texts: Human ancestor reproduction after chromosome fusion

texts: I read somewhere that human chromosome 2 is the result of 2 primate chromosomes fusing together somewhere along our evolutionary journey. This is why we have 23 chromosomes while other primates have 24. My question is this: for the first ancestor whose chromosomes fused to have 23 chromosomes instead of 24, how did he reproduce? Don't offspring receive half of their genetic makeup from each parent, so if one parent has 23 chromosomes and the other has 24, how would that work? I know that there have been animals with different chromosome counts being bred together, but the offspring typically have issues and are sterile, so even if the difference in chromosome count was not a problem, wouldn't the offspring between an organism with 23 chromosomes and one with 24 be infertile, thus leading to the end of animals with 23 chromosomes? Would there have to be two organisms of different genders experiencing the same chromosome fusion at the same time in order to avoid this problem? I'm just a bit confused as to how this would work exactly.


texts: Does DNA contain information beyond protein synthesis?

texts:
It's well known that genetic information is stored in DNA.  As far as I know, DNA only has information at the protein level.  What about higher levels, such as organelles, cells, tissue, organs? Is there any known carrier of information at that level? If not, what guides those levels of structure?

Hypothesis: Above the protein level, there is no real genotype/phenotype.  Instead, it's all done through cell division.  So, there is no split between information and embodiment.  Instead, it's through a prototype-duplication model: cells grow and split, creating more cells.  As for differentation into different types of cells, and organization into tissue and organs: the information and control systems for that are currently unknown.


texts: Ultra-violet radiation and Bacteria in Petri Dishes

texts: My partner and I are planning on doing a science fair project on how long bacteria can be exposed to UV radiation. We were wondering what the noticable effects would be if we held a UV lamp to bacterial colonies in petri dishes. Would the bacterial colonies shrink?


texts: Two different Leucochloridium infected snails - different species?

texts:
In the last three days, I have found two snails infected by some species of Leucochloridium. I found them in my garden in the south-west of Sweden. Now I'm wondering if they are the same species or not.

One has broodsacs with green stripes and looks like a typical Leucochloridium paradoxum, and the other has brown stripes, which makes me think it's a Leucochloridium variae, but I've seen it mentioned that their appearance can vary.

Update: I have learned that there is only one (documented) species of Leucochloridium in Sweden, so maybe I should close this question, but I would still like to know if there is a way to tell the difference just by appearance.

And here they are in animated form in case that is helpful:


texts: Relationship between bacteria size and temperature?

texts:
I'm, doing a research in a TOC (total organic carbon) degradation in a BAC (biologically active carbon) filter for the grey-water treatment. Recently, I started to wonder if there is a relation between bacteria size and temperature. If anyone know any research paper or did a research by himself/herself where such relation has been checked, it would be of a great help.

Thanks in advance.


texts: How much DNA (or genes) do homo-sapiens and ursus arctos (brown bear) share? There are articles online that indicate that humans share xxx% of DNA with Chimpanzees, bananas, and other assorted organisms, but I can not find how much humans share with brown bears.


texts: In an experiment qPCR was used to determine viral load. Alongside this conventional PCR was also performed and ran on an agarose gel. However I do not understand why both methods would have been used, any insight would be greatly appreciated?


texts:
Ive been taught that its based on genic balancing.
But I recently saw this question that has caused me some doubt.

I thought it would be the 1st option but unfortunately they said it to be the 3rd.
But in the answer key, they mention the same line of that of the 1st option.
Ive only been taught genic balance in a general sense .I solved by finding the ratio of no. of X chrom. to no. of autosomes. It would help if someone could give me some clarity.


texts: What causes muscle spasms with muscles that are not in the heart  ? Could it be some sort of stimulus overload that causes a massive contraction?


texts: Did cyanobacteria commit evolutionary suicide by producing oxygen?

texts:
I heard this story from one of my friends:

  Cyanobacteria can convert carbon dioxide into oxygen through
  photosynthesis, so the concentration of oxygen in the atmosphere kept
  going up over a long period after their appearance. Finally, those
  oxygen poisoned cyanobacteria through some mechanism, which
  effectively killed many of them. As a side effect, the oxygen produced
  lead to the evolution of fishes and other fantastic creatures,
  including human beings.

I wonder whether it is true. After some searching, I found that cyanobacteria can perform photosynthesis. However, I can't tell whether oxygen is poisonous to them.


texts: How fast does the rotor in ATP synthase spin?

texts: I'm sure the exact frequency varies, but does anyone know roughly how many revolutions per minute / second the rotating center part makes?


texts:
How deadly is a stab in the back?

Video games, movies, and other fiction would have us believe that a backstab against a foe with a modestly-sized blade leads to immediate and certain death, having a 100% success rate and causing death virtually instantaneously.  How close is this to reality?  How does the lethality of a puncture wound to the back compare to such wounds delivered to other areas of the body?  What is the primary target in such an attack in terms of internal organs, and what variables effect its projected success?


texts: Probabilities of mutations in telomeres?

texts:
Frankly I am a programmer, I've been looking at sites like NCBI and others, but couldn't find what I was looking for so if someone can help:

Can you give me the probabilities of

mutations in Saccharomyces Cerevisiae's telomeres.
Probability of having an insertion
Probability of having a deletion.
Probability of having a substitution.

The reason I need this is that I want to generate true-telomeric data based on, the telomere structure consensus.


texts: If not, is it impossible for DNA to have enzymatic activity?


texts: HLA typing between siblings to identify a genetic disorder

texts: If a patient  suffering from a complex array of signs and symptoms for a disease and is having an 8/8 loci match with his sister who suffers no such symptoms can you conclude that the disease is an X-linked recessive disorder? Can u rule out autosomal dominant disorders and autosomal recessive disorders from the diagnosis?


texts:
Question: The red and white feather pattern of a  bird is determined by a gene that has two alleles, band R and W,which show codominance.  Some birds have completely red feathers (RR),some parrots have completely white feathers (WW), and others have red and white feathers (RW).In a population of 630 birds that is at Hardy-Weinberg equilibrium, 202 parrots have completely red feathers. How many birds in this population would be expected to have either red or white feathers?

Is this question asking for what is the carrier proportion-2pq? The answer is supposed to be 321 but I keep getting 309. I did 202/630= p^2=0.32= 0.566. Then q=1-0.566 =0.434. Then I did 2(0.434)(0.5662)= 0.49. Then I multiplied 0.49 x 630 to get 309. If any one can point out what I did wrong I would really appreciate it!!


texts: How does the body respond to blood donation; are there any possible risks?

texts:
Can blood donation cause any harm to the donor? I have been told so, but cannot find any references supporting this claim. I have also learned that our body will replace the lost fluids within 24 hours and the RBCs within weeks. Can blood donation still cause health issues for our body?

This is not a personal medication question, and I mainly want to know how the body responds to blood loss and what mechanisms that monitor the altered levels of blood volume? To me, it would also be unethical by medical doctors to withhold the possible risks of blood donation to prospective donors, but it might also be seen as unethical to discourage a person willing to donate blood from doing so, so there might be a conflict of interest here.


texts:
If a hermaphrodite animal (like slug, snail, etc) finds a partner they can mate immediately.

If another animal with "normal" reproduction (lets say a mouse) finds a partner they can only mate if they are opposite genders.

So it seems logical that the hermaphrodite way of reproduction is more successful than the "normal" way.

But it is not, as far as I know all higher developed species are using, the standard way of reproduction (male and female).

Why? What are the disadvantages of hermaphroditism?


texts: Can elementary alternative splicing events be combined in more complex events?

texts:
I'm a computer scientist who is trying to understand alternative splicing. As the title says, I'm here to ask you if, from a biological point of view, elementary/basic alternative splicing events (such as exon skipping, alternative 3'/5' splice site...) can be combined into more complex alternative splicing events. If it is possible, how common is it?

Just to clarify my question, let A->B->C be a transcript made up by three exons (A, B and C). Biologically, is it possible to obtain a new transcript A'->C in which exon B has been skipped (exon skipping event) and exon A has been "cut" at a different splice site producing A' (for instance, alternative 5' splice site event)? Can I obtain also A->C' (exon skipping of B and alternative 3' splice site of C)? Another example could be the following one. Le A->B->-C->D be a transcript. Can I obtain a transcript A'->B'->D?

From a combinatorial point of view, I can combine all the events and all the exons in many different ways but from a biological point of view, are all the possible combinations plausible?

If so, can you please point me to some articles describing how alternative splicing events can be combined?

Thank you and sorry if this has been asked and answered already (but I didn't find anything regarding it).


texts: Is there a special reason why ferns are so early in evolution?

texts: Reading about plants in history it seems that ferns where already in the Devonian period (400 million years ago) growing. Probably the climate in that time was very different from now, but what made them so good surviving in that time?


texts:
I am trying to find orfs with Glimmer. At the end, Glimmer gives me a .predict file with the orfs and a corresponding raw score.

When I look at the documentation, it says about the score, "This is 100 times the per-base log-odds ratio of the in-frame coding ICM score to the independent (i.e., non-coding) model score. It gives a rough quantification to how well an orf scores that can be compared between any two orfs." You can look here for the documentation-

https://ccb.jhu.edu/software/glimmer/glim302notes.pdf

But what does the score really mean in an absolute manner? How do I realize for an orf, if the score is significant or not?


texts: Which bacteria takes the longest to double?

texts:
Currently I am writing a lab report on the enumeration of bacteria.
E.coli takes about 30 mins to double. That is going from 1 bacteria to 2 bacteria.

I want to know which bacteria takes the longest to double? Do some bacteria take a day to double?

Thank you for the help.


texts: The hyphae are the branching filaments that make up the mycelium of a fungus. Hyphal compartments are part of the hyphae. What are they exactly?


texts: Why I cannot find dendritic cells in blood smear?

texts:
According to many sources including Wikipedia, there are haematopoietic stem cell derived dendritic cells in the blood.

figure 1 - haematopoietic cell lines - ref

Despite of this, when I examine a blood smear, I cannot find dendritic cells and I did not find any blood smear example on the internet, which depicts dendritic cells.

figure 2 - blood smear cell lines - ref

Why is that?


texts: Why are fingerprints different even in identical twins?

texts: Why are fingerprints different from person to person? It can't be genetics. Even identical twins has different sets of fingerprints. What is the deciding factor that form and shape our fingerprints?


texts: Why do the two hemispheres of the brain control the opposite sides of the body?

texts:
Why does the left hemisphere control the right and the right hemisphere control the left? I googled it but didn't find a good answer regarding this. Could someone explain?
Does this adaptation help in the speed of transmission of nerve impulses?


texts: Why do some people become more aggressive when tired?

texts:
Why do some people become more aggressive when they are tired? I've been thinking about this question for a few days and my 'hypothesis' is that the neural activity in the prefrontal cortex lessens as the brain prioritises the other more primitive parts of the brain. Is it also so that the amygdala becomes more active when tired for some reason?

I've tried to search for answers on Google but can't find any satisfying ones. Optimally, I'd like to see brain scans and have them explained, but maybe that's asking for too much.


texts: What is the most specific behavior we're able to control or induce with optogenetics?

texts:
Optogenetics is very widely used in neuroscience to study how behavior is controlled by populations of neurons.  For example, in a highly cited 2011 Nature paper, Lin et al. show that they can induce aggressive behavior in mice by stimulating neurons in hypothalamus. However, it would seem that there are many different reasons for why a mouse can turn violent. It might be in pain, it might be defending its offspring, it might be competing with other mice for something, or it might just be sustaining brain damage and is unable to control its behavior (and we know that optogenetics in the absence of stimulation induces aberrant activity in mouse brain and sometimes results in  seizures: Aberrant Cortical Activity in Multiple GCaMP6-Expressing Transgenic Mouse Lines)...
So my question is: what are the most specific and precise behaviors we can control and induce using optogenetics today?


texts: Is there a molecular basis to intelligence?

texts:
Is there any explanation, gene(s) or whatever detected, that are co-related or explicitly related via mechanical bio-molecular (or at any other level) models that explain the higher or lower intelligence found in different individuals of Homo sapiens?
If so, which and how do they work?


texts: Why sudden stresses cause stuttering and/or other impairs in children?

texts: The question is simple: Why sudden stresses cause stuttering and/or other temporary or permanent impairs in children (and even adults)?


texts: What is the best way from remove background signal from a band when doing Western blot image analysis?

texts:
I am doing image analysis of a Western Blot in Image J. I have calculated the total intensity of my protein bands of interest through outlining each band using the rectangle tool in ImageJ, and calculating the area and mean intensity. I have multiplied the area with the mean intensity to obtain the total intensity. However, I want to remove the background signal from each protein band of interest.
The background adjusted protein signal would be calculated as: (protein band mean intensity - background band mean intensity) * (area of protein band). On my blot, I have two isoforms of my protein of interest that were detected by the antibody, and I want to subtract the background from all bands for both proteins.
The way I am calculating the background, is for each lane, making a rectangular selection near the top of the lane where there is no labelling against any protein. The length of the rectangular section is equal to the length of the lane. However I am not sure how wide the rectangle for the background should be. From what I have seen online, there is no fixed method for calculating the background signal.
Are there any ways to determine how wide you want the band for your background to be? E.g. should the width of the band for the background be equal to the width of the protein band of interest, or can it be wider than that?
Additionally, how can you know if you have made the rectangular band for the background too wide?
Any insights are appreciated.


texts:
I have been seeing this animal for the past year and I am wondering: "Which species is this?" It has hair and is orange. It has the black spot at the end, but this seems to be the last part because it walks in the other way (in the direction of the part without the black spot). At the other end is smaller reddish spot. It seems that it has 6 legs, but I am not sure because it turns on the right direction quickly. These legs seems to be concentrated on the first side. Its average speed is around 1 mm/s. Maximum speed is 2 mm/s. It is pretty small, around 4 mm, so I can't see more details. Below is the photo with the millimeter paper.

I placed it in a small paper envelope (2×5cm) for one day and it is still alive. Additional pictures:
Top:

Bottom:

Data about the location:

Northern Italy, 100 km from the coast
altitude: 700 m
room temperature: 21 °C


texts:
What is the Pianka's Index?

How does it work?
How can one calculate this index?
How often is it used?
In what context do people usually use it?
Can one infer any statistical significance with this index?


texts:
Assuming the sequence shown is read left to right, what is the sequence of the protein produced?

sequence: 5’-ATGTACTTCCATCTGGAATAG-3’

MY ATTEMPT: I know RNA is synthesized 5 to 3.  This is throwing me off because if we read the above sequence from left to right then we are going to synthesize 3 to 5.  If I ignore this for now, I get an mRNA of 3'-UACAUGAAGGUAGACCUUAUC-5'  from this i could easily get the protein looking at a mRNA to protein chart.  Is this correct?


texts: What is "beto carotene" and how can it turn lakes pink?

texts:
The BBC News article Pink lake in Australia attracts and delights tourists describes an artificial salt lake in Westgate Park, Melbourne, Australia that tuns pink around February and then in "late Autumn, until cooler temperatures restore it back to blue."

I am not sure about the autumn part as it's in the southern hemisphere, but my question is about the color change.

Could they mean beta carotene rather than beto carotene?
And if so, does the pigment stay inside the algae or is it released into the water to produce this color change?
And why pink, rather than the orange color we associate with carrots?

  In those conditions, the lake's algae produces a red pigment called beto carotene

  The lake's pink colour typically lasts through to late Autumn, until cooler temperatures restore it back to blue.


texts: I'm mostly interested in the maroon and white ones in the center, or the purple and white ones in the front left corner.  They were in bloom in a garden in July at the Buffalo Harbor.  Any help would be appreciated!!


texts:
Connected to What is happening when we get a tan? - Why do some people burn while other people tan?

Very pale people tend to just burn while other people tan very nicely, what causes this difference?

I assume it has something to do with pigmentation - so what is the pigmentation in our skin actually doing in order to protect us from getting a sunburn?


texts: What does the term 'modified residue position' in phosphorylation mean?

texts:
Does it mean the position of the amino acid in the protein sequence, or something else?

For example, I came across the phrase "S 368 phosphoryation" where S is the modified residue and 368 is the modified residue position. What does it all mean?


texts: What happens to the nitrogen when an oxygen machine delivers only oxygen?

texts: My father recently began using an oxygen machine. He would like to know where the nitrogen goes when the machine takes in air and puts out only oxygen.


texts: How can I save bacillus strains on filter paper without an -80 degree freezer?

texts: I want to save my bacillus strains but I don't have access to a -80 degree freezer.  What are possible alternatives?


texts:
In the sentence: "Bacteriophage (viral) polymerases are typically monomeric polypeptides".

I know that polypeptides are chains of amino acids monomers. But what is a "monomeric polypeptide" and what other kinds of polypeptides are there?


texts: Is human "sperm warfare" a concept supported by biology?

texts:
I've recently read the "Sperm wars" book by Robert Baker. It deals with human sexuality and infidelity. The main premise of the book is that  human male has different kinds of sperm:

Regular sperm for fertilization
Toxic sperm that kill competitor sperm (similar in concept to white blood cells)
Slow, inactive sperm to block channels in female cervical filter

According to the author, when a female engages in infidelity or group sex, the sperm actually "goes to war" killing competition and preventing passage through cervical filter.

Are there are indeed different kinds of functional sperm in humans, and are their functions involved in sperm competition / warfare? In other words, does human sperm not only fertilize the egg, but also to block passage of competitor sperm and even kill it?


texts:
I currently have a waterweed (elodea) preparation for my optical microscope but i can only see some of the structures (membrane, wall, chloroplasts and the nucleus).

Now I want to see more (Like the Vacuole, Peroxisome, Mitochondria, Amyloplast, Ribosome, Golgi Apparatus, and endoplasmatic reticulum if possible with an optical microscope)

I know there are contrast media like the lugol's iodine solution (iodine-potassium iodide solution) but what will it show? And are there more?

Thanks in advance


texts:
Ancestral facial hair.
Our closest ancestors, the chimpanzee and bonobo, both grow facial hair around the mouth area. What is noteworthy is that this is the case in both males and females of the species.
Female chimpanzee with facial hair:

Dichotomy of facial hair in humans.
Our own species has a notable dichotomy in facial hair between males and females. I'm interested in what broadly speaking are the theories on facial hair. Could it be as simple as sexual selection over tens, or hundreds of millennia?
A previous answer eludes to a sexual selection direction, but my question is primarily why do human females not grow nearly as much facial hair as their male counterparts? Is this just a typical sexual dichotomy? I suppose here I am interested at a molecular level - is beard growth absent, or suppressed in women?
Speaking physiologically androgen is a hormone that drives hair growth and this hormone is more prevalent in males. Although females do have vellus hair coverage on their face, the thicker androgenic hair isn't typically present. A cursory search didn't reveal to me if this is due to less follicles in the first place so androgen would have little effect, or less hormone release.

To answer the question "Why do men grow facial hair" I think three smaller questions are raised:

What is the point of facial hair? (If there is any beyond sexual selection...)
What selected thick androgenic facial hair out of human females?
At a molecular level, have females lost the "facial hair gene", or gained a "facial hair suppressor gene"?


texts: How does the age of a parent affect the chances of occurrence of certain genetically transmitted diseases?

texts: Do genetically transmitted age-related diseases (like hypertension, arthritis etc.)have the probability of occurring at an earlier(younger) age in the offspring if they are born at a later age to their parent(s)?


texts: difference in genetic instuctions between male and female

texts:
I'm a computer science graduate so please bear with me the following computer program :
mov  ecx, -1
INC  ecx
consist of 2 instructions (mov,inc) each working on specific data , can genetics instuctions be expressed in the same way ? if so what is the difference between male and female(humans) when it comes to the number of instructions and the difference if any (eg , n-instuctions being exclusive to female ... etc) ?

Edit#1
:what I mean by instructions is something like a computer program and a programming language commands.


texts: Ephedrine or pseudoephedrine indirectly central alpha2 mimetic?

texts:
I started to think this problem by first thinking if the alpha2 mimetism is possible in either case.
It seems to be indirectly in either one.
Ephedrine seems to have more prominent effect in CNS.
So I propose that Ephedrine has indirect central alpha2 mimetic effect.

Is ephedrine central alpha2 mimetic?
I think one evidence about that would be if there is a alpha2 receptor which is activated by ephedrine somehow indirectly.


texts: Does anyone know a good pancreatic-cancer metastasis cell line?

texts:
Researching about pancreatic cancer. We have mostly "main-tumor" cell lines in our lab, and I´m currently looking for cell lines originating from metastases (liver, lung, etc.).
Does anyone know a well-established pancreatic-cancer-metastasis-cell line?


texts: Do hormone drugs affect whether a person feels sexual attraction to males or females?

texts:
I know that ingesting testosterone and other hormonal drugs may stimulate libido and increase sexual desire.

But I wonder, if a man ingests female hormones such as estrogen, will he experience sexual desire towards other men or not?

Similarly, the other way around, whether a female ingesting male sexual hormones will experience desire towards other women?

The question is motivated by the interest to know whether transgender people, particularly, the MtF transsexuals engaged in prostitution experience genuine attraction to males.


texts: If a healthy human is at a certain muscle state and then experiences muscular atrophy solely due to disuse/lack of exercise, is it easier to gain that muscle back than if the human had never reached that certain muscle state. If so, is there a name for this effect. The reason I'm wondering is because it seems like muscle mass was definitely periodic in ancient times when food would become scarce during the winter, and that an increased ability to put back on muscle might have developed evolutionary-wise. I thought that this would fit best in biology, let me know if this isn't the case.


texts: Do creatures exist which can stop their hearing at will?

texts:
Many people would love to have the ability to shut out noise while sleeping, in the same way that we have eyelids to shut out light. If this capability exists in nature, it could offer clues to researchers in the field of sound proofing.

Are there creatures which are capable of 'switching on or off' their hearing capabilities at will? At least partially?

I don't see why this cannot be evolutionarily possible. If perception of sound was necessary to know a predator was approaching while the creature slept, then according to evolution, creatures would not have had the ability to shut out vision either.


texts: What is the rationale behind tapering of immunosuppressant dose a while after transplant?

texts:
MMF, Cyclosporine, Prednisolone, Tacrolimus the dose of whatever immunosuppressant used is reduced in around 6 months - 1 year after the transplant.

What is the rationale behind this?

Wouldn't any allograft, howsoever old, still remain foreign? Does the body learn to consider the graft self? Or is the response still there but the destruction is reduced?

Why should a new graft elicit more response than an old one?


texts: histamine inter-cellular and cytoplasmic binding site

texts: I noticed that HRH (histamine receptor) has an inter-cellular and cytoplasmic binding site of anti-histamines which are equal in binding energy. Does anyone know what is the function of the well formed cytoplasmic ligand binding site?


texts: Why is there an apparent reduction of reptile species near the Mississippi River?

texts:
The USGS Gap Analysis Program published a map of reptile species richness in the U.S. There is a conspicuous reduction in reptile richness along the Mississippi River corridor. Why might this be?

From USGS:

  This map of reptile species richness in the U.S. is derived from the
  USGS Gap Analysis Program’s (GAP) national reptile ranges dataset. The
  map represents the total number of reptile species summarized by
  12-digit hydrological units (HUCs). Light blue HUCs have the lowest
  number of species while red HUCs have the highest.


texts: How many traits can a multivariate breeders equation handle?

texts:
The multivariate breeders equation (MBE) by Lande predicts the change in a trait $\Delta \bar z$ (response) as

$\Delta \bar z = G \beta$

where $G$ is a genetic variance-covariance matrix and $\beta$ is a vector of the selection coefficients. What are the limitations on the number of traits the MBE can tolerate? Is there a theoretical limit on the number of traits $G$ and $\beta$ could contain? Or does the calculation lose power with increasing complexity?

Theoretically as an example, could I take the expression of 10000 genes, compare them to fitness to to make a 10000 row $\beta$ vector, and generate a 10000 * 10000 G-matrix from estimates of male and female gene expression in some lines, and then put them through the MBE?


texts: By bullying, I mean individuals harassing others with name-calling or violence but not for the purpose of gaining resources such as with extortion or theft. The only explanation I've thought of is that bullying offers practice for types of extortion that do result in increased resources.


texts: How are vaccines and inoculations different?

texts: If so are vaccinations more safe? If so how? And how is the vaccine a magical invention?


texts:
http://blast.ncbi.nlm.nih.gov/Blast.cgi

In this website, when I want to apply the psi-blast algorithm on a sequence, under the section of algorithm parameters , what does PSI-BLAST threshold mean? The question mark says it means that:

  Set the statistical significance threshold to include a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.

Another parameter is there called pseudocount. Did not understand that too. Could not understand what this means, someone please explain in simple language.


texts:
I am aware of the post here 'Optogenetics - How do microbial opsins work?'
however it is a bit too technical for me. I am struggling to understand how the neurons can be genetically engineered to produce these light-sensitive molecules in optogenetics, and how genetically engineering the neurones is even a usable method considering it seems you would have to genetically engineer the neurons one by one. So I suppose my question is: in the trials run of optogenetics so far (with mice), how where the neurons made to respond to the light stimulus?

Also, I was wondering whether the principle behind optogenetics- controlling calls with light- could be used for other treatments e.g. to kill cancer cells?

My biology knowledge is limited to A-Level (final year of high school), however I really want to understand this topic thoroughly, so detailed but not too technical answers would be much appreciated! Thank you!

EDIT: I just wanted to add two more quick questions...

Are the light-sensitive molecules (which I now have read are channelrhodopsins) present all along the axolemma, or just the membrane of the soma of the neuron? (I hope I used those terms correctly!)
Wikipedia says that these channelrhodopsins are non-specific (with some exceptions: The L132C mutation (CatCh) increases the permeability for calcium and generates very large currents.[17] Mutating E90 to the positively charged amino acid arginine turns channelrhodopsin from an unspecific cation channel into an anion channel. This chloride-conducting channelrhodopsin (ChloC) inhibits neuronal spiking when illuminated with blue light.[18]). How then can these channels work, if any cation can diffuse any way through the channel?


texts: I am new to BioInformatics, I want to know what is gene expression level and how it is determined.. Anyone who can answer this silly question.


texts:
How exactly do our eyes see an inverted image of what we are looking at?
Does it have something to do with the shape of our lens (i.e. convex)?


texts: Is human vision sensitive to frequency or wavelength?

texts:
In a vacuum, there is a one-to-one correspondence between light frequency ($\nu$) and wavelength ($\lambda$), ie. $\lambda=c/\nu$. But in a refractive medium, $\lambda=v/\nu$, so while the frequency may remain constant, the wavelength may not.

I've seen that in biology, wavelength is mostly used. But, I recall reading that human vision is sensitive to frequency. So, is human vision sensitive to wavelength or frequency?


texts: Why don't rates of cancer increase generation to generation?

texts: As cells divide, they accumulate mutations that can sometimes cause cancer. Gametes have to divide like any other cell, and thus generation to generation mutations should accumulate in people's genomes. However, it doesn't appear to be the case that cancer rates increase as a species ages. Why isn't this the case? Is the process of development itself a filter that ensures that most of the cells in the body are "far from cancer"?


texts: Are all tastes just a combination of sour, sweet, bitter, etc.?

texts: For example, can the taste of pineapple be isolated to just a certain amount of "salty-taste-triggering-molecules" and "sweet-taste-triggering-molecules" etc.? Can our current understanding of the gustatory system predict the taste of a new substance (for example we could predict it tastes like chocolate) just based on the amount and ratios of these molecules?


texts: How do drugs tests check so many substances?

texts:
There are about 170 drugs banned for sports and many other drugs that can be used in crimes.

How can blood tests practically detect so many different substances? Do they divide the sample into 170 different micro samples? How are sports and criminal blood tests arranged to be comprehensive?


texts: Estimate of total number of oncogenic mutations

texts:
So there are a number of ways point mutations can hyperactivate or inactivate genes. But realistically there are only some small number of point mutations ever observed for a particular gene in cancers. An example is the JAK2 mutation: c.1849G>T p.V617F chr9:5073770 which is almost the only JAK2 base substitution observed in leukemias.

Is there some estimate of the number of substitution loci ever observed in cancers?


texts: If excess sodium is bad for humans, why don't our bodies just remove it?

texts: This is one of those questions where I realized two everyday facts don't connect for me. Excessive sodium in the diet is supposed to be bad for us. But surely our bodies have mechanisms for getting rid of excess sodium. (I don't know the details, but I know enough about neurons to know that our cells can move sodium when they need to.) Why don't our bodies just keep our sodium levels at a healthy level?


texts: Can ' functional' stress 'forced upon' a cell actually cause cell mutations when they divide and reproduce?

texts: If a group of cells are forced to go beyond their regular biological parameters that they should be under given ' healthy' functioning and while existing in these stressed states some of the cells divide and multiply would the added stressful states make them mutate?


texts: Have any mutations or genetic loci been associated with exceptional longevity in humans?

texts:
Individuals that avoid age-related diseases into later life are known as 'exceptional survivors', and have increased longevity compared to their 'controls' (those that were born at a similar time, yet have 'aged' and died sooner). The Leiden Study determined that in these long-lived individuals there is a considerable genetic component contributing to the survival [Schoenmaker et al] (although this could equally be epigenetic - or even more likely, a combination of both).

I have read about studies that have identified genetic mutations that cause premature aging phenotypes (for instance mutations in the WRN gene cause Werner's Syndrome [Yu et al]).

I have yet to discover any studies that determine any genes/regions associated with resistance to age-related disease (i.e. those that age 'well'). My question is whether anyone knows of any such studies?

Arguably studies that have looked into predisposition to age-related diseases have found some mutations - for instance mutations within the 9p21 genetic locus (i.e. p16INK4a/CDKN2A) have been associated with heart disease and stroke independently (2 age-related diseases) [Wahlstrand et al]. Therefore individuals without any of these risk-increasing alleles could be considered predisposed to exceptional survival - but I see this as separate to my question. Are there any protective alleles/genes/loci that increase 'global' survival? Are there a few protective alleles, or many with small effects? Or are the exceptional survivors just without any disease-causing/risk-increasing alleles?

I am interested in published research (of course), but also in peoples general perceptions of the topic; there are plenty of theories of aging and longevity, but few facts - so please state what you 'believe', and explain why this is the case.

Thanks for your time.

p.s. I am aware that you can genetically modify lab models (e.g. C. elegans eat-2 mutants [Lakowski et al]) to live longer. I am interested in naturally occurring variants, specifically in humans (or that at least relate to human aging).

Update (11 May 2012)

I have found a study, published earlier this year, that finds a single genetic polymorphism to be associated (after correction for multiple testing) with centenarians [Sebastiani et al]. The SNP is in TOMM40/APOE (in LD), which is certainly interesting given the previous links between APOE and Alzheimer's (an age-related disease).

However, I am not convinced by the experimental design; they use age-at-death in centenarians as their cases (having genotyped them), and they use alive population controls as the controls. Whilst there is unlikely all these individual will become long-lived, a better design (to gain more power) would have been to use individuals who have died from 'premature' (e.g. between 60 and 70) age-related disease. So I am still waiting for a convincing study, but this does look promising!


texts: Difference between Genus, Genus sp. and Genus spp

texts:
What is the difference between the three following sentences?

There is significant increase in Bifidobacterium
There is significant increase in Bifidobacterium sp.
There is significant increase in Bifidobacterium spp.

Of course, this could be applied to any genus.


texts: For what reason(s) is allolactose, instead of lactose, the "natural" inducer of lac operon repressor?


texts: What is the meaning of the "d(...)2" notation when writing a DNA sequence?

texts:
When the sequence of a DNA oligo is written as d(CGCTAGCG)2 what is the meaning of the d(...)2?  Why would it not simply be written as CGCTAGCG?

I recognize this sequence is the complement of itself.  Is that what this notation indicates?


texts: Tradeoff between pathogen adaptability and infectivity

texts:
Is there a kind of inverse proportionality relation between a pathogen ability to infect new hosts and its ability to evade the immune defenses/medication?
The background:
The question is motivated by another one asked recently, which draws an apocaliptic scenario of SARS-CoV-2 adapting to vaccines and exterminating the mankind. My answer is that SARS-CoV-2, while being highly infectious, is not capable to such a degree of adaptation. In the same time, the examples of organisms highly adaptable to the immune defenses and/or medication, such as HIV or pathogenic bacteria, are usually less infections (at least to the extent that they cannot be transmitted through thin air). This anecdotal evidence seems to suggest that highly infectious pathogens are less capable of adaptation, whereas highly adaptable organisms are less infectious. I could justify it from the population genetics point of view: a pathogen that is both highly infectious and highly adaptable would exterminate its hosts and go extinct. This explains why such organisms do not exist, although it does not exclude an apocaliptic scenario, where such a pathogen does exterminate the mankind ;) However I would go further, claiming that there is a trade off between higher infectivity and being able to adapt to a changing environment. So I am looking for a coresponding principle in population genetics or perhaps even in ecology (e.g., a tradeoff between the replication rate and the adaptability).


texts: Do neurons have agency with respect to modulation of spike timings?

texts:
I am aware of the mechanism of Spike Timing Dependent Plasticity (STDP) and its ability to cause Long Term Potentiation (LTP) and Long Term Depression (LTD). So far, I've been viewing neurons as input-output devices. However, there seems to be a problem with approximating neurons this way. If all they do is sum the inputs and produce an output, then it seems as if LTP and LTD as caused by STDP would be purely a function of the inputs from the environment. This would leave animals without any meaningful agency.

I would be much more comfortable with the idea that neurons actively try to optimize some parameters by competing with each other, perhaps by varying the timing of their spikes. Is this picture consistent with neuro-scientific findings?


texts: Why are my faeces black in color after eating Oreos

texts:
Why are my faeces black in colour the morning after I eat some Oreos?

Day 1 : Eat a handful of Oreos & the next morning your stool is black.
Day 3 : Eat a handful of cocoa flavored biscuits & the next morning your stool is normal.
Day 5 : Eat a handful of Chocolates & the next morning your stool is normal.

I'm aware of the beetroot digestion story, and how it doesn't happen to everyone. What is surprising in the case of Oreos is that it just takes a
handful of Oreos to turn the stool black. But with any other biscuits or chocolates, my faeces are normal.

I don't have anything other than anecdotal evidence but a lot (NOT ALL) of my friends have had similar experience. Just Googling "Black stool after eating Oreos" & I see a lot of people (not all) having similar experience. Do note that to my knowledge it doesn't affect my body in any way.

Why is that the case? Why doesn't it happen to everybody?
What ingredient in Oreos makes it happen? What is the physiological underpinning?
Asking this question with curiosity than caution. Looking for biological/biochemical perspective.


texts: Do I not have any alleles from my mom's mom & my dad's dad?

texts: So, I have an XX, & I got an X from my mom, & an X from my dad. My dad would have gotten his only X from his mother, & my mother could have gotten the X I got from her father or mother. That would mean I did not get either X gene from either my mom's mom or dad, or my dad's dad - does that mean that I have "less" of their genetics in me? Say I got my mom's dad's X, would that mean I have less of my mom's mom's genetic traits?


texts:
Context: Trying to exterminate a clothes moth infestation.

Supposing you have a room with clothes moths, or rather, with clothes moth eggs and larvae.

Suppose then, that you remove all of the soft furnishings, all of the clothes, all of the carpet, and you thoroughly clean and vaccuum to remove as much dust and hair as possible.

Would one predict that the remaining larvae would then immediately pupate into moths, in response to this food deprivation?

I know that lots of plants will suddenly flower or fruit if they perceive that they are at risk of dying, in order to reproduce before they die. I believe the moths are essentially just a reproductive phase of the moth, so I'd be unsurprised if they did pupate.

On the other hand, I imagine pupation takes a lot of energy and food reserves (not to mention needing material for the cocoon), so I can imagine that they might be unable to do this?

Which way do it go?

Will moth larvae pupate in response to food deprivation


texts: DNA modifications other than 5-mC/5-hmC/5-fC/5-caC in vertebrate genomes?

texts: Other than 5-Methylcytosine and the more recently discovered 5-Hydroxymethyl, 5-formil and 5-carboxylcytosine DNA modifications found in DNA sequences, what are other DNA modifications present in vertebrate genomes? There is apparently a whole bunch of modifications that can be found in prokaryotic and eukaryotic genomes, but I would like to know which ones have been found relevant in vertebrate/mammalian genomes of the eukaryotic ones.


texts: Is "tonic activity" common for neurons firing in the brain?

texts:
I've been reading about Dorsal Raphe Nucleus, a serotonin- rich part of the brain. I noticed mentioning of "tonic activity" - regular pulsing that releases neurotransmitters. On top of this "tone" the nucleus can fire bursts of spikes(action potentials?) that further increase neurotransmitter concentrations for a short time.

Is this kind of tonic firing common throughout the brain, or is it DRN specific?


texts: Comparing maintenance energy costs of plant biomass vs bacterial biomass

texts:
Im interested if anyone has an idea if this research has been done or how you would approach it.
What is the energetic maintenance cost of (e.g) 2kg of some given bacterial cells vs 2 kg of a plant (like soybean).
Bacteria have less DNA to maintain per cell, less organelles, they dont fight gravity (not sure if this one matters), and probably have less active transport mechanisms. I guess the amount of energy they need just to maintain their biomass is much lower than a plant.


texts: What options exist to quantitatively detect enzyme activity in non-model insect tissue?

texts:
Evolution/genomics person here: what are the options to measure the activity or presence of broad categories of enzymes--like peroxidases or catalases--active in a specific tissue (in a non-model insect)?

I understand that antibodies, e.g. ELISA, may be one approach but am unsure if it's the best option or what the alternatives would be. Are any sequence based-approaches available, if I know the peptide sequence (or at least a specific function domain, ie Pfam ID)?


texts:
If a plant was given sunlight even during the night, with appropriate constant intensity during day and night, will the plant be able to maintain health and normally photosynthesize throughout the day?

Does it depend on specific plant species? If so, are there particular categories of plants that may have problems with all-day photosynthesis?


texts: Is fat distributed proportionally around the body?

texts:
One guide I have been using to tell me if I really am gaining a lot of weight is a ring around my 2nd last finger on my right hand, if I can slip it on and off without any resistance then I'm fine, however I've been basing this from the notion that if I gain weight it's proportionally distributed around my body, as such, if I get fatter so do my fingers

So I am wondering, is fat distributed proportionally around the body (ie. if your waist gets bigger then your fingers will get bigger along with it)?


texts: How does non-homologous end joining (NHEJ) work?

texts: I was reading about non-homologous end joining (NHEJ) in my molecular biology of the gene textbook but the explanation provided in the text was rather vague to me, and I was not able to understand it completely. I understood that NHEJ can be used as a repair mechanism when double-strand breaks in DNA occur. The two broken ends are then joined together. What I didn't understand is how this is done. The two broken ends won't always have complementary bases so, won't this lead to mismatched bases? How is this problem fixed? I really need a detailed explanation of how NHEJ occurs please.


texts: How important is non-binding site of protein?

texts:
Just a curious question:

What will happen if i remove most protein sequence that encoded for non-binding site of Restriction Enzyme to make a new enzyme, can the new restriction enzyme still work?


texts: Can TGF beta family induce all somatic stem cells?

texts:
I think this is not possible.
Conclusion about this preview article TGF-$\beta$ family signaling in stem cells:

  While TGF-$\beta$ family signaling regulates stemness of normal and cancer stem cells, its effects are diverse and depend on the cell types and physiological state of the cells.

Can TGF-$\beta$  induce all somatic stem cells?


texts: How long does it take to form a peptide bond?

texts:
What is the time taken to form a peptide bond in vivo or in vitro? It isn't mentioned in my course on protein structures. I was just curious to find out  if any  time scale is known?

Given that prokaryotic and eukaryotic cells have difference ribosome structures, is there any chance that the time might vary between species or even within species?


texts: What's the plant name? It is climber or creeper plant..like money plant...help me finding its name...it has seven to five lobes


texts: Mother's physiological response to baby crying

texts:
I have read several articles [1,2] that talks about the physiological response in mothers when their babies cry. Is there any studies performed and published that show that this is not true ?

https://www.sciencenews.org/blog/growth-curve/how-baby-cries-bore-mom%E2%80%99s-brain
https://www.livescience.com/36964-baby-cries-women-men-brains.html


texts: can a protein recognized by antibodies not be immunogenic?

texts:
I have a protein that is produced with the baculovirus system that is recognized by antibodies generated by immunization of rabbits with the same protein produced in E. coli. However the baculovirus protein did not induce an antibody response when I immunized some pigs.

Could it be that the baculovirus protein is not immunogenic? Even if the same protein is recognized by antibodies? If the rabbits produced antibodies with a protein that did not have post-translational modifications, how can not be immunogenic when the modifications are added?


texts:
I'm thinking of creating my own laser tag system and am a bit concerned about the eye safety aspect. Most of the homebrew system I've seen use the TSAL 6100 diode(http://www.vishay.com/docs/81009/tsal6100.pdf).

From what I've gathered from hobbyist forums it should be totally eye safe. However the math doesn't add up, my math could be wrong, read probably is, but I couldn't find any conclusive data that would disprove it. Also I cannot manage to factor in what effects lenses would have, which are a must to keep the beam from having to large a spread. Here are my calculations.

First off using the inverse suqare law and a TSAL running at 1Amps (from what I've read most players run it at 1.5 Amps) at the minimum distance of 200mm we get the following result:

Ee = 1.5W/sr / (0.2)^2m = 37.5W/m^2 (the 1.5 W/sr is from the TSALs datasheet at 1A)

The irriadiance of 37.5 is a bit high, but it's still under the 100W/m^2 safety limit for the cornea.

The same equation done at a distance of 100mm however yields an Ee of 150 W/m^2 which is above safety levels. Assuming you don't point a tagger in your face and start firing of shoots you'll be safe.

What I'm curious about is how a lens affects the safety characteristics. Assuming a lens with a focal length of 100mm. Won't the irradiance be the same with the irradiance at a distance of 100mm from the IRLED.

My math and understanding of the principals could be wrong, but I was curious if anyone could put my mind at ease.

I've also made a rough calculation of the retinal hazzard.
R(lamb) = 0.33 rad
(angular subtense) alpha= 5mm/200mm = 0.025 rad

We'll use an alphaeffective = 0.011rad and that gives us an emission limit for the radiance of 545mw/mm^2/sr

and our iriadiance is Lir = 1500mw/sr * 0.33 / (5mm)^2 = 99mw/mm2/sr

that's way below the limit, but if we modify that active light source to 1mm it becomes 495, which is skirting the line.

(the tec doc doesn't define an active light source size, at least I couldn't find it so I used 5mm )

Again the above calculations are for a source without a concentrating lens. What would happen if we added a lens in the mix? Would it stay in the safe zone? How does pulsing the diode effect intensity? I'm guessing it lowers it, but if anyone could manage it, I'd like a numerical demonstration that it brings it closer to safer bounds.

The above calculations are based on the folowing OSRAM paper (http://www.osram-os.com/Graphics/XPic2/00052113_0.pdf/Application%20Note%20Eye%20Safety.pdf), which explains the principles involving


texts: Epistasis when interacting loci are codons within a single gene

texts:
There is epistasis when the effect on the phenotype of one gene is influenced by one or more other genes (called modifiers). Is there a similar concept when the effect on the phenotype of one site within a gene is influenced by one or more other sites within the same gene?

For example: Think about an opsin (a light sensitive protein) that gets activited when hit by a wavelength of, say 500nm.  If the mutation A124S (at position 124 the aminoacid A is replaced by the amino acid S) exists, then the protein is activated when it gets hit by a wavelength of 560nm but this shift occurs only if there is a V (instead of a I) at position 95. Hope you get the idea! Are there specific words to describe such phenomena?


texts: Is the swimming pool water harmful to frogs who jump in? If so, how?

texts:
Here is an odd question:

Frogs have permeable skin. Indeed, via capillary action, frogs absorb water through their skin.

Chlorine is in principle a harmful substance. I am sure what percentage of chlorine is in swimming pools usually, but the pH level is kept to around 7.4. This is the desired pH level, as a pH of 7.4 is the pH-level in human eyes and mucous membranes.

One of the "common wisdoms" I had growing up was that if a leopard frog (i.e. The Northern Leopard Frog, rana pipiens) jumps into a swimming pool, it must die soon, because the chlorine would kill it. However, I now doubt this is true.

So, do frogs die from swimming pool water? If so, why? What exactly is killing them? Chlorine poisoning?

PS: I am having difficulty finding the correct tags for this question. Any help is appreciated.


texts: Why do diseases in the tap water of developing countries affect people from developed countries more?

texts:
My siblings and I went abroad to a country that doesn't have drinkable tap water, but we did not know this at the time as the people who lived there used to drink it all the time with no issues.
One day, we all decided to drink a glass of water from the tap and we all ended up in a hospital and were really ill (I'm unsure of what we had as it was a while ago). We were told it was due to the tap water and were advised to only drink bottled water in the future as the tap water is unsafe.
My question is, why did the tap water only affect us but was fine to drink for the residents there? Is it maybe because our bodies are used to clean tap water?


texts: What kind of insect can this be? This appears to be just a shell after and insect went through a metamorphosis process

texts: What kind of insect can this be? This appears to be just a shell after an insect went through a metamorphosis process.


texts: Name (and meaning of the absence) of the white semicircle at the base of the fingernail?

texts:
At the base of fingernail, there is a white semicircle (see on the first picture). But sometimes there isn't one.

My questions are: what is this white semicircle on the fingernail, and what causes it? What is the explanation when there it isn't on all of the fingernails (see on the second picture)?


texts:
When I was walking in my garden at night I saw this small glowing insect, can you identify what is this insect?

Location: Middle-East Palestine

Size: Length about 1 CM

This image in the dark (see the light of the insect)

These images taken by flash.


texts:
I recently heard a radio show where two callers claimed that their blood types had changed. One caller claimed that he was born O-, but recent tests said he was A+. Another caller claimed to change from AB- to AB+. Both callers claim that they had multiple tests before and after the change.

What I noticed is that both cases claim a conversion from Rh- to Rh+, or from type O to some other type. These could potentially be explained by a person carrying a gene for Rh factor or some other blood type, but failing to express the protein. Then the gene starts expressing, changing their blood type.

Of course both stories could be false, intentionally or otherwise. This is purely anecdotal evidence, and one caller claimed that her blood type change was due to extraterrestrial interference. I couldn't find any better documented cases of blood type changes after a quick search on the internet, so I thought I'd ask here.

Are there any documented cases of a change in blood type?


texts: I understand that Circle of Willis is a circulatory anastomotic system that provided blood to the brain.  I want to understand if this system is unique to humans or does it exist in other species or mammals to be more specific?


texts:
Several of these were on my potato plants in Washington state, USA. This one about 7mm in length, some were a bit larger. They were moving in an inchworm-like fashion, but only by touch - I don't think they have eyes.

This specimen was photographed after placing in isopropyl alcohol, which changed the color (it was almost white while alive) and the shape somewhat.


texts: Why don't weak detergents lyse the nuclear membrane?

texts:
A low concentration of a non-ionic detergent lyses the cell membrane, but leaves the nuclear membrane intact. Both are phospholipid bilayers, so why is only the cell membrane lysed?
Under these conditions, are the membranes of other organelles lysed?


texts: Prevalent large (>=90kDa) maintenance protein/loading control

texts:
I was wondering if anyone had recommendations for good, large (hopefully 100kDa+), control proteins that would be present in most mammalian cells.  I'm working mostly with tissue samples from humans and mice, and airway epithelium in particular if that matters.  So far the best I've thought of is HSP90, but that is far from ideal for a number of reasons.  My target proteins are between 125 and 210 kDa.  To improve resolution, we've run pretty much everything under 90kDa off the gel.

That removes the old standbys like actin or GAPDH.  I understand that the protein levels could vary between cell types for a good loading control target.  Bonus points if you know a good antibody clone to it.


texts: What is the active site (not metal binding site) of tyrosinase and other monooxygenase/oxidoreductases?

texts: On https://www.uniprot.org/uniprot/P07524, tyrosinase is shown as a monophenol monooxygenase. However, the UniProt database only shows a metal (copper) binding site, when there is presumed to be an actual active site that performs the reactions, other than the metal binding site. Are there any clues to find the actual reaction active site for a monooxygenase? Please include the sources, if there are.


texts: On which chromosomes were the traits studied by Mendel?

texts: In his experiment with peas, Mendel mainly studied two traits : yellow/green colours and round/wrinkly shapes.  I've heard that the pea genome is very large and its sequencing is a challenge. However, is there any information about the chromosoms involved in the traits on which Mendel worked ?


texts:
I am using Neutravidin Agarose beads to isolate biotinylated RNA. The thing is, in the manual it says to use 8M Guanidine-HCl, pH 1.5 for elution biotinylated molecules. As far as I know it is a very harsh elution buffer. Do you think it would effect my RNA? I have isolated my RNA with TRIzol which also contains Guanidine salt but the concentration is not that high.

As a second question, do you know other ways to elute my biotinylated RNA from beads?

Thanks!


texts: How to incorporate intraspecific variation in discrete characters in comparative analyzes?

texts:
I'd like to run a multivariate analysis (Pavoine et al. 2011) that aims to disentagle the effect of environmental gradients on traits, considering its autocorrelation with phylogeny and space. It uses the RLQ approach and works with both discrete and continuous traits. However, I don't know how to incorporate intraspecific variation in discrete traits.
For example, I recorded categories of pigmentation on organs of several amphibians, but for some species, these categories vary among individuals. One way would be including individuals as polytomies at the species level, but this would make the test quite hard to interpret.

Thank you in advance,
Diogo


texts: Can CRISPR-cas9 be used to insert a large gene?

texts: I would like to insert a 1500 bp or longer gene to the broken site in E.coli (or may be bacillus subtilis which support NHEJ) after cut with Crispr-Cas9. Is this possible for both NHEJ or HDR?


texts: Role of neuraminidase in preventing polyspermy in humans

texts: Neuraminidase is a hydrolytic enzyme present in the acrosome of human sperm. It removes neuraminic acid (salic acid) from glycoproteins. I have read in a book that due to this reason it (the enzyme) prevents polyspermy. Can anyone corroborate both of these statements?


texts: How are baselines for extinction rates established?

texts:
At the time of 2010, the UN Environment Programme estimated that 150-200 species of plant, insect, bird and mammal become extinct every 24 hours, and, that this is nearly 1000 times greater than "natural" rates. (source, para. 5)

My question is: How are baselines for extinction rates (regarding plant & animal species amongst the entire Earth) established, to then be able to say if an extinction rate for a given species is "normal" or not? What factors are considered most relevent?


texts: As it is really beneficial for all organisms, why are animals, especially mammals (I don't know about other vertebrates) unable to synthesize cellulase enzyme in their body? Is it linked to some DNA defects or have we not evolved from cellulase producing bacteria?


texts: Can formalin fixed tissue stored in absolute ethanol be used for histology?

texts:
Can samples which have been stored in buffered formalin and the moved straight to absolute ethanol be used for histology?

I know that the samples normally need to go through a series of ethanol concentrations (70%, 80%, 90%) for dehydration before they reach absolute ethanol, but can you still use samples that have been immediately immersed in absolute ethanol? Or would the rapid dehydration cause too much distortion?


texts: Is this tall, white tree in central Australia a kind of Eucalyptus?

texts:
This is near Alice Springs NT, Australia, about -24°S latitude, 550m. Area is arid but it's in a maintained park.

I don't know the exact size, but the photo is hand-held from the ground and clearly the tree is quite tall.

I only have this one photo to work with (it's not mine). I've added some cropped sections of the same original image below for easier viewing.

It reminded me of the tree I saw in the linked video below, which is likely a Eucalyptus considering the koala context.

I don't need an exact species, just confirmation of my genus hunch.

Oh! No koalas were seen in the tree eating leaves at the time, which would have made a "differential diagnosis" easer.

From Koala Bears and Eucalyptus - Periodic Table of Videos at about 02:10 (Sir Poliakoff reminds us a few times in the video (himself as well) that koalas are not "bears"!)


texts: Are peppers on the same plant genetically identical?

texts:
I'm a hot pepper growing enthusiast and on one unknown super hot cross there is significant variation in pod size and shape.

What causes significant variation of pod shape and size on the same plant? Environmental factors? Genotype/genetic factors?

Also, what is a hot pepper phenotype? What makes a phenotype a phenotype?

Appreciate any input!


texts: Difference between "wash" and "rinse" in biotechnological procedure descriptions

texts:
Is there a difference between "rinse" and "wash" in sentences like this:

  Following the staining, the sections were washed twice with deionized water, then dehydrated using ethanol solutions of incrementally increasing concentration (70%, 80%, 96%), cleared using a xylene substitute, embedded in the mounting medium and coverslipped.

Can we use "rinsed" freely in the place of "wash" here, or are there nuances of meaning?

I know the difference between the two verbs in non-specialized English, but I'd like to know if there's a difference in a biotech procedure context.

Google Ngram search gives the following for "sections were washed, sections were rinsed":


texts: What are "primary amino acids and secondary amino acids"? Context: analysis of amino acid content using reversed-phase HPLC

texts:
In a Russian document I'm translating, an HPLC system is used to analyse the amino acid content of a substance.

The detector wavelength is set at 262 nm for "secondary amino acids" and 338 nm for "primary amino acids". But what are those?

I googled and found a lot of mentions with exactly these wavelengths being used, but I haven't been able to quickly understand how a "primary" amino acid differs from a "secondary" one. Is it that the secondary amino acids are the products of the destruction of the primary amino acids (those that initially existed in the substance)?

What is the difference between a "primary amino acid" and a "secondary amino acid"?


texts: What kind of memory is "keyboard/keypad memory"?

texts:
I work in IT and I have observed many people who cannot remember their iPhone passwords or computer passwords off the top of their head. However, if presented with a keyboard or a phone with a functioning keypad, they can instantly remember exactly what their password or passcode is.

I'm curious to know what this kind of memory is called. Since it's somewhat related to visuals, but not necessarily (you don't need to look at your keyboard to type out your password.)


texts: How deep underwater could you breathe using a tube which breaks the surface until the water pressure makes it impossible to inhale air?

texts:
I'm struggling with a question asking how deep you can breathe underwater using a hollow reed before the water pressure makes it impossible to inhale. The question asked to use this data of maximal respiratory pressures:

The question also gave a hint that for every metre below the surface, hydrostatic pressure increases by 100 cm H2O.
I'm seriously lost on this question, from my research, all I could find was that a difference of approximately 50 cm H2O is needed in order to inhale, but I'm unsure if that is information I should deduce from the table instead of looking up. Even knowing that information, how would I then find out how deep that means you could breathe? Any help would be greatly appreciated.
Thanks


texts: Kegg in Cytoscape: how to get plots with reaction IDs in place of EC numbers using KeggScape?

texts: I found a KeggScape manual page representing Kegg reactions in Reaction ID format, but I couldn't find how to get a Kegg plot with reaction IDs in place of EC numbers. Does anyone know?


texts: How does a plant grow before photosynthesis is possible?

texts:
During photosynthesis, a plant translates CO2, water and light into O2. I assume the carbon C is further used for the growing process. I wonder how the plant grows before the time where photosynthesis is possible, i.e. before there are even leaves, in which photosynthesis occurs.

To what extent does the plant grow from the seed/the minerals in the ground?
How much carbon are relevant for which parts of the plant and at what times of the evolution of the plant?

I don't know if there are only these life periods of the plant, i.e. if there are other major biochemist-of-growing changes, than in the comparison before and after the plant got leaves. So are there other relevant aspects to this? If there are leaves present, is the rigid structure of the plant only coming from the CO2 in the air and not from the ground anymore?
The answer will probably depend on the plant. So here is another formulation of the question:

What are typical characteristics of different plants in this regard? I.e., how do common species of plants manage their C consumption before (and after) the development of leaves?


texts: What happens if we continuously stimulate a mimosa plant?

texts:
I know there is some mechanism in humans by which we start to ignore a certain stimuli if it persists for a long time (e.g., we don't feel our shoes all the time !).

Can the same thing happen in Mimosa pudica? Can it again get it's original arrangement of leaves if it is stimulated without interruption?

I think it should do this, otherwise it will not be able to grow if it is surrounded by bushes from all the sides as it will be stimulated constantly and so will be unable to photosynthesize properly.


texts:
Yesterday, my brother brought a strange fruit resembling Lychee (but much bigger in size). Here is a pic of it:

When cut it, it had smell like banana and fibers were like of the chicken meat, though taste was more or less like banana (sorry have no pic of that).

Can someone kindly help me identify it?


texts:
I have read many papers that refer to cell type, cell state and cell function, but I haven't found an explicit definition for each of these terms.

For example this paper (Brown et al. 1994. J General Virology 75: 2367-2377) refers to cell type and cell state without providing an explicit definition of both terms.  I have a vague idea of what these terms mean but a more explicit definition would help me greatly in understanding them.


texts:
I've got petri dishes with a base agar layer ready for E. coli culturing. However, I do not have soft agar in which to dilute the E. coli before pouring it on to the plate.

Any suggestions on what substance I can use to substitute for soft agar, or how I might be able to make it? I have the following at my disposal from the lab at school:

Tryptone base agar
Nutrient broth
MacConkey agar

The original soft agar medium had the following composition:

10 g Bacto™ tryptone
9 g Bacto™ agar
5 g KCl
1000 mL water


texts: Which surfaces contain no epithelial tissues and which epithelial tissues are vascular?

texts:
Epithelial tissues are found on all the surfaces of the body; including external surfaces and surfaces of organs etc.
Are there any surfaces which do not have epithelial? I have read in my book that almost all the surfaces has epithelial tissues but there are some exceptions. What are the exceptions?

Similarly, almost all the epithelial tissues are avascular. But there are some exceptions which are vascular? Which epithelial tissues are vascuar?

*I'm talking about a human body.


texts:
I would like some help identifying this mushroom I found in my yard.
Location: Southeast Georgia
Near Pine trees after heavy rainfall
Color: Light brown to Dark Red, biggest is about 4 inches in radius


texts:
In many places it says PGF2-alpha.
Now, I am thinking PGE2 is a substype of PGF2-alpha.
However, I am not sure.

Is dinoprost PGE2?


texts: What causes the shape of the dense structure in this "giant squid egg" sac?

texts:
The YouTube video Swimming Next To Giant Squid Egg shows a giant egg of a squid and/or an egg of a giant squid. Text in the video's description includes the text quoted below, which indicates that the "egg sac containing hundreds of thousands of baby squid."

Question: The egg sac is mostly transparent and contains an optically dense structure with a very striking shape. If I didn't know it had hundreds of thousands of individual organisms, I'd think there was a brain developing at the top and a body forming below it. Is this shape just random? Does it change over time? Does it represent motion of all the little squids swimming around? It looks to me like it could be a slow-motion murmuration for example.

screenshots from the video linked above; click each for a full size view or just watch the video.

  MANDATORY ONSCREEN CREDIT - Ronald Raasch

  A team of divers filmed a rare glimpse of a huge transparent egg sac containing hundreds of thousands of baby squid.

  The stunning underwater video was filmed by Ronald Raasch, 48, as he was diving with two other team-members from the research vessel REV Ocean in the cold waters outside Ørsta, Norway.

  On October 5, the team of divers was swimming back to shore after visiting a WWII shipwreck about 200 metres from the coast, when they had a once-in-a-lifetime encounter with a mysterious object.

  Floating 17 metres below the surface and 15 metres above the ocean floor, was a giant transparent orb which the divers quickly identified as a 10-armed squid’s egg sac.


texts: What are the characteristic structures of bacillus M. tuberculosis and what they cause?

texts:
I answered to this question:

  In most forms of the disease, the bacillus M. tuberculosis spreads slowly and widely
  in the lungs, causing the formation of hard nodules (tubercles) in the
  respiratory tissues and form cavities in the lungs.

and got zero points.

What is the correct answer to the question?


texts: How many species of mites live on the human body?

texts:
How many known species of mites regularly live on the human body?

I've always heard that most people have eyebrow mites. This source  mentions 2 species of face mites, Demodex folliculorum and D. brevis,  that also regularly live on humans, but I'm wondering if there are in fact other species of mites that also call human bodies home. If so, how many? And where do they live?

Note: I'm not talking about disruptive mites such as scabies,  but mites that go less detected.


texts: Can someone tell me where can I find detailed text about mechanisms of evolution of dominance? Or, if it is possible, I would be grateful if someone will tell me about them here.


texts:
With many foods today containing chemicals, agents and preservatives etc... What biological criteria must a new food and its constituent components satisfy biologically, to be defined as edible?

For example do they look at the chronic/acute affects of chemicals in the body?

This question is just limited to chemicals, if a new fruit was discovered, how would it be decided if it was edible or not?


texts: Why is the Patellar reflex not triggered when the tendon is extended slowly?

texts: I have been previously told that the Patellar reflex (knee-jerk-reaction) exists to prevent the hyper-extension of the patellar tendon.  Yet if the impact to the tendon is delivered slowly - i.e. by pressing down on it rather than striking it - there is no reflex response.  Why is this, as surely the tendon is being extended by the same amount?


texts: Can platypuses communicate via electroreception?

texts: I know at least some electroreceptive fish are capable of basic communication with other members of their species via varying their own bioelectric signals.  However, I can't find any information as to whether platypuses (or, for that matter, any of the handful of other electroreceptive mammals) are capable of communicating in a similar manner.  Does anyone know if they're able to do this?


texts:
Does doing sports makes a human require more magnesium and – if any – how strong is this effect?

Do athletes take magnesium supplements (e.g. pills of magnesium carbonate) because they build muscles and therefore need more of it as their muscle masses increase, or is magnesium consumed by muscle activity (e.g. by causing a chemical reaction which the human body can't undo so it has to excrete the reaction product and get new magnesium from food)?


texts: What does it mean for muscles origins and insertions to be the other way around in the right than left limb?

texts:
Herbert Srebnik writes in Concepts in Anatomy:

  In the right limb, the muscle's origin is proximal to the joint and
  the insertion is distal to it. In the left limb, the muscle's origin
  is distal to the joint and the insertion is proximal to it.
  (The text appears next to an image of the biceps brachii)

What does that mean? What does it tell this paragraph tell me as someone new to human anatomy?


texts: How are viruses in vaccines weakened in a laboratory

texts: I would like to know how viruses in vaccines are weakened or attenuated in a laboratory


texts: What would happen if some neurons are unmyelinated?

texts:
I know that cold receptors have myelinated axons and heat receptors don't.

From a physiological perspective, what could be the consequences if cold receptors were unmyelinated? Would that pose some detrimental effect?


texts:
Under which keyword would you try to find out more about the grouping behaviour which looks like this? Does anybody recognizes such behaviour, or know an animal species which uses it?

My tries: threshold group behaviour (threshold here is the group size - if bigger than 5 individuals == stable), or gravitational group behaviour?

After step 6 the group disintegrates (for example due to foraging) and mechanism starts by step 1. Important thing is that the location of forming stable group is always different.


texts: Cell biology - Resting membrane potentials

texts: Why do we say there is an overall negative charge on the intracellular side of the plasma membrane at rest, and an overall positive charge on the extracellular side when both potassium and sodium are positively charged ions, and they are in relatively equal amounts on either side? It seems to me that both sides should be positively charged, and I can't get my head around it.


texts: Identification of protozoa under microscope

texts:
I observed maybe Protozoa from standing FRESH water and from slowly flowing FRESH water. I am complete dilettante. Can you tell what these creatures are?

https://www.youtube.com/watch?v=6D5ck3zNJzA&t=474s

Thank you.

Added picture for to be more specific


texts:
After looking through the PhyloCode, the only thing I found that looked like an example was in Article 9, Chapter 4:

  A node-based definition may be abbreviated "<A&B" or "<A&B&C&D [etc.]".

  A branch-based definition may be abbreviated ">A~Z" or ">A~Z∨Y∨X [etc.]".

  An apomorphy-based definition may be abbreviated ">M(A)".

Then from the following lines, I assume that that is actually how the names would appear in print:

  The system of abbreviations used here adopts the following conventions: > = "the most inclusive clade containing"; < = "the least inclusive clade containing"; & = "and";  ∨ = "or"; ~ = "but not"; A, B, C, etc. = species or specimens used as internal specifiers; Z, Y, X, etc. = species or specimens used as external specifiers; M = an apomorphy; () = "of" or "synapomorphic with that in"; >∇ = "the most inclusive crown clade containing"; <∇ = "the least inclusive crown clade containing". The inverted triangle meaning "crown clade" resembles the representation of a crown clade on a phylogenetic tree diagram.

I'm wondering if one could clarify what an actual real-world Clade name would be using the PhyloCode. Maybe just a few examples or even just one. For example, there is this fern Equisetidae, a subclass of Polypodiopsida. Altogether it has this set of names:

Kingdom     Plantae
Subkingdom  Embryophyta
(unranked)  Tracheophyta
(unranked)  euphyllophytes
Class       Polypodiopsida
Subclass    Equisetidae

I am wondering how you would rewrite this using the PhyloCode. If it's too complicated or requires a bunch of additional work to initialize a basic set of codes or something, then that would be good to know too. But from the documents I've seen, it seems to suggest one can translate existing Linnaean classification terms to the PhyloCode somehow. My attempt at it without having gone thoroughly through the whole document is this:

A = Plantae
B = Embryophyta
C = Tracheophyta
D = euphyllophytes
E = Polypodiopsida
F = Equisetidae

So the full name of it would be something like A>B>C>D>E>F. Or maybe it's more like this:

A = Plantae
A>B = Embryophyta
A>B>C = Tracheophyta
A>B>C>D = euphyllophytes
A>B>C>D>E = Polypodiopsida
A>B>C>D>E>F = Equisetidae

Looking for some help on better understanding how to translate existing Linnaean terms/species to PhyloCode. Wondering if you are actually renaming things like Tracheophyta, which has a descriptive Latin name, to A>B>C, which is a non-descriptive identifier. Thank you.


texts: Why is the skin of European bog bodies brown?

texts: What causes this? Is it to do with decay or is it to do with substances within the bog dying the skin?


texts: Why isn't phosphorus or nitrogen a limiting nutrient for animals?

texts:
Nitrogen and Phosphorus are usually the limiting nutrient for plants, especially for algae.  Phosphorus is used for DNA, ATP and phospholipids, and Nitrogen is used for pretty much every protein a cell might want to produce.  That is, their need for biological processes is not tied specifically to photosynthesis: anything that lives is going to need them, pretty much for anything it might want to do.  It would make sense for them to be a limiting nutrient for almost anything that's trying to grow, plant or animal.

Yet for animals the limiting "nutrient" seems to always be energy, ie: food.  Why aren't animals limited by lack of nutrients in the same way that plants are?  Obviously animals need these nutrients, too.  Or to reverse the question, why do plants need so much more phosphorus/nitrogen than animals do?

My best guess is that an animal's digestion of plant material is relatively inefficient energy-wise but relatively efficient nutrient-wise.  So for an animal to eat enough food to have sufficient energy to survive, it's probably eaten more than enough Nitrogen and Phosphorus for its needs.  But I'm just guessing and I can't find any data that would back up that guess.


texts: Effect of sleep deprivation on pupils and pupillary responses

texts:
What is the effect, if any, of sleep deprivation on pupils? Specifically:

Are pupils more dilated/constricted?
Is the pupillary response to light any different?
Anything else?


texts: Do humans have enough biological differences to be grouped into races or subspecies?

texts:
After my online research on the subject, I learnt that, biologically speaking, many scientists believe that there is no such thing as a race. Homo sapiens as a species is only 200,000 years old, which has not allowed for any significant genetic diversification yet, and our DNA is 99.99% similar. I've read statements that there can be more genetic variation inside a racial group than between different racial groups, meaning that, for example, two individuals from the same "race" can have less in common with each other than with an individual from another "race".

Wikipedia on Race (human classification) quote:

  Scientists consider biological essentialism obsolete, and generally discourage racial explanations for collective differentiation in both physical and behavioral traits

Q1: If Homo sapiens has no races (according to biologists), why are we so different morphologically? (hair/eyes/skin colour and even athletic performance seem to differ between human populations)

Q2: Is it common for other species too, when genetically close populations have very different morphological traits? Are there any other mammal or animal species that exhibit biological diversity comparable to human diversity, and how do taxonomists treat these species? (excluding intentionally bred domestic species to keep the comparison fair)

The question has been paraphrased to emphasize that it is the biological debate that is in question, not the sociopolitical. I.e., why is there no consensus in evidence and opinions of scientists?


texts: Can an oncoming stroke/seizure, be stopped by a setup consisting of a brain-computer-interface (BCI) that immediately detects the variation in wave-form, and then another machine that neutralizes the anomaly by sending a measured voltage to select areas of the brain OR by Transcranial Magnetic Stimulation?


texts:
I have learnt that our immune system distinguishes self from non-self by using MHC. So a mother during pregnancy should also develop antibodies against the fetus as it is also a genetically different individual. Answering by saying that antibodies won't cross the placental barrier seems wrong as there is so much research going on this thing that such a simple explanation wouldn't suffice.
Why doesn't the mother reject the baby?


texts: Which extinct creatures were most genetically distant from everything alive today?

texts:
The more distant the common ancestor of two creatures the more genetically distinct the creatures will be. For example I am more genetically distinct from a mushroom than an ant. I am more genetically distinct from an ant than a fox. Etc.

Extinction in the deep past has cut off some evolutionary branches. Which extinct creatures (including all living organisms) were most genetically distinct (alien) from living creatures today?


texts:
We're in the process of welcoming sheep, thus setting up the fences, now inside on of the areas, there is a small tree. Never seen leafs like this before. I suspect this to be some sort of anomaly/disease ?.
I identified 2 oddities : the branches are chorros-like and some leafs have small, vivid red appendices growing on them

Could anybody identify the tree?
are the branches and leafs 'normal'
3 is there any danger for the sheep? (toxicity) ?

Region : South-west France
Size: About 2 meters

Overall picture :

Details :

Closeup:


texts: In my understanding, the evolutional function of berries is to be eaten and pood out somewhere else, so that the seeds of the plant spread. Is this so? Then why are some berries poisonous?


texts: Which domains or motifs are capable of attaching to both DNA and RNA?

texts: Domains or motifs of transcription factors are catalytically active to attach to the nucleic acid of any type. Where could I find a list of domains or motifs which are able to attach to both DNA and RNA? for example KH domains bind to either RNA or single-stranded DNA.


texts:
Several species of the tree genres Betula have a white bark,especially when they are young. This is quite peculiar to trees - at least in central Europe; so I'm wondering if there is a ecological reason behind it.

The first idea I have is that they protection against the sun. But normally protection of nature against the sun is to make the opposite: put more pigments in the skin, so that the sun does not damage the underlying DNA.
If this is the explanation, how do other tree species protect against this?


texts: Self-thinning: slope of log (biomass) vs log (density) is -1/2 whereas slope of log (weight) vs log (density) is -3/2, why?

texts:
In self-thinning or intraspecific competition (more relevant for trees I guess) why does logarithm of Biomass vs logarithm Density give you a slope of -1/2 whereas logarithm of Weight vs logarithm of Density gives you a slope of -3/2? Biomass is mass (or quantity) of an organism per volume(or area), weight is mass scaled by gravitational acceleration which is a constant, unless the organism you are dealing with is very very tall. So the plots can be shifted accordingly but shouldn't slopes be more or less the same ?

source: Ecology: Concepts and Applications
by Manuel Molles
www.mheducation.com/highered/product/ecology-concepts-applications-molles/M0077837282.html

.


texts: Why doesn't the concentration of one ion affect the concentration gradient of another ion across a plasma membrane?

texts: In the initial stages, some ion channels across the plasma membrane open to allow for ions to flow down their concentration gradient into or out of the cell. I understand that each ion's overall electrical potential across the membrane would affect the other ions', thus affecting their transport across the membrane. However, I don't understand why the concentration of ions aren't taken as an overall concentration because surely, if we are looking at diffusion of ions caused by Brownian motion, then all molecules on either side of the membrane would affect the other molecules on that respective side of the membrane?


texts: How to characterize stability of a protein from Trp fluorescence vs [denaturant] curves?

texts:
A colleague of mine has taken Trp fluorescence measurements from a dimer in combination with various ligands, over a range of denaturant concentrations.

The idea is that ligands which bind more tightly to the dimer will stabilize it and delay changes in fluorescence. This is what our data look like:

Total fluorescence decreases, probably due to quenching from the denaturant. Papers I've seen using this method show it's possible to calculate the fraction of denatured protein by analyzing displacement in peak emission wavelength. However, they use monomeric proteins with few Trp, whereas I have a dimer with several Trp plus some additional variability introduced by the different ligands.

Additionally, we have data from a scintillation proximity assay that indicates ligand affinity is ordered as 1<...<5 and 6<...<11. Ideally, we would like to replicate this same ordering through the analysis conducted on the data above. I would appreciate any suggestions of methods that will allow us to carry out such comparisons.


texts:
The neck seems like an odd place for it. All other neck anatomy must interface between the head and abdomen (trachea, esophagus, circulation, spine etc).

Surprisingly I have not been able to find any explanation for the thyroid’s location.


texts: Is there a good field methods book that covers terrestrial ecology?

texts:
In the past I have used Limnological Analysis by Wetzel and Likens and Methods in Stream Ecology edited by Hauer and Lamberti to develop labs and research methods for courses and projects with an aquatic focus.

These books detail the standard methods of lotic and lentic ecology with some emphasis on utilizing the methods in undergraduate or graduate level courses.

I am now developing a biogeochemistry course that is not limited to aquatic systems and I am looking for a summary of field methods for terrestrial systems.

Is there a book that summarizes terrestrial field ecology methods similar to Wetzel and Likens and Hauer and Lamberti?


texts: Is it possible to grow a fertilized human egg entirely outside the woman's womb?

texts:
Many science-fiction movies (for example, The Island) show the possibility of growing a fertilized human egg cell (from the beginning to the end) outside the womb of the woman.

This means that you have to create the exact circumstances for the fertilized egg cell to develop into a human being. These exact circumstances coincide, obviously, with the womb of a woman.

Doesn't this require a woman, where those circumstances are exact, which means the only place where a fertilized egg cell can grow is the woman itself? So basically I'm saying that you need a woman (the womb is connected to the entire body) to let the single fertilized egg cell into a fully grown 9 months baby.

Well, this isn't exactly true: after development for 5 months or so in the womb, an artificial environment can take over, which is possible with current technology. But to devolop the fertilized egg right from the start is another story? Can it be done, or is it impossible (of which I'm certain, but nevertheless I ask this question)?


texts: Why do plants flower in different seasons?

texts: I know how it is controlled (photoperiodism), but I wonder why all plants don't start to flower in spring? Is it connected with ecological niche?


texts: Studying the epigenetic variability, can I use SNPs?

texts:
So, I'm trying to study the effects of epigenetic variability on the brain structure. Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed in the brain region? I don't have environmental data, just the SNP information.

Since epigenetics refers to the variations in the gene expression without changing the DNA sequence, I don't really understand if there could be a connection.

Any help would be appreciated, thank you!


texts: Does anyone know what this purple plant is? (picture taken in Turkey)

texts: Is anyone familiar with this plant species, picture taken in the Dalaman region of Turkey. It has large purple leaves.


texts: Controlling for phylogenetic signal - what is statistically appropriate?

texts:
I am currently collaborating with a fellow PhD student. We are both in the same Biology department, but my collaborator is more of a natural historian, so I am handling the statistical side of things.

He has published a few papers using only Brownian models and Pagel's $\lambda$ (with a different collaborator). However there seems to be a plurality of different methods available - Grafen, Blomberg, and Martin, to name a few. OU models seem inappropriate for our data since we have relatively small phylogenies (Cooper 2016). The literature seems to indicate that Pagel's $\lambda$ is more robust than Blomberg's $\kappa$, and in general an okay method to check for phylogenetic signal. I've also found that some people throw everything and the kitchen sink at their data, and then compare log-likelihoods, AIC, BIC, with log-likelihood ratios for any nested comparisons.

My first question is then, should you have any a priori assumptions of which method will be appropriate for your data?

I am still new to PCM so I used old R scripts and an AmNat paper (from 2019) as my reference. I am also using the same phylogenies as that AmNat paper. From that paper, and from those scripts, only two models were used, a Brownian model (which is essentially $\lambda$ = 1, anyways) and an estimate of $\lambda$. They compared the two models, chose the more appropriate model by log-likelihood ratio and that was it.

My second question is, shouldn't you always compare your models to a model with fixed $\lambda$=0?

For example, I have the following output in R,

#Brownian Model

pglsModel_BM <- gls(sum_dep ~ ContGroup, correlation = corPagel(1, phy = UltTree, fixed = TRUE), data = temp, method = "ML")

#Estimated Lambda Model

pglsModel_E <- gls(sum_dep ~ ContGroup, correlation = corPagel(0.50, phy = UltTree, fixed = FALSE), data = temp, method = "ML")

###Output of comparison is...

             Model df      AIC      BIC    logLik   Test  L.Ratio p-value
pglsModel_BM     1  3 528.4584 534.5344 -261.2292
pglsModel_E      2  4 528.0454 536.1468 -260.0227 1 vs 2 2.412992  0.1203

###ANOVA output of preferred model

Denom. DF: 54
            numDF  F-value p-value
(Intercept)     1 7.039370  0.0104
ContGroup       1 6.480427  0.0138

And the Brownian model got the go ahead. It seems that Brownian is treated as a null model, but I can't wrap my head around why $\lambda =0$ isn't also a null model or the null model. Moving forward with my assumption,

###Adding in a lambda=0 model

pglsModel_0<- gls(sum_dep ~ ContGroup, correlation = corPagel(0, phy = UltTree, fixed = TRUE), data = temp, method = "ML")

###Using anova for model comparison

             Model df      AIC      BIC    logLik
pglsModel_0      1  3 524.0962 530.1723 -259.0481
pglsModel_BM     2  3 528.4584 534.5344 -261.2292

###checking out the 0 model...

Denom. DF: 54
            numDF   F-value p-value
(Intercept)     1 289.67228  <.0001
ContGroup       1   0.21234  0.6468

I realize the differences are rather small, but all methods point to $\lambda  =0$ as the 'more likely' model.

My third question is -- although, possibly answered by the second question -- do we assume that there must be some amount of phylogenetic signal due to shared history, such that it is suffiecient to only test for $\hat{\lambda}$ and compare to $\lambda = 1$?

Note: Just to be sure, I compared all Brownian models with corBrownian to their $\lambda = 1$equivalents, and got the exact same outputs.


texts: Do we know how dangerous six-eyed sand spiders are?

texts:
The Sicariidae family contains the well-known and dangerous Loxosceles spp. (fiddle-backs, violin spiders).

The family's other two genera, Sicarius and Hexophthalma (six-eyed sand spiders) have reputedly exceptionally cytotoxic venom, although they live in sandy deserts and rarely come into contact with humans.

Quite common in the exotic pet trade is Sicarius thomisoides (formerly terrosus).  I would be particularly interested in how dangerous this species is likely to be - many are now claiming that research has shown it to be minimally dangerous.  I'm not sure what work this is based on - perhaps this paper? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2767091/


texts: Is it common to have multiple recessive traits in humans?

texts: I just started thinking about my phenotype and realized I got multiple recessive traits. I have attached ear lobes, my blood type is O-, I got green eyes (I think eye color in polygenic but still somewhat recessive), a few years back I was in the control group of a study that was looking for a link between an allelic variant and the development of diabetes mellitus in patiences with another disease I forgot which, I was the only homozygous among all control patients! so you get the point. I am just wondering if anyone has any notion of how often humans present multiple recessive traits, maybe in terms of allelic frequency or something like that, or where can I find information about it. And maybe if there is something health related that may be worth knowing. I mean apart from a minor allergy I'm a really healthy person, but I may have predisposition to something.


texts: Radial Basis Function Network (RBF Network)

texts: In the Wikipedia article on radial basis function network, I didn't understand what was meant by "center vector for neuron i", in other words "center of the RBF units called also prototype".