:
This beautiful insect was found in Kenya today - and we don’t know what it is. We think it may be a mantid of some sort?!
Nairobi kenya, croton trees, cape chestnuts, bougainvilliea, there is quite a lot of lichen on the trees.
Despite looking to be the size of someone's arm, it's about 2” long!
Needless to say, no-one had a good camera at the time. Just phones!
The colour of the insect is very similar to the lichen on the trees (hence the mention above).
Someone suggested it was a 'grizzled mantid' Gonatista grisea (Fabricius), but we didn't think they are found native to Kenya - and likewise, we don't see a protuberance on the back of grizzled mantids... Still hoping for an answer.
You can see it also has very small wings, which I hear is a feature of some mantids - micropterous mantids.
I don’t know anything about these - someone said ‘some sort of bark mantis’ - which, for insects would probably mean that it’s bite is worse than its bark...


texts: How are single-stranded binding proteins removed from the lagging strand during DNA replication?

texts: The lagging strand, downstream of the Okazaki fragment, is covered in single-stranded binding proteins (SSBPs) during DNA replication. What is the mechanism which ensures that SSBPs are removed from the lagging strand to allow for the binding of the next Okazaki fragment?


texts: Visibility of a cell membrane under microscopic Imaging

texts: When we see any cell under a microscope the membrane surrounding the cell is opaque. But then if the cell membrane surrounds the cell in all the three dimensions how come we can see through the cell membrane and have a look at the organelles inside if the membrane is also covering the cell from the top and not just at the boundries on the object plane.


texts: Why are valves preferentially affected in endocarditis?

texts:
The inside of the heart is covered by endothelium throughout. Why are valves predisposed to endocarditis? I know it can affect other structires like the septum, chordae etc. But why the valves? Especially bacterial endocarditis.

Wouldn't a place on the ceiling of the atria be quieter and have less turbulence?

Robbin's Pathology says that valves derive nutrition from the surrounding blood and there vessels but mostly on the proximal side. So it might not be due to nutrition.

Are there theories for this?


texts: Is there any reason the common housefly continues to return to an area?

texts:
This might come off as a really silly question. But I'm wondering (especially in the case of food) if there is any reason a fly would continue to try and sit on top of a piece of food even after swatting it away. I assume (it could be misconception) that it is instinctive that animals and insects would leave an area if it is harmful / dangerous to their existence after having close encounters more than once. Is this not the same for the fly?

I have this question mainly because I recall waving a fly away several times while eating lunch, and I couldn't understand why the fly wouldn't just find another place where there is food or somewhere safer.


texts: External sensory stimuli that awaken a person from sleep

texts:
An external sound or touch can awaken someone.

Can a light? It would have to be very strong, but part of the reason might be that it would have to penetrate the eyelids.

And can a smell or taste?

When we are awake, the impact of sensory stimuli and of changes in them depend on which sense is stimulated.

My question concerns the kind and strength of impact the stimulation of each sense has when we are asleep, in relation to what is needed to wake us up.

Note

Thanks to @Mithoron for linking to another question, asked on this website by @Taladris. That question is certainly quite similar to this one and its answer contains some relevant material, even if the answer is not of high quality because of course our senses are "dimmed" when we are asleep and of course it is not true that "that we respond to our own names in a similar fashion in sleep and in wakefulness". The present question asks specifically about awakening because of sensory input. I believe I am sometimes awakened by smells, although it is hard for me to tell whether or not I am right. Part of my question asks for views or facts concerning whether people can be woken by smells at all. This is different from asking whether we can smell when we are asleep.


texts: What protocol does the nervous system use?

texts:
I just read How does an inhibitory synapse communicate to the cell body of a neuron? and found myself asking this question ... hopefully I'm not asking the same thing

Any body possessed of a nervous system probably has hundreds of neurons. At one end of the neuron is the nervous system, at the other - the organ.

A neuron is connected to several others in the vicinity through it's dendrites.
When a 'signal' (for want of better word) is put on the system bus - how does a neuron know whether it has to act ( contract/relax it's associated muscle/organ ) on the signal, or pass it on ( forward ) after amplification of the signal, if necessary?

Is there something like a chemical protocol to identify the target neuron/group-of-neurons that form the destination?


texts: I read this article but it didn't explain much. Is the fact people like to cuddle pets with fur connected anyhow with our past when our ancestors had fur as well - and therefore could evolve an instict to enjoy hugging someone furry as an expression of friendship.


texts: What are the effects of enzyme exposure to high temperatures?

texts:
Question: After enzymes are exposed to high temperatures and undergo denaturation, then returned to their optimal temperature and renatured, can the enzyme's active site return to it's original shape and will it function at the same level of efficiency as it did before being denatured and renatured?

Some background I wrote to the question:
I am just beginning to learn Cell Biology, I hope what I've written is correct.

When you raise the temperature of an enzyme, at first it will increase the efficiency of the enzyme's activity, but eventually as the temperature rises, the enzyme with stop functioning and undergo denaturation, which means that the 3D formation of the protein is unraveled, so it doesn't function anymore. From what I've managed to research, the high temperature changes the shape of the active site in the enzyme, which is what allows the enzyme's activity in the first place.
I know that some proteins cannot be renatured (like adding heat to an egg will fry it and there is no way to unfry it), but some can be renatured (like heated milk, when it cools down the protein bonds will reestablish themselves).

But will the enzyme's active site return to it's original shape and manage to function at the same level of efficiency as it did before? Or is the damage permanent?


texts: Do the right-handed people tend to use the right side teeth of their jaw to chew food more often than the left-handed people?

texts: And vice versa, do the left-handed people tend to use the left side teeth of their jaw to chew food more often than the right-handed people?Or the frequency of food chewing distribute fairly to both sides of the jaw?


texts: Do we know a complete list of nutrients that humans must ingest to live?

texts:
When the people who are making "nutritionally complete" foods like Soylent are developing their product, how do they know that they've covered all their bases? You need to have protein, carbohydrates, fats etc., but what about vitamins or minerals?

Has science produced a commonly accepted list of all the nutrients that humans need to live?


texts: I read that roughly 20% of all species of mammals are bats. Is there a good explanation for why bats have diversified so much compared to other mammals? Is it because bats' ability to fly allows them to fill niches that are completely out of reach (pun intended) of other mammals? If so, how is this reconciled with the coexistence of bat populations and bird populations?


texts: What is the biological reason for a burst appendix being potentially lethal?

texts:
Given that the appendix does not seem to be used by the human body, what is the biological reason that it is potentially lethal when this organ bursts?

Also, what would cause the 'burst'?


texts: Anomalous base pairing of nucleotide tautomers

texts:
What tautomers base pair with what bases?

I know that adenine pairs with thymine and guanine pairs with cytosine normally. My question is what does the imino form of adenine base pair with? Regular cytosine? What does the enol form of guanine base pair with? Regular form of thymine?

I cannot find any books discussing this issue and Google is of no use. However, my professor wants us to know how tautomers base pair.

I tried base pairing cytosine with adenine but does the -NH2 group on cytosine really hydrogen bond with the imino -NH group on the adenine tautomer?


texts: mRNA Sequencing Basepair from Polyadenylation Site?

texts:
I was wondering how many basepairs are usually sequenced with mRNA/cDNA illumina methods from upstream of the polyedenlation site?
Thanks.


texts: what is the integral of PAR radiation over total solar radiation

texts:
This paper say 48%: What is the maximum efficiency with which photosynthesis can convert solar energy into biomass? -Zhu 2008

Also why does Zhu use 740 nm at high end of PAR wavelength!

My calculation says 43% (also using 7440 nm)

Have you done this integral? What did you find


texts:
I came across a reference to dAT joining in my reading of Genentech by Sally Hughes. The technique is described in passing as a technique for joining DNA fragments used around the late sixties to early seventies (likely prior and after, too, of course).

A quick query into earlier visits of the topic on the exchange returned no relevant results, but the results may have been have been obscured by the copious references to the neurologic "DAT" term (dopamine transporter).

Please provide a quick explanation to this concept/technique if you're familiar.


texts:
Let's say that the threshold potential of a neuron is +40 mV to make a muscle twitch. Now suppose we have two signals of +20 mV. So, this signal will cause the twitch in muscle because it has reached the threshold potential.

Suppose that we have many signal of +20 mV. Will this cause a lot of twitch, the same twitch or no twitch at all in the muscle? In other words, how will the twitch be greater?

Please be a little simple.


texts: Do hydrogen ions contribute to water potential?

texts: I was thinking about lysosomes and how they maintain an acidic pH inside themselves by pumping H+ ions from the cytosol. Do hydrogen ions set up a concentration gradient that causes water to move by osmosis? If so, why doesn’t water rush in to the lysosomes to raise their internal pH?


texts:
So I want to make Congo Red TSA. My instructor gave some hints but I still have some questions:

I start by making two stock solutions: 20 mg/ml of congo red and coomassie in two different falcon tubes. To prepare 30 ml of each, would I dissolve 600 mg in sterile water?
The final concentation in a 500 ml TSA solution needs to be 40 μl/mL of CR and 20 μg/mL of coomassie. How do I calculate the amount of solution needed for the TSA?


texts: Can the value of heritability be greater than 1?

texts: Heritability defined as genetic variance divided by total variance seems to be bounded between 0 and 1.  However, I see a way of calculating heritability on this page (http://www.radford.edu/~rsheehy/Gen_flash/Tutorials/Linear_Regression/reg-tut.htm) with:  2*Covxy / Varx.  However, a result calculated in this way could be greater than 1.  What am I missing?


texts: How to safely sterilize urea-containing growth medium?

texts:
I'm using urea-containing growth medium for experiments with bacteria (1-2 l/day). After the experiment, the growth medium has to be sterilized and disposed. I did this so far by autoclaving, but our technician complained about the ammonia smell that develops (urea breaks down when heated, releasing ammonia).

I'm pretty sure the amount released into the air is not dangerous (I've emptied the autoclave several times), especially if you don't purposefully breathe in the first gust of air that comes out after opening, but I think it's useful to look into alternatives. Also I'm not sure if the autoclave might get damaged on the long run.

Does anyone have experience with this? Do you see a way to sterilize larger amounts of growth medium reliably without heating?


texts: Nervous stimuli and neurotransmitters and impacts

texts:
As far my knowledge, in body parts generally **acetacholine ** is the neurotransmitter. Which is responsible for most nervous impulses.

Consider a body part, say, foot. Only one  nerve reaches here. When ant bites there, the impulse of pain and irritation moves from there ;

Secondly, when some soothing agent comes there the impulse of comfortness moves from there

Now, neurotransmitter is the same, nerve is the same, but different impacts are observed.

My teacher said that the impulse moves to different parts of the brain.

But how are the impacts really understood, analysed and sent to different regions ( as entrance of all stimuli enter through the same brain stem,)

In short,

My question is that how does our brain analyses two different stimuli when neurotransmitter is the same, nerve is the same and enter the brain through the same brain stem. They must be going to different regions of the brain but how is that decided


texts: Insects do have a nervous system, even if it isn't nearly as complex as that of other animals. Can insects or other arthropods sense pain? Does their aversion to harmful stimuli suggest that they can 'feel' pain in the sense that other animals seem to?


texts: How is Cas9-gRNA-tracrRNA complex lysed in mammalian cells?

texts: I am interested in degradation of Cas9-gRNA-tracrRNA complex. I would like to understand how do the cas9 enzyme, gRNA and tracrRNA degrade in mammalian cells (with references, if possible).


texts: Earliest to use media after autoclaving?

texts: I am autoclaving media to use later to inoculate yeast. How much time do I have to wait before using the media and adding the culture? Can I use it a few hours after autoclaving?


texts: Does animal blood, esp. human, really have similar salinity as ocean water, and does that prove anything about evolution?

texts:
It is an often-repeated claim that human, and in fact all animal blood is salty because we evolved from aquatic organisms, and that blood has a similar concentration of salts as ocean water, or at least as primordial ocean water.

Is any of that true? Does science know what the salinity of the oceans was billions of years ago, and was it indeed similar to the blood of today's organisms? Does that knowledge prove anything about evolution and the origin of life?

I am wondering, because I tried to Google for the answers, and unfortunately all I could find were creationists referencing each other how it couldn't possibly be true because evolution is a lie in the first place etc., and they claim that there is no empirical research that would compare salinity levels of organims' cells and ocean water.


texts:
I have been asked to talk about (constrained) optimisation like $$\max_{x,y} f(x,y)$$ $$\mbox{Constrained by } g(x,y) = 0$$

for high school students with applications to biology. However, I can not think of a single good example from biology that actually uses optimisation.

The existing application is proving what the optimal linear regression line is given by, but this is rather tedious to do and not really a fun exercise for high school students, which is why I hope you might have a great application that I can use.


texts: How to confirm secondary structure formation of Precursor miRNA on gel?

texts: I want to fold precursor-miRNA into its secondary structure and then confirm it on gel. At first, I heat it in annealing buffer at 95°C for 5 minutes and cool down slowly. Then I run it on gel but the samples are at same position as the original dilution.


texts:
I can't seem to find any conclusive information about the origin of Myxomatosis. According to Wikipedia

  It was first observed in Uruguay in laboratory rabbits in the late 19th century. It was introduced into Australia in 1950 in an attempt to control the rabbit population.

However I find this passage unclear.

Was this a naturally occurring disease that we then used as a means of population control, or did we have a hand in its creation?


texts:
Are there poisons that affect only mammals but not reptiles or crustaceans?
E.g. hemotoxins which affect hemoglobin but not hemocyanin or specific Na+ channels?
Looking for a "nice" poison/disease as idea for a fictional story to explain survival of reptiles/crustaceans vs. mammals.


texts:
I am wondering about one thing. I have read different accounts of this (prior to reading it on Wikipedia), so I am wondering.

Here are the two versions I have read:

asparagus leads in a certain percentage of people to a smell that has to do with a reaction of asparagusic acid. That is: not every human body creates the reactions leading to the "smelly" thiol (sulphuric) compounds.
asparagus leads to the processes of the aforementioned asparagusic acid in everybody but only a part of the population is able to smell those compounds.

Which one is true? Or is perhaps some other version I haven't heard about.

btw: The Wikipedia article on asparagus references both versions, too. So I am hoping for a definite answer with references to the respective scientific papers/studies.


texts:
Why does masturbating seem to be like an addiction?

What controls or initiates the urge to masturbate?

Is it good or bad or both and why is it so? I have heard guys who say that the do it regularly. Also there is a relaxing feeling; what generates that?


texts: Biological validation of computationally determined gene-gene interaction

texts:
How can a computationally determined three-way gene interaction be biologically validated? What kind of assays or tests must be performed using cell/tissue-based and/or mouse models to prove that the three genes may indeed have a joint effect?

Let's say, it is easier to identify and validate gene interactions that involve transcription factors like FOXM1. Consider a three-way gene interaction in Breast cancer - FOXM1-BUB1-CHEK1 - that can be tested for direct interactions via western blot and reporter assays. But such interactions may or may not be interesting - given the fact that transcription factors may be affecting expression levels of other genes. Most computational studies are focussed on identifying gene interactions based on coexpression or co-occurrence. There is literature on computationally identifying AND/OR relationships between interacting genes. I don't have a specific example to provide but, for argument sake, if we did suspect that three genes are interacting in an AND like manner, how do we biologically validate this finding? I'd also appreciate if you may have comments on the usefulness of such findings, particularly, with regard to designing more efficacious combination therapies against a disease".

Thanks


texts: In my biology class we got the question if saltwater fish need to drink. We need to use the term osmosis, but I cannot think of a valid answer and we were allowed to ask help.


texts: What are some atypical examples of positive transcriptional cooperativity?

texts:
Cooperativity in gene expression is an important feature of many regulatory networks. Described using the Hill function, the most common example is a transcription factor (TF) that when bound to its target regulatory site, increases the rate of binding of other transcription factors (usually through TF-TF dimerization).

There are numerous example of TF dimerization-based cooperativity in the literature. However, I am trying to find examples of positive transcriptional cooperativity that involve mechanisms other than TF dimerization. In the dimer model, an unbound TF binds to its cognate promoter (containing multiple enhancers) with a certain affinity. With the first TF bound, another identical TF now has increased affinity for its target - binding to the enhancer and binding (dimerization) to the first TF. The expression profile is sigmoidal (near binary) and represents sharp on/off switching in activity.

Although peer-reviewed articles experimentally or theoretically characterizing alternative mechanisms are preferred, I'm also interested in user hypotheses and discussions that are more speculative. Specifically, I'm interested in positive cooperativity that occurs without feedback from the regulated genes.

One potential mechanism could involve a DNA-binding TF consisting of a transcriptional activator domain and a chromatin remodeling or DNA methylation domain. When the TF binds it not only activates transcription but remodels local chromatin. If the remodeling increases affinity for the next TF, they act cooperatively (and positively). Perhaps something similar to this has already been described.


texts: Can a hormone be absorbed into the body digestively?

texts:
Obviously, to act most hormones must be present in the bloodstream. What happens if a hormone or hormone-containing food is consumed normally? Is there any way for the hormone to reach the bloodstream?

A related question is whether hormones are destroyed by digestive enzymes and chemicals, which include hydrochloric acid and bile salts. If hormones are destroyed by these chemicals then it may be impossible for them to enter the blood stream.


texts: What does effect would Sulforaphane have on Kennedy's Disease?

texts:
Sulforaphane is a isothiocyanate found in cruciferous vegetables including broccoli and cauliflower. Its 2D structure is as follows:

It's been found to serve as a histone deacetylase 6 (HDAC6) inhibitor and to inhibit androgen receptor expression in prostate cancer cells.1 This caused me to become curious as to whether it would do the same in lower motor neuron cells and thus manage to prevent their polyglutamine-induced death and thus halt the progression of spinobulbar muscular atrophy (SBMA; Kennedy's disease).


texts: Why hasn't life on Earth reached an evolutionary stable strategy?

texts: I heard in some YouTube video that cheetahs only existed 5,000,000 years and according to https://en.wikipedia.org/wiki/Extinction, extinctions are occurring all the time so I assume life on Earth hasn't reached an evolutionary stable strategy. I know some species like ants are in an evolutionary stable strategy and most species are close to their evolutionary stable strategy because the system of the rest of the species is changing so slowly but why hasn't the system of all life on Earth reached an evolutionary stable strategy. Could it be that it's destined to never reach one? That doesn't necessarily mean there isn't one. According to https://en.wikipedia.org/wiki/Evolutionary_game_theory, the side blotched lizard has 3 forms undergoing cyclic evolution so it's destined to never reach an evolutionary stable strategy if the state of the rest of the species on Earth doesn't change. There's another case of cyclic evolution where rabbits outcompete wolves when there are very few rabbits and wolves outcompete rabbits when there are a lot of rabbits? Why are there so many species that have existed for no more than 5,000,000 years instead of the system of all life on Earth being stable with a few species undergoing cyclic evolution? What's causing the current state of all life on Earth to keep on not being evolutionary unstable?


texts: How do plants store energy by potassium battery?

texts: Plants have a so-called potassium battery system for energy storage/conversation. Wikipedia only has a reference to a technical article. Can someone explain it in a layman's language (or refer to a non-technical article)?


texts: How can we quantify the effect of pancreatin (biological enzyme) on the clarification of milk powder

texts:
Alright so I'm trying to quantify the rate at which casein (protein constituent of milk powder) is converted into a product (I am unaware of) by pancreatin (a biological enzyme that speeds up the reaction). I've attempted researching what the product of the reaction is erroneously given I couldn't quite determine the answer.

All I know is that this enzyme essentially allows casein to convert into whatever thus clarifying any water it would be poured into. Casein remains in suspension (opaque) and then progressively reacts and clarifies the water. How to quantify it on the other hand, I haven't merely got a conceivable clue.

Yes, this question is broad, perhaps you could inform me of any other notions that pertain to this experiment and thereby aid me in my pursuit of an answer.


texts: Do swarm of the same species attack each other?

texts:
What happens when two swarms find each other?

For example: When a swarm of bats, of the same species, go through another bat swarm. Do the bats attack one another or they simply merge into a bigger swarm?


texts: Forward or Reverse Strand: Is there a difference when encoding genetic devices?

texts:
Background:
In synthetic biology, and also in nature, there are lots of examples of genes in both the forward and reverse orientation. It seems in synthetic biology/bioengineering, most genetic devices are, by default, encoded on the forward strand unless there are concerns of readthrough from one expression unit to another, in which case one of the expression units is included on the reverse strand like below:

It also seems that genes are sometimes in the reverse orientation for no apparent reason, especially in plasmid backbones:

The Question:
My question is, ignoring issues of potential readthrough, does it matter which strand a genetic device is encoded on? So in the example below, would there be any difference between A and B, or does it not matter? Also, does whether it's on a plasmid compared to a genome matter? I'm specifically interested in bacteria here.

This seems like it should be a simple question to answer and I'm sure I'm just missing something, but I can't find anything about it.


texts: Is Klebsiella pneumoniae found in the throat of healthy people?


texts: Multistability in the lactose ultization network

texts:
Reading the paper here, I'm confused about the production of figure 4d. The method of production is detailed in the supplementary information under the heading "Theoretical phase diagram".

Specifically, I'm confused about the use of theta and what it means. I have tried reproducing the figure using MATLAB and the parameters in the paper to see whether I can understand it better, but nothing quite works out.

To be clear, the paper obtains a steady state result for a series of ODEs:
$$
    y = \frac{\alpha  (1+(βy)^2)}{ρ+(βy)^2}
$$
Then rearranges as a cubic:
$$
    y^3 −αy^2 + \frac{ρ}{ β^2} y − \frac{α }{ β^2 } = 0
$$
Apparently, a general cubic with two identical roots has the
form:
$$
    (y-a)(y-a)(y-aθ) = y^3 - (2 + θ)ay^2 + (1+2θ)a^2 y - θa^3
$$
The paper then equates coefficients:
\begin{align}
    ρ &= (1 + 2θ)(1 + 2/θ)\\
    aβ &= \frac{(2 + θ)^{3/2}}{θ^{1/2}}\tag{did you mean?}
\end{align}
And claims that these are the parametric equations that describe the graph in question. When plotting these equations, I get nothing like the graph. I can't really see where it comes from.

The graph in question and some equations are reproduced here on the last page:
http:// web.mit.edu/biophysics/sbio/PDFs/L7_notes.pdf


texts: Where can I find historical data on world-wide ecology parameters?

texts:
I hope this is the right StackExchange forum for such a question.

I'm looking for large data sets on world-wide ecology parameters, such as annual temperatures by latitude, annual rainfall, CO₂ and O₂ concentration in the atmosphere and in the oceans, data about the insect population, plants, algae, and so on.

Is there any research institute or NGO collecting such data and making it available to the public?


texts: Why do bacteria need mRNA? Isn't the DNA free floating without nuclear membrane so why doesn't the tRNA read the code directly off of the split DNA strands? (ofcourse after helicase splits them). Wouldn't this be more efficient?


texts: How can we know or measure pain in animals?

texts:
Is there any standard way to know how much pain an animal feels when it gets hurt like when a bird loses it's wing or hen when killed etc. All pain sensation points?

Hey I'm new to biology. :)


texts:
I'm tying to understand the mechanism of paired end illumina sequencing, however I dont't  understand why index primer 1 and index primer 2 are used.
paired end illumina sequencing (YouTube).


texts: Determining limiting nutrients from a graph

texts:
The question was
Which of the following statements is supported by these data?
A. Phosphorus was the first limiting nutrient followed by nitrogen.
B. Nitrogen was the first limiting nutrient followed by phosphorus.
C. Phosphorus was limiting but nitrogen was not limiting.
D. Nitrogen was limiting but phosphorus was not limiting.
E. Neither nitrogen nor phosphorus was limiting.

The answer was B: Nitrogen is the first limiting nutrient followed by phosphorus, but I do not know why. I thought it would be only phosphorus as the Nitrogen values are always greater than the control values.


texts:
Reading the recent ScienceAlert article "For the first time, living cells have formed carbon-silicon bonds", it is stated that despite the relative abundance of silicon in the surface of the Earth, there are no silicon based lifeforms.

Specifically, the article asserts:

  Why silicon has never be incorporated into any kind of biochemistry on Earth has been a long-standing puzzle for scientists, because, in theory, it would have been just as easy for silicon-based lifeforms to have evolved on our planet as the carbon-based ones we know and love.

I have read the question and answers "Why are we carbon-based?", which looks at the importance of carbon, what I am seeking information of is why carbon and why not silicon in the first place. So, therefore my question:

Why is it thought that silicon based lifeforms never flourished on Earth?


texts: How does DNA damage increase the activity of p53?

texts: I understand the steps leading up to the halting of the S-cdK checkpoint from there, but I can't find the mechanism by which DNA damage actually increases the activity of p53.