texts: Understanding intra and extracelullar concentrations (membrane potential)

texts:
I have 4 question (not homework)

What happens to the cells membrane potential if:

a) Na+ outside rises by 40mM

b) K+ inside rises by 10mM

c) K+ outside rises by 10mM

d) A- (impermeable ion) inside rises by 100mM

e) Na+ outside decline by 50mM

So my answers are:

a – hyperpolarisering (more negative)

b – Depolarisering (more positive)

c – Hyperpolarisering

d – Depolarisering

e - Depolarisering

I think it like this:

Membrane potential is the DIFFERENCE in electrical potential inside and outside the cell. When we say a cell has a resting potential of -60mV we mean that the cell has 60mV LESS than the extracellular space.

So when I am asked what happens if all of a sudden, the extracellular space increases in mV (first question) then I can say that the difference is now GREATER than 60 mV, it is now in fact 100 mV, as the extracellular space has increased by 40 mV, then plussing the already established 60 mV.

Is this the correct way to think about these problems?


texts:
Could you help me solve this problem:
AAbbCC is crossed with aaBBcc and the offspring re-crossed with aabbcc. Considering that A and B are linked and their distance is 12 mapping units, while the gene C is not linked to them, find the percentage of the offspring that will have phenotype aabbcc.
I used this method to solve it (I know it's not correct but I don't know where I am mistaken):
P: AAbbCC x aaBBcc
F1: AaBbCc
AbBbCc x aabbcc
Since the distance between A and B is 12, their recombinant frequency is 12%
88% then is the recombinant frequency of the parental
Dividing by 2, 44% is the RF of parental AB/ab and 44% of parental aa/bb
In conclusion, since gene C is not linked, I calculated the probability to obtain cc from CC x cc, and that's 1/2
So my final result is: 0,44 x 0,5 = 0,22 = 22%


texts: Do insects' muscles become stronger with exercise?

texts: I am curious to know if insect muscles become stronger with exercise, because I have seen many insects get tired out, but I have never seen one get stronger. They always seem to become permanently weakened from excessive exercise. Do they get stronger like people do?


texts: Does chromosome cross occur over male and female or vice versa?

texts:
My understanding is homologous chromosome pair, which means male and female chromosome inside the DNA. So if that's homologous how does male do with female? Does it flip over and change direction, that could not happen as male chromosome 1 (say) is indistinguishable from female?
And what about the XY chromosome in male,say?
I know some are pseudoautosomal, but most are normal sex chromosome nucleotides.
So what about them?


texts: How are amino acids neutral at physiological pH?

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Amino acids with non‐ionizable side chains are zwitterions when they are at physiological pH, pH 7.4. This is what my book says. But I do not understand why. The Pka for a carboxyl group is around 3 and the pKa for an amino group is around 9. So the isoelectric point should be around ( 9+3) /2 = 6 for an amino acid with no ionizable side chain. At pH 7.4 it would be slightly negative, would it not?

Also what exactly is a basic amino acid? Is that an amino acid that has a PI value of more than 7?

Thank you.


texts: Why does it hurt when water touches cuts?

texts: Why do we feel a burning sensation when water touches cuts/wounds? People suggest applying oil over cuts while bathing to prevent water touching it, but water is heavier than oil so it shouldn't work, but it does, Why?


texts: Are there anatomical differences between male and female mammal brains before action of hormones?

texts: is there any evidences of these differences during development stages prior to hormone driven sexual differentiation? mice studies ?


texts: Selection of recombinant host by color selection method

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In recombinant DNA tech,
To select a recombinant host from non-recombinants, we have different types of techniques available.

The one I'm talking about is the color selection method with the use of 2 markers(one antibiotic resistant gene for eg. Ampicillin, and the other Z-gene).
We use Z-gene as the reporter gene.
We use vectorless E. Coli as the host cell here.

Now, when we add add Ampicillin to the petri dish containing all of the variants (transformants and non-transformants), - the non-transformants will die.
The transformants survive.

Now, we add X- gal to the replica of this petri dish, and we see some of the colonies turning blue due to the action of the enzyme β- galactosidase, which in turn is produced by the intact Z-gene in the plasmid.  That means our blue colonies are the non-recombinant ones.

My question is-

The medium taken in the petri dish should contain glucose too , shouldn't it? Otherwise the recombinants would too give the colour reaction (X-gal is a homolog of lactose) due to the Z-gene present in their chromosomal DNA (operon concept).

The question maybe silly since it's kind of obvious we have to supply basic necessities for the growth of bacteria(which obioviously is glucose).

Just wanted to confirm in case we don't have glucose available ! =p


texts: What is the relationship between protein-protein interaction networks and metabolic networks?

texts:
I am trying to find out how these networks can be linked together. I know that Protein-protein interaction networks and metabolic networks both fall under the Intra-cellular type of biological networks that describe the cellular functioning. But what is the relationship between them?

Thank you very much.


texts: Is $F_{ST}$ a probability and a correlation coefficient?

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$F_{ST}$ is one of the most famous and most important statistics of all of evolutionary biology. Yet, many people misunderstand it or misuse the classical results from the literature on $F_{ST}$ (Whitlock and McCaughley,1999).

Fixation Index in infinite islands model

In a panmictic population, the probability of identity by descent $F(t)$ in generation $t$ is the probability of sampling the same allele twice plus the probability of not sampling the same allele multiplied by the probability of identity by descent in the previous generation

$$F(t) = \frac{1}{2N} + \left(1-\frac{1}{2N}\right) F(t-1)$$

, where $N$ is the population size. Here I am assuming diploid population and no mutation. In an infinite allele model, these probabilities must be weighted by the probability that none of the parent migrated in the previous generation.

$$F(t) = (1-m)^2\left(\frac{1}{2N} + \left(1-\frac{1}{2N}\right) F(t-1)\right)$$

, where $m$ is the migration rate between any two demes. Setting $F(t) = F(t-1) = \hat F = F_{ST}$, assuming that $m$ is low and solving for $F_{ST}$ yield to the classic result from Sewall Wright

$$F_{ST} = \frac{1}{1+4Nm}$$

Definitions of $F_{ST}$

$F_{ST}$ was defined by S. Wright as

$$F_{ST} = \frac{var(p)}{\bar p(1-\bar p)}$$

, where $var(p)$ is the variance of allele frequency among population and $\bar p$ is the overall average allele frequency.

From Nei (1973)

  Wright showed that the variation in gene frequency among subpopulations may be analyzed by the fixation indices or F-statistics. He derived the formula
  $$1 - F_{IT}= (1 - F_{IS}) (l-F_{ST})$$
  where FIT and F1s are the correlations between two uniting gametes to produce the individuals relative to the total population and relative to the subpopulations, respectively, while $F_{ST}$ is the correlation between two gametes drawn at random from each subpopulation. $F_{IT}$ and $F_{IS}$ may become negative, but $F_{ST}$ is nonnegative.

Question

In the derivation of the fixation index in infinite island model, $F_{ST}$ is a probability of identity. In the quotation from Nei (1973) (and other sources), $F_{ST}$ is presented as a correlation coefficient. In Wright's and Nei's definition, I don't see the relation from the equations to either a probability or a correlation coefficient. Can you help to clarify this for me?

For example, I would expect that $E\left[\frac{var(p)}{\bar p (1-\bar p)}\right] ≈ \frac{1}{4Nm+1}$, where $E[X]$ is the expected value of the variable $X$. Can you demonstrate that this is true?


texts: What happens when cells in your body run out of telomeres?

texts:
In my biology book I read about an experiment where the genes encoding telomerase were 'knocked out', but they could still live a normal life and no adverse effects were noticed until the 6th generation of offspring (although it did not say what the effects were).

I have often often heard how longer telomeres indicate longer life potential, but what happens when you run out of them? Would rapidly proliferating cells be affected before others? Do the cells then just stop dividing or would they continue to divide? If they continue to divide what would the effects be?


texts: What species have had their genomes sequenced/are being sequenced?

texts:
The human genome project released it's first complete genome nearly ten years ago. Since then many species have also been sequenced.

I am trying to find a list of completed (and possibly ongoing/initiated) projects sequencing other species along with some very basic summary data such as number of genes (divided amongst the sex chromosomes and autosomes), length of DNA, number of chromosomes etc.

This is for a presentation I am giving at a conference and would make a nice addition to my talk.


texts:
Following from this question: What is the evolutionary advantage of death?:

Is there any evidence that human bodies have systemic self-destruction built into their developmental program? I'm not talking about the cell death response, which I know is an important part of growth, development and cancer prevention.

I've read some things about telomere-shortening but don't know if this is a cause or an effect.


texts: Why seeds won't sprout given excess water?

texts: What would cause a seed to not sprout despite showing signs of germination given excess water? Oxygen, temperature, and light were sufficient for germination and sprouting in seeds of a slightly lesser amount of water.


texts:
I am using the (one sample) capture recapture for estimating hidden human population. One sample method uses purely frequencies of capture to estimate population. One of my colleague suggested parametric bootstrapping method to assess the variability of the population size estimate. I tried to research online a little about this parametric bootstrap method but I just still don't understand how it is performed. I know bootstrapping is basically resampling data with replacement and then calculating the variance of it. However how do I perform parametric bootstrapping (I assume the frequencies of capture follows Poisson Distribution) on capture recapture data? Do we treat the frequencies as datas, i.e. so if f(1)=100 and f(2)=9, our data has 100x 1 and 9x 2 and then resampling this? Is probability of daily capture the parameter $\lambda$ in Poisson distribution?

I guess what I am trying to ask is, how do you perform the sampling bit of a parametric bootstrap [in capture recapture]?


texts: Estimating population divergence time with a single mitochondrial marker

texts:
Is it possible to estimate population divergence time with a single mitochondrial marker?

Here is additional information for my specific case:

Mitochondrial marker: Cytochrome Oxidase Subunit 1 (COI)
Molecular clock rate for COI for my taxon of interest: 1.29-1.96 % per million year
Age of the taxon: ca. 2.69 million years
Number of individuals per population: 10


texts: How can humans hear low frequency sounds using the cochlea which is tiny compared to wavelength?

texts:
Humans can reportedly hear sounds as low as 31 Hz. If we consider the speed of sound in air to be 1125 feet per second, then a sound at 31 Hz will have a wavelength of about 36 feet.

Normally, to capture a sound or other wave, we need an antenna that is at least as long as the wavelength of the signal we are attempting to receive.

But with the ear this is plainly not possible. If the cochlea of a human ear were to be unrolled, it would have a length of about 1 inch. Thus, in the sense of being an "antenna" it would seem to be far too short to be able to receive a 31 Hz signal, yet somehow it does.

How does the ear sense such low frequency sounds?


texts: Which direction are wild beehives combs oriented?

texts: Is it on the North-South axis, the East-West axis or some other orientation?


texts: What is meant by 'fixing' of an antigen presenting cell?

texts: Can someone please explain what does 'fixing' of an antigen presenting cell mean?


texts: Why should collected blood from patients be analyzed as soon as possible?

texts: I'm looking for the possible factors influencing blood samples. What happens to the blood cells esp. WBCs/PBMCs after 8 hours of blood draw? For example, I know that granulocytes may cause oxidative stress and that may affect the viability of WBCs. What else could have an effect on blood samples that we can't store them for a long time at room temperature?  Thank you.


texts: Pathogenesis of Chronic Venous Congestion in Lungs?

texts: I am thinking how CVC in lungs lead to the left-sided heart failure.


texts: How can a pathogenic bacterium be avirulent?

texts: Streptococcus pneumoniae R6 is a pathogenic bacterial strain but it is avirulent. How can a pathogen be avirulent. What does it mean if a pathogenic bacterium is avirulent?


texts: Evolution equations of a 2-gender age-structure model?

texts:
This sounds a bit complicated but I want to grab more feelings on age-structured problems. Less than 2 days to the exam so I appreciate any help.
So suppose we get 4 age classes in a population census and we don't count the people in the eldest age class again. We model females and males separately. Let $u_{i,n}$ and $v_{i,n}$ be the number of females and males in age class $i$ at census $n$, respectively. $s_i$ and $t_i$ are the fraction of females and males, respectively, surviving from age class $i − 1$ to $i$. $m_i$ is the (expected) number of children from a female in age class $i$.
If a fraction $\alpha$ of births are females and $1 − \alpha$ are males, what are the evolution equations for (1) $u_{1, n}$ to $u_{4, n}$ and (2) $v_{1, n}$ to $v_{4, n}$ respectively?

I tried putting forward the Leslie matrix for female: $$\begin{bmatrix} \alpha s_1 m_1 & \alpha s_1 m_2 & \alpha s_1 m_3 & \alpha s_1 m_4 \\ s_2 & 0 & 0 & 0 \\ 0 & s_3 & 0 & 0 \\ 0 & 0 & s_4 & 0 \end{bmatrix}$$ Is this correct?

If I try to repeat the thought process in part 1, we must use $u_{i, n}$ to write out the equations for males in the 1st age group, i.e. $v_{1, n+1}$ (unless both gender can give birth): $$v_{1, n+1} = (1-\alpha)t_1\left(\sum_{j=1}^4 u_{j, n} m_j\right).$$ Is this a way to determine "the evolution equation for $v_{i, n+1}$ in terms of the population structure at census
$n$"?

In case I have to find the gender ratio (e.g. for a certain age class or overall) in census $n+1$ or in long run, should I find the largest eigenvalue of both Leslie matrices for both gender, and proceed to find the respective eigenvectors for both gender, and then add the terms together to compare?

Thanks in advance.


texts: Could deutrium oxide be used to make organic compounds with Deutrium instead of hydrogen?

texts: I am wondering for prokaryotes if Deutrium Oxide could be made into Deutrium Glucose or other biological compounds with Deutrium.


texts:
GFP ( green fluorescent protein) can show green fluorescence. And its fluorescence is due to the tri peptide chromophore which is given in below I was wondering, can we observe fluorescence, if we denature it by boiling at 95 degree celsius? Say can we observe fluorescence band in SDS-PAGE?

I assume it can show some fluorescence as it is not due to any cofactors etc.


texts: Could biofilms float and survive in the sulfuric acid clouds of Venus?

texts:
The atmosphere of Venus is composed of 96.5% carbon dioxide, 3.5% nitrogen, and traces of other gases, most notably sulfur dioxide.
The main cloud deck is located in the 48-70 km altitude range and is composed mainly (75-96%) of sulfuric acid droplets, with a temperature of 27$⁰$C and a pressure of 0.53 atm at 55 km.
But to put the acidity into perspective, the mass loading of the droplets is 10 mg/m$³$, while the density of CO$_2$ at that altitude is about 950 g/m$³$.

Despite these harsh conditions for life, could biofilms float and survive there when certain bacteria species producing hydrogen could live within them ?

Nostoc commune for instance,is a  colonial species of cyanobacterium which forms a gelatinous mass for protection and can withstand acidic exposure and other extreme conditions like desiccation and high and low temperatures.
In addition the cells contain pigments that absorb ultraviolet radiation, which enables it to survive high levels of it, and in some cells nitrogen-fixing occurs.

There are also bacteria, like Enterobacter aerogenis, which produce hydrogen, and when it could live inside the gelatinous mass it could provide  the necessary buoyancy to float within the clouds of Venus.

Assuming the biofilms could be provided with the necessary trace elements, could they be airtight to some degree, to even float in the air with gas vesicles for buoyancy ?


texts: Are there any animal species other than humans & chimps that engage in tribal conflicts?

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i.e., between tribes within the specie.

(For chimps, see, e.g., https://news.nationalgeographic.com/2016/01/160130-animals-insects-ants-war-chimpanzees-science.)

Am seeking examples to develop taxonomy of such conflicts, e.g., for resource acquisition, enslavement, etc.


texts: What is the translation termination efficiency in mammalian cells?

texts: When I express proteins in bacteria I put at least two stop codons at the end of the gene to increase the termination efficiency. Is this the case in eukaryotic cells too? If I put a single stop codon is there a risk for the ribosomal complex to readthrough and continue translation?


texts:
What techniques do rats use to open a walnut? What are the traces they leave in nature?
I have a book on traces that wild animals leave in nature, but it only explains squirrels (splitting the walnut in two halves, using their teeth as a lever) and mice (gnawing a hole into the hull of the nut). I am interested in the two common European species of rats, brown rat (Rattus norvegicus) and black rats (Rattus rattus).


texts: Can organ-accumulated iron get shed again?

texts: Hemochromatosis can lead to an accumulation of iron in some organs. If the accumulated amount is not too high, will it go down again upon correction of blood iron levels?


texts:
We know that an action potential is produced by an active cell membrane when the stimulus reaches a certain threshold. When it does, an action potential fires, and when it doesn't, nothing happens.

There are dozens of videos online painstakingly illustrating this point, using examples going from plumbing to pebbles falling down a paper towel.

But this is such a simple idea. There doesn't need to be analogies. When I push a button, something moves, when I don't push it, nothing moves.

But what is the fundamental principle behind this? What biochemical device causes this all or nothing phenomena?


texts: Simulating Drug Entry in Protein and binding?

texts: Is there any simulation protocol or paper which can simulate the dynamics of drug entry and  interaction with the target protein?


texts:
I do not seem to understand the concept of Quantitative Trait Loci(QTL's), can anyone explain it to me in detail? Reading the wikipedia article helped somewhat, but I do not understand it well.

What I understand:

-quantitative traits = a number(quantity) of phenotypes(traits) that vary

-To "make" a QTL, one must "map" the phenotypical traits to the genes that they are believed to propagate.

-This is done by AFLP-PCR, or Amplified fragment length polymorphism, according to wikipedia at least. This process cuts the genomic DNA into pieces and then amplifies the target region with primers via PCR. Then it is visualized using some type of gel technique?

-I am not sure how this gel data then allows the mapping of phenotypes to genes. I know gel electrophoresis can help to identify the length of a gene or region of a gene if using a ladder to compare.


texts:
In my textbook, it is stated that after the closure of potassium voltage-gated channels and during hyperpolarization, potassium leakage channels allow potassium influx passively and this returns the cell to its normal polarised state. I don't understand why will potassium ions enter the cell against its electrochemical gradient ?

My textbook quote :

  during Hyperpolarizatio: The Leakage K+ Channels tend to drive the membrane potential from hyperpolarized state to the resting state as they drive K+ ions inward


texts: How does the number of chromosomes evolve through generations?

texts: Mitosis is a complex mechanism that, through mutations and crossover, determines how a chromosome is composed. But at that point, the number of chromosomes is already determined: how can this number evolve through generations? What mechanism is involved?


texts: I'm a runner (cross country) and I'm always amazed at how fast Olympic sprinters are. There's a lot of hype about those in the 100-meter dash being the fastest in the world, and we're constantly seeing the 100-meter time dropping. But is there a limit? How fast can human being, propelled only by its own energy (i.e. without any external assistance) run?


texts:
On average, how many cells divide each day in a human being?
How long does a cell wait before dividing itself ?

I have tried to look on the internet but surprisingly the answer is difficult to find..


texts: Would boiling water kill microorganisms in clothing that had feces spilled on it?

texts:
Lets say there is a piece of clothing that had a small amount of human feces that spilled on it.

Would placing that clothing in boiling water destroy the microorganisms on that clothing?


texts: Can nature create codes and specified complexity?

texts:
Is there an example of nature creating codes or specified complexity? It is said by Creationists that codes can only come from minds, and since DNA has a code, it was created by a mind.

Is this true? If false, can you explain how unguided, unintelligent nature could create coded specified information? Just as a note to show where I'm coming from, I am an Evolutionist.

But I have to admit, this appears to be a very, very strong argument in favor of special creation by an intelligence.


texts: Microarray chips allow us to conduct many expression experiments in parallel to each other but they can be used only once as far as i know. Are there reusable microarray chips? Have people ever tried it? If there are, are they becoming more common? If people do not choose to use them even though they are in the market, what can be the reasons?


texts:
Is there more pressure on the heart when lying down flat as opposed to lying down with head and knees slightly elevated?
Also is there more pressure on the heart standing up as opposed to lying down in either a flat or with head and knees slightly elevated


texts: How to give a biological interpretation to this phase portrait?

texts:
Consider the following system and analyze its behavior.
$$\begin{array}{rl} \frac{dA}{dt} &= A \left( 2-\frac{A}{5000}-\frac{L}{100} \right)\\ \frac{dL}{dt} &= L \left(-\frac{1}{2}+\frac{A}{10000} \right)\end{array}$$

The analysis
It has $3$ equilibrium points. I know the stability of the three points but I am not sure if I interpret the meaning of them correctly according to the phase portrait. $x_1, x_2$ are saddle points and $x_3$ is stable point they are
$$\overline x_1=(0,0)$$
$$\overline x_2=(10000,0)$$
$$\overline x=(5000,100)$$
According to the phase portrait I think the behavior of the system is described as:
For every point $(A,L)$ given in the first quadrant, where $A$ is the number of aphids at time $t$ and $L$ is the number of lady-bugs at time $t$, we'll have that in the future, the maximum number of lady-bugs and aphids it's going to be $(5000,100)$ respectively. This also means that both population will never going to extinct.
Even in the case where there were just a few number (near 0) of lady-bugs, their population will grow and will be establish also.
My question
Did I miss something important in the biological description to the phase portrait?


texts: Could anyone please identify this Indian bug?

texts: Photographed by a friend recently in central India. next to Panna Tiger Reserve.


texts: Is plaque formed even if you do not eat anything?

texts:
Some people report that their gum and dental health improves when they are fasting. Many forums contain crazy amounts of misinformation and claims which are unsupported by serious scientific research, so many people attribute various effects of fasting to their body being "purged of toxins" and all sorts of other nonsense.

I have noticed one of these effects on myself when I'm fasting - my teeth get somewhat sticky in the evening. The same effect is reported by many people on the aforementioned forums. On normal days when eating food, this does not happen.

It's pretty certain it's not some sticky toxins being excreted by the teeth. So what is it? I strongly suspect that it's just normal plaque, which would otherwise be abraded by chewing on food. But I always assumed that plaque is formed by food remains in the mouth, so it leads me to the question:

Is plaque formed even when one does not eat any food?

Citations of scientific literature are welcome.


texts:
In glycolysis, 2 ATP molecules are produced from each triose phosphate molecule (to give a total of 4 ATP produced; 2 net produced as 2 were initially used up in the reaction).

I don't understand how this would be the case, as each triose phosphate only has one phosphate group available to form ATP from ADP, meaning that one ATP is produced per triose phosphate. I know this cannot be the case as this would mean a 0 net production of ATP defeating the purpose of glycolysis, but i can't get my head around why.

out of curiosity, would the other remaining two phosphates that are required come from other sources, i.e. 2 phosphates + the 2 phosphates already from the two trios phosphate molecules to give us the 4 ATP molecules (2 net ATP)

Many thanks in advance.


texts: The second law of thermodynamics and the cell (3 questions)?

texts:
How is that the cell maintains internal order, yet it discharges heat (disorder) to the surrounding?
If the cell is supplied with materials for metabolism and growth by the surroundings (disorderly environment), then how does that disorder generate order inside the cell?
When we zoom out from a single cell to a multi-cellular organism, will the net value of internal order of cells decrease disorder which would contradict the 2nd law of thermodynamics?
Note:I would appreciate serious informative answers. The questions are important for me no matter how silly they may look like for you.


texts:
This may sound trivial, but...

Protein is sourced from plants and animals. Pepsin and HCl digest meat (animal protein). Does pepsin also digest plant-based proteins?

I took a look at few articles online and this. None seems to explain what I am after.


texts: Mitochondria variability per tissue in humans?

texts: I would like to know the distribution of mitochondrial content per tissue type in humans. I understand the simple metric that energetically active or energy requiring tissues will have more mitochondrial content, however is there any study/link for a more quantitative estimate ?


texts: Consider a codon of the form NNK (where N = Adenine, Cytosine, Guanine or Uracil & K = Uracil or Guanine).  How many codons are now available? I know if all were available there would be 4^3 = 64 codons. How many are possible now? When I have tried combinations manually I got it to be 32, is this correct?


texts: Identifying a creature that appears to be a worm wrapped in a cocoon

texts:
This creature was found on a bed. At first, I thought it was a piece of lint, but then it suddenly moved. I picked it up in a paper towel and put it in an eye cream containers, which it is currently in. I believe this means that it is pretty strong, since it appeared to have pulled itself all the way up from the floor, to the top of the bed, then across to the other side of a King-sized mattress.

It appears to be a worm wrapped in a cocoon. It is pretty short, being small enough to fit inside an eye cream container.

The creature is a pale yellow-white/cream, with brownish-red tips on each end (unless it can somehow turn around without exiting its casing). It looks from the side as if it has a rather flat face, one that comes to a slight bump at the bottom, but is pretty much flat. The casing is light grey, with some small portions that appear to be almost the same color as the organism, just slightly darker. There is an opening at each end of the casing, which the organism uses to slide slightly out. It has never fully come out of the casing. The edges of the openings at each end are white. The casing seems to either be made out of or covered in dust.

It can create a substance that is sticky and strong enough to support its weight. I cannot tell if the substance is created by the 'worm', or the 'cocoon'. A thread at each end of the casing is connected to the side of the container by the substance. When I accidentally detached one end of the casing, the entire thing began to shake violently when held so that one end was hanging. It wouldn't stop until I had turned it so that both ends were touching the side of the container. Within minutes, though, it had reattached the broken end. Minutes. Not hours, but one minute.

The holes at each end of the cocoon can either grow or shrink closed. I believe this allows us to tell which opening is in use. If it is nearly shut, it will come out the other end.

It appears to be nocturnal, since it doesn't move during the day, but it is very active at night. It also appears to react to light. If some is put on it, it will poke out to look around.

It has survived for four days straight without food, as far as we know. We put a small piece of lettuce in with it. However, there are two small, brownish things on the bottom of the container. This may be its excrement.

The creature moves by reaching out with its 'tentacle/worm', grabbing onto something (including the ground), and pulling itself forward.

I cannot tell if the creature is attaching to the container's side to climb, or because it is morphing. If that is the case, then the outer shell may be a cocoon. It did detach itself from the side of the container, and first hid under a ledge of lettuce, but now has wrapped itself in lettuce.

To summarize: can someone please help me identify this creature?


texts: What do ants do with human finger nails?

texts:
There is place in my house where I cut my nails. Here, there is an ant hole where an ant colony is seen.

Whenever I cut my nails from here, they take my nails inside their hole. I was wondering what they do with them.

Do they protect their houses with them or feed them to their young ones?


texts: Can bacteria be killed by purely physical trauma?

texts:
In a question over on Skeptics Stack Exchange, I half-jokingly listed "blunt force trauma" as a means by which a bacterium could be killed. That makes me wonder if it really is only a joke or whether such an assault is plausible. The webcomic xkcd also did an episode on the possibility of physically attacking a cell (though not a bacterial one).
There are plenty of resources on how bacteria can die from biological processes (e.g. infection with a bacteriophage, biological effects of antibiotics, etc.), chemical attacks (e.g. membranes getting lysed with bleach), temperature (i.e. cooking), and radiation, but have bacteria ever been shown to be vulnerable to a direct physical assault such as being hit with a hammer, cut with a knife, thrown onto a hard surface, twisted until they burst, or being drawn and quartered?
I do know that many common weapons that are generally effective against animal life (swords, axes, clubs, assault rifles, etc.) do not have the exact same properties at the microscopic scale, but does that mean that physically beating a bacterium to death is absurd or is there a known way to kill a bacterium using only physical force?
To be clear, I recognize that our normal means of killing unwanted bacteria - cooking food to prevent food poisoning, treating bacterial infections with antibiotics, cleaning hard surfaces with bleach, applying rubbing alcohol to wounds, etc., are probably effective enough that most people don't bother pulling out that old Wild West six-shooter they have in the closet or the antique sword hanging on their wall the way they might consider them if attacked by a bear or wolf, but that's not the question.


texts:
One of the tenets of Darwin's theory is the survival of the fittest, ie adaptation of features that allow a species to adapt better to its surrounding environment. I am wondering that given the right conditions, is there a possibility of a more "complex" species, say humans, back-evolving into a less "complex" species, say a dog? Is there anything in Darwin's theory or some experimental proof that excludes such a possibility?

EDIT (4/19/12): Thanks for all the responses! I definitely agree with the fact that we are no more complex than dogs or Drosophila, hence the quotes surrounding complex in the question. I learnt a lot from the answers and don't think there is any one answer that is the best, but read together, they drive home the point. Thanks all!


texts: HIV and effectiveness of inhibitor cocktail over single inhibitor

texts:
I'm looking for clarification on the answer to this question. It's in my biochemistry class but I figured this is more Biology than Chemistry, so I'm asking it here.

The question is:

  One of the more effective treatments for HIV-positive individuals has been for them to take
  protease inhibitor cocktails. Certain proteases are required for the virus to mature and these inhibitors prevent them from functioning. A cocktail of inhibits means that numerous inhibitors are used at once. Why would a cocktail be more effective than a single inhibitor?

My answer to this is that there could be more than one mutation of the virus, and with each mutation a variation in specific protease. So, the protease cocktail would defend against a wider range of the mutated virus.

Is this correct? Is there an answer that might involve describing epitopes?


texts: Finding out the best concentration for my plant extract to be used as drug for diabetes

texts: I am using plant extract of Ajuga parviflora and found out that it possess anti-diabetic properties by using alpha-amylase inhibitory assay. I used various concentration 250 µg/ml(29% inhibiton of alpha-amylase), 500µg/ml(37%),750µg/ml(46%) and 1000µg/ml(63%). Basically, alpha-amylase results in increase in glucose level after eating food. So  i wanted to know that how could i find out that what is the best concentration of my plant extract to be used as drug.


texts: The human organism knows what we have to eat?

texts: My mother has told that if your organism needs a vitamin, you want fruits include that vitamin. For example you have lack of C-vitamin you would like to eat lemon. Is there any explanation for it, or just it is a myth? The human organism knows that what we have to eat?


texts: What's the point of glycolysis in fermentation?

texts:
In order to initiate glycolysis, 2 ATP are necessary. In the glycolytic process, you generate an additional 4 ATP, which results in a net gain of 2 ATP.

If you don't undergo glycolysis, however, then you have an extra 2 ATP not being used. If you do glycolysis, you still got only 2 ATP. Am I missing something here?


texts: By what mechanism can hypoglycemia induce fainting?

texts:
Hypoglycemia (Low blood sugar) is said to be among the potential causes of human-faintings. I was wondering by which mechanism this happens. Google search results are abundant; there are lists of various causes and solutions, but I couldn't find a direct answer to my question.

Is it a controlled reduction of heart function to save energy? Is it an uncontrolled shock reaction (malfunction)? I'm looking for an answer along those lines.

Thanks.


texts: Hypothalamic breakdown and effect of temperature on membrane lipids

texts:
I'm in my last year of high school and doing a research assignment on thermoregulation. In the excellence level exemplar for the standard, a student made the statement:

  Once the body's internal temperature is well above the optimum range, important enzymes start to denature, phospholipids start to destabilise, and cell membrane lipids begin to dissolve. As a result of this, important organs in the trunk of the body are unable to carry out important metabolic processes. If the temperature continues to rise it causes tissue damage which could cause disability depending on its severity. It also causes the hypothalamic thermostat to break down, meaning the body can no longer have control of the core temperature.

However, I have been unable to find any sources which mention destabilisation of phospholipids or the dissolving of membrane lipids. I have also not found anything on tissue damage or the cessation of the hypothalamic thermostat.

Are these things true? And if so, could someone please direct me to a reliable source which states this?


texts: Influence of eating at late night on sleep

texts:
I have often heard the saying that one shouldn't eat a mountain of food because blood will go to the stomach and it'll be difficult to sleep well because the stomach can't rest at night.

I see that the blood goes to the stomach when you eat something to digest the food. Have any studies been done on whether it does actually affect the quality of sleeping?


texts: what is the classification of this stream insect?

texts: This insect I found from Southers region of Bangladesh. Its limbs are larger than its body.and the picture shows its dorsal part.


texts: How does the bear mother ensure her cubs don't escape during hibernation?

texts:
I have some questions relating to bears- more specifically, the brown bears we have in Scandinavia.

When they go into hibernation, do they fall asleep as we know falling asleep? If a bear mother brings her cubs into the den, how can she keep track of them? How can she make sure they don't wake up, leave the den and get lost in the snow?


texts: Can we change one's genome into the genome of somebody else

texts: If I (grown-up individual and not just an egg after fertilization) wanted your exact genome, would we be able with today's technology to change my genome into yours?


texts: At what point, when connected, do DNA strands become a helix?

texts:
When synthesizing DNA strands and beginning to "connect" them, how quickly does it become a helix?

In this answer, canadianer says

  The helical structure is more stable than the "straight" form (because of base stacking interactions), and so it forms spontaneously.

This then makes me think of the following scenario: say one is constructing two strands of DNA out of deoxyribonucleotides. Then, one begins connecting them with hydrogen bonds. Before the hydrogen bonds are added, my understanding is the two strands would be straight and not helical (if this is wrong, please correct me on this) so at some point as the two strands are connected, it would "spontaneously" become helical.

The question, then, is at which point. After one "connection"? Two? All of the connections necessary to complete the piece of DNA?


texts: Does body temperature affect human lifespan?

texts:
If a human body were somehow to be kept at a cold temperature (say 30C) for the entire life of the given individual. And somehow the brain could be fooled into thinking that this 30C feels nice and warm.

Would that given individual live longer as a consequence?
What effect does a tempreature have on lifespan?


texts: Are there hybrids that emerge as a new species?

texts:
We know a couple of hybride (mammal) animals (http://www.rantpets.com/2015/06/03/15-strangest-hybrid-animal-breeds-you-didnt-know-existed/) and perhaps even more and perhaps even insects like the Drosophila.

But are there animals which arise as a new species? And by species I mean animals who can't breed with the species of their parents but can interbreed succesfully with their own species ('brothers' and 'sisters'). Only leaving out pre-mating mechanisms in case they don't get offspring (so that only Post-mating isolating mechanisms counts)

See also: Have we ever observed two drosophila lineages that evolved reproductive isolation in labs?
Have scientists ever produce a new species in laboratory by means of natural selection?


texts: Are there any drugs that target the lipid envelope of viruses?

texts:
Many drugs go after the unique viral enzymes but do any target their lipids? Viral membranes are of course similar to the host membrane but might have a different composition and do have a different curvature and protein composition. Is anybody aware of research or even existing drugs that attempt to hit the lipid envelope of viruses to limit them?

There are evolved molecules that target the lipid membrane, for example. A subgroup of those pore-forming toxins are cholesterol-dependent, so they might target a membrane high in cholesterol over one low in it. I'm trying to think out of the box here whether properties of the viral lipid membrane could be exploited in a similar way.


texts:
We have this cute little tree in our front yard (Denver CO):

Unfortunately we have to get our water main replaced and this tree lies right in the path of destruction. Anybody know what species it is? And, in your opinion, is it worth saving?


texts: How are bubbles formed and how do they make dough rise in bread?

texts:
So we took in biology that carbohydrate is broken into $\ce{CO2}$ and ethanol. But all I see in my mind here is that since gas is inside the dough then the gases will try to get out expanding the dough and rising it and I know that ethanol will rise as it is baked. However I am not sure how and why are bubbles formed in the first place or how they're related to this at all and does the ethanol taste stay in bread or is it completely removed once rised?

I heard on another resource that;
"It is because air bubbles get stuck inside, and when the bread bakes, the holes appear."

How does bubble getting stuck inside lead to holes appearing? it is confusing me.


texts: Anaerobic Respiration vs Aerobic Respiration during physical activity

texts: So I was wondering about the difference between aerobic and anaerobic respiration on the context of burning calories. While swimming we can choose to keep our head up and breathe, or keep our head below water for a stretch. Which will burn more calories for that time and why? And does anaerobic respiration cause fatigue of the brain due to insufficient oxygen?


texts: How does estrogen influence collagen synthesis?

texts: Through what mechanisms does estrogen interact with collagen synthesis? Especially in the context of elevated estrogen levels and genesis of purpura simplex .


texts: What is the proper quick freezing /snap freezing protocol for pancreatic tissue?

texts:
I would like to do a quick freeze on pancreas from mice. I want to then make sections (30 µm thick).  The idea is to preserve a fluorescent staining done in vivo.

I do not know if I should place my fresh tissue directly into liquid nitrogen, then embed the tissue in OCT, and then freeze everything in cold isopentane?

Or do I have to embed the fresh tissue in OCT first, prior to putting everything in nitrogen?

Or is there another protocol to do quick freezing in order to do sectioning?


texts: Are dominance hierarchies always maintained through violence?

texts: Is there a species in which a dominance contest cannot escalate to a fight? I don't know of any but I'm not a biologist.


texts: Why did they expect Astronaut Scott Kelley's telomere shortening to accelerate? (they got longer!)

texts:
The NPR News article and podcast Scientists Share Results From NASA's Twins Study says:

SCOTT KELLY (NASA Astronaut): You know, the symptomatic stuff is fine. I don't have any long-term negative feelings, physically, from being in space. Now, there's the things you can't feel. And hopefully, I will never learn that those are a problem.
GREENE (Host): Those things you can't feel - well, it turns out they are as small as the protective structures at the ends of his chromosomes.
MARTIN (Host): Yeah. These are called telomeres, and normally, they get shorter with age. But what about in space?
SUSAN BAILEY (Principle Investigator): What we wanted to do was evaluate telomere length in both of the twins before and after so that we could see, you know, where they started and then where they ended.
MARTIN: Susan Bailey was one of the scientists who answered this question. She expected the stresses of space to shorten telomeres quicker.
BAILEY: And, in fact, we saw exactly the opposite thing - that during spaceflight, he had many more long telomeres than he did before he went up. So that really couldn't have been more of a surprise to us.

See also Radiation Biologist Dr. Susan Bailey Studies the Cellular Clocks of Astronaut Twins
Question: Why did investigators initially believe that Scott Kelley's year in space would accelerate the rate of telomere loss, relative to his baseline rate and the rate of his identical twin brother on the ground? What would be the postulated mechanisms?


texts: How can mosaic segregation be used in C. elegans? Can it tell us where a given gene is expressed, or needs to be expressed for worm survival?


texts: Strength of Female Chimpanzees vs. Male Chimpanzees?

texts:
Where can I find studies done on the strength dimorphism between male chimps and female chimps?

For example, "one-arm pull strength is 300 pounds for male chimps and 200 pounds for female chimps"


texts: Is the autonomic nervous system only activated by internal stimuli?

texts:
My professor claims that the autonomic nervous system is only activated by stimuli from organs but I really feel like I've read that it can be activated by outside stimuli, although I'm not sure what receptors that would be.

Is my professor right?


texts:
As far as I know and could understand from reading about HIV, T helper cell is one of the main reasons to develop AIDS in patients infected with HIV virus, that because the absence of helper T cell suppresses the immune system because no T cell cytokines released to allow other white blood cells to attack or release antigens.

Q1. Did I understand it correctly?

Q2. Now if my understanding is correct, why don't scientists find a way to produce T cell cytokines in the lab? and then inject it to patients with HIV? wouldn't that in theory revive the immune system and perhaps heal them or at least make them live longer?

P.S. My knowledge is close to nothing in this topic, so excuse me if the question itself is wrong :)


texts: Prader-Willi Syndrome and Angelman Syndrome?

texts:
On the website http://www.whatisepigenetics.com/fundamentals/2/ it states that

  the imprint disorders Prader-Willi syndrome and Angelman syndrome, display an abnormal phenotype as a result of the absence of the paternal or maternal copy of a gene, respectively. In these imprint disorders, there is a genetic deletion in chromosome 15 in a majority of patients. The same gene on the corresponding chromosome cannot compensate for the deletion because it has been turned off by methylation, an epigenetic modification.  Genetic deletions inherited from the father result in Prader-Willi syndrome, and those inherited from the mother, Angelman syndrome.

To me it seems like this is suggesting the same problem in both Prader-Willi and Angelman sydrome- lack of expression of a particular gene. However in Prader-Willi syndrome it is the paternal chromosome that is missing and the maternal copy of this gene is silenced by methylation and the reverse applies for Angelman syndrome. Therefore it seems that in boh cases the problem is the lack of expression of this gene. Why, then, if both are caused by lack of expression of this gene, do these two illnesses have such different symptoms (constant hunger in Prader-Willi syndrome and mental disability and jerky movements in Angelman syndrome)?


texts: Difference between dysentery and bloody diarrhea

texts: The difference between diarrhoea and dysentery is quite clear; but the appearance of blood in stool or bloody diarrhoea is a very confusing term when compared with dysentery. Are they different in the amount of blood or their etiology or pathogenesis or something else. I searched a lot in the internet and medicine and pathology books but nowhere I could find a straight answer. If anyone knows about it please reply with proper reference and values (if its about the amount).


texts: What is the maximum amount of different bacteria in the drinking water in Europe?

texts:
I am looking for a statistical amounts which are allowed.
Some students say it is 0 for all bacteria, which I think is false.
I found this USA source.

I found there

Total Coliforms (including fecal coliform and E. Coli) mg/l. No more than 5.0% samples total coliform-positive (TC-positive) in a month.
Giardia lamblia: 99.9% removal/inactivation.

What is the right place to look for such information?


texts: How does an antisense RNA molecule restore protein function in CF patients?

texts:
I am researching a treatment for cystic fibrosis (CF) called Eluforsen and I am trying to understand the mechanism by which an RNA molecule can restore proper protein function. In many research articles I come across the same sentence:

"Eluforsen, is an antisense RNA oligonucleotide designed to bind specifically to the mRNA region around the F508-encoding deletion and to restore CFTR protein function."

But I cant find any literature explaining how an antisense RNA molecule can restore function of a protein on its own. When I think of antisense RNA I think of  RNA interference not restoring protein function.


texts:
What is the name of the marine egg or living being that is transparent like a jelly fish or a Venus girdle, with a shape like a DNA or better like a chain of infinites, long as half of a hand and large as half of a hand nail?

Imagine a DNA-like strand but with no internal "sticks", white-ish, 10 cm long and 2 cm wide

Alternatively, how do I narrow my research in order to find the name of what I saw underwater?

The image seems too simplified but I just saw something like that, pretty simple, essential and little.


texts: What are most common natural causes of death?

texts: What are most frequently occurring natural causes of death?


texts: Does creatine-phosphate (CP) supplementation regenerate NADH?

texts:
I have the following facts:

It is possible to convert ATP <-> creatine vice-versa. (ref - non scientific)
CP supplementation protects against metabolic syndrome. ref1 ref2
Fructose digestion depletes NADH via TG synthesis. ref

I assume that CP supplementation regenerates not just ATP, but NADH, if it is depleted, and so it restores the redox balance in the liver. Both ATP and NADH are similar energy storing molecules, so I guess there is a biochemical pathway which converts ATP to NADH, or there is a pathway, which regenerates NADH using CP. Am I right, if so, which pathway is it?

note:

I might be wrong. From one of the references:

  Taken together, this study provides direct evidence that creatine reduces lipid accumulation in hepatocytes by the stimulation of fatty acid oxidation and TG secretion.

So maybe ATP is enough to prevent TG accumulation in the liver.


texts: Humans have nails, horses have hooves - but they are always exposed. Why are cats' claws retractable rather than always exposed? Is it related to "Why are there nail growth differences  between humans and other mammals?"?


texts:
Firstly I would like to apologise if this is not correct place to ask this question, as it can be seen more as chemistry and not biology question.

I was looking around for data on psychedelic substance called 25i (25I-NBOMe) . It was fist synthesized in 2003 and is somewhat 'new'. I have found some data on overdoses and they are few, however I could not find any specific data on mortality to dose rate nor on LD50 (Dose where 50% of people would die). Wikipedia is quiet in this regard.
Judging by the dosage it being active in sub-milligram doses (600–1,200 µg) it should not be very lethal compared to most, should it?

Where could I get data on LD50 for 25i (25I-NBOMe)?


texts: Why isn't meiosis II called mitosis (as the chromosome number doesn't half)?

texts:
Meiosis: a type of cell division that results in four daughter cells each with half the number of chromosomes of the parent cell, as in the production of gametes and plant spores.
Mitosis: a type of cell division that results in two daughter cells each having the same number and kind of chromosomes as the parent nucleus, typical of ordinary tissue growth.

After meosis II we have the same number of chromosomes as before. So why isn't meiosis II called mitosis instead?


texts:
It is commonly accepted that birds are descendants of dinosaurs. It is nice that not all dinosaurs died out.

Are there other animals, descendants of dinosaurs,
 that survived ? (Maybe not till our time, but survived the time when most dinosaurs died).

By the way, what made flying dinosaurs survive and not die like other dinosaurs?


texts: Why do we blink instead of winking each eye independently?

texts:
Question

Why do we blink both eyes at the same time rather than winking each eye as needed?

Why would winking independently be better?

The benefit would be a minor improvement whereby a person would receive continuous sight of the area of vision shared by both eyes.  I'd also assume that it would be more likely for the wink-as-needed mechanism to evolve than the blink-as-needed mechanism were there no benefit to blinking over winking.

Why then has evolution favoured blinking?

My guess at why is that the overhead on our brain of switching between binocular vision to monocular vision is more significant than the overhead of momentarily pausing our visual processing.

I also believe that some animals don't blink, but wink; e.g. chameleons.  This supports my theory as their eyes operate independently, so their brains would have to cope with the variance in each eye's information anyway.  That said, their wink is different; i.e. they roll their eye inside their head, rather than having an eyelid.

Research so far

I found a couple of Reddit posts:

https://www.reddit.com/r/explainlikeimfive/comments/2kzx4s/eli5_why_does_blinking_take_me_almost_no_effort/ - explains why blinking is easier than winking; but only based on how we are rather than how we got there (i.e. why evolution would have resulted in different muscles for winking vs blinking).
https://www.reddit.com/r/explainlikeimfive/comments/3mijgw/eli5_why_do_we_blink_with_both_eyes_at_same_time/ - doesn't have any hard fact answers; just discussion of opinion.


texts: Is homocysteine converted to glutathione during oxidative stress?

texts:
From the paper titled "The basis for folinic acid treatment in neuro-psychiatric disorders" by Ramaekers et al., 2016:

  On the left side of the figure, the purine metabolite GTP serves as the substrate for the GTP-cyclohydrolase I enzyme (GTPCH) to produce tetrahydrobiopterin (BH4), which is the co- factor for enzymes producing dopamine, serotonin and NO.
  At the upper right of the figure the trans-sulfuration pathway is shown.
  It converts accumulated homocysteine to the anti-oxidant glutathione during oxidative stress.

Is this so? Is it true that this pathway is only active when the cell is under oxidative stress conditions?

Or maybe the authors meant to say that the pathway converts homocysteine to glutathione, which is later used to counteract oxidative stress?

Here's the figure from the paper:


texts: Has the gestation (pregnancy) period for humans always been 9 months?

texts:
At this point in our evolutionary progress, the expected human gestation period is (roughly) nine months long. My question is, has this duration of time always been the same for homo sapiens? Or, are pregnancies getting longer/shorter?

My attempts so far: upon searching online, I was only able to find a single reddit thread, of which didn't provide much of anything. And then, on Wiki's page for gestation it provides a link that should contain content on the "evolution of gestation related features for mammals", however, the link revealed itself to just be a page that outlines all mammalian evolutionary developments, and I'm not able to find the forementioned gestation specific information within it.


texts: Why do fruit flies go so close to large reservoirs of liquid when they are likely to fall in due to surface tension?

texts:
I had accidentally left out half a glass of red wine by the windowsill when I went to sleep. As anyone knows, if you do this with a window cracked you will get quite a few fruit flies near it in that time(region dependent obviously).

I noticed that many of them had simply fallen in as there was nearly nothing on the sides of the glass. What causes this behavior in a likely death scenario? Is it only exhibited during extreme hunger? Would this also not likely be an evolutionary cost or is that outweighed?


texts: Is there any specific reason behind why we dream? Why do we sometimes get weird and unusual dreams? Sometimes we can't even recall what we dreamt of. Why does this happen?


texts:
Why do babies of any mammal tend to play ? From humans to small dog pups, cubs of a lion, baby bears, etc.

*I am not sure if the tag I chose is correct or not. Please correct me if I'm wrong.


texts:
I notice many wikipedia articles, courses, pathway sites use a different abbreviation for the same enzyme. Eg: Wikipedia lists the abbreviation of phosphoglycerate mutase as PGM, whilst wikipaths lists it as PGAM in the glycolysis pathway. Then there's enzymes like glyceraldehyde 3 phosphate abbreviated either as GAPDH or G3PDH. This has led to many confusions, particularly when the enzyme abbreviation is completely different to the gene abbreviation, eg: protein kinase A (PKA).

For the official names of genes, I'm using genenames.org. I thought it might be common practice to abbreviate an enzyme with its gene abbreviation, but I see this is problematic due to many enzymes being encoded by multiple subunits and genes from different locations.

Is there a site, or a way, to unambiguously know the correct, and most widely recognized, official name/abbreviation for an enzyme, like there is for genes?


texts: What is the relevance of the constant in the clearance equation?

texts:
I have seen the equation for drug half lives described variously as (0.7xVd)/Cl, (0.693xVd)/Cl, and (ln2xVd)/Cl.

What is the origin of this numerical constant in the numerator? What does it signify?


texts: Mutation Rate in Multicellular Eukaryotes

texts:
I always hear people saying that the mutation rate is around $10^{-6}$ or $10^{-7}$. I don't even know if this number is the mutation rate of genes or of a single nucleotides and I actually (almost) never seen a referenced estimation of the mutation rate.

I know there is an impressive variance in mutation rate depending on the species we look at and depending on the genomic region we look at. Various other factors also influence the mutation rate such as ecological factors (thermal stress for example).

In multicellular eukaryotes, what is a good estimate of the mutation rate per nucleotide, per gene and per genome? How does real values vary around these estimates?


texts: Do squirrels and blue jays play a role in oak tree distribution?

texts:
White oak (Quercas alba) acorns have lower tannin levels than red oak (Quercas rubra) acorns, therefore animals tend to eat the white oak acorns before red oak acorns.  Animals such as squirrels and blue jays will often catch red oak acorns for later consumption when the tannin levels have lessened or when food sources are scarce.  Since red oak acorns are more likely to be hauled off, cached, and forgotten about wouldn't this cause red oaks to be more widely dispersed than white oaks?  By this I mean that white oak trees would be spaced closer together than red oaks.

Source 1: https://www.allianceforthebay.org/2017/09/the-complicated-relationship-between-acorns-and-animals/

Source 2: https://link.springer.com/chapter/10.1007/978-1-4419-0378-5_6?no-access=true


texts: Why is human vision restricted to 400-700 nm?

texts: Across the electromagnetic spectrum, 400-700 nm is a narrow spectrum of frequencies and focused in the region of short wavelengths. For example, radio waves cover a large range of frequencies unexploited by the visual system. So what biological reason is there that evolved us to use such a small frequency bandwidth for vision?


texts: What do you call that part of the muscle that connects directly to the bone?

texts:
When you open up a chicken leg or a clam and you remove the meat, there is this little part that is connected to the bone and is not easily scraped off.

What is this part called and what mechanism does it use to connect to the bone or the shell?


texts: How can microarrays be used to quantitatively determine level of gene expression?

texts:
This is probably a stupid question because I don't fully understand how microarray experiments work. I'm trying to understand how microarrays work but I'm confused about something which I can't seem to get around without fully understanding how microarrays work, which seems impossible without understanding this.

I understand the principle of how microarrays work. But I don't get how microarrays can tell you how much mRNA is expressed in one kind of tissue vs another kind of tissue. Wouldn't that depend on how much tissue you started with? So if you started with more cells of one kind you will get more mRNA/cDNA and so the intensity of fluorescence at the corresponding spot on the microarray will be greater. So even if the amount of gene expression is lower in one type of tissue the corresponding spot on the microarray might show a greater fluorescence intensity compared to the other type of tissue if more tissue was used.

Also another related question: if you put the mRNA you obtain from cells through PCR will you get the same proportion of mRNA as before PCR? From what I understand PCR can be used to make more mRNA before doing the microarray but because PCR is a random process I'm not sure if it will affect the proportion of mRNA.

Hopefully my questions make sense.


texts: Staining cells for FACS at 4 degrees or ambient temperature

texts:
I'm sorting a 293 derived line. One thing that is worrisome for me is cell viability after the sort. Usually I have been staining and washing at room temperature (on the benchtop) on a nutator. I have been reading that most sorting procedures indicate that you should be doing this at four degrees in the dark. It is my understanding that this helps with clumping, but is this at the expense of viability? Does the cold cause these cells to apoptose?

Currently my procedure is the following -

Using HBSS + 1 mM EDTA + 1% BSA (sort buffer) I suspend approx 10-15 million cells per/mL.

Stain with primary
Spin at 300 x g for 5 minutes
Add 15mL of sort buffer, spin again
Stain with secondary in 1 mL of sort buffer
Wash x2 with 15mL
Strain
Sort

One thing I can do to minimize cell death is do a live/dead stain (we just added that capability). The other thing I read was to use 50% FBS in your collection tube.

The other thing that might be of concern is that if we are doing many sorts, then some of the tubes may be sitting in sorting buffer for a long time in the queue. How long is too long?

Lastly, we use puromycin and blasticidin as selection markers for our libraries and we usually add these right to the sort after we replate. Should we wait a while?

Thanks for the advice


texts:
Now, before you flag this question as blatantly off-topic, I claim to have a scientific basis for this(!): not some drug or remote control, but parasitic infection.
While reading about behavior altering parasites and parasitoids, I found this:

Parasites that induce behavioral changes in their hosts often exploit the regulation of social behavior in the brain...For example, Toxoplasma gondii attaches to the hypothalamus rather than target a specific cellular pathway; this broad targeting leads to a widespread increase in host dopamine levels, which may in turn account for the loss of aversion to cat odor...This rise in dopamine levels induces a loss of aversion to cat odor in the rats, increasing the risk of predation by cats, T. gondii’s definitive host.

Now, if a parasite can prevent mice from being afraid of cats, how hard would it be for another parasite to prevent humans from caring about each other's life(!)? Can a parasite develop some method by which it can alter behavior of humans in such a way that they just start killing each other for no reason? How easy/hard would it be for a parasite to do so?
Note: although it is just a curiosity question about whether it is possible or not, giving some description of neural pathways which stimulate social behavior in humans and how they are regulated would be much more appreciated.


texts: Will a dog develop similar feelings with a robot as like human?

texts:
I think we are connected to the world by Biochemistry first and then physical and verbal interactions. If a robot feeds a dog regularly, pampers it and cuddles it regularly, would it develop the same feeling to the dog as it would have developed with a human?
A sci-fi robot like Ultron from Avenger movie.


texts: Why do people cut back on kilo-calories?

texts:
I am learning about specific heat in science and I learned about how the specific heat for water is called a calorie, but that is different to what is on the food label.
On the food label, that calorie is actually a kilo-calorie. My teacher went on to explain that if somebody handed you a bowl of ice-cream that contained 500 Calories (i.e. Kilo-Calories) then, that was enough to raise 500kg of water 1°C.
If a kilo-calorie is just raising your body temperature, why do we cut back on calories?? What effect does a kilo-calorie have on your body other than raising your temperature?

P.S. How can we burn calories?? This seems, at least to me, like an abstract thing... burning heat....


texts: How to calculate the geometric mean titer (GMT) of titers from a haemagglutination assay (influenza)?

texts:
I got a list of Influenza-specific antibody titers from a hemagglutination inhibition assay.

They look like this:

40
640
160
<10

One site says: “The swine influenza HI scale is geometric: 20, 40, 80, 160, 320, 640 (successive values increase by a factor of 2). The geometric scale is logarithmic. It is best to express an average influenza HI titer as a geometric mean. A geometric mean is calculated by averaging the logarithms of the test values and then converting the mean to a real number. This prevents a few obviously high positive values from making the mean unrealistically large.”

What does that mean for my sample? How do I deal with <10 in this calculation? This is surely not rocket science, but honestly I don’t get it right now.


texts: What happens to Km when enzyme concentration is *very* high?

texts: Let Km be an empirical measurement of a certain enzyme with concentration [E]. Theoretically, this value is constant and shouldn't vary when [E] goes up or down. Now let [E']=10*Km. Under this concentration of enzyme, it's clear that if [S]=Km, V0 cannot be 1/2*Vmax (as there's only enough substrate to saturate 1/10-th of the enzyme molecules). What's happening here, and how does this relate to the derivation of the Michaelis-Menten equation?


texts: how to clone a gene fragment in two direction as sense and antisense in vector

texts: I have a sequence ATG GGG CCC TTT AAA TAA and want to use it as antisense RNA in my vector. How should I clone it? I am confused with the direction of my clone. I looking for the direction and sequence of the clones.


texts: Does Spinning dancer has anything to do with your eyesight

texts:
I came across the spinning dancer as part of the brain test to determine left brain vs right brain dominance.

I saw the dancer is turning clockwise. The other people around me saw it turning clockwise for the first time, but soon they got confused and said they saw it turning it in both direction.

I know the tips of how to see it anti clockwise, but no matter what I do I always see it clockwise. I have shown it to a number of people and all of them could see it spinning in both direction after looking at it for longer time.

I am the only person who has never see the dancer turning in both direction.

My question is does this has anything to do with my eyesight? I have very limited(almost blind) eyesight in my left eyes. This is from birth.

Does my visual impairment has anything to do with this or does this mean anything else?


texts:
As the question states, got curious and I was wondering if monogamy is an innate human behaviour or is it because of how we built society (religion, traditions, etc.)?

Let's say we go back in time, would we see humans settling down with a single partner at a time and caring for their children as a couple for life or would they reproduce with several leaving the mothers with their children?

Thanks!


texts:
Inspired by this question, I want to ask a question about centrifugation.

Suppose a protocol says : 10 min at 2500 rpm . Can we instead centifuge for 5 min at 5000 rpm or 20 min at 1250 rpm ?


texts: Nature Scientific Reports vs. BMC Genomics

texts:
I do not know if this question to suitable here or not. I posted it as I think biologists can help me in this question. If not suitable here, then I am sorry for that.

I have written paper which I spent about 3 years working on it and it has nice findings and original sequenced data (deposited in NCBI). I submitted the paper to "Genome Biology" and I got editorial rejection but they offered to transfer the paper to "BMC Genomics". However, my supervisor refused this and suggested that we submit to "Nature Scientific Report". I tried to convince him to go to BMC Genomics because it is more focused journal and it is better for my CV, however, he said the second one is better because it has better impact factor and it is Nature! (Impact factor: 5 for Scientific Reports vs 4.04 for BMC Genomics).

What do you think as I am really confused which one to select?


texts: Question: Annotation search in scientific literature

texts:
In a scientific paper I have been studying ("Predicting Novel Human Gene Ontology Annotations Using Semantic Analys" S.Draghici et al., 2010), I have read that authors checked the accuracy of their annotation predictions by searching on available literature the scientific evidence of their discoveries.

So, for instance, if they predicted an annotation X, they would search for scientific papers that prove that the predicted annotation is correct.

I think I could use the same method for my annotation prediction experiments, but how to do it? How to search evidence of a certain annotation by browsing literature?

Should I just visit PubMed website and use annotation id as keyword for search? And which source (EntrezGene, etc) id should I use?


texts: Which condition is most likely to cause a buildup of materials in the lysosome?

texts:
Stated below, I must answer a question related to lysosomes. I am unsure of the answer, and have explained my reasoning after the question.

Lysosomes contain hydrolytic enzymes that derive from the endoplasmic reticulum (ER) and work best under a pH that is different from cytoplasmic pH. These enzymes, called lysozymes, use this low pH to degrade damaged macromolecules, but they are able to spare their own protein and enzyme contents.

Which of the following conditions is likely to cause a buildup of materials in the lysosome?
A. inhibiting the protein synthesis in the ER
B. decreasing the supply of amino acids to the cell by half
C. providing the cell with more nutrients so that more protein can be made
D. having a mutation in a lysosomal proteinase that renders it more resistant to self-digestion
Reasoning: I know that A and B are strongly incorrect, as decreasing the number of proteins or the building blocks of proteins is unrelated to the toxins and waste that is built up in lysosomes. However, even though I am leaning toward D as there would be a buildup of toxins because of it, I am unsure if C would have some merit as perhaps if there is an increase in protein synthesis, there would be an increase in waste. Is my reasoning for C and D incorrect, and which answer would be the most appropriate (with explanation included, please)?


texts: Was site-directed mutagenesis used to study the effects of sickle-cell anemia?

texts: The title says it all. I am inquiring whether or not site-directed mutagenesis was used to study the effects of sickle-cell anemia/figuring out that specific amino acid mutation was the problem.


texts: Transformation of coordinates found in PDB

texts:
According to the PDB guide there are some coordinate translation matrices found in PDB file:
ORIGXn                  Transformation from orthogonal  coordinates to the
                        submitted coordinates (n = 1, 2, or 3).
SCALEn                  Transformation from orthogonal coordinates to fractional
                        crystallographic coordinates  (n = 1, 2, or 3).
MTRIXn                  Transformations expressing non-crystallographic symmetry
                        (n = 1, 2, or 3). There may be multiple sets of these records.

For example, in 10gs complex from RCSB I see:
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.012543  0.000000  0.001805        0.00000
SCALE2      0.000000  0.011055  0.000000        0.00000
SCALE3      0.000000  0.000000  0.014557        0.00000
MTRIX1   1  0.945333  0.099229  0.310644       -5.48795    1
MTRIX2   1  0.099832 -0.994906  0.013998       21.83043    1
MTRIX3   1  0.310451  0.017779 -0.950423       27.67516    1

I want to do 3D voxel reconstruction of some part of the complex stored in PDB. What is the purpose of those matrices, do I need to apply any of those translations to the coordinates stored in PDB to "standartize" the data and obtain the same coordinate system and same grid for different PDBs? Or they are just related to the data which was submitted by authors and are needed for inverse translation? Or something else? Thank you very much!


texts: What fraction of embryos fail to be born? And why that high?

texts:
In the book Developmental Biology by Scott F. Gilbert and Michael J. Barresi, it says:

  Most human embryos die before being born. You survived.

So how come is that true???

And what percentage of pregnant women lose their unborn child(ren)?


texts: How do anaerobic bacteria produce ATP for their own cellular activities?

texts:
Anaerobic bacteria utilise glycolysis:

Glucose + 2 P + 2 NAD+ => 2 ATP + 2 H + 2 NADH + 2 H2O + 2 Pyruvate

followed by fermentation:

Pyruvate + NADH => Lactate + NAD+

The resultant NAD+ formed can then be used again to break down more glucose molecules in glycolysis to produce ATP.

However, besides NAD+, glycolysis also requires an input of 2 ATP at the beginning (for the phosphorylation of glucose to glucose 6P, and fructose 6P to fructose 1,6 BP)

Since only 2 ATP is produced from glycolysis initially, would these 2 ATP be reused in another round of glycolysis?

If so, how do anaerobic bacteria produce a net amount of ATP for cell activities and growth?


texts: Sitting in a closed room filled with regular air - for how long will the air last?

texts:
The question has implicitely a lot of variables attached to it:

volume of the room
activity
how closed the room is
size of the person (I'm 168cm long and 64 kg heavy)

That could probably be turned into some formula and I am interested in scientific insights.

But at the end of the day my question is actually of very practical nature. I have a small room - about 1m x 2m x 2.5m = 5m3 - and I would like to use it as super-quiet place for meditation, reading etc. - hence calm activities, no excessive moving around. To improve sound proofness I'll probably also increase the sealing of the door and there is no ventilation - no air exchange.

Now if I close the door - how long can I expect to stay there without the air quality deteriorating to a level where my mental processes start to be impaired by it?


texts:
Ankylosing Spondylitis (AS) causes inflammation around joints and the growth of syndesmophytes that may eventually fuse vertebrae. I'm familiar with the genetics (HLA-B27, IL1A) related to the condition, but I can't find any information about the mechanism that causes the actual growths to occur.

My current assumption is that AS causes the over-production or under-production of a particular compound or enzyme at the growth site, but I can't find any studies or papers that explain this. Is the mechanism known? Is it directly related to abnormal levels of a particular substance?


texts: How to determine the actual flux in the human metabolic model of a cell line?

texts:
The problem to be solved is to determine what the flux values are for the different reactions in the human metabolic model.

As far as I understand, a good way to do that would be to use gene expression data to calculate a flux, but I am not sure that is a good idea or if it is even possible.  I am not very sure of what is the correct process to do this.

Thanks for any help or suggestions!


texts: Do free computer programs exist that can simulate drug permeability in bacterial membranes?

texts: I am currently trying to make derivatives of a molecule in hopes of making it more permeable to bacterial membranes. I wanted to know whether there are any bacterial membrane simulating programs where I can dock my molecule and see its predicted permeability. Preferably, I would like to use a free program that is known to be trustable/accurate.


texts: Why is absorbance at 280 nm for protein solution going up when I measure repeatedly?

texts:
I have been measuring my protein solutions' concentrations by diluting them in water 20 fold with a final volume of 100 uL and then measuring the absorbances of these solutions in 96 well plates with plate reader. I don't remember having any problem up until today.

I used 20 mM phosphate buffer instead of water to dilute them today and measured the absorbances at 280 nm repeatedly three times and the absorbance for one of the solutions went up from 0.043 to 0.068 (absorbance of 20 mM phosphate buffer is 0.030 at 280 nM with same volume); I stopped measuring after third one but it would probably go higher as I measured until I hit a plateau.

I measured absorbances of two proteins and only one of them went up that much, other one went up from 0.071 to 0.088; if this were to be concentration dependent I would expect the second solution go even higher but it didn't happen.

I know there may be differences in UV absorbances if protein is folded or unfolded; would it be that dramatic? What is the reason for that increase? I will be grateful for an explanation and a practical solution to the problem.

NOTE: I increased the total volume to 200 uL by simply adding 100 uL of 20 mM phosphate buffer into all wells and the signal increase slowed down a lot; there is still some increase though with 0.001-0.003 increments in each measurement.


texts:
What has to duplicate before cell enters M phase?

DNA
histones
centrosome
mitochondria (any other organelles?)
condensins (not sure?)

have I forgotten anything?

Thank you in advance!


texts: Why does the right bundle branch not have any terminal filaments in the IVS of the human heart?

texts:
Dubin's "Rapid Interpretation of EKG's" briefly describes this part of human physiology but doesn't explain the reason behind it.

Is there a specific advantage of the human heart having this characteristic, or is it a flaw/useless trait?


texts: How can I tell if a protein has been denatured?

texts:
So i recently done an experiment using egg albumin, and we had 5 test tubes. the goal was to see if they have been denatured.
1- heat
2-acid (HNO3)
3-base (NaOH)
4- Alchol (ethanol)
5- heavy metal ions (AgNO3)

So some of the test tubes became cloudy/milky and some clear. Is it the clear ones that has been denatured? I don't know how to tell.

Thanks in advance :)


texts: Does prolonged exposure to low pitch but low volume noise affect hearing or stress?

texts: This is similar to another post but not quite the same... At work, our ventilation system produces a constant low pitched sound - like a rumble - as well as the sound of air blowing through the vents. It's not very loud, we can certainly talk, even whisper to each other, but when it shuts off, it's like a huge weight off my shoulders. My ears don't really pop but there's sort of a slight "tingling" sensation - like when the blood starts flowing to a hand or foot that fell asleep. You can usually hear several people in the same room say "Ahhh" as in we are all glad the noise has stopped. I have worked in this location for over 10 years and in that time I have developed tinnitus which is probably attributed to a number of bad behaviors as a youth. But I was wondering if this constant noise could contribute to the decline in hearing? Also, that sense of relief when the noise stops makes me wonder if the constant noise adds to our stress levels?


texts: Is it inevitable that antibiotics will become useless in the future due to bacteria immunities?

texts:
Antibiotics are developed in an ever smaller amount due to the difficulties of discovering new ones. Bacteria, on the other hand, keep "finding" more ways to render antibiotics ineffective, and they are doing it faster than new antibiotics come to market. It seems that by a simple qualitative assessment at some point in the future all antibiotics will be ineffective.

However, there are 2 things I could think of that can suggest otherwise:

Antibiotics which were rendered ineffective long ago can be reintroduced since it's possible that the bacteria mutated away from their defense mechanism. This would allow for cyclic reintroduction provided we have enough types of antibiotics to sustain the cycle.
Antibiotics which bacteria can't defend against.

Are any of the above 2 possible futures? Can it be (at least theoretically) proven that antibiotics in point 2 can exist? Are there any other methods to "win the antibiotics war against bacteria" (assuming we are losing it as I assessed)?


texts: Range of feasible coefficients in an unlimited growth model

texts:
If you are given an unlimited growth model in the form:

$\frac {dP(t)}{dt} = k P(t)$

Obviously the population growth would never be unlimited, but let's presume for the moment that we are introducing a species into an environment where there is the possibility for unlimited growth, at least on for a given time -- i.e. invasive species.

$k$ is some rate of growth of the population at time $t$, denoted by $P(t)$

What are some feasible values of $k$? In other words, if a number is way above or way below $k$, where would I know that the research I am reading is preposterously off-base?

I am sure it is different for different types of animals, including mammals, birds, bacteria, etc.


texts: Do factors other than concentration gradient and membrane permeability affect the diffusion potential?

texts:
If, hypothetically, the concentration gradients and the permeability of 2 different ions (Na+ and K+ for example) in 2 separate solutions are the same, will the diffusion potentials be different?
I'm trying to gain an intuition for the concept of diffusion potential and equilibrium potential.
It read this topic from 2 physiology textbooks but haven't really found an answer anywhere. I understand that the diffusion potential is the potential difference generated when an ion moves through a membrane down its concentration gradient. I also know that it is determined by both the concentration gradient and the permeability, but, does the type of ion itself matter if the charge on the ions is the same?


texts: I read that the length of telomeres in Dolly was shorter, because the DNA was taken from an old sheep. Shorter telomeres may lead to early aging. What is happening now with cloning? Do we use a telomerase to restore the length in a donor cell?


texts: What makes a 'sense'? Is fatigue (tiredness) a sense?

texts:
I have watched to new episode of Scishow on that scientists added 3 new senses (Thermoception, Proprioception and Equilibrioception) to our 5 sense list, and was wondering what makes a 'sense'?

Wiki definition:

  A sense is a physiological capacity of organisms that provides data
  for perception.

Does that mean fatigue (feeling tired) is a sense too?


texts: Do you know of ways that help a plant to produce more flowers?

texts: In Crocus sativus, or saffron crocus, the most commercially important part is the stigma of flowers. Each plant produces one flower (so there is more than one plant in this picture) and each flower has three stigmas (stigmas are red in this picture). What are the possible mechanisms to produce more stigma in a plant for commercial cultivation?


texts: Advantages of Monogamy over Polygamy and Vice Versa In Nature?

texts: Some animals take on a single partner, possibly for life, while others have multiple partners over their lifetime, possibly even at the same time. What are the advantages to each approach, and how much is conscious choice verses instinct?


texts: Maximum Allometry of aquatic mammals omitting Kleiber's Law

texts:
As far as I understand, blue whales cannot get any physically larger due to the extremely demanding caloric intake it has on consuming large quantities of krill, not due to any other physiological reasons, as it for what limits a land animals's, being their bones not being able to support their own weight.
Be that the case, how big can an aquatic mammal be, in terms of volume and/or mass?
Would other organism's, such as Hydrozoa, to name one example, display any difference in this regard?
For reference on the Blue Whale size being limited by caloric consumption, here is a link on a study:
https://science.sciencemag.org/content/366/6471/1367.abstract
Goldbogen, J. A., et al. "Why whales are big but not bigger: Physiological drivers and ecological limits in the age of ocean giants." Science 366.6471 (2019): 1367-1372.
APA


texts: Spatial sequence of autumn leave colouring: top to bottom

texts: Leave colours on trees seem to vary on the same tree from top to bottom. Leaves higher up are already further ahead in the shedding process. What's the reason for this tempero-spatial gradient?


texts: Will tagging a protease with HlyA for secretion inactivate the protease?

texts:
We are looking to secrete the protease proline iminopeptidase by attaching the secretion signal HlyA to the protease in a gene circuit. Since the natural HlyA secretion sequence in Escherichia coli isn't cleaved from the protein, it will remain attached to the protease in the extracellular matrix.

Will the protease still function and cleave the peptide chain at the n-terminal proline residue with the HlyA signal still attached?


texts: What is the name of this flowering plant?

texts:
My mother is in hospice, and this beautiful flower is outside her window. She would like to know the name of "her" flower.

The flower is growing in Eastern Kansas and we are approaching the first day of summer here


texts: How the chaotropic agents help in purification of DNA molecule?

texts: Those plants which are rich in secondary metabolites and polysaccharides DNA isolation can be done using certain chaotropic agents? can any one explain how it works?


texts: Transcript(omics) terminology: cDNAs, ESTs, RNA-seq, etc

texts:
I've worked pretty frequently with genome and transcriptome data for several years now, but I'm still not 100% sure I understand the proper usage for certain terminology related to transcripts and transcriptomics. Let me give it my best shot.

cDNA: in general, this term corresponds to any DNA that is derived from an RNA template via reverse transcription (complementary DNA); however, it is often used to refer to full length cDNAs, DNA sequences that correspond to complete mRNA molecules
EST: expressed sequence tags correspond to cDNA (sub)sequences obtained from a single read of a cDNA sequencing experiment
RNA-seq: this refers to the use of high-throughput sequencing technologies to characterize entire transcriptomes, such as by transcript assembly or expression analysis

Here's my concern: I've seen ESTs described as "one-shot" or "single-pass" sequences, which I interpret to mean a single sequence read. However, they are also typically described as being hundreds of base pairs in length (Wikipedia claims about 500-800bp in length max), which (currently) limits this definition to reads derived from Sanger-style sequencing.

Does this mean that a short read derived from a high-throughput sequencing platform is not an EST? Is this distinction based on read length? platform? throughput?

Due to technical limitations, short reads are often assembled before they are used for other downstream analysis. I have sometimes heard the contigs belonging to these assemblies as ESTs, but this doesn't seem to be consistent with the previous definitions.

Is our terminology becoming inconsistent due to the rapid improvements in sequencing technology, or am I missing or misinterpreting something?


texts: Is it in principle possible to revive an extinct species having no living relatives?

texts:
Is it, in principle, possible to revive an extinct species having no living close relatives but whose DNA and other tissues have been preserved?

What about the case where there are no living individuals of a species but there are some living somatic cells?

What about the case where only individuals of only one sex are alive?


texts: Can a plant be induced to accelerate transpiration?

texts:
Just what the title states.
I wonder whether it is possible to fire a chemical switch - sort-of like injecting adrenaline in a human, to accelerate a particular process in a plant. For example, transpiration.


texts: Colorblindness in females and random X chromosome inactivation

texts:
From Annenberg Learner:

  Because the X is inactivated randomly in cells, one cell could have the maternal X inactivated, while the adjacent cell could have the paternal
  X inactivated. This causes a pattern of gene expression called mosaicism, which occurs when different alleles of X-linked genes are expressed in different cells.

However, this seems at odds with colorblindness being more likely in males.  From Wikipedia:

  The genes that produce photopigments are carried on the X chromosome; if some of these genes are missing or damaged, color blindness will be expressed in males with a higher probability than in females because males only have one X chromosome, whereas females have two and a functional gene on only one of the X chromosomes is sufficient to yield the necessary photopigments.

Question: If X chromosomes are randomly inactivated cell by cell, shouldn't the fully functional photopigment-producing gene be inactivated approximately half the time?  In which case, wouldn't we instead see females with colorblindness with higher frequency as males, but experiencing colorblindness to a lesser extent?  (After all, two X chromosomes means two chances for a dysfunctional gene.)

I'm guessing I'm missing a piece of the puzzle here, e.g., perhaps the relevant cells "know" to inactivate the dysfunctional X chromosome, or perhaps it's to do with X chromosomes only being incompletely inactivated.


texts:
As far as I know, all land life depends on plants for survival. Plants convert sunlight to energy using photosynthesis, herbivores consume plants, and carnivores consume herbivores. All the energy is coming through the sun and being gradually processed by this food chain. If plants were removed from the system, all animals would eventually die as they would run out of energy.
Do fish and other water creatures also depend on plant life in the same way?


texts: How is the rate of gluconeogenesis controlled in the cell?

texts:
As far as I am aware, all steps in glycolysis are readily reversible except the phosphorylation of glucose, the phosphorylation of fructose6 phosphate, and the phosphorylation of phosphoenolpyruvate to pyruvate. I understand how control of the rate of glycolysis can be achieved through allosteric means (for example glucose 6 phosphate inhibiting hexokinase in muscle cells, phosphofructokinase being under allosteric control of the ATP/AMP ratio in muscle or hormonal control via glucagon in liver), however how is the rate of gluconeogenesis controlled compared with glycolysis? When a cell has a high rate of glycolysis, then as the rate of forwards reaction increases the concentration of substrate for each gluconeogenesis reaction also increases. Thus there must be some way to shut off the gluconeogenesis enzymes.

I would be grateful if someone could explain how the relative rates of glycolysis and gluconeogenesis are controlled, and perhaps if this varies according to the cell type (muscle/liver cells etc).

I was also wondering whether every cell is capable of gluconeogenesis. I was considering putting this on a separate post so that there is only one question per post, but I thought that it is quite a short question so it may be better to put it here.


texts: What temperature should mammalian B-Cells be stored at outside of the incubator?

texts:
I'm working with murine B-cells. The general protocol is to keep cells on ice to keep them from dying but I've noticed that it makes these cells aggregate and precipitate out. I've heard suggestions that these cells should just be kept at room temperature. How would I be able to determine which conditions at which I should be keeping my cells?

I was trying to collect cells to prepare them for cell binding studies to antibodies and then assess the cells on a filterplate. Typically, you keep them on ice to pause the metabolic state as well as to prevent endocytosis of the bound molecules. However, that shift seems to cause settling. How do you troubleshoot the appropriate temperature to process cells and what are the usual scientific justification for making such decisions.


texts:
The section of retina shows a layered arrangement of the various retinal cells. Starting from the inside (where the light strikes first) is the nerve fibre layer, ganglionic layer, amacrine cell layer, bipolar cell layer, horizontal cell layer and finally rods and cones (and that too in inverted position, i.e. the actual receptor portions are farther inwards).

  Why is this stratification inverted? If the receptors would have been the innermost cells, they could have received the maximum
  quantity of unaltered light. Does this "inverted" arrangement, i.e.
  arrangement with the receptor cell behind a screen of several other
  layers not hinder the process of photoreception by blocking a lot of
  incident light and hence the formed image? What is, if any,
  advantage of this reverse arrangement?


texts: What is the death mechanism of an electrocuted Mosquito?

texts: While using the Electric bat, does the mosquito get killed by primary electrocution, or it secondarily by burning?


texts: What DNA does a self-fertile plant's seedling have?

texts:
Some plants are said to be self-fertile. An example is Prunus tomentosa.

Assuming that no cross-pollination happened with other plants, if a self-fertile plant such as prunus tomentosa produces a seedling, what DNA will the seedling have? Is the seedling's DNA an exact copy of the parent plant's DNA, or do the genes get rearranged?


texts: What are an internal and external exons?

texts:
I read the book: Essential Genetics and Genomics It has a table summarizing the properties of the "typical" human gene:

It has a gene feature Size of internal exon, what internal means in this context?

When I searched for it I found mentions about external exons, but found no definition.

I strongly suspect they mean:

External exons are the first exon right after the 5' untranslated region and the last exon just before the 3' untranslated region and all the other exons are internal exons.

As turned out this was almost right, but had a mistake which is wonderfully pointed out in the accepted answer.


texts:
If Humans are evolve from Monkeys, there must be stages in the evolution process, when it was 1% human and 99% monkey, 2% human and 98% monkey  and so on. This is because evolution was a very slow process that occurred in a span of thousands of years. So we expect there must be fossils of this intermediate stages under earth. These intermediate-stage fossils must be many times in no. as compared to 100% human or 100% monkey.

But why do we do not discover these intermediate fossils?


texts: Identify this insect, found in Central Vietnam, with long antennae, black wings, and red body

texts:
Last year this insect landed on my hand when visiting the My Son city ruins in Central Vietnam.
I've been trying to identify the insect, but until now without result.

Can you help me? Or do you know who could?


texts: "Immortal Genes" common to all organisms?

texts:
Author Sean B. Carroll mentions that there are about 500 genes common to all organisms. They have to do with the essential DNA machinery and so forth.
What are these genes? Where can I read more about this fascinating concept?
When you google immortal genes you get mentions of Sean B. Carroll. What term do others use for these genes?

"When we compare the genomes of Archaea, bacteria, fungi, plants, and animals, we find about 500 genes that exist in all domains of life... The functions of immortal genes are central... processes such as decoding DNA ... and making proteins. All forms of life have depended on these genes since the origin of complex DNA-encoded life early in Earth's history." (Making of the Fittest, pg 79)