texts:
I'm trying to understand N50 on the wikipedia. But I was unable to get a sense of the definition:

  Given a set of contigs, each with its own length, the N50 length is
  defined as the length for which the collection of all contigs of that
  length or longer contains at least half of the sum of the lengths of
  all contigs, and for which the collection of all contigs of that
  length or shorter also contains at least half of the sum of the
  lengths of all contigs.

Is there a simple example that illustrates this definition? Furthermore, why do we need this statistic? What does it really tell me? Do we want a higher or less value?


texts: HOW is the Gallbladder attached to the liver

texts:
The gallbladder’s function is to store bile from the liver which is delivered through the cystic (bile) duct.  The cystic artery is also connected to the gallbladder to deliver blood.  (Correct me if I am wrong about any of this.)

However, when I was watching a gallbladder surgery video on YouTube, in the process of removing the gallbladder the surgeon clips the bile duct and artery which I understand but he/she also cauterises the gallbladder off the liver.  I also understand that The cauterisation is to prevent bleeding.

BUT the question is WHY is the gallbladder attached to the liver in the first place?  WHAT purpose does being attached to the liver serve? Does it provide stability? Because I always thought the gallbladder just sits beneath the liver.  Most importantly, HOW is the gallbladder connected to the liver?  (This maybe be more of a chemistry question), what bonds is it connect through, what/which biomolecule connects it and why is it that biomolecule/ bond that is used.

As watching the video,  I also noted that the surgeon didn’t clip the cystic vein, or even mentioned it.  Maybe I am wrong and he/she did clip the cystic vein but I didn’t see, would you also be kind enough to explain to me why the surgeon didn’t clip the cystic vein or if he did why it wasn’t pointed out.  Also tell me more about the cystic vein where is it located because it’s very hard to find clear diagrams with them...(is it because it’s small)


texts: Possible? When a pregnant woman suffers an organ damage, fetus would send stem cells to the damage organ to help repair it?

texts:
I am quite sure that there is this blood-placental barrier between the mother and the baby so that nothing (except a type of antibody) can pass through it.

But I remember reading somewhere that when a pregnant woman suffers an organ damage, fetus would send stem cells to the damage organ to help repair it.

Anything to support that?


texts: What moth is this and how do we get rid of them?

texts: This bugs are everywhere in my house and we've tried so many home remedies, but they won't leave. Can anyone help us!?


texts:
Is there a relationship between bio heat equation (found here) and exercise intensity as described here
That is I am trying to include the effect from exercises to the tempertaure variation in skin. I am trying include the term $Q_e$ which measures the heat generated from exercises,
 to the known bio heat equation

So that it would be modified as
.
So I would like to know if there is a relationship between metabolic heat generation and exercise intensity.


texts: Is the quiescent centre only found in monocot roots?

texts: I read that the quiescent centre is present between the dermatogen and calyptrogen. As calyptrogen is only present in monocot root, does that mean quiescent centre is only found in monocot roots?


texts: How to store vegetables in the refrigerator: In plastic bags or not?

texts:
My wife and I are having a debate similar to this one:

I claim that it's better to take the fresh veggies out of the bags and put them in the crisper with humidity control because:

That's what the crisper with humidity control is for.
If they are in the (plastic) bag, the humidity control is pointless.
It's easier to notice vegetables in their early stage of rotting (it doesn't feel right to throw out an entire bag of rotten cucumbers or zucchinis before we got a chance to enjoy them).
It's more pleasing to the eye. It's more convenient.

She claims that it's better to leave the fresh veggies in their supermarket bags when putting them in the fridge because she could swear she noticed that they rot more slowly when left in their bags.

As you can see from the few links in this question, I tried to conduct my own search on the subject, but all answers seem to be opinions or "experiences", not an authoritative answer based on scientific research or knowledge.

So I am hoping that with the help of biology professionals (or students) I can finally find an authoritative answer to the question: Do vegetables really last longer if they are kept in their (supermarket) plastic bags when put in the crisper?

Update: I found this formal excerpt from the refrigerator's manual:

  Low (open) lets moist air out of the crisper for best storage of fruits and vegetables with skins.

  Fruit: Wash, let dry and store in refrigerator in plastic bag or    crisper. Do not wash or hull berries until they are ready to
  use.    Sort and keep berries in original container in crisper, or
  store in a    loosely closed paper bag on a refrigerator shelf.
  Vegetables with skins: Place in plastic bag or plastic container and store in crisper.

  High (closed) keeps moist air in the crisper for best storage of fresh, leafy vegetables.

  Leafy vegetables: Wash in cold water, drain and trim or tear off bruised and discolored areas. Place in plastic bag or plastic container and store in crisper.

While this seems a bit more authoritative (because it comes from the manufacturer of the refrigerator), it still leaves quite a few questions open:

If leafy vegetables should be "placed in plastic bag or plastic container and stored in crisper", why set the humidity on "High"? How does humidity get the lettuce inside the plastic bag or plastic container? (is it sealed?)

Assuming that some humidity does get into the bag, why is the bag needed? Why not let humidity flow freely?


texts: Is there a better lysis buffer than this for fungal DNA extraction?

texts:
I've being using this lysis buffer for fungal DNA extraction,lysis buffer - 400mM TRis-HCl(pH8.0), 60mM EDTA(pH8.0), 150mM NaCl, 1% SDS and containing 40microgram/ml RnaseA.

It is keep giving very light bands on 1% agarose gel and shear appearence. After extraction I have to follow PCR and sequencing. If there are inhibitors, how can I get rid of those ?


texts: Found on the ground on dried cottonwood leaves in southern Utah.


texts: Parallel DNA double-helices with Watson–Crick base-pairing: Why do they not occur?

texts:
I know that parallel DNA helices exist and are governed by Hoogsten base pairing, but why can’t they be possible with Watson-Crick pairing? In the diagram below, if we were to flip one of the strands while keeping the other the same, it appears as though hydrogen bonding is still possible.

The only specific suggestions that I could find was because of the DNA replication process and the negative polarity of hydoxyl group on the phosphates. Moreover, after flipping one strand, the DNA nucleotides form enantiomers. Are these possible reasons, or are there others?


texts: Are there known minimal marine ecosystems that are stable?

texts:
A more entertaining phrasing of the question would be "what would a marine ecologist put into a perfect aquarium?"

I was reading about Prochlorococcus, among other photoautotrophs, and found that they seem to get their nitrogen from ammonia, which must be produced by some other organism. This set me off wondering what different species I would need in a hypothetical aquarium (how big that would have to be is another question, I guess), such that a sustainable ecological equilibrium occurs (one different from everybody dead, I guess), only requiring sunlight and air from the outside.

I realize that I'll have to put other components like iron etc in the water, but let's say I only put some fixed amount in during setup. What exactly that would have to be is probably another can of worms, so let's keep that out of this question as much as possible.

Has there been research towards such model ecosystems, and are there known minimum configurations?

It's hard to give an authorative "no" to this answer. But maybe there's research that looked for such a system and failed, or maybe marine ecologists use model cultures in their labs that show instabilities (meaning the culture dies, you have to replace the water, or keep adding fertilizer, or keep removing some waste) which allow some generalizations.


texts: When forming an enzyme-substrate complex in a spontaneous reaction, why free energy increases?

texts:
We ate food, and then food was digested into proteins, carbohydrates...
Does not digestion break bonds within food macromolecules? and thus free energy decreases? why when looking to the curve we see an increase in the free energy and then a decrease?


texts: What are these maggots, and how to get rid of them?

texts:
These maggots are just over 1cm long. They appeared suddenly, in great numbers, and in many rooms all over the apartment (central Israel).

What are they?
Is there a less heavy-handed way to get rid of them than calling in an exterminator?


texts: How's maturation different from differentiation/activation of B lymphocyte?

texts:
I was reading Wikipedia that said $-$

  In mammals, B cells mature in the bone marrow, which is at the core of most bones. In birds, B cells mature in the Bursa of Fabricius, a lymphoid organ.

So it's got the name B-lymphocyte.

My questions:

Is the transformation of Haemotopoetic stem cell to Immature B-cell called maturation of B-lymphocyte and the transformation of Immature B-cell to Mature B-cell through a Naive B-cell called differentiation/activation of B-lymphocyte?

The maturation occurs in Bone-marrow and Activation/differentiation in Spleen or lymph nodes. The whole process maturatiion + activation is called development. Am I correct?

Note: My understanding of Immature B-cell is that it is a cell in the series of B-cell development that expresses BCR (an IgM) for the first time. While Mature B cell is a B lymphocyte which after interaction with antigen has turned into either Plasma cell or Memory cell.


texts:
Why aren't the antibodies in the mother's milk digested by the infant's digestive system?
Enzymes like pepsin have been found to be present in infant's digestive system(1). Though the pH in the stomach of infants is high(The gastric pH of neonates between 2 and 13 days increases from 3.5 to 5-7 for 2 h after ingestion of human milk)(2) activity of pepsin like enzymes from mother's milk itself or infant's stomach is appreciable(1). Moreover tryspin function in infant's intestine is equal to the level in adults by the age of one month(3). Many more proteases are also seen in both mother's milk and in infant's digestive system(1). If this is the case why are antibodies present in mothers milk not digested by the infant?
I have two hypotheses regarding this

Glycoproteins by their nature cannot be digested by the enzymes in infant.
Antibodies are present in such large amounts that many of them are undigested by chance.

I have no idea whether either of these are true. Any ideas will be appreciated.
References:
(1)Thérèse A. Holton et al. Following the Digestion of Milk Proteins from Mother to Baby.Journal of Proteome Research 2014, 13 (12), 5777-5783
(2)Mason, S. Some aspects of gastric function in the newborn Arch. Dis. Child. 1962, 37 (194), 387-390
(3)Lebenthal E, Lee PC. Development of functional responses in human exocrine pancreas. Pediatrics. 1980, 66(4), 556-560


texts: Do animals like Seals feel cold on their skin?

texts:
Whenever there is a documentary about animals and you get to the colder regions, you will hear about Seals and their layer of blubber keeping them warm.

But the skin is on top of the blubber, in direct contact with the cold water (and air). Do they feel the cold outside the way a human would?


texts: Violation of the law of energy conservation between photosynthesis and respiration?

texts: For the production of one glucose molecule in the Calvin cycle a plant uses 18 molecules ATP, but when the same glucose molecule is oxidised — first in the cytoplasm and then in the mitochondrion — it can obtain approximately 36-38 molecules ATP. How is the theory of conservation of energy maintained here?


texts: Release of Nor-Epinephrine by presynaptic beta receptors

texts:
Presynaptic alpha-2 receptors on stimulation decrease the release of nor-epinephrine by certain mechanisms where as activation  of beta presynaptic receptors increase or facilitates the nor epinephrine an effect which is opposite to the alpha receptors
How does this facilitation of nor-epinephrine occur by the pre-synaptic beta receptors


texts: I've harvested IPTG induced E.coli BL21DE3 cells' suspension culture by spinning at 5000 rpm/15 min/4 degrees C. The pellet after spin looked pale pink colored. What could be the reasons?


texts: I am trying to determine whether or not my sequencing data has more/less non-synonymous mutations than would be expected. My understanding is that there is some fixed ds/dn ratio for the human exome that I can use to calculate this. Is this true? And how might I calculate this?


texts: Can anyone identify this species of spider?

texts: These spiders are all over everything on my padio in New Hampshire. Can anyone help me identify what they are?


texts: Species Identification: Bulbous root on plant, Southern California, USA

texts:
In Southern California, I was pulling out some roots and grasses and weeds in our backyard, and I noticed something weird. It appeared like there was a grape-sized bulb of something connected to one of the roots below the top layer of dirt. I didn't puncture it or anything, but do you have any idea what this could be?

It reminded me of two things: an air sack on kelp and a potato.

Edit: I took some more photos, and I tried to break it apart. I was able to break it in half with one hand, easier than a potato but harder than a grape. It was a little juicy inside. I took more photos too.

Edit number two: We have dandelions. Does this seem like it could be a potato dandelion?

Edit #3: So we have a lot of Dandelions and I thought these roots appeared to be connected to dandelion plants, so at first I thought they were potato dandelions. However, we I pulled out a different plant nearby, and it had very similar looking tubers connected to the roots. It was a small plant, but here's the picture, and a picture of a larger plant that I think is the same species as this one, but mixed with a bush. Can anyone positively identify it?

Edit #4: Here's more pictures of the plant I'm seeking to identify, which appears to be a more developed individual on a neighbor's property, and it even has berries:


texts:
The question is not about the very basics, but more about where the line separating the neutral theory from the rest of population genetics lies.
One often reads/hears claims that "the findings of the neutral theory are still disputed" or that "there's no experimental proof for its validity". It is hard to accept these claims wholesale, since:.

It is hardly in doubt that some mutations are neutral
It is hardly in doubt that neutral or even slightly deleterious mutations may fix in the population due to genetic drift, or that beneficial mutations may fail to fix for the same reason.

I therefore interpret such statements as attacks on specific points of the neutral theory, or its most sweeping claims (e.g., that most mutations are neutral), or perhaps as attacks on specific meaning of the term. Moreover, such wholesale rejection seems to ignore that the theory may have very different degrees of validity for different organisms (say, more likely to be true for RNA viruses than for mammals).
I will appreciate clarifications of these points.
Update
Here is an article that raises several issues regarding the applicability of the neutral theory framework to bacteria: Neutral theory, macrobial practice: challenges in bacterial population genetics


texts: Found this bugger crawling across my laptop.  Any help identifying would be appreciated.  After a bunch of googling it appears to be close to a lady beetle larva.  I am located in north east USA.


texts:
Recently we've been learning about Microarrays, and the typical method seems to be to run a two channel microarray where your RNA from each cell is labelled with a different fluorescent marker, and then the relative intensity of the fluorescent label can be used to identify a ratio of relative gene expression.

I was wondering if it would be possible to use a larger quantity of DNA sequences on the array and then run a number of sets of RNA fragments - for example, say you extract RNA from cells from a cell culture at constant time intervals, then you label them with fluorescent markers which are orders, and then scan the fluorescent labels to find out how the expression varies over time?

Why wouldn't this work?

Thanks!


texts: I have seen a Cooper hawk sitting on a low branch above my small Koi pond 3 times in 4 months. The books and net say they eat birds and some mammals but I wonder if he is looking at my fish ? Or snakes or frogs ?  As I write this I had a thought, song birds come down to a shallow part of the pond, that may be what the hawk is after. But I still wonder about the original question.


texts: Why did the Brain develop in the front in most organisms?

texts: I was wondering: why most, well, pretty much all organism with a brain have it right in front of their bodies or at the top.


texts: Can Listeria monocytogenes endotoxin act as an A-B toxin?

texts:
I think no, but I am not sure since Listeria is Gram-positive and probably has lipopolysaccharide (exception among Gram positive bacteria).

Can Listeria monocytogenes' endotoxin act like exotoxin A-B?
(In which component B lets component A inside the cell and component A causes the toxicity.)


texts: What are the different ways an exon gets spliced?

texts: Exons are produced by more than one mechanism, e.g. splicing out introns after transcription, if I remember correctly. Please list all mechanisms.


texts: Doesn't the sarcomere contract during isometric contraction?

texts: During muscle contraction, the lenght of the sarcomere changes, length of myocyte changes and so does the length of muscle. However, if the length of muscle is not changing length as in isometric contraction does it mean that the sarcomeres are not contracting?


texts: Can someone identify this flowering bush from the US?


texts: Effect of histidine on the binding affinity of HisP

texts:
I was asked the following question by my teacher:

  A gene regulatory protein called HisP regulates the enzymes for
  histidine biosynthesis in the bacterium E. Coli.  HisP is a protein
  whoes activity is modulated by histidine.  Upon binding histidine,
  HisP alters its conformation, dramatically changing its affinity for
  the regulatory sequences in the promoters of the genes for the
  histidine biosynthetic enzymes.

  If HisP function sas a transcriptional repressor, would you expect
  that HisP would bind more tightly or less tightly to regulatory
  sequences when histidine is abundant? Why?

My own attempt at a solution:

Less tightly.  If histidine is abundant, HisP's job is to stop the histadine pathway as a "repressor."  If HisP binds less tightly to promotors, the pathway should not produce as much histadine.


texts: Why does hemoglobin electrophoresis in sickle cell trait gives two bands but not three?

texts:
Electrophoresis of hemoglobin from a patient with sickle cell trait (carrier for sickle cell anemia) shows two bands. Why not three?  Since there are two beta chains in each hemoglobin, it seems to me they should have three types of hemoglobin: HBB/HBB, HBBs/HBBs, and HBB/HBBs. Does the HBB not form hybrids with HBBs? Aren't both polypeptides produced in the cell?

*HBBs signifying mutated beta chain


texts:
The Varicella zoster virus causes chickenpox in children and shingles in adults.
When the virus attacks as shingles, one of its distinguishing characteristics is that it only affects one side of the body. (As shown in the link and verbally identified by a doctor I spoke to). This happens because the nerve cells themselves are infected - and are partitioned on different sides of the body.

At first the rash appears similar to the first appearance of hives;
however, unlike hives, shingles causes skin changes limited to a
dermatome, normally resulting in a stripe or belt-like pattern that is
limited to one side of the body and does not cross the midline.[13]
Zoster sine herpete ("zoster without herpes") describes a person who
has all of the symptoms of shingles except this characteristic
rash.[16]
 From Wikipedia

My question is: What is the name of the category of viruses that affect only one side of the body?


texts: How do plants benefit from their seeds being buried?

texts:
Common planting advice, when starting many plants from seed, is to bury the seed some small distance under the soil.  It seems like most plants (at least members of class Dicotyledonae) will grow a root, lift the seed casing out above the surface, then the cotyledons push off the seed coat.

My question then is: why is it recommended to put the seeds below ground at all?  It would seem that dirt only serves to interfere with the first stages of growth.

I can guess at a few reasons:

To keep moisture around the seed
To make sure the root hits dirt no matter which way the seed is oriented
To prevent predators from eating the seed
To keep the seed in place

Absent these reasons, is there any reason to have soil sitting on top of a seed?


texts: What role does the eardrum and ossicles play in hearing, versus cilia?

texts:
Modern electronic sound recording equipment employs a physical membrane that triggers the piezoelectric effect in a metallic element, to transform sound waves into electric signals.
I had always thought that the eardrum (or tympanic membrane) was the main instrument of hearing in vertebrates, that it physically transduces sound waves into nerve signals. However, in looking into it, I find that the eardrum transmits sounds to inner ear anatomy, where more structures are encountered before the sound waves become nerve signals.
I also find that small hairs, cilia, are sensitive to sound, and appear to be what actually turns sound waves into nerve signals, perhaps analogously to rod and cone cells in the eye. These cells line the ear canal, and when I read about them, they seem to be the real mechanism of hearing, and not the ear drum or inner ear bones.
At this point I'm confused as to actually how sound waves are transduced into nerve signals in vertebrates. Can someone explain the the roles of the various parts of anatomy in vertebrate hearing, in the overall, big picture? What roles do the large parts play, versus the microscopic cilia?


texts: What would be the scientific name of this worm

texts:
I saw this pic while crawling online and it was a bit different for me to predict which worm is this.

Source: http://www.seafishingtackle4u.com/softbaits/ragworms-latex-lures/

It appears somewhat different form other annelids as parapodia or setae are somewhat transparent and very attractive too.

What worm is this?


texts: In the NCBI Taxonomy tree what does "no rank" mean?

texts:
NCBI publish their taxonomy browser at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi

While many taxa have a well defined rank (Order, Family, Genus etc..), some of them have "no rank".

For example, Amniota:

  Taxonomy ID: 32524
  Genbank common name: amniotes
  Inherited blast name: vertebrates
  Rank: no rank
  Genetic code: Translation table 1 (Standard)
  Mitochondrial genetic code: Translation table 2 (Vertebrate Mitochondrial)

What does "no rank" mean?


texts:
What is a gene driver and what does C765 stand for? Is Gal4 a transcription factor?

Source: "Dynamics of Dpp Signaling and Proliferation Control"


texts: What are the limiting factors for gene length and number of exons?

texts: I recently downloaded gene annotations for Homo sapiens from Ensembl for some bioinformatic analysis. The vast majority of the gene annotations have 20 exons or less, although there are some that have as many as 250. I know enough about gene annotation to take these predictions with a grain of salt, but it got me thinking...what are the biologically relevant factors that might limit the length, exon number, etc of a gene? Is there any real possibility for a gene to have 50 exons? 100 exons? 250 exons? From a biological standpoint, where is the line drawn and why?


texts: If everybody DNA is different then how blood can match even with matching blood group?

texts: We know that everybody's DNA pattern is different in the world. Then how can ´we transfer blood from one person to another person and this person can survive ?


texts: Why does flatulence vary in temperature and smell?

texts:
Quite simply, why do some farts feel warmer than others?  Some feel regular, while others feel like lava.  What causes this?

If there is no real temperature difference, why do I perceive some to be warmer than others?  Does this contribute to the smell?  I've notice the hotter they feel, the worse they smell usually.


texts: Is it possible to know the sex of a bird using blacklight?

texts:
In the case of birds that have sexual dysformism, is it possible to notice it by illuminating them with blacklight?
In my case I have a cockatiel (Nymphicus hollandicus) which is a lutino. They do not have a visible sexual dysformism due to their color, but when I illuminate them with black light I see points under their wings and lines on their tail.


texts: mVenus fluorecent protein, life time? luminosity?

texts:
If fluorescence proteins get excited by radiation, how long does it usually take for the excitation to decay (at room temperature)?

I guess, if the life time is too long, the luminosity will be very low. Do you know something about how luminous the fluorescence can be?


texts:
This isn't exactly homework but I'd like to treat it as such. I'm asked to find the probability that both (III: 2) and (III: 3) are carriers given that (II: 7) and (III: 1) exhibited the recessive trait (affected individuals are marked black in the pedigree below).

Denoting the affected individuals with $aa$ (and so the dominant allele is denoted $A$), I was able to determine the following:

Both (II: 1) and (II: 2) are carriers.
Both (I: 3) and (I: 4) are carriers.
At least one of (I: 1) and (I: 2) must be a carrier.
The probability that (II: 6) is a carrier is $\frac{2}{3}$.

The answer is supposed to be $\frac{1}{3}\times\frac{1}{4}=\frac{1}{12}$.

I'm mostly confused as to how to approach this one case at a time. Suppose (II: 6) is indeed a carrier. Then if (II: 5) is homozygous for $A$, then (III: 3) has a $\frac{1}{2}$ probability of being a carrier; if (II: 5) is also a carrier, then (III: 3) has a $\frac{2}{3}$ probability of being a carrier.

Since the event that (II: 5) is homozygous is mutually exclusive from the event that he is heterozygous, would I just add these probabilities (i.e. $\frac{1}{2}+\frac{2}{3}$)? Then multiply by the $\frac{2}{3}$ of (II: 6)? This would give $\frac{7}{9}$, which doesn't seem to get me any closer to the right answer.

A different approach I tried was multiplying the respective probabilities for the (II: 5) events above, which gives $\frac{1}{3}$ and thus one factor of the provided answer. If this is right, and it seems to be, I'm not sure how to apply this to the (III: 2) side of the pedigree.


texts:
This question is background research for a science fiction / fantasy novel, my knowledge of genetic is very basic.

It seems obvious to me that for genetic disorders that are autosomal recessive, if those disorders prevent affected individuals from reproducing, the carrier and affected rates in a population will naturally be smaller. I'm not sure if this is the entire reason why say, blue eyes are more common that cystic fibrosis, but it definitely seems to be a contributing factor.

My question is this: say you have a (fictional) autosomal recessive trait that does not prevent reproduction. Let's call the initial carrier rate in the population for this trait C and the initial affected rate A.

In case it matters, the fictional trait I'm considering might reduce the chance of reproduction (as the people may be shunned, or considered less desirable as a mate) but there is nothing preventing reproduction. Something like "bright purple hair" where there is a stigma against affected individuals -- "your hair marks you as tainted" or something. I'm thinking A is around 0.1% (1 in 1000 births). (And if I understand the math right, C would then be around 6%, or 1 in 16 -- so that C * C / 4 gives A.)

Now let's say an oppressive government decides to prevent all affected individuals from reproducing (but carriers are left alone). Let's assume a 100% success rate for the government at rendering affected people infertile thus preventing their reproduction. What will happen to C and A over time? Is there some simple way to estimate how they will trend over several generations?
I don't need exact numbers but I'm having trouble with even coming up with a guess.


texts: Why does meiotic recombination disrupt the independent assortment of genes on the same chromosome?

texts:
There are many sources that say that genes that are "linked" by being on the same chromosome assort with each other -- that when an allele is passed on that the gamete containing said allele will also contain every allele from the chromosome rather than simple allowing everything to assort independently.

There are also many sources that say during meiosis there is recombination, hence, why aren't all genes completely random?


texts: In organ transplantation the transplant is rejected by the body's immune system , but is it possible if along with organ transplant if bone marrow transplantation is carried out from the same donor , then will the Cell Mediated immunity still reject the graft ?


texts: How many water molecules will be generated when single nucleotides are used to make this RNA: 5’-UUAACCGUCAG-3’?

texts:
Based on what we learned on condensation reactions, how many water molecules will be generated when single nucleotides are used to make this RNA: 5’-UUAACCGUCAG-3’

I had an online biology quiz with this question, and I thought it would be one molecule for each nucleotide, for 11 total. The answer I have been given is 10. I feel like I am missing something obvious.


texts: How effective is spraying disinfectant on streets?

texts:
I always wondered how effective spaying disinfectant onto outdoor ground is.

Source: Wikimedia

I understand that viruses and bacteria will sink down to the ground. I further understand that pedestrians may transport it across the area via their shoes, which shall be prevented.

Is the outdoor concentration of virus/bacteria particles really that high, that it helps to approach them with disinfectant?
Wouldn't it dilute too quickly?
Will the disinfectant droplets effectively touch the particles to inactivate them?

To me this looks more like this done to show "something" is done.


texts: For how long and how cold should I perform ethanol/isopropanol precipitations of RNA or DNA?

texts:
Precipitating nucleic acids using either isopropanol or ethanol is a very common operation, and I've read some very different protocols on the duration and temperature the precipitation should be performed.

I've seen anything from precipitating at room-temperature and centrifugating immediately without any delay to precipitating at -20 °C over night in various protocols.

Is there any published data about the influence of duration and temperature on the yield of the nucleic acid precipitation?


texts:
Very simple cells, such as Nanoarchaeum equitans, require a host to provide certain essential ingredients for life. Complex life-forms (like humans) require a whole ecosystem of other life-forms to survive (either externally, to provide food, or internally, in a symbiotic relationship).

What is the simplest cell that has been discovered so far that can live in an environment where there are no other life-forms, not even in a decomposed state? Does such an organism exist, or is all life inextricably dependent on other life?


texts:
I'm trying to get a better understanding of quantitative genetics by reading Lynch and Hill 1986. I'm getting stuck with some notation that's used right at the beginning referring to the mutant and WT alleles at a given loci.

2ai is the genotypic value for WT homozygous
(k+1)ai is the genotypic value of the F1 heterozygous
 0 genotypic value for the non-existent "mutant" homozygous

From my understanding, a is the additive genetic effect and k is the dominance coefficient. I understand that 2ai is the additive genetic effect at this particular loci which moves this trait away from the population mean for this trait.

Can someone explain the (1+k)? I understand that there could be dominance between the new and old allele, but I don't understand why 1 needs to be added to the dominance coefficient.


texts: How should "the human genome" be interpreted?

texts: What does sequencing "the human genome" mean? Don't individuals have unique genomes?


texts: How much of the genetic differences between humans and chimpanzees are due to genetic drift?

texts: Both natural selection and genetic drift play a part in changing our DNA over time. Are there trustworthy estimates how much of the differences over the whole genome between us and chimpanzees are due to genetic drift and how much is due to natural selection?


texts: Do cockroaches lay eggs in human flesh when they "bite"?

texts:
Recently, I discovered a "bite" by a cockroach, and not only is the "bitten" area red and swallowing, and more specifically, it have a big hole in that area, but when I clean it with hydrogen peroxide solution, something is happening, that is, a yellowish/greenish thing comes out from the holes from each infecting area.

Do cockroaches lay eggs in human flesh when they "bite", and much more importantly, would hydroxide solution kill the eggs and parasites inside those of those holes?


texts: Which shades/hues of color are easiest to distinguish for humans?

texts:
I'm trying to represent data graphically and am using a variation of hue/lightness to distinguish one data point from the next. I would like to use a color that would allow me to convey most information visually.

What I'm interested in is which color I should use. I've read somewhere that humans are most capable of distinguishing shades of green, that is a human can differentiate more shades of green than any other color. Is it true?

Has there been any studies to distinguish the number of shades that a typical westerner can distinguish? I'm looking for information like : ### shades of green, ### shades of red, ### shades of cyan, etc.

Thank you for your input!


texts: does the amount of blood circulate in a body is same before and after amputation?

texts: if a person loose his hand in an accident do the blood flows through his body is equal to the volume of blood before accident? how human body manage with that blood which is deserved by the missed body part? if human body have such a mechanism. does it effect other body parts? or is there any change in the proportion of blood flows through different arteries?


texts: properties of lamps for indoor plant growth

texts:
Ikea has a brand of hydrophonic start kits called vaxer. Part of their offering consists of lamps that aid in the cultivation of the plants (example1, example2 and example3). There are other companies offering lamps that should help plants grow. Here is an example on ali-express.

When I compare the lamps from ikea as well as others I find it hard to figure out what lamp may be preferable for my hobby projects at home. I recall seeing a documentary where it was suggested that plants prefer red and blue light because that is the colour they themselves do not emit back. This makes me wonder why the ikea lamps don't have these colors.

I'm new at this field but I may be interested in investing in some lights for some indoor hobbying. When considering this though, what are properties of these growth lights that are important as far as plant growth goes?

In my particular situation I am not concerned with heat but more the correct type of light and the costs of electricity.


texts: How does the specificity to bind to antibody differs between 'hot' and 'cold' antigen in radioimmunoassay?

texts: This question is in relation to radioimmunoassay. In this assay, the 'cold' antigen replaces the 'hot' antigen. Why is it so, if both the antigens are same and hence their specificity? Does the radioactive molecule change its specificity?


texts: Protein bands not visible after sds page coomassie dye stain

texts:
I am working with cell wall protein of Candida albicans and cryptococcus neoformans but after protein extraction and run on SDS PAGE my bands are not visible after coomassie staining. Can anyone tell me how to concentrate the protein so that bands can be seen on coomassie stain.
I am using Ammonium Carbonate buffer for extraction of protein. Also, the bands are visible on silver staining.


texts: What does "operationally soluble" mean, re. Tax10 enzyme?

texts:
I am trying to work out whether the enzyme Tax10 is soluble or insoluble. I need to know if some buffers won't work with Tax10. I am trying to confirm Tax10 activity, having confirmed protein expression and having purified it.
Any help would be much appreciated! Thanks :)

Context:

Walker K, Long R, Croteau R. 2002. The final acylation step in taxol biosynthesis: cloning of the taxoid C13-side-chain N-benzoyltransferase from Taxus. Proc Natl Acad Sci USA 99(14):9166-9171.

  The TAX10 gene overexpressed from pSBET yielded a ≈50-kDa protein (determined by SDS/PAGE), consistent with the size of the encoded enzyme, and this operationally soluble recombinant enzyme from preparative bacterial cultures was partially purified by anion exchange (DE-52) and ceramic hydroxyapatite chromatography.

(p.9169, below Figure 3)


texts: How do ribosomes interpret stop codons as selenocysteine and pyrrolysine?

texts: How does the protein synthesising machinery determine that UGA and UAG in mRNA should be decoded as selenocysteine and pyrrolysine, respectively, in certain circumstances, rather than as stop codons?


texts:
Today, first  time in my life I ate seafood. It was a squid and a calamar. Note that I am biology layman, so please be merciful :(

While dissecting my food I noticed that the tissues of those creatures were homogenous white mass. Completely different than with pork or chicken, where you can easily see the directions of muscle fibers and different groups of muscles. Just looking at a chicken wing tells you which muscle does what.

But why are squids and calamars so homogenous? How is it possible they work? Why is it like that?


texts:
Can a gene be expressed under the T7 promoter in an E. coli strain (e.g. DH5 alpha), which does not have the T7 polymerase gene encoded in its genome? In other words, is T7 promoter leaky?

To be more specific, how is it possible that a regular E. coli strain, which does not encode for the T7 polymerase, can grow on kan selective media if it was transformed with a plasmid that has the kanR gene under T7 promoter?


texts: I just want to confirm the species of the tree in the middle of the picture. Is it the "Flame of the Forest"? This is taken in my school campus. Thanks in advance!


texts: How to map the Gene name to its Gene Symbol?

texts:
I am learning in Gene data lately so I apologize for the silly questions in advance. I read a paper for a cancer on human which found some important genes. For example, the paper listed one of genes in its name as

gene1:    chromosome 12 open reading frame 52

May I know how I can find its corresponding gene symbol as

C12orf52

Is there a mapping table or  tool I can use ?

Thank you very much,


texts: Photosynthesis in oxygen free enviornment

texts:
If a plant is grown in an oxygen free enviornment would it live longer in light or darkness?

It is evident that oxygen would compete with carbon dioxide during various processes like competing with carbon dioxide for reducing power, also oxygen quenches the excited electron of chlorophyll etc.

But all these effects to me don't give any sense of the extent of oxygen on these reactions. What does the absense of oxygen have on the system? Except ofcourse the plant not being able to respire properly.


texts: Do ants or other insects sleep, and if so why?

texts:
I was thinking yesterday about insects (as there was a spider in the house, and I couldn't help but think of anything else, even though they aren't insects), and I started to wonder if ants sleep?

After thinking about it for a while I decided that they might sleep, but then what would be the purpose of sleeping for them? My limited understanding of the need of sleep is that it is used for the brain to compartmentalise the events of the day and allow memories to be formed. But ants don't really have to think about much during the day, given that they act more as a collective than an individual. Or in the case of other insects, they have simpler more instinctive brains which rely on taxis, reflexes and kineses.

So, do ants and other insects sleep (or do they have a different type of sleep to us) and what would the purpose of it be for them?


texts: How much would it cost (more precise the better) if i wish to start a diy bio lab in my own house. Assuming that all I want is a functional set and to create maybe simple things like glowing bacteria/glowing fish/deadly virus（jk)


texts: Does Vasa deferens produce any secretion in the Human Body?

texts:
I got this doubt while attempting the following question:
Q. Secretions of which structures are essential
for maturation and motility of sperms?

a. Epididymis

b. Vas deferens

c. Seminal vesicle

d. Bulbourethral gland

(1) a, b only

(2) b, c only

(3) a, d only

(4)a,b,c

The ans given for the above question was (4) a,b,c
I understand how the seminal vesicle, being a gland can secrete substances but I am unsure about how Epididymis and Vasa deferens are involved in the secretion process.


texts: Does the assembly of the PLC transcription complex utilize phosphorylation in binding of the GTFs?

texts: in the recruitment of general transcription factors during transcription initiation is phosphorylation utilized?


texts: In this poisson distribution in olfactory receptor (OR) pseudogenes neutral mutation rate, how is the mean used?

texts:
The 2005 paper A comparison of the human and chimpanzee olfactory receptor gene repertoires describes a poisson distribution, with a mean of 0.701

From that mean, how is the gene disruption rate of 1kb per year calculated? And, how is the age 3.86 Ma for relaxation of selective constraint calculated from (0.451/0.701)·6 Mya = 3.86 Mya?

The parts of the paper,

TL;DR How is mean = 0.701 used to calculate stuff in that paper?


texts: Is our color vision calibrated to sky, vegetation, and blood?

texts:
Our color vision is based on three types of receptors (cones) which are sensitive to three distinct locations on the spectrum:  420–440 nm, 534–555 nm, and 564–580 nm.  We label them "red", "green", and "blue", but these names are arbitrary.  However, their locations on the spectrum may not be arbitrary.

I notice that they correspond to the colors of the three most important things in our natural habitat:  sky (the above), vegetation (the below), and blood (the sign of potential food or alarm, depending upon whether you are the hunter or the prey).

Am I on to something here, or am I just dreaming in technicolor?


texts: Systems identification in small neural network

texts:
When analyzing data from cortex, we often try to understand what each neuron does in terms of its inputs from other neurons - a specific kind of a systems identification strategy. Most current approaches use generalized linear models for that purpose (Review article).

For very small systems like the worm c.elegans it must be possible to record from all neurons at the same time, at least optically. How well can we understand the output of each neuron based on its inputs in such simple systems? What are the best databases to ask such questions?

The reason I am asking this question now is because the human brain project that just got roughly a billion dollars in funding basically needs such data for every cell in the whole brain.


texts: What kind of mushroom is this in central Europe?

texts:
I found some mushrooms in the forest and I'd like to know what kind it is, for being able to tell how to protect the trees from it.
Growing Info
growing location: central Europe, forest
host plant: beech tree, alive
season: late Summer (Sept. 15th 2020)
The area where the mushrooms were found is a typical beech forest with unusually low water levels, as the last few summers have been drier and warmer than usual. I presume the trees suffer more from these mushrooms because the trees are weakened due to the hot weather and little rain.
Some of the mushrooms dry out while on the host tree.
Picture Taking Conditions
The closeup pictures were taken at home. This was after transporting the mushrooms and storing them in the fridge for 2 days. They got a bit squeezed during this procedure.
Pictures
host tree:

host tree from below:

multiple mushrooms, pic A:

multiple mushrooms, pic B:

bright mushroom, pic A:

bright mushroom, pic B:

bright mushroom, pic C:

cream colored/older mushroom, pic A:

cream colored/older mushroom, pic B:

cream colored/older mushroom, pic C:


texts: I see a lot of studies on GWAS not filter out for linkage disequilibrium or even make the slightest mention of it. Why is this the case? I would imagine that you want to keep SNPs that are only in linkage equilibrium to promote independence (and besides, without it an additive model makes no sense)


texts: Does 405 nm light set off phosphorescence in the eye?

texts:
While playing with a blue/violet laser (5 mW, 405 nm) tonight, I noticed that on dark, non-fluorescing surfaces, the beam reflection was trailed by what looked like a dimmer reflection of the beam. The effect was most easily observed when I moved the laser in a circular motion. The apparent 2nd reflection was not produced by a side lobe of the laser diode, as it always trailed the main reflection, regardless of clockwise or counterclockwise rotation. Also when I stop moving the beam, the second 'reflection' quickly merged with the main beam reflection.

I doubt it is caused by phosphorescence of the material (cloth) I was lasering, as it also showed up when I pointed the laser at the floor, other sorts of cloth and painted walls.

So, do rods, cones, visual purple or other eye components phosphoresce when hit with deep blue light?


texts: Why does depolarisation by high intracellular K+ trigger calcium channels opening?

texts: I have learnt that in pancreatic beta cells, glucose being metabolised in the cell causes a high ATP level, which triggers ATP-dependent potassium channels to close. This means that potassium can't leave the cell anymore, which depolarises the membrane and causes voltage-gated calcium channels to open and release calcium into the cell to trigger insulin release. I don't understand why this happens, because both potassium and calcium being positively charged. Wouldn't this depolarise the membrane even more? I thought this would be unfavourable.


texts:
As far as I'm aware, chloroplasts produce energy through the use of photosynthesis which essentiall converts CO2 and Water into Glucose (I'm an engineer by trade so really wracking my brains to the last time I studied biology formally).

The pigment in chloroplasts, chlorophyll, makes the plant appear green due to the fact that it absorbs red and blue light, reflecting the green.

My question is this, would it be possible to extend the light spectrum absorbed by the chloroplasts, perhaps through the use of very careful genetic engineering and manipulation of the pigments contained within, in order to increase their energy absorbtion rate.

In essence, could you could make them absorb a wider range of frequencies for use with photosynthesis and thus enable much faster glucose/ATP synthesis?

If this were possible, how much of an evolutionary advantage would it provide?


texts: How and when does the regeneration of cells that have died start?

texts:
I assume that the replacement of cells that have died (or been removed by any means) doesn't work on a single cell level but starts only when some critical number of cells have died.

My question is: How is this signaled (to the regenerating cells), and how is the critical number encoded, i.e. the signal threshold at which regeneration starts?


texts: What is open complex in E.coli DNA replication?

texts:
The E.coli DnaB helicase is essential for replication initiation from the chromosomal origin of replication ( oriC ) and is present in vivo as a protein complex with six monomers of the DnaC ATPase protein and six ATP molecules (Wickner and Hurwitz, 1975; Lanka and Schuster, 1983). DNA replication initiation at oriC begins with binding of multiple molecules of the bacterial DnaA initiator protein to a 9 bp repeats (DnaA boxes). This binding promotes destabilization of nearby AT-rich sequences, resulting in unwinding of the DNA double helix and the formation of an open complex.

I looked up in DNA Replication by Arthur Kornberg, Tania A. Baker (the authors who probably coined this term), Google and Google.Scholar but didn't stumble upon any definition.

What is it actually?


texts: why does translation occur more frequently than transcription?

texts: In our textbook it says that translation occurs more in a cell than transcription but I couldn't find anything that explains why it happens


texts:
As I know evolution comes bit by bit mutation by mutation

How sex evolved which requires a major change in at least two individuals one to become male and one to become female ?

When that happened as we can see sex in all animals and most plants?


texts: Was HindII the first restriction endonuclease to be extracted?

texts:
Background:

Guided by wikipedia and pmc I found this paper by Hamilton O. Smith. and .Daniel Nathans.

  A
  restriction
  enzyme
  is
  a
  component
  of
  a
  restriction-modification
  system
  of
  a
  given
  specificity
  within
  an
  organism.
  The
  R-MT
  system
  consists
  of
  two
  enzymatic
  components,
  a
  restriction
  endonuclease,
  and
  a
  modification
  enzyme
  sharing
  similar
  (or
  identical)
  recognition
  specificity.
  We
  would
  like
  to
  propose
  that
  the
  genus-species
  designation
  be
  used
  as
  an
  R-M
  system
  name
  according
  to
  the
  following
  rules.

  (1)
  The
  genus
  and
  species
  name
  of
  the
  host
  organism
  is
  identified
  by
  the
  first
  letter
  of
  the
  genus
  and
  the
  first
  two
  letters
  of
  the
  species
  to
  form
  a
  three-letter
  abbre-
  viation
  in
  italics.
  For
  example:
  E.
  coli,
  Eco
  and
  H.
  influenzae,
  Hin.

  (2)
  Strain
  or
  type
  identification
  follows
  the
  genus-species
  abbreviation
  in
  non-
  italicized
  symbols,
  e.g.
  EcoB
  or
  EcoK.
  In
  cases
  where
  the
  R-M
  system
  is
  genetically
  specified
  by
  a
  virus
  or
  pla,smid
  the
  italicized
  genus-species
  abbreviation
  of
  the
  host
  is
  given
  and
  the
  symbol
  for
  the
  extrachromosomal
  element
  follows
  in
  non-italics,
  e.g.
  EcoPl,
  EwRI,
  etc.
  In
  occasional
  cases
  where
  it
  might
  be
  necessary
  to
  specify the
  host
  strain
  as
  well
  as
  the
  extrachromosomal
  element
  the
  strain
  identification
  symbol
  may
  be
  inserted
  parenthetically,
  e.g.
  Eco(B)Pl.

  (3)
  When
  a
  particular
  host
  strain
  has
  several
  different
  R-M
  systems,
  these
  are
  identified
  by
  Roman
  numerals,
  thus,
  the
  R-M
  systems
  from
  H.
  injluenzae
  strain
  d
  would
  be
  HindI,
  HindII,
  HindIII,
  etc.

Main question:

Now HindII was -

extracted from  Haemophilus influenzae
the strain was strain Rd, so d
and it was the 2nd enzyme to be isolated? Hence II.

So how is it the first Type II RE?

  H.O. Smith, K.W. Wilcox, and T.J. Kelley, working at Johns Hopkins University in 1968, isolated and characterized the first restriction nuclease whose functioning depended on a specific DNA nucleotide sequence. (wiki)


texts: Question regarding an Escherichia coli reaction

texts:
With respect to this link
http://www.biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN-14479
Here the enzyme is mentioned and the two reacting compounds. Now , my question is
1. When these two compounds react, do they initially get attached to the enzyme before reaction?
2.If they Do both these compounds get attached to the enzyme, what is such an interaction called? Protein compound interaction??


texts: What is an interaction motif with respect to protein sumoylation?

texts: While am reading about protein sumoylation this morning I got stuck on sumo interaction motifs and consensus motif line. I heard the the word motifs for the first time. What does motifs mean in this context and What does canonical Sumo consensus motif ΨKx(D/E) mean also? Would you please elaborate the formula and thanks in advance.


texts: Why does a stomach come before the gizzard in birds?

texts: Since the gizzard is for mechanical digestion, shouldn't that happen before the stomach digests the food with acids? (to make the morsels smaller)


texts: Burns' "To a mouse" - what species of mouse?

texts:
What's the most likely mouse species Robert Burns is referring to in his poem "To a Mouse, on Turning Her Up in Her Nest with the Plough".

Burns farmed near Ayr, which is on the Firth of Clyde in Scotland. So the mouse of his poem would have to live in that area in the late 18th century. The creature obviously was living in an open field in December in a nest made of "leaves an' stibble [stubble]". From the poem's title it appears like the nest was constructed underground. "Sleekit" refers to sleek coated as in shiny fur. A clue to the mouse's diet is given by "A daimen icker in a thrave", ie grain. According to Wikipedia: "Scotland has no population of the Edible or Hazel Dormouse, or of the Yellow-necked Mouse, and the Harvest Mouse's range is limited to the southern part of the country."

The poem is here: http://en.wikipedia.org/wiki/To_a_Mouse


texts: I see how large trees and weeds that are capable of splitting concrete, and realized that I have no idea what this phenomenon is officially called. Google was no help, suggesting root pressure, but that's an interior force for water and sugar transport, not what I was looking for. Is there a name for the act of plants growing through things like concrete and rocks on their own, independent of weathering?


texts: Why is the rough ER necessary to make extracellular proteins?

texts: It is my current understanding that free ribosomes synthesise proteins to be used inside the cell, and the rough endoplasmic reticulum is necessary to make proteins that are to be secreted by the cell. Is this correct - and more importantly, if so, why?


texts: Why is the chemical of an hexose not sufficient to ID the molecule?

texts:
Here is the homework question I have to answer to

  The Chemical formula C6H12O6 can mean any number of different hexose sugars that share the same chemical formula. To tell the hexoses apart, you would need to see their structural formula. This is because they are ___________ of each other

My thoughts are ...


texts: Why Do Healing Wounds Feel Warmer To The Touch?

texts:
I fell over on my bicycle trying to avoid running over a rattlesnake, and ended up badly skinning my knee. It immediately began to bleed, but soon clotted.

It has been 2 days now and it has formed a thin scab and is healing well as far as I can tell. I was chilly from the air conditioning, and I noticed the wounded knee was much warmer than the healthy knee. It was very warm, while the other was rather cold to the touch.

I read here about skin healing, and thought, maybe it is because the blood rushed there to clot the wound. But, the wound is already clotted and sealed and the worst is over. So my question is:

Why is my wound and the area around it so much warmer days after the injury?


texts:
I'm really stuck on this question. I'm being asked to find the half life of a drug.

The Vd is 50L/kg. The clearance is 0.1 L/hr/kg. The patient weighs 70 kg.
Equation is:
T1/2 (halflife) = 0.693 * Vd / Cl.
I keep getting 0.693 * 50 / 0.1
               = 346.5
The right answer is 14.4 days but I can't figure it out.
Thanks in advance


texts:
I have a general understanding of the Bohr effect, and that Hemoglobin's affinity for oxygen will shift depending on the conditions of the lungs and tissues. However, I'm struggling with the following question; I feel as though I'm getting caught on the less-than-ideal answer choices, but I want to make sure I'm not missing a basic principle that could reason this answer more clearly.

Q) Which of the following best describes how a shift to the right in the dissociation curve results in more oxygen delivered to tissue?

A) The distance between the curves at 100 mmHg is less than the distance at 40 mmHg

B) The distance between the curves at 100 mmHg is more than the distance at 40 mmHg

C) On the right-shifted curve, Hb will pick up more O2 in the lungs

D) On the right-shifted curve, Hb will pick up less O2 in the lungs

My reasoning for choosing A is less-than-ideal: let me explain. First, I've been taught that a good rule-of-thumb for oxygen affinity is that Leftward shifts are related to the lungs, while Rightward shifts are related to the tissues. Therefore, because the answer choices C & D refer to right-shifted curves and the lungs, they can be eliminated. However, I'm not convinced this "rule" is so absolute - I can imagine that the curve can shift left & right within the tissues and the lungs. For the sake of argument though, I'll assume the rule works and eliminate answer choices C & D. Then, I can also eliminate answer choice B because it's not a true statement. As a result, I arrive at answer choice A. However, I don't feel as though it quite answers the question. Can anyone please provide some insights as to my reasoning, and/or perhaps what I'm missing? Thank you!


texts: Is it known how the first viruses formed?

texts:
The oldest known virus is known to have infected prehistoric insects 300 million years ago. A virus is basically a parasitic strand if DNA or RNA encapsulated in a protein coat. It enters cells by "wearing" a protein coat made out of proteins needed by a certain cell (e.g. Lung cells and flu virus).

Now, my question:

Do we know how viruses naturally formed? To simplify the question, if we went back to the first virus, how would it form?

Note that I am looking for a scientific answer, and not wild-ass speculation. While I can accept some degree of speculation the accepted answer will NOT be based entirely on speculation if it is avoidable.


texts: Where can I upload non-human Genotype data?

texts:
I have genotype data from few chicken population and I want to (need to) upload them somewhere online with free access. I have searched the web but I haven't found any place for non-human genotype data!

Does anyone have an idea where I can upload it, which is publicly available and user friendly?

bests


texts: What is the name of the species of this butterfly?

texts:
Well,I am from India and live in the northern part of the country.I commonly find these butterflies during winter or spring seasons.

The original image shot is:


texts:
I have lets say 10ng/uL of RNA. How can I convert it to picomole?

I need it to calculate how much magnetic beads I need. This is the product: http://tools.lifetechnologies.com/content/sfs/manuals/dynabeads_m270_sav_man.pdf

I do not know how much beads should I use.


texts: Why do the carbohydrate groups in glycoprotein hormones decrease the rate of metabolism? And increase the half-life?


texts: Is there a scientific name for the field of study focusing on the hemispheres of the brain and their control of opposite sides of the body?

texts: I'm assuming this field of study would focus on motor controls, movement, and exercise, but it could also focus on activities which strengthen the corpus callosum or stimulate a specific half of the brain.


texts: I would like to know the specific determinants for formation of IgG dimers. My understanding is the stem of the antibody is a homodimer of two heavy chains, covalently bonded through two disulfide bridges called the hinge region. Is there any association between the constant region? My reading would suggest no but I have not found a specific reference as such.


texts:
This question is related to the recent Wuhan outbreak. Currently, mortality rate for the virus is somewhere around 2-3%. This is much lower than say, SARS (9.5%) and MERS (34.5%).

As a thought experiment, the main cause of death of the above viruses tends to be pneumonia (direct and secondary). If pneumonia leads to a higher rate of infection, then (indirectly) would such a virus would become much more deadly over time?

Do viruses such as the coronavirus self-select for higher rates of mortality, e.g. by leading to pneumonia, thus causing more phlegm and coughing?

Related to the above, how quickly can such mutations arise?

Sources would be really appreciated!


texts:
How do biologist trace evolutionary history of virus, is there any article on this issue,
e.g. how scientist got to know that coronavirus evolved from bat or camel or pig?


texts: Are homozygous carriers of the CCR5-Δ32 allele fully immune to all known strains of HIV?

texts: Or is there documented evidence of even one homozygous carrier contracting HIV and staying infected?


texts: Effects of beer on muscle recovery after exercise

texts: I noticed it several times that when I drink beer (even one bottle) after some heavy workout, the next day my muscles are more stiff than other times, and not the same way... Is it because that lactate and NADH levels are raised both due to the anaerobic training and alcohol metabolism?


texts: Travelling with tissue samples in RNAlater

texts:
I've been in Brazil collecting some samples (ants) and need to travel back to to the UK with - I've got their brains stored in RNAlater, which have been in the freezer at -4C for a bit less than a month. On the Fisher Scientific website it says that they can be left at 37C for a day in solution before the RNA can begin to degrade. I've got a long journey home which could take up to 3 days in the heat (it's around 38C at the moment here) and involves stopping off through Morocco.

Has anyone travelled with samples in RNAlater like this before in elevated temperatures and got good results from their RNA extractions? Would you reccomend trying to source some dry ice for the journey?


texts: If a gene altered causes cancer and creates a protein for cancer can the new protein be isolated in some way?

texts: In the above title question, can the protein thats altered not be isolated (to separate out from other proteins) somehow?  Is there nothing that can bind to the specific cancer proteins that will not bind to other proteins?


texts: Why don't onion root tips show mitotic stages?

texts: It was back in the winter that we did the Onion root tip experiment in college. We were able to see wonderful stages but now in this monsoon-autumn transition the root tips hardly show any mitotic stage. Why is it so?


texts: How fast the brain recover itself at sleep? What can be done to accelerate this process?

texts:
In Computer Science we have "Big O Notation" to describe how efficient is an algorithm at processing some task. Those can be linear, time constant, exponential among others.

Using that analogy, How much time the brain needs at sleep to recover itself from an intensive day at work/over stimulation/training/learning/etc?

After it reach it's "specific time", I know that we dream, and that can take very few minutes. Last night I've dreamt of hardest college exams, even done my last one in 2011. So, dreaming time is a period where the brain clean itself from toxins? I've waked up early, so I should have "dreamed a litle bit more" to recover, or the dream it's just the output imaging of the brain recovery process?

What can I do to recover faster? Things like dimmer and silent ambient help better than the total time slept? How they affect and interrelate? If you can provide technical and scientific papers, it will help a lot!

Thanks a lot for your time and patience!

Edit: "Typed Bio O instead of Big O".


texts: Why does white light viewed through optical chopper appear purple/blue?

texts:
I looked at a light like the one shown here through a fidget spinner (I believe I was observing near where the "blades" meet the inner portion) and noticed that it appeared purple/blue, particularly when viewed for a prolonged period (I looked at the reflection of sunlight from snow and observed this as well.).  I believe this is either an optical effect (the spectrum is convolved with the Fourier transform of the "chopping function or pulse" ) or has something to do with the eye/my perception.

So what's going on here?


texts: Are humans the only mammals that are known to display homosexuality?

texts:
REQUEST: In this post I do not refer to, nor do I encourage reference to, any ethical/moral/emotional aspects of homosexuality. So please don't start an pro/anti- LGBT campaign in the comments section.

Are mammals (other than humans) known to engage in homosexual activity of any sort?

From the way I see it, homosexual activities carry no evolutionary or reproductive benefit: No offspring produced, no continuation of species...hence pointless.

Yes, I get that the "need to mate and to produce and protect offspring" is hard-wired into every (normal) mammalian brain. If I've interpreted this correctly; intercourse is a fairly energy-expensive act so if there were no immediately clear "incentive" for mammals to mate they wouldn't mate at all, hence heralding the decline and eventual extinction of a species. Nature solved this conundrum by ensuring that the brain would perceive intercourse as highly pleasurable, thereby securing the necessary "incentive" for mammals to mate.

The only "flaw" here, is that simply stimulating the genitals is sufficient enough to elicit a sensation of pleasure. So there's no real need to go through all the trouble of finding a suitable animal of the opposite sex and "do it" to feel good. A sufficiently intelligent mammal would soon figure that out; so this opens up two more possibilities: 1) Masturbation and 2) Homosexuality. (Since this post's on Homosexuality, I'm only going to deal with the latter)

So, a mammal intelligent enough to figure this out would have three options before it : 1) Heterosexual activity, 2) Masturbation, 3) Homosexual activity; the last two options being a way to bypass Nature's original intent.

So before I continue, I want to make what I mean by "homosexuality" very clear:

a) A being that displays option 1) or both 1) and 2) is heterosexual.

b) A being that displays options 1) and 3) [and maybe 2) too] is bisexual.

c) A being that displays option 3) or both 3) and 2) is homosexual.

[Just to make it explicitly clear, a homosexual will always steer clear of option 1)]

So let me just put all of that together and re-phrase my question:

Q- Are there any known instances where a (non-human) mammal consciously avoids heterosexual acts and instead prefers to engage in homosexual activity

Personally, I find this doubtful, since the existence of homosexuality (among humans) is the unintended result of Human self-consciousness/intelligence, something that other mammals apparently lack.

HOWEVER: (Considering another possible reason for homosexuality)

If occurrence of homosexual tendencies is (also) due to, say, the stochastic, faulty "hard-wiring" of the human brain due to mutation or damage to neural tissue (I'm not sure if this really is one of the reasons for homosexuality), then it would seem plausible that other mammals could also be affected by this stochastic "fault" and thereby display homosexual tendencies.


texts: How did scientists establish the reactions that occur in metabolism?

texts: How did scientists establish that macromolecules like proteins, carbohydrates and lipids are synthesized from other molecules with intermediate products by living cells. Did they observe this under microscope. I want to know this because I am studying bioenergetics and while studying photosynthesis and cellular respiration I have doubt that whether this all stuff is correct or not. I hope that you will help me to clear this doubt.


texts: Confused about definition of bulk flow of water by osmosis

texts: As a teacher of high school and introductory college chemistry, I used textbooks that defined osmosis as a flow of water (only) through a membrane that prevents other substances such as dissolved salts from passing through.  But in more advanced text, discussing osmosis through aquaporins in the plasma-membrane, bulk flow by osmosis implies that the water carries along dissolved substances.  So which is it:  pure water or a solution that moves by osmosis?  (I'm somewhat naive about biology, as my degrees are in physical chemistry and metallurgy.  Biology is way more complicated!)


texts: How to predict future generations from heritability

texts:
The heritability of human intelligence is estimated to be around 0.5. There are of course various estimates, some lower, some higher. But let's work with this value of 0.5 for the moment.

I wanted to know how this relates to the trait value of future generations and read a bit about it. For example, in some related posts:
how should one interpret heritability is it related to r2
why is a heritability coefficient not an index of how genetic something is
how to interpret the breeders equation

Turns out the breeders equation gives us an idea about that. But we need a second variable: Selection.  I read that selection is based on the reproductive success of individuals with a certain trait value.  But how would I calculate this value?  Let's assume that the reproductive success is higher, for humans with higher intelligence. Let's simplify and say, the fertiliy rate of above average indivdiduals is 2.10 and the same value for below average individuals is 1.90. How would I plug those numbers into the breeders equation?

I tried the other way around. We know that intelligence is increasing over generations in western civilizations (see Flynn effect). Again, estimates vary (and can actually be negative) but we can work with an increase of 2 IQ points per decade. So lets say 5 IQ points increase from one generation to the next in a western civilization population. That would mean:

S = R/h²
S = 5/0.5 = 10

What would this value of 10 mean? How does this boil down to the reproductive success of individuals with certain trait values?


texts: Need to solve a "pseudo-metabolic" network for rates

texts:
following problem:

I have data on a certain complex association network (from monomers 1 ... 8 to complexes of all combinations, such as, 12 ... 13 ... 18 and so on until 12345678, so that I know

the structure of the network (255 vertices)
the edges of the network
the concentrations of the vertices

From this data I now wish to infer the preferred route(s) of assembly for those complexes - which should be the rate constants for the edges, such as 1 --> 12 or 145 --> 1458. Does that make sense?

I have now tried various standalone applications for network creation/analysis as well as R packages. Metabolic flux analysis seemed promising for me, but it turned out that it only works with set external concentrations and assumes steady-state for all metabolites within the network. Which is not the case for me. Do you know of any alternative method?

Thanks and best wishes,
Simon


texts: What is a gene transcript, how is it different from an allele?

texts:
Within human genetics,

My current understanding of a transcript for a particular gene is that it's the exact nucleotide sequence and position of a particular instance of said gene in some individual.

My current understanding of an allele is that it's a less granular breakdown of the instances of a gene in a population.  That is to say, one allele for a particular gene likely covers many (millions of?) unique transcripts for that particular gene, and groups them together due to their tendency to all have a similar phenotypic expression.

Is this correct?


texts: What biological processes can affect the temperature of the shadow a tree casts?

texts:
Assuming two trees have similar shape and leaf coverage, could differences in the biological processes among them lead to differences in the temperature of the shadow they cast?

What biological processes occurring in plants could affect this? I was thinking that transpiration will cause heat loss, and photosynthesis also absorbs energy, so these would contribute. What other processes that occur in a tree could affect the dissipation of heat causing cooler shade?

Has there been any studies specific to rates of transpiration and photosynthesis, and the effect on shade temperature?


texts: Many studies claim that humans need 8 hours of sleep. During sleep there are several different stages, from stage 1 to 4 as well as REM sleep. However, are all these stages actually necessary? If yes, what are the importance of each stage, if no, which stage(s) are/is insignificant?


texts: I found this plant near the MSU, Moscow, Russia. Could someone help me to identify it?


texts: What virus properties affect their airborne contagiousness?

texts:
What properties of a virus affect it's ability to be transmitted by air? I assume it must be able to withstand different temperatures and be smallish in size?

For example why is influenza very easily transmitted by air but the ebola virus is not?


texts: Any evolutionary explanation for human blood groups?

texts: What is the explanation of people having blood types from an evolutionary perspective?


texts: The phosphate in hydroxyapatite Ca5(PO4)3(OH) is a strong base, PO4^3-, and the hydroxide is also a base, OH-. I was talking with a biologist the other day about if bone resorption (at a level that causes elevated calcium and phosphate) also causes alkalosis. He did not think so, but mentioned that it might be buffered or compensated for. In general, does bone resorption cause alkalosis?


texts: Which life is supported in sterilized 100% pure water?

texts: As sterilized 100% pure water does not contain any mineral and ion, so which type life can survive in sterilized 100% pure water?


texts: Is there are evolutionary explanation for why humans and primates are ticklish? How might it have evolved?

texts: Tickling is a rather interesting phenomenon: When humans or apes are touched in certain areas like the armpits or sides, we respond with laughter AND frantic attempts to stop the assault. Obviously our ticklish areas tend to be very vulnerable, so it makes sense that we would want to protect ourselves, but why do we respond with laughter? How might both of these reactions to tickling have evolved? Do they have the same evolutionary purpose or different ones?


texts: Merge several .ab1 sequence files into a single FASTA file?

texts:
I have several .ab1 files generated from Chromas. I want to merge all of them into a single FASTA sequence file. How can I do this in an automated way?

Note that I don't have Chromas installed (the files were generated by someone else). I am using linux, so open-source, command line tools are preferred.


texts: When did the mammalian outer ear evolve?

texts:
All Eutheria and Metatheria have outer ears, and as far as I found out, monotremes once also had them, so they seem to be universal for mammals. Did other synapsids have them, too?

I know that soft tissue doesn't fossilize well, but isn't there any other way to find out, like muscle attachment? Has it something to do with mammalian ear bones?


texts: Biostatistics: Pollen dispersal directionality

texts:
What Information am I looking for?

Think about a tree that is sending pollen all over the place. Because of wind, most pollen grain will go toward one direction. Imagine, we split the 2D area around the tree where pollen grains fall into two half disks of equal size. We chose the disks so that the number of pollen grains falling into one half-disk is minimized and the quantity of pollen falling in the other half-disk is maximized.

The information I need is what proportion of pollen grain falls into each disk? Is it $\frac{0.5}{0.5}$ (in which case the wind would have no effect) or is it something like $\frac{0.8}{0.2}$?

Where to get the information from?

I was reading this paper about pollen dispersal directionality and was trying to extract the info I need.

On pages 4 and 5 they explain their analysis under the section statistical procedure. More specifically, in the first paragraph of the 5th page, they seem to describe the meaning of the parameters that are trying to estimate. One of them is the so-called directionality parameter $\delta$. I don't understand how to interpret this parameter $\delta$.  This parameter is part of a logistic regression I think (although the authors do not characterize it as such) of "mating success" $y$ against variables $d$ ("distance") and $h$ ("height") and an angular variable $a = \cos(\alpha_0 - \alpha)$.  ($\alpha_0$ is the "presumed prevailing direction of effective pollen dispersal," which apparently is not estimated from these data.)  The corresponding parameters of the model are $\beta$, $\gamma$, and $\delta$, respectively, hence

$$\phi_j = \Pr(y_j = 1) = \frac{\exp\left(\beta d_j + \gamma h_j + \delta a_j\right)}{\sum_{k=1}^r \exp\left(\beta d_k + \gamma h_k + \delta a_k\right)}$$

where the index $j$ ranges over all $r$ "male(s) in the neighborhood."

Their Results

Using maximum likelihood, they found that the directionality parameter, $\hat\delta = 0.56$ (SE = $ 0.15$; bottom of page 6).

Question

How can I relate their finding to the information I need (even if it is just a rough approximation)?

I think I have to understand the so-called directionality paramter $\delta$ Can you help me to interpret the meaning of this parameter $\delta$?

Reference:

Burczyk, Adams, & Shimizu, Mating patterns and pollen dispersal in a natural knobcone pine ... stand.  Heredity 77 (1996) pp 251-260.

Not receiving any answer on Biology.SE, I asked the same question here on Mathematics.SE but sadly, the question doesn't receive any attention!


texts: What causes the complementary copy of an RNA molecule to separate?

texts: I have recently read an article which explains that, in the RNA World hypothesis, an RNA molecule gets 'scanned' by nucleic acid, catalysed by a different specifically-folded RNA molecule, to arrange itself complimentarily to the original molecule. However, what causes the new, complementary molecule to detach from the original molecule? I always hear people say that this complementary base pairing allows the RNA molecule to reproduce, but I never quite understood: how? If complementary bases tend to bind together, shouldn't the newly formed structure then be stable? What causes the actual reproduction?


texts: mRNA with Pseudouridine and 5-methylcytidine?

texts:
I am making mRNA by in vitro transcription for transfection purposes. There is a lot of literature about how protein expression is increased and innate immune activation is decreased by substituting uridine for pseudouridine and cytidine for 5-methylcytidine. I decided to try this, but my yield was lower and the mRNA was shorter than when using natural nucleotides. The papers all say they made the mRNA by simply using the new nucleotides in their in vitro transcription kits, but they never mention any further changes to the protocol. Now I would assume that since pseudouridine and 5-methylcytidine are a little different from the normal substrates for RNA polymerase that they might not be incorporated as quickly and the resulting reaction rate would slow down. It might be possible that the Polyadenylate polymerase that adds the polyA tail doesn't recognize the modified mRNA as well. Both a slower reaction rate and less efficient tailing could make a lower yield of shorter mRNA.

Does anyone here have any experience with IVT using modified nucleotides and can suggest something to improve yields?


texts: Number of spindle fibres during Metaphase?

texts:
During metaphase, the chromosomes are arranged on the equatorial plate and are attached to spindle fibres. After S phase, can the cell be said to attain the configuration of 4n?

Also, during metaphase, since two spindle fibres (one from say right centriole and other from say left centriole) are attached to one tetrad, so can it be said in a well defined pattern that for a human being, 46*2=92 spindle fibres are formed in order to proceed with mitosis? Also how would the number vary in case of Meiosis I and Meiosis II?


texts:
Pair-end mapping (PEM) is a technique that allows to detect structural variants in DNA by obtaining paired-end reads and the comparison of their positions in a reference genome.
Then among libraries that had insertion of 500bp, 2kb, 10kb and 40kb which one would you pick to detect the following inversions?

a) an inversion mediated by inverted repeats of 20 kb at its breakpoints

b) an inversion with clean breakpoints (no inverted repeats)

c) an inversion mediated by inverted repeats of 1 kb at its breakpoints

My guesses:

a) 40kb, as if it were to be smaller than the inverted repeats length, the pair ends may align inside and nothing would be detected

b) Medium size, as if it is too small it wouldn't probably cover the area desired, and if it were bigger it would overlap too much (anyway data is needed for and answer is a blind optimization)

c) 2kb. same reasonings as a) and b).


texts:
In this question about the fires in the Amazon rainforest, a user responds with

  It [the Amazon] is still a part of nature and burning it can narrow
  the diversity of both plants and animals, which can have consequences
  on the whole planet.

What are the negative consequences of a narrowed biodiversity to the planet?


texts:
For most animals, the whole bottom of their face sticks out and they have a snout with a mouth and nose at the end.  But humans have a flat face and just a nose that sticks out.  We used to have the whole face sticking out, but our jaws got smaller and smaller.  Because our noses still needed space to do their job, they had to stay sticking out.  People who come from very cold areas have bigger noses than people from where it is hot, so they can warm the air up more.

Why has our nose evolved with the nostrils facing down? Is it because we were water animals, and that would help with water coming in?


texts: How does inorganic phosphate inhibit alkaline phosphatase?

texts: I want to know how is inorganic phosphate able to inhibit alkaline phosphatase.


texts: How standardized is lab-grade skim milk?

texts:
I was surprised to learn in the answers to this question that in many cases the preferred cryoprotectant for many organisms is skim milk, rather than something more simple and well-defined like glycerol. And indeed, Sigma will happily sell you lab-grade dried non-fat cow's milk for lab-grade prices.
It seems to me that this could potentially cause significant variability and reproducibility issues. Milk is pretty sensitive to the condition of the producing animal, and when dealing with a cow we're talking about a very large and complex source that's not hyper-standardized like lab-grade rodents.
I don't seem to be able to find anything much about specification on Sigma's site, however (the spec sheet for milk has only the obvious like "opaque white fluid").
Does anybody know to what degree lab-grade milk is actually standardized, and if this should be a concern for protocols like cryoprotection?


texts: Concept of mean systemic filling pressure

texts:
Mean circulatory filling pressure (MCFP) in humans was defined by Guyton as "the pressure that would be measured at all points in the entiere circulatory system if the heart were stopped suddenly and the blood were redistributed instantaneously in such a manner that all pressures were equal".
Now according to many physiologists, there must be a location in the vascular network where the pressure is completely independent of the cardiac activity, and this pressure must be equal to the MCFP. Apparently, this was already noted by Starling in 1897. The entire point is well explained in this article.
I have read this article and some others introducing the concept of MCFP to medical students; many of them report the same observations made by Guyton, Starling, etc., but a point which is never addressed is why there must be a location in the vasculature where the pressure is independent of cardiac activity.
I feel like getting a satisfactory answer to this question would greatly improve my understanding of hemodynamics, so I would be very grateful if you could explain the concept to me.


texts: Is there a measure for degree of reticulation in a phylogenetic network?

texts: When working with phylogenetic networks, how does one talk about reticulate (i.e., web-like) the branches are? Is there a standard measure of this?


texts: Today I found several of these in my back garden in Sydney NSW, Australia (specifically the north shore). They seem like flowers, except I don't see any attached plant and they have a weird brown goo around the mouth. I've never seen anything like this. Any ideas?


texts: Are antibiotic-resistant bacteria necessarily less virulent than their original strain?

texts:
In the absence of antibiotic treatment, is there a reduction in the average severity of disease caused by resistant strains of pathogenic bacteria compared to wild-type ones?

I would assume that bacteria that have adapted to be able to withstand antibiotics would have to allocate extra resources in order to counter the antibiotics, making them perhaps less growth-efficient than the "original" (non-resistant) strain.


texts:
I've been reading a lot about Hi-C lately, and this has been bothering me.  So far as I can tell from reading around, the topology is related to the conformation of the linear chromosome.  This seems like a fairly pointless description however, as they should all have the same topology.  A "conformation", in my understanding, is the chromosome being folded into a particular geometry.
On the other hand though, I guess if two genes were brought together to form a loop, they would also form a "hole" (the gap in the loop).  But this seems like a weak connection to make, just because two chromosome regions are paired doesn't necessarily mean they were bound and formed a loop.  It seems the "topology" would "best" be seen after a 3D reconstruction from the pairs data, showing the predicted geometry, and from there you could see how many putative loops and such there are, and thus start to determine the topological properties.
The last possibility I was thinking was that this is in reference to network topology implied by a contact matrix.  This seems the most likely to me, but also the least implied (to me, at least) in the literature I've ever read.
All of this has me wondering if I've missed something about the meaning of "topology" here, as opposed to just "conformation".  I'm wondering if there is a consensus on the precise meaning of topology in the genomics/Hi-C context.


texts: Do the centrioles in the centrosome differ in their angle to one another?

texts: The centrioles in the centrosome are often shown at an orthogonal angle, does this arrangement differ between samples, as in, does the daughter centriole show up in different sides of the mother centriole, or on the distal end rather than the proximal end?


texts: map list of proteins into an already built network

texts:
I have a built reliable network which can be downloaded from here
http://www.filedropper.com/mynetwork

This network is bulit using Cytoscape. Now I have a list of proteins IDs, for example

set1: Q9Y4Y9, P62310, Q9Y4Z0
set2: Q9Y333 ,P62312, O15116
set3: Q9Y4Y9, P62310
set4: Q9Y4Z0, Q9Y333, O95777, P62312
set5: O14497, P51532, Q8TAQ2, Q92922, P60709, O96019

I want to know if it is possible to map the above IDs to the built network? I don't mind using another algorithm, or software , only the result is important

Thanks


texts: How did mitochondria make energy long ago?

texts:
I've learned that mitochondria is thought to have been eaten by a larger cell, resulting the mitochondria to be part of a bigger cell. Well, here's my Q. If you look at how mitochondria works, you find that in order to initiate the TCA cycle, you need to have pyruvate acid.

Then does this mean that when mitochondria was all by itself, there were pyruvate acid around it? I mean, isn't pyruvate acid a complex molecule, therefore, cannot be abundant??? How could this be?

Furthermore, if cell A swallowed a mitochondria, then that cell A should provide mitochondria with NADH and pyruvate acid. How could this be? Did ancient cells produce NADH and pyruvate??


texts:
What causes the trees to develop gnarls? I can't find anything on internet other than dictionary definitions.

Are they caused by a mold, like the burls?


texts:
I am studying copy-number variation. I am reading

  C. H. Mermel, S. E. Schumacher, B. Hill, M. L. Meyerson, R. Beroukhim, and G. Getz, “GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers,” Genome Biol., vol. 12, no. 4, p. R41, 2011.

Here, it is written that

  Segmented copy number profiles represent the summed outcome of all the SCNAs [somatic copy number alterations] that occurred during cancer development. Accurate modeling of the background rate of copy-number alteration requires analysis of the individual SCNAs. However, because SCNAs may overlap, it is impossible to directly infer the underlying events from the final segmented copy-number profile alone.

It is not clear to me how a segmented copy number profile represents the summed outcome of all the SCNAs. Is it because different alterations can be present in the same sample, or can alter the copy-number in different moments, or both?

And, do they overlap spatially, temporally, or both?


texts:
The following questions were on the slides for my biotech course and I haven't been able to find any information on what the answer is.

What is the difference between Leloir and Non-Leloir glucosyl transferases?


texts:
I've been thinking about this question for awhile, since reading this question: What causes adenosine build up in the brain when awake?

We know that a couple of things will block adenosine receptors: caffeine and hops. If you're overloaded with adenosine and it's early in the day, coffee (or other caffeine sources) make you feel alert by tricking your brain by blocking the adenosine receptors. The dubious downside is that when it finally quits blocking the receptors, you've got a much bigger load of adenosine. Which might not be a downside if it means you fall asleep more easily and deeply.

But what about just clearing the adenosine?


texts: Has any large-scale origin-of-life simulation/experiment been done?

texts:
I have been thinking a little about the origins of life, and was further inspired by this question: How did the first self replicating organism come into existence?

I can accept that we don't quite know exactly how, but has any large-scale/long-term simulation been carried out?

There have been experiments but they seem to have been on a small scale. As an example, according to the Abiogenesis page on Wikipedia, some experiment which spontaneously formed peptide structures was carried out by Sidney Fox during the 50s and 60s.

What would be really interesting is if there had been some experiments or simulations carried out during a very long time, plausibly allowing for extremely low-probability structures to form. I doesn't matter whether this simulation/experiment has been carried out in a lab or as a computer simulation. There is of course the interesting but old "Conway's Game of Life" simulation, but according to my search efforts nobody has really tested it on a very large scale and in 3D.

Again, I'm looking for something extensive, like a decades-long single lab experiment or a simulation that has been run for years.


texts: Why is Silene virginica, colloquially known as Fire Pink, endangered in Florida? What factors besides human industrialization are affecting its survival there?


texts: What are the carbohydrates that are found in white rice?

texts: From this Wikipedia page on rice, it is mentioned that 100g of rice contains 80 g of carbohydrates, of which 0.12 g is "sugar" and 1.3 g is "fibre". I believe the "fibre" refers to dietary fibres that are not absorbed by the body and are just passed out of the body. However, I understand "carbohydrates" to be almost the same as "sugar" so what is the difference between the two terms as used in this context. I am guessing that "sugar" refers to simple monomeric units of carbohydrates while the rest of the "carbohydrates", excluding "sugar" and "fibre", is in the form of starch polymers, namely amylose and amylopectin. Could someone help to verify my understanding?


texts:
How is love induced between humans? Say, between mother and child, couples, etc.
Does the phenomenon of love exist in other mammals, too?


texts: What is the name of this green plant with thin leaves?

texts:
I've seen this in Scotland between Balmaha and Inversnaid:

A higher resolution is here: https://commons.wikimedia.org/wiki/File:Balmaha-Inversnaid-9.jpg

What is the name of this green plant with very thin leaves?
(I guess it was most of the time about 60cm high, but I don't quite remember)


texts: Besides hemoglobin, what proteins are present in red blood cells?

texts:
I knew that mature red blood cells (RBCs) lacked nuclei, but I wasn't aware until just now that they also lacked ribosomes and mitochondria. Most cells in the human body all contain a common laundry list of housekeeping proteins and RNAs (including mitochondrial proteins and ribosomal RNAs), but I guess RBCs lack a number of them. Do they still have all of the other organelles? Obviously hemoglobin (and to a lesser extent carbonic anhydrase) makes up a large portion of the dry weight of RBCs, but are other proteins still present? If so, what are their relative abundances?

For example, do red blood cells have any of the normal metabolic (i.e. ATP producing) proteins? Obviously they don't have any of the TCA cycle proteins, but do they still have the glycolysis ones?


texts: Why do we use DNA sequencing methods such as shotgun?

texts:
I am learning about DNA cloning for the first time. What I understand is that, in order to clone DNA, we break-up the original gene into shreds. Then try to piece it back together.

Why exactly do we do this? Instead wouldn't it be better to clone one base at a time? Basically in pseudo code:

old_dna_strand = 'ACTCATGCGAGCGTCAGTAGTACGTACTG'
new_dna = ""
for base in old_dna_strand:
    new_dna+=base

That looks a lot more easier and a lot less prone to errors. Why do we have weird methods such as shotgun?

Thanks in advance. Let me know if i should clarify or update anything in this question.


texts:
Why are special visceral efferent nerves are named as such?

They are supplying motor impulses to muscles of pharyngeal arch, which are both skeletal(facial) and visceral(laryngeal) 1, so why only visceral in name?
Why the name special?

I tried wikipedia but didn't find any information.


texts: Where in the body are self antigens important? In terms of central tolerance and autoimmunity, but also in terms of T cell activation?


texts: Coalescent theory - independence of coalescent times

texts:
Let $T_i$ be the time to coalesce from $n(t)=i+1$ to $n(t)=i$, where $n(t)$ is the number of sites that have not coalesced yet. In the below example the maximum $n(0)=6$.

As I understand it, many mathematical developments in coalescent theory depends on the fact that the random variables $T_i$ are independent (but not identically distributed). In other words...

$$f_{T_n, T_{n-1}, …. T_3, T_2}(t_n, t_{n-1},….,t_3, t_2) = \prod_{i=2}^n f_{T_i}(t_i)$$

What are the assumptions for this equation to hold true? Below are some suggestions

No selection
Selection is not varying through time
Stable population size
Random mating
Both sexes have the same genetic background
Both sexes have the same variance in fitness
...

source


texts: How would evolution explain parastitic wasps?

texts:
I read this article about wasps that can do "brain surgery" on cockroaches.
https://www.wired.com/2014/02/absurd-creature-of-the-week-jewel-wasp/

How does evolution create such a thing?

The brain surgery along with many of the other steps in the reproduction process seems to be very precise.  Any error here or there could lead to a bad result
Even if by happenstance the first wasp figured out a good way to do brain surgery, how would its offspring know to do the same thing?

Thanks.


texts: Gene duplication and subfunctionalization

texts:
I’ve been intrigued by gene duplication and want to learn more about it.

I’ve read the following from here:

  several studies suggest that the proportion of duplicated genes
  retained in vertebrate genomes is much higher than is predicted by
  this model [4-6]. This has led to the suggestion of an alternative
  model whereby complementary degenerative mutations in independent
  subfunctions of each gene copy permits their preservation in the
  genome, as both copies of the gene are now required to recapitulate
  the full range of functions present in the single ancestral gene. This
  was formalized in the Duplication-Degeneration-Complementation (DDC)
  model [7] in a process referred to as subfunctionalization.

Can someone explain this?  What is meant by “both copies of the gene are now required to recapitulate the full range of functions present in the single ancestral gene”?

Can you suggest any other good articles on gene duplication?


texts:
Today we found this kind of fish on the shore of Baltic Sea near Gdansk (PL). It is a very thin "fish" with some kind of a needle in place of nose. It was about 5 cm long and very lively. What is the name of the species?

PS. Kids caught it into a bucket just to take a pic - we released the creature just after the photo session :)