texts:
When chromosomal crossover occurs, two matched chromosomes swap matched sections of their chromosomes. My question is: how does the cell select where to to make the break on both chromosomes? Is it based on some attempt to match sequences on the two chromosomes, or purely on distance from the centromere? The mechanics of the former could be achieved by breaking the two strands of each chromosome at different places. The mechanics of the second is a simple walk from the centromere with a random(?) selection of where to cut.

The purpose of this question: if the process is based on distance from the centromere then it would provide an explanation the presence of junk DNA. Successful crossover requires that the number of functioning genes on the two chromosomes not be radically altered in quantity. A failed crossover would result in at least one of the gametes being non-viable, reducing fertility. If crossover is based on centromere distance then the location of genes becomes a factor in the success of a crossover, erecting a fitness barrier between populations with radically different gene placement, even if gene content is identical.

If this is a question without an answer, currently, one way to address it would be to try to cross breed knockout mice that don't have junk DNA with ordinary mice that do. If the fertility of the cross breeding is significantly lower than than knockout with knockout and normal with normal, or if the cross breeds are less fecund, then that would provide evidence for position based crossovers, and a function for junk DNA in the crossover process.


texts: What are the mechanisms that cause bananas to ripen? How is or isn't it related to the banana peel ripening?

texts:
So recently our commercial kitchen got some bunches of bananas with a curious feature. On the inside they were firm and delicious (no jokes, please), on the outside they looked incredibly sickly. Specifically, they had this grey/green/brownish yellow with lots of black spots, some of them with depth.

Situational details: these are Cavendish bananas, and a weekend of ripening in the open air did nothing for them.

This got us curious about the mechanisms of banana ripening - it's clearly not as closely related to how good the banana is to eat as we previously thought! Can someone explain it more?


texts: What does this biomass measurement mean and how to translate it to volume

texts:
This is probably a softball question but because of the nature of the term, it's difficult to Google.  I am not a biologist, I am a web developer.  :-)

What does this measurement mean (it is a measurement of biomass production): 50 g m-2 d-1

I believe it means 50 grams per square meter per day - but not sure why there are '-' signs in there.

And perhaps more complicated, it is possible to translate this measurement to volume (either cubic meters or ideally cubic feet)?


texts: Why do we have two kidneys but one liver?

texts: Both the liver and the kidneys are involved in "cleaning" our blood. But why we have one liver and two kidneys? I can just as well imagine that we have two livers and one kidney. Is this just a coincidence?


texts: Can you help me identifying an insect I saw?

texts:
I'm a student of biology and yesterday we went to the fields to collect some plants for our herbariums.

Suddenly one student of our group said that he saw a very strange bug that he thought that was related to the family of wasps/hornets.

He pointed to some dried bushes and that insect was hidden inside. I could not do a photo but I hope that you could help me identifying this bug since it surprised me a lot (and even scared me a bit).

From what I remember, this insect had an enormous abdomen (around 5-7cm long and 3-4 cm wide) that had a similar shape to the abdomen of wasps and hornets. The rest of its body and head were very small (around 1cm). It had no wings and I think it had no "hair".
It was mostly black with very few red marks/stripes.

I've been "researching" a bit and the most similar insect I found on the web was the Dasymutilla occidentalis but the insect I found had no hair (or rather I believe so), had a much bigger abdomen and was way bigger than the average "Cow Killer". Also, this bug is native to the US and I live in southern Europe, so I think it's very unlikely that this insect lives here as well (I've found no information about Dasymutilla occidentalis living in my country)

The exact location was (in UTM): 30T 0462625 4447661
(East of Madrid, Spain)

I know this description may be vague, but it is all I've got and I'm very curious about that insect I found. It would be great if you could help me


texts: Do you know of any disease where HLA / MHC association discovery has led to better treatment or management?

texts:
If we discover an association between a disease and a particular HLA type (MHC class I or class II molecule) then it may provide us with some insight into the disease in a very basic way. However, will it provide us with a therapeutic target? Or second best, will it provide us with information that is useful for diagnosis or management? I am looking for examples. Do you know of any?

The most obvious is in transplantation where one would use HLA typing to match donor to recipient but that is not the same as using knowledge of an HLA type to target, treat, diagnose, prognosticate.


texts: Why are some genes dominant over others? What is the mechanism behind it?

texts: If I have a brown eye gene which encodes the protein that is responsible for the brown color and have a blue eye gene as well, what is the reason that my eye color is brown? How does one gene maintain dominance over the other?


texts: Can swallowed fingermails, hair, or skin get caught in your appendix?

texts:
There is a common saying in my place: If you eat your skin, hair or nails, it will be deposited in the cecal (Vermiform) appendix, and can cause appendicitis. (This is mostly told to children to discuourge them from eating their own.)

Is there any reality in this statement? In the case of hair and nails they are dead cells, but what is the issue with skin? Skin is normally living and the cells are active.

So is there any problem digesting ones own skin?

Do nails, skin and hair must be trapped in Vermiform appendix?


texts: Use of beta-2 microglobulin staining to assess frozen tissue sample integrity

texts:
In a Russian paper I'm reading the authors use staining for beta-2 microglobulin (B2M) to make sure that a variety of frozen tissue samples still express antigens on their surface, so that these samples could be used to assess the activity of an antibody they are researching.

The authors write that "since virtually each cell expresses B2M on its surface, this assay ensures that other antigens have remained on the surface of the examined cells as well".

Is there a special term for this kind of check? Is this anti-B2M staining a routine procedure, and are there papers dedicated to this procedure? I haven't found relevant papers.


texts: Coefficient of relationship and path of coefficient

texts:
A path of coefficient of relationship is defined as

$$\rho_{AO} = \left( \frac{1}{2}\right)^n \sqrt { \frac{1+f_A}{1+f_O}}$$

This SE post discusses this definition

From this, the coefficient of relatedness between two individuals $B$ and $C$ is defined as

$$R_{BC} = \sum \rho_{AB} \rho_{AC}$$

, where $A$ is (I think) the last common ancestor of $B$ and $C$. The sum is over all possible path coefficients.

Source: Wikipedia

I am a little bit confused, I don't really understand this formula. One reason is the following. Let's assume that  $B$ has 2 paths and $C$ has 3 paths to go to $A$. If we denote $\rho_{AB,i}$, the path $i$ (or the $i^{th}$ if you prefer) between $A$ and $B$,

$$R_{BC} = \rho_{AB,i} \rho_{AC,i} + \rho_{AB,j} \rho_{AC,j} + \rho_{AB,k} \rho_{AC,k}$$

But the path $\rho_{AB,k}$ does not exist because there are only 2 paths between $A$ and $B$ (which are denoted $i$ and $j$). Also, there is no reason to count the path in a specific order and not another one. If we change the order we count the paths between $C$ and $A$, we can get:

$$R_{BC} = \rho_{AB,i} \rho_{AC,j} + \rho_{AB,j} \rho_{AC,i} + \rho_{AB,k} \rho_{AC,k}$$

, which is obviously different from the previous calculation of $R_{BC}$

Can you help me making sense of these formulas?


texts: Does ribosome associated with RER separate from RER after finishing protein synthesis?

texts: After ribosome associates with RER because of its specific signal sequence, and then when cotranslation translocation is finished, does ribosome return to free floating ribosome at cytosol? Or does it stay as combined condition?


texts:
Taken from Ian Freshney's Culture of Animal Cells:

  The enzymes used most frequently for tissue disaggregation are
  crude preparations of trypsin, collagenase, elastase, pronase, Dispase, DNase, and hyaluronidase...

What does crude mean in this context?


texts: Identify this insect - genus, species (orange, black)

texts:
Please help identify this insect - genus, species and anything interesting about it. Do the colors matter in the identification?

Note, this is posted separately due to comments in this other thread.


texts:
According to this

Blastocyst & Embryo Freezing in IVF

  Embryos can be frozen at the pronuclear stage (one cell), or at any stage after that up to and including the blastocyst stage (5-7 days after fertilization).

Given that freezing normally destroys mammalian cells1 why can early stage embryos survive being frozen?

Reference:
1: Shier, W. T. (1988). Studies on the mechanisms of mammalian cell killing by a freeze-thaw cycle: conditions that prevent cell killing using nucleated freezing. Cryobiology, 25(2), 110-120.


texts: What are the physiological roles of Hydrogen sulfide?

texts:
I am thinking why hydrogen sulfide has its effects in the body.
For instance, it is one Salmonella's virulence factor.
I am not sure if such a balance equations holds

H2O + H2S ←→ ...

Actually, I miss here some factors because I am not understanding the biochemistry enough to answer this.
I think H2S can exists in some sort of ionic form.
Hydrogen sulfide reminds me of ammonia.
I think it inhibits some systems.
By which mechanisms?

It is mentioned in many places the empirical effects: signaling functions similar to NO and CO.
But I am interested in how this happens.
What is the rate of adhesion of H2S to hemoglobin for instance?

H2S can change to sulfite and thiosulfate in mitochondria which are then excreted into urine.
I think most of the biological effects are done before these forms.
But in which forms?


texts: Can anyone identify this colorful snake found at Pulau Ubin in Singapore?


texts: I learnt that lignin impregnates xylem cells, causing the cytoplasm to die due to the inability of water and nutrients to pass freely, hence creating hollow tubes adapted to transport materials. This means that in order for the cytoplasm to die and the tubes to be hollow, lignin needs always be present.. However lignin is not present in all xylem vessels... Lignin is the woody tissue that only forms the trunk of a tree. So how do these cells hollow out in other parts of the plant/tree to create empty transport vessels..??


texts:
I would like to find an accurate definition of disease risk for virus ecology.
I am searching in articles and in none of them this term is defined, they only mention it.
Schematic of the relationship between habitat heterogeneity and disease risk.
Disease is greatest in fully cultivated plants, intermediate in wild plants
that are tended by humans in anthropic habitats, and lowest in fully wild plants.
On the other hand, biodiversity is highest in the habitats of wild plants, and
lowest in those of cultivated plants.

Roossinck, M. J., & García-Arenal, F. (2015). Ecosystem simplification, biodiversity loss and plant virus emergence. Current opinion in virology, 10, 56-62.
I have defined it as the probability of a host to develop a disease. However, I have the feeling that this definition is somewhat lax.


texts: What does the nucleus look like in S phase of Meiosis?

texts:
I was watching an animation video about Meiosis and this is what the video shows (pics attached.)
It shows that before synthesis, each chromosome exists as single chromatid and then after replication, it has a sister chromatid. I am confused because germ cells are diploid, so shouldn't the S phase look like this?
It should start with 23 chromosomes (46 different DNA's) and then replicated to 46 chromosomes (92 different DNA) which then get assorted into 4 different cells?


texts: How many phosphates are in the 5' end of a DNA strand?

texts: I know that the pyrophosphate of a NTP is hydrolysed so that it can create enough energy for the synthesis of DNA. But if we want to get specific we can know for sure that the 3' end of the DNA strand has got one phosphate because the phosphate is having a bond with another nucleotide. But what could be the reason for the 5' end to have only one phosphate and not 3? Could it be the energy providing or that the structure has to be consistent or something else that I can't think of?


texts: Can bacteria or other microorganisms be killed by applying pressure?

texts:
Can you smash a bacteria (or any microorganism) and kill it?
Let's say there is millions of microorganisms on a table. When you put your finger on the table, will or can you kill at least some of them ?


texts: Does blowing 'HOOO' vs 'HAAA' release different amounts of CO2?

texts:
Near the end of an experiment during one of my lab courses one day, I blew like 'HOOO' (where the air you blow is cold) onto a small container of water which had a pH probe. Then, I blew like 'HAAA' (where the air you blow is hot).
I noticed that, perhaps by sheer coincidence, the pH of the water decreased by a small amount when I blew like 'HAAA'. My hypothesis was that maybe blowing like 'HAAA' released more CO2 which was absorbed by the water, making it more acidic.
Unfortunately, I didn't have enough time to test my hypothesis further and we aren't going to use the pH probes for the rest of our experiments, so I can't test it later on, either.
So, I'm wondering: does blowing 'HAAA' release more CO2 than blowing 'HOOO'? Or was this purely a coincidence?


texts: What determines the spiral direction of plants?

texts:
Some plants and vines spiral clockwise as they go along (right direction) and some spiral anticlockwise (left direction). What determines which direction they spiral along? At first, I believed it to be determined by which hemisphere you are in (influenced by the Coriolis Effect), and this result could be tested by finding spirals in both northern and southern hemispheres and comparing their directions. However, the very first spiral I found seemed to cripple that idea.

The spiral I found spirals first in the right direction, then suddenly decides to spiral in the left direction, and then further along in the right direction again. Since the Earth does not arbitrarily change its rotational direction, this phenomenon must be explained by some other explanation. The change in rotational direction seems to be abrupt, almost like a catastrophic event. A few that I thought of:

1: Arbitrary. The spiral seeks merely to latch onto something, and will try both directions to see if either work out.

2: The spiral is somehow influenced by the night day cycles. Since the spiral switches from right to left back to right having been subjected to two sudden changes, the only large changes I can think of is the day night cycle.

-I live in Australia by the way


texts: I am not talking about chemotherapy or radiotherapy. So, if it exists, what is the best biological technique to cure cancer as of now?


texts: Why don't antibiotics affect mitochondria?

texts: Given that mitochondria are evolutionarily closely related to bacteria, and antibiotics kill bacteria, why don't antibiotics also kill mitochondria?


texts:
In the Miller-Urey experiment the probability of the chemical origin of life under (hypothetical) early Earth atmospheric conditions were assessed. For that water, methane, ammonia, and hydrogen were sealed in a bowl, heated and struck by artificial lightning (see this for the experimental setup). After cooling the mixture down several complex organic molecules (e.g. amino acids) were found by paper chromatography.

So my question is what would happen if instead of using early Earth gases, one puts a concoction similar to current or early atmospheric gases found on/expected to once be found on Mars.

Is it possible to foresee how well that experiment might do and what results it could bring?


texts: Why are monocotyledonous plants considered more evolved than dicotyledonous?

texts:
Why are the following characteristics advantageous for a plant?

to have atactostele instead of eustele
to have less stamens
to lose secondary growth
to switch to anemophily pollination (also if it's not always the case)
to use the cotyledon as storage media instead of endosperm

Why are there so much similarities between liliopsida and gymnospermae?


texts: Implanted neural recording system vs Electroencephalography

texts:
Can someone help me to understand why in nowadays the scientists develop implanted neural recording system to measure and collect neural signals? Why the use of the electroencephalogram is not sufficient to record neurons? Which is the difference between these systems?

Thanks in advance


texts: How does the snail shells' fertilizer compare to regular fertilizers?

texts: May I ask about the quality of the fertilizer derived from the shells and their effectiveness compared to other fertilizers on the market ?


texts:
I am currently reading a "book" (rather an article) called "Protein Modelling & Molecular Docking: Modeller, Autodock".

The abstract starts with the following sentence :

  Polyketides are a large family of complex enzymes synthesized by
  polyketide synthases.

Before reading this article, I knew nothing about polyketides. I looked it up online, and I saw that they were secondary metabolites, which adds up with the rest of the article. However, I could not find any mention of some polyketides being enzymes, hence my question:

Are some polyketides enzymes or is this a simple mistake in the article ?


texts: Can we use differential equations for population that is discrete?

texts:
Population dynamics is often modeled using ODE. For example one common model is logistic growth model:

$$\frac{dx}{dt} = k.x.\left(1-\frac{x}{C}\right)$$

where x is population size, k is rate constant for growth, C is carrying capacity.

But population is a discrete variable. It is not continuous. It always takes whole numbers. You can have a population of 3000 fish, but not 3001.2 fish.

Then how can one use population as a dependent variable in a differential equation?

Integration of the ODE, given above, will give me a function to calculate size of population, x(t), at time t, when size of the population at t = 0, was x0. We can specify a whole number for x0. Here, x(t) can be a real number with fraction, but a population size is always a whole number.

How does one tackle this anomaly?


texts: How do cells become differentiated using epigenetics despite having the same genome?

texts:
How is epigenetics used in the differentiation of cells and is this the only thing that is used? I've seen that transcription factors play a role but are these simply proteins that initially write the epigenetic code or something different altogether?

I've written this explanation of how I understand it currently. Please tell me if this is right or wrong.

How do our cells become specialised if they have the same genome? The answer lies in the fact that gametes have most of their epigenetic information taken off at fertilisation, (apart from small sections like at IAP retrotransposons) so it’s like a clean slate. The zygote cells divide to form many identical cells that have the capacity to become any cell in the body.
Proteins in the egg then bind to certain genes and regulate their expression by adding epigenetic markers like methyl groups and histone modifications. The proteins created from these genes then go to control the regulation of other genes and so on, until all the cells have different epigenetic markers put on them that mean they produce different proteins in different quantities to serve different functions in the body.


texts:
How does the rosette structure of synthase cause the cellulose synthesized to be aligned next to each other?
I just cannot visualise how a rosette structure can be able to cause the celluose to be aligned next to each other at all.


texts: How does temperature affect photosynthesis?

texts:
I am doing a lab for biology and my teacher required me to do this virtual lab. However, it does not make sense when seeing the results of the lab. In 30 second trials, it shows that there are 16 bubbles at 10C, 6 bubbles at 25C and 19 at 40C. This should not happen as 25C is near the optimal temperature (at least in respiration) but it shows the opposite.

Is the site wrong or am I wrong?

Site link: http://www.kscience.co.uk/animations/photolab.htm

Constants: 50 Light intensity, full disolved co2, white light color.


texts: What is the smallest visual unit perceptible to the human eye, like a pixel? (esp. in visual static)

texts:
If you close your eyes, you can often see visual static, where individual pixel-like things are much more visible than with the more smooth, crisp images one gets with open eyes. This led me to wonder a few things:

Is there a name for this unit, like "pixel"?

What is the biological correspondent? A single rod or cone or something?

Are the individual pixel-like things making up the static noise the same underlying mechanism (and size) as the smallest perceptible units of vision one gets when actually looking at something? I suppose this is related to visual acuity. I've read that the cause of static is suspected to be excitation of neurons, but that's not what I'm asking.

Thank you.


texts: What animal does this skeleton belong to?

texts:
I was exploring around the outskirts of a local lake this afternoon (central Kentucky, USA), and came across the following skeleton:

The length of the remains is somewhere between 9-12".

Can someone tell me what animal this is from, and what part of the body it is?


texts: How do I identify and then isolate a Gene that codes for a particular observable phenotype. It is a novel bacteria and I do not know the gene sequence or the protein that it codes for.


texts:
A common precaution for preparing EtBr-agarose gels is to add EtBr only after the gel solution has cooled somewhat, because EtBr is a dangerous mutagen. Supposedly, adding it to a hot liquid allows EtBr vapors to get into the air and everyone's lungs, where it can act as a carcinogen.

In addition to this are commonly seen special procedures for handling EtBr vials and gels (fresh nitrile gloves, avoid contaminating other work areas, special waste disposal rules).

However, there's also some saying that EtBr isn't all that mutagenic and all this care is over the top.

What's the reality? Just how dangerous is EtBr, especially in amounts used at a typical biological lab? How long does the danger persist? Are even trace amounts hazardous (for instance, touching a "clean" pipette without changing gloves after working with EtBr)?


texts: If all the brain ever "sees" is action potentials, how do we know that one set of action potentials denotes a flash of light, another one signifies a loud sound, etc ?


texts: Does the vagus nerve supply the human thoracic diaphragm?

texts:
The vagus nerve (CN X) passes through the oesophageal hiatus of the diaphragm at the vertebral level T10.

But does the vagus nerve actually offer any nerve supply to the diaphragm?


texts: What are all possible vectors for unicellular human parasites?

texts:
I got the given question. They want the following pieces of information about protozoological human parasites:

  disease - parasite - vector.

There are 10 proteogenic diseases at the Wikipedia. I added the corresponding parasite and the vector next to them:

Malaria - Plasmodium - Apicomplexa
Amoebiasis - Entamoeba histolytica - sarcomastigophora
Giardiasis - Giardia lamblia - no vector
Toxoplasmosis - Toxoplasma gondii - no vector
Cryptosporidiosis - Cryptosporidium - Apicomplexa
Trichomoniasis - Trichomonas vaginalis - no vector
Chagas disease - Trypanosoma cruci - insect
Leismaniasis - Leishmania donovani - sand fly vector
Sleeping sickness - Trypanosoma brucei gambiense - tsetse fly vector
Dysentery - Entamoeba histolytica - sarcomastigophora

I am unsure what I should answer to the question since it is asking "all" possible vectors for unicellular human parasites.
There are many possible diseases, much more than the given ten in my opinion.
It seems also that there are many possible ways of getting the infection for each disease.

I hope that I am wrong in my statements.
It is my first course in Parasitology.

What would you answer to the given question?


texts: How can I accurately predict proper transgenic protein function/structure from different species?

texts: I am currently building a synthetic system in E.coli, and am often faced with the need to use genes from other distant prokaryotes. I know that myself and most of my colleagues resort to an educated trial and error approach. Besides the obvious (elimination of introns from eukaryotes, codon optimization, genetic relatedness), is there any predictable or semi-rational way of knowing if a transgene for a different organism will function properly in any given organism?


texts: What is this thing? It is hairy mostly a cocoon, and i saw a white worm pop out of it. It is spreading rapidly

texts: I suspect it is originating from the mud. This has some plastic bits with it. They are spreading all over my walls. I think it is some  kind of cocoon for worm. Should it's rapid growth in terms of number be a matter of concern? found in Bangalore, India,


texts: How does cold water help to overcome high fever?

texts: Why cold water helps to overcome from high fever in body? As fever is inside the body and we're applying cold water over the body!


texts:
As indicated in this question, what do you think is is the best explanation for the observed progeny, is it because distance between genes affects recombination frequency? My main concern is question b).

Any help would be greatly appreciated thanks in advance!!


texts: Are there issues with filling PCR tubes to capacity?

texts:
I'm planning to scale up a PCR reaction, and I'm wondering if filling the PCR tubes to the maximum volume of 200 ul would be a problem. It would mean a lot less pipetting as I would only need 1/4 of the tubes.

The typical protocols I've seen always use 50 ul for a PCR reaction, I'm wondering if there are any issues with larger volumes, e.g. differences in heat transfer, that could cause issues if I scale up the volume in one tube.

Is scaling up the volume problematic? Any specific aspects I should consider?


texts: What is the volume of menstrual flow in non human hominidae?

texts: I'm looking for reliable data related to menstruation in animals, with especial focus on apes. I have found that some articles and cientific studies point that only chimpanzees have copious menstruations, but there is not refrence to the volume of menstrual flow at all, and what is more intriguing this alleged copious menses are not consistent with two important observations, first that in a studied carried on some captive female chimpanzees only a keeper reported an observation of menstrual flow in a female on one single day (and the researchers didn't agree it was actual menstruation), and the second one that field researchers reported of a period of adolescent infertility in young female chimpanzees, about two years in which they have intercourses but not pregnancies, and yet they didn't notice a sign of menstruation.


texts: What is meant by "neurotransmitters flooding the brain"?

texts:
I frequently hear expressions like "Dopamine flooding the brain" or "X neurotransmitter flooding the brain" used to communicate with general audiences. For example: "Following [orgasm]? oxytocin floods the brain, causing feeling of deep connectedness between people"

What exactly do they mean by "Oxytocin flooding the brain"? I'm interested in where and how it happens. Do they mean that excess neurotransmitters are released in the synaptic cleft? Is it localized to some brain areas, or is it indeed throughout the brain?

If they are indeed talking about the synaptic cleft, then I'm interested in how such "flood" triggers the change in state - the answer to this question suggests that the half life of dopamine is only about 2 seconds in prefrontal cortex. Assuming that the half life of oxytocin is similar, in the "oxytocin floods the brain and produces feeling of connectedness" example, does it mean that a single burst of oxytocin(x seconds in synaptic cleft) is enough to produce such feeling, or are they talking about sustained release or some kind of release loop mechanism?


texts: How do we know with so much detail the molecular structure and composition of some molecules?

texts:
I can't understand how can we get to and be so sure about so detailed information about the molecular structure of certain substances. How do we get this information? What tests are used to such?

Let's take for example somatostatin:

you can see it is a big and extremely complex molecule, and my question is, how have we arrived to this structure? How can we know this to such detail? What tests do we use to know this?


texts: How to use Transect-based sampling to select sample trees

texts: I was wondering if you help me how to use Transect-based sampling to select sample trees


texts: What causes decomposition of human body after death? Here it says autolysis, while Here it says that bacteria decompose the body. If bacteria decompose the body, why don't they do while we are living?


texts: This is a tree that I have been growing. I'm wondering if this is a mulberry, and if so, what kind?  Location is Arizona.


texts: What causes very high pitched sound in one's ear?


texts: How do I make conclusions from the autoradiograph of a Southern blot?

texts:
Here's another question taken from "Concepts of Genetics," Klug et al (10ed), revolving around a paternity test. PCR and a Southern blot were carried out in order to determine whether 3 chimpanzees (lanes 3, 4, 5 in the blot below) were the "legitimate" offspring of 2 potential parents (lanes 1 and 2).

The question makes a point of saying that the primers used to bind to the chimp DNA originates from humans, and that they "flank highly polymorphic sites in human DNA that result from variable numbers of tandem nucleotide repeats." My first question is what exactly does "flanking" mean in this context? It sounds to me like the human DNA "mirrors" the chimp DNA, and so makes it good enough to use as a primer, but I'm not sure.

I've come across a few other examples not in the text about how to infer whether a potential parent is indeed a parent based on whether the offspring's lane contains bands found in both the maternal and paternal lanes, which leads me to believe I can rule out the chimp in lane 5.

I'm given five answers to choose from to decide which of the offspring, if any, are legitimate:

None
A only
A and B only
Not enough data; more polymorphic sites should be examined
No conclusion can be made because "human" primers  were used

Main questions: Does that fact that we're using human DNA as primers cause any problems? Do we know enough from this blot to determine paternity?


texts: What are some potential consequences for attempting to cure Type one Diabetes?

texts: Type one diabetes has been in my family for a few generations. As a carrier and having a mother with the disorder, I've done a lot of research on it. As I am completing my High school Biology course, I've gotte a better understanding of how the disorder may be treated. (Stem cell therapy, gene replacement, etc). Here's a hypothetical scenario: Scientists develop a modified virus that contains a normal person's beta cell genetic makeup, injects it into the pancreas, and reproduces. The virus and beta cells reproduce, and the body detects the virus, but not the beta cells. (or neither, and the virus is not harmful). The beta cells create insulin, and the Diabetes is cured. Would this work, and would this hurt the immune system? Would it be possible for the scientists to blunder and either create too potent a virus or too much of the virus?


texts: How is C4 pathway more water efficient than C3 pathway in photosynthesis?

texts:
In the C3 pathway:

1 H2O molecule is required for the fixation of 1 CO2 molecule.

In the C4 pathway:

The only H2O molecule used is in the calvin cycle, so 1 H2O molecule required for fixation of 1 CO2 again.

So, how is C4 pathway more water efficient? I tried looking up more detailed diagrams, but I couldn't find one which gave any different (H2O consumed) to (CO2 fixed) ratio. Any help is appreciated.


texts: Why are there no large animals with chloroplasts?

texts:
Mitochondria and chloroplasts display similarities with bacteria that led to the endosymbiont theory. This theory states that an early ancestor of eukaryotic cells engulfed an oxygen using non-photosynthetic prokaryotic cell. Eventually, the engulfed cell formed a relationship with the host cell 1n which it was enclosed, becoming an endosymbiont (a cell living within another cell). Indeed, over the course of evolution, the host cell and its endosymbiont merged into a single organism, a eukaryotic cell with a mitochondrion. At least one of these cells may have then taken up a photosynthetic prokaryote, becoming the ancestor of eukaryotic cells that contain chloroplasts.

So my question is,  why is it that all the cells that took in the chloroplasts became plants or other simple animals but not large mammalian or reptilian animals?  Is there a limiting factor that restricted chloroplasts from being beneficial to large animals? Why is it that large plants can have both chloroplasts and mitochondria but not relatively larger animals?


texts: What is the most reliable tumour suppressing gene for NSCLC?

texts: I was looking at some tumour suppressing genes that can be helpful in diagnosing lung cancer (particularly NSCLC - Non-small-cell lung carcinoma) at an early stage. I came across a few such as p53, etc. However, as a beginner (and someone who has never pursued higher studies in biology), I do not have much knowledge as to which is the most reliable and the most extensively documented tumour suppressing gene for NSCLC.


texts: What are the minimal chemical requirements for a food which we all can eat?

texts:
I've been puzzled by the following though experiment for the past few days:

I want to make my own food from scratch, but I do not know where to start from.
I want to be 100% sure that what I eat will never contains something that can damage my body. For example: If you buy something from the local market you can not be 100% sure that it's safe to eat. (99.9 % maybe... but that's not 100%)

I want to ask you to tell me, how can I make a food that I can eat, or should I say - live on it, for the rest of my life, that's 100% safe, I can control every aspect of it's creation and has many combinations of taste because I love diversity.

Thank you for your time : )

Edit:
Because I realized my question is very broad and indeed is a little... too much scientific I want to close it. But before I do so, here's what I had in mind:
I wanted to take some chemical elements, put them in a jar, run some electricity, heat, whatever through it, filter it, do some additional processing and eat it.
 I wanted to know if the stomach can take it, because I was going to eat food that's not hard to digest.


texts: Suspensory ligaments: why are they ligaments?

texts: Don't ligaments connect bone to bone? In the eye for example, the suspensory ligaments connect the ciliary muscle to the lens, which obviously aren't bones. Is this just one of those instances where the terminology isn't that precise and you just have to memorize the exception?


texts: Test of antibiotic A for sensitivity as surrogate of antibiotic B

texts:
I am reading the WHO Global Antimicrobial Resistance Surveillance System (GLASS) - Manual for Early Implementation. it mentioned some of the drug-bug combination that will be put under surveillance in page 8 of the following link, I have screen-captured the page below that I have some questions.

http://apps.who.int/iris/bitstream/10665/188783/1/9789241549400_eng.pdf

For S. aureus, Cefoxitin is selected for surveillance, but the remarks mentioned that Cefoxitin is a surrogate for testing susceptibility to oxacillin (methicillin, nafcillin). I know S. aureus showing resistance to methicillin is MRSA, but why test for Cefoxitin but not test methicillin directly?

The same question goes for S. pneumoniae for Oxacillin as a surrogate for testing reduced susceptibility or resistance to penicillin. Why not directly test for penicillin?

Sorry that I am not a microbiologist, just a data analyst recently working on microbiological data, hope that I won't be asking something too stupid.

Thanks!


texts: What are the evidence that all life today descended from a common ancestor (LUCA), and which organisms (if any) challenge the concept?

texts:
If I understand correctly, the concept of the LUCA (last universal common ancestor) is based on the hypothesis that archaea and bacteria share common ancestry.

In the realm of mathematics, the same discoveries have often been made more than once, in different places. Sometimes (like with calculus) these independent discoveries were made almost simultaneously. Sometimes the discoveries appear to  be totally unrelated (Hipparchus affirmative compound propositions before 100 BC, and David Hough's work on inserting parentheses in 1944).

If "life" started on Earth in some kind of primordial soup, it is conceivable that it started not once but many times, in different places and at different times.

How strong is the evidence that bacteria and archaea do not represent quite separate discoveries of "life", which (because of the nature of the chemical substances that they use) happen to share a number of features, such as DNA?


texts:
Spotted this outside my window today. Looks like an orb-weaver, but I can't tell whether it's a regular garden spider or not. What species could this be?

This picture was taken in Bangalore, Karnataka, India.


texts: Why does cyanide inhibit CuZnSOD, but not MnSOD or FeSOD?

texts:
Different types of superoxide dismutase (SOD) contain different metal ions (Zn, Cu, Mn, Ni, or Fe), all of which allow them to catalyze one reaction, dismutation of superoxide anion, O2−. Cyanide can block this reaction, but only in CuZnSOD.

What is the (bio)chemical mechanism behind cyanide inhibition of CuZnSOD and why doesn't it occur in FeSOD or MnSOD?


texts: What are some examples of interbreeding between species that are separated by 5 million years or more?

texts: Interbreeding is constrained with that the offspring shares the gene pool of the parents. What are some examples of interbreeding that has occurred, where the two species were separated by 5 million years or more?


texts: Which side of the DNA helix is used for describing SNPs?

texts:
In genetic research I often come across references to single-nucleotide polymorphisms (SNPs).  An example is rs3184504(C;T).  As far as I understand it: In this case rs3184504 refers to a specific point in the DNA genome, and (because this one occurs in a non-sex human chromosome) it indicates the nucleotides at that point in each copy of that chromosome.

But how does one determine which strand of the DNA helix it references?  Is there a convention?  Or is the strand indicated in the SNP reference (in this case rs3184504)?

If one strand is C;T then the opposing strand will be G;A ... but in the context of the gene in question I assume it matters which strand is referenced in the SNP.  E.g., if the code following this SNP on the chromosome in which rs3184504 has C is:

CTCGA...
GAGCT...

this is a different genotype from the SNP indicating a C on the other strand:

GTCGA...
CAGCT...

So the SNP description is only meaningful if it also indicates the strand, right?  If so, how does the SNP descriptor do that?


texts: I saw this on Facebook today and have tried researching it myself, but I have had no luck.


texts: Could murder be modeled as an infectious disease?

texts:
Background

  "When swine flu hit the population it spiked in certain areas and
  tapered off in neighboring regions, it hits hardest where people have least protection and this pattern is more pronounced (here)"

Apparently incidences of murder spreads in a similar pattern to infectious diseases such as swine flu according to a 26-year study of the city of Newark, New Jersey (summary).

Questions

It would be interesting to hear your opinions, but some interesting questions I would like to ask are:

To what extent could murder and the epidemiology infectious disease
patterns resemble each other?
What factors could you suggest may lead to their apparent
similarities?
Given that murder could be modeled as an infectious disease could we
apply epidemiological interventions to murder?


texts: Total number of pleura in the exoskeleton of cockroach

texts:
Basically as far as i know cockroach consists of 10 terga and 9 sterna but what are the total number of pleura present in the cockroach.

Pleura are situated between tergum and sternum of a body segment and help in the articulation of terga and sterna.

What would that be in the case of the 10th abdominal segment in which sternum is absent ? Are pleura present there? If yes then what is their functions at that place?


texts: Effect of the health of the male parent at the time of conceiving

texts: Does it matter at all in determining the traits of a baby what the current health of the father is? For example, let's say I got diabetes at the age of 40 because of the poor lifestyle choices. Will the baby be any different from how it would be if it was when I was say 26?


texts:
Why is the malate-aspartate and the glycerol-3-phosphate shuttles located in the cytosol and intermembrane space?

The krebs cycle happens in the matrix so why wouldn't they push electrons from the matrix and into the intermembrane complex for oxidative phosphorylation??


texts: What wasp like insect breeds in clay pots with dead spiders?

texts:
I found several small clay pots of oval/cigar shape roughly 2cm long in a rarely used window in the house, because a wasp like insect was flying into a small cavity of the window.

I removed one and found dead spiders inside.

I let the rest of the nest alone and closed the window again. I guess I don't have to bother them if they aren't bothering me.

I'm wondering what type of insect is that building such nests? It looked like a cross between a wasp and a hornet.
As far as I know, wasps and hornets build their nests from wood, which gives them a paper like material. This one however is made from soil/dirt.

I'm also not sure if spiders are the only food. But given the street lamps outside, I suspect that spiders are very available and easy to catch.

The region is central Europe.


texts: Why is Adam's Apple more prominent in males? Is it due to bigger voice box pushing the cartilage more, or is the cartilage indeed bigger than that in females? I am assuming bigger voice box as males have a "deeper" sound. Is it correct to do so?


texts: Do neurons secrete multiple neurotransmitters, or just one type?

texts:
I know that neurons communicate between each other by filling the junction between dendrites with neurotransmitters.

What interests me is if a single neuron only works with one type of neurotransmitter(ex: serotonin), or if it can secrete/receive all of them (serotonin, dopamine, etc).

If a neuron can secrete all, then can all dendrites secrete and respond to all neurotransmitters, or is it one per dendrite (one branch only works with dopamine, another one with serotonin, etc)?


texts: How does extracellular potassium ion concentration and calcium ion concentration affect the excitability of a cell?

texts:
When extracellular $K^+$ concentration increase by a certain amount, excitability of cells is higher because the resting potential shifts toward a higher equilibrium potential of $K^+$, therefore causing depolarization. However, when there concentration of extracellular $Ca^{2+}$ increases, excitability of cells decreases. If $Ca^{2+}$ and $K^+$ are both positively charged ions, what is the cause behind their opposite physiological effects?

I'm not a biology student, so detailed answers would be kindly appreciated. Thank you!


texts: Enzyme Inhibitors: Using in vivo in yeast

texts:
I find listed on the Sigma-Aldrich site a large list of enzymes & corresponding inhibitors. e.g. For the enzyme squalene synthase the inhibitor listed is "Zaragozic acid A trisodium salt"

Would this mean that if I added the right amount of this chemical to, say, a Yeast cell culture I might expect to get reduced activity of Squalene Synthase which is native to yeast and catalyses the transformation of FPP to Squalenes.

Would this even be a reasonable thing to try if I had a goal to block Squalene synthase? Or am I interpreting how these inhibitors ought to be used incorrectly? Can they be used with in vivo cultures at all?


texts: Hormonal terms Somatotrophin or somatotropin?

texts: Are Somatotropin and Somatotrophin hormones the same? It's confusing because when you type in Somatotrophin in google, it says, "a growth hormone secreted by the anterior pituitary gland.", but there's no Wikipedia about it. But when you type in Somatotropin, there's whole Wikipedia for this stating that it's a growth hormone. I am 100 % sure that there is a difference between these two terms: tropin and trophin because Wikipedia itself says not to be confused with these terms and has articles separately for these two terms. So, Can anyone help me be clear about these two terms?


texts:
I have a Dracaena Marginata which started to have some white spots. They turn out to be some kind of "mold"

which can be removed when swapping the leaf and then leaves some discolored spots

They usually appear when the leafs get yellow (because of it, or because I have forgotten to water for too long) and seem to be more present at the base of the leaf.

What is this?

And more importantly: is it a problem for the plant? (minor issue, though it is a gift from my children) or for me? (major issue, and death sentence for the plant)


texts:
This tree has red samaras.

Location: Toronto

Size: medium-sized tree

Date: July 26th, 2020

What is it?


texts: Is this European(western), Eastern(northern) or another Hedgehog?

texts:
Yesterday this little guy ambushed my bicycle, thankfully tire-hedgehog contact was avoided at the last moment. Now I am wondering which one is it. Going by wikipedia maps and photos it should be either European/Western (Erinaceus europaeus) or Northern (E. roumanicus).

Sadly due to nocturnal nature of Hedgehog, "smart"phone camera and general willingness of Mr. Spikey to quickly leave area of incident this is best photo I have:

Incident occurred in Poland, Europe, around 21:30 local time.


texts: How can a three-base codon evolve from a two-base codon?

texts:
Inspired by this question among others.

It's widely suggested that the current 3-base codon system of encoding protein sequences in DNA evolved from an earlier 2-base codon system. This makes sense if you look at the coding sequences themselves but I fail to understand how it can evolve? Wouldn't any shift wreck the coding of all existing proteins?

Perhaps they could overlap, but wouldn't even that produce nonsense and how would it shift to non-overlapping codons? Perhaps both systems could run in parallel, but how would anything useful come from that in the short term? What selective of advantage of 3-base coding could be strong enough to overcome any disruption?

Has anyone developed a coherent model of what intermediate stages might look like?


texts: Do miRNA and antisense RNA do essentially the same thing?

texts: Don't they both just disrupt RNA so it can't make a protein? If so, then what is the difference between the 2?


texts: What advantage does lactose have as the main sugar in milk?

texts:
Most organisms have lactose as their main sugar in their milk.

What advantage does lactose give have over sucrose (Which is a common sugar in the plants, so it makes sense for it to be present in milk)

Is lactose synthesis easy? Or is the enzyme B-galactosidase easy to make?

Or is it more easily digestible, allowing mammalian infants to get energy faster?


texts: What molecular processes are involved in pseudopodial extension?

texts: I am curious as to the processes and mechanisms involved in the extension of pseudopodia in amoeba. How does the cell know and control the direction and extent of pseudopodia formation at a molecular level? I am not particularly interested in the taxes that amoeba recognize, but rather the mechanism of response to these taxes.


texts: What Animal is This Skin From? A Wooly Mammoth?

texts: I was at the American Museum of Natural History in New York City today, and I saw the skin pictured below. Because it was next to stuff about wooly mammoths, I thought it might be a mammoth skin. However, there was no sign accompanying the skin. What is it from?


texts: What is this insect that showed up after I left food out? How can I get rid of it?

texts:
These bugs showed up after I left some food out. I noticed a significant reduction after I cleaned up my place, but now they're back again. They're pretty small, but can you guys help me identify these bugs. I need to look up how to get rid of them.

I live in the Midwest.

I realize the quality is not the best.


texts: What do viruses do during incubation period?

texts:
For example, there is an incubation period of around 1 to 3 days for common cold, and that of AIDS can range over to decades.

What do viruses do actually do during the incubation period?

What triggers them to turn active again?


texts: Do restriction enzymes on read 3' to 5'?

texts:
Every chart of palindromic restriction enzymes I've seen lists their restriction sites from 5' to 3', something like this:

EcoR1 cuts GAATTC between the G and A:
          5' NNNGAATTCNNN 3' --> 5' NNNG____ AATTCNNN 3'
          3' NNNCTTAAGNNN 5' --> 3' NNNCTTAA____ GNNN 5'

Will restriction enzymes match and cut a site if it's running antiparallel? For example, will EcoR1 cut this sequence?

5' NNNCTTAAGNNN 3'
3' NNNGAATTCNNN 5'


texts: What was the evolutionary advantage of having seeds so large that they could only be dispersed by megafauna?

texts: I understand that fruits like the avocado and the osange orange are so large and unwieldy that their evolutionary "intent" was to be consumed whole by megafauna that are now extinct. What I don't understand is why there was selection pressure for such a relationship to develop. Wouldn't it be to the plant's advantage if its seeds could be dispersed by more types of animals? What advantage does the plant get by limiting seed dispersal to a small set of large animals?


texts: Are Na+/K+ active pumps and K+/Na+ "Leak" channels same as given in the figure?

texts:
Na+/K+ channels maintain the resting potential with other sodium and potassium channels. Then what are these "Leak" channels? are they the same Na+/K+ pump in a special condition? If so, what is it?

Source of Image: Guyton and Hall- Textbook of Medical Physiology


texts: Is a single polynucleotide necessarily and always a nucleic acid?

texts:
I am confused. I know that a DNA molecule is made of two polynucleotides.

But does each polynucleotide represent one nucleic acid? If so, a DNA molecule is made of two nucleic acids, right?

Or do the two polynucleotides (that form a molecule of DNA) make up only one nucleic acid? If so, a DNA molecule is only made of one nucleic acid, right?


texts: Why do telomere lengths not predict differences in life spans among species?

texts: We read that ageing is related to cell death when we run out of telomeres at the end of our DNA molecules. Humans live roughly for 70 years - the traditional three-score years and ten. This compares with the great apes, such as chimps and gorillas, which live for about 40 years. So we would expect the great apes to have fewer telomeres than humans. In fact the reverse is the case. Humans have telomeres of about 10 kilobases in length whereas the equivalent length in chimps and other great apes is about 23 kilobases. So what is going on? Why do we live longer?


texts: Linkage disequilibrium with multiple alleles and loci

texts:
Linkage disequilibrium $\left(D\right)$ for two bi-allelic loci is defined as:

$$D=X_{11}X_{22} - X_{12}X_{21}$$

where $X_{11},\ X_{12},\ X_{21},\ X_{22}$ are the frequencies of the haplotypes $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$ respectively (the subscript number correspond to the two different alleles and $A$ and $B$ correspond to the two different loci)

My questions are

How is $D$ defined for more loci and a greater number of alleles?
How is $D$ defined when the number of alleles differ from locus to locus?


texts: Why is the resting potential of a neuron so close to the equilibrium potential of K⁺?

texts:
I know this has something to do with the K+ leak channel. I just don't understand how.

I know that 3 Na+ are pumped out for every 2 K+ pumped in. This makes the cell interior net negative.

I know that K+ is allowed to leak out slowly via K+ leak channels.

How does this place the resting potential of the cell so much closer to the equilibrium potential of K+ than Na+?


texts: How are lysosome membranes protected from the attack of hydrolases?

texts:
Lysosomes are a bit like the suicidal bags of cells. They help to clean cells, have an acidic pH and contain a large number of hydrolyzing enzymes.

But why don't these hydrolyzing enzymes attack and destroy lysosomes' membranes?


texts: Is there a biological determinant for right- or left-handedness?

texts:
When I was very young, I was sent by parents to examination where I was told both my hands are dominant in the same way. My parents preferred to make my life easier and chose to focus on my right hand development.

However, all my life I find myself naturally using my left hand - with a knife, to lift things, etc. Yesterday something happened that really twisted my perspective - I was playing bowling and I really sucked at it. And then, the moment I started playing with my left hand, I got perfect strikes.

I use my delicate motor abilities a lot with my right hand (drawing for instance), and now I wonder - how can I tell if I used the correct hand all my life?


texts: What culture medium should we use for tap/drinking water bacteria?

texts:
We are a group of high school students from Manila who is performing an investigatory project on a topic that we chose which, at first glance, seemed simple, but turned out a bit complicated. We're trying to test the effectiveness of SODIS of solar water disinfection in killing bacteria.

I previously asked a  question here at Stack Exchange and we consulted our teacher about the answer we received. According to her, at our level, it is best to use culture media. Our testing will be qualitative. We won't be identifying the specific type of bacteria. Rather, we will observe culture media if anything grows in there.

She gave us an assignment to research about what medium to use. Due to inexperience and lack of knowledge on what we find on the internet, we resorted to ask here again.

For bacteria commonly found in tap water, what culture medium do we use? We found mentions of Legionella, Salmonella,  E. coli, and Anabaena sp. in our research.

In this article, we found different types of culture media. TSA captured our attention because it is a "general type." Nonetheless, we're not that sure about what "general" means if it means it can be used for the bacteria I mentioned above. There's also EMB that appears to be used in two of the bacteria we mentioned.

Edit:
It appears that not all culture media is good for student use. According to this article, only LB Agar, Nutrient Agar, and Tryptic Soy Agar can be used by students. Among these three, is there something I can use?


texts: I caught my first queen but I'm having trouble identifying her. Could anyone help me out? She has a reddish brown body and black legs.


texts: Identify this plant from the Netherlands with big white flower

texts: The picture was taken today in the Netherlands. Can you identify this plant species?


texts: Why can CO₂ be transported dissolved in plasma?

texts: Is it because CO2 is more soluble in water or has it got to do with the alkaline pH of plasma ?I here mean only aqueous CO2 transport from body cells to lungs.


texts: How to induce a steady increase in cyctoplasmic [Ca2+] in HEK293T cells? And is there any simple marker/method to confirm it?

texts:
We are trying to find out whether increase or decrease of cytoplasmic calcium concentration affects the interaction of two proteins, using co-IP in HEK293T cells as a readout.

In different forums and papers I have found that to increase cytoplasmic Ca2+ levels in non-exciteable cells, there are three major categories of compounds. Ionophores (A23187, Ionomycin), Agonists of InsP3-PKC signalling (carbachol, ATP) and SERCA inhibitors(Thapsigargin, CPA).

However, different papers and different people on use  different concentrations and durations of treatments. Since a lot of the drugs generate rather transient spikes, I realize that the timing is crucial here. Since, we do not have the resources for the optimisation of [Ca2+]-sensing dye imaging, I am also wondering whether there is a simpler way of roughly assessing [Ca2+], perhaps by by analyzing a marker protein/RNA using Western Blot or qPCR?

Thanks a lot!


texts: What chemical test can be used to tell apart meat and plant-based meat?

texts:
Long story short, I thought about this question and simple Google searches weren't enough. I know there must be some nutrient that can only be found in one of the meats but not the other, but I can't seem to search for it.

For this scenario, just assume that the 2 meats are exactly the same in terms of texture, color, consistency, taste, etc., to the point where only chemical tests can tell one apart from the other.


texts: Why do some cells like myofibrils have multiple nuclei?

texts:
I see that myofibrils (muscle cells) contain not one, but multiple nuclei.

Why is this so?
Do all the nuclei participate in cell division?


texts: Given identical twin males, Michael and Douglas, Douglas and his wife have four children, all of whom are girls.  Michael and his wife have only one child, a boy, and are expecting another. What are the chances it will be another boy? If Michael and his wife have more children, what are the chances they will all be boys? Is there any support/evidence for, or a study about, one twin of an identical pair will have children all of the same gender and the other twin will have children all of the same (or opposite) gender?


texts:
Can a tree whose roots have died due to whatever reason, let's say due to ringing, still draw water up? I personally doubt so but I believe that since all forms of conducting water up a plant requires only passive actions, such as root pressure or capillary action, and that having a dead tree root will not result in leaves dying, hence transpiration can still take place. Is it hence derived that a tree is able to continue taking up water even if their roots died, or, does it depend on the woodiness of the tree?

Edit: I still got no answer


texts: I've been reading lately about primary (which I understand completely) and secondary (which I do not understand that well since I'm not very good at chemistry) structure of proteins. My question is: Can two proteins have equal primary structure but different secondary structure?


texts: Can this image be the result of a Western Blot?

texts:
I am currently researching image manipulation in the life sciences and stumbled upon a Western Blot looking very similar to the image below.

For creating the image I have cut out the blot using the Fuzzy Select Tool of GIMP and then greatly adjusted the local contrast of the blot as well as the background. By using the Fuzzy Select Tool some pixels of the original background are also captured. That is why the blot shown has a brighter background around the edges. I normally would not expect to see bright edges around a blot.

While I know how Western Blots look when they are captured with a digital camera, I do not know about techniques like Chemiluminescent Blotting (I am an undergraduate student in Computer Science). Maybe there is a blotting technique that results in an image like the one i created.

Is it possible to get a Western Blot result like this without inappropriate modification of the image?


texts: Why doesn't life produce diamond, graphene, nanotubes, etc? Could it?

texts:
It seems that life is really good at assembling carbon into extremely complicated molecules (e.g. DNA). Graphene is stronger than any materials currently used by biology. Diamond is harder than any biological materials. Do we know about some inherent difficulty that prevents this? Is there any reason to think that humans will never be able to genetically engineer say, bacteria/fungi/ourselves, to produce diamond, graphene, carbon nanotubes, etc?

I'm looking for specific metabolic hurdles that would make this difficult or impossible. (For example, enzymes/proteins can't do that for this reason, or ATP metabolisms don't have enough energy to form the needed bond.)


texts: How high into the air are spores of molds commonly occurring?

texts:
I understand so far that most of the air surrounding us contains mold spores so that given the right environment and a food source they start to grow. I assume this is true for air close to the earth. But how high mold spores are still common?

To clarify: I don't want to grow mold, I want to know how high into the air on earth mold spores are usually common.


texts: Why do I often see male robins with female robins?

texts:
Even when it is not breeding season for robins I still often see male robins with female robins. But why?

I know that the male robin often chirps to find female robins within his territory. I also know that the male robin puffs his chest to try to impress a female robin.

But I have seen out in the country that even during the fall and late summer the male robins are still with female robins. I don't know whether it is to raise their fledgling chicks or what because only in videos and pictures have I seen robin chicks and robin eggs.


texts:
There is strong evidence that chromosome 2 in humans is a fusion of two chimp chromosomes (i.e. common ancestor of chimps and humans) as explained at wikipedia here

The question is what are the odds of a similar event occuring at random in newborns?

I have read conflicting reports, some say these things happen in about 1 out of a 1000 live births, while others placed the odds at somewhere around 1 in 7 billion.


texts: Understanding entropy and the second law of thermodynamics as involved in metabolic processes

texts:
My AP biology textbook, (the 10th edition of Campbell Biology) states entropy as being the disorder or randomness of the atoms involved in any matter, but Khan Academy says that this example isn't quite right, and is too simplistic of a way of explaining the concept. And the TedED video I watched goes on talking about quanta and stuff ...

The online definition I was able to find of entropy on Wikipedia states the "The entropy of an object is a measure of the amount of energy which is unavailable to do work. Entropy is also a measure of the number of possible arrangements the atoms in a system can have. "

I'm confused how it's both at the same time and how they're related. And how does this even relate back to Biology again???


texts: What exactly are "feeder cells"? A paper I'm reading says they harvested the cells and then plated them onto feeder cells. What is the purpose? Is in order to promote growth?


texts: Can excessive carbonated drink consumption lead to elevated red blood cell levels?

texts:
I've recently had a blood test and the results displayed elevated levels of erythrocytes as well as hemoglobin. (As a result my hematocrit levels were also above average)

At my workplace there is a water cooler which also has an option to dispense carbonated water (this is just regular ol' carbonated tap water) and usually over the course of the day I tend to drink quite a lot of the stuff.

Since erythrocytes/hemoglobin deals with O2 and CO2 transport, I was wondering if my daily consumption of carbonated water is a plausible cause for the additional erythrocytes that are being pumped out?


texts: Why do stars disappear when I look at them?

texts: I've noticed that when I'm out at night stars seem to vanish when I focus on them. I assume the reason is physiological and not astronomic. Why does this happen? I would expect that things would be more clear when I focus on them.


texts: Poly-symbiosis? What's the name for this?

texts:
A mutually beneficial relationship between two species is called symbiosis.

If multiple symbiotic relationships exist with a single common (dominant) species, is this called 'farming'?


texts: What is the difference between transformation and transfection? How do both of these methods work?


texts: Animals as organ donors and organ's life expectancy

texts:
Recent attempts to find reliable organ donors was using genetically-engineered (GE) pigs as heart donors.
The pig's DNA is altered so that its tissues will appear identical to the patient's tissue and will not be attacked by the patient's immune system and rejected. A pig's heart is anatomically close enough to a human heart to fit to the task. All it takes is to make a GE and raise it until it is of the right age.

The issue is as follows: a human's life expectancy is much higher than that of a pig. If the patient is young enough, and the transplant succeeds, then the human will live far longer than the average pig. Will the heart hold-up throughout the lifetime of the human, or will the human need a new heart in say a decade or two?

EDIT: I have realized that actual attempts were so far limited to valves, and not entire hearts or other organs. Looking for an analogy in a human-to-human transplant, or animal-to-animal experiment, what would happen if the organ receiver is much younger than the donor itself? will the transplanted organ live the lifespan of the donor (its "original" lifespan), or will the transplant extend the life of the organ to that of the receiver?


texts: Why does throat 'burn' when you've got a common cold?

texts:
Apart from pain when swallowing, there's also a persistent feeling of throat 'burning' in the same area.

What causes it and why does it feel that way?


texts: Can antimicrobial peptides be called antibiotics?

texts: Antibiotic peptides are present in almost all multicellular eukaryotes. So can they be called antibiotics ? ( which are usually defined only for fungi and bacteria )


texts: Why is PCR possible to amplify DNA template before Sanger Sequencing for unknown DNA sequences?

texts: Most of the informations show that both PCR and cloning can be used before Sanger Sequencing to amplify the DNA template. But how is it possible for us to design the primers if we don't know the DNA sequence yet? So, in my opinion, only cloning is possible to amplify the sequences. Can anyone tell me how PCR can work in this way? Thank you!


texts: I have checked on Wikipedia which says that sprouted mung beans has way less protein than normal one, while on web you will find articles saying sprouted beans are best, which is true, how do I eat unbaked mung bean anyway without any processing they are so hard. Does soaking moon beans overnight really reduce protein content drastically ?


texts: How is excretion of metabolic wastes from a cell related to its size?

texts: As with anything that is taking place within a cell, the metabolic waste too must be proportional to the size of the cell. In particular the surface area to volume ratio. But how is the waste excretion related to the concept of above ratio and how to determine it?


texts: Is there any commercial vector technology platform for boosting recombinant protein production?

texts:
I am a novice in biomedical industry. Our team would like to search new vector technology for boosting recombinant protein production. It's difficult to google a firm that provide those plasmids.
Dose anyone know if one exists?
Thanks!


texts: Why does the iron content differ in different species on seeds?

texts: Iron can be affected by pH of the soil but why does each species actually have a different iron content. What causes it? What genes cause it?


texts: Links between Genetics and Personality Types

texts:
This topic was visited briefly in the thread, Genetic Effects on Personality, but I was surprised not to find more on it. (Is there a taboo I don't know about? What's the ethical stance on this nowadays?)

(An answer in that thread mentions serotonin receptor genetics specifically as having strong links to personality, but provides no explicit references.)

The question: What links have been measured between genotypes and personality outcomes within personality frameworks/models like the Big Five?

Related:
 - An Overview of Personality Models?
 - Genetics and Intraversion/Extraversion


texts: Connect the inner and outer space of cell with a wire, will there be electricity?

texts: There is a potential difference, but ions can not go through wires, right? Though there is a electric field, but there is no electron source, I am thinking the answer is no, or will there be some chemical reaction?


texts: What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation?

texts:
In prokaryotic translation, how critical for efficient translation is the location of the ribosome binding site, relative to the start codon?

Ideally, it is supposed to be -7b away from the start. How about if it is -9 bases away or even more? Will this have an observable effect on translation?


texts: Does crossover happen between chromosomes from grandparents?

texts:
Rephrasing question: does crossover happen after sperm and egg meet each other, but before formed fetus starts to grow?

As I understand sperm and egg of human are haploid cells. That means this cells undergone meiosis and chromosomes crossover before meet each other. If so then crossover happened between a pair of chromosomes which came from parents of the parent of the fetus, not between chromosomes of mother and father of the fetus.

Am I wrong?


texts: What is meant by electron transfer potential?

texts: I was reading a text and came across the term. What does it mean? The sentence said 'The driving force of oxidative phosphorylation is the electron transfer potential of NADH or FADH2 relative to that of O2. '


texts: What kind of worm is this in my food? (Tuna sandwich from canned tuna)

texts: Can I have some assistance identifying this worm which was in a tuna salad sandwich I purchased from a local co-op in Minneapolis MN?


texts: Confusion regarding photosynthesis and respiration in plants

texts:
During 24 hours there is a time in i.e. twilight when plants neither give oxygen nor carbon dioxide why is it so?

This also suggests that neither of the two vital processes i.e. respiration or photosynthesis is being carried out.

Well,
during twilight there is not enough sunlight so photosynthesis may  slow down or even cease but what about respiration?


texts: How does an embryo know where to grow limbs etc

texts:
For example you have a cell or already a bunch of cells. Those cell(s) divide and after several week you have a grown organism, for example a human with limbs, several different organs etc.
However, how do cells know where up, down, left, right etc. is?
I know left and right can be defined clearly in physics, for example by the Wu experiment verifying parity violation really occur.

However how do cells define those directions? What are the mechanisms for them to grow into a certain direction and tell other cells to attain a certain property?


texts: What is the outcome of a human population starting with only 2 individuals?

texts:
Starting with a human population N = 2, is there any way the genetic variability seen today could have come about? I don't know that much about meiosis, but isn't there a very limited number of alleles that could be passed on by the parents? Without a population to start with, wouldn't the lineage eventually turn into clones of each other like the cheetahs are now?
Are there any known mechanisms besides mutation that replenish the variability in alleles?


texts:
A father with gene AC has a child with gene ACC. Where did the nondisjunction occur? (Meiosis I, Meiosis II, none of the above)

I do not know because both Meiosis I and II have the possibility of producing gametes with n+1. Is there something I'm missing here?


texts:
I want to get my head round this once and for all so if you guys could help me would really appreciate it! I understand lesions to the optic nerve. It is the other nerves that I find difficult.

So far this is my understanding, please correct me if I'm wrong. The cranial nerves do not decussate generally with exceptions being CN2, CN4, CN7 and CN12. That means if a lesion affects Cranial Nerve 1, 5, 8, 9 and 11 or the respective nucleus there is either sensation loss or atrophy of the muscle (dependent on what the nerve does) of the ipsilateral side. For example in a lesion affecting CN6, the eye cannot look out in the side of the lesion.

In the case of CN4, I'm not too sure what happens but I imagine if there is damage to the nucleus the opposite side is affected (meaning superior oblique in the contralateral side will not work). If the nerve is affected, it is typically the ipsilateral side. The same I imagine is true for CN12.

In CN7, the forehead is bilaterally innervated so if the upper motor neurone is affected eyebrows can be raised but the lower side of the face is affected ipsilaterally. In a lower motor neurone lesion, there is complete loss of one side of the face ipsilaterally.

Am I correct?


texts: I just wanted to ask that in a given RNA, If there is a start codon and no stop codon, is it still considered mRNA, I mean can it be translated to a protein ?


texts: Will renal blood flow decrease in response to dehydration?

texts:
If dehydrated, does the correction of ECF osmolarity happen slowly enough for ECF (and therefore plasma) volume to be temporarily depleted and therefore reduce renal blood flow?
If dehydration is taken to mean ECF hyperosmolarity, would fluid not just move out of cells to restore normal osmolarity, without affecting ECF volume or renal blood flow?


texts: I’d much appreciate help figuring out what kind of spider this is. I’m in Western Washington, in the northern suburbs of Seattle. Its outside, on the eaves of the house. Particularly wondering if a yellow sac spider.


texts: Which components grow in size but not in number and which grow in number but not in size?

texts:
During growth of an individual animal some components of the body grow in size but not in number (type 1) while some others increase in number but not in size (type 2). Which of the following is correct?
(A) type 1: bones and muscle cells; type 2: hair follicles, red blood cells and epithelial cells.
(B) type 1: bones and red blood cells; type 2: hair follicles, muscle cells and epithelial cells.
(C) type 1: hair follicles and muscle cells; type 2: bones, red blood cells and epithelial cells.
(D) type 1: epithelial cells and bones; type 2: hair follicles, red blood cells and muscle cells.

I know muscle cells only grow in size. I am unsure about hair follicles, which is why I am confused between options A and C. I am also confused about bone growth. Does it ever increase in number? It would be nice if someone could clear that up.


texts: When analyzing whether selection favors an allele that allocates indiscriminately, should the initial frequency of the allele be considered?

texts:
For example, Refardt, Bergmiller & Kummerli (Proceedings Royal Society-B, 2013; http://rspb.royalsocietypublishing.org/content/royprsb/280/1759/20123035.full.pdf)
model bacteria that have been infected and that commit suicide  in order to prevent the spreading infection to the rest of the population.  They do so even though relatedness is low, approaching zero.

Two questions:

In section 3c, they write

  (A)ltruistic host suicide cannot evolve with $r=0$ because populations
  go extinct before invasion of the Abi trait is possible.  Thus, we
  predict marginal relatedness ($r < 0$) to be required for successful
  invasion.

I am assuming this is a typo and they mean $r>0$?
In a situation in which altruism is not directed toward any particular individual(s) but is rather allocated to the whole population, doesn't $r$ depend upon the frequency of the allele that is engaging in the altruism?  If it is a new mutation and there is no other allele in the population to receive the benefit, then r=0.  If the allele has gained fixation, $r=1$ and selection is much more likely to favor the altruism.

What is a way of modeling whether selection will favor fixation of a new mutation that allocates benefits to the population but not any particular individual (e.g., by committing suicide), given that the new mutation is not shared by (m)any other individuals and consequently, $r$ is initially very low?  I would think there is a way of determining the odds that genetic drift would lead the new mutation to develop a substantial enough frequency to increase the odds that the resources would benefit holders of the allele.  But I am unfamiliar.


texts: Can bacteria, viruses, and cancer cells be destroyed by resonance?

texts:
Radiotherapy has been used to treat cancer.

Can the resonances by coordinated electromagnetic waves (and/or other forms of waves), of various frequencies, amplitudes and pulse rates, directed from various directions, be used to destroy harmful viruses, bacteria or cancer cells in a human body, without damaging the other parts of the human body?

(* NOTE * This question was posted here in Physics Stack Exchange too, but is possibly going to be closed in that forum as some claimed it is not so much about Physics.)


texts: What are different firing rates in different regions in the human brain?

texts:
Could it for example be that neurons that are concerned with high-order thought and medium-term planning fire more slowly, or is it expected that all neurons rather fire more or less at the same rate?

Here is an article on the average firing rate: http://aiimpacts.org/rate-of-neuron-firing/

Is the assumption that the measurements tend to be biased by accounting only for visually responsive cells warranted?


texts: What slope do I need to prove a hypothesis?

texts:
I am conducting an experiment for school in which I am measuring people's heart rates as music plays at different tempos. My hypothesis is that as the tempo of the music increases, so will the subject's heart rate. After recording data from many subjects, I will use linear regression to find the overall function to represent my data.

What slope would I need on my function to prove my hypothesis correct?


texts: Can pathogens enter the bloodstream if the epidermis has been scraped off?

texts: Assume that the epidermis has been scraped off by a fall (not just scratched). Also assume that the dermis is completely untouched. Does this allow pathogens to enter the body more easily, or does the dermis still provide adequate protection?


texts: How does transition of osmoregulation occur in fishes when they migrate from sea to rivers and vice-versa

texts:
From my high school level knowledge I can recollect that there are two types of migration in fishes-

From marine to fresh water
(like in Hilsa which grows in the marine water but migrates to the fresh water only for reproduction and then the young return back to the marine water)
From fresh water to marine
(like in eels that live in the fresh water but migrate to the marine water to reproduce)

The only mechanism I had read about osmoregulation in aquatic organisms was via the ionocyte cells in the gills of the fish.

So my question is:

How do they change their osmoregulatory mechanism during this migration?

Just a follow-up:

Are there any other mechanisms by which they osmoregulate


texts:
I am not able to identify this bug/insect.
I stay in Dubai and have been noticing this bug/insect in my apartment since a week now. It is so tiny that it's difficult to notice. The image below has been taken using a DSLR by placing it on a book page and cropped to more than 100% zoom.

I don't know the source, can feel it crawling on my skin and that's the only way to see it. One good thing is it cannot fly.

I went through all the questions about insect identification, but couldn't find any closest match for this. I also compared it to a book lice, but it's nowhere near to it.

I suspect it bites and leaves the skin itching with red spots similar to a mosquito bite.
Does anyone know about this bug if it is harmful, and how to get rid of it?


texts: What are necessary parameters for a tissue scaffold to be biodegradable?`

texts:
I am a mechanical engineer with little biological experience, but I have recently been looking at tissue scaffoldings.

My current understanding is as follows, but may be flawed. I would appreciate any feedback: The purpose of tissue scaffolding is to provide a structure where there is none, and to facilitate healing. The tissue scaffolding is typically porous because it must facilitate the transport of cells during the inflammatory phase of healing, while the scaffold also later provides an interface and structure for the growth of new cells. It can essentially replace extracellular matrix.

I understand that these scaffolds need to be made of inert material so that there are no reactions with the body. But I know that some tissue scaffolds are meant to be biodegradable, so that once stronger extracellular matrix is established, the body can go back to doing its job. But, arent biodegradability and inertness mutually exclusive?

I also understand that a major issue with tissue scaffoldings is the compatability of specific scaffold materials with corresponding tissues, and that there are issues with adherence, etc.

I was hoping to gather some more insight as to what types of challenges tissue scaffolds typically encounter, how they are dealt with, and why? I'm also in scaffolding materials' use to deliver drugs, but that may be an issue to discuss on another day.


texts: Are transgender people born physically different from others?

texts:
Are all children born with only either male or female body parts (other than exceptions), or is there actually a natural third gender with the physical characteristics of both genders, e.g. the child has the genitalia, or reproductive organs, of both sexes?

According to Wikipedia they are only either male or female when born. They only feel different later on in life.


texts: Will eukaryotic RNA fold in the same way in prokaryotes?

texts: As far as I know, there are no specific eukaryotic or prokaryotic factors that aid in RNA folding other than cellular environment (salt and ion concentrations, dissolved molecules, etc). Are there any factors to consider when introducing eukaryotic RNA in prokaryotes? Is it possible to predict the proper shape and folding upon introduction to a prokaryotic cell?


texts: Can spp. be used for taxa other than genus ? For example Noctuidae spp. meaning certain genera in the Noctuidae family.


texts: Is it possible to estimate tree height from stump/breast diameter and species?

texts:
Kindly pardon my poor knowledge, my area of expertise is not biology.

I am currently working on project where I have access to tree's stump and breast diameter and its species. We are trying to estimate tree's impact on microclimate on its surrounding.

To simulate it, we need approximation on tree height. So is there a database or textbook I can refer which provide information on estimating tree height from these features?

I understand that there would be no absolute value here but rather a distribution.


texts: Confusion about the duration of different phases of the cell cycle such as G1, G2 & S

texts:
We all know that normally most of our cells (which are alive and have nuclei - except for cells such as "stem cells", "red blood cells", etc) spend most of their lives in interphase.
But the Interphase itself is also composed of other parts, other stages, including G1, S, and G2.
Is the staying duration of the most human cells in each stage(G1,G2 & S) is comparable to the other stage?
For example, is it true to say that:

"Most human cells, which have the ability to divide(passing the cell cycle), spend most of their lives on stage G1 than S phase or vice versa."?

Usually, which stage is the longest or shortest?
It is quite clear that the G1 is normally longer that G2 and as far as I know the G2 is the shortest stage in interphase, but what about G1 and S?
Is stage S usually longer than G1?
Is there any information?


texts: Why are skin tactile receptors considered to be phasic receptors?

texts:
A phasic receptor by definition is one that quickly adapts to change. In terms of neuron firing, this means that it does not trigger another firing because the receptors are used to the stimulus.

But when I place my fingers on my arm, I continuously feel pressure. Does this mean that skin receptors are only phasic in the sense that it will fire as soon as it is touched and does not prolong this touching sensation?


texts: Are bleach solutions still routinely used in biochemistry laboratories to rid surfaces of bacteria, viruses, certain enzymes, and nucleic acids?

texts:
Decades ago I would stop by biology and biochemistry laboratories to see what was up, and I noticed a ubiquitous presence of a squirt bottle of bleach solution. When I asked what it was for I would get different answers in different laboratories. They ranged from disinfection of surfaces by accidental bacteria or phage contamination to denaturing of certain specific proteins or nucleic acids thought to be threatening to certain types of experiments.
Experimental techniques have developed dramatically over the subsequent decades.
Question: Are bleach solutions still routinely used in biology and biochemistry laboratories to rid experimental surfaces of bacteria, viruses, certain enzymes, and nucleic acids? If so, how can one solution be so reliably useful across all of these cases?


texts: Do all cells of a plant contain chloroplasts?

texts: If the answer is no, then how do plant cells tell whether they need to keep chloroplasts or not? What kind of signals are used, and how are chloroplasts eliminated?


texts:
I am wondering exactly what a-fib is (causes and symptoms).

I would really appreciate having a sample of an EKG with it (because in my limited research, I have found it nearly impossible to find just a sample piece of an EKG that has a-fib on it) with your answer, so I can actually get an idea of what it looks like. With the sample EKG, I would love to have a normal one beside it so I can kind of analyze the differences between the two.

Note: This is not and never was a homework question!


texts:
Do all sea creatures that have scales have to have fins?

Do we know of any sea creatures that have only scales without fins?

I'm especially interested in fish that have scales but no fins.


texts: What is the purpose of the AraC gene in pGLO?

texts:
The AraC gene activates in pGLO from my understanding in the presence of arabinose. Arabinose is present as a metabolite from other metabolic in the e.coli cell. Is it that there's no termination marker, so transcription continues to the GFP gene?

In addition, does AraC contain parts that are encoded 5'->3' and 5'->3'?


texts: Wondering if there are any open databases out there that specify the branching and flowering patterns of plant species, similar to algorithmic botany book.


texts: What are haplotype blocks and what is the effect of hybridization on these?

texts:
In this PDF, there is a quick definition of haplotype blocks.

  A haplotype block is a set of closely linked alleles/markers on a
  chromosome that, over evolutionary time, tend to be inherited
  together.

Also look at this definition:

  We defined a haplotype block as a region over which a very small
  proportion (<5%) of comparisons among informative SNP pairs show
  strong evidence of historical recombination. [We allow for 5% because
  many forces other than recombination (both biological and artifactual)
  can disrupt haplotype patterns, such as recurrent mutation, gene
  conversion, or errors of genome assembly or genotyping.]

Although in the abstract they say:

  haplotype blocks: sizable regions over which there is little evidence
  for historical recombination and within which only a few common
  haplotypes are observed.

But the first definition confuses me because it really looks like the definition of linkage disequilibrium:

  linkage disequilibrium is the non-random association of alleles at
  different loci in a given population.

Which means that they are inherited together (non-randomly inherited).
The other definitions don't seem to agree in the same paper...

Just as a reminder a haplotype is: "The set of alleles found on a single sequence is referred to as a haplotype."
(Hahn, M. W. 2018. Molecular Population Genetics. Sinauer Associates, Incorporated, Sunderland, Massachusetts.)

So:

What are haplotypes blocks precisely and compared to LD? How to estimate haplotypes blocks?
Why is this an important concept (what is it informing us, why would want to study that specifically)?
What influences haplotypes blocks and how is it useful to get some information when doing genomic analysis (can we account for that)?

Here are 2 relevant resources on the subject:

Daly, M. J., J. D. Rioux, S. F. Schaffner, T. J. Hudson, and E. S.
Lander. 2001. High-resolution haplotype structure in the human
genome. Nature Genetics 29:229–232.
Patil, N., A. J. Berno, D. A.
Hinds, W. A. Barrett, J. M. Doshi, C. R. Hacker, C. R. Kautzer, D. H.
Lee, C. Marjoribanks, D. P. McDonough, B. T. N. Nguyen, M. C. Norris,
J. B. Sheehan, N. Shen, D. Stern, R. P. Stokowski, D. J. Thomas, M.
O. Trulson, K. R. Vyas, K. A. Frazer, S. P. A. Fodor, and D. R. Cox.   2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science
294:1719–1723.


texts: Why are there seven entries for Pimpinella dioica in the Catalogue of Life?

texts:
And six for Haliclona digitata, and five for Ichneumon varius. A couple of the duplicate entries are synonyms for other species, which is understandable, but most are the "accepted name". Shouldn't there just be one Pimpinella dioica? By my count there are 3068 species with two or more "accepted name" entries in the 2014 database. Where do these duplicate entries originate? Do they serve a purpose or are they errors?

Probably a question for catalogueoflife.org forums, but they don't seem to have any discussion area, so seeing if anyone here can answer.


texts:
Stanford Medicine's OCD page says that

  Many investigators have contributed to the hypothesis that OCD involves dysfunction in a neuronal loop running from the orbital frontal cortex to the cingulate gyrus, striatum (cuadate nucleus and putamen), globus pallidus, thalamus and back to the frontal cortex.

What is a neuronal loop? I have looked it up on DuckDuckGo with no usable results.


texts: Find the concentration of free receptors in a solution of 90% free ligand and 10% receptor-ligand complex, knowing only the value of kD

texts:
I could use some guidance on how to utilise the equation for the disassociation constant kD to find the concentration of free receptors [R] in a solution containing 90% free ligand [L], and 10% bound [RL] complex.

The Kd of the receptor-ligand interaction = 10^-8 mol l-1

Where Kd =  ([R][L])/([RL])

I assume as a percentage I could state, [L] = 0.9 and [RL] = 0.1, but am not sure if I'm taking the right approach.

Any clarification on this would be appreciated.


texts: How are the boundaries of a gene determined?

texts: What statistical processes and methods are used by geneticists/molecular biologists to know where one gene starts and one ends?


texts: what's the difference between traditional genetic engineering and and CRISPR?

texts:
While at school, I learnt about restriction enzymes and how you could insert foreign DNA into an organism.

When I first heard about CRISPR I thought it was very similar except much more precise/targeted.

It seems however that CRISPR only allows editing (substituting nucleotides)

What are the differences, advantages, etc?


texts:
From Wikipedia:

  Studies have observed dreaming in mammals such as monkeys, dogs, cats,
  rats, elephants and shrews. There have also been signs of dreaming in
  birds and reptiles.

Have there been such signs in any invertebrate species?


texts: Can we graft a tree with cells from the seed directly?

texts: Are there any limitation to the grafting so we could only graft a branch to another tree? Could we just use cell from the seed, or just a sprout, to graft onto the tree of the same species?


texts: Why don't people seem to die from salmonella in bites?

texts:
As far as I know, reptiles have salmonella in their mouths as part of their digestive process. Every time I hear about someone being bitten by an python or alligator or monitor either at a zoo or in the news or from a private owner, it seems like whoever is bit recovers with ease.

How come something as virulent as salmonella that can evade an immune response doesn't cause whoever gets bitten to nearly immediately become septic? Is it because salmonella only attacks epithelial tissue and there isn't much of that deep in an arm or leg?


texts: Are stem cell lines cryogenically preserved or commercially available like HeLa cells are?

texts:
There are HeLa cells, which were taken from sick cancer patient and now is growing worldwide in different laboratories for experiments. HeLa cells can be kept because they are immortal and so they are an instance of immortal cell line.

What about stem cells? They are also immortal. Such cells can be taken from normal healthy person and also kept forever. Do scientists do this? Why don't we hear about it then? For example, they are distinguished in Wikipedia article, referred above.

Are there some special properties of stem cell lines, making them different? For example, being low differentiated they may be useless for experiments.


texts: What is the biological principle of this "holotropic breathwork" technique?

texts:
Holotropic breathwork is a non-drug technique developed by Stanislav Grof used in psychotherapy. The therapy as a whole is usually called holotropic breathwork (at least by Grof himself) and will most probably rely on a range of effects. However, I am mainly concerned about the core technique, which leads to hallucination and a changed state of conciousness (i.e. being half concious and having a distorted perception of time).

As quick googling does not reveal any specific information of the technique, I will describe a demonstration of an amateur enactment of something which was stated to be based on the same principle as holotropic breathwork. (I consider the respective people very irresponsible to have done this without trained assistance, it is probably very dangerous, do NOT try at home!)

A person squats curled near a wall and breaths as quickly and as heavily as possible for a few minutes. After that they quickly stand up in front of the wall and another person pushes them quickly in the chest and presses them strongly against the wall behind them. The pushed person collapses completely, their muscles relaxed, they even don't have the time to close eyes and you can see their eyeballs rolling around freely. They are in this state for about 15 seconds and then wake up reporting vivid hallucinations. Some of the people said that their perception e.g. of sources of light and surfaces were altered for another several hours.

So, what is the biological basis of this collapse and hallucinations? (It would be perhaps good to also comment on the possible risks.)


texts: Just that. It seemed weird for me not to find anything on Google. But I still think that they might be edible.


texts:
I was reading from Odum about Liebig's law of minimum.

It said that

  the law is appicable in steady state condition i.e. when the inflow of energy and material balances out the outflow.

I got two questions:

1.Here what is actually in steady state? Photosynthesis? or Plant community? or Biotic community?

2. Inflow of energy and material balances out the outflow.

What is the net material/energy that is flowing in an out of a system? Could it be amount of light absorbed and amount of glucose and O2 produced respectively? He used the word balances which means they are not equal actually but proportionate I suppose.


texts:
I am neither a student nor really advanced in biology, I am just writing a tabletop role-playing game scenario that I want as realistic as possible. In the story, the players find an old laboratory where genetic mutations were studied, but as the electricity is off since 40 years, most of the embryos are "rotten". I still need to have some embryos still "fresh" so someone could get DNA from it and continue the experiment.
Problem is, I thought about formol (the experiment is supposed to have taken place in the 1980's, so the health problem is not one right now), but I've read that formol alters and destroys the DNA. I've seen older ways with alcohol, but the process doesn't seem as efficient.
What liquid (or technic) could have been used in the 80's to preserve embryos and their DNA so we could still exploit it 40 years later, and with not electricity?


texts: I am learning normalizations, I wonder when log2 and quantile normalization is used in each situation, may I ask if there is any material that compare these two types especially in microarray expression matrix for differentially expressed gene analysis? Thank you!


texts: Measuring genetic distance: $F_{ST}$ vs. Nei's distance

texts:
As far as I'm aware, Nei's genetic distance is quite old compared to $F_{ST}$. However, I have recently read more papers that utilized Nei's genetic distance alongside with $F_{ST}$. As I'm not very familiar with Nei, what are some advantages it has over $F_{ST}$?

Does Nei's genetic distance suffer from ascertainment bias?