texts: Are mesophyll cells the same as parenchyma cells?

texts: I read in my biology textbook that ground tissue is constituted by parenchyma, collenchyma and sclerenchyma.It was also mentioned that, in leaves the ground tissue was made up of thin walled chloroplast containing cells called mesophyll cells.


texts: Electrocardiogram: Missed beats in presence of Ectopic beats or Premature Atrial/Ventricular Contraction beats

texts:
I have been working on analyzing Electrocardiogram data.

So far, i have identified Ectopic beats and Premature Atrial/Ventricular Contraction beats.
I am working on identifying Missed Beat in the Electrocardiogram.

The definition of Missed Beat is:
"The characteristic of a missing beat in ECG is the unexpected absence, together, of P-, QRS-, and T-waves."

My question is, do we have to consider missed beats in presence of Ectopic or Premature beats also ??
For example, if an ECG contains premature/ectopic beats, then should the R-R interval between these beats should be compared to R-R interval between normal beats to search a missed beat ??


texts: What species of bird inspired Nebraska's nickname Bug-Eating State?

texts:
Nebraska's early nicknames include Bug-eating State, inspired by a bird. One reference describes it as the "“bull bats (Caprimulgus europaeus).” However, that's the Latin name of the European nightjar.

I'm therefore assuming Nebraska's nickname was a reference to a native nightjar species - but which one? Of course, it could have referred to multiple species, or all of them.

I just wondered if anyone might know if this nickname referred to a particular species. If that can't be answered, it would be interesting to know if there's a species that's a likely candidate. For example, is there a particular nightjar that was especially widespread or common in Nebraska in the late 19th century?


texts:
Estimations (or measurements) of bite force is usually conducted for toothy predators like sharks, theropod dinosaurs and crocodiles. For example: Tyrannosaurus had a bite force of about 57 kN (about 5.7 tonne-force) while a 5.2 meters long Saltwater Crocodile (Crocodylus porosus) recorded a 16,700 Newton bite (by Gregory M. Erickson). See my earlier question Reference for the bite force for Nile Crocodile for reference.

However, although paleontologists agree herbivore ceratopsian dinosaur Triceratops had quite a strong bite due to large jaw muscles anchored to (part of) the frill, and sharp hard beak. However, as far as I am aware, no one ever tried to quantify how strong is Triceratops bite. But maybe there are some estimations in paleontological literature and scientific research. So to sum-up my question:

  What is the bite force of a fully-grown bull Triceratops?

Size for reference: Triceratops length was 8-9 meters and weighed 6-12 metric tonnes.


texts: Is "monosexual" still a valid term in biology?

texts: I read an older article where they talk about species being strictly monosexual as opposite of being hermaphrodite, etc [1]. After an extensive googling and reading about how everybody has to be at least a little bit homosexual, I am still not clear about this. Is monosexual still a valid term to be used in biology? If not, what is the correct term referring to a species that has separate sexes over the entire life-cycle?


texts: Can nociceptors die because of too much mechanical stress?

texts: In martial art people hit their body (e.g., with small bean bags) to become more insensitive to pain. Can the sensory neurons die during this procedure? I think this is just an urban legend. Instead, I think the skin receptors desensitize, but they don't degenerate by the constant mechanical stress. However, I cannot find any research in the topic.


texts: Protostomia classification and characteristics

texts:
While working through a practice test for my final exam in an introductory organism biology course, I came across this question:

Protostome characteristics include which of the following?
a) a mouth that develops secondarily, and far away from the blastopore
b) coelom formed by schizocoely
c) radial body symmetry
d) spiral cleavage
e) none of the above

After reading the answers a few times over, I just moved on because I couldn't figure out how to answer. My first instinct said that both (b) and (d) were correct, but the answer is (e).

After some thought, I've come to a few ideas how this could be true.
1. The wording is incorrect, the definition he provides for protostomia says "body cavity formed by schizocoely," and "spiral determinate cleavage."
2. These two characteristics are not present in all protostomes (i.e. spiralia evolves after ecdysozoa, and platyzoa have no body cavity).

Just looking for some clarity or closure regarding this.


texts: just a quick question. Is the tissue fluid the same water potential as the cells it surrounds? I am a bit confused because if it was lower it would cause water to leave the cell and if it was higher water would enter the cell and both aren't really good for the cell. I believe tissue fluid is isotonic, am I correct?


texts: Under what circumstances will a human neuron divide?

texts:
I read somewhere that a mature neuron loses its ability to divide, except for very specific situations. I was unable to find the description of those situations. What are they?

(I'm sorry I'm not saying where I read that, but I simply can't find it.)


texts: How do exon tandem exon duplications occur in the genome?

texts: By this I mean in cases where tandem exons are introduced by replication slippage how would a DNA polymerase by chance duplicate an entire exon cleanly (i.e. from exact start to exact end) when it doesn't even know what an exon is?


texts: What are the molecular mechanisms that make the turtle brain more resistant to hypoxia?

texts:
I know that turtle brains, particularly those of individual species that hibernate and burrow are particularly resilient to hypoxia and any tissue damage secondary to a hypoxic event.

What are the known molecular mechanisms behind this resiliency?  Does it have to do with the ability of their blood to store/release oxygen over extended periods, or is it molecular factors in the neural tissue that protect it from insult?


texts: Can the dendrites of sensory neurons be a meter long?

texts:
The typical textbook structure of neurons is a cell with a short dendritic tree and a long axon. The dendrites receive information and send it to the axon via the cell body (soma). The axon is a long structure designed to send the information to distant parts.

A neuron. source: ASU School of Life Sciences

In sensory neurons of skin receptors, however, the dendrites are considered to receive information about the outside world, i.e., the dendrites are the receptive parts of sensory neurons. They generate action potentials that are sent to the soma. But I've been told that the soma of sensory neurons are located in the dorsal root ganglion of the spinal chord?

Does this mean that the dendrites of sensory neurons are exceptionally long? Suppose I feel a prick in my finger, do the pain receptors really have dendrites a meter long all the way to the dorsal root?


texts: How can the same transcription factor be both an activator and suppressor of the same gene?

texts:
For example, hunchback in moderate concentrations is an activator of kruppel, but a suppressor of kruppel in large concentrations.

From what I've seen in literature, that's because the kruppel's enhancer has several binding sites for hunchback: some responsible for activation, while others for suppression. But why would hunchback in moderate concentrations bind only to activation sites, and why would higher concentration "change its preferences"? What chemical mechanism is responsible for this preference?

P.S. I provide hunchback and kruppel as an example, but this is a general question: how could the same transcription factor be both an activator and suppressor of the same gene?


texts: Hydrophobic interactions in the helix-turn-helix

texts: This slide states that the second helix works to stablize the configuration of the two helixes via hydrophobic interactions. What exactly is this hydrophobic interaction? In other words, what molecular interaction does the second helix have with the recognition helix?


texts: Are there any biological obstacles prohibiting lighter-than-air organisms?

texts:
Why there are no organisms that use cavities filled with lighter-than air substances (e.g. hydrogen) to fly and remain in air?

Given that there are a lot of fish and algae that use similar cavities to float, it is surprising that no organism utilized the same mechanism to fly.


texts: Do species other than humans have distinct daily feeding patterns?

texts:
I have a general interest in complex adaptive systems and I have found that nature and the organisms within it is a perfect natural case of a rich adaptive system with a lot of possibilities for gaining insight in general about the nature of complex adaptive systems.

My mind accidentally started thinking about the common human feeding pattern breakfast-lunch-dinner and I sought reference points in nature, realizing that I'm not aware of any specific cases where the feeding pattern of animals other then humans follow a distinct pattern, in contrast to a constant, stochastic or mainly opportunistic search for food.

In the case of humans there is probably a very strong cultural cause for our very distinct feeding pattern, but that is not necessarily to say that these patterns only can occur in species with a highly developed culture.

How does the scientific body of observations look like here? Is there any research or empirical observations about the feeding pattern of animals?

For example, I would of the top of my head assume that some common reasons for these patterns to develop could be connected to e.g. the 24h circadian rhythm, dependencies to availability of food, or internal dependencies on behavioural organization in social species.

Of course it's likely that many organisms do not have the luxury of spending a significant time on other activities then acquiring food, but nevertheless we can see that some animals have evolved into a situation where they don't have to constantly be in the search for food, but instead can spend time on other activities increasing their fitness, like engaging in social interactions, searching for and seducing sexual mates, exploring their environment and migrating, building nests and so on.

To clarify what kind of observations I'm imagining could happen, take these speculative examples:

  Some species of birds have a significantly higher feeding activity in the morning, where they after a night of inactivity have depleted their daily energy resource and when the insects, their main source of food, starts to activate after a cold night and are still cold and slower/easier prey. After this the birds only have an opportunistic approach to feeding which is enough to satisfy their energy need, and they spend more energy on pruning, calling for potential mates and engaging in territorial battles.

  Many primates engage in collective feeding sessions where they as a group travel to a known area rich with food where they spend a couple of hours before they retreat back to a different location for socializing and digesting the food. One reason for this behaviour can be that there is a high risk of predation at these food-rich areas, as the predators learn that these places are frequently visited by prey.

  Feline predators on the savannah are usually concentrating their hunting in the night as the darkness gives them an advantage of stealth and surprise. This is why they in daytime instead spend a considerable amount of time on resting, engaging in activities regarding social hierarchies, order and bonding with the pride, while most often only opportunistically engaging in hunting.

Do we have a body of knowledge here?

While it would be close to hand to start trying making lists of observations like this, which certainly would be interesting in itself, the intention of this question is to get a good overview on the subject. Are patterns like these common or uncommon? In the cases where they are found, what are the common factors and what can be identified as the underlying causes?


texts: The least complex animals with ability to dream

texts:
People can dream, dogs can dream, cats probably too when they are sleeping.

What about other creatures?

Can a bird dream?

Do rats have dreams?

Are there any studies about that kind of thing? What is the most simple organism that have brain structures that allow them dreaming during the sleep?


texts: Why does colchicine not affect the source plant itself?

texts:
Colchicine, being a mitotic poison that blocks spindle fibre formation, should affect its source plant. It should also stop its cells from dividing. So how do they grow?

I think that there might be some cells that synthesise it seperated (by many layers of cells) from other cells. So the rest cells are not affected.


texts: What type of fish is this- Cabo San Lucas, Gulf of California side

texts: Can anybody tell me what this fish is?  Caught in Cabo last week, actually closer to San Jose, with a Joe's Flies 1/4oz spinner.  Cool looking fish for sure, just can't seem to find it online of what it is??


texts: Can gene-gene interactions result in gene expression?

texts:
I am building a project on Inferring Gene Regulatory Networks using ARACNE and PCA-CMI algorithms, and the input to these algorithms is taken from the DREAM3 challenge.

The format of the input data is shown in the image.

Now according to what I studied, a Gene Expression Matrix has its rows represent genes, columns represent samples such as tissues or experimental conditions and the numbers in each cell refer to the expression level of a particular gene in the particular sample.

And that Gene Expression is the process in which information from a gene is synthesized to obtain Gene Products. The process of Gene Expression is that it undergoes a transcription process where a transcription factor attaches itself to the gene and then results in the formation of gene product.

But the input data apparently shows gene-gene interactions.

As a result of this I am extremely confused.

Any kind of help would be greatly appreciated. Thanks.


texts: Why did the indigenous peoples of northern Asia and America not evolve the same physical characteristics as people of Nordic ancestry?

texts:
I was watching DW's documentary on the Arctic the other day, and I was struck by how the indigenous peoples of the far north seemed - visually speaking - to fit into two categories. On the one hand, there are the peoples of northern Europe, with their pale skin and their preponderance of blue-eyed and blond-haired individuals. On the other hand, there are the Yakuts, Inuit, Aleuts and many more, whose physical similarities - they all seem to share an East Asian-looking bone structure, as well as black hair, deep brown eyes and a skin tone akin to white coffee - belie vast differences in language, culture and belief. Why did northern Europeans evolve these distinctive physical traits while other northern peoples did not? It's probably worth noting that the physical and temporal separation between, say, the Finns and the Nenets is much less than that between the Yakuts and Inuit.
It might be helpful to approach this by splitting up the different characteristics:

Pale skin: Of all the physical characteristics, pale skin seems to confer the most obvious advantage: better absorption of sunlight, and the various benefits connected therewith. Although I've not carried out any kind of systematic analysis, non-Nordic northern peoples do not seem to have a lighter skin tone than their southern neighbours (i.e. the Chinese, Japanese, Native American, etc peoples).
Blond hair and blue eyes: These are the most striking physical differences between Nordic and non-Nordic northern peoples, however it's not clear - at least to me! - what advantage they confer in high latitudes. Is it just blind chance that these characteristics evolved in northern Europe, and not in, say, Central America? If it's not blind chance, why did these characteristics evolve in northern Europe, but not in other northern regions?
Other characteristics: I have read that there are other characteristics, e.g. greater height, associated with high latitudes. Do Nordic and non-Nordic northern peoples have any of these characteristics in common? If there is divergence here, how might it be explained?


texts: How does the cardiovascular system improve upon repeated, strenuous exercise?

texts:
New here, hopefully this is the right place to post this question.
It's widely known that repeated, strenuous aerobic exercise gradually improves the capacity of one's cardiovascular system — $\text{VO}_2$ max, cardiac output, etc. The U.S. NIH, for example, states the following:

Over time, regular aerobic activity makes your heart and lungs stronger and able to work better.
When done regularly, moderate- and vigorous-intensity physical activity strengthens your heart muscle. This improves your heart's ability to pump blood to your lungs and throughout your body. As a result, more blood flows to your muscles, and oxygen levels in your blood rise.
Capillaries, your body's tiny blood vessels, also widen. This allows them to deliver more oxygen to your body and carry away waste products.

Unfortunately, I have not been able to find information about the actual biological processes that happen during repeated exercise which trigger these effects. Is it some combination of hormones? Is it a form of muscle hypertrophy of the heart?
Frankly, the subject fascinates me, and I'd be grateful if someone with knowledge about this could share it!


texts: The length of a bone is caused by growth of hyaline cartilage which is then replaced by bone tissue. How do cells know whether they should grow the hyaline cartilage? What are the key molecules that trigger the synthesis of hyaline cartilage?


texts:
So far all I have found is this:
https://www.biostars.org/p/132527/

My guess is that some alleles, for whatever reason, bind to things like transcription factors 'moreso' (for want of better word - affinity maybe) than others. Or maybe some alleles are more likely to get methylated, for example.

I feel my understanding is very much bare bones. Is anyone able to go through it a  little more comprehensively? Thanks


texts: Is there a database containing sequences of human cell lines?

texts: I'm looking for the whole genome sequences of several human cell lines, e.g., A549 or Ea.hy.926. Is there a database specifically dedicated to human cell lines?


texts: Why are vaccines for polio taken orally while vaccines for TB need to be injected?

texts: My thoughts are that maybe the TB antigens necessary to produce an immune response are proteins; therefore they can be digested in the stomach and small intestine. But I may be wrong though. I am confused why I can't say the same for polio vaccine.


texts:
In this experiment, we transformed a truncation of the NFAT protein sequence into a plasmid vector to be expressed in E.Coli as a fusion protein with GST.  We also attempted to transform the normal plasmid without NFAT so that we could get GST alone.  After growing up these colonies and selecting positive colonies, we lysed the e.coli.  We collected some of this lysate for SDS-PAGE.  We then put the lysed GST and GST-NFAT solutions in separate columns with glutathione beads.  GST binds glutathione.  We washed the column and collected some of the wash for SDS-PAGE.  Finally, we eluted the GST and GST-NFAT off the column and saved some for SDS-PAGE.

I have attached a picture of a successful version of the SDS-PAGE.

You want to direct your attention to the first lane, the Molecular Weight Marker (MWM).  The rest of the lanes should be interpreted in sets of 3.  The first of the three is the crude lysate, the second of the three is the first wash, and the last is the eluted protein of interest.  The important lanes for my analysis are 8-10 and 11-13.

I will explain what I know from this SDS-PAGE gel so far.  I know the weights of the different bands in the molecular weight marker because I was given a copy of the different proteins in the marker.  From this information, I was able to confirm that I isolated my protein of interest in lane 13 and isolated GST-alone in lane 10.  I also understand the reason why the lysate lanes are darkest, followed by the wash lanes, and then very clean protein of interest lanes.  Also, note that the marker and the elution lanes were loaded with 10 microliters while the other lanes were 2 microliters each. However, there are some things that I do not understand from the gel.
(1) Why are the bands so diffuse/low resolution.  I imagine it may be overloading the wells, but I am not convinced because I followed a set procedure.
(2) Why is there large amounts of streaking, especially in lanes 5, 8, 9, 10, and 11.
(3) I isolated my protein of interest because it was a fusion protein with GST (or just GST alone), and then eluted the protein off the glutathione beads via excess glutathione wash.  Theoretically, the lanes for the elutions should be free of everything except the protein of interest and glutathione then.  This mostly holds true for lanes 4 and 9, which should only have GST and glutathione.  However, lanes 7 and 13 should only have GST-NFAT and glutathione.  The lanes are not as clear however and seem to have stained numerous other proteins.  What is going on?
(4) I was told by a professor that the second band in lane 13 (the GST-NFAT lane) was a degredation product.  How can this be?  The band does not correspond to the weights of NFAT alone or GST alone.  Also, if the NFAT-GST was degraded, wouldn't there be two bands of degredation product?
(5)  Why do the GST-alone lanes have what looks like doublet-bands?  (Lanes 4, 10).
(6)  If we eluted the proteins of interest with excess glutathione, which has a very low molecular weight, why doesn't it show up on the gel?  Is it possible that it ran off before everything else?
(7)  I have a list of the weights of the bands of the molecular marker.  Yet, there is an extra band at the bottom that does not show up on my list.  Is it possible my list is incomplete, or is there something else happening?

Finally, I have attached a picture of a failed SDS-PAGE gel.

The only thing that I definitively know was a source of error is the fact that my buffer level fell during the run (due to a leak).  The results of this gel are accurate (Lanes 2-7 correspond to lanes 8-13 on the above gel, and the results are almost identical) yet the gel turned out horribly.  How can the buffer falling cause this result?  Or is there something else that may have contributed to this weird pattern?  Finally, the lanes are not as distinct in this gel as the first gel, yet the same comb, and thus the same size and spaced wells were used.  So why was there so much bleed between lanes/ lack of space between the lanes?

Thanks in advance for any help.


texts: What are the different, high-level programs along which a eukaryotic animal cell can follow?

texts:
What are the different, high-level, disjunct (mutually exclusive at one particular point in time) programs or pathways along which a eukaryotic animal cell can follow? Examples of programs would include growth, cell division, senescence and quiescence. Are there programs that differ between cell types?

Any I'm missing? If so, references much appreciated.


texts: Why does hypocalcaemia cause increased muscle contraction?

texts: Calcium is needed for  muscle contraction, so how does hypocalcaemia cause increased sustained contraction?


texts: Identification: creepy dangling spiderthing

texts:
Can anyone identify this creepy mess dangling from the cieling of my garage on a few strands of spidersilk? The thing is 5cm.

Should I burn down my garage and move to another country (Currently Belgium)?


texts: Computational engineering of protein binding pocket

texts:
I have an X-ray structure of an enzyme with reported activity to a small molecule.
This activity is rather low since it is not the native substrate.

I can run molecular modeling simulations (e.g. using DOCK) to estimate the enzyme's binding behavior to different compounds. However, what I would like to be able to do is to mutate the binding pocket so that it better binds my small molecule of interest.

Exploring all possible amino acid substitutions is computationally too expensive, so I am wondering whether smarter ways of looking at this problem have been developed.

Can someone point me in the right direction? I've searched Google but can't really find a straight forward answer


texts: Focusing on flowering plants, are there reasonable explanations why pentaploids would be more fertile than triploids?

texts: For the genus Rhododendron, triploids are sometimes fertile but pentaploids appear to be often fertile. Once Rhododendron seedlings gets above the triploid level, aneuploids not near euploid appear to become more viable at least in greenhouse situations. What mechanisms best explain this increase in fertility of odd ploidy and viability of aneuploids as ploidy levels increase?


texts: Do these large spiders in Taiwan belong to different species?

texts:
I see both of these spiders (and others) frequently on hiking trips outside of Taipei. Their large webs are often high overhead between trees but can be right across a hiking trail that hasn't been used in a few days, which can make for some excitement.

The two individuals shown in the photos were quite large; both had a body length of about 5 cm not counting legs.

They have similar body shapes but very different color. I don't know if they are completely different species, or different sex or different age.

I mostly see "Spider #2", and usually they are around 3-4 cm in body length. I see  "Spider #1" much less frequently, and I don't think I have ever spotted a smaller individual, but that could just be due to lower frequency.

Spider 1:

I spotted this on on this plant, but once disturbed he started climbing up a vertical thread back into the threes.

Spare photos: 1, 2

Spider 2:

I see these more often than Spider #1.

Adjusted brightness, contrast, sharpness to make the structure of the web more visible:

Spare photos: 1


texts: How should species density be calculated for a clumped distribution?

texts:
Lets imagine 5 plots of different size are sampled for a target species:

plot#  count  area(m^2)  plot_density
  1      1       5         0.2
  2      3       2         1.5
  3      0      10         0.0
  4      5       1         5.0
  5      2       6         0.33

What is this species' density?  I see two ways to calculate the density that give completely different values.

The first way averages the density at each plot:

$$
\frac{\Sigma(\frac{count_i}{area_i})}{5} = 1.41/m^2
$$

This seems OK but it doesn't do much to control for changing plot sizes.  For example if plot 3 above was 10 times larger the density would still be the same.  In a situation where plot sizes are determined by the environment (say, under natural cover objects) this seems less than ideal.

The second way totals the counts and the search area and divides them:
$$
\frac{\Sigma(count_i)}{\Sigma(area_i)}=0.46/m^2
$$

I prefer the second method because it seems to describe the animals' density more accurately. And I would be happy to use the second method, but my issue is that I am unsure how to calculate a summary statistic for method two since a mean was never calculated.  Method one gives a standard deviation of 2.1. What is the standard deviation for method two??

One possible solution I've come up with involves breaking the larger plots into 1m^2 plots and dividing the number of animals across those smaller plots.  So now I have 24 1m^2 plots with the following "counts":

plot#  count  area(m^2)  plot_density
1-5      0.2       1         0.2
6-7      1.5       1         1.5
8-17     0.0       1         0.0
18       5.0       1         5.0
19-24    0.33      1         0.33

Now, using the first equation above I get:
$$
\frac{\Sigma(\frac{count_i}{area_i})}{24} = 0.73/m^2
$$
With a standard deviation of 1.26.

Is this a reasonable approach?  Is there an established solution to this problem?


texts: In a tumor, why hypoxic regions have access to glucose?

texts: The Warburg effect is ubiquitous in cancer. It consists of the upregulation of glucose uptake, glycolysis, and subsequent lactate secretion, sometimes by over 200 times, in cancer cells as compared to normal cells. A common explanation for this phenomenon is that tumor cells can be oxygen deprived, because they are far away from the diffusive range of oxygen in the blood supply. But if that's the case, then how are they close enough to blood supply to have access to enough glucose? How can glucose diffuse to places where oxygen cannot, even if oxygen is a much smaller molecule?


texts: A doctor might give bicarbonate (HCO₃¯) to a patient who is breathing very rapidly. What is the doctor assuming about the patient’s blood chemistry?

texts:
The answer is:

The doctor is assuming that the rapid breathing is the body’s response to low blood pH.
(Source: Campbell Biology)

But this answer doesn't make sense. Why would the doctor give the patient even more CO2 if the patient is already suffering from an excess of CO2 that is causing the low body pH?


texts:
While reading about primary structures of protein, I came across the following image.
What do the numberings $n-1, n, n+1$ in the below image refer to?
I thought about it : The amino acid residues are numbered from 1 to n starting from the N-terminus to the C-terminus .
But the image below shows only a part of the protein.. so why is the last residue numbered $n+1$ instead of $n$ also, why is this shown as termination?

I looked out few papers.. but they seem to be very technical and beyond the scope of my understanding.


texts: What is the disadvantage of having no anticoagulation after pulmonary embolism?

texts:
Is chronic anticoagulation always given after pulmonary embolism?

What are the risks or disadvantages

if anticoagulation is not given?
if terminated early?


texts: How did dolphins acquire their dorsal fin?

texts:
I had been thinking bout atavism when I saw a picture of a dolphin. I had seen it before, but suddenly the dorsal fin startled me.

How did this dorsal fin evolve? Is it some atavism from eons ago, a revived feature, or a new development altogether? (Strong evidence of the former would be if the genes ruling dorsal fins in fish and dolphins would be similar.)

I've seen this How and why did mammals go back to the oceans?, but it doesn't ask nor explain about the dorsal fin.


texts: I'd like to know the name and a few details of a certain time-keeping structure in the human brain

texts: I once heard of this structure on the Discovery Science channel and have since forgotten the name. The details I remember about it were that it is the central time-keeping device for the brain located in the geographic center of the human brain. The DSC only mentioned it in passing to describe a person with an abnormality in this structure. Can someone post some reliable research links and a short description of it? I don't trust google much and am not good at using it, so thanks!


texts: Color of DNA, available absorption energy levels of DNA molecule, mutations

texts:
I have done a couple of DNA separations and observe that the clumped strands of DNA are white.

Is that an artifact of the chemicals used in standard separations? Or is it indeed the case that the DNA molecule in standard conditions does not absorb many or any photons in the visual range?

If that is right, can we use this as evidence for why visible spectrum light doesn't cause mutations, unlike say higher energy photons in the UV range?

Looking forward to your thoughts.


texts: Difference between flexion and contraction?

texts:
i asked this to my anatomy teacher and he said there is no difference but when it comes to specialy in body building when you say to flex their bicep they freeze their upper limb in order to do that but when you say contract your bicep they only isolate it an shortens it.
am I right with my reason?


texts: What are the risks of elevating the legs too regularly and when tired?

texts:
I started to to think the pathophysiology of elevating legs high next to the wall too often and when you are tired.
I think possible manifestations

some damage to valves of the veins (No!)
because of collateral circulation, rhombus, heart damage, ... (No! Only in pathological situation but cannot be considered here. I think here that the risk of thrombus leaving legs is higher when you elevate your legs.)

Other side is when you should do this.
To do regularly like every evening - may not be the right way to go.
If you are tired and you do this, the vasomotor tonus is already lower so smooth muscles can less help to keep the blood so much more stress to the valves.
Cardiac output is also less because of tiredness so lymphatic drainage is less.
Elevating legs will move more lymph and blood to the middle of the body.
So less lymph and blood can be moved back to legs when you tired.

What are the risks of elevating legs for too long time in Short time and Long time?
Is there any advantage in elevating legs like increasing blood circulation of our body?

In what manner would elevating legs harm valves?

There should be no damage to valves because the direction of the blood circulation does not change.
Blood is only going from legs to heart.
I think the vasoconstriction of smooth muscles occurs first in the legs.
This returns some blood to the legs.

How is lymph made - -?

Lymph is made in lymph nodes.
After leaving the node, it is rich in lymphocytes.
After leaving digestive system, it is rich in triglycerides so called chyle.
I think after leaving legs it is also rich in triglycerides.

[W]hat is the danger of lymph leaving the legs?

I think the effective lymph (that one used in legs) is coming from the lymph nodes of the legs.
Some lymph can be made in lymph nodes of legs so no danger of lymph leaving legs.
However, some may come from the region of coxa.
How long distance can lymph travel as effective unit of immune system?

If all lymph nodes are working, there is no danger of lymph leaving the legs, I think.
If there are problems with lymph nodes of legs, then there may occur some constitutional symptoms of legs - but not sure about how fast.

Does the heart get tired like your head does, or like muscles after exercise?

No.


texts:
I've been hearing the term passed around, and my own research has led me to some very high-level papers which propose new tools for accomplishing RNA engineering.

From the abstract of one of the above linked papers:

  These methods advance our ability to develop broadly applicable genetic tools and to elucidate the underlying sequence-structure-function relationships that empower rational design of complex biomolecules.

It seems as though we are edging close to designing fine-tuned lifeforms. It's easy to jump to exorbitant conclusions, so I'd like to make sure I understand what this is all about.

My questions are:

What exactly is RNA engineering and what can it accomplish (in plain english)
What are the implications of the advent of RNA engineering tools


texts: What is the etymology of the intermediate filament , Vimentin?


texts: Growth rate oscillation in the a population of non-interacting bacteria

texts:
I have come across this theoretical paper claiming that if you start a batch culture from a single E. coli cell, the exponential growth rate of the population defined as $$k = \frac1N \frac{dN}{dt}$$
could oscillate for as long as 30 to 40 generations. In this equation, $N$ is the number of cells, and $\frac{dN}{dt}$ is the rate of change of the number of cells with time.

My question is:

  Have these oscillations been ever observed? This seems like a very simple experiment. Looking for references.

Edit: As mentioned in the paper, the "oscillations are hidden to the optical density measurements which provide a proxy for the total mass of the population" and not the number of cells.


texts: Is there any academic reference that shows α-tubulin is around 50-55 kDa? The only thing I found is some data sheets from companies. I need the real reference.


texts: Why do animal teeth get darker if exposed?

texts:
I was wondering why the teeth of cats (And dogs, as far as I know, plus possibly some other animals or even humans) get darker if they are exposed to air / light?

Example:

(See the lower end of the tooth, which sticks out if the mouth is closed. No, the cat was not resisting, just slightly annoyed.)

So, my question is:

Why does this happen?
Would it happen to human teeth, if they would stick out of the mouth like the ones of cats do?

My guess is that it has something to do with the teeth reacting to air and corroding, but all my knowledge about biology comes from two years of biology in school, so I'm asking here.


texts: Can a virus be transmitted from a sweating person out to another person?

texts: In the sport of Jiu-Jitsu, close contact with many partners is common. Many times these partners are sweating profusely (Yuk), which in turn drips on the other person sometimes into the eyes, nose, and yes mouth. I am just wondering if viruses can enter in this way.


texts:
I have a plant fossil that my dad once found for me at a beach in Denmark, Europe about 15 years ago.

Is it possible to identify what kind of plant it is? There is a fossil water bubble suggesting that this plant lived under water.
What kind of process did the plant undergo in order to become a fossil?
Is it possible to find out how old it is?


texts:
In my texbook it is written that for non- vascular seedless plants the dominant generation  is the gametophyte as the gametophyte generation is larger and longer lived.
Is the criteria for dominant generation?-( Which generation the plant spends most of its life in?)


texts: Why are Aardvarks capable of burrowing given their size?

texts:
I was wondering if large animals could possibly dig extensive burrows for themselves to live in. The polar bear burrows, but snow is not dirt. The aardvark goes about 4' long, ~150 lbs: similar to a sheep. I think the aardvark might be the biggest dirt-burrowing animal, the only sheep-sized burrower.

I wonder why.

Is there anything special about the aardvark that at its size it burrows, while other burrowers are smaller?


texts:
The last time I came across this question was when I was in high school. And the explanation I was given is that epiglottis works like a valve, it prevents foods from getting into the windpipe. Still, if I google the majority of the top results agree with this answer.
Recently I got interested in rabbit anatomy after I bought a pair as pets. I learned they are "obligate nose breathers due to their epiglottis positioned rostrally to the soft palate". Then I tried to revise my understanding of epiglottis and that let to some sources that claim that epiglottis is not essential for swallowing. For example:

  It was at one time thought that the epiglottis acted as " the lid of
  the larynx"; it was supposed that during deglutition it fell back like
  a flap over the laryngeal aperture in order to prevent ingress of food
  or water. This erroneous view as dispelled by Stuart, who proved that
  during swallowing the epiglottis actually moved forwards, to be
  squeezed between the base of the tongue and the rest of the larynx.
  This view cannot be disputed by anyone capable of judging, and the
  truth of it is borne out when observing a patient whose epiglottis has
  been almost entirely destroyed by lupus, but whose powers of
  swallowing remains unaffected.

Negus, VE (1927). "The Function of the Epiglottis". Journal of Anatomy.

  Controversy has continued for well over 100 years regarding the role
  of the epiglottis in deglutition. We describe the effect of isolated
  epiglottectomy on swallowing success in a case series of 3 adult human
  subjects with isolated epiglottectomy due to trauma, surgery, or
  cancerous erosion. The patients were 42, 51, and 70 years of age, and
  swallowing was analyzed objectively with videofluoroscopy. All
  subjects exhibited successful swallowing with all food types: thin
  liquid, puree, and solid food. Specifically, the patient with
  traumatic epiglottectomy exhibited rapid swallowing success, the
  patient with surgical epiglottectomy exhibited a short period of
  dysphagia due to postoperative edema, followed by swallowing success,
  and the patient with epiglottectomy due to cancerous erosion of the
  entire epiglottis exhibited long-term adaptation, with successful
  swallowing maintained. We conclude that the epiglottis is not
  essential for successful swallowing in humans, because individuals
  can readily adapt to isolated epiglottectomy and avoid tracheal
  aspiration.

Leder, Steven B et al. “Epiglottis is not essential for successful swallowing in humans.” The Annals of otology, rhinology, and laryngology vol. 119,12 (2010): 795-8.

Judging from google searches and Wikipedia entry on the topic it seems the dominant view is: epiglottis prevents food from getting into the trachea. But many research like the ones  I have mentioned above says that people can swallow without epiglottis. How to make sense of these apparently contradictory claims?

Edit: My question is not the same as the question suggested. The suggested question seeks the function of "hyoepiglottic ligament" which is a ligament that connects epiglottis "to the upper border of the body of the hyoid bone". My question is related to the function of epiglottis itself in the background of contradictory claims found in the literature.


texts: Can cancer cells transmit from one organism to another?

texts: I know cancer cells are very resilient, so would it be possible for them to survive outside of the original organism for long enough to be absorbed by another? Furthermore, would that type of "infection" be possible?


texts: Can beavers control the direction a tree falls?

texts:
We humans can easily control the direction a tree falls by making a number of strategic cuts, essentially creating a hinge:

This prevents trees from falling on equipment and people and sets them up in a good location for the subsequent processing steps. I'm curious if beavers also perform directional felling and, if they do, how do they choose the direction (eg to fell the tree towards the damn, in a river, away from thick brush, etc)?

In this picture (and others), it appears as though the beaver has created a hinge. Is their any method to their technique or do they just start chewing and hope for the best?


texts: This is from Bangladesh though I am not sure it's native here


texts: Is there any free database when one can check the gene frequency in a healthy population? For example I would like to check it for genes like BIN1, CLU or CR1. On the English Wikipedia I found a gene frequency for APOE gene (for example: 79% for e4 and 7% for e2), and it was linked to the specific publication. I wonder if one need to look for specific publication when looking for information like that or there is any database with such information available?


texts: Do sea sponge cells transfer nutrients to each other?

texts:
Does a sea sponge cell transfer nutrients or energy to their neighboring cells or is their only symbiotic relationship that they are connected to each other forming a structure?

The sea sponges that I'm talking about are the ones that can be broken apart and naturally reassemble themselves.

YouTube of the sea sponge I'm talking about.


texts: What is the difference between a polysaccharide and a macromolecule?

texts:
I'm having trouble understanding the difference between "Polysaccharide"
and "Macromolecule".

I know that polysaccharides are made of chains of monosaccharides.  In addition, I know that macromolecules are made of monomers.

But what is the difference?


texts: Can't identify this fish caught off NC coast

texts: It was caught approximately 35 miles off the coast of North Carolina. I've been a charter fisherman for more than 25 years and never seen anything like it. Thanks for your help!


texts: Simple protein graphics software for stick models

texts:
Anybody know of a good free molecular graphics system that allows PDB file input? I prefer that it does not use Java. I also prefer that it is online, although I would consider recommended software with a simple download process.

I am looking into trying to display a stick version of one of the chains of a protein, and want a program that can help me easily do this.

I have tried using FirstGlance and Protein Workshop, but FirstGlance is difficult to navigate through and the Protein Workshop doesn’t do stick models.


texts: Why do I want to urinate when I touch water?

texts:
I've noticed that whenever I come in contact with running water (especially when I do my dishes), I have a desire to urinate. A quick Google search (link,link) gave me few different hypotheses:

Cold diuresis. Being in contact with cold water reduces temperature on the skin, which then constricts blood vessel to reduce heat loss, thereby increasing blood pressure and prompting the bladder to release excessive fluid.
Afferent innervation. I wasn't able to comprehend all the details of the process, but it seemed like this hypothesis is pertaining to the nervous system than circulatory system, hence different from first hypothesis.
Learnt psychological response. Second article linked above argues that this is a conditioned reaction, where even the sound of tap water triggers the desire to urinate. While it did not mentioned specific details of how this happens, I'm also assuming that this hypothesis is different from aforementioned hypotheses, because this hypothesis sounds more like a psychological response than biological reaction.

Which one of these hypotheses accounts for the desire to urinate when in contact with water? How exactly does it happen? If there is any other reason, feel free to add in the answer.


texts:
This one was found in the woods of northern Poland. It was about 5 cm long and crawling pretty dynamically. For me it seemed a little too big for a butterfly larva.

What is it called?


texts:
What is the difference — if any — between "higher plants" and "vascular plants"?

On Wikipedia, "higher plants" redirects to "vascular plants", which seems like an indication that both terms are essentially the same.

Is one of the terms preferred over the other?


texts: Could a human become infected with rabies in such a way that even prior vaccination wouldn't stop the infection?

texts: Given the highly persistent nature of rabies after entering the brain, I was wondering whether certain ways of exposure to this virus could be risky even for a previously vaccinated individual. I understand that no vaccine is 100% effective, but would the risk of infection be particularly increased in case of exposure at some particular site on the body? Which mechanisms of the rabies infection would play role in this situation?


texts: I notice mold likes to grow on silicone caulk. I find it odd since silicone is mostly inorganic and doesn't contain any nutrients for mold to grow on unlike soil and clothing. Can mold metabolize silicon?


texts: Why is Homo sapiens not categorized as an invasive species?

texts:
According to Invasive Species Advisory Committee (ISAC), the definition of the invasive species is “a species that is non-native to the ecosystem under consideration and whose introduction causes or is likely to cause economic or environmental harm or harm to human health.”

But considering the following facts, why is this species not categorized as an invasive species?
Homo sapiens:

is non-native to the most of the ecosystem which it is inhabiting, since it originated from a certain area of Africa and spread quite recently.
has often caused environmental problems by decreasing the local species after its introduction, as it is known that the number of species in the planet is drastically decreasing ever since the advent of Homo sapiens.
is likely to cause the same problem after introduced to new environment where homo sapiens hasn't inhabited yet.

http://www.invasivespeciesinfo.gov/docs/council/isacdef.pdf


texts: I distinctly remember an episode of NOVA from the early 1980’s that concerned itself with gold. One of the points that was made was that there are trace amounts of gold in the human body, specifically in the heart, and without this gold our hearts wouldn't beat. I've never been able to find another citation of this. Is this true?


texts: Is there a consensus on the CaMV 35S minimal promoter sequence?

texts:
We have an algal enhancer element and a transcription factor that probably binds it. Basal expression of the enhancer element or full promoter driving luciferase in tobacco protoplast was extremely low. I heard this could be overcome by fusing it to a minimal 35S promoter fragment but I can't seem to find a clear sequence for this minimal promoter.The best I could find was on the cambia website where they say it is -90 http://www.cambia.org/daisy/promoters/242/g1/250/264.html

1) Does anybody have experience with increasing the expression of enhancer elements like this?
2) And what sequence did you use for this?


texts: Method to recognize the age of a firebug from the pattern on its back

texts:
Can I recognize the age of a firebug from the pattern on its back?

If yes, what pattern shows what age/stage?

Below is what I extrapolated from Wikipedia, but is there a more precise scale with more steps? (I could not find more than this with google).

Nymph: Adults:


texts: How does one calculate the resolution of a crystal structure?

texts:
Considering that I have a diffraction pattern of a crystal, how would I calculate the resolution of a structure in Angstroms? How does that value differ from the information that I would get from the beta-factor?

I'm aware that the resolution can be calculated by Bragg's law but how does that provide details for the entire structure?


texts: What happens to snakes that swallow rodents as a whole?

texts: As we all know, a few species of snakes swallow rodents as a whole. My question is what happens to the teeth and bones of these animals? Won't they cut into the flesh of the snake and hurt it? Are the digestive acids strong enough to dissolve bones and teeth? Even so, I'm sure the process takes time, and during this period won't the snake get injured?


texts: Can I explain the kinetics of a ligand looking at the ligand-protein co-structure?

texts:
Can I explain the kinetics of a ligand binding to a target protein (association and dissociation rates) by looking at the protein-ligand co-structure?

Editing my question after a few comments:
I have a set of ligands targeting the same protein. These ligands show different kinetics properties, i.e. different association and dissociation rates. Would it be possible to explain why they have a different kinetics if I had the x-ray structure of the different protein-ligand complexes? Would I be able to say that ligand A has a slower dissociation time compared to ligand B because it makes for example 3 H-bonds instead of 2? How accurate would this conclusion be? Would I need in any case MD simulations?


texts: What's the advantage of autocrine signalling?

texts:
In the antibody-mediated immune response, when the helper T cell gets activated by the costimulus (IL-2 and TNF-α secreted by the APC) which in turn produces IL-2, IL-2 acts in an autocrine manner. I'm just wondering why does IL-2 have to be secreted? Why doesn't it just exert an affect while it's already inside the helper T cell? What's the point of autocrine signalling?

I hope the answer isn't going to be, "Well, that's just the way it is..." because paracrine and endocrine make sense and have advantages, but autocrine just seems a bit extra.


texts: What are the trade-offs between polymerase chain reaction (PCR) vs Loop-mediated isothermal amplification (LAMP)?

texts:
I've heard that LAMP could be a good alternative to PCR for DNA strand amplification and detection because the equipment required is cheaper, more portable, and the amplification is faster since all happens at a single temperature.

Since this system has clear advantages, I'm curious what are the downsides that prevent it from completely overtaking PCR/qPCR?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862059/ mentions some disadvantages:

  However, this technique has some limitations. Complexity of multiple primers’ designs for multiplication of new gene regions and selecting the suitable regions in the gene sequence for efficient design of primers, complicated product having cauliflower-like structures with different sizes, lack of commercial kits based on LAMP technique and complexity of this method mechanism are some of its drawbacks limiting its popularity among the researchers; and it not as common as PCR-based method.

but they just don't seem that important compared to the large benefits for diagnostic usage.

For example, from this video https://www.youtube.com/watch?v=L5zi2P4lggw I understand that more primers are needed, but is it that hard to "just create a few more primers"? Aren't those just deterministically determined from the target DNA of interest in this  case?

I can see why the cauliflower structures matter for certain applications, e.g. I guess those messy strands are not going to go through an Oxford Nanopore pore for sequencing, but do they matter when we just want to know if the DNA of interest is present or not?

Related articles:

https://www.researchgate.net/post/What_is_the_difference_between_a_PCR-RT_and_loop-mediated_isothermal_amplification_LAMP
https://www.ncbi.nlm.nih.gov/pubmed/22051073

I later learnt that there are other isothermal amplification amplification schemes out there as well, maybe  I knew about those I would have asked a more generic isothermal question:

RPA
which is apparently used in Abbot ID NOW system according to this and is being used for Covid-19 diagnostics.
HDA
NASBA
NEAR
Strand Displacement Amplification


texts:
A plasmid is a small DNA molecule that is physically separate from, and can replicate independently of, chromosomal DNA within a cell.

In general, in eukaryotes, episomes are closed circular DNA molecules that are replicated in the nucleus. Viruses are the most common examples of this, such as herpesviruses, adenoviruses, and polyomaviruses. Episomes in eukaryotes behave similarly to plasmids in prokaryotes in that the DNA is stably maintained and replicated with the host cell.

Source is wikipedia.


texts: Why human hair is losing its color over time?

texts:
Human hair is losing its color over time, that's a known fact.

I would like to know why, meaning what biological processes are involved in this?

Also, is it part of the DNA somehow, i.e. the exact rate of losing the color is known when one is born?


texts: Can a relationship exist that is mutualistic/parasitic/etc. but not considered symbiotic?

texts:
Wikipedia definition of symbiosis: "Symbiosis (from Greek σύν "together" and βίωσις "living")[2] is close and often long-term interaction between two or more different biological species."

Wikipedia definition of mutualism: "Mutualism is the way two organisms of different species exist in a relationship in which each individual benefits from the activity of the other."

In intro biology class, I (and many other people, I'm sure) was taught that mutualism is a type of symbiosis. However, now that I think more about it, it seems like some relationships that are mutualistic don't appear to fit the definition of symbiotic. Some relationships are clearly mutualistic and symbiotic (humans and gut flora, for example) but other relationships (like bees pollinating flowers) are mutualistic but don't appear to fit the definition of "close and often long-term interaction". The same of course goes for parasitic, ammensalistic, etc. relationships as well.

Thoughts, anyone?


texts: Do cold blooded animals generate any heat?

texts:
In explaining energy and work to an 8 year-old I said that all conversion of energy generates heat as a by-product.  For example, cars generate heat in their engines and running generates heat in our bodies.  Then the 8 year-old said, except for cold-blooded animals.

So my question is, do cold-blooded animals generate any heat in their conversion of stored energy (food, fat, etc) into motion?  If they generate heat, why are they cold-blooded?


texts: Flow Cytometry to learn about Cell cycle

texts:
I am posting my Flow Cytometry data here again because I realize that there are many people who are willing to help me, and I can learn a lot from you guys.

In this cell culture Lab, we use Cell U-937 Lymphoblast. And we want to learn how can we analyze cell cycle by using flow cytometry.

Could anyone help me to explain how to read the flow cytometry result related with cell cycle? I will be very glad to learn from you guys.

Thanks in advance!


texts:
I "inherited" a plant and was trying to identify it (to understand how to take care of it - plants usually have a hard time with me).

I belive this is a sentry palm (from photo matches gathered on Internet) but my leaves seem much more narrow than the ones on the pictures.

The plant is in France and is probably not a fancy one (in the sense that it should probably be available in Ikea or a general plant store).


texts: Why are human children more likely to get lice (nits) than adults?

texts:
By my own experience, lice seems to be prevalent in the hair of human children, but not in adults.

My question is Why are human children more likely to get lice than adults?

Assumptions:

Can be referred to lice/louse/nits


texts:
I'm 20, in about 6 months I turn 21. For some time I've been wondering whether there are natural, non-surgical and non-pharmaceutical ways that humans can continue to grow after reaching adulthood.

Please answer only if you are certain about this or you can reference any
trustworthy source.

Thank you a lot friends.


texts: Does preservation in ethanol alter leaf litter mass?

texts:
I have benthic samples that were collected with an Ekman dredge from some small ponds.  The samples contain quite a bit of coarse particulate organic matter (CPOM, basically dead leaves).  I would like to quantify the amount of CPOM in the samples but they were preserved with 70% ethanol in the field.

Is there any evidence that ethanol preservation alters benthic CPOM mass?


texts: Can anyone expolain this? Cell culture vials have strange hair-like condensation patterns

texts:
What is the hair-like polymer that condenses on the caps of the plastic cell vial? Inside vial are cells in a mixture of FBS and DMSO. The vials were frozen slowly in a special isopropanol-filled container (isopropanol does not touch the vials) to -80 degrees celsius, then put on dry-ice to move to a liquid nitrogen cryogenic freezer. The hair-like crystals appear to be water, but bend toward my finger when nearby, similar to the static attraction.

I suspect the has something to do with DMSO/isopropanol leaking out, and the very low temperatures cause this strange condensation pattern, but I'm not sure.


texts: Are there any DNA base sequences that are fully conserved between the genomes of all humans?

texts:
That is, they don't differ throughout the entire population. I understand of course that we can't DNA sequence every human, so by "fully" I mean there's an incredibly small probability of there being a mutation retained in a living individual.

Also by the genome I'm referring to the consensus of all the cells composing in the individual.

I guess my question is really, where are the crucially important sections of DNA that are simply unmodifiable without being incompatible with life?


texts: Why don't vaccines cause bacterial resistance?

texts:
Since bacteria can evolve to overcome antibiotic use, why wouldn't they be able to evolve to overcome antibody or cell-mediated immunity?

(One possible explanation: antibiotics have only one target while vaccines elicit antibodies against multiple targets and multiple T-cell epitopes. Even more targets arise when comparing sub-unit vs inactivated vaccines, where the number of targets are extremely higher using inactivated vaccines, containing whole bacterial cell.)


texts:
Can anyone identify this caterpillar we found on a cauliflower? This was the only photo we could get of it.

Location : Ceres, Fife, Scotland


texts: Do hornets return to the same nest after winter each year?

texts:
I have what I think is a hornet nest on the soffit of my house.

The nest has been removed, however, the hornets keep rebuilding. Also, they have started to swarm the sewer vent pipe (not shown in photo).

If fail to get rid of the hornets this fall, will they return to the same nest next year (or overwinter and continue to live there)?

I'm not sure if this is relevant or not:

To give you an idea of what kind of winters I am dealing with, I am near Toronto, Ontario; the temperature goes down to -25 degrees Celsius.


texts: Are RNA transcripts always synthesised from the same DNA strand?

texts:
The DNA is read 3'->5' (and RNA synthesized 5'->3'). But due to the DNA strands having to be complementary, it seems to me that the origin can only appear on the correct side of the ORF on one of the strands. And even if it were possible to synthesise RNA from the other strand, due to the directionailty of the strands/RNA the RNA transcript would then code for the protein in reverse. Surely the reverse synthesis of a protein, even if containing all of the same amino acids, would lead to dfferent folding and thus only on eof the proteins is correct?

Now that I am considering the origin, it seems likely to me that the strand on which the origin is dictates which strand acts as the RNA template (perhaps both starnds can, however for a given GENE the RNA is always synthesised from the same strand.

Is this the case? I have read this post: Majority of transcripts are from sense strand? however I found it slightly confusing. I think what the answerer said is similar to what I have suggested here, however I am not quite sure. Would greatly appreciate some input.


texts: Rosetta ab initio prediction and protein-protein interaction fitness help

texts:
I have designed several proteins which I predict have interactions with another protein using the sequence based Conjoint Triad Method. I would like to know which ones structurally are predicted to dock and have interactions. I have Rosetta installed and have looked at the examples a little. Rosetta doesn't have much "how to" documentation on protein design and fitness selection. Could someone please walk me through the process line by line of taking a fasta with a series of proteins through rosetta's ab initio pdb generation and then how to and where to look for a fitness of each proteins interaction/docking? Also I read in "Design of Protein-Protein Interaction Specificity Using Computational Methods and Experimental Library Screening" page 91 that it was possible to generate specific protein combinations that map to a structure using Rosetta. How do you do that?
thank you :)

Rosetta commons links to additional software add ins but omits the crucial Sparks-X. I found Sparks-X from at this webpage. And I found that the code for make_fragments.pl needs to have many changes made for it to run properly. Several files are listed in make_fragments.pl. Two files without links pdb_seqres.txt and entries.idx are found at RSCB, below.

The NCBI nr database requires about 100 gigs of free space to properly load and process. Anything less than that results in errors.

make_fragments.pl requires a single gene in a fasta file. multiple genes in the fasta file cause it it crash.

Psipred nolonger has a dat4 so this line needs in make_fragments needs to have the dat4 removed.

"$PSIPRED sstmp.mtx $PSIPRED_DATA/weights.dat $PSIPRED_DATA/weights.dat2 $PSIPRED_DATA/weights.dat3 $PSIPRED_DATA/weights.dat4 > psipred_ss",

My make_fragments does not always finish it sometimes gives an error

ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!

This error was caused by a ^M in the fasta file removed with vi.

I'm attempting to bypass the fragment picker with csrosetta toolkit from .csrosetta.org/

libstdc++6 32bit version must be used for talos+
I used a Ubuntu 32 bit machine to copy the /usr/lib/libstdc++.so.6 and uploaded it here.
http://www.mediafire.com/?j0133qqwiilsuz1

cs-rosetta does not create fragments for unknown reason. I have emailed the creator and I have emailed rosetta commons support as well. For now I recomend the on-line server roberta.

There are examples of how to use prepacking and docking in rosetta_tests.

PPI can be designed by docking a protein to another protein then running sequence tolerance. Though the resfile doesn't seem to be able to limit the changes to certain nt at this point.

Sequence tolerance has an extra rotamer bug and fills up memory and the page file for certain proteins if the "ex" series flags are use. It also sometimes ignores the resfile so double check the initial scripts results before begining a multi-generational study.

Ab initio relax has a bug which prevents it from running twice in the same directory. Remove default.out to rerun the structure prediction.

Docking can be forced to one location by using a constraints file but the radomize and spin options must be turned off for it to work properly.

-constraints:cst_weight integer
-constraints:cst_file cstfile

http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/de/d50/constraint_file.html

http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/summaries.html


texts: Probability of Extinction under Genetic Drift

texts:
Here is the Wright-Fisher model of genetic drift:

$$\frac{(2N)!}{k!(2N-k)!}p^kq^{2N-k} \Leftrightarrow \binom{2N}{k}p^kq^{2N-k}$$

where $\binom{2N}{k}$ is the binomial coefficient.

This formula gives the probability of obtaining $k$ copies of an allele at generation $t+1$ given that there are $p$ copies of this allele at generation $t$. $N$ is the population size and $2N$ is the number of copies of each gene (this model applies to diploid population only).

From this formula, how can we calculate the probability of extinction of an allele in say 120 generations starting at a given frequency, let's say 0.2?

and

How can we calculate the probability of extinction rather than fixation of an allele present at frequency $p$ if we wait an infinite amount of time?


texts: How can co-dominant alleles work in flower petals?

texts:
I am studying gene inheritance, and I understand complete dominance/co-dominance and incomplete dominant penetrance in flowers. I know how to recognize each case.

However, how does co-dominance work? If I understand correctly: when a gene is transcribed, both alleles are transcribed. Hence, for flower petals, if I have a "red" allele and "white" allele, and there is incomplete dominant penetrance, I get rose petals. However, if both alleles are co-dominant, why are petals either red or white? Aren't both alleles transcribed? Or perhaps, in the case of co-dominance, heterochromatin is responsible for shutting down one allele in lineage cells?

I hope that I am expressing myself correctly. Thank you very much for your time!


texts: What is possibly wrong with my gel electrophoresis when i don't see bands of DNA ladder?

texts:
![enter image description here][1]

What was possibly wrong in my gel electrophoresis when I didn't see bands of DNA ladder?
I'm running a 2% electrophoresis gel (65v for 2h) to confirm the presence of qPCR amplification products, I can see the gDNA bands, is only the ladder that don't appear.


texts: What gives diarrhoea caused by Cholera its milky colour?

texts: The diarrhoea caused by the Cholera bacteria is a milky colour, also known as 'rice-water' like. Why is this? I have a fairly good understanding of how Cholera acts on the body.


texts: Is Berlin patient immune to HIV after bone marrow transplant?

texts: Is the Berlin patient here : https://biology.stackexchange.com/a/39364 become immune to HIV after bone marrow transplant? Or in other words: Can he get HIV infection again?


texts:
The Chinese Idiom The mantis stalks the cicada, unaware of the oriole behind (螳螂捕蝉，黄雀在后), which the story behind the idiom comes from Shuo Yuan(说苑), refers to those who are attracted by immediate interests without thinking about the possible dangerous results.

In reality, do mantises stalk cicada? Moreover, are cicadas stalked by birds?


texts: what kind of bonds join the okazaki fragments

texts: During DNA replication, the synthesized okazaki fragments adjacent to each other are joined up directly by DNA ligase-catalyzed phosphodiester bond formation. Can someone point out to me which part of this statement says it's false? All I know is that the fragments are joined together by DNA ligase, which can only mean the part about the phosphodiester bond is wrong, but arent the 2 nucleotides joined by a phosphodiester aka nucleotide bond?


texts: Is there a biological reason for spreading food intake into breakfast-lunch-dinner?

texts:
I keep hearing over an over how humans can satisfy their entire daily caloric need in one sitting at a fast food restaurant. At the same time I'm looking at the kitchen plates, cups, etc, and they also seem to be getting bigger.

This makes me ask the question - was breakfast-lunch-dinner a concept invented because people:

Could not make enough food?
Could not make food fast enough?
Could not make food with high enough caloric intake?

I'm thinking along the lines of: you can make only so much tasteless porridge and stuff it in your mouth before it gets cold. At the same time I know that gorillas and some other primates have a very long (8 hours?) feeding session of eating raw vegetation throughout the day.

Is there a biological explanation why human food intake should be spread into X distinct sittings?


texts: Does drinking water from stainless steel increase hemoglobin?

texts:
I'm pretty sure iron molecules will be present in water.

Cooks who use iron or stainless steel pots increase the amount of iron they consume


texts: Does homeopathic or herbal treatment of cancer have any scientific recognition?

texts:
Even though we have a very high tech society, cancer is still a serious issue. We humans still are not entirely capable of fighting cancer.

Radiation and chemotherapy are still considered the best methods for treating it and frequently, even these don't work. And, as for this disease, it is a phenomenon of uncontrolled cell growth that has lead to the death of many people. Within these main two treatments, there is plenty of controversy surrounding applying radiation and chemo in a proper sequence.

However, there are also some different methods known and available on the market to treat cancer. Among them, homeopathic and herbal treatments are the most common. So, my question is, do they really work and is there any scientific evidence of that?  If yes then what is it?


texts: What is the smallest touch sensation that a human can feel?

texts: What is smallest touch (pressure) sensation that a normal, healthy person (not hypersensitive nor insensitive) can feel on the palm of the hand?


texts: Signaling pathways with Receptor Tyrosine Kinase clarification

texts:
This question is regarding signaling pathways with RTKs, Receptor Tyrosine Kinase.  The picture posted has one thing wrong with it and I am supposed to figure out what that is.

What I have come up with so far is that the Ras protein shown that goes on to activate RAF, has GDP attached to it.  This cannot be true from what I understand, as Ras must have GTP bound to it in order for Ras to stay in it's closed conformation.  The closed conformation is what activates the rest of the signals.

I am wondering if I am correct in my assumption, or if there is something else in the diagram I am missing.


texts: Nocioception (pain perception) in subcutaneous tissue

texts: There seem to be no nocioceptors (pain and temperature sensitive nerve endings) in subcutaneous fat. there are nocioceptors and other receptors in veins running through fat, but these can be avoided. Does this mean that subcutaneous fat can be cut, or otherwise traumatised, such as with diathermy (burning) without causing pain?


texts: Examples for oscillatory behaviour in the human body

texts:
I'm looking for examples in the human body which show periodicity, more precisely, I'm looking for examples of oscillating reactions that occur in the human body which can be modelled using the Hamiltonian of the harmonic oscillator.
for example, as someone mentioned to me before, the circadian rhythm is controlled by the oscillation of protein concentration. I wanted to know if there are some examples from biologists perspective?
I want to read more about it, and I will be grateful to hear more examples so I can look for information about it online or if anyone could refer me to some reading material regarding this subject.
Thank you very much for your time and attention.


texts:
I recently found these two winged ants near a colony. There were 5, but 3 flew away.

Location: Nassau/The Bahamas. November 19, 2017.

Are they queens? And What species?


texts: Is lemon water an alkalizing agent in the body?

texts:
I was recently having a discussion with someone about whether lemon water actually increases the pH of your body (by which I assume they mean the blood); their claim was that once Citric acid was metabolised it results in an increase in pH due to the "anionic properties of citric acid".

I looked around on the internet at it would seem that this is a common claim circulating around health forums: Example 1, Example 2, etc.

Now to me this sounds like something which cannot possibly be true and appears to be a crazy health fad (they seem to spuriously appear and gain popularity now and again), and I cannot find any scientific papers or articles to support or refute their claim.

Can anyone provide a reliable scientific reference or provide a reasonable scientific explanation (preferably accessible to a layman with only A-level (college level) understanding of chemistry and biochemistry) which either supports or refute the claim that drinking lemon water (citric acid) increases the pH of the blood?

I have crossposted this to Chemistry.SE as well, as it is a crossover between chemistry and biochemistry.


texts: What is the distinction between F' plasmid and R plasmid?

texts: Is there a difference between an F' plasmid that has taken up a chromosomal gene that conveys antibiotic resistance, and an R plasmid? Is a bacterium containing an R plasmid and yet lacking an F+ plasmid capable of horizontal gene transfer by conjugation?


texts: Does *E. coli Dh5 Alpha* strain has the ability to degrade polyethylene?

texts: Does E. coli Dh5 Alpha strain has the ability to degrade polyethylene? What are the bacteria that can be used as a control in the research of polyethylene degradation?


texts: How do special NK cells get to the uterus?

texts: When an embryo is creating a placenta in the uterus, some special kinds of Natural killers cell of the mother will move and gather towards this placenta (for exmaple for growth components increasing blood of the placenta). But how do these NK cells know where to go....do they kind of 'smell' the uterus?


texts: What can be the reason for yellow and dark marks on leaves?

texts: The plant in our office started to have this strange marks, what can be the reason for that kind of marks? how can we cure the lovely plant?


texts: Why do some plants develop a shiny layer that looks like plastic?

texts:
I noticed some plants that look almost as if they were made of plastic and am wondering what and why that is. Here is a sample photo:

My guess is that this might be some sort of waxy cuticle that protects the plant from either water loss or pests.


texts: How long does a mosquito take to land on a host, bite, and fly off?

texts:
How long does a mosquito take to land on a host, start its bite, end its bite and then fly off?

And what about different species?

I am most interested in human hosts.

References to web sites or books would be appreciated.

I cannot find this even after extensive trawling of Google.


texts: What percentage of individuals infected with COVID-19 don't have symptoms?

texts:
There are various statistics estimating mortality of COVID-19 infections, based on how many diagnosed people have died. These numbers are used by various media to extrapolate how many people will die if the disease spreads uncontrollably.

However, what is missing here are the undiagnosed infected (due to their immune system fighting the virus fast enough and thus only presenting with mild, or no, symptoms).

Do we have any data or estimates for the percentage of infected people that are asymptomatic?


texts:
Does a human body decompose in a completely sterile environment ? If yes, what decomposes it ? And how fast ? What happens in vacuum ? Can it remain exactly the same ?

Thanks


texts: Is there a critical size for a bacteria colony forming?

texts:
I am a maths student doing a project based on modelling bacteria and phages. In one of my models the bacteria population reaches a population size of ~450 cells.

Would a colony of bacteria this size be at risk of completely dying out if there was an environmental change (e.g. pH or UV)?
Also, is there such a thing as a critical colony size? e.g. if a colony of a certain type of bacteria falls below this critical size then the probability of a colony forming would be very low.


texts: Is there a free software for manual sequence annotation?

texts:
I'm looking for a software that would allow me to make a quick graphical annotation of the structural features of a sequence. Something that would look like what you get in jalview, with your sequence on top and tracks at the bottom that highlight which part is an alpha helix or a beta sheet.

My final annotated sequence would look like this:


texts: (Genetics) Is a silencer the same as gene silencing (heterochromatin)?

texts:
Is silencer the same as gene silencing?
I know that gene silencing refers to those heterochromatin concentrated at the telomeres or centromere. It is also related to methylation. But what about a silencer. Are they the same? Or is silencer an opposite of enhancer (repressor)?


texts:
I was trying to look up what the poison in Chinaberry is, however, with the exception of a couple related compounds was able to find no information on the poison. What chemical makes up the Chinaberry poison, and what is this chemical's concentration and LD50, if known?

Edit: The Chinaberry I am referring to is Melia azedarach


texts: histones in the Hershey / Chase experiment

texts: When DNA is injected into the cell why aren't histones(protein) also injected and why wouldn't the radioactive sulfur therefore also be present in the infected cell


texts: What is the difference between natural selection and adaptation?

texts: From what I've read it seems that the only actual difference is that creationists use adaptation and people who believe in evolution use natural selection. But otherwise, from my understanding, the two terms are synonymous. Is that correct?


texts: What is this furry, long-limbed, presumably tree-dwelling creature?

texts:
Can anyone identify the species below? I believe the picture was taken at the Museum Of Zoology in Cambridge so maybe someone cleverer than me could narrow it down using their collections search.

Of the species I know, it looks most like a tarsier to me. Is there any relation?


texts: Is homosexuality an adaptation in humans?

texts:
Homo sapiens have menopause - as some other mammals (e.g. some Cetacea) - a phenomenon where older females live for decades after the end of their own reproduction.

Perhaps homosexuality, that looks to hold at 10% levels in any population, may be just the same sort of adaptation?


texts: How is e-value calculated in BLAST 2 sequences (BLAST+)?

texts:
In the BLAST+ packages, you can align two sequences instead of searching a database:

tblastn -query seq1.fa -subject seq1.fa

The web BLAST documentation states that e-values are calculated from the nr database:

  Because BLAST 2 Sequences uses the size of the current nucleotide or protein nr database to calculate Expect values, you may need to significantly increase the Expect threshold in order to see shorter alignments.

However, the command-line documentation explicitly states that you cannot provide both a database and a subject sequence:

-db <String>
BLAST database name
 * Incompatible with:  subject, subject_loc
-subject <File_In>
Subject sequence(s) to search
 * Incompatible with:  db, gilist, seqidlist, negative_gilist,
   db_soft_mask, db_hard_mask

How is the e-value calculated when using BLAST-2-Sequences on the command line? (I am fairly certain I do not have the nr database downloaded.)

Thanks!


texts: Michaelis-Menten Kinetics: Does measuring apparent Km and Vmax take into account competing reactions?

texts:
I am learning about why it is important to measure Km and Vmax for each experimental setup because measuring the "apparent" Km and Vmax includes enzyme inhibitions of which one might not be aware.

However, what if there are entire reactions going on that are consuming the product or substrate that are not known? Are these accurately aggregated into the Km and Vmax measurements?

Here are some of the links that I read through:
http://www.bio.upenn.edu/media/pdf/courses/F02/BIOL202/Handouts/BIOL202.ApparentKmandVmax.pdf

http://en.wikipedia.org/wiki/Enzyme_inhibitor


texts: Evolution of protein and protein efficiency

texts:
Suppose we have a bacterial protein that performs a function and let's say we can measure the efficiency of the protein. Let's say we have two species, species A and B, both of which have this protein. One of these species, species A, is close to the common ancestor of A and B, in terms of evolutionary distance, while B is farther although for both cases, it took two speciation events to end up with species A and species B.

Let's say for both for species A and species B, we measure the protein efficiency in different environments. The species A protein has the efficiency highest in an environment most similar to its own and the same is true for the species B protein. But let's say we have two situations:

When species A protein has best efficency, it has a lower efficiency compared to species B best efficiency
Species B protein best efficiency is lower than the species A best efficiency

In these two cases, what conclusions can we make in particular about the evolution of the protein itself? Can we show that the protein evolved to a degree to suit the different environment of species B compared to species A?


texts: Difference between imputing and typing in GWAS studies?

texts: In genome-wide association studies (GWAS), what is the difference between imputing and typing? Are they the same?


texts: How lymphocytes in lymphatic system get oxygen?

texts: We know that the gas-transporting protein hemoglobin is absent from the lymphatic system. So, how does gas transportation takes place in lymphatic system? Is mere diffusion from surrounding blood vessels sufficient for lymphocytes and lymphatic endothelium to survive?


texts: Recommendation for a molecular biology book that explains how we know what we know

texts:
My background is in math and I know very little about biology.  The few biology books that I've looked at seem to explain what is known (or what is believed), but don't really explain how we know what is known.  For a specific example, when I hear that "DNA makes RNA and RNA makes protein", I would like to know things like:

How do we know that DNA makes RNA?
How do we know that RNA makes protein?
How do we know that there is such a thing as "protein" in the first place and how do we know what it is?
How do we know that there is such a thing as RNA and how do we know what RNA is?

Can you recommend any books that do a good job of explaining how we know what we know in molecular biology and genetics?


texts: Link between macro lncRNA and DNA looping

texts:
I was wondering if anybody knows some publication about macro lncRNA (very long unspliced RNAs) or more generally a transcribed RNA that may lead to cis-DNA looping of genomic regions overlapped by the (macro) lncRNA transcript ?

Thanks


texts: I have seen these on my hands recently and I am wondering what they are. Urban Setting. South Central Pennsylvania.


texts:
This was a test question, and I'm not too sure about the answer.

Which statement about phenotypic plasticity is false?

a. Because the plasticity of a phenotypic trait may be costly to maintain, it will not be favoured in stable environments.

b. A trait that is an adaptation will not vary with environmental conditions within one generation.

c. Phenotypic plasticity can itself be an adaptation to varying environmental conditions.

d. Variation in phenotype among populations of a given species across different environments is only caused by phenotypic plasticity.

If you could explain the answer to me, that would be great.


texts:
I would like to know the steps the body takes to heal a broken bone and what happens if it cannot heal properly.  I am not looking for advice or explanations on resting and not doing activity, I am genuinely interested in understanding the outcome if activity is not stopped

Here is the scenario:

A rock climber develops a pain in the lower part of their middle finger.  The pain is not so bad so the climber continues to climb for four weeks, but the pain has not gone away.  The climber decides to go to the doctor fearing they have an A2 Pulley tear.

To their surprise the Doctors tests show no A2 pulley tear but rather a minor stress fracture of the Proximal Phalanx.  The doctor says stop climbing, however the climber has several trips planned and does not experience any pain while climbing nor a loss of strength or power while climbing.  The only time pain is felt is when the lower part of the middle finger is squeezed.  Because of this the climber decides to continue climbing as they just love it so much.

Question:  What will happen to a stress fracture in the finger if adequate rest is not given?

I understand the first thing the body does is try to stabilize the break and then starts to repair.  What happens if it is continually used and not given the chance to properly heal?  Will the climber just have a sore spot on their finger for the rest of their life or will it progressively get worse and worse?


texts:
In the body, the liver holds between 90-110 grams of glycogen in storage, while skeletal muscle storage makes up another 400 grams.

If a person exercises and depletes both stores, when a carbohydrate source is consumed, which of the stores is replenished first?


texts: Insect identification - pantry moth vs clothes moth

texts:
Are the following insects a pantry moth or a clothes moth? I live in Europe, if geographical location is of importance in this case.

The insects are about 7 - 10 mm in length.

For several months I have been fighting with recurring invasion of pantry moths and those were caught in pantry moth pheromone trap. However, the specimens seem  to be smaller than the pantry moths that I have been fighting a couple of months before (I have read that clothes moths are smaller) and I have seen some flying near the wardrobes. I couldn't find traces of infestation in the food as well. Is it possible for clothes moth to be attracted by pantry moth pheromones?


texts: What is bilateral symmetry in "bilateria", an actual symmentry

texts:
Wikipedia defines bilateria as :

  animals with bilateral symmetry, i.e., they have a head ("anterior") and a
  tail ("posterior") as well as a back ("dorsal") and a belly
  ("ventral"); therefore they also have a left side and a right side.

By symmetry, I understand that divisions of the body along some plane be similar. Now, if you have a head and tail, isn't the horizontal symmetry lost (head and tail look different) ? Similarly, for a vertical division, a different looking belly and back also destroys symmetry along this axis.

An organism whose head and tail are exactly the same (you can't even make out if something is head, and the other, tail), is perhaps "actually" bilaterally symmetrical (along the horizontal axis).

What am I missing here ?


texts: Which of the nicotinic acetylcholine receptors (nAChRs) catalyse the release of the neuromodulators mentioned below that's caused by nicotine?

texts:
Neuromodulators: acetylcholine, norepinephrine, epinephrine, vasopressin, histamine, arginine, serotonin, dopamine, autocrine agents, and $\beta$-endorphin.

I am aware that agonists of the $\alpha_7 $ nAChRs improve cognition in Schizophrenia, presumably by catalysing the release of histamine, norepinephrine and/or acetylcholine.1,2 I also know that $\alpha_7 $ nAChRs antagonists reduce $\Delta^9$-tetrahydrocannabinol (THC) self-administration in mice presumably by suppressing dopaminergic activity in the nucleus accumbens or by inhibiting the activity of the CB1 receptor.3 Selective CB1 antagonists also manage to reduce nicotine dependence.4 Also I know that the activation of the $ \alpha_3 \beta_4 $ nAChRs in the adrenal medulla catalyses an epinephrine and norepinephrine release.

Reference List (Oxford Style)

M Hajós, BN Rogers, 'Targeting alpha7 nicotinic acetylcholine receptors in the treatment of schizophrenia.', Current Pharmaceutical Design, 16/5 (2010), 538-554.
LF Martin, WR Kem, R Freedman, 'Alpha-7 nicotinic receptor agonists: potential new candidates for the treatment of schizophrenia', Psychopharmacology, 174/1 (2004), 54-64.
M Solinas, M Scherma, L Fattore, J Stroik, C Wertheim, G Tanda, W Fratta, SR Goldberg, 'Nicotinic α7 Receptors as a New Target for Treatment of Cannabis Abuse', The Journal of Neuroscience, 27/21 (2007), 5615-5620.
C Cohen, E Kodas, G Griebel, 'CB1 receptor antagonists for the treatment of nicotine addiction.', Pharmacology, Biochemistry and Behavior, 81/2 (2005), 387-395.


texts: Is there a non-bacterial source of lipopolysacchrides

texts: I am wondering if there are any other non-bacterial sources of LPS. To my understanding, lipopolysacchrides (LPS) are components of the outer leaflet of gram-negative bacteria, but are there any other sources of LPS such as fungi?.


texts: How much energy is required to blind someone?

texts:
As I understand the ravages of sunlight upon the (human) eye; the cause of ocular damage and blindness is too much energy delivered to the cones and rods that ultimately make up our eyes; so the questions arise:

How much light can a (human) rod take?

How much light can a (human) cone take?


texts:
Nearly all volcano plot I've seen tend to be roughly symmetric around the y-axis, with a fairly equal number of up- and down-regulated genes. What are the potential reasons for a volcano plot that is heavily unbalanced (i.e., many more negative fold change genes than positive)?

In my analysis, I have identified two populations of patients within a disease cohort, representing the "interferon high" and "interferon low" sub-populations. I then calculate differential expression between these groups, and visualize the results with a volcano plot (log(p-value) of differential expression vs. log(fold change)). The volcano plot is quite asymmetric, with a maximum log2 fold change of 1 on the positive end, and a minimum log2 fold change of -3 on the negative end, with many more genes significantly down-regulated in the IFN-low population.

Is it reasonable to suppose that there are lots of genes up-regulated in IFN-high, with no down-regulated genes defining this population, or is there something else going on?


texts: Programming Languages for Bioinformatics

texts:
Good day everyone,

I am very much interested in math, biology, and programming; ideally I would like to study bioinformatics and, as such, was wondering what languages are typically used by bioinformaticians? Particularly for fields of bioinformatics relevant to biochemistry, virology, and immunology, what are the most useful programming languages to know, as well as their strengths and limitations? (i.e. in what setting would it be better to program in C++ than Python, is R good to know and if so why, etc.)

Thank you in advance.


texts:
Why do humans find baby animals like cats, dogs, ... so cute?

As these are potential competitors (when grown up!) or even natural enemies (like e.g. tigers, leopards, ..), the protection instinct (reasonable for the babies of your species) should therefore not apply.

I can't imagine any reason why evolution let mankind adore foreign species that much.
Maybe only humans liking the enemy's kids survived, because they weren't killed by the baby's parents.

What is the evolutionary reason?


texts: How to remove duplicate results from BLAST?

texts: If I run BLAST using a protein sequence (e.g. human p53), I get many matches to the same protein, presumably from different research projects. As you can see from the screenshot, all are similarly named and close to exact matches. Is there any way I can filter the results to get unique genes only?


texts: Bacteria resistance to natural antibiotics?

texts:
It is a known fact that bacteria develop immunity to antibiotics. Why then did not all bacteria develop immunity to natural antibiotics like penicillin in the fungi?

It is for sure that fungi did not care to continue killing all bacteria so that them won't be able to develop immunity (as we're adviced today to use antibiotics carefully, in order not to develop a superinfection)..

Looking at all the time span that bacteria and fungi exist, it seems unlikely that there'd be any bacteria left not yet immune to penicillin at all. However, that's not the case, the antibiotic is still a rather successful one.


texts: What is the quality rate of intrinsic autoregulation in the heart?

texts:
Autoregulation is the maintenance of constant blood flow to an organ in spite of fluctuations in Blood pressure.
It involves the relaxation of myocardium and contraction.
It is local.

I know that autoregulation is best done in the brain, well in kidneys and badly in skeletal muscle.
I am interested how it is in the heart.
I think it should be at least good.
Brain can be thought more important.
However, I am not sure.

How good is the autoregulation of the blood flow in the heart?


texts: Do Pthirus gorillae remain in gorilla leaf nests after gorillas migrate and abandon them?

texts: Gorillas build leaf nests to sleep in. Do the lice which parasitise gorillas, Pthirus gorilla, remain in gorilla leaf nests after gorillas migrate to new regions (and abandon the old nests)?


texts: What are some characteristics of venules and arterioles?

texts:
I know that the vascular system of the human body is organized in the
two, "ever branching", structures of the veins and the arteries. These two
structures stem from their connections to the heart and stretch and
branch throughout the body.

The two structures are interconnected through capillary beds,
responsible for the interactions between the blood and the
extracellular liquid, surrounding the tissue cells of the body.

The capillary beds are connected to the arteries and the veins through
small vessels, venules, branching out from veins and arterioles,
branching out from the arteries.

The capillary beds consist of a web of capillaries, vessels small and
thin enough to allow exchange of nutrients and waste between the blood
in the vessels and the extracellular liquid surrounding the vessels as
well as the cells of the body.

Now, I realize that the capillary beds must be ubiquitous throughout
the body, sustaining every part of the body but the circulatory system
itself.

I am eager to find out more about the venules and arterioles. Looking
at the structure of veins and arteries, how prevalent are the smaller
blood vessels? Are the arteries and veins "fuzzy" with arteriole and venules or are the small vessels more sparse? Do they emanate from large vessels as well as smaller ones? How do their presence interfere with vascular interventions or
even drawing blood for blood tests?

I'd be happy for information in these matters.
Cheers
Mats


texts:
I am conducting research and these insects were found on my biological sample (sections of pig's femora placed in an artificial water setting).

My location: Mississauga, ON

What species of insects are these?


texts: Need Help Identifying this Critter (Insect?)

texts: This creature is hanging out on my kitchen window. I live in Western Maryland, US, near the Potomac River. The creature is about 3 inches long (measured from tip of mandibles to tip of tail). Does anyone know what it is? Is it dangerous? Rare? I've been living here about a year and have never seen one before.


texts: What is the distribution of the major ions across a neuronal membrane for a human neuron?

texts: I have searched for the ion distributions across the membrane of human neurons on the internet but almost all the information refers to the giant axon of the squid. Could anyone give me the ion distribution across the membrane of a human neuron?


texts: When was it discovered XY chromosomes decide the sex of a child in humans?

texts:
Several stories are told from before-genetic-age (books and movies are my reference, the one present in my mind is Marie-Antoinette by Copola) in which we can always see that women are blamed for giving birth to a girl - when it was a boy which was "required".

How did mankind's (man) society took the discovery of the fact that the sex of a human baby is decided by the Y or X chromosome carried in the masculin genes within the sperm fertilizing the female's egg. (at least this is what I learned in school decades ago).

When was this fact discovered and by whom?

(The occasion for this question is Nettie Stevens 155th birthday today)


texts: Why were dinosaurs not as smart as humans are?

texts:
According to http://en.wikipedia.org/wiki/Dinosaur, Dinosaurs were the dominant terrestrial vertebrates for 135 million years.
They had a lot of time to evolve. My question is: why were dinosaurs not smarter than us, and why was their society not complex like ours is?


texts: Why is the pituitary gland located in the brain?

texts: Why is the pituitary gland located in the brain in humans, instead of elsewhere in the body? Why would this be an evolutionary beneficial adaptation?


texts: Does bioluminescence occur in humans too?

texts: I read that Japanese researchers have developed very sensitive camera that recorded bioluminescence in humans; is it possible and if so what is the mechanism behind it?