texts:
In this amazing video, at 26:03 we see this image

We now know that the telomerase contains a sequence complementary to the telomere sequence and so is able to do what it is capable of doing in this image.

My questions : What if we make a piece of dna with  five GGGGG at the 3' end ? Will the telomerase not work, as the RNA in telomerase has the sequence AACCCC and so won't be able to form complementary strand ? If so, has such a mutation been detected in any organism ie it's telomerase is unable to work just because it has a random insertion(maybe during replication) of one of the nucleotides in the telomere at the 3' end ?


texts:
I grew up hearing the mantra

excess salt causes heart disease

I had a vague understanding that it caused deposits in the body or something. Now that I give it more thought - I come up with three vaguely plausible explanations for this:

kidneys have a fixed limit on how much sodium chloride they can filter from your bloodstream in a day
excess salt has an effect on oxidation/redux reactions or acid/base levels that means your body's chemical reactions aren't performing optimally
the excess ions mess with other reactions in the body

When I take the 'devils advocate' argument in my mind - my plausible arguments are:

how can salt cause deposits in the body? It would simply dissolve in the bloodstream
surely the body has sufficient chemical mechanism to flush out surplus sodium ions

Now the author here makes the following claim:

The entire field of research around salt is a colossal [stuffup], for a fairly simple reason: sweat is salty. If you sweat, due to exercise or high temperatures, you lose about 1g/L of sodium. So right off the bat, all the research that's trying to find a population-wide correct amount of sodium to eat is on a wrong track, because there's no such thing.
But it's even worse, because most of the research doesn't measure the amount of sodium people take in through food, it measures the amount of sodium they lose in urine. This isn't their intake, it's what's left after losses, so it's confounded by exercise.
And it's even worse than that, because while the actual studies indicate that there's no benefit from cutting salt intake, some high-status organizations once said there was, and are acting as though they can't take it back without losing face.
The overall result is that there are a bunch of people shouting "less salt!" and a bunch of people shouting "the same amount of salt!" and no one has any model of how much salt they actually need, so they occasionally end up deficient.

In addition, the article here claims:

...there are the epidemiologists whose research appears to point in the other direction. They track the connection between salt and deaths from heart attacks and strokes, and their studies indicate that while heavy salt eaters did die sooner, there is little evident danger from the average American’s intake.

My question is: What is the evidence that mammals are unable to process excess sodium chloride?


texts: Is the ability to roll your tongue or not truly inherited or genetic? What I have gathered from school has been contradicting with evidence I found elsewhere.


texts: Questions in Regards to Isolating Promotor Region for Recombinant DNA Techniques

texts:
For a while now I have been trying to isolate the promotor region of this Protein.

Using sticky end PCR, I need to isolate this promotor region so it has paticular sticky ends for the purpose of placing it into a plasmid. However, I have a couple of questions on how to do this:

A. For inserting it into a plasmid, how precise does the sequence have to be? It is nearly impossible to find a restriction enzyme which lines up exactly to the start codon. How far can I deviate away, while still allowing the protein to be transcribed properly (on the plasmid)?

Thanks.


texts: Where does this equation in the electrophysiology literature form come from?

texts:
In my studies I keep coming across the form of an equation that is used in many different mathematical models for voltage gated ion channels. The most general form I have found is in the 1977 paper Reconstruction of the action potential of ventricular myocardial fibres by Beeler and Reuter. Each ion channel has a gating variable $y$ whose differential equation depends on functions $\alpha$ and $\beta$, both of which take on the general form:

$$\{\alpha,\beta\}=\frac{C_1\exp[C_2(V_m+C_3)]+C_4(V_m+C_5)}{\exp[C_6(V_m+C_3)]+C_7}$$
where $V_m$ is the membrane potential and each constant is determined to have different values depending on the channel, system, etc.

My question is where does this form come from? In all of the papers I have come across they seem to just use this form with numbers chosen to fit their data without explanation as to why this form is actually used. The Beeler and Reuter paper cites the 1952 paper by Hodgkin and Huxley, but it seems like H&H use simpler forms of this equation primarily motivated by just fitting the data rather than illuminating any underlying mechanisms. Therefore, I do not understand where this form in the B&R paper comes from that so many papers later on use as well.

Does this form come from assumptions about the workings of the ion channels, if so, what are these assumptions, and how do they give rise to this form? Or is this just a general form found to fit many data sets fairly well, and if so why was this chosen over other functions that could probably do the same thing?


texts: Construct picture of person's face from DNA

texts: Would it be possible to construct a picture of a person's face from his/her DNA?


texts: Evolution of umbilical cord and reason of its elongation

texts:
To answer a question myself, recently I've read that

  Years and years ago, a long umbilical cord enabled a woman to grasp her baby after birth and run away from predators"

Update:

$Question:$ How umbilical cord is evolved and what's the reason behind it's elongation?

There is at least one position that supports this claim:

  So why 61 cm? Umbilical cords of whales, porpoises, goats and other
  mammals are rela- tively shorter than the human cord. Walker and Rye
  of Cambridge surmised in the British Medical Journal in 1960 that
  prehistoric humans evolved length for protection. Nature's purpose was
  to allow the mother to pick up the newborn without disturbing the
  placenta. The event of breast feeding would then separate the placenta
  - an event which could attract predators. Having the fetus in tow would allow escape for mother and child.

(title: Silent Risk, auth.:Jason H. Collins). Well, right now I feel confused a bit...


texts: How to gather life-history traits data on bird species?

texts:
I am looking for a data base of life history traits for bird species. Is there such data base? If not, what are your advice on how to collect those data? Is there a handy website that list characteristics of birds around the world? I started to gather those data using wikipedia (and the references anytime wikipedia actually have reference) but it is very cumbersome.

The kind of data I am looking for are:

Reproductive age
Average lifespan
Average gestation time
Number of eggs per reproduction event


texts: Does increased cell turnover cause cancerous mutations?

texts:
If a certain set of cells or tissue are undergoing a lot of reproduction and repair cycles for some reason, does this inevitably lead to cancerous growths? If the mutation rate exceeds the normal 'background' mutation rate for the tissue will these extra mutations eventually cause cancer?

As user Luke said below; does an increased rate of replication increase the rate of mutations.


texts: When the leaf length ranges are given in a plant species' description, what do the numbers in parentheses represent?

texts:
Referring to a plant species, a paper I am reading (see citation below) says: "Blades are 4–5(6) mm long and (0.5)1–1.5 mm broad."
I understand the numbers 4-5 and 1-1.5 would be the ranges, but what do the numbers 6 and 0.5 in the parentheses represent?
Domínguez, Y., Valdés, C. M. P., & de Miranda, V. F. O. (2012). New features of Cuban endemic Pinguicula filifolia (Lentibulariaceae) and considerations on its habitat and ecology. Flora-Morphology, Distribution, Functional Ecology of Plants, 207(11), 838-841.


texts:
I'm working with a protein that doesn't have any homology to other proteins so it will likely require ab initio structure prediction. However, since I don't work for a structure prediction lab and I don't have a stringent requirement to have a high resolution structure, I'm fine with a 6-10 angstrom resolution prediction to help me visualize the protein.

I'm imagining I-TASSER to get an initial idea of the topology. SWISS-MODEL doesn't find any homologs to template against. I'm trying to avoid using Robetta since it will probably take a month. What other low-resolution webservers should I test?

Alternatively, you could just tell me to suck it up and submit it to a month-long prediction.


texts: Geometric Interpretations of the DNA Double Helix

texts: In mathematics, a helix is a shape which has constant curvature and constant torque (see Wikipedia here. What are the biological implications of the DNA double helix having constant curvature and torque, or is there none?


texts: Are there any viruses that integrate their DNA into organellar DNA?

texts:
It is known that many viruses (e.g. retroviridae) integrate in the nuclear genome of their host as part of their cycle. However, I'd like to know if integration can happen in organellar DNA (cpDNA and mtDNA) as well.

I've found a paper proposing that some chloroplast genes have a viral origin; however, the virus would have been present into the ancestral alpha-proteobacterium that later became the chloroplast, so no direct chloroplast infection is involved.

There is also this almost identical question on ResearchGate, but frankly the answers there are not satisfactory.


texts: Energetics and Products of Pepsin/HCl Protein Digestion

texts:
What are the energetics of protein digestion during which the enzyme pepsin is "activated" (whatever that means) by HCl?  I've looked and been unable to find anything like a chemical equation that includes an energy term.

Of course, pepsin, being an enzyme, is not used up in that sought-for equation.  Is HCl used up?  If so, what are the products?  How and in what form is the chlorine removed, assuming the HCl is consumed in the equation?


texts: Could someone recommend an introductory book on epidemiology?

texts: I'm hoping to learn the basics of epidemiological methods, terminology, etc. I come from a background in statistical economics, and I'm moving into the economics of public health. I don't know if epidemiology uses separate statistical methods, but I presume it does. I know discussion questions aren't recommended, but please list any reasons you have (personal experience, ease of introduction, etc.) for texts you would recommend.


texts: protocol for pulldown of DNA breakpoints?

texts:
Is there any method to do pulldown enrichment of DNA breakpoints from a cell? I have found this paper reporting a method to enrich for the DNA single-strand breakpoints from meiotic recombination events:
 Khil PP, Smagulova F, Brick KM, Camerini-Otero RD, Petukhova GV. 2012. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. Genome research 22: 957–65.

I would like to know if there is something like that which will work on any status of the cell cycle, not only meiosis.


texts: How come all my family have brown eyes and I have blue eyes?

texts:
My whole family tree up to my grandparents have brown eyes,

I have blue eyes, how come?

I don't know if it matters but I have not received enough oxygen at birth, doctors said it's probably the reason I'm left handed while my most of my family is right handed


texts:
I've found this bird.

Does anyone know what is it?


texts: How would you model the evolution of two genotypes across generations?

texts:
Say you have a genotype A that produces x offspring and another genotype B that produces y offspring, where x>y.  These x offspring are of genotype A but with modest differences in fitness due to mutation and these y offspring are of genotype B but with modest differences in fitness due to mutation.  How would you model how many offspring these x offspring can themselves produce and how many offspring these y offspring can themselves produce as a function of the quantity their original parents produced?

Obviously, you could say that each descendant of genotype A produces x and each descendant of genotype B produces y, but that would unrealistically benefit genotype A, since realistically, one of B’s offspring could have a chance to be fitter than A’s by developing a favorable mutation or one of A’s offspring could have a chance to be less fit than B’s by developing an unfavorable mutation.
You could say that each descendant of genotype A and B produce (x+y)/2, but this would not be fair to genotype A, since it is fitter, so its offspring would probably be fitter than B’s offspring.

You could use the breeder’s equation and say that each of A’s offspring produce xh+m(1-h), where h is the heritability of fitness and m is the population mean, and that each of B’s offspring produce yh+m(1-h).  But this is also unfair to genotype B because all of its offspring are less fit than all of A’s offspring, since x>y.  So, what’s a way of modeling how resultant mutations might occur, such that B has a chance of producing some offspring that are fitter than A’s offspring?


texts: How exactly does marijuana damage brain cells?

texts: I've heard that THC can cause permanent damage to brain cells. I've also heard this reffered to anti drug propaganda. Another theory i've read is that temporary effects reduce intelligence but long term results are not affected. If Marijuana does cause permanent brain damage how does it do so? How exactly does it kill the cell?


texts: During a large forest fire, what is the evacuation behavior of birds?

texts:
I'm interested in birds' behavior during large forest fires. Do they fly away as soon as they smell smoke, or wait until seeing fire itself? Do they fly away in flocks, or individually? Do they ever try to return to the area later, or just abandon it for good?

Interested mostly in average forest birds like jays, cardinals, finches, etc.


texts: DNA replication: How many DNA polymerase molecules work in parallel?

texts:
Background research

I am aware that DNA polymerase works in pairs, at least. This is to process both opposite stands of a given chromosome. The 3'-to-5' "leading strand", and 5'-to-3' "lagging strand" simultaneously. This two-DNA-polymerase process is beautifully shown in this TED talk by Drew Berry.

I have not checked any non-online sources but simple Google queries failed to answer my questions below.

Question

Within a single Eukaryotic cell, is the process of DNA-replication carried out by just a single pair of DNA-polymerases? Or do multiple pairs of DNA-polymerases work in parallel?


texts:
I'm interested in amplifying a sequence for further use with Gibson Assembly. I want to create overhang regions in my DNA fragment so there would be complementarity to the plasmid I'm trying to insert it in.

I was informed by a colleague to work with "flagged primers" though I can't find any literature online.  Can anyone explain this concept to me?


texts: Synthesis of an additional DNA in Pachytene and Zygotene

texts: I've read, that in Pachytene and Zygotene additional DNA material is synthesized, about 0,3, 0,1% respectively. Why is it so?


texts: Composition and quality of mushroom spores

texts:
Message to moderator(s):
This question was deleted since it looks similar to a question in another SE.
However, the question being asked in this SE is completely different. Would that be a strong enough basis to restore this post?

From this source, it states that:

  Living spores have been found and collected in every level of earth’s atmosphere. Mushroom spores are electron-dense and can survive in the vacuum of space. Additionally, their outer layer is actually metallic and of a purple hue, which naturally allows the spore to deflect ultraviolet light. And as if all this wasn’t unique enough, the outer shell of the spore is the hardest organic compound to exist in nature.

With regards to a mushroom spore's electron density, having an outer metallic / purple layer, and the hardness of its outer shell, have these things been confirmed in biological experiments?


texts: Help identifying this bird from Southern Brazil

texts:
I've seen a few of these birds at my university located in the extreme south of Brazil.

I noticed they usually stay on wet areas and like to eat small critters, such as worms and young tadpoles (I'm not completely sure about the last one).

I also noticed they usually stay alone in a particular area or, at maximum, two in the same location.

Also, here we also have many Southern Lapwings, which are in the breeding season, and one of them sometimes attacks the bird in the picture (for apparently no reason). When attacked by the Lapwing, this bird bristles the feathers of his neck and just dodges the Lapwing's attacks.

Does someone know what bird is this?

P.S.: Sorry for the bad picture. I couldn't get closer to it.


texts:
Recently, I saw this video but I couldn't find out if it's CGI or if it's an actual jellyfish. If it's real, what explains its beautiful bioluminescence pattern? And could the output from the ROV thrusters rip it apart (in the video description it says so)?
Photo:

Location: off the East coast of Africa.
Size: unknown, but it can be compared to the objects in the surroundings.
Additional info: footage taken in 2013.


texts:
I was told in a physiology lecture that alcohol inhibits gluconeogenesis because 'NADH produced from ethanol catabolism leads to product inhibition'.

But is NADH not a reactant coenzyme of gluconeogenesis? It would make more sense if NADH inhibits glycolysis by product inhibition.

So, what is wrong here? Or is it because of some other reason why alcohol inhibits gluconeogenesis and leads to hypoglycemia?


texts:
Well, insecticides are used to kill insects.
I have always wondered why are herbal / natural insecticides more effective in killing insects than chemical ones. I have read this at many places but havent found a reason for it.
Also why don't insects develop resistance to herbal insecticides while they do for chemical ones?


texts: If plants "alternate generations" between sporophytes and gametophytes, why don't we say the same of humans?

texts:
I've been reading on Wikipedia about how plants alternate generations between a diploid sporophyte (usually the dominant part) and haploid gametophyte (in flowering plants, the pollen and ovule sacs).

Mammals also produce haploid gametes. But in mammals we don't describe the gametes as a separate generation that alternates with the dominant "sporoid." The gametes are just the organism's means of reproduction.

What is it about plant reproduction that warrants describing their gametes as a separate "generation" or "phase"?


texts: How to calculate the Position Weight Matrix score?

texts:
Can anyone explain me how to calculate the Position Weight Matrix score?

I know the formula, but I don't understand it. I have a table with the frequences of nucleotides, and a table with the PWM scores:

Frequences of nucleotides:

Position:            1       2        3        4        5

A                    0       0.9      0.1      0.6      0.2
C                    0       0        0.2      0.1      0.2
G                    0       0        0.1      0        0.1
T                    1       0.1      0.6      0.3      0.5

And I have the corresponding PWM scores:

Position:            1       2        3        4         5

A                            1.848   -1.322    1.263    -0.322
C                                    -0.322   -1.322    -0.322
G                                    -1.322             -1.322
T                    1      -1.322    1.263    0.263     1

But, I have no idea how this scores are calculated.
The formula is:

But I don't understand this.

Can anyone explain me step by step how I can calculate this scores?

I especially don't understand how to calculate p(b,i).

Thanks! :)


texts:
I've read that the bacterial capsule protects the bacterium from phagocytes and prevents water (and nutrients, possibly?) leakage from the bacterium.

A less organized and less dense version is called a slime layer. It seems that the slime layer has similar functions, according to Wikipedia.

What are the differences between the effects a capsule and a slime layer bring to a bacterium?

I thought about the followings:

The capsule covers most part of the bacterium, so adhesion proteins and transport proteins on the plasma membrane do not work effectively, whereäs with a slime layer, more proteins on the plasma membrane are exposed to the exterior, making them work more effectively.
Maintenance of the capsule takes more energy than that of the slime layer simply because there are more glycoproteins in the capsule.
Bacteria with capsules are less likely to lyse than those with slime layers.

Is there anything else significant that goes on this list? Or are there any points I made that are not true?


texts: Reason for name "Motile sperm domain-containing protein 2" if it has nothing to do with sperm

texts:
I am interested in a gene with the name "motile sperm domain-containing protein 2".

The entry for the human gene in uniprot suggests that it does not have any relation to sperm or spermatogenesis.

If this is so, why does the name make reference to sperm?


texts: What is this? Found crawling across ground under oak tree. Six arms waving, I broke off 1 trying to pick it up. Less than 1 inch long

texts: Crawled like snail.  No slime trail.  Less than one inch.  Six arms, I broke one off.


texts: Is Hydrogen gas present in biogas, and does it spontaneously ignite?

texts: Is Hydrogen gas present in biogas? As it is highly inflammable, may it ignite the other gases like methane?


texts: How far in evolutionary distance is the P-distance estimator "accurate"?

texts:
I'm reading Yang's computational molecular evolution and in the very first chapter it says the P distance is a "simplistic distance measure" between two sequences. It is the number of different sites / the total number of sites.

However, because back mutation and multiple hits cause inaccuracy it become weak over longer distances (large number of generations to most recent common ancestor, MRCA, I guess).

  "The raw proportion p is usable only for highly similar sequences,
  with p <0.05 (5%, approximately)."

How far back in divergence time do we have to go for this p<5% to be violated? I assume it has to do with the mutation rate right? I'm trying to get a sense of scale on this for myself. Are we talking a distance of just a few generations (within species), the distance between two closely related species, or an even greater distance?


texts: How do roots absorb water instead of presence of waxy - material suberin in the form of casparian strips on the wall of endodermis?

texts: I found that in the endodermis, the tangential and radial walls have deposition of the waxy, and hence water-impermeable, material suberin in the form of casparian strips. The endodermis comes before the vascular bundle so how is water absorbed in roots?


texts: Aseptic technique: a single technique, or any technique fulfilling criteria, or collection of said techniques?

texts:
My friend just used the following sentence in her lab report:

  Aseptic technique is used in this step:

I immediately felt something was wrong. She used the term as if it were a specific technique. Is her usage correct, and if so is "aseptic technique" indeed a specific technique with a specific procedure?

Rather, I thought "aseptic technique" referred to any technique that involves complete sterilization of a certain environment or apparatus/instrument. If this were right, then perhaps "an aseptic technique" should be used instead?

Further still, if "aseptic technique" refers to the collection of all techniques that involve sterilization as described above, the perhaps it should have been "the aseptic technique" instead?

Which one(s) is/are correct, grammatically and semantically (hence conveying the concept accurately)?


texts: Seen in the med and have it in my garden


texts: What happens to the red blood cell in CaCl₂ solution?

texts:
Here's the problem:

One red blood cell is placed in a hypertonic solution of NaCl, another is
placed in a solution of CaCl2 equimolar with the NaCl solution. What
would you expect to happen and why?

My reasoning is that the red blood cell will shrink due to water loss by osmosis when placed in hypertonic NaCl. It will shrink even further due to the larger osmosis gradient due to there being such low concentration of Ca2+ normally in the cell. However, I'm not sure if this is right so could someone please explain the correct answer?


texts:
I noticed a really huge, beautiful web on my porch last week, and tonight, I discovered its resident. I'm thinking it's an Araneus diadematus (Cross Orbweaver), but I was hoping for some confirmation.

Can anyone confirm this or offer a better suggestion?


texts: Do blind birds bob their head when they walk?

texts: Birds try to keep their heads still for short periods of time between steps to improve their ability to see. You can find amusing videos of chickens used as small video camera stabilizers. But does this happen to blind birds? Is it something all birds do regardless of their ability to see?


texts: What motivation is there to create general, cross-species neural models which account for the variation between species in different environments?

texts: The main components of human neuroanatomy have been mapped out. What attempt has there been to map a broad (many-species) spectrum of functional parts of the nervous system? Such a mapping could be useful in behavioral ecology, which associates functional behaviors with driving environmental forces.


texts:
I spotted these two in my garden.  What is this insect?  He had firm control over the wasp and was just hanging on by one leg.  He appeared to hold on until the wasp stopped moving and then flew away with it.

I live in Ohio (USA). The wasp was a bit less than 2cm long while the other insect was about 2.5cm long.


texts: How valid is Schwartz's criticism of molecular phylogenetics?

texts:
A proponent of the human-orangutan clade, Jeffrey Schwartz argues, in this paper [1], that molecular phylogenetics is largely based on a baseless assumption.
To sum up, according to him:

this type of phylogenetics relies on overall similarity, rather than cladistic considerations, to infer relationships. He claims that even parsimony algorithms (albeit traditionally contrasted with distance-based methods) group taxa on the basis of overall similarity.
this reliance on overall similarity is based on the baseless and questionable assumption that sequence evolution is gradual and continuous.

Could you tell me if his objections and paper hold water, and how valid they are?

[1] Schwartz & Maresca, 2006, "Do Molecular Clocks Run at All? A Critique of Molecular Systematics", Biological Theory, Springer.


texts:
What is the difference between Coding Sequences (CDS) and cDNA?

Are Coding sequences the sequences that is transcribed to mRNA and cDNA in contrast DNA obtained by reverse polymerization of matured mRNA?


texts: Human Anatomy and Physiology - The Muscoskeletal System

texts: In the human limb skeleton can you identify a bone which is rather feeble and does not have much role in supporting body weight or maintain posture, and doctors use pieces of it to transplant to other broken bones, where necessary?


texts: What's the name of this green fruit with little pikes fallen from a city tree on the pavement?

texts: What's the name of this green fruit with little pikes fallen from a tree on Paris (France) pavement ?


texts: Why there are no RBCs in lymphatic vessels?

texts:
I know the following.

Leukocytes (white blood cells) are made in the bone marrow, and naive leukocytes go to the blood vessels. So, leukocytes mainly exist in blood vessels.
Endothelial cells wrapping the capillaries have some gaps, but too narrow for RBCs or leukocytes to leak out (or for bacteria to invade. So, bacteria go to lymphatic vessels).
When leukocytes are needed (like when some foreign molecules invade), leukocytes such as macrophages get out of blood vessels to the tissue of interest by the mechanism of  extravasation.

My question is, why there are no RBCs in lymphatic vessels? Is it because they cannot do extravasation, while leukocytes can?


texts:
List the following proteins in the order of decreasing evolutionary
  conservativeness of their primary structure:

  Somatotropin.
  Catalytic subunit of a DNA – polymerase.
  Histone H1.
  Prolamines (storage proteins of cereals).

What I think : I am sure that 4th one should be last. I believe that H1 sequence is not that important as I had read somewhere that a cell can survive even without H1 histone. I also think that catalytic subunit is most important. So, according to me the order should be : 2,1,3,4.

Am I right ?


texts: Expected time for a neutral allele to reach a frequency of $p_1$ when starting at frequency $p_0$

texts:
Kimura and Ohta (1968) showed that the expected time for a neutral allele to reach fixation (given that it will reach fixation) is

$$\bar t(p_0)=-4N\left(\frac{1-p_0}{p_0}\right)\ln(1-p_0),$$

where $p_0$ is the initial frequency and $N$ is the population size.

From their work, can we generalize this result to calculate the expected time to reach a frequency of $p_1$ (given that this frequency will be reached at some point), where $p_1$ is not necessarily equal to $1$?


texts: Alternatives to ethidium bromide for staining small nucleic acids?

texts:
While ethidium bromide works well for staining larger single-stranded RNA or double-stranded DNA molecules, it doesn't stain smaller nucleic acids very well. I observed that at around 20 bases and below single-stranded nucleic acids are difficult to see with EtBr-staining unless the nucleic acids are highly concentrated.

What are good alternatives for observing small nucleic acids in polyacrylamide gels? The main consideration would be ease-of-use, and it should be possible without any unusual equipment.


texts: Why do the size of the phase 1 notch vary among cardiac cells?

texts:
The size of the phase 1 notch varies among cardiac cells. It is prominent in myocytes in the
epicardial and midmyocardial regions of the left ventricular wall  and in ventricular Purkinje fibers. However, the notch is negligible in myocytes from the endocardial region of the left ventricle.
What's the reason?


texts: How is it possible for the absolute fitness to be more than 1?

texts:
The wikipedia definition of Absolute fitness is "the ratio between the number of individuals with that genotype after selection to those before selection. It is calculated for a single generation and must be calculated from absolute numbers."

But in one generation there are no reproductive events so it should be theoretically impossible for the population to be larger after the selection event than before it (since no reproduction is taking place).


texts: Rice left in water for several months - what biological reactions or growths would occur?

texts:
In an attempt to make a hair care product, uncooked white basmati rice was left in an air-tight container half filled with tap water for several months.

When opening the container, the smell was extremely foul and disturbing, one of the most revolting things I have ever smelt.  It was worse than the smell you would usually associate with yeast, alcohol, or mold.  This horrid smell immediately spread to the entire property and took many hours of fan extraction to remove.  It was worse than the smell of sewage.

I rinsed the container used and cleaned it in the dishwasher several times at 75'c.  After several dishwasher cycles, the disgusting smell remains.  It makes me wonder what kind of biological or chemical product has been created that even a dishwasher cannot neutralise or sterilise at high temperatures?  Is this a safe substance?  This is especially concerning as this recipe exists on several hair care forums; is it widespread misinformation caused through malice?

I believe this is a valid scientific question about microbial life so on that basis I would not expect it to be down voted.

The substance looked like water with rice or rice starches dissolved in it; it was murky with a whitish colour.  There was no air bubbles which could be visually observed, although the murky texture could have been caused by micro-bubbles. The smell was very strange, unlike anything I have smelled before.  The closest description I could give is that of sewage, yet it is more disgusting than the smell of sewage if that is relatable at all.


texts: Why are enzyme-catalysed reactions slower at lower substrate concentration?

texts:
Suppose I'm using 200 nmoles of enzyme and 2 mmoles of substrate. The enzyme should be saturated but if I use 50 mmoles of substrate, the reaction will be faster. Why?
I just can't get it! Even at lower concentration of substrate the enzyme is saturated (all enzyme molecules are engaged in the reaction) but still the reaction rate is lower.


texts: I'm looking for an online source with images of the eye disease trachoma. I'm looking preferably for resources from a credible source that have images from each stage of the disease.


texts: What species of butterfly is this? Picture taken on 9-18-2018, near Helena, Mt

texts: Butterfly picture taken on the 18th of September 2018 at an elevation of 1800 meters (6,000 feet) near Mount Helena in Montana, USA.


texts: Why is it thought that protein folding is determined solely by amino acid sequence?

texts: It seems that it is a generally accepted idea that protein folding is completely determined by the sequence of amino acids, but why do people believe that? Is it simply that no example of a protein with two different functional foldings (possibly with different functions) is known, or is there some theoretical reason that it would be impossible for such a protein to exist?


texts:
I need some help in identifying this critter. It was found in southeast Georgia in a home I am renovating. There were several around the sink and toilet bowl.

Approximately 5 millimeters long. Stripes black/dark gray. Tapered end seems to be moving as though it was the head. Bulbous end has two extrusions like antennae?

Thanks in advance.


texts:
Why does one combine PCR and cloning as ways for amplification of sequences? Don't they produce the same result? I was reading the paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1864885/ and got confused by the following passage:

  Cloning and Bisulfite Genomic Sequencing

  Each bisulfite-converted DNA
  sample was subjected to PCR by primers that did not discriminate
  between methylated and unmethylated sequences, using a GeneAmp PCR
  core reagent kit (Applied Biosystems). The primer sequences are listed
  in Table 1, and reaction conditions are listed in Supplemental Tables
  1C and 1D (available online at http://ajp.amjpathol.org). Each
  subsequent PCR product was TA-cloned into pGEM-Teasy vector25
  (Promega) for transformation into Escherichia coli strain JM109,
  according to the manufacturer’s instructions. Clones were picked
  randomly and colony PCR was then performed using vector primers T7 and
  SP6 to amplify the cloned inserts. Cycle sequencing was performed
  using BigDye version 1.1 (Applied Biosystems) and an automated
  capillary DNA sequencer Genetic Analyzer 3100 (Applied Biosystems).
  The sequences obtained were aligned and compared using SeqScape
  software (Applied Biosystems). The completeness of bisulfite
  conversion was first confirmed before scoring. The CpG sites sequenced
  as cytosine or thymine residues were scored as methylated or
  unmethylated, respectively. The methylated site frequency was
  calculated for each sample by dividing the total number of methylated
  sites over all cloned CpG sites.

Can someone comment on what purpose the cloning serves when the amplification is already done by PCR?


texts: What are some of the general characteristics of the DH5 alpha strain?

texts:
I can not find some useful sources unfortunately.

Please tell me about some important characteristics of DH5 alpha.

What makes DH5 alpha suitable for the gene cloning?


texts: Sources for common laboratory Saccharomyces strains?

texts: I'm used to working with bacteria - some of the more common laboratory strains sometimes come with an order from some vendors.  What's the most convenient source to order common straings of Saccharomyces for lab work?


texts:
Relation between clownfishes and sea anemones is a classic example of mutualism. I wanted to list the species of sea anemones that are involved in this mutualism but I got lost.. Could you help me with that?

How many species of sea anemones which host clownfishes are there? Could you list them?


texts: Integral membrane proteins have functional asymmetry i.e. they have two different domains of proteins performing different functions. these proteins have Tyr and Trp amino acid residues at the interface between the lipid and water.Because these amino acids have dual nature that their side chains can interact with both extracellular aqueous environment as well as hydrophobic lipid phase and another generalization about amino acid location relative to bilayer is described by "positive inside rule": The positively charged Lys,His, and Arg residues of membrane proteins occur more commonly on the cytoplasmic phase of membranes.My question is that why only positively charged amino acids are faced towards cytoplasm why not negatively charged amino acids or other amino acids are favoured here?


texts: Doesn't osmosis violate the law of conservation of energy?

texts:
Osmosis seems very counter-intuitive to me. I will try to explain my doubt with the following thought experiment:

Consider a huge container divided into two by a semi-permeable membrane. We add equal levels of water on both sides. On one side, dissolve some sugar. After some time, there will be a net movement of water to the sugar containing side of the container. This will increase the level of water on one side and decrease it on the other. If we create a huge hole in the membrane (large enough for both water and sugar molecules), then water will rush from one side to the other, equalizing the levels. If we were to somehow place a turbine at this hole, we could generate quite a bit of energy. Where did this energy come from?


texts: Can someone suggest me good opencourseware links for learning computational biology basics?

texts:
My internet is slow and I have only 1GB data usage allowed for this month. And I want to make maximum out of it for learning some basics of computational biology.

Which are the best online course (freely available lectures) suggestions for me?


texts: What is the evolutionary advantage of having polymorphisms in MHC?

texts:
The MHC genes are widely polymorphic and hence cause an issue in tissue matching pre-transplantation. Why is there such a polymorphism?

I know that different polymorphisms in MHC can lead to variation in the immune response to the same offender. But then, if there is a difference, shouldn't there be a selection for those that mount a better response?

So, why the polymorphism?


texts: What difference in proteins radius of gyration can be considered significant?

texts:
In molecular dynamics simulations of proteins, the radius of gyration is often used to assess the compactness of a protein.
When comparing two protein radius of gyration, what difference can be considered significant 1 angstrom, 5 angstroms, 10 angstroms?
Significant meaning: yes it is definitely more compact or no it is definitely not more compact.
I have been searching through but can't find any reference related to that.


texts: Can Palisade Cells Survive Independently?

texts: I have been intrigued by this question. Can palisade cells survive independently from its parent plant in a chemical environment? For example, if we were to separate a palisade cell from a plant and place it in sucrose solution, how long would it survive?


texts: Why is sarcoma more prevalent and common in right heart?

texts: Ewing's sarcoma or Ewing sarcoma is a malignant small, round, blue cell tumor. It is a rare disease in which cancer cells are found in the bone or in soft tissue. It is more common in right heart than left heart? Why? Which one is more dangerous?


texts: DNA Topology. Question on twists and writhes

texts: Hi guys there is a question which has been driving me crazy ever since I saw this video(https://youtu.be/az2c6UbEdug). At 4:50 the guy says that when a right-handed circular DNA starts forming a right handed interwounding writhe the DNA must adjust by twisting more(You can see the number goes up to 8 from 5 in the equation) and that when an interwounding writhe is done in the opposite direction it must twist less. To me this doesn't make sense at all. I thought that as you interwound to the right the twisting should lessen and when you interwound to the left the twisting should increase. Can someone explain(or show a very clear diagram/illustration which explains this) please??


texts: What type of creature makes those mounds?

texts:
Location: South Ireland,
Appeared: 2020
Nearest river: 500 meter down hill south
Water is running down the hill also but there’s drainage to not flood the grass
Seen before: potted plant
I  used earth like this from a different location to plant a potted plant into a plant pot and those type of mounds happened afterwards in there also. Just on a smaller scale.
Never seen anything move though. Probably night active.


texts: What kind of factors determine how someone looks according to their race or ethnicity?

texts:
From what I read, race is considered the biology, the physical traits inherited by ancestry. Ethnicity and nationality have to do with social construct and cultural identity. This is almost the same things as sex and gender, where the former means the biological characteristics, and the latter refers to the social identity.

So, is there any relationship between race, ethnicity, and nationality? For example, Asians have a different cuisine than Europeans, which consists of whole grain and wheat, which explains why they are generally shorter? What makes them have slanted eyes? Is it because they have been known to look up at the sun constantly that they developed that characteristic over time?

What makes Mexicans have black hair, brown eyes, and medium skin, or have higher foreheads? Again, does this have to do with the cuisine that they have, or something else?

The only explanation I have heard about race is that melanin affects the colour of the skin. It is always sunny in Africa, which is why Africans have really dark skin, despite the fact that all of humanity derived from Africa. Europeans lived in more cloudy weather, so their skin became paler. I'm sure there's more to these findings.


texts:
What kind of bat is this? I saw it flying quickly between trees in Buckinghamshire, UK, at about 4pm in September (so about three hours before sunset). I think it might be a common noctule but I was surprised to see that there are something like fourteen other British species to choose from.

Sorry the photo quality isn't amazing but it was hard to capture anything at all!


texts: Why do small organisms make faster movements than big organisms?

texts:
I hesitated to ask this question because it seems so obvious and intuitive. However, I am not able to explain this tendency.

Background

It seems to me that small organisms make faster movements than big organisms. I don't mean that they are able to travel at higher speed (the cheetah is a big animal and is the fastest terrestrial species) but I mean that their movement are fast, quick and their members undergo high acceleration.

Examples

I would guess for example that the legs of a tiger beetle (clade of fast sprinter beetles) (see movie) undergo much higher acceleration than the legs of a cheetah (fastest terrestrial organism on earth) (see movie). To avoid taking the extreme, I would think that the legs of a Drosophila (see movie) undergo higher acceleration than the legs of a dog (see movie). The organism that is able to create the fastest acceleration is the mantis shrimp. Wikipedia says:

  Both types (smashers and spearers) strike by rapidly unfolding and swinging their raptorial claws at the prey, and are capable of inflicting serious damage on victims significantly greater in size than themselves. In smashers, these two weapons are employed with blinding quickness, with an acceleration of 10,400 g (102,000 m/s2 or 335,000 ft/s2) and speeds of 23 m/s from a standing start. Because they strike so rapidly, they generate cavitation bubbles between the appendage and the striking surface. The collapse of these cavitation bubbles produces measurable forces on their prey in addition to the instantaneous forces of 1,500 newtons that are caused by the impact of the appendage against the striking surface, which means that the prey is hit twice by a single strike; first by the claw and then by the collapsing cavitation bubbles that immediately follow. Even if the initial strike misses the prey, the resulting shock wave can be enough to stun or kill the prey.

Finally, note that Gabel and Berg (2003) show that the flagella can rotates up to 270 Hz.

Questions

Am I right to think that small organisms tend to make faster movements than big organisms?
If yes: Why do small creatures make faster movements?

Does it has to do with time for chemical diffusion?
Does it has to do with mechanics? ($F=ma$... But muscles are smaller as well).
Does it has to do with the resistence of biological tissues?
...


texts: It is around 2 inches long, one inch wide, fat, hazel coloured with black specks and has short antennae. It's got a lot of cobwebs on its legs, since I found it in a corner in my house. It was found in North America.


texts: Is the amount of blood that flows through every vein and artery per minute really a constant?

texts: I was listening lectures from Mark Saltzman via Open Yale Courses. Now, if I did not understand him wrong, he said that the amount of blood that travels through every vein and artery in our bodies per minute is a constant. Five liters of blood go through the aorta every minute, and since the blood circulation is a closed system, also every other vein/artery must pass that amount of blood per minute. Is this true? How could I (mathematically) show that it is true?


texts: Why do sharks continually regrow their teeth?

texts: Other animals don't do this. What is unique about sharks that requires them to regrow their teeth over and over, or what benefit does it provide them (that wouldn't also be evolutionarily advantageous to other animals)?


texts:
The answer to "How do some plants grow in salt water, while others die?" offers some hints as to how salt-tolerant plants store salt by shifting it out of cells, and also can deal with higher salt concentrations in cells, but what happens after that?  Do the plants somehow excrete the salt? Store ever-increasing amounts in more and bigger vacuoles? Convert it into something more useful by chemical reactions? Reach equilibrium concentrations with the water in which they grow and rely on osmosis?

It seems to this layman that plants growing in salt-water in the tropics will transpire quite a lot of water, and if that's replaced with salt water, they'll take up quite a lot of salt.


texts: How many colors can colorblind people really see compared to normal color vision?

texts:
A person with normal vision, it seems, can see 7,000,000 colors.

How many can a colorblind person see?

I'm not as much interested in the exact number, or the technicalities that might exist due to different types of color blindness (let's just consider the most prevalent colorblindness, which is red-green I think) but I'm more interested in how low or what percentage would that number be w.r.t. to the normal vision? Is it like half, or only 10%, or much closer like 90%?

This is sort of a follow up of this question. If 3 cone cells can see between 7,000,000 colors, how many would 2 see?


texts: How do a particular arrangement of atoms become self aware?

texts: At the simplest level, we're all just atoms, animals, plants and humans alike. But what I don't understand, is how a particular arrangement of atoms such as us can become self aware, and be able to not only understand our environment, but manipulate it to our will? How is that even possible?


texts: Any kind of online "molecular modeling playground"?

texts:
I'm wondering if anyone has ever made a tool to try out new molecular modeling/simulation algorithms, where the tool itself handles the "boring" tasks of loading PDB files, building chains of amino acids from sequence so that the atoms can later be assigned coordinates by user scripts, rendering rotatable graphics in 3D, etc., but where the user can then write scripts that loop over the coordinates, do some kind of math, and then modify the structure. That way you could experiment with new force fields, integrators, etc. Something like TurtleToy does with plotter graphics.
There are obviously molecular modeling tools with scripting capability, but quite a few have licensing restrictions and also they are commonly intended as ways of splicing together existing algorithms and modeling "recipes" in new sequences. The actual simulation code is often "buried" deep in complex codebases and spread across multiple files that must be compiled together just to get something working. Clearly something like an energy minimizer written in for loops in a language like Python won't compete in terms of speed with GPU-accelerated parallelized C++, but it can be written completely from scratch to test out completely new algorithms, and if seamlessly integrated with a rendering component that accepts redraw calls from in the script, it's a quick way to visualize "what is this doing to my protein structure?" in real time as you single-step through your algorithm (and the rendering overhead probably makes speed a moot point there anyway). That way if you want to quickly see "how does my method compare to the existing ones in CASP" or something, you have a "playground" to try it out.
If I'm looking for this I'm sure others have too, so I'm wondering if it exists. An even potentially more interesting feature would be the ability to execute scripts as "filters" over the PDB, something like "Find all sequences of length 5-20 amino acids in the PDB for which this expression evaluates to "True", align them using the following transform, and plot them in this canvas". But I can see where the PDB might not like people doing this as it could bog down their servers from all the fetches, so this may be a bad idea. But allowing people to operate on their own PDB files would obviously not be a problem if the tool were around.


texts:
I'm studying Neuroscience and Fruit Flies are a pretty big deal but I don't know as much as I think I should about them.  Are there and comprehensive sources that I could read?

I'd like a review of all the important parts of the nervous system, where they are, what they do, and how they connect.


texts: Consequences of abnormal blood pressure unrelated to cardiac output?

texts:
A question from Kaplan's MCAT Biology Review asks:

In bacterial sepsis (overwhelming bloodstream infection), a number of capillary beds throughout the body open simultaneously. What effect would this have on the blood pressure? Besides the risk of infection, why might sepsis be dangerous for the heart?

The answer is:

Opening up more capillary beds (which are in parallel) will decrease the overall resistance of the circuit. The cardiac output will therefore increase in an attempt to maintain constant blood pressure. This is a risk to the heart because the increased demand on the heart can eventually tire it, leading to a heart attack or a precipitous drop in blood pressure.

I had always viewed blood pressure as a means to achieve appropriate blood flow, and a system with lower resistance would simply operate with lower pressure (via Ohm's Law). However, the answer implies that maintaining normal blood pressure is a goal in itself, such that the body would naturally raise cardiac output to dangerous levels in order to maintain it.
Can someone help explain:

Does blood pressure play a role in blood circulation that makes it more important than just a means towards appropriate cardiac output?

What are health consequences of abnormal blood pressure unrelated to cardiac output from a biochemical perspective? If I search for "abnormal blood pressure" I'll get broad symptoms like "dizziness" that don't explain its effect on different tissues that cause the symptoms.


texts: How are human rotaviruses generally transmitted?

texts: I know rotaviruses are double stranded RNA viruses and i am wondering if the human transmission is similar to the modes of veterinary transmission.


texts:
We can perceive sensation of pain if we are poked on any part of the skin.  Does this mean there is a nerve ending at every point on the skin?

Does this also mean that each of these nerves go all the way to the brain as single strands so that the brain can distinguish between the touch at any two distinct locations?


texts: How are different types of cells created from zygote?

texts:
In the process of mitosis that starts from zygote, how do different cells appear? What happens that some cells become one type and some another?

For example, is there a cell that divides into a blood cell and a skin cell?


texts:
I was watching the video at this link:
http://www.bbc.co.uk/news/science-environment-17436365

The speaker says that a cell is taken and its original DNA content is stripped out and replaced with synthetic DNA.

Does this mean scientists are not able to create a synthetic cell yet? Is this why they use existing cells, stripping them out and replacing the DNA?


texts: What is the meaning of the word 'bin' in the context of RNA-Seq?

texts:
I have a question from a book about RNA-Seq. I would like to know the meaning of the word "bin" in the below cited paragraph:

  RseQC has several nice features not found in the other programs: (a)
  When calculating read distribution between different genomic features,
  it reports also several bins upstream and downstream of transcripts.


texts: What are non-heritable changes to genomes?

texts:
I am told that mutations are heritable changes to the genome.

So this begs the question - what are non-heritable changes to genome?


texts: Is my understanding of the Bergmann's rule correct? (mass is secondary)

texts:
According to Wikipedia, Bergmann's rule applies because animals living in colder areas have greater  surface-area-to-volume ratio. If I understand that correctly, the advantage of the bulkier bodies of the polar animals isn't really about having a greater mass but about having a shape more closer to a sphere - which usually means having a greater mass.
Am I right?


texts: Can estimating the likelihood of protein sequences adopting functional enzyme folds show life is too complex for evolutionary timescales?

texts:
An acquaintance provided me with this article1. I can't understand for sure what it is about.

My acquaintance said that it proves that time for generation of even the simplest proteins is on a larger timescale than evolution history (billions of years).

I'm asking you, is that a valid conclusion to be made from this paper? What is in this article that might drive someone to that conclusion?

Axe,D.D. (2004) Estimating the prevalence of protein sequences adopting functional enzyme folds. J. Mol. Biol., 341, 1295–315. http://www.ncbi.nlm.nih.gov/pubmed/15321723


texts: Are cloned spieces significantly more vulnereble to deseases than sexually reproducing species?

texts:
I would like to be able to compare the risk for species to go extinct implied by their reproduction mechanism in the very short term. Imagine we choose some species A that can reproduce both sexually and asexually and then we make three clones of earth and in one clone we spread 1 million specimen of A that are all reproduced sexually. In another one 1 million that are all asexually reproduced (not in one generation but in like a 100 generations) and in another one 1 million of cloned specimen of A. now I want to compare the probability of each of these three going extinct in 10 years assuming the next generations would also be reproduced like their parents of course.

At the end I would be happy to know if the reason I get for this question depends on how sophisticated the immune system of that specie is.

So if I can fill in the following table with normalized numbers from 1 to 100 I would be so happy.

╔═════════════════════════════╦═════════════════════════════╦═══════════════════════════════════════════════════════════════╦═════════════════════════════════════════════════════╗
║ disease toleration score    ║ clones of a single specimen ║ asexual reproduction of the same specimen through generations ║ sexual reproduction of a couple through generations ║
╠═════════════════════════════╬═════════════════════════════╬═══════════════════════════════════════════════════════════════╬═════════════════════════════════════════════════════╣
║ sophisticated immune system ║                             ║                                                               ║                                                     ║
╠═════════════════════════════╬═════════════════════════════╬═══════════════════════════════════════════════════════════════╬═════════════════════════════════════════════════════╣
║ casual immune system        ║                             ║                                                               ║                                                     ║
╠═════════════════════════════╬═════════════════════════════╬═══════════════════════════════════════════════════════════════╬═════════════════════════════════════════════════════╣
║ simple immune system        ║                             ║                                                               ║                                                     ║
╚═════════════════════════════╩═════════════════════════════╩═══════════════════════════════════════════════════════════════╩═════════════════════════════════════════════════════╝

Right now my intuition tells me it should be something like this:

80 85 100
40 50 70
1  15 30

But I know I can be so wrong.

Please note that I don't want the single "Correct" answer to this question. I would be happy enough with the best "wrong" answer from a biologist. I mean if you know some things and you have some ideas about it that are not so bad but you are not so sure and you think maybe in future science will prove you were wrong. Just tell me that incomplete answer. I just want to learn something more than what I know now. I don't want an ultimate answer.


texts: DNA quantification in a high school bio lab

texts:
I'm working on a project in a high school bio lab (so limited resources), and I need a way to quantify the concentration of DNA in a PCR product. I can't use spectrophotometry (cheap spectrophotometers at school can't measure absorbance at 260nm), and any fluorescent dyes are out of the question as we don't have a transilluminator. Right now I'm looking at measuring absorbance change in a visible-light dye like crystal violet or methylene blue, but there isn't enough data on quantification using these dyes. Can anyone suggest anything?

Thanks.


texts: Does sleeping fewer hours than needed cause common cold?

texts: Does sleeping fewer hours than needed cause the common cold? If so, how?


texts:
I recall an obese patient who was referred to a transplant clinic as his stitch wounds hadn't healed after a year. While there's a myriad of side effects caused by immunosuppressive medication after transplants, the usual healing process for patients that underwent the same procedure is around one to two months1.
It's not an isolated example, as patients with very high BMIs can be considered ineligible for transplantation because of the post-surgical complications that follow, namely, delayed wound healing and increased chance of infection. It does not seem to be dependent on diabetes or merely low metabolism rates caused by a sedentary lifestyle (some of the patients perform well in exercise tests and monitor and control their blood glucose levels) and as such, BMI tends to remain the only (imperfect?) factor.
Why does a large percentage of body fat or a high BMI delay or impair healing?
It seems counter-intuitive to me because, as I understand it, the two major parts of the healing process involve 1) a great range of proteins for the creation of new vessels, tissue etc., and 2) The energy needed for the different processes, such as the mitosis of the cells. If blood glucose levels are close to normal and there isn't much of an insulin resistance, then surely it's not a problem of availability for either of the parts to play their role?
Clarification: I restrict the scope of the examples to transplant surgical procedures as what I state is more likely to be factually correct due to  personal experience. I would expect wounds other surgical operations to follow the same patterns, but I could be wrong.

[1]: That is an extreme case, especially considering the possibility of effects of diabetes, obesity and steroids compounding. However, there's a general trend.


texts: Why don't we speak of medial and lateral rotation of the forearm? And pronation and supination of the upper arm?

texts:
Why don't we speak of medial and lateral rotation of the forearm?

I notice we speak of forearm supination and forearm pronation, but why not medial and lateral rotation.

It seems to me that if we take the diagram of the human with palms forward, which I understand to be the neutral position one is meant to start from.. then forearm pronation looks to me like a medial movement. So why not medial rotation?

And similarly with upper arm.. why don't we speak of pronation and supination of the upper arm?  We speak of medial and lateral rotation of it..


texts: Why can't we observe haplotypes directly?

texts:
I am completely a noob to biology and DNAs, but recently I am looking into EM-algorithm used in the case of re-constructing haplotypes from genotype data.

I am just wondering what exactly in the process of DNA data collection prevents us from observing haplotypes directly.


texts: How usable is the Human Metabolic Model to predict biomass?

texts:
In order to use the Human Metabolic Model for Flux Balance Analysis of specific cancer cell lines, we would like to know what sort of flux values have been determined for the Human Metabolic Model.

Basically, how usable is it to predict biomass production in humans (to some extent)?  If it is not very good for this, what other options are there?

Thanks very much!


texts: Does pupil size affect image focus in persons with no lens?

texts:
If an individual has no lens like Claude Monet (who had them removed).

They should be able to still focus the images they see in a well light area if they shrink their pupils to a very small size like the Moken people right?

But they won't be able to see well at all in dim light, as focusing would require them to dilate their pupils which would make everything  very blurred.

Is this right?


texts: Competition with other individuals of the same species vs. adaptation pressure from predators

texts:
It is often said "You don't need to outrun the cheetah, just the other gazelles", thus emphasizing that greater part of the adaptation pressure comes from competing with other individuals of the same species and not directly from predators/parasites (which are seen as more indirect forces similar to the living conditions imposed by the environment (climate, geophysical factors, etc.))

My question is:

Isn't there a difference between competing with other individuals of the same species for food, habitats (i.e. resources) and competing with them in avoiding being eaten?


texts: Do men have a higher genetic variance than women?

texts:
I've heard that with the  distribution of our genome women have less variation on the bell curve than men.

Is there any basis for this? It was my understanding that women have more genetic variation than men due to having two X chromosomes and there being more variation on gene expression within the X chromosomes.

I've also seen a theory that with traits linked to genes on the X-chromosome in women being averaged across the genetic variants found on each of a woman's two X-chromosomes, this would reduce the likelihood of extreme traits (men have just one X-chromosome, precluding this averaging process).

Is there any biological possibility for men to have more genetic variation than women, and if so what would be a potential reason for it?


texts: Why don't fish get hurt with so many sharp fish bones? And why don't fish feel pain when they swim? Don't those sharp fish bones stick into the flesh while swimming?


texts: In which direction plants' root grow in weightlessness?

texts:
As far as I know, roots of plants grow to the direction of Earth's gravity - this is called gravitropism.

But what happens if plants are in space? Are they able to perceive gravity in state of weightlessness? Either way, where do they grow their roots in those circumstances?

Note: this question may fit better either to Space.SE or to Astronomy.SE, but I was not sure about it.


texts:
We know that almost all cats are solitary.
How did the Lions (Panthera leo) end up social animals? Do we have an explanatory evolutionary path describing how the Lions became social while the rest of the felines remained solitary?

I'm not asking what general rules apply to evolution, but, rather - what evolutionary path has led to this specific outcome.
I know a bit of evolutionary game theory. No need to reiterate the obvious. I'm asking if we know the mechanism or the evolutionary pressure in this particular case.


texts: Why cannot there be multiple sources for same species origins?

texts:
We often associate Africa as the geographical location of the origin of humans. Why cannot there exist multiple geographic locations of origin (given same environmental conditions)?

The same argument exists for other species as well. So what is the basis of the common ancestor (from single geographical location) theory?

Please give me references so that I can read more on this subject.


texts: Open databases for copy number variations similar to TCGA

texts: The Cancer Genome Atlas(TCGA) has open data for copy number variation(CNV) from at least 10k different cancer patients. They offer two types of data, CNV data from tumor and CNV data from normal tissue samples. Is there any other open databases that offer CNV data from at least one cancer type?


texts:
Apparently, there is an advantage to having 6 legs in the insect world. What is that advantage, if anything? Why would such an advantage exist for insects, but not for other, larger land animals?

What do those middle legs do that the front and hind legs cannot, if anything? Are they really essential, or do they just generate more muscle power?


texts: Are there any antigen electronic sensors?

texts:
Is it possible somehow to attach antibody to silicon or to other electronic component chemical, and have electronic detector of correspondent antigen?

Does such devices exist?


texts: How is the antigen against which autoantibodies are formed, identified?

texts:
Say we suspect some new autoimmune disorder in a patient, and we collect blood for serology.

How are self antibodies differentiated from normal ones in the collected sample?
Once they are identified, how is the antigen towards which it is directed known?

Are there assays for this? Or is it identified by the structure of the variable region? Can a simple IHC be done on all body tissues using the purified isolated antibody to localise the protein?

I mean, what is the root for suspicion of an antigen? Like, what caused ANCAs (anti-neutrophil cytoplasmic antibodies) to be suspected in systemic lupus erythematosis (SLE)?


texts: Is there any kind of antibiotic effective against fungi?

texts:
I know that antibiotics usually have properties affecting specifically bacterial cells, like by inhibiting peptidoglycan synthesis. but do any antibiotics exist affecting eukaryotic cells, like yeast or other fungi? I read in a text that "most" eukaryotic cells are resistant against antibiotics and that confused me.

Regardless of whether it can be used against bacteria or not, is there any kind of antibiotic effective against fungi, or any kind of eukaryotic cell?


texts:
I am stuck in trouble while pouring LB agar onto my petri dishes. I had to add kanamycin to my plates just before it started to solidify, out of forgetfulness, which I tried to mix using the tip. The plate was such a disaster! Is there a way to melt the agar in the plate and re-solidify it evenly.
I use falcon sterile plastic petri dish.


texts: Origin of human intelligence and thought

texts:
I've been debating this topic with a friend of mine and we can't get to a common answer. She argues that we don't descend from any Chimpanzee or Orangutan because, if we did, they would also have the cognitive thinking ability that we have. I am arguing that a high protein diet allowed the first humans to have the possibility to develop a higher memory, intelligence and other mental procedures.

But after all, what would be the real origin of the intelligence? And if animals do have intelligence too, why isn't theirs as advanced as us.


texts: What is the biological basis for a human's ability to think clearly and be aware while "fighting/competing"?

texts:
I'm interested in learning more about the biological systems or hormones or parts of the brain that affect short term (<15 minutes) ability to concentrate attention on the task and be aware of the situation.

I'm particularly interested in humans who are engaged in an activity that can be perceived as threatening: martial arts, competitive video games, sports and other activities which may be considered "fight or flight", but a scenario in which the person has chosen to stay and fight.

To clarify the question further: What is involved in the ability to make decisions based on the competitive situation itself, instead of responding with pre-learned techniques and tactics? In one case, a person may be aware of what his/her opponents are doing, while in other cases the same person may "rush in blindly" and attempt to execute techniques that were learned and worked before, but will not work in the current situation.

What influences this choice of responding versus acting on prior knowledge?


texts: Shortest route for a Nitrogen atom from fossil fuel to a protein in your body?

texts:
Millions of years ago fossil fuels originated from plants. A nitrogen
  atom from fossil fuel is now inside in a protein molecule in your
  body. What is the shortest path that the nitrogen atom could have
  taken starting with plants that lived millions of years ago, until the
  protein molecule in your body. Use those points:

  consumers
  producers
  reducers
  fossil fuels
  $NO_x$

I guess the route could be producers -> reducers -> fossil fuels -> consumers -> $NO_x$

But this could be wrong, because NO does not have to be produced by consumers.


texts: What is the name of this plant? It was found in a village in Bangladesh, in the month of February.


texts: Do allergens have structural similarities to pathogens?

texts: The conventional popular explanation of allergies is that the immune system confuses allergens with pathogens and reacts to them as such.  Is there any merit to this explanation?  If so, I would expect it to be possible to predict which proteins would be allergens by their structural similarity to pathogens.  Is it?  If not, how else could we explain which proteins are allergens and which aren't?


texts: Predicting progeny of recessive mutations using recombination

texts:
I was asked this question on a test and got it wrong, but I'd like to know how to do it.  The answers are shown in the blanks below:

  You are studying two recessive mutations in the fruit fly D.
  melanogaster. The red_ mutation causes flies to have red bristles
  (wild-type flies have black bristles) and the shiny- mutation causes
  flies to have shiny eyes (wild-type flies have eyes that are pebbly).
  You mate females from a true-breeding strain with red bristles and
  pebbly (wild-type) eyes to males from a true-breeding strain with
  black (wild-type) bristles and shiny eyes. F1 females are then mated
  to males that have red bristles and shiny eyes to produce F2 progeny.

  If you analyzed 1000 male progeny in the F2 generation, how many flies
  of each possible phenotypic class would you expect, if:

  The two traits are determined by two autosomal genes that are 15 cM
  apart:

Red bristles, pebbly eyes:_____ 425_______
Red bristles, shiny eyes: ______75____
Black bristles, pebbly eyes:____ 75_____
Black bristles, shiny eyes:____ 425______

My attempt:

So I know the 15cm=recombinants/parentals * 100 but I don't see how that formula can help.


texts: Why are prokaryotic promoter sequences written 5' to 3', when transcription proceeds from 3' to 5'?

texts:
It seems that the promoter regions are written from the 5' to 3' direction. My lecture notes, for example, give the -35 and -10 promoter regions sequences like so:

Wikipedia seems to agree, on their article about promoters.

However, RNA polymerase transcribes in the 3' to 5', as in  it reads the template strand in the 3' to 5' direction. In that case, why aren't the promoter regions written also in the 3' to 5' direction?

Meaning, instead of the -10 sequence being 5'-TATAAT-3', why is it not 3'-ATATTA-5', in agreement with the direction of transcription?

My intuitive guess is that the $\sigma$ factor recognises the promoter region in a 5' to 3' directionality. But I cannot find any information to back up this guess. Additionally, if this is true, how could it have been determined (experimentally)? Furthermore, whatever the answer is, does it also apply to transcription in eukaryotes?


texts: What DNA has the most info for getting a person's likeness?

texts:
I understand that DNA can come from hair but also from other places.

Let's suppose a person gets their DNA mapped by a company (there are some companies claiming to offer analysis of DNA.. e.g. maybe $200 and maybe some may send the DNA on a DVD)

I understand from this link that human DNA should fit on a DVD

https://stackoverflow.com/questions/8954571/how-much-memory-would-be-required-to-store-human-dna

Would it be possible to get a person's likeness..  if not now, then in future, based on the DNA I might be able to get sent to me digitally.

And presumably the DNA of a 28 year old would be the most ideal for getting (in a computer program) the likeness/image of that person at 28 - the age the DNA was taken?

I hear of the cost of sequencing the human genome to be millions or billions.. Is that more about scientists figuring out what the DNA does, rather than capturing it all?

For example, if I got my DNA captured by a company for $200, then in 50 years time or the future when technology develops, could I use it to produce a likeness of myself?    Or would what a company would send me, not really be all my DNA or be vastly insufficient to create a likeness?

I'm interested in if the kind of test that copmanies off for $200 provides all the information to create an exact replica.

Is a complete replica of a person possible in theory? (e.g. if in future they have a machine to build somebody from DNA) (with the information gathered and that could be sent to the customer by a DNA test for $200, or is it impossible even in theory because the DNA collected and sent is insufficient?)

I'm more interested in the possibility of (in theory) getting a really good likeness, than the personality of a person.

If a company only collects Saliva, is that just a fail.. would they need hair too and DNA from all sorts of human parts, in order to get a good likeness? or better likeness?  Or would it not matter whether it's the hair or the saliva?


texts: Young family members to learn genetics - Amino Labs?

texts: I'm an engineer but want to learn about biology with a niece and nephew who are early teens. I saw Amino Labs (https://amino.bio/) and thought because I work a lot with my hands, doing hands on exercises would be a good way to learn. I don't like text books and don't think my niece and nephew will appreciate a text book. Has anyone used Amino Labs? Any suggestions?


texts: Stability of RNA including Thymine nucleobase

texts:
Does an RNA double strand containing the nucleobase T instead of U has a lower free energy?
Or more precisely: There are tabulated values for the change in free energy of the canonical neighboring base pairs here.
Do you know of any source where values for neighboring base pairs of e.g. GT/CA got compared to GU/CA?


texts: Why arteries  pulse? How superficial an artery has to be for pulse to be measured manually?


texts: Problem with epoxy silane (Random results in glass silanization). What are crucial points to look at?

texts:
I`m trying to immobilize an antibody onto the glass surface by means of GPTOMS (glycidoxypropyl trimetoxy silane). Using the same protocol (silanization in toluene or acidified ethanol (see below)) I get different results any time, what are key points to check?

Looking through literature on immobilization, I see a lot of articles where authors use APTES (aminopropyl triethoxy silane) and only a few using GPTOMS, why? Epoxy group seems so atractive...

For toluene:

Rince slides with water
Ultrasonicate them in isopropyl alcohol for 3 min, dry them
Put for 3 minutes into piranha solution
Rinse with distilled water
Treat with oxygen plasma for 3 min
Slowly put slides into 2 or 4 % silane solution in toluene, incubate for 3 min
Rince with toluene and isopropyl alcohol.
Put them on dry heater (max temp. of ours is 97 C, most protocols say 110 C), incubate an hour

For ethanol:

Rince slides with water
Ultrasonicate them in isopropyl alcohol for 3 min, dry them
Put for 3 minutes into piranha solution
Rinse with distilled water
Treat with oxygen plasma for 3 min
Put slides slowly into 2% silane in ethanol solution (silane + alcohol + acetic acid (pH 4,5-5,5)), incubate 3 minutes
Rince slides with ethanol
Put them on dry heater (max temp. of ours is 97 C, most protocols say 110 C), incubate an hour


texts: Are there any fluorescent proteins capable of transforming 500-600 nm light to 400-500 or 600-700 nm?

texts:
In order to improve photosynthesis, which doesn't use 500-600 nm light, I wonder if that light can be transformed into useful light?
The idea is to transfect photosynthesis organisms with the gene for that protein to improve growth.


texts: What is known about the precise molecular mechanisms involved in asthma?  For instance, is it known why the bronchi tissue alteration cannot be reversed?  Were any new mechanisms discovered in the last decade or so?


texts: How is chloride concentrated in nerve cells?

texts: Bear, Connors and Paradiso describe in depth the electrical behaviour of the neuron. This depends upon a 20:1 concentration within the cytoplasm of potassium ions AND chloride ions. All subsequent activity revolves around potassium and sodium ion channels and pumps. No mention is given of how the initial chloride concentration is created and its subsequent regulation. Obviously there has to be a chloride pump but there’s no mention of it. Any help would be appreciated.


texts: Primary function of the enzyme lipoprotein lipase

texts:
I read here and here that the function of lipoprotein lipase is to facilitate fat uptake and storage in adipose tissue. Could anyone provide a slightly more expanded explanation, without going into too much detail, and without the use of too much jargon (I am not a biologist). I have read the wikipedia page, but sadly I didn't understand it....Thanks !

Edit: One of the things that is confusing me is what "fat uptake" means in this context.


texts:
I am viewing (through edX ) an introduction course to computational neuroscience. In the second lecture, the Hodgin-Huxley model is considered. I am going over some of the questions and have encountered a problem with one of them (a picture of the exercise is attached below). I have a strong background in mathematics, but my background in biology is yet very poor. I am having a hard time connecting the biology to the math. Can anyone help with this question:

Thank you!!


texts: Do bacteria with capsular antigen always have a capsule?

texts:
Assume some bacteria have capsular antigen.
Do these bacteria always have a capsule?
I think not, I think the antigen only makes it possible.


texts: Does the necessary Carbon Dioxide need to be in the atmosphere for mammals?

texts:
In the answers to this question, we've learnt that carbon dioxide is necessary for mammalian life, but is it necessary in the atmosphere/to breathe it in?

Or does the act of respiration give a human (or other animal) enough carbon dioxide to fulfill all of the functions that carbon dioxide is needed for?

Or, phrased another way, if you put an animal in a carbon-dioxide-free atmosphere, and continually removed the carbon-dioxide that they generate upon respiration/exhalation, would they get enough carbon dioxide to fulfill these requirements:

fatty acid biosynthesis (FAS)
mammalian/bacterial biotin-dependent carboxylation reactions.
blood pH regulation


texts:
Found in Malaysia, South East Asia. Small insect with wingspan of around 1 centimetre. Its back legs and abdomen are pointed away from the wall.

Front View:

Diagonal View:


texts: Does probiotics bacteria from yogurt live in the mouth too? Does it populate the mouth/throat or just the gut?

texts:
Yes I was basically just wondered this as I've taken probiotics in a pill form but those only go to the gut. I guessed the mouth needs probiotics too and I wondered if yogurt can accomplish that.
I also found conflicting stuff on the internet: some say enzymes in the mouth kill the bacteria in yogurt, others say yogurt helps bad breath for example which means it does have beneficial bacteria that live there in the mouth probably.


texts: How do Kangaroo mothers deliver the correct kind of milk to the correct joey?

texts: Mother kangaroos are able to rear multiple joeys (young kangaroos) at different stages of development at the same time. According to Wikipedia, "the mother is able to produce two different kinds of milk simultaneously for the newborn and the older joey still in the pouch." What biological mechanisms are able to ensure that the correct joey gets the correct kind of milk? Do different teats produce different types of milk and somehow the joeys know which teat to suck from; or is each teat able to deliver both types of milk and the teat is able to tell from the mouth conformation (or something else) which type of milk to deliver?


texts: Are humans the only primates being engaged in group sex?

texts:
There are quite many examples of humans being involved in group sex. I won't say it is a common thing and won't say whether it is "natural" or "cultural" (but "cultural" only means induced to majority by minority).

What I'm asking is if there are any other primates being involved in group sex (or how is it called in biology?). Under "group sex" I mean a sexual intercourse where several males or females can see other males and females being involved in sex too, right as they themselves are.


texts: Why does this karyotype start numbering at 11?

texts:
Here is some image I found for karyotyping a chromosome:

Why does the band numbering start at 11? When I count other things I usually start with the number one, and in some cases zero. Eleven seems random.


texts:
Question:

Two dominant non-allelic genes are 50map units apart, the linkage is:
(A) Cis type
(B) Trans Type
(C) Complete
(D) Absent/Incomplete

My take:
After a lot of searching on the net I found that 50 map units =50% recombination frequency. And no recombination happens  when it is 50 map units or more than that.
But there is no information given about cis and trans linkage with that of map units.
Even though the answer for the above question is absent or incomplete (d),the options bugged me to ask this question
Is it possible to guess cis /trans linkage when map units are given? If i am wrong please correct me. Thanks in advance !


texts: Is it "easier" for researchers to detect evolutionary ancestry than distance in the evolutionary tree?

texts:
I'm a researcher in another field who has wandered into a problem with applications to biology.  I hope to sell my results by making the following statement:

  Given two species X and Y, it is "easier" for biologists to decide whether or not X is an evolutionary ancestor of Y, than it is for them to determine the distance between X and Y in the (unknown) evolutionary tree.

Question 1: Is this statement true in any meaningful sense?  Is it cheaper, less time-consuming, or more accurate to measure ancestry than to measure distance?  Or are the two tasks roughly the same?

Question 2: A reference request - what papers/textbooks could I read/cite to back up this statement?

Thank you!


texts: What came first? The DNA or the DNA polymerases?

texts:
I know this sounds a lot like chicken and egg question and while the latter has an answer, I am intrigued about the former.

A modified form of the question would be, in the course of abiogenesis, what formed first? The DNA or the proteins (hence enzymes and DNA polymerases)?

The principle behind it is that the DNA needs an enzyme to replicate.(DNA pol)

But DNA pol itself, being a protein, needs a DNA pol A/B/C gene on the DNA! (Transcription and translation) Not to mention all the other proteins required for transcription and translation.

Same is the case for RNA and RNA pol.

If the DNA/RNA formed first, how did it replicate without a protein?
If Protein formed first, then how did it came to existence without DNA/RNA?

Let's make a big assumption and say that nucleic acid formed for the first time and replicated without proteins. Is it possible for nucleic acids replicate without proteins? For example, a abiogenetically formed DNA sequence just randomly attracted its complementary strand and whatever could fit, fitted and somehow the phosphodiester bonds were sealed sans proteins. That sounds too implausible.

Would love if somebody provides sources with evidences of DNA/protein abiotically forming de novo sans enzymes, genes.


texts: How to find miRNA binding sites on a specific gene?

texts: I am trying to find miRNAs that bind to the 3'UTR of a specific gene. What is the best way of doing that (that is, with a good scoring analysis that is most commonly used by researchers in this area)? I would also like to know the other possible methods if there are multiple ways of doing this.


texts: What is the mechanism of action of lithium-induced polyuria?

texts: I was reading in my pharmacology textbook on lithium in treating bipolar disorder, and I was curious to know if there was any specific action lithium takes to produce symptoms such as polyuria and polydipsia. Any help would be great. Also, what is the most common way to monitor lithium levels in the body?


texts: Building a PDB file from amino acid sequence of non-folded structure

texts:
I am interested in experimenting with folding simulations and algorithms for arbitrary sequences. I'm wondering if there is an easy way to convert an amino acid sequence into a PDB file for further simulation. To be clear I only want the primary protein structure.

If possible, I'd like to be able to characterize the bonds as well so that I can treat the molecule as a rigid body with rotational joints. Does anyone know something that can do this?


texts: Why haven't prey evolved the ability to always outrun their predators?

texts: I can understand why some prey can't outrun a recently evolved species. However, since cheetahs have existed for so long, why haven't its prey evolved to always outrun it, driving cheetahs to extinction. Is it because the cheetah population size is so much smaller than the population size of most of its prey species that its prey species are under very weak natural selection to outrun cheetahs? Is it that those that can run faster have more other biological costly traits?


texts: How deep does water have to be so a mosquito can lay viable eggs in it?

texts: I read about this idea for a mosquito trap (with a rather tactless name) where the idea seems to be that because the water available for the mosquito eggs is so shallow, they will die somehow or not be viable. Mosquitos are pretty small though, wouldn't they not need much water for the eggs to hatch?


texts: Say I was conducting an experiment for photosynthesis. If I moved light closer to the plant, what effect would this have on the process of photosynthesis?


texts: Is there a website that shows population sizes?

texts: I'm looking for a website that shows the population sizes of a species (doesn't matter which) as a function of time at a geographic coordinate. Is there a government website or other free database with such information?


texts: What is the difference between organelle membranes?

texts:
Cells and organelles are contained in lipid bilayers. I'm particularly interested in eukaryotic organelle bilayers and the biophysicochemical differences between them.

Many papers assume a difference in membrane characteristics and some like Anderson et al., 2007 have categorised the relationship between these characteristics and protein function in depth.

Do any reviews or comprehensive studies exist in the field that compare the thickness of the membrane, the rigidity of the surface, any differences in lipid entropy, or the overall charge inside and outside across different types of organelle membranes?


texts:
I really need to know what Ercc1-/- / DAT-Cre+  mean. I think the 1st part means that the mice don't have the Ercc1 gene (knockout). But what about DAT-Cre+?

This question arised from reading the following paper: "Inefficient DNA Repair Is an Aging-Related Modifier of Parkinson’s Disease" (Sara Sepe et al).

Ercc1-/- / DAT-Cre+ mice are mentioned several times, For e.g.:

  Ercc1−/−DAT-Cre+ mice are viable and normal at birth. At 26 weeks of
  age, specific deletion of Ercc1 in DA neurons mice elicits reduction
  in tyrosine hydroxylase (TH) immunoreactivity in the SNpc and in the
  striatum (Figures 1A and 1B). Aging profoundly exacerbates SNpc DA
  neurons reduction, as evidenced in 52-week-old Ercc1−/−DAT-Cre+ mice
  (Figure 1C). Damage is limited in DA neurons and other populations
  remain unaffected, as indicated by unchanged NeuN immunoreactivity
  (Figures 1A and 1B). Overall, these findings demonstrate that Ercc1
  function and NER are essential to preserve integrity of the DA
  circuits in time.


texts: We know that the adaptive immune system recognizes foreign particles when their proteins are expessed of the the surface of T-cells, complexed with MHCs. But MHCs present only short peptides of length 8-11 amino acids long. How is it that every antigen has one characteristic 8-11 residues long stretch in some protein of its which none of the host's protein has. Conversely, how is it that this 8-11 amino acid long peptide, which the body is recognizing as foreign is not found in any protein of any cell of our body?


texts: Are all chromosomes equally susceptible to mutation?

texts: The humans have been around for a few million years, other organisms longer yet. Changes that occur in the genome and propagate (may) eventually throw a new species ... or atleast branch off the old one. Are there any chromosomes out there that may be more susceptible to mutation than their neighbours?


texts: Difference between Sphyraena obtusata and Sphyraena novaehollandiae

texts:
"Striped barracuda" is the common name for both Sphyraena obtusata and the Sphyraena novaehollandiae.

Here's links to both fish species from fishesofausralia.net: S. novaehollandiae and S. obtusata

Are they the same fish just found in different parts of Australia, or are they completely different species? If they are different species, what is the difference between them?


texts: Does the mutation CCR5-delta 32 increase the genetic info?

texts:
My understanding is that the mutation CCR5-delta 32 caused the CCR5 co-receptor to be of a different shape, resulting HIV virus to not be able to attach itself to it.

My question, this shape/mutation, is it a result of a more or less information in the genetic information of the person with the mutation as compared to one without it?


texts: Why does hypertension occur in obstructive sleep apnea?

texts: What is the physiological mechanism behind systemic hypertension resulting from obstructive sleep apnea?


texts: I've found this spider in my bathroom today, never seen one like this, especially since I'm living in part of Europe ( Bosnia, Balkans ) that isn't known for being promised land for spiders. This one was somehow aggressive, when I touched him with an object, he immediately launched himself from the roof using his net, and when landed, he raised his "bottom"?! I've sprayed him with some water, and removed him as seen on picture, didn't want to kill him, but I'm interested if this is some venomous kind, because his head was blood red, and I've never seen this in my region


texts:
What does single channel microarray mean?
When is it used?
 Thank you for your case in advance.


texts: Concentration of a specific promoter in a cell?

texts: I want to simulate transcription activation by a given transcription factor (TF) with known kinetics. The binding rate $k_{on}$ is given in $\mu M^{-1} s^{-1} $, describing a bimolecular reaction mechanism (second order reaction kinetics). However, what is the concentration of a specific promoter in a cell?


texts:
I have read that DNA polymerase requires a primer to bind to the DNA, but I am confused as to why this is the case. When DNA undergoes replication in the cell, there are no primers in the nucleus. Why are they needed in PCR?

Many thanks :)


texts:
I have read that there are proteins in oat which are similar to those in soy, milk and eggs. I know nothing about biochemistry, and I'm struggling to decipher the info i find..
the closest Ive got to an answer is albumin - which i believe to be a group of proteins, all present in the above?
Can you be intolerant to albumin? or a derivative of?

a simpilar version of the question - what is the name of the protein(s) found in milk/oat/eggs and soy, if any?

the reason for my question, my daughter has a milk/egg/oat (protein) intolerance and I'm just interested to find out if its a particular protein (or group of), or if its an intolerance to random things.

Many thanks!


texts: What is mean by the term "an organism's genotype is its specific combination of alleles for a given gene"?

texts:
an organism's genotype is its specific combination of alleles for a given gene

What is meant by this? Is it talking about heterozygous and homozygous (like GG or Gg) or is it talking about the nuclear bases?

Thanks


texts: Is α-keratin a fully functional protein?

texts:
Is α-keratin before it coils with another polypeptide, makes chains, and build intermediate filaments a fully functional protein?

I mean, is the single monomer of α-keratin a protein or does it have to become a dimer to become a protein?


texts: What happens to our body when we undergo a sudden temperature change from 40℃ to 20℃?

texts: We know that a glass gets cracked when it undergoes sudden change in temperature. But what will happen in the case of a human body if it changes from the maximum(>35℃) to the minimum temperature(<35℃) suddenly?


texts: Can any one provide online free degenerate primer designing software. I have tried couple of them like CODEHOP is one where BLOCK formatting step finding difficulty, can anyone help me out....


texts: Is there a known minimal stretch of DNA that can distinguish any two people in the world?

texts: I imagine this could be used as a universal Identifier.


texts:
Almost everyone nowadays wants that nice summer tan, but what exactly is going on beneath the skin? I've heard a few different theories about tanning - such as a tan is nothing but the pigmentation in your cells burning, but is this true?

My questions:

What exactly is happening to our skin as we tan?
Are pigments being burned (like I was told in school), or is pigment being produced by the cells. ?

Bonus related question:
 Why do some people burn and others tan?

Bonus related question: https://biology.stackexchange.com/questions/35719/how-does-our-tan-disappear


texts:
In north Italy were I live I have two plants of laurus at the two sides of a garden. One of them has some sort of parasite on its leaves.

Someone know something about it? Leaves are covered with something like an oil.


texts: Can specific B-cells be created in a lab?

texts: Instead of creating protein sequences, could that stepped be skipped and just have B-cells created to manufacture a particular type of immunity?


texts: How does a blunt force stimulate histamine to develop early stages of inflammation?

texts: I know that viruses and sharp forces can stimulate mast cells by cut or by a virus infecting them and then release histamine. How can blunt force do this and cause inflammation? It doesn't have the above process. And how will the macrophages, neutrophils and plasma cells  react to this type of inflammation when there is no bacteria or viruses to swallow and create antibodies for?


texts: What external signals do tell catadromous fish to go from the sea to the rivers?

texts: What signals do tell catadromous fish to go from the sea to the rivers? Is it photoperiodicity? Are there any other signals?