texts: Conservation Law in Gene Regulatory Network modelling

texts:
I was going through the GRN modelling from Chemical and enzyme kinetics
by D. Gonze & M. Kaufman (PDF). The gene has 2 sites for activator/repressor. It say the DNA $D_0$ combines with activator/repressor at one of the sites leading to $D_1$ and then $D_1$ combines with $X$ again leading to $D_2$. It says then then total DNA is conserved in the reaction leading to $D_{Total} = D_0 + 2D_1 + D_2$. I want to ask why is there "2" with $D_1$ shouldn't it be $D_{Total} = D_0 + D_1 + D_2$. What I am talking about is given on page 49 of the document.
$$D_0 + X \leftrightarrow D_1$$ $$D_1 + X \leftrightarrow D_2$$
For first chemical reaction the rates are $k_1$ and $k_{-1}$. For the second reaction the chemical reaction rates are $\alpha k_1$ and $k_{-1}$.
Also, what will be the rate of the reaction for $D_2+X\rightarrow D_3$ when the DNA has 3 sites instead of 2.


texts: What is the average age of my flesh and my bone?

texts:
A study reported in the New York Times on August 2, 2005, claims that the average age of all cells in a middle age human is 7-10 years. This was based on new techniques at the time that allowed for very precise measurements of carbon-14 in human DNA.

My question is partly regarding whether or not this claim has been confirmed, changed or improved upon in the 12-odd years since the original study.

Mainly however, my question is simply: What is the average age of the flesh, bone and body as a whole of a middle-aged human?


texts: How did evolution support sports, fun, entertainment etc

texts: We know that many animals entertain themselves by playing games. But sports actually increases risks of death,or at least accidents. So why did evolution choose it? And why did evolution decide to make us look for entertainment every now and then?


texts: Why do bacteria die in a high sugar content environment?

texts:
I was reading some questions in the test bank. Then in Chapter 27, I wonder why the answer is A. (undergo death by plasmolysis). Is the high concentration of sugar that kills them or the effects of sugar on bacteria?

  Reece et al. Campbell Biology Test Bank. 9th ed. Boston: Benjamin Cummings / Pearson, 2011: 563.


texts: Why bovine serum albumin is used in mass-spectroscopy and how to interpret such data?

texts:
In the paper Network organization of the huntingtin proteomic interactome in mammalian brain, there is a description of a mass spectroscopy experiment where Bovine Serum Albumin (BSA) is added to a sample lysate and the same lysate without BSA was used as the control. I have a working knowledge of how mass spectroscopy works but I could not understand why BSA is used in this experiment. Can anyone help me?
This is probably a very trivial question. Excuse my ignorance, I am not a biology major. I tried google search to get an explanation for this but I didn't find anything satisfactory.


texts: Why is it called "Ebola virus disease", not just "Ebola" or "Ebola disease"?

texts:
Why do scientists (pretty consistently) call it Ebola virus disease, rather than just Ebola, or Ebola disease?

Many other diseases are caused by viruses, but they don't seem to have this detail of terminology.  Nor do you hear the analogous terminology for bacteria.

For example:

Rubella is caused by the rubella virus.
Influenza is caused by various influenza viruses (genus names Influenzavirus A/B/C).
Some strains of E. coli (pathogenic E. coli) cause disease, but you never hear E. coli bacteria disease.


texts: Industrial melanism is an example of natural selection. Can it be considered as a evolution due to anthropogenic action?


texts:
I am trying to find out what controls what exons are spliced out, and I keep coming across the term cis regulator, but I cannot seem to find a clear explanation of what happens...

Thank you in advance :)

EDIT: to clarify, I have tried to read the Wikipedia article on alternative splicing and I get the main idea (some exons being cut out of the mRNA with the introns to produce the mature mRNA, I think...) but I don't understand the 'mechanism' section, I.e. What controls which exons will be cut out? And what enzymes 'splice' the mRNA- how do they do it in the right place, and stick the mRNA together again?


texts: How was gene therapy able to cure diseases through the transformation of actively dividing cells?

texts:
I thought that gene therapy, when performed on target cells that regenerate themselves constantly, can be effective for a limited time only. I.e., the effect gradually wears off after a while, depending on how fast the target cells renew themselves. In other words, the patient needs to continue receiving gene therapy every so often to keep getting desired effect.

On the other hand, when targeting cells that do not divide/renew, such as an eye, gene therapy can and actually did cure blindness once and for all, and the patient no longer needs gene therapy injections.

So what about the other diseases that gene therapy allegedly cured? I think they include blood disorders like hemophilia and some serious immune system disorders? I thought they mainly involved cells that do regenerate, like bone marrow and liver?


texts: Can the immune system stop plasmodium from being active?

texts:
Suppose a female Anopheles infected with Plasmodium bites someone and transmits Plasmodium to their body.

Can that person's immune system be strong enough that it can kill the Plasmodium before it starts entering into red blood cells to rupture them?


texts: How to secrete a recombinant protein from E. coli?

texts:
What are some secretory pathways that can be used to secrete a recombinant bacterial enzyme from E. coli?

I have a recombinant protein (29kDa) that I will express in E. coli BL21 cells.  For now I have been sonicating E. coli to extract the enzyme, but in the future I would like E. coli to secrete the enzyme.


texts: Is faster breathing during exercise linearly more efficient?

texts:
Evolution's an amazing thing. It has this incredible ability to optimize variables, and often these optima can then be learned by people to gain insight into various biological phenomena.
In exercise, as intensity is increased, breathing tends to get faster and change in pattern.
I'm interested in how this change in exercise corresponds to oxygen uptake and carbon dioxide clearance.

Is the breathing style and speed associated with high intensity exercise linearly more efficient at absorbing oxygen and clearing carbon dioxide as intensity increases?

Is oxygen uptake and carbon dioxide clearance a limiting factor in exercise capacity, and to what degree does breathing style and speed associated with exercise help in this regard?


texts: Why does the face turn pale in dangerous situations?

texts: I know what the effects are of a dangerous situation on the brain, i.e., an activation of the hypothalamic-pituitary-adrenal (HPA) axis which eventually results in an increased heart rate and elevated blood pressure. However, I do not understand why enhanced blood circulation would result in a paling of the skin? Do red blood cells actively change direction?


texts: Why have whales and dolphins not evolved to have gills?

texts:
It seems at first glance that it would be an evolutionary disadvantage for a sea creature to have to come up to the surface on a regular basis in order to breathe, so why are there animals (e.g. whales and dolphins) which still need to do so?

If there is some advantage to breathing from the air instead of using gills, why haven't animals such as sharks (or indeed fish in general) evolved to do this instead?


texts: Where does the gluteus medius attach to the greater trochanter compared to the gluteus minimus attachment?

texts:
Where does the gluteus medius attach to the greater trochanter of the femur  compared to the gluteus minimus attachment? Is it above, below, next to it, etc.? Ideally I'd like to know the distance as well and location relative to the greater trochanter.

What I have found so far: some diagrams place the gluteus medius attachment below the gluteus minimus attachment, some place it above and some place it next to it at the same height.

Example of diagram placing the gluteus medius attachment below the gluteus minimus attachment (image source (mirror)):

Example of diagram placing the gluteus medius attachment next to the gluteus minimus attachment (image source (mirror))

Example of diagram placing the gluteus medius attachment above the gluteus minimus attachment (image source (mirror)):


texts: Why are C4 plants mainly tropical plants?

texts:
Why is it that most C4 plants are tropical plants?

As far as I am aware the C4 cycle does not prevent water loss; so having it exist in tropical areas does not serve these plants any good other than preventing photo-respiration. Hence I do not understand why it is solely found in tropical plants and not plants from other areas as photo-respiration is a problem not limited to tropical areas

Reference:
http://lifeofplant.blogspot.sg/2011/10/c4-and-cam-photosynthesis.html?m=1


texts:
I read this Wikipedia article about Playgirl, It is made especially for females. but Its Spokesman Daniel Nardico revealed subscriptions are generated more from males.

  In a February 2010 interview with the Associated Press, Playgirl
  spokesman Daniel Nardico stated that he considers the magazine
  appealing to both men and women, although the audience is
  predominantly male

I found another source here to claim,

  They did not find a single study that showed that women had a higher    sex drive than men.
  But Majority found that men had higher drive than women.

Why females don't have much sexual desire when compare to males?


texts: Are all fusion genes somatic in origin or can fusion genes be germline?

texts: Fusion genes should have an origin.These are essentially hybrid genes that are translocated in its entirety. Eg. BCR-ABL, EML4-ALK are known to be implicated in cancer pathogenesis. Do these translocation events occur somatically or is there a possibility for it to be inherited?


texts: How much generation of hamster's family it takes to get first bad mutations

texts:
So if I have two humsters and they start to reproduce themselfs then how much generations of hamster's family it takes to get first bad mutations?

The info here does not help to find answer https://www.reddit.com/r/askscience/comments/32x33j/how_do_animals_like_hamsters_and_snakes_avoid_the/

Thank you!


texts: How does one insert cas9 into animal cells?

texts: How could cas9 be inserted into cells by researchers looking to edit a genome? I imagine for engineering bacterial systems you could just put in the cas9 coding region in an expression vector, but is that how it is also done for eukaryotic cells?


texts: What does the acronym ‘PIN’ stand for referring to PIN proteins in plants?

texts:
There are so called PIN proteins, or PIN-formed proteins, in plants. What does this acronym mean?

Wikipedia briefly explains the function of the protein but not the origin of the name.  It's not explained even in the link-linked review paper, if I'm not missing something.


texts: Genetic pros or consequences of children born to parents of mixed nationalities?

texts:
I've gleaned a potentially flawed impression over time that a more diverse gene pool should, in theory, result in healthier progeny. Something about dominant genes promoted over recessive genes..

As a result of the above, I always assumed I should favor a mate from another region if I want to have children, thus hopefully ensuring the children have a diverse mix of DNA bits to assemble out of.

I'm an American male (almost 38), and by a curious chance I find myself dating a Russian female (almost 29) who is in a US PhD program. We've been together a little over a year, and we've discussed marriage/children. So far so good.

However there's an observational wrinkle.. She sometimes associates with a local group of Russians and I tag along. Not long ago at a gathering with several young families, of which I think many are mixed-national (Russian and American), I was discouraged to observe what I thought was a disproportionate number of children with various disorders. If memory serves, there were 2 or 3 autistic and one down syndrome child out of about 11 or 12 kids of the same age.

[It might be worth noting that this is a church group. Church might provide a kind of social safe-haven that allows these families, particularly the children, to socialize with fewer concerns. As such it might make sense to see them in greater numbers.]

Anyway, suddenly I'm doubting my prevailing assumption about genetic diversity and wondering if there is a correlation between autism and the children of parents of mixed nationalities.

In this article, I read:

  In the studies conducted in Nordic countries, a statistically
  significant 58% increased risk of autism was observed among the
  offspring of mothers born abroad.

So I find myself vexed. Is there a propensity for genetic challenges in children born to parents of mixed nationalities?

(FWIW I realize our ages dip into another risk factor, but I'm specifically asking about regional genetics.)


texts: Why does a cockroach not die even after decapitation?

texts: Why does a cockroach not die after its head is cut off?


texts: Did the Broadbill Swordfish population fully recovered?

texts:
Regarding the Broadbill Swordfish Xiphias gladius:

I read Richard Ellis "Swordfish: A Biography of the Ocean Gladiator", Chicago University Press, 2013. The chapter about industrial-strength fishing described that up to the late 20th century, swordfish population was decimated due to overfishing. In chapter 11 he discusses whether the swordfish is endangered and describe the late 1990's conservation efforts. It says that there is a rise in swordfish population in the North Atlantic (but say we don't know if the population fully recovered to its heydays) and say there is little information for the Pacific and Mediterranean populations.

I found some info in https://www.fishwatch.gov for the North Atlantic and North Pacific population, saying that north Atlantic and western north Pacific are not overfished and not subject to overfishing (I think this is good), while the eastern north Pacific is not overfished but subject to overfishing. The ICCAT published a report Atlantic, ICCAT 2017 which is hard to read. What I understood the north Atlantic is not overfished while the south Atlantic population is overfished and in danger.
For the Pacific, see Pacific, ICCAT 2018, which says that the north central and western Pacific are not overfished:

  Overall, the base case model indicated that the WCNPO swordfish stock is not
  likely overfished and is not likely experiencing overfishing relative to MSY-based
  or 20% of unfished spawning biomass-based reference points.

These reports are hard to read for non-expert, so I ask here few questions about the populations of swordfish:

Is the swordfish endangered species?
Is the swordfish population sustainable?
Per population P = { North Atlantic, South Atlantic, North Pacific, South Pacific, Indian, Mediterranean }:

3.1 Is the population P endangered?

3.2 Is the population is safe (non-threatened) or least concern?

3.3 Did the population fully recovered and reach a healthy size?


texts:
I'm looking for papers quantifying the validity of ontologies such as GO.

I'm relatively new to using annotation terms, and I often hear things like "annotation is messy" and "GO is good but it's not perfect." So I'd like to find papers that give numbers for just how messy.

I'm looking for answers from any experts that have a sense of the "quality" of GO terms (however you want to quantify it). For example, what fraction of terms are just wrong? The more computational parts of me want to sum up GO (or other ontologies) with a few descriptive validation statistics. e.g. "GO terms have an 80% precision and an R^2 of 0.6."

I'd like to see a few more examples similar to this paper that shows that a good fraction of GO ontology can be rebuilt from the ground up from independent data. That seems like one way to validate GO quality. They include this line about lack of GO validation in general literature: "... problems [with consistency and bias] are difficult to assess due to the lack of any definitive gold standard for the rigorous validation of GO."


texts:
I had always assumed that protein folding is an independent activity that occurs after translation is complete. However, recently, I learned that intermolecular forces begin shaping the peptide bonds as they exit the ribosome, while translation is still occuring.

This leads me to ask: when do the "stages" of protein folding take place? What is a general "timeline" for protein folding? For example, when do secondary and tertiary structures begin forming? Or, when do things like chaperones bind and act?


texts: A limit to birds affinity for high vantage points

texts:
Birds seem to have a natural affinity for high vantage points, including power wires, the tops of trees, and the sides and tops of buildings.

However I presume the top of the Burj Khalifa is not packed with birds, flyover video of cities full of skyscrapers suggest this would not be the case.

Q: Therefore, is there a cap, if so at what height, where higher is no longer better? Perhaps the birds vantage point is reduced by going higher.

Related, but I feel different: Why do crows sit on treetops even when it is cold?


texts: How could you measure the rate of light reactivity/ photosynthesis of a cell in a lab setting?

texts: For a lab I must take Volvox protist cells and expose them to specific wavelengths of light. How would I know they're even reacting? The assignment I've been given does not explain what I should even be looking for. I know that they do photosynthesis, so I was thinking of looking for signs of photosynthesis occurring, but I have no idea how to tell if even that is happening.


texts: I was wondering what organelles are in an onion cell, because, based on the labs we are doing in my biology class, I only saw a nucleus and cell wall. My friends and brother say there are all the organelles that you would find in a typical plant cell, but I can't find any evidence anywhere. I need to create a model and it's due in a week.


texts: What's the longest functional transcript known?  I'm wondering about RNA length post splicing, so not including introns.


texts: Spider identification: male black widow?

texts:
Unfortunately I didn't snag a picture but I found a small spider with reddish legs and enlarged fangs in Victoria, BC, Canada. The spider was very quick and looked similar to pictures of male western black widows I found online. The difference was that the spider I found had a light brown body but pictures I found online typically had white stripes.

Is it likely the spider I saw was a Western black widow or are there other species that look similar in this region?


texts: Proteins folds: relation to splicing and post-translational modification?

texts: Is the secondary structure pattern of protein folds related in any way to alternative splicing and post-translational modification?


texts: What can cause incompatible sticky ends to be ligated?

texts:
Actual question

I have reason to believe (details see below) that in a ligation I carried out, an EcoRI sticky end (EcoRI: G'AATT_C) and an XmaI sticky end (XmaI: C'CCGG_G) were somehow ligated together, a process during which at least the EcoRI site was lost: the plasmid had a BamHI site very near the XmaI site, and a BamHI/EcoRI digest produced only one band compared to three bands in the undigested control (three conformations of circular plasmid).

How could ends as incompatible as EcoRI and XmaI be ligated?

Detailed Background or: Why I believe incompatible sites were ligated

This is chronologically further to: What are common causes of unexpected ligation products?. Briefly: I digested two plasmids, one with EcoRI and XmaI (p1), the other with EcoRI and AgeI (p2) [XmaI and AgeI produce compatible sticky ends], then carried out a ligation between a 1.4kb insert isolated from p2 (structure EcoRI-1.4kb-AgeI) into the 3.4kb backbone isolated from p1 (structure XmaI-20bp-BamHI-3.4kb-EcoRI). After transformation, I tested the ligation product by digest with EcoRI and BamHI, which should produce again 3.4kb + 1.4kb. The gel was poor quality but allowed the conclusion that there were different ligation products.

Repeating the EcoRI/BamHI digest and gel more carefully showed there were only two variants: Variant A (8 colonies) produced the two expected bands 3.4kb and 1.4kb. Variant B (4 colonies) only produced a clear 3.4kb band, nothing else visible in the lane: in other words, it only carried either an EcoRI or a BamHI site and was in total smaller than variant A (confirmed by undigested controls). Thus, I conclude that B was simply the same 3.4kb backbone, re-ligated without the 1.4kb insert. Since the BamHI site was untouched in the backbone during the preparatory EcoRI/XmaI digestion, I assume that the EcoRI site was not recovered during the ligation of variant B.

(The ligation was carried out overnight at 16 deg C, using Promega T4 DNA ligase and buffer and a molar ratio of 3:1 insert:vector at a total volume of 20uL. The E.coli for transformation were Invitrogen OneShot Stbl3 and have been routinely and successfully used in the lab for a long time. The analytical digestion used Promega EcoRI and BamHI in Buffer Multi-Core, which Promega claims offers 75-100% efficiency for both enzymes. Incubation was 1.5h at 37°C.)


texts: A timeline of the odds for survival for fertilized eggs and fetuses

texts:
I'm looking for data to build a timeline of the odds for survival of a fertilized egg, i.e.,

What are the odds it'll last a week?
What are the odds it'll last a month?
2 months?
(and so on until)
What are the odds of it being born?

I am interested in the odds with the usual level of care in an industrialized nation (and a mother that is not trying to abort the fetus).


texts:
I was bitten by this insect (no big deal, but I cannot identify it). I took a picture of it (with my phone, so the picture is not great). I was sitting under some sort of vine tree (downtown though), and I think it fell from it. If that helps it happened in mid July 2016, in Montreal, Quebec, Canada.

I looked on several resources for biting insects in Montreal but I could not identify it. It was very small and yellow.

Also, the insect bit me, took some blood, and left me with a light burning sensation for about 10 mins. I am not a specialist at all in this, and I know nothing about insects, so I apologize for what I am going to write, but if I was to describe it, I'd say it was a weird mix between a very small yellow lizard (for the shape of the first half of the body) and a quite furry(for how it looked under). The head was shaped like a sharp triangle.

That's all the information I have, I hope that helps you identifying it!


texts: When touch and pain are caused by heat/cold or pressure how are the nerve cells triggered?

texts:
I suppose that when your skin is smoothly touched by any cold/heat or pressure we feel that because our AB cells notice this due to a kind of change in the nerve cell.
But when you touch something hot but not noxious how is that registered different from something what is cold or puts pressure on the skin. How works their mechanisms differently?

A step further is when due to heat/cold or pressure inflammation is started. I read that there are for each stimuly different receptors available. But what is the difference between an inflammation caused by heat/cold and pressure. How can heat create a different cascade of enzymes compare to pressure while both are inflammations and not adding any chemicals of themselves?


texts: T-cell "exhaustion" in patients with Covid-19

texts:
Following up on my previously asked question, which asks how COVID infects T-cells in immune system.

Here's a study that shows that recovered covid patients have "exausted t-cells". To quote:

  T cell counts are reduced significantly in COVID-19 patients, and the
  surviving T cells appear functionally exhausted. Non-ICU patients,
  with total T cells, CD8+T cells CD4+T cells counts lower than 800/μL,
  300/μL, and 400/μL, respectively, may still require aggressive
  intervention even in the immediate absence of more severe symptoms due
  to a high risk for further deterioration in condition.

Is this normal for other coronaviruses (like the common cold)? Also is it possible that this immune damage can be a long-term effect, similar to HIV?


texts: How is CO2 related to acidity in plant cells?

texts:
Why does increase in concentration of CO2 in a plant cell increase the acidity of the cell sap?

Thank you


texts: Is there a way to determine corresponding differential equations from fitted Hill equation parameters

texts:
I am currently doing some work with GCaMP, a genetically encoded calcium indicator. According to the literature the Hill equation parameters for GCaMP6m is $K_d=167\pm3\, \text{nM}$ and $n=2.96\pm0.04$. Usually the "derivation" of the Hill equation assumes that a number of binding sites equal to the the Hill coefficient, but I understand that the Hill Coefficient should be interpreted more as an effective "interaction coefficient" rather than an actual indicator of how many calcium binding sites GCaMP6m has. This is certainly true here, since GCaMP is a fusion of GFP and Calmodulin, which has 4 calcium binding sites.

However, given that $K_d=167\pm3\, \text{nM}$ and $n=2.96\pm0.04$, is there a way we can formulate a set of differential equations describing the kinetics of calcium binding to GCaMP? Both "intuitive" ways I can think of don't seem to be valid. If we take the naive approach similar to the Hill equation "derivation" we would end up with equations like
$$\frac{\text dc}{\text dt}=-k_\text{on}c^n(g_T-g_c)+k_\text{off}g_c$$
$$\frac{\text dg_c}{\text dt}=k_\text{on}c^n(g_T-g_c)+k_\text{off}g_c$$

Now, $n=4$ is invalid because this would not produce the correct equilibrium behavior determined experimentally. However, $n=2.96$ would also appear to be invalid, as it doesn't correctly give the actual number of calcium ions taken up per GCaMP molecule.

Therefore, my question is how can we set up a correct (or reasonably correct) set of differential equations for a reaction given experimentally determined $K_d$ and $n$ that are more of "effective" parameters rather than literal ones?


texts: explanation of conjugation experiment in bacteria

texts: In this paper (On the expression of a structural gene) I am confused about what is being plotted in Figure 6. The x-axis contains the fraction of radioactive day and y-axis contains the enzyme formation (I assume this is just the concentration of enzyme like Figure 5?). Different point shapes are different times after mating. If so, why are there multiple points of each time? Why are there multiple measurements for say 48 mins past mating? Is the correct interpretation that for each condition, they are showing the fraction of radiolabeled material for each number of day post thaw, like figure 5? It is unclear.


texts: Difference between "controlled release" vs "prolonged release"

texts:
My sister is using the epilepsy drug Tegretol which has both CR and retard (previous naming for prolonged release according to https://www.medicines.org.uk/emc/product/5932/smpc) versions in different countries. Given the active ingredient is the same (carbamazepine), would there be any difference between the effects of the two drugs in terms of preventing seizures?

Here are the boxes for the two versions:


texts: Heterozygosity and the Wright-Fisher model

texts:
I was reading the textbook Probability Models for DNA Sequence Evolution by Durrett. In chapter 1, he discusses the Wright Fisher model and the coalescent theory which I am interested in.

He defines heterozygosity as the probability that two copies of an allele are the same. In theorem 1.3, he derives the expected value of heterozygousity, but what he seems to derive is the expected value of the probability that two allelles have a common ancestor. This does not seem to be the same as heterozygosity to me. Am I missing something here?


texts:
Recently researchers present evidence that the platypus is at risk of extinction.

Source

How do researchers know that a species is at risk of extinction?  I mean Earth is so large, said species could be deep in the Pacific ocean or somewhere else that has been thoroughly explored.


texts:
https://youtu.be/B3_S3Uj18G8

In this video, inappropriately titled autistic rabbit, we see the rabbit first lying motionless before suddenly starting to spin around and jumping around.

What caused it to behave this way? Is it suffering from a disease?

I'm sorry if this is off topic. Please direct me to the appropriate site if it is.


texts:
From Solomon et al, 2013 ACC Synthetic biology and from this video :

Here, there are 2 competing reactions for glucose - one with glk as enzyme and other with gdh as enzyme.
In the graph, y axis is gluconate yield and x axis is glk activity. Logically, as glk activity increases, gluconate yield should decrease.
This is the case for most of the graph. But why is there an increase in gluconate production initially(when glk activity is somewhere between 0.2 and 0.27 )?


texts:
The 2018 study {1} mentions that:

  The healing process
  of injured tendons includes tenocyte migration which occurs
  from intact regions of tendon into the wound site.

What causes tenocytes to migrate from intact regions of tendon into the wound site, and how do they move?

References:

{1} Dursun, Gözde, Mersedeh Tohidnezhad, Bernd Markert, and Marcus Stoffel. "Effects of uniaxial stretching on tenocyte migration behaviour." Current Directions in Biomedical Engineering 4, no. 1 (2018): 313-317. https://doi.org/10.1515/cdbme-2018-0076


texts: What is the etymology of the name Anemiaceae for a family of ferns? I assume that it's from the name Anemia for one of its genera, but that is equally mysterious. Obviously it has no blood, but what fern does? I have been unable to find an answer by searching the internet.


texts: Was mammal body better suited for some type of the marine environment than the body of fish?

texts: When some of the land mammals came back to the oceans, they seem to be successful in the competition with fish at least in some environment even though they seem to have a huge disadvantage in the need of breathing above the water. So how did they succeed in the competition with fish?


texts: What is the closest species to humans in animal kingdom?

texts:
I presumed chimpanzees were the closest relatives of us. However, after watching this TED Talk, it seems bonobos are closer to us both in skeleton and behavioral similarity than chimpanzees. I once read in The Magic of Reality that we share quite a lot of common FOXP2 gene letters with chimpanzees, but there isn't any mention on similarity between us and bonobos in that book. Here is the excerpt:

  You can tell that FoxP2 is the same gene in all mammals because the
  great majority of the code letters are the same, and that is true of
  the whole length of the gene, not just this stretch of 80 letters. Of
  the total of 2,076 letters in FoxP2, the chimpanzee has 9 letters
  different from ours, while the mouse has 139 letters different.   And
  that pattern holds for other genes too. That explains why chimpanzees
  are very like us, while mice are less so. Chimpanzees are our close
  cousins, mice are our more distant cousins. 'Distant cousins' means
  that the most recent ancestor we share with them lived a long time
  ago.

  Monkeys are closer to us than mice but further from us than
  chimpanzees.   Baboons and rhesus macaques are both monkeys, close
  cousins of each other, and with almost identical FoxP2 genes. They are
  exactly as distant from chimps as they are from us; and the number of
  DNA letters in FoxP2 that separate baboons from chimps is almost
  exactly the same (24) as the number of letters that separate baboons
  from us (23).

So which species is closest to us, chimpanzees or bonobos?


texts: Do all tumors - both benign and malignant - form when proto-oncogenes and/or tumor suppressor genes experience mutations? Were all malignant tumors once benign?


texts: What bacteria results in a Gram +ve cocci and catalase +ve? What test comes next?

texts:
Results so far.
We are trying to determine unknown microorganisms in intro to microbiology course. I first did gram stain and they were all cocci morphology, purple color and clumped together  (actually I'm not so sure if clumped is right word, but they definitely were not in chains and I didn't see any isolated coccus, so if that's qualifies as clumped then they were clumped.
So I have a gram+ here.
Next I did catalase test and got bubbles on slide; I put thick chunk of the unknown on slide and dropped 2-3 drops of ${H}_{2}{O}_2$; instant bubbling.
Next test.
So now I will test for coagulase but I'm uncertain what a positive or negative result will tell me about he organism and whether this is the terminal test (for ID-ing organism I mean)
My notes say that positive for coagulase indicates S. aureus.
But does that mean that it is unnecessary to do the Mannitol test at that point then? Or is Mannitol used as a confirmation test?
Further, if unknown tests negative for coagulase, my notes say that if its also novobiocin sensitive (pos) then it is S. epidermidis.
But my same question then is, is it necessary to still do the mannitol test?


texts: Why does the hydrolysis of ATP increasing entropy increase the Phosphoryl-‐transfer Potential?

texts: I am currently taking a biology class. I do not understand this concept. I understand that the electrostatic repulsion of the negative charges, resonance stabilization and hydration stabilization all contribute. However, I do not understand why an increase in entropy would help. Wouldn't it be more favorable to have less entropy in a system?


texts: What are the ploidy levels in major groups of organisms?

texts:
If total number of chromosome in the cell is x, then for-example;

Are all animals diploid (x= 2n) ?

Are all fungi haploid (x= n) ?

Are all plants diploid (x= 2n) ?

Are all Protists diploid (x= 2n) ?

Also, what is the ploidy of archaea and bacteria?

Thank you very much.


texts: Why is the outer circle of human mitochondrial DNA ‘heavy’, whereas the inner circle is ‘light’?

texts: Why is the outer circle of human mitochondrial DNA "heavy" whereas the inner circle is "light"?


texts: What does "thermodynamic equilibrium" mean for an enzyme-substrate complex?

texts:
From Fersht, Enzyme Structure and Mechanism p. 87:

  The Michaelis-Menten mechanism assumes that the enzyme-substrate
  complex is in thermodynamic equilibrium with free enzyme and
  substrate.

In my understanding what this means is that the (E-, S- and ES-concentration dependent) rates of association and dissociation have equated.
So we're kind of in this situation:

where "product" would be referring to [ES] and "reactant" to [E] and [S]. Does that make sense?


texts: How much time does it take for an evolutionary change to take place?

texts:
I think I've read that in humans, it takes either 50,000 or 100,000 years for a mutation to fixate. But I've looked into the books I thought it mentioned it and I can't find it. I know there are theories that behavioral modernity has arisen before 40,000 years ago, and that modern humans evolved from Homo heidelbergensis, Homo rhodesiensis or Homo antecessor, some 100,000 to 50,000 years ago,  but I don't know if this implies the same. Anatomically moderm human . On the other hand, this other article (7 years old now)  says evolutionary change might take 1 million years (Not so fast).

How much time takes for an evolutionary change to take place in animals in general, but also in humans in particular? (if there is any difference between humans and the rest of the animals. I know mutations don't take the same time to spread in animals than in bacterias, for example)


texts:
Where is the line usually drawn between macroevolution and microevolution?

I thought that, although similar processes govern both, the line was at the species level, with macroevolution being changes at the above-species level and microevolution being changes within a species (something like changes in allele frequencies).  (So it's a question of timescales?)

However, I heard someone talk about microevolution among different species of Drosophila, specifically referring to copy number variation.  Was the choice of "microevolution" to describe this process (more likely) due to the similarity between Drosophila species or the type of change in the gene? Or at this level, is the distinction rather arbitrary?


texts: Is an egg classified based on the species inside it, or by the species that laid it?

texts: Basically what I'm asking is if an animal of species x were to lay an egg, and the animal inside that egg happened to be the first member of a genetically new species y, would the egg be considered an x egg or y egg?


texts:
According to Korde et al. (2010):

  Male breast cancer accounts for less than 1% of all cancers in men and less than 1% of breast cancers.

This raises the question: Why do most breast cancers occur in women?

Two plausible explanations I can think of:

A male is less likely to get breast cancer for anatomical reasons (such as a smaller quantity of breast tissue, or breast tissue that is less susceptible to cancer),
Women have higher significantly levels of estrogen, which is linked to mutations that cause breast cancer (see Cavalieria et al. (2006)).

Although, I have no evidence to suggest that either of these is predominant factor.


texts: Is the information in the brain stored in the connections rather than neurons?

texts: Can I imagine the difference between the model of the grandma neuron and the model of interconnected neuron network so that the information isn't primarily stored in the neurons (respectively in their states) but in the connections between them.


texts: Why does the "all-or-none" principle hold true for only single nerve cell, and not a bunch of nerve cells?

texts:
I've read this from wikipedia:

  ... This relationship holds only for the unit of tissue; for nervous tissue the unit is the nerve cell, for skeletal muscle the unit is the individual muscle fiber and for the heart the unit is the entire auricles or the entire ventricles.

https://en.wikipedia.org/wiki/All-or-none_law

I know about all-or-none principle but i don't understand this statement. What it is trying to imply? I am not sure my question title is reasonable because of my less understanding.


texts: Do fish break a water molecule to absorb oxygen?

texts: How do fish separate oxygen from H20 & consume it? Do they break the water molecule and absorb  the oxygen only?


texts:
I tried the all powerful google to answer this question - but I am not getting the answer I seek. I know we turn darker because the skin produces melanin. The question remains - why darker?

I am a physicist and it would make sense to me that the bodies response would want us to turn whiter- since a higher albedo would reflect more UV radiation. It seems that evolution took the way of absorbing more and more UV radiation by this melanin and then converting it to heat. Which begs the question as well - do black people get hotter than white people given the temperature is constant? Although this a side point to my original question.

What sparked this question was the use of thousand of black balls being dumped into LA's water reservoir in the hopes to reduce evaporation. Again... BLACK balls. This makes no sense to me - why the heck not use white balls to reflect more sunlight?


texts: How do researchers define the region a lead SNP encompasses?

texts:
As I understand it, a lead SNP captures the variance for all unmeasured SNPs in a region due to it's low p-value and high linkage disequilibrium. However, in different papers the region size differs (e.g. from 500kb +/- to 1mb +/-), how are these sizes chosen and why do they differ?

Edit to add examples:
Xia et al. Transl Psychiatry. 2017 Aug
"Genome-wide association analysis identifies common variants influencing infant brain volumes"
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5611727/
-500kb region

Polushina et al. Transl Psychiatry. 2017 Dec
"Analysis of the joint effect of SNPs to identify independent loci and allelic heterogeneity in schizophrenia GWAS data"
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802566/
-1mb region


texts:
I don't think "non-human" animal like cat, dog, bird or fish think about future while sleeping.

I think when sleeping, the "non-human" animal will feel rather think about anything. I think when sleeping, the "non-human" animal will feel  their breath just like when we are meditating. So, when we meditate we will feel our breath like "non-human" animal that are sleeping.

Do "non-human" animal like cat, dog, bird or fish think about future while sleeping?


texts: Why don't we have vaccination against all diseases caused by microbes?

texts: People can be vaccinated against certain diseases. Principle of vaccination is to use live attenuated load or inactivated. My question is - why we dont have vaccination against all diseases which are caused by microbes?


texts:
One thing i can not still comprehend about the immune system is the following:

A bacteria is first recognized by neutrophiles. But then neutrophiles have to have the ability to release chemotaxines upon the recognition (or the bacteria?)? Its not mentioned anywhere in my script how macrophages and other non abundant innate immune cells come to the source of an infection in details.


texts: Why does my simulation not support the idea that inbreeding is bad?

texts:
After reading this post, I wrote some code to simulate inbreeding.

  We have a population of $N$ creatures. Each creature has two genes, which come in two forms: recessive (a) and dominant (A). The creatures' initial genomes are random. At each stage, the following happens, in order:

  Each creature with the recessive phenotype (aa) dies with probability $p_R$.
  Each creature with the dominant phenotype (AA, aA, or Aa) dies with probability $p_D<p_R$.
  Each creature then decides to have children with probability $q$. Each creature that decides to have children chooses a mate (see below) and has three children with that mate.

  I wrote two different kinds of creature, incest-averse and incest-seking. Each time I ran the simulation, the population consisted of either all incest-averse or all invest-seeking creatures.

  An incest-averse creature chooses a mate randomly and uniformly from the set of its non-siblings.
  An incest-seeking creature chooses a mate randomly and uniformly from the set of its siblings. If it has no siblings, it just randomly picks anybody.

In practice, since each union produces 3 children, the incest-seeking creatures almost never fail to have siblings after a few generations.

What I found was that whichever type of creature I used, the results were the same: the frequency of the aa genotype plummeted to almost zero. I used the parameters $N=100$, $p_R=0.1$ $p_D=0.05$ $q=0.022$.

Presumably my model is in some way too simple. What am I not taking into account?

Source code


texts: What's the longest intron in the human genome? Discarding isoforms were a long intron spans more than one exon, i.e. what's the longest distance between two exons without another exons in between.


texts: Why do Humans not produce Vitamin C like other mammals?

texts:
Why do most mammals produce their own Vitamin C?

Why do Humans not?


texts:
I am doing EMSA with Thermo LightShift Kit. I have a 150 bp biotin labeled probe which has been PCR amplified, gel eluted and sequenced. When I load samples on 5% native polyacrylamide gel, I see a non specific band in my control and samples along with suspected shift. Can anybody please help with an explanation of this band and possible troubleshooting?
Image Details:
Lane 1 and 3 are controls rest are samples

My binding reaction has HEPES ph 7.9, KCl, DTT, Glycerol, MgCL2, Poly (dI.dC) and NP-40
Lane 1 and 3 are my negative controls ie binding reaction mix + labelled probe
Rest are binding reaction components mix + probe + nuclear extract
Nuclear extract was made using Thermo NE-PER kit
Thanks!


texts: What does q stands for in Gq/11 alpha subunit?

texts: Sorry for asking, I am not capable to find what does the q stands for in Gq/11 alpha subunits.


texts:
If NADPH returns to being NADP+, then that means one proton and two electrons have been incorporated into 1,3-BPG. If only one proton and one electron were attached to the carbon in 1,3-BPG (removing phosphate), I’d understand, since there’s a single covalent bond between carbon and hydrogen which establishes stable octets. But there’s another electron hanging around. What happens to this one? Or am I totally mistaken about the whole process?

This is the chemical formula for G3P:

The Lewis diagram below shows the top part:

As stated, NADPH gave off 2 electrons, yet only one is needed to bond with carbon (orange). Where did the other electron disappear to?


texts: Immunotherapy for tumours which do not have TSA

texts: Is immunotherapy possible for tumours which do not have Tumour Specific Antigens (TSA)? If so, doesn't targeting those tumour cells also target other healthy cells, thus causing autoimmunity ?


texts: Species-ID: What is this thing attached to my wall (California, USA)

texts:
I found this thing attached to my wall next to my garden. I live in Simi Valley, California, USA.

At first I thought it was a caterpillar and I left it alone, but after 2 or 3 months I don’t think it is a caterpillar anymore. I touched it today for the first time and it moves. What is it?


texts: What would happen if all magnesium was removed from a person's body?

texts:
Magnesium is essential to bodily functions. It enables ATP from which most energy is produced in cells. It regulates over 300 biochemical reactions in the body. It is important to the transfer of nutrients through cell walls. It stabilizes the structure of DNA and RNA.

What would happen to a person if some alien micro-organism totally depleted his/her body of magnesium? How quickly would they die? (Yes, there may be a sci-fi story being written here.)


texts:
I can understand the allele notation when is in the form rs8176719(T;T) or rs8176719(G) but recently i found this ones rs8176719(T;-) or rs8176719(-;T).

So im confused, rs8176719(T;-) is the same as rs8176719(T)? or is the location is important ?

Thanks .


texts: What allows grass eaters to digest cellulose?

texts:
Scientists are saying that it was a small step for the Panda to move from a meat diet to a grass diet. The article only refers to differences in the Panda's skull, presumably for better chewing.

I've also heard that the Japanese are able to digest Nori because they have the right gut biome because Nori has been part of their diet and the appropriate bacteria has developed over time.

Does that suggest that if the cellulose of bamboo and other grasses were pre-chewed by mechanical means and the right bacteria were introduced into the human gut that we would likewise be able to digest grasses?

Related story


texts: Is Asteraceae and Compositae the same family?

texts:
I'm wondering what taxonomic family sunflowers (Helianthus) belong to. Although it's mentioned it belongs to family Asteraceae it is also a composite flower. So it belongs to Asteraceae or Compositae or both?
And do they refer to the same family or to different families?


texts: Why do the ancestors of birds still exist?

texts: If I am not mistaken, scientists believe that birds are evolved from reptiles. Why do the ancestors of birds (that is, reptiles) still exist?


texts: How do rodenticides with delayed effect work?

texts:
Most modern rodenticides are claimed to cause death no earlier than several days after ingestion.

That's quite strange - once a chemical was ingested it will be absorbed in the digestive system and enter the blood stream and rapidly spread around the body (something like within ten hours - that's what most human medications claim in pharmacokinetics sections of their manuals). I'm pretty sure a rodent is very similar to a human in terms of digestive system functioning.

Then how do rodenticides not kill the rodent earlier than in several days after ingestion?


texts: Independence of Light independent reaction in photosynthesis?

texts:
Inspired by a question asked to me by a classmate, I have the following question about Light-independent (dark phase) reactions in photosynthesis:-

  Let us suppose an algae sample was exposed to light for a considerable
  time so that maximum( if there is a limit) NADPH concentration was
  achieved. Now if the sample is placed in dark and radioactive
  ¹⁴CO₂ bubbled, will the cell be radiolabelled after some time of
  bubbling continuously?

I guess the answer depends on the active life of ATP and NADPH , the products of light reaction. If they are considerably stable, such that they are in sufficient concentration for executing Calvin cycle although their production (apart from respiratory ATP production) has ceased due to absence of light. If they are, then the ATP and NADPH produced during the initial exposure period will carry out carbon fixation with radioactive carbon and hence radio labelled sugars will be recoverable from the sample. If not, they will quickly degenerate (by hydrolysis, utilization or likewise) and they will be unable to carry out fixation after some fixed time after stopping the light.

What, under normal conditions, should be the time after which the light-reaction products are no longer capable of fixing CO₂ by Calvin cycle? And, ultimately, will the presence of radioactivity in sugars for the scenario above depend on the species of plant?

[I am ignoring all radioactivity due to dissolution of ¹⁴CO₂ in cytoplasm]


texts: What made this pile of tiny poops at the base of an old oak? Eastern Long Island, NY

texts:
I ran across three trees (all with cavities) that had mounds of these small droppings at their base. These were approximately 50-100 meters from the shore of a salt marsh on the east end of long island.
We don't have porcupines, and I've never seen such piles associated with squirrels, so my first thought was bats. Any ideas?


texts:
This one is too basic question:

I just came across $Ihh^{-/-}\ $ mouse. Is that means this mouse devoid of that gene Ihh. What is this sign called and are there other such representations?


texts: How did so many types of larvae become known as worms?

texts:
How did it come to be that so many types of creatures typically known as worms are actually insect larvae? Silkworms are not actually worms at all, but larvae of a type of moth. Another example being the Maguey worm, which is supposedly the worm in some types of tequila and also not a worm, actually also a type of moth-larvae?
I find it curious that Wikipedia would have a creature with the word worm in its title, and then the first thing they tell you about it is that it is actually an insect. These are just the two examples I came across, there are probably more.


texts:
My physiology book says that cell specialization is so great that no cell in the body could be called a typical cell.

I don't understand the above sentence, why couldn't there be typical cells? After mitosis don't we get two typical cells? Or what is meant by the sentence??

Thanks in advance!


texts:
On Wikipedia article about Urine specific gravity we can read:

  A specific gravity greater than 1.035 is consistent with frank dehydration.

What is frank dehydration? How it is different than regular dehydration?


texts: What is operating temperature of the human brain?

texts:
I've heard several times that human brain can die in temperatures over 40 °C, or under 10 °C, as an engineer I'm curious.

In what temperature region can brain properly work?

And just an underlying question what is a TDP (thermal design power) of human brain?


texts: Why aren't plants' roots as diverse as leaves?

texts:
I have been doing some gardening recently and I suddenly realised that all plants have superficially identical non-woody roots of the same size from gigantic trees to small fruiting plants and vegetables. They are all white, no more than 1 mm across, long and flexible with no distinguishing marks. Only when the root start to become woody do they become different in appearance.

Leaves are very diverse even when they have just started to grow, i.e. before they have reached their full size. I can recognise many different plants from their smallest leaves alone but I wouldn't be able to differentiate plants by looking at their roots. So why aren't roots anywhere near as diverse as leaves?


texts: With supercomputers doing calculation in petaflops ($10^{15}$ Calculations per Second), have we crossed the speed of Human Brain?


texts:
All knowledge of biology I have comes from online and after speaking for a brief period of time with someone from a biological education it is very clear that I have no knowledge of the pronunciation of all the necessary jargon I have learnt.

For example: Chordae Tendineae, Squamous Suture, Loop of Henle

How have people overcome this issue? I have searched online for pronunciation videos and whatnot, but very often they pronounce them differently to each other and it is impossible to know who is correct. I also do not want to learn the IPA for English.


texts: Western Blot: Fischer ECL substrate 2:1 instead of 1:1?

texts:
i recently developed a b-actin-ab-incubated PVDF-WB-Membrane with the Thermo Scientific Pierce ECL Kit. According to the manufacterers orders i mixed Reagent 1 and Reagent 2 1:1. But unfortunately i got kind of "unbalanced" bands (on the right side of the picture). Then someone gave me the tip to try to mix the reagents 2:1. For this substrate i got the result on the left side which actually looks much better.
Has anyone of you had the same experience and can anyone explain to me why this is so?
Is it "legal" to do so, or does it alter somehow the results of my experiment?

Yours,
p1ssn3lk3


texts:
I am running PCR reactions with different sets of degenerate primers and I want to know what should go into the master mix

My usual master mix:

DEPC water
PCR buffer (-Mg)
25mM MgCl2
10mM dNTPmix
cDNA

On ice I add my forward and reverse primers to the appropriate PCR tubes, add master mix to each PCR tube, then right before I pop them into the thermal cycler I add taq and mix.

Is this a proper way of doing it? I get product but I'm thinking maybe I can improve it by changing what I add to the master mix. For example, is it better to add taq instead of cDNA to the master mix and then add cDNA before I start the PCR? Is it okay to add both cDNA and taq to the master mix together?


texts: Why does rotational cleavage take place in mammels like humans. What is its significance?

texts: What is the actual reason behind the rotational cleavage that takes place in humans? Why does it happen? If it doesn't occur, what will happen


texts: Do SARS-CoV-2 virus particles really travel through filopodia and "emerge from the tips"?

texts:
Watching the new University of California San Francisco video Coronavirus forces cells to produce tentacle-like structures that infect neighboring cells I saw

The growths spread out, and coronaviruses emerge from the tips, ready to infect neighboring cells.

The caption on the video page includes the following:

When a cell is commandeered by SARS-CoV-2, however, these same kinases behave in ways that disrupt normal cell function and transform the host cell into a virus factory. Cell division comes to a halt, inflammation pathways are activated, and the cell even begins to produce tentacle-like structures known as filopodia, which protrude from the cell's surface and may serve as molecular highways that help the virus spread rapidly to neighboring cells.

Question: Do SARS-CoV-2 virus particles really travel through the induced filopodia and "emerge from the tips" of at least some kinds of human cells? Are they transported along the microfibers to the ends as part of this process? If so, how is this known? Images here and elsewhere seem to shown the virus particles dotted randomly along the filopodia and other areas of the cell surface as well.


texts:
I found this on a forest in Mexico City. It was kind of a warm day (around 15°C). It had been raining a few days prior and it was quite humid, but not suffocating.

This orange thing was on top of a rotting tree. I thought it could be Dictydiaethalium... maybe.

When I moved it it produced an orange slime.


texts: Is gut bacteria Succinivibrionaceae's low methanogenesis understood well enough for GM of cattle gut bacteria to be considered?

texts:
After watching the Periodic Table of Videos episode linked in this question I watched the episode Wallabies and Methane where Sir Poliakoff says (a bit after 02:00):

So the point of this paper was that Wallabies have different bacteria in their stomachs, which which instead of producing methane, produced succinic acid, which is the diacid of butane.

 Succinic acid, Source
The paper he references seems to be Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies Pope, P. B. et al. Science 29 Jul 2011: Vol. 333, Issue 6042, pp. 646-648 DOI: 10.1126/science.1205760
Question: I can not understand the abstract, and the paper is paywalled. Presumably much more work has been done since its publication in 2011. How well is  Succinivibrionaceae's low methanogenesis understood; well enough for the genetic modification of cattle gut bacteria to be considered?

Abstract
The Tammar wallaby (Macropus eugenii) harbors unique gut bacteria and produces only one-fifth the amount of methane produced by ruminants per unit of digestible energy intake. We have isolated a dominant bacterial species (WG-1) from the wallaby microbiota affiliated with the family Succinivibrionaceae and implicated in lower methane emissions from starch-containing diets. This was achieved by using a partial reconstruction of the bacterium’s metabolism from binned metagenomic data (nitrogen and carbohydrate utilization pathways and antibiotic resistance) to devise cultivation-based strategies that produced axenic WG-1 cultures. Pure-culture studies confirm that the bacterium is capnophilic and produces succinate, further explaining a microbiological basis for lower methane emissions from macropodids. This knowledge also provides new strategic targets for redirecting fermentation and reducing methane production in livestock.


texts: Do Marsupials have a standard classification system for their blood groups?

texts:
I've seen a limited amount of animal blood groups listed...like dogs, cats, horses, etc. But what blood types do marsupials have?

To clarify, what I want to know is if the species has a classification system similar to the ABO blood group? For example: Blood Type A, Blood Type B, etc.
Or in the case of Dogs, the classification system is labeled as: Dea 1.1, Dea 1.2, etc.


texts: How is the activation energy lowered in an enzyme by just orientating the reactants closer to one another?

texts: If the activation energy is lowered, bond strength has decreased. How does purely orientating the reactants closer to one another lower the activation energy in a protein? The only thing I can think of is steric strain.


texts: Why are P and T waves curved and not straight (ECG)

texts:
The P and T wave are in shape of a curve while the QRS complex is in straight lines.
What is the reason this is happening?


texts: Why was the intramuscular route selected for palivizumab administration to infants, instead of the subcutaneous route?

texts:
The majority of monoclonal antibodies administered by an extravascular route to adults are administered subcutaneously.  Does anyone know or have hypotheses about the reasoning behind why palivizumab and motavizumab were designed for intramuscular administration?  A key point may be related to the fact that they are administered to infants as young as one week old, rather than adults.

FDA documents are at this link:  https://www.accessdata.fda.gov/drugsatfda_docs/bla/2003/103770Orig1s5033.pdf


texts: ID Request: What is this frog? Eastern Long Island, NY USA mixed hardwood forest

texts:
Apologies for the potato quality photos, but can anyone ID this frog?
My son found a few frogs living under a porch at my father's house, which is situated in a mixed hardwood forested area of eastern Long Island, NY. I say "living" because he sees them sitting just at the edge of the low porch every day for a while now.


texts: Can 5 alpha reductase inhibitor drugs work for life or do they lose effectiveness?

texts: Do 5 alpha reductase inhibitor drugs like finasteride and dutasteride lose their effectiveness over time? Why do some drugs, like in an HIV regimen, work for a prolonged time without tolerance whereas other drugs, for example antidepressants, have tolerance issues after a short time?


texts: Shine-Dalgarno sequence and expressing proteins

texts:
Shine-Dalgarno sequence present in the prokaryotic mRNA plays a role in initiation of translation. In eukaryotes a Shine-Dalgarno like sequence is present but does not play an important role in initiation of translation.
We often try to express a eukaryotic gene in a prokaryote. For example : expressing insulin gene in E.Coli.

My question : If eukaryotes do not have the shine dalgarno sequence , then how can a eukaryotic protein be expressed in a prokaryote ? (I am especially interested in knowing about this in case of cDNA expression)


texts:
I have had a few difficulties finding answers for the questions below. I have tried answering the first two myself; but, I am not sure they are correct or not. And I am not too sure about the third one.

In which structure of the brain does the axon from the spinocerebellum tract synapese? Is it the cerebellum?
Are the cell bodies of axon in the gracile tract located at the dorsal root, tectospinal tract located in cerebral cortex?
Which region  of spinal cord carries feed-forward information to help accommodate for upcoming motor movement?


texts: Are there any organisms, extant or extinct, that have only one neuron?

texts:
Nervous systems are useful in one way because they allow for integration of complex information. They are also useful because they transmit information very rapidly, over a large distance.

However, that last function can be done without an actual nervous system; presumably, all you need is one cell. Some individual sensory neurons can transmit an impulse at 120 m/s, which in and of itself would be useful in many circumstances.

So, are there any species that have only one neuron? There may have been many one-neuron creatures in the early days of animal evolution, but it's also possible that nerve nets appeared together, as a unit. I also suppose there are some small multicellular organisms that have a single excitable cell, but it's up for debate whether we should call those "neurons" or not.


texts: In my biology textbook, it says that mosses are avasculer and do not have xylem like spermatophytes. So by what means do mosses transport nutrients ?


texts: Who is organizing the heartbeat and its roles in the body?

texts: Throughout the decades we heard that the heart is the only muscle whose nervous system is not acting. So who is he responsible for organising the heartbeat and its roles?


texts: Are there any examples where 'magic bullet' drugs have worked in cancer treatment?

texts:
Magic bullets are drugs that can be administered on a micro local scale. In this context administration/binding would occur in or near the tumour by exploiting the different surface antigens that cancers expose. Basic lectures teach that a "magic bullt" drug could attach via an mAb (attached to the pro-drug) and then a conjugated enzyme cleaves or converts the pro drug to a drug. This would eliminate a lot of side effects from chemotherapy.

Use in clinical trials. Some mAbs have started to be used in clinical trials, almost 40 years after they were first proposed. My question is simply; have there been any cases of mAbs being used as a successful treatment for any disease? If not, what makes the R&D of this drug type so difficult?


texts: Why when measuring turbidity do we use the minimum wavelength?

texts:
As a preface, I read a few other related posts and was able to gather some knowledge, though without any background in physics I am having some trouble here piecing together a coherent view. I looked up videos of Beer-Lambert law on Khan academy and it gave a relationship between transmittance and absorbance as
$$Transmittance (T)=\frac{I_1}{I_0}$$ $$Absorbance(A)=-log_{10}(T)$$
Further, this post points out that turbidity is absorbance, and describes to be in relation to diffuse-reflected and scattered light?
Taking a step back, we see okay, turbidity is really just a measure of 'murkiness' and the amount of light that is scattered as a consequence. What about this diffuse-reflected light? And then this post says scattering is really just the sum of refraction and reflection. I don't think that is correct though, as this video shows refraction and reflection and scattering are different concepts, in so much as refraction is the bending of light as it passes through one medium to another, reflection occurs when light hits a smooth or shiny surface and bounces off, and scattering happens when the surface is rough sending the light in different directions. Then this post here. appears to detail out what would be a satisfying explanation but I haven't taken physics. Are there any good videos that might help better explain these topics?
Then, thinking about absorption my chemistry textbook talks about radiation and I had this concept in my head about light being absorbed then admitted at different wavelengths and I feel like that is true and perhaps that is where we are getting the relationship between transmittance and absorbance?
Bringing it back to the question that brought all this up, through other questions we were able to determine the answers to be To measure levels of pigment production it would be best to use the light of 450 nm, and to measure it turbidity would be best to use the light of 560 nm. In other words, for pigment production, we use the maximum value of absorbance and for turbidity the minimum value. The question we have is why this is the case? The most we were able to come up with is that the color of the Chlorella bacteria is green and that things are green because that wavelength of light is reflected, and that the wavelength of green light is 560 nm. I guess we can't use green light to measure the amount of green pigment because the light that would be returned would be a combination of reflected light (how much green pigment) + scattered light(not green pigment but returns green light) + (some combination of absorbed and reradiated light??). So we wouldn't be isolating the information we are after? If we want to know how much "green" is present this would be best measured by measuring the wavelength of light that is the least reflected, or the most absorbed, so the green pigment absorbs most of this light and the light that is not absorbed will tell of how much green stuff was there to absorb it. When it comes to the why for turbidity I am a tad stuck and I think it is because we appear to have a mixture of definitions above. Perhaps some more concise definitions will shed light. It appears the answer to "why can't we use green light" may help to give a possible answer, as the scattered light is the measure of turbidity and that would be with some margin of error, what we have isolated?


texts: Where in the world does blue eyed whites originate from?

texts:
I know that there were no blue eyed people until ~6000 years ago due to a mutation and all blue eyed people have a single common anchestor.

But where in the world does it originate? I assume it originates from somewhere in Europe but is it known more specifically where like Scandinavia, Eastern Europe, and so on or is it impossible to know?


texts: Does hypothalamus regulate posterior pituitary gland?

texts: We have the hypothalamus-anterior pituitary-endocrine axis, but is there a similar chain of command for posterior pituitary gland such that oxycotin and vasopressin are regulated by some tropic hormones?


texts: Why does the SARS-CoV2 virus not remain infectious forever? Or does it?

texts:
Given that the majority of biologists do not currently consider viruses to be alive, a virus can never die.  It can, however, get destroyed by long exposures to soapy water, alcohol, and apparently certain frequencies of UV light.

Why is an individual SARS-CoV2 virion not infectious forever?  Or is it?


texts: Eukaryotic cell lysate-based protein expression efficiency

texts: What is average efficiency of eukaryotic cell lysate-based protein expression systems in terms of (mg of protein expressed) / (mg of lysate) ?


texts: Understanding common identifier codes (IDs) in biology databases

texts:
I know this is very basic but I would like to understand it and it's difficult to know where to begin with a new database.

I have the output:

sp|Q9NZT1|CALL5_HUMAN

However I'm not sure exactly what this is referring to.

Is Q9NZT1 q unique identifier?
Is CALL5_HUMAN unique too?
Should one use both together to get information?
How many types of ID are there?


texts: Which information can be obtained from a list of gene names?

texts:
Lets say I only have a list of gene names. I know they are up regulated and I know they are related to cancer.

What information can I obtain from having only the names of genes? For example is there any way to find a gene-gene interaction, or anything else? Is it possible to retrieve any information by having only the name of the genes?


texts:
Why elders advice not to drink water after eating banana? Is there any science behind or is it a myth?

Found a website supporting this (so called?) myth.


texts: This insect was found in my garden in India on the evening of August 07, 2019. It's rainy season here.


texts: Can oral bacteria be targeted by white blood cells?

texts:
Today I was told from a dentist that a leukocyte is much larger than a bad bacterium. So a leukocyte cannot remove bad bacteria when they hide in very places like the space between the gums and teeth for example, because leukocytes cannot exit the body.

So am I right that a colony of bad bacteria cannot be removed from the oral cavity by leukocytes, because they are too big to exit the gum?


texts: Why are low throughput methods more trustable for protein interaction?

texts:
I read that protein interactions found using high throughput methods are less trustable than those found using low throughput methods.

For example, searching for interaction of BRCA2 on BioGRID, I got this result.

So, we won't be sure about the interaction of BRCA2 with SIRT1 as it has been found with a high throughput method.

My question: Could you give me a very simple explanation of what is the meaning of high and low throughput techniques ? (I have a vague idea reading it on web but I am not satisfied with my understanding.) Why is high throughput not reliable in this case?

One reason I can think is that they involve mostly in vitro studies.


texts: How can we determine which chromosome came from which parent?

texts:
In this article there is a graph (figure 1) describing different levels of methylation in the maternal and paternal chromosomes after karyogamy.
How can the researchers identify which chromosome originates from each parent?


texts: We all know CO₂ as a waste product of metabolism . Does CO₂ have any helpful role , apart from having a role in pH of blood ?


texts: Why to choose a grammar from a lot of grammars that can describe structure of proteins?

texts: Why do we choose a grammar from a lot of grammars that can describe structure of proteins? Usually, there are a lot of (maybe infinite) grammars that can describe one language. Why do we choose a specific one? Especially the language of proteins of gene just has finite sentences or words.


texts: The genotype of a hybrid plant from a cross and its determination?

texts:
Question

I know about crosses Inheritance and this question is about Test Cross.
I want to know if we can determine the genotype of hybrid plant by crossing with a pure recessive parent from Filial generation 1 or if we require more generations to know the genotype?

My thoughts

if the plant is homozygous then no need if it is dwarf as we know that dwarf genes are recessive but if the phenotype is tall then we have to find its genotype whether it is Tt or TT. I have come across a MCQ : the genotype of hybrid plant obtained from a cross can be determined by crossing the plant with - . To me the ans should be Pure recessive parent at F1 generation. But ans given is Pure recessive parent at F2 generation


texts: What do breeders call the effect when a breed resists modification?

texts:
It is impossible to breed a blue rose or a cat with a bulldog shape. This is because breeding is limited by gene variations in the population.

What do breeders call this effect?

UPDATE

I guess this term is from medieval and/or handicraft breeders, not modern and hi-tech.

UPDATE 2

I am speaking not about principal impossibility but just about observable or tangible barrier. We can be sure that it is possible to turn dog into cat in billion years, but it is much harder than turn German Shepherd to Yorkshire Terrier, which is possible for hundreds of years.

So, there are are two main types of changes, ones take hundreds of years, others take hundreds of millions of years. Former require genetic recombination while latter require genetic mutation.

This barrier was felt by breeders in practice and caused some versions of anti-evolution beliefs.

I need to know how this barrier is named.


texts:
I had someone gift me some old firewood along with some other wood I had purchased from them.  I was told the wood in question is popple.  However, it was in pretty bad shape and much of it had a mushroom/fungus growing on it.

Does anyone recognize this fungi?  The trees lived in central Minnesota, and sat close to a lake for a year or so.


texts: method for DNA extraction for human mucus(nose) or earwax?

texts:
What is a simple method for extracting human DNA from nose mucus or earwax?

I tried googling for methods for DNA extraction for human nose mucus or earwax and couldn't find any. I assumed that if one can extract DNA from hair, which has few cells with non intact nucleus'  then the same could be done with earwax, which also has few cells or mucus? The simpler the method, the better, given I am an undergrad with low experience.


texts: Role of Prevalence in Estimating Coronavirus Mortality

texts:
Let there be a sample of 10,000 people.

100 of them have a fever. You test them for COVID19 and they all come out positive.
5 of them die, 9 of them end up in intensive care.
The estimated mortality is 5%, and estimated intensive care rate is 9%.
What about the 9,900 asymptomatic people who did no get tested?

Scenario A: All 9,900 asymptomatic people would test negative for COVID19.
Scenario B: All 9,900 asymptomatic people would test positive for COVID19 because of a combination of high rate of asymptomatic carriers and high false positive rate.
End result:

Scenario A: true mortality rate is 5% and true intensive care rate is 9%.
Scenario B: true mortality rate is 0.05% and true intensive care rate is 0.09%.
the numbers are fictitious, but the point is simple - we can't estimate mortality without knowing the prevalence

Question:

Where are we right now between scenario A and scenario B? Or put another way, are there any ongoing studies/reports which take into account this factor?


texts: How is information sent from the skin to the brain?

texts:
Say you have a needle, and you poke a very specific area on your left thumb.
A signal gets sent from that nerve up your spine and into your brain.

How does the brain know exactly where this signal has come from to such accuracy?

Does each nerve in every conceivable part of the body have a unique path that goes up the spine and into the brain, so that's how the brain knows where it came from?
Or does the nerve encode the signal as data which travels up a generic nerve, and the brain decodes the information, which contains the "address" of the particular spot that was stimulated? If this is the case, how are the data encoded? Binary?


texts:
Location: East Anglia, UK.

Approximate size (including legs at full span; like in the image): about 3cm.


texts:
My sister is in 9th grade biology and her teacher avoided answering the question of how we actually study the inside of a cell. I haven't taken biology in a while but I'd like to give her an answer.

Can someone roughly summarize how we actually learn about what goes on inside a cell? Just mentioning a few of the most common or used techniques would be fine.

Note: I hope this isn't a bad question. It's a bit vague. But I didn't want to leave her without a decent answer.


texts:
I read about the regulation of Calvin cycle by thioredoxin which activates key enzymes essentially by converting disulphide linkages on inactive enzymes into sulfhydryls. Another regulatory mechanism is the pH control. The enzymes work at a slightly alkaline pH which is established as soon as the proton gradient is set up by the light reactions. But aren't these two mechanisms contradictory: at alkaline pH, the sulfhydryls $-SH$ groups, being acidic, will dissociate by giving up a proton and will be more stable in the dissociated form.
In general I fail to understand how pH will decide which bio-compounds will dissociate into proton or hydroxyl.


texts: What could cause no pain but sense of touch?

texts: What could cause a mammal to have and respond to a sense of touch with only isolated numbness but not feel pain?


texts: Hypersensitivity Simultaneously in Ear canals

texts:
I got experimental data where hypersensitivity (i.e. tonic pain when touching ear canal) was recognised for about 100 minutes.

I do not know which type of hypersensitivity is this one.
IgM can reach ear canal, I think (not sure) - it is just in the limit.
If IgM cannot reach ear canal, then the hypersensitivity must be caused by

humoral immune system

which is responding slowly to the trigger.

It is proposed that this cannot be contact dermatitis because

the reaction happened simultaneously in both ear canals

after irritating ear canals with plastic the subject is not allergic.
Irritation was also a selected signal which resulted in the dynamic cycle of bass music by Beats earphones.
It was studied the effect of the specific signal with bass music on the movement on the inner membrane on the subject with problem in maintaining the inner physiology of ear itself (also repeated cycle of ear infections during childhood).

Can IgM reach ear canal?

The hypersensitivity was simultaneous in both ear canals.
I did not know before that you can get hypersensitivity reaction in ear canals and also simultaneously.
I think hypersensitivity is not in normal condition.
There must be some etiological factors (probably neuronal) that can cause it.

There are other organs which can have hypersensitivity too.
So I started to think what is the trigger of hypersensitivity.

My conjecture is about Secreted substances of endothelium (EDRF, EDCF).
There are three types of substances secreted by the endothelium

NO
Endothelium hyperpolarising factors
Endothelins

NO is the most important one.
But what is its role in the hypersensitivity of ear canal is unknown to me.

What is the mechanism of hypersensitivity of our body and particularly in the ear canal?


texts: Do macrophages engulf material in the epidermis?

texts: This question comes from how tattoos work.  From what I understand, the ink particles are something like 100 nanometers in size, which is too big for macrophages to remove them in the dermis.  What I would like to know in that case is are macrophages able to go into the epidermis, or is that too far for them?  In other words, would material in the epidermis just leave the body after that part of the skin grows out?


texts: Do couples having children later in life act as an evolutionary mechanism?

texts:
Ok, this may be just wild nonsense and I have to warn that my knowledge on the subject is limited.

I was reading about how in some countries people choose to have children later in life. After that this question came to my mind?

If human couples chose to have children later in life, lets say 40s 50s - disregarding keeping an younger self gamete preserved - wouldn't this result in the people less resistant to the effect of aging being unable to reproduce,  creating a more longevous generation? thus enabling future generations to reproduce even later lenghtening the average lifespan of humans?

ps: After reading this sounded a little too eugenic, by no means I'm trying to make this an legitimate theory or suggest an experiment, it's just a doubt - maybe good for some science fiction story...


texts: How do minute changes in an organism, as a result of evolution, get carried over to next generation

texts:
The theory of evolution states that random variations in organisms occur to better suit their surroundings. We take for example a bacteria's flagella. There's a bacteria who has a tube kind of structure that it uses to inject toxins in other cells. Structure of flagella and this tubular structure is very similar. So biologists state that this is clear evidence for evolutionary process wherein this tubular structure underwent gradual changes that resulted into a flagella.

Now my question is, minute changes did occur to this tubular structure, but how do those changes get carried over to the next generation? Almost all components of a cell are created as per the instructions coded into DNA. So does it mean that every minute changes that occur to an organism get recorded into DNA so that they can be carried over? In above example, assume, that a few proteins got accidentally attached to the tubular structure that will help the structure to rotate. Now when this temporarily changed bacteria gets divided into a new one it will have lost that change. So to actually carry over this "beneficial" change would the bacteria have changed its genome? How does this happen? What is the basal mechanism that supports evolutionary changes?


texts: Can a portion of human skin cells be modified in some way to generate light?

texts: I have come across some species of living organisms who are able to emit light at whim. Can that ability be incorporated into a portion of human skin (a specialized tissue)?


texts:
There is only hydrogen bond different.
Cortisol is synthesized by our body, while cortisone is given to the patient.

Why you cannot give cortisol directly to the patient?
I think the reason is metabolism that cortisol will break (probably in liver) and not be useful.
Or expansive to produce.
Cortisone however can be given.

What is the physiological difference between cortisone and cortisol?


texts: Powdered meal replacement vs regular meal

texts:
Can a person live with this alternative nutrition? Of course, assuming that eating pleasure is assumed the same.

The nutrients that contain are far better than average meal a person eats the majority of times, al least me. However, since is not solid food, do our digestive system need to work harder?

Scientific reports would be appreciated, comparing these two modes of feeding.


texts: Where does the first oxaloacetate comes form in the citric acid cycle?

texts: Oxaloacetate forms together with acetyl-CoA citric acid. Now oxaloacetate is used but also re-used again in this cycle. But where does the first oxaloacetate comes from? Is that from the mother or produced by DNA or....?


texts: What does it mean when a protein has a different excitation spectra than wildtype, but the same emission spectra?

texts:
We have a GFP mutant that displays a different excitation spectra with emission at 510nm than the WT. However, their emission profiles with excitation at 490nm are the same, and we do not observe the same trend.

We're confused as to what might be happening.


texts: Why do people look different after a long sleep?

texts: What happens during a long sleep that makes people look odd when they have just woken up?  Why doesn't the same phenomenon occur in the case of a person who lies down for an extended period of time, but stays awake?  I've noticed that some nights seem to make a bigger difference than others in the appearance of the sleeper, but haven't noticed a pattern.


texts: What does it mean when N-Fold coverage of read of sequence? Details will be much appreciated if a link provider with brief explanation.


texts: Does the speed of muscle contraction within a single sarcomere differ between people?

texts:
Of course the number of muscle cells can be different person to person. But within a single sarcomere, are we all the same?

Would the frequency of the protein motor binding and release cycle different for each person? And if that is a constant, then do we all attain the same speed of muscle contraction?

If not, what causes the different speed?


texts: Why my proteins are migrating like this on SDS-page?

texts:
I'm trying to make a SDS-page of total proteins extracted from algae but I'm encountering two problems. First, when I depose my proteins in the wells the sample goes down and then it starts to move up the sides of the well. Second the result of my run looks like this:

so my bands are not visible and I have like a vertical smear on the sides of the lane.

The buffer used to extract proteins contains Tris, NaCl, EDTA DTT and Glycerol and my loading buffer is a 5x commercial dye with B-mer.

Thank you!


texts: Is there a difference between sleeping late and waking up late vs sleeping early and waking up early?

texts: For example, if I sleep at 1 AM and wake up at 10 AM, will it negatively affect my health opposed to sleeping at 10 PM and waking up at 7 AM?


texts:
I understand (a little) that there are biological clocks and reason that after a certain amount of time organisms die. I'm wondering if that is something inherent in our DNA or in biology/chemistry in general. EG, is it possible that there could be a complex organism that would not die and would just regenerate it's cells In Perpetuam? I'm specifically interested in mammals and even more specifically interested in humans. But, I would be interested in hearing about other organisms like bugs, fish, plant, algae, etc.

I'm not asking if this practical, do we know how to do this, etc.. I just want to know theoretically if living forever is biologically possible, as far as we know. If not, is there an estimated upper limit?


texts: Are humans the only species who drink milk as adults?

texts:
I was drinking a glass of milk the other day and that got me thinking that no other animal to my knowledge drinks milk past their infant stages. One could argue that cats might but it isn't good for them to do.

Are humans the only animal that are able to drink milk as adults and not have it cause issues?

Of course, I know some people do have lactose intolerance too.


texts: Which cells produce HCl produced in stomach? Don't these cells get destroyed by HCl?

texts: Which cells produce HCl produced in the stomach? Or is HCl produced due to the translation of proteins. Don't these cells get destroyed by HCl?


texts: Is water movement across cell membrane purely diffusive or it always requires channels?

texts:
If we see nephrons, in the descending part of Loop of Henle (LoH), water movement is allowed but solute movement is not. On the contrary, in ascending LoH, solute movement is allowed but not water. What exactly restricts this movement?
I am particularly interested in understanding the movement of water across cell membranes and then answering the above query.


texts: Why is chromatin not condensed during interphase but is in prophase

texts:
Cell cycle goes through three processes:

Interphase
Mitosis
Cytokinesis

Why are chromatins not condensed during interphase but instead condensed at prophase of mitosis? What makes them condense at prophase?


texts: Identification of an insect from Florida

texts: Any entomologists or there that can identify this bug? I live in north Florida, found this guy in my bedroom and thought it was a bedbug but I think it was too big, about half an inch long.


texts: How far can locust swarms expand and beplague?

texts:
March 2020 is the the latest map that I see. I'm asking about all relevant species of locusts. What's the maximum effective range for these locusts swarms? Southern Europe? China? Japan?
I read Michel Locoq's answer on Dec 9 2013 but it doesn't answer for swarms.

In 1988, locusts swarms travelled some 5000 km non-stop from West Africa to the Americas. Several waves of locusts arrived between 7 October and 4 November 1988. This was not at all a single event. There is other examples: migration of swarms from Africa to British Isles in 1954, migration half-way across the Atlantic in 1865 and 1916, etc.
Desert locust can resist to starvation and cold temperatures. Just a few days without food is not too much for an insect living normally in desertic areas, migrating during months for food and humidity for its eggs. And they can survive quite well at low temperatures. I have seen swarms crossing the Atlas mountains in Morocco, they can settle in the snow and start again when the sun appears. No need for human help (and what kind of help for large swarms of bilion of insects ?) to cross the ocean. it's just a good flying insect. Its flying capacity is so developed that there is no genetic differences between mauritanian populations and populations from Pakistan.


texts: Can a bumblebee hive be positioned high above the ground?

texts:
We'd like to set up a hive for bumblebees and I wonder if it can be positioned high above the ground, for example on a balcony.

As bumblebees usually nest in holes in the ground, I'm somewhat concerned if they'd find the hive comfortable and be able to navigate back to it.


texts: Why is it that guttation is most commonly observed in the morning?

texts:
Knowing that guttation occurs through a plant's hydathodes due to root pressure forcing liquid water out of the leaves, I am curious as to why so many small drops of water are observable on plants in the morning. Could this potentially have to do with the moisture in the air at night vs day? Since humidity tends to increase at night?

Thanks in advance!


texts: Can trichoptera and lepidoptera be distinguished with the naked eye?

texts:
Are there any tell-tale signs which one could use to distinguish adult trichoptera from lepidoptera? To me, trichoptera just look like moths:

One method would presumably be to touch its wings and see if scales come off, but what if we assume we don't want to catch it?


texts: How does blue, yellow and orange coloured light affect photosynthesis?

texts:
I've been conducting an experiment with different colored light and photosynthesis, and so far my hypothesis states that red light will grow the plant, green will slow or kill it, and white will grow it as normal.

I'm wondering what would happen with blue, yellow, and orange.

Thanks.


texts: Can you knockout a gene specifically in the dorsal root ganglion in adult mammals?

texts: Since the dorsal root ganglion is so small, would that be easier than the entire body?


texts: What does it mean: carrying the stably integrated gene

texts:
Reading this study
http://www.nature.com/cr/journal/v23/n10/full/cr2013122a.html

They writing

  Multiple exogenous and endogenous genes can be simultaneously activated
  by CRISPR-on

  We tested single, double and triple activation of a TetO::tdTomato
  transgene and the endogenous SOX2 and IL1RN genes (Figure 3A) in
  HEK293T cells carrying the stably integrated TetO::tdTomato transgene

Could you please help me to understand: They talking about exogenous gene. But saying "carrying the stably integrated". Does that mean that this gene (TetO::tdTomato) is in the cell genome (integrated to genome)? If so, what is the meaning of exogenous here?

Thank you!


texts: Why is fructolysis independent of glycolysis?

texts:
In glycolysis, glucose is converted to fructose-6-phosphate before further breakdown. However fructose, instead of being phosphoryated to fructose-6-phosphate by glucokinase (and thereafter to pyruvate via glycolysis), yields fructose-1-phosphate in the reaction catalysed by fructokinase.
Why is this so?
It should be just as easy to phosphorylate fructose to both compounds. Wouldn’t it be more economical to use a single reaction, so everything would be easier to regulate? As there are several disorders that arise from the deficiency of enzymes used in fructolysis, wouldn’t there be a selection pressure against two separate metabolic pathways?
Edit:
Thanks for David's criticism; I see the confusion, I actually meant that it is mainly metabolized in the liver. I don't really have any real sources as I do not have access to much and quite a large portion of online resources is behind paywall. After a bit of digging I was able to find an overview that reiterates most of my claims. Sorry for not being able to provide more.

In the liver, fructose is rapidly converted to
fructose 1-phosphate via fructokinase. Fructose 1-phosphate is then converted into the trioses dihydroxyacetone
phosphate and glyceraldehyde via aldolase B.

The liver can extract 40–70% of dietary fructose in
both rats and humans. The high efficiency of
fructose extraction by the liver is due to the fact that the
liver is the main source of GLUT-5. Anatomically,
the liver is the first organ to receive absorbed nutrients
via the portal vein; in that way, it contributes to fructose
extraction. In contrast, the liver accounts for a smaller
percentage of glucose extraction for glycogen restoration

Above are two excerpts from Chapter 19 - Fructose-Induced Hypertriglyceridemia: A Review. This source also (albeit vaguely) states that the resulting triose phosphates (glyceraldehyde and dihydroxyacetone phosphate) can and will enter pathways like glyconeogenesis, gluconeogenesis etc.

Up until this point in fructose metabolism, there have been no rate-limiting steps and, as a result, there is an increased amount of substrate leading to metabolic pathways from triose phosphate (i.e. glycolysis, glycogenesis, glyconeogenesis, lipogenesis, and fatty acid esterification).

Another source for my assertion that fructose is mainly metabolized to fructose-1-phosphate (Elsevier's Integrated Biochemistry):

Unique Characteristics—Aldolase B Specificity
Fructokinase, like glucokinase, is found primarily in the liver. Unlike hexokinase and glucokinase, it phosphorylates the sugar at the C-1 position. Aldolase B, which is specific to the liver, works on both F1,6-BP and F1P. In extrahepatic tissues such as muscle or adipose tissue, fructose is phosphorylated to F6P by hexokinase.

Also, a possible lead, from Fructose: Absorption and Metabolism. Encyclopedia of Human Nutrition:

The allosteric inhibition of PFK effectively reduces the rate of glycolysis and decreases hepatic glucose uptake overall. In contrast, the entry of fructose carbons through the pathway proceeds without this limitation.

Using different enzymes (and therefore a different pathway) allows regulation of glycolysis in the liver without unnecessarily affecting fructolysis.


texts: What are limitations of giving birth to a baby from a frozen embryo?

texts:
Recently the story of a woman giving birth to baby girl from an embryo frozen 24 years ago hit the news. After an in vitro fertilization the embryo was frozen on 14 October 1992(
Article in the Guardian)

So I wonder about the limitations concerning freezing embryos. Especially the following questions came to my mind:

How much time after the embryo has been fertilized has passed before
he was frozen?
How much more time after fertilization could pass before the embryo
has to be frozen?


texts: Does taking a shower have the same effect on muscles as warming up?

texts:
When playing sports, coaches and trainers are always very clear that it is necessary to warm up and stretch. But sometimes athletes sometimes want to get an extra stretch in and don't want to go through the hassle of warming up.

Will taking a hot shower warm up muscles or does an athlete sctually have to do physical exercises like jogging in order to be ready to stretch?

I know this sounds like a question I could go on the physical fitness SE, but I'm really hoping for an answer involving thermodynamics and I doubt I'll get that there.


texts: What ecological niche do disk shaped fish exploit?

texts:
I looked up "Early Triassic" to get a sense of what that meant and I ended up on this image of marine life at the time. I noticed some disk shaped fish (#8 in the picture:  Bobasatrania (durophagous actinopterygian)) that looked, to me, like Permit or a Sunny.

I wondered, what ecological niche are disk shaped fish exploiting? Why is this particular body type repeating itself 250 million years later?

EDIT per answers:
I view them as same thing. I don't mean to suggest an animal can only exploit one niche, nor that a given niche can only be exploited by one animal. For example, birds with short, thick beaks like parrots eat seeds that are tough to crack. They give up the ability, perhaps, to get at some more delicate flower nectars. Brightly colored poisonous animals are easier to spot, but they are poisonous. So, over time, they are, as a specie, less likely to get eaten. What do disk shaped fish give up by being disk shaped, and what do they gain?


texts: Why do bulls-eye rashes look like they do?

texts:
People infected with Lyme Disease often present with an erythema migrans ("migrating redness") rash. Most often, these rashes are in the shape of a bulls-eye.

Rash image.

Presumably, this is a reaction that many of our bodies have to the Borrelia burgdorferi pathogen.

Lyme disease also sometimes presents with different-looking rashes, and other pathogens also sometimes produce a bulls-eye-looking rash. CDC Link on Lyme Disease Rashes and Look-alikes.

What causes the bulls-eye shape of these rashes?

Thought process: A gradient of redness from the site of the tick bite makes sense--an immune response might be strongest at the bite site--but I'm still stumped on why there would be a spot of redness surrounded by a no-rash-ring surrounded by a rash-ring.

Note: If I remember correctly, external links to images are usually frowned upon. Although the images linked in this post aren't super graphic, I decided to make them external links for the sake of anyone who is sensitive to medical images.