Effect and functional role of voltage-gated channels on dendrites I'd like to understand better the effect and functional role of voltage-gated channels on dendrites.

What I believe to have understood:

It is important that a more distal post-synaptical potential (PSP) arrives at roughly the same time and with roughly the same strength at the soma than a more proximal PSP generated at the same time (to give them comparable weights and to detect that they were synchronous). Let me call this the goal of adjustment.
Achieving this goal is the main function of (properly distributed) voltage-independent channels on dendrites (→ Rall model)
The main function of voltage-gated channels on axons is unattenuated signal transport.
Voltage-gated channels on the dendrite lead to non-linearities.

The immediate physical effect of voltage-gated channels on the dendrite is hard for me to imagine and understand. But even harder to understand are the (specific) functional advantages and disadvantages of those channels.

Some possibilities come to mind:

They allow to achieve adjustment better (more precisely) or in some other way more efficiently.
They allow to achieve other goals better or more efficiently (which are only poorly achieved without them).
They allow to achieve completely new goals which are not achievable at all without them (by having some magic computational powers due to non-linearities).
They may have disadvantages (which should not exceed there advantages, otherwise they would not exist), e.g. by distorting PSPs in an unwanted way.

I know that there is a lot of literature on the topic of dendritic processing, but not so many gentle introductions. A gentle introduction - answering some of the following question  - would be welcome. And of course immediate answers!

Do voltage-gated channels on dendrites (distributed as they are) allow to achieve adjustment better or in some other way more efficiently?
Which other goals do they allow to achieve better or more efficiently?
Which new goals do they allow to achieve?
Can their extra computational powers be pinned down?
Which disadvantages do they have (possibly)?

[I believe it wouldn't make sense to split this question into five: they are too strongly related, aren't they?]

As on axons, one immediate effect of voltage-gated channels on dendrites is the generation of spikes (called dendritic spikes as opposed to action potentials). These typically have higher local voltage thresholds than on axons. They seem to play a major role in long-term potentation. But it's not obvious for me how, and which other "implications in neuronal communication, memory, and learning" they might have.


Fertilization of an egg by two sperm What happens when two sperm fertilize an egg?  This can be either naturally or by experiment.

This phenomenon is called polyspermy and results in an embryo which is not viable. This is because it has more than the usual two sets of chromosomes (one from each parent), but one from the mother and multiple (depending on how much spermcells enter the egg) from the father.

To avoid this, most species (including mammals) have protective mechanisms against it. The so called cortical reaction which starts upon fertilization (the first sperm penetrating the zona pellicula) and releases cortical granules to prevent further sperm cells from entering.


Are releasing-hormones and release-inhibiting hormones from the hypothalamus ever present in the blood? Our teacher said that these two hormones are normally never present in the blood stream, and to be carfeul of it if it comes as a question. I'm not conviced to be honest, is this true?

I think your teacher means that these hormones only go from the hypothlamus to the anterior pituitary gland, where they stimulate hormone secretion. Like, for example, of the FSH or LH, who are stimulated by GnRH. GnRH is not present in the systemic sirculation, but it's definately present in the one between the hypothalamus and the APG. FSH and LH are though. I don't remember the name of the small blood-system between the hypothalamus and the APG, but I don't think it's connected to the systemic circulatory system.


What portion of America needs the Flu vaccine for herd immunity effects to become substantial? I've been looking at the effectiveness of Flu vaccines, which are in my subjective opinion abysmal, and the concept of herd immunity.  I see many articles which argue that we all need flu shots to help support the weaker individuals via herd immunity.  However, I see very few documents actually indicating how effective this process is.

Most of what I have found on the topic is interested in the Herd Immunity Threshold (HIT), which appears to be the point where vaccinations drive the Rq of the disease (reproductive rate in the presence of the vaccinations) below 1 such that the disease spreads to fewer and fewer people with each generation, like removing the heat from a fire such that it cannot sustain itself.

There are two particular aspects of this which I believe are required to answer the question which I cannot seem to find a good answer for, which have been preventing me from answering my question:

What is R₀, the basic reproductive rate, for influenza?  I have seen estimates ranging from 1.2 to 3.  As best as I can tell, even a poor vaccine would be very effective if it was 1.2 but it seems like it would do very little against the higher R₀ values.
How substantial of a knee in the curve is there regarding the number of immunized individuals vs. the herd immunity effects?  If there is no substantial knee in the curve, that should indicate that there are valid herd immunity arguments for influenza even if the vaccines are substantially ineffective.  If the knee in the curve is sharp, then herd immunity arguments would only be valid if we could reach that threshold.

It appears some of these questions may have been answered in "The vaccination coverage required to establish herd immunity against influenza viruses" by PedroPlans-Rubió in 2012, but I do not have any access to Preventive Medicine, the journal it was published in.

Quoting Jhung et al. 2011 talking about H1N1 2009 epidemics

  Although estimates of R0 from past pandemics vary, the R0 of previous pandemic influenza viruses generally range from 1.5 to 1.8 for the 1957 H2N2 and 1968 H3N2 pandemic viruses, and 1.8–2.4 for 1918 H1N1 influenza A strain, with a high estimate of 5.4 by Andreasen et al [see also White et al]. During the current pandemic, White et al used CDC case-based data from 1368 confirmed and probable cases with a date of report on or before 8 May 2009 and estimated the reproductive number of pH1N1 virus to be between 2.2 and 2.3. Estimates decreased to 1.7–1.8 after adjustment for increased case ascertainment during the initial pandemic period. In a sensitivity analysis making use of previous estimates of the mean serial interval, White et al estimated that the reproductive number was between 1.5 and 3.1. Fraser et al used data from the initial outbreak in Mexico to estimate R0 in the range of 1.2–1.6. Yang et al used reported case clusters in the United States to estimate R0 to be 1.3–1.7. Most estimates of R0 for pH1N1 virus, therefore, have indicated that the virus was at the low end of transmissibility, compared with the strains that caused the 1918 pandemic, and was comparable to or slightly less transmissible than the strains that caused the 1957 and 1968 pandemics.


How many times has SARS-CoV-2 mutated? According to

Coronavirus has mutated at least once

  The novel coronavirus that has infected thousands of people across the
  world may have mutated at least once — meaning there may be two
  different types of the virus causing illnesses, a new study conducted
  by Chinese scientists suggests.

  Scientists with Peking University’s School of Life Sciences and the
  Institut Pasteur of Shanghai in a preliminary study found that one
  strain — type “L” —  of the virus was more aggressive and accounted
  for about 70 percent of the strains analyzed. The second — type “S” —
  was less aggressive and accounted for about 30 percent of analyzed
  strains.

But also several webpages theorized the virus has mutated before passing from animals to humans.

This page What we know about the Wuhan virus says

  This virus belongs to a family of viruses known as coronaviruses.
  Named for the crown-like spikes on their surfaces, they infect mostly
  bats, pigs and small mammals. But they mutate easily and can jump from
  animals to humans

and

  Where did the new coronavirus come from? The new virus likely came
  originally from bats, scientists say. It isn’t known exactly where or
  how it jumped to humans, though. Viruses from bats often infect
  another mammal first and then mutate to become more transmissible to
  humans.

though

  Coronaviruses can also jump directly to humans, without mutating or
  passing through an intermediate species.

Is something more known about this? Is it possible the virus has mutated twice in a period of time of months?

This question makes a number of incorrect assumptions and I don't have time to correct them. The short answer is that the virus has mutated probably hundreds of times since it entered humans in late 2019.

The lower figure on the NextStrain.org ncov page, "Diversity", shows the known mutations that have been identified so far. As I look at it now, there are maybe 100-200 shown there, but that will change daily and I can't be bothered to count them.

Is it possible the virus has mutated twice in a period of time of months? Of course it is. That's what we expect from coronaviruses. It would be shocking if it did not.

The default assumption (based on a vast amount of experience with coronaviruses and many other viruses) is that these mutations are neutral and do not affect the virus in terms of fitness, virulence, or transmissibility in any way; they are occasionally useful in tracking sources, but unless you have spent a lot of time looking at virus phylogenetic trees for several years, your interpretations of these mutations are almost certainly wrong.

An example of people making claims based on unfamiliarity with virus evolution is the "two different types of the virus" claim. That claim is addressed by MacLean and colleagues in their Response to “On the origin and continuing evolution of SARS-CoV-2”. Summary:

  Two of the key claims made by this paper appear to have been reached by misunderstanding and over-interpretation of the SARS-CoV-2 data, with an additional analysis suffering from methodological limitations


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

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

YouTube of the sea sponge I'm talking about.

yes choanocytes handle the bulk of sponges digestion and transfer nutrients to other cells. in some species Amebocytes also perform a similar function.


Presence of MHC on red blood cells Do red blood cells have no MHC? (I have often heard that they do not.)

If so why are they not destroyed by immune cells?

They do not, at least not normally or noticeably.  MHC I occurs on all nucleated cells, and red blood cells do not have nuclei.  If they did indeed have MHC on them, blood transfusions would be as successful and as tricky as organ donation.  There are reports of MHC detection on red blood cells, but the amount is orders of magnitude smaller than elsewhere, only present for certain MHC alleles, and often transient.


Does opening the lid of the spectrophotometer affect my results? If I'm performing an experiment using a spectrophotometer and I mistakenly forgot to close the lid on the spectrophotometer, would that affect my results?

It depends on the construction of the spectrophotometer, the wavelength of light you're detecting, and the sensitivity/accuracy that you're demanding of the result.

In the past I have used spectrophotometers which were completely missing their sample lid, with no appreciable detriment to the result. Several things were in my favor, though. The light path from the sample to the detector was suitably collumated, such that any light that wasn't coming from the sample was blocked. I was attempting to detect far UV wavelengths (e.g 260 nm), for which there is little to no ambient source - attempting to detect a wavelength at the peak of a fluorescent light wouldn't have been as successful. I also didn't need highly accurate results, and I was able to dilute my sample such that it fell within a region (~50% absorbance) that is least sensitive to small changes in the amount of light being received.

In your case? If you can retake your measurement "properly", then I'd recommend doing so. If not, you can run some tests (like user aaaaaaa suggests) with some other similar sample, seeing if the absorption readings for that wavelength are affected by having the lid open.


Can stem cells from male convert to cells of female-only organs, and vice versa? As we know, stem cells can convert to different cells of other organs, can male use their own stem cells to convert it into cells of female-only organs(and vice versa)?

I am assuming you are talking about embryological stem cells and embryological development of genitalia.

The answer is no.

Male stem cells have XY chromosomes. Y chromosome is the sex determining chromosome with SRY gene that determines testes development. Absence of the Y chromosome leads to female development by default. That is why XX forms women and there are people with only one X chromosome which are women. (Turner's syndrome)

It might be possible that SRY gene undergoes a mutation and the gene isn't expressed. There are Y chromosome linked diseases.

You should read up about Y chromosome and development of genitalia.

https://en.wikipedia.org/wiki/Y_chromosome
https://en.wikipedia.org/wiki/Development_of_the_reproductive_system


Calvin cycle:synthesis of glucose For synthesis of one molecule of glucose,six turns of calvin cycle are required.

One molecule of carbon dioxide combines with ribulose bisphosphate (RuBP) to form a stable product of two molecules of phosphoglycerate (PGA). This is called carboxylation. Then 2 molecules of PGA undergoes reduction to form 2 molecules of phosphoglyceraldehyde (PGAL).

My question is whether there 2 molecules of PGAL goes in the regeneration of RuBP or in the synthesis of glucose.

The quick answer is "both", but the stoichiometry is not 1-to-1. The stoichiometry of the calvin cycle doesn't add up when thinking about a single molecules making one "turn" of the cycle. There is only one carbon (CO2) added, but three carbons (in PGAL) leave, which obviously cannot work.

What's happening is that multiple molecules are processed at the same time. The cycle is of course just a set of enzymes that continually catalyze their reactions, so there are always lots of molecules available for enzymes act on, and the cycle doesn't "get stuck" just because things don't add up in a single turn. The "regenerating" steps between PGAL and RuBP produce 3 molecules of RuBP from 5 molecules of PGAL (15 carbons total). Carboxylating these 3 RuBP molecules adds 3 carbons, so that one PGAL molecule can leave the cycle.

The reason for this odd stoichiometry is that the cycle needs to turn 3-carbon sugars (PGAL) into 5-carbon sugars (RuBP), which is rather complicated. Several enzymes work together in a complicated series of reactions to achieve this. A good resource for learning about the details is the MetaCyc database, where you can explore all the molecular details of the pathway.


Do animals suffer from "Human" mental disorders? It is tragic, but apparently Killer whales and Dolphins can commit suicide too (e.g. here)...

This suggests they can become depressed. I wondered whether they were "clinically" depressed like many people are, and what other mental illnesses have been observed in animals in general.

Questions

Which mental disorders have been observed in animals? Which animals?
What is the prevalence of these mental disorders in those animals?
Are the causes and treatments of these disorders similar to Humans?

Strange thought

Organisms that have not evolved the ability to make "conscious choices" cannot decide to end their life.

You will be hard-pressed to find any scientific data on this question. Psychology in humans is already a difficult study, at times failing to demonstrate results with real scientific rigor. When studying animal psychology, you face another substantial barrier - language. Although some primates have been taught to communicate with sign language, the best of them are still far from the level of proficiency of a human. We can measure brain activity and observe behavior, which can lead us to strong suspicions about what is going on in an animal's mind, but very little can actually be proven.

Mostly, all we can do is speculate about such questions. You will find some veterinarians out there who treat pets for mental conditions, but you will find at least as many people calling them quacks as those who believe in the validity of their work. And certainly, they can't prove to you that a treatment has helped an animal. It's subjective.

If we see an animal do something which in a human might reliably be interpreted as a sign of depression, it's possible that this interpretation is appropriate for the animal as well. It's also possible that there is some totally foreign unrelated explanation. The problem we find when trying to scientifically discuss matters which cannot be proven scientifically is that scientists must be careful to state what they know and nothing more. So they might say "We cannot prove that the porpoise is depressed", or "Science cannot prove the existence of a God." This is often misinterpreted as evidence against the finding - that the porpoise is not depressed; that there is no God. This is a fallacy. Rather, we should recognize that we have different ways of exploring questions like these.

I can't prove it to you, but I know that my Beagle had a rich emotional life. I know this because I spent huge amounts of time with him. He was a close friend of mine. I would just as soon question whether my wife has real emotions as my dog. I can't prove that my wife's emotions are real either, but I don't have to. It would be silly to assume that everything she shares with me is some sort of evolutionary programming, and not real emotion. Now, when I extend this to cetaceans, I must admit that I don't have any friends in those circles. So I can only guess.


How does axon guidance system precisely targets specific axons? Axons find their way to the terminus by responding to axon guidance molecules (AGMs) that attract and repel growth cones or make them stir. This I understand.

Through a very specific combination of AGMs, a precise path can be layed out that an axon cone will follow even across half the brain. This I also understand.

What I don't understand is that in developing brain, there are millions of axons moving to their termini at the same time, and millions of AGMs released all over the brain. When an axon departs on a journey to reach an AGM at the opposite end of the brain, it will probably pass by thousands of other AGMs and yet ignore them all.

When an AGM is released, there are like thousands of neurons nearby, and yet they all will ignore it but some single neuron across the brain will reach for it.

I can think of two possible explanations:

There are unique AGMs for every neuron that no other neurons will
follow (but it doesn't seem to be the case).
There are somehow very specific instructions wired into EACH neuron aka ignore five netrins, then follow the sixth, then ignore two more, and then follow the ninth one till you reach it (but how is it possible to program every neuron in the brain like that?).

So, how does it work in reality?

In a nutshell, I would say neurons do have "specific instructions."  However, it isn't so much "ignore netrin X amount then stop."  It's more like "express receptors 1, 30, 48, and 62" which as a unique combination gets the growth cone where its going and prevents it from forming an erroneous connection along the way.  I've provided more context below that might help this make more sense.

A number of factors come into play with proper axon pathfinding and guidance, but I think the two below are sufficient for this:

There are different receptors present or absent on the cell surface depending on what cell type it is, which allows different cell types to respond only to specific cues. However, most developing axons express multiple types of receptors, so they can respond to multiple guidance cues (or respond to a cocktail of different cues).
There are non-diffusible signals present along the path in which the axon is growing.  You can read about one type here: https://www.nature.com/articles/nn.2231.  The main point about non-diffusible cues is that they can either stabilize the growth cone (which might promote growth or initiate the formation of a synapse) or they can repel the growth cone.  Therefore, they play an important role in informing the growth cone what is and is not the proper target.

There are now two things from your question should bring it all together.  First, you state that the precise path comes from a "specific combination of AGMs."  Exactly! The key word here is "combination."  Because there are so many AGMs that can affect the growth cone in so many ways, the combination of receptors (and intracellular secondary messengers) expressed on the growth cone and how they work in concert is what's critical.  Second, you state that growth cones will "ignore" potential targets as they pass them by.  That might sort of be the case (i.e., if a growth cone doesn't have a receptor for something the target is expressing, it won't "grab onto" or respond much to its presence).  However, it may also be that these potential targets express some non-diffusible cue that repels the growth cone, and it doesn't recognize that spot as a its final destination.

This article can also help provide more insight on the nuances of axon guidance:  https://dev.biologists.org/content/145/10/dev151415.long


Is there any free software similar to CellDesigner that allows me to represent large networks of biochemical reactions in the human body? I continually have to review multiple articles, in multiple journals. These articles present how various enzymes, proteins, lipids, carbohydrates, etc. intervene in the processes that lead to certain pathologies (generally neurodegenerative). I have used Celldesigner and Freeplane, but Freeplane is very general software and CellDesigner provides reduced work spaces. I would like to know if there is any other free software that works for this purpose (I usually work in Linux).

Here is a list of such programs. It is an old post but most of the tools it lists appear to still be functional. I found this by just googling "celldesigner alternatives", which is always a good idea to search first for these things.

I have used cytoscape and it is ok, maybe too general also for your purposes. For very simple purposes I have used KEGG pathway in the past, which is in addition to the others.


How can I align more than 2 sequences locally? ClustalW and Omega of EBI and Blast of NCBI, both globally align sequences. Smith waterman of EBI aligns sequences locally, but works with just two sequences. How can I align more than 2 sequences locally?

You have to do it pairwise (there is no other option).

You can do that with BLAST or even SSEARCH (Smith-Watermann). If you have a fasta file of your sequences then do this:

make index of your sequences using makeblastdb -dbtype nucl -in <yourfastafile> -out <yourdbindex>
Run BLAST with your <yourfastafile> as input and <yourdbindex> as database with desired parameters. This will do a pairwise alignment between all sequences

Similar strategy can be used for SSEARCH.


Fastest observed biologically evolution rate? Fastest possible evolution rate?

What is the theoretically quickest evolution rate?

For example, I could calculate this as the number of offspring an E. coli colony can generate at once * (time frame/time per generation) * mutations per generation, and then assume every organism on earth had this same evolution rate.

Is there a generally accepted value, perhaps based on mass of organism?

Theoretically, it really depends how crazy you want your model to be! Also it depends what you mean by "evolution rate".

Let's consider a very simple and quite crazy model. Let's assume that by evolution rate you mean the difference between mean phenotype between one generation and the next. Let consider a trait (which heritability is $h_N = 1$) which takes only two values $x_1$ and $x_2$. In a given generation, half the individual carry the trait value $x_1$ and half the trait value $x_2$. If the relative fitness of $x_1$ and $x_2$ are 1 and 0 respectively, then the evolution rate is simply $| \frac{x_2 + x_1}{2} - x_1 |$. Allow $x_2$ and $x_1$ to be very big values and the rate of evolution will be very fast. In the most extreme case, $x_1 = \infty$, then the evolution rate is simply infinite.


Creative ways to deactivate alpha-amylase taken from fungi I can deactivate $\alpha$-amylase in ways such as extreme temperature controls, pH controls of the solution it stays in, or adding salt to the solution.

However, are there any other unique or elaborate ways to deactivate the enzyme? (maybe the lock-and-key hypothesis also works for enzymes AND enzymes?)

Amylase inhibitors have attracted much attention because of their potential in treating type 2 diabetes.

You can inactivate most enzymes by using a specific inhibitor. One class of inhibitors consists of molecules that resemble the substrate molecules but are not acted upon in the same way. These will bind to the active site and will prevent the substrate from binding. An inhibitor of many amylases is acarbose. This is a competitive inhibitor which means that inhibition is overcome by high concentrations of substrate.

And if that isn't enough to get you started here is an entire thesis on the topic of amylase inhibitors.

If you want to permanently block activity the ideal compound would be one which binds to and covalently modifies the active site, destroying enzyme activity. This would be an irreversible inhibitor. I haven't been able to find a reference to such a compound however.


DNA Structure and Function In a strand of DNA, why does identifying the 3' side and the 5'side matter? Or the 3' --> 5' strand and the 5' --> 3' strand? Also, what is a single strand of DNA called, is it just a helix, or is the helix just the backbone?

A double strand is a helix, as the basepairs move with a horizontal angle with each step to the next basepair. Identifying the sides is important for DNA-replication and RNA synthesis as the way DNA is read is from 3' to 5' so that the complementary bases can be ''glued'' together from 5' to 3' in which the phosphate groups bind to the OH groups of the other molecule by a polymerase reaction.
Disregard first answer.

There.


How does the body make sure that Vasoactive Intestinal Protein reaches only the target tissue? Vasoactive Intestinal Protein (VIP) is a 28 amino acid neuropeptide that has several effects in several systems. These include the cardiovascular system, respiratory systerm, urinary system, immune system, etc. Furthermore, some of the effects appear to clash with each other. For example, studies have shown that VIP can have an antidipsogenic effect, while some have shown that it induces the secretion of vasopressin. Vasopressin is usually secreted when there is not enough water in the body. Thus, it seems contradictory that the hormone would induce cessation of thirst and secretion of vasopressin.

The hormone is  a paracrine mediator. This makes sense since limiting the distance that VIP travels allows for the hormone to only reach the intended tissues. However, it is also a neurohormone. Which means that it travels through blood and I would assume that it causes a myriad of effects. My question is, how does the body make sure that VIP does what is intended to do?

Vasoactive intestinal peptide (VIP) acts in the intestine, brain, kidneys, lungs, heart, blood vessels, etc. (Cardiovasc Res) and its effects all lead to the same goal: to improve the delivery of blood, glucose and oxygen to the tissues, so it's not a problem if it acts on different tissues simultaneously. Specifically, VIP stimulates thirst, water retention and blood flow through the coronary and pulmonary arteries, dilates bronchi and breaks down glycogen to glucose, among other.

VIP can act via the nerves as a neurotransmitter or via the blood as a hormone:

  In research animals and in humans, VIP, administered into the coronary
  artery or intravenously, increases the epicardial coronary artery
  cross-sectional area, decreases coronary vascular resistance, and
  significantly increases coronary artery blood flow. High frequency
  parasympathetic (vagal) nerve stimulation also releases endogenous VIP
  in the coronary vessels and heart and significantly increases coronary
  artery blood flow. (Cardiovasc Res)

In humans, VIP stimulates water retention and thirst:

1) VIP stimulates the secretion of renin:

  VIP has now been shown to produce an increase in renin release in a
  number of species, including humans. (Ann N Y Acad Sci)

The activation of renin-angiotensin-aldosteron system results in water retention.

2) VIP stimulates the secretion of vasopressin (Cardiovascular
Research). Vasopressin stimulates water retention. Since vasopressin (arginin-vasopressin or AVP) is dipsogenic (stimulating thirst):

  given the established dipsogenic effect of AVP in the nonpregnant
  state... (JCI Insight)

and since VIP stimulates the secretion of vasopressin, VIP is also dipsogenic.

Now, there seems to be some conflict in the studies about VIP being dipsogenic or anti-dipsogenic in rats:

  VIP was found to have no effect on drinking when injected centrally
  and peripherally in the eel, although it is dipsogenic in the rat
  after central injection. (ResearchGate)

  Intracerebroventricular administration of vasoactive intestinal
  peptide strongly inhibited drinking in rats deprived of water...
  (Neuropharmacology)

Not to go in the details, but there may be different circumstances, for example, the level of dehydration, in which VIP can act differently...


What is this animal that hides in dustlike structure? I'd like help identifying the species of animal in these two photos. There's some dust(or dust-like substance) with something alive inside of it (possibly a larva or I don't really know what to call it). This appeared in a couple of hours in the wall. Please, try to even just guess what this could be (I can't think of anything!). Very odd...
I don't even know what tags I hsould use for this!

Thanks in advance

new photo

This is likely a case-bearing clothes moth (Tinea pellionella).
Though more information and a better image would aid in confirming that to be the case.

Here are some pictures:


Can radiation equilevant to 1 CT (computer tomography) scan causes significant changes in human body? I've read that CT scan causes radiation equivalent to few hundreds of ordinary X ray scan. It sound scary at the first look of it but I wonder is it the amount considered significant? Can dosage equal to the 1 CT scan significantly increase chance of developing cancer or other adverse effects?

As a rule of thumb you can say that a CT scan exposes you to a higher dose than a X-ray examination, due to the different techniques. For CT scans a number of single 2D photos is processed into the 3D models. However, the dose strongly depends on what body part is examined. See a part of this table (the complete table can be found in reference 1):

The additional risk for most examinations is low to very low and since we don't get x-rayed on a daily basis this is a risk which can be tolerated. Besides this, there are other exposures to radiation which also accumulate, but where people usually don't hink about it. These are for example smoking and flights at great altitudes. See the answer from @anongoodnurse for some more details on this.

References:

Radiation Dose in X-Ray and CT Exams
The 2007 Recommendations of the International Commission on
Radiological Protection
AAPM Response in Regards to CT Radiation Dose and its Effects


Transformation efficiency I accidentally spun down the cells after heat shock treatment before adding the media into the tubes while doing transformation? will the transformation work?

This is hard to answer since we don't know the exact conditions you chose, as these are rotation speed (or better g), how long you spun them down and also if you used a cooled centrifuge or not. It's also important how gentle you resuspended the pellet.

However, I would plate these cells, no matter what happened since you are at the last step of the procedure and have nothing to loose. Do the usual dilutions you use for plating your cells and then add another plate with undiluted transformation mix. If you have only very few surviving cells after your mistake you might get your clones on this plate. If it doesn't work, you will have to repeat the transformation.


Mathematical Biology Jobs/Prospects? I'm a junior math major starting to take his first courses in Algebra, Analysis, Topology, Nonlinear and Partial Differential Equations, etc.

I am just considering my career options at this point and somebody told be biotech/biology could have some interesting work. So I have come here to hear some advice if that is okay! Is there anything highly mathematical about the search for anti-aging or achieving the whole "biologically immortal" thing? I just don't know about any of this stuff so please inform me :)

PS: I also know Prob/Stats at a decently advanced level. So there's that too. Thanks!!

Off course you can! Here are career paths for you as per my limited knowledge:

BioStats

There are lot of applications in this domain. For example in Microarray Gene Expression or Proteomics analysis (for example, this paper).

Bioinformatics

Sequence alignments use common techniques like Dynamic Programming, Probabilistic or Heuristic methods, etc.

Computational Biology

There are lot of applications like Lagrangian and Eulerian Mechanics (Computational Anatomy), Computational Phylogenetics (Computational Evolutionary Biology), etc.

Systems Biology - In Systems Biology, you can have applications in:

1-) Probability and Hypothesis Testing - usually used to find associations between genes (Ref: S. Krawetz (ed.), Bioinformatics for Systems Biology, DOI 10.1007/978-1-59745-440-7_8, Chapter 8)

2-) Stochastic Modelling of Biological Patterns - ODEs,PDEs (applied to lot of problems), Markov Chains, HMM, PSSM are common mathematical implementations in this domain.

3-) Population Genetics - uses Statistical models (for example Genetic Distance), exponential equations (for example, Cumulative Effect of Mutation)

P.S: Here are some tools you might be interested in:

1-) Bioconductor - one of the main reasons why R is preferred language by BioStatisticians.

2-) BioPython

Wish you best of luck with your career!


Explanation of ECG in MI using an electrostatic model I found a paper presenting an electrostatic model to explain the ECG recorded in various leads. This model essentially calls for considering the depolarization wavefront to be the major contributing factor to the potential difference measured at the leads, especially the limb leads, by means of an aggregation of momentary dipoles with dipole moments organised according to the direction of propagation. It is also used in this book here, under the ECG section under Measurements of cardiac function.

The paper does not explain the observed ECG deformities in case of MI in detail. ST elevation, is a common finding in most MI cases. How do we explain this in light of the aforementioned model?

My thoughts

In the normal case, ST segment is isoelectric, as there is no depolarisation/repolarisation wavefront propagating. How is this isoelectric nature compromised in MI? Assuming most infarcts include muscle death or damage due to focal insufficiency of coronary circulation, even if a region of heart was dead, during the ST segment, the graph should show an isoelectric line (no deflection) as the living tissue will either be depolarised or polarised, (but not switching states) and the dead tissue will have either a completely obliterated membrane polarity or an altered polarity throughout the cardiac cycle. In any case, no part of the heart will be switching its polarity then. Why is then, some resultant dipole (which indicates a propagating wavefront of altering polarities)obsereved during the ST segment?

  alternative model
   To explain the elevation, this book (pg 522) provides a two cell model, and explains that the anoxic damage somehow
  causes the basal depolarised state of the cell to have a lower
  membrane potential difference, which causes all the segments of the
  ECG except the ST segment to be lowered, making the ST segment appear
  raised. I don't understand three things regarding this explanation.
  How will anoxic damage cause such a specific alteration in the polarity and the subsequent action potential? How can this two cell
  model be extrapolated to the whole heart with a focal infarct? How
  does this explanation be reconciled with the model presented at the
  head of the question?

Let me know if the question appears too broad and needs to be split, or if my assumptions are wrong in any way.

MI-Myocardial Infarction

PS:-  I seem to have lost the touch with the formatting on this site, and hence don't know which tags to use. Will take some time to get back :)

The concentration of K+ inside the cell is 30 time more than outside. Hypoxia causes loss of this intracellular Kalium and consequent/premature repolarization when measuring the potential of action.

As the all the ECG theory is Vector based, any abnormality in the electric pathways and myocytes will result in changes of ECG.

This picture depicts the ST changes due to different extension of injury. In addition, the explanation on this site will probably resolve the issue of understanding.

ADD

The article explains the ECG phenomena as a result of electric propagation of dipoles. If the dipoles propagate towards the lead we get upward wave etc.

As the electrostatic model takes the whole heart as one dipole (as a sum of multiple dipoles) the minor infarcts can be missed on ECG. It is an actual fact, this is why other tests are important (for example, the troponin test).

The confusion point in your understanding is a "dead" tissue. In a case of infarct there is an hypoxic damage which leads to elevated permeability of the cell membrane with resulting K leak (as I explained above there are 30 times more Kalium inside the cell than outside). This means that "dead" area will have abnormal depolarization/repolarization pattern just because there are multiple "non grouped" dipoles in that area (look at the picts). There are diastolic and systolic theories of ST elevation, but none of them has won the battle yet.

With time the scarring tissue replaces the infarcted myocardium and in that case the ST-segment will not be affected and will look nearly normal. This is the case you meant as "dead" tissue - scar tissue does not leak any electrolytes and consequently the ST segment is not affected in a chronic stage.


Macrophages and what they consume Do macrophages in the dermis consume any foreign invader to the body, or simply pathogens and cellular debris?  For example, would macrophages consume vitamins or medications injected into the dermal layer of the skin?  Thank you

Macrophages and dendritic cells generally recognize large foreign complexes. They often do this through the recognition of pathogen or damage-associated molecular patterns (PAMPs or DAMPs). Otherwise, cell-mediated pathways involve cyto/chemokines which direct macrophages and the like in the region. We also have to consider, does the compound in question belong in the region, or is it insoluble amongst the tissue? In these cases, the compounds are also degraded/engulfed. So how does the body go about recognizing small, soluble foreign molecules?

These are called haptens. If these small molecules can bind to a larger carrier complex in your body, so that it now looks like there's something foreign, regardless if the initial carrier complex was foreign or not, this may present cause for immunologic reponse (as in the mechanism of urushiol, the toxin in poison ivy). There are certain T-cells, like NKT and γδ T cells, which can "see" these antigens despite their lacking a type I or II MHC presentation.

The short answer is it depends on what the injected drug does once it begins interacting with your physiology. Vitamins, on the other hand, are regularly uptaken by cells for metabolism, and I wouldn't imagine macrophages engulfing exogenous vitamins outside of it's needs on their own.

Source: Cellular and Molecular Immunology, 8th ED.


Development of radial symmetry in starfishes and other animals How does nearly perfect radial symmetry arise in an animal like the starfish? My confusion lies in the fact that cells are fluid & amorphous, & that these characteristics seem to make it difficult to form symmetric structures. Many of the sources I've read describe the formation of the blastula but not the development of the five arms following that. Also, at one point in the development it is bilaterally symmetric. Furthermore, some species of starfish can regrow from a single arm.
What process mediates the formation of radial symmetry in a developing organism? Is it that arms grow individually & there are cascades of cellular signaling that mediate the production of new arms until the desired amount is reached or is it something else? How do the arms of the starfish remain evenly spaced?

That is the field of developmental biology which deals with organizers. Cell organizers are processes, genes and signalling proteins cells use to communicate / send and receive information from their neighbors, so that their spacial distribution in the body regulates their development.
The cells also have gradients of signaling proteins inside the cytoplasm, and cell polarity, so the cells know which way round they are:
"A spatially distributed signalling cascade can create step-like activation profiles, which decay at successive distances from the cell surface, assigning digital positional information to different regions in the cell. Feedback and feedforward network motifs control activity patterns, allowing signalling networks to serve as cellular devices for spatial computations."
All metazoans use the same types of organizers to develop different patterns of cells, so starfish use the same genes as mice to organize their axes. They are early metazoan genes/ Precambrian. Here is an in depth answer to your question: www.ncbi.nlm.nih.gov/pmc/articles/PMC5307799/
The cells know where they are, because they are receiving multiple signalling proteins from further away in the animal. Here is a picture of Bicoid morphogen in fruitflies:
The signalling proteins are received from cells far away, and that signals to other cells to make different kinds of signalling proteins to organize the local neighbors.

Given the complexity of metazoan morphogenesis, there are very many organizers and we only know a few of them. The axis formation is related to the Nodal gene which uses some kind of axial/mid-line located organizers to control symmetry, there are documentd about LRO: left right organisers, in starfish its the same chemistry in a different geometry. The Nodal biochemistry: https://youtu.be/kO8k9aiQJsQ?t=189


How do you differenciate between the eukaryotes and prokaryotes? I wonder how we differentiate between the eukaryotes and prokaryotes.

Eukaryotes:

  Eukaryotes (also spelled "eucaryotes") comprise animals, plants, and
   fungi—which are mostly multicellular - as well as various other groups
  that are collectively classified as protists (many of which are
  unicellular).

Prokaryotes:

  Prokaryote (also spelled procaryote) comprise any organism that lacks a
  distinct nucleus and other organelles due to the absence of internal membranes. Bacteria are among the best-known prokaryotic organisms.
  The lack of internal membranes in prokaryotes distinguishes them from
  eukaryotes.

Isn't there any other method to know what organisms are eukaryote or prokaryote?

There are lots of ways to distinguish between eukaryotes and prokaryotes, as listed by microbiologynotes.com:

Difference:             Eukaryotes:                Prokaryotes:
-------------------------------------------------------------------------------
Size                    > 5µm                      1-2µm by 1-4µm
Nucleus                 Nucleus with nuclear       No true nucleus; nucleoid
                         membrane
Complexity              Usually multicellular      Unicellular
Chromosome              Multiple linear; histones  Usually single circular;
                                                    no histones
Cell Division           Mitosis, meiosis           Binary fission
Reproduction            Involves meiosis           No meiosis
Zygote                  Diploid                    Merozygotic
Genes                   Expressed individually     Operons
Gas vacuoles            No                         Possible
Mesosome                Yes                        No
Ribosome                Found on membranes         Distributed in cytoplasm
Mitochondria            Usually present            No
Chloroplast             Possible                   No
Cell wall               Simple if present          Freq. present, complex
Endoplasmic Reticulum   Possible                   No
Golgi apparatus         Possible                   No
DNA usage               Transcription in nucleus,  Transcription at the same
                         translation in cytoplasm   time as translation
Duration of cell cycle  Usually long (hours)       Usually short (<1 hour)

N.B.: I have used the list on microbiolgynotes only as an outline, editing as needed.  For instance, Mitochondria is not necessarily present in eukaryotes, neither are chloroplasts.  Also, I have not included everything, since I do not presently have the time to verify everything.


Are there parasitoids of mosquitoes ? (other than nematodes) Outside of nematodes, are there any examples of organisms that are parasitoids of mosquitoes ?

I could not find any example in literature so far. I'm notably interested to know if the most known mosquito genera (Aedes, Anopheles, Culex...) have already been described to be parasitized by other insects (e. g. parasitoid wasps), and if this is a common phenomenon in nature.

It happens I just found an answer to my question in a recent review book by George Heimpel and Nicolas Mills. It appears that for now we do not know any  parasitoid of mosquitoes.

Quoting chapter 1 :

  "Most insect herbivore species are attacked by
  one or more parasitoid species, but some major
  arthropod pest groups appear to be entirely free
  of parasitoid attack. For instance, we know of no
  parasitoids that attack mosquitoes or other biting
  flies with aquatic larval stages, and no parasitoids
  that attack phytophagous mites or adelgids."

Source:
Heimpel, G., & Mills, N. (2017). Definitions and Interactions. In Biological Control: Ecology and Applications (pp. 1-18). Cambridge: Cambridge University Press. doi:10.1017/9781139029117.003


How to do desalt reaction by passage through a Micro Bio-spin 6 column? I want to perform the bisulfite sequencing on rRNA to detect the 5-mC. I followed this protocol

•    DNA-free™ DNA Removal Kit (Invitrogen)
•    Purified RNA, Treat RNA according to manufacturer's instructions.

Adjust DNAse-treated RNA to a volume of 10 μl.

2.Sodium Bisulfite Treatment of RNA EpiTect Kit (Qiagen)

•   DNAse-treated RNA preparation
•   PCR thermal cycler
•   Micro Bio-spin 6 columns (BioRad)
•   GlycoBlue coprecipitant (LifeTechnologies)
•   Cooled microcentrifuge

3.Transfer DNAseI-treated RNA solution into a PCR tube.

Add 42.5 μl freshly made bisulfite solution (EpiTect kit) and mix thoroughly by pipetting.
Add 17.5 μl DNA stabilization solution (EpiTect kit) and mix thoroughly by pipetting.
Place samples in a thermal cycler and run the following program to deaminate RNAs:

•   70 °C: 5 min
•   60 °C: 60 min
•   Repeat steps (i) and (ii) two to six times (depending on target RNA abundance and predicted secondary structures)
•   25 °C—hold

7.Desalt reaction by passage through a Micro Bio-spin 6 column according to manufacturer's instructions.

Add 1 volume (70 μl) of 1 M Tris–HCl (pH 9.0) and incubate at 37 °C—30 min for desulfonation.

9.Precipitate RNA by adding sodium acetate (pH 5.2) to 0.3 M, 15 μg GlycoBlue coprecipitant and 3 volumes of 100% ethanol and incubate at − 80 °C for ≥ 1 h.

10.Pellet RNA by centrifugation at 4 °C for ≥ 30 min at top speed.

11.Wash RNA pellet with 75% ethanol.

12.Air-dry ≤ 5 min at room temperature.

Store deaminated RNA pellet until further use at − 80 °C.

In the step-7 I got stuck. i do not know whether do I have to use flowthrough or do i have to elute from the column.

Ref. https://www.sciencedirect.com/science/article/pii/S0076687915002335?via%3Dihub

Maybe you can take a look at this. I found it through google when searching for the manual as well.
http://www.bio-rad.com/webroot/web/pdf/lsr/literature/4006051.pdf


Cellular demand for antioxidants Antioxidants such as ascorbate and glutathione serve to inactivate radicals and counteract spontaneous oxidation reactions, such as unwanted disulfide bonds in proteins. These systems are cycles, where a "spent" antioxidant (say, oxidized glutathione) is convert back to its reduced form by another reducing agent, usally NADPH.

My question is, how much NADPH (or reducing equivalents) does a cell devote to this antioxidant defense? What is the flux, in molar amounts per unit time, through these systems? Does it represent a large portion of the energy metabolism of cells?

I am guessing that the flux is quite large, but I have never seen any data on this. Most likely it varies a lot between cell types, but I would be happy to see any numbers. I think this is important for understanding antioxidant chemistry in cells, yet it is rarely discussed in the literature.

Most experiments to try to get at this type of question use stable isotope tracers to measure NADPH production from the various pathways that can make it, and then subtract away the amount that's predicted to be needed for growth/anabolism (based on the observed growth rate and biomass composition). I think this paper is by far the best example:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104482/.

Quote:

  The overall demand for NADPH for biosynthesis is > 80% of total cytosolic NADPH production (Figure 4b), with a majority of this NADPH consumed by fatty acid synthesis. At least in transformed cells growing under aerobic conditions, most cytosolic NADPH is devoted to biosynthesis, not redox defense.

Note that these are fast growing cells without additional oxidative stress. Interestingly, what the authors find is that imposing additional oxidative stress doesn't actually change NADPH production that much, but it slows down growth as more NADPH is used for anti-oxidant defense (Extended figure 9).

For skin cells, the situation might be a bit different, at least in terms of the increase in NADPH production upon oxidative stress. You might look at this paper: http://www.cell.com/molecular-cell/fulltext/S1097-2765(15)00456-6


Best methodology to compare computed phylogeny tree with taxonomy? I have computed a phylogenetic tree using an alignement of sequences, and I would like to :

Compare it to the "known" taxonomy (uniprot/ncbi which I know is not
the most up to date one) and extract a metric of how "divergent" it
is.
[Optional] Visualize the differences (I can probably come up with a
solution for that one, but if someone knows of a nice tool to do so
?)

What are the best metrics / tools / methodologies to do such a comparison ?

Thanks !

Take a look at the ape package in R. It has a function called cophyloplot which allows you to visualize two trees like so:

Which is well described in this question (also the source of the image).

There is also the dist.topo function which produces a metric which describes the topological distance between two phylogenetic trees. I don't know if this is what you mean by "divergent" but I hope it helps.


Subtracting shared DNA with half-sibling I want to note that I am not a biologist. I've been on a nearly 20-year search for the identity of the parents of my 4th great grandfather (not an easy task.)
I'm using ancestry.com DNA, GEDmatch, and family trees of my matches in hopes of using DNA triangulation to find my ancestors. In addition, I have a half-sibling who also had his DNA tested which allows me to find common ancestors on this side of the family.
I read the article "Relatedness" on the topic of inherited parental dna with two half-siblings and I'm not sure I understand what the writer means when she says:

In other words, you and your half-brother should be able to figure
out what part of your DNA came from your mom.  And if you subtract out
that shared DNA, what is left must have come from your dad!

My first thought was that a person and their half-sibling wouldn't inherit exactly the same DNA from their mother, could they? For example, the mother has two different alleles for some trait. Her son could get a copy of one and the daughter could get a copy of the other. Therefore, in the author's example, how could subtracting out the shared DNA with the brother give the girl the ability to identify exactly which DNA must have come from her dad?
I read on and the author addresses this by saying:

One brother inherited the green version of the mother’s chromosome 2, while the other brother inherited the blue version.  This means that none of the chromosomes match!  So testing wouldn’t tell the brothers which version of chromosome 2 came from which parent.
It turns out, though, that it’s really unlikely that siblings would
have two totally different versions of a chromosome.  This is because
of something called recombination.

She's talking on entire chromosomes here which is different, but it doesn't seem to address fully why the girl should be able to 100% identify what DNA came from her dad by subtracting the shared DNA with her brother. I read that half-siblings share 25% of the DNA, but the mother here surely contributed more than 25% to each of her children.
In practice, my half-sibling shows a genetic relationship to people on our shared parent's side that I do not (and likewise, I have genetic relationships to people on our shared parent's side that he does not.) Therefore, I'm positing that my brother and I each inherited some different DNA from our shared parent.
I would take the writer's word for it, but I'm confused. Where am I going wrong? (Sorry about the bad biology background.)

The website is just wrong when it says for DNA tests on a person and their half-sibling:

  In other words, you and your half-brother should be able to figure out what part of your DNA came from your mom.  And if you subtract out that shared DNA, what is left must have come from your dad!

Consumer autosomal DNA tests do not identify which of the two chromosomes present in the sample a detected variant can be assigned to.  The tests show only the two variant values detected at each location tested, and not which chromosome they come from.

Using this data from two tests, comparisons can show stretches of chromosomes which have matching patterns of variants which indicate with good probability that the corresponding pieces of chromosome have the same origin.  The tests do not tell you about the source of the pieces outside these stretches.

Each of two half-siblings do get half of their autosomal DNA from their common parent.  On average, half of the DNA each gets from that parent will also be inherited by the other half-sibling, and so will show up as matching stretches when the tests are compared.  Thus half-siblings will show around 25% shared DNA (around half of the 50% that comes from the shared parent).

Given a matching stretch of DNA results, one can determine the DNA variants that came from the other, non-shared, parent for the locations within that stretch of chromosome.  However, the locations outside the set of matching stretches cannot be identified with a particular parent (without testing of the parents).

There are two spots on that web page that do get this right.  One is in this diagram:

In the above, the bracketed area does identify the associated parents, but the unbracketed areas cannot be so identified.  (The colors shown are not reported by the DNA tests, so you can't just "follow the color" to identify matching chromosome areas outside the brackets.)

The other spot the web page gets it right is in this paragraph:

  By finding the shared DNA, the brothers can find the pieces of the 23 chromosomes that came from their shared parent, just like we did for chromosome 1.  Any genetic information from the DNA on the corresponding sites on the other 23 chromosomes will tell the brothers about their fathers.

Outside of these two places the web page seems to mislead one into thinking that all the DNA can be associated with the correct parent, which is not the case without the parents being tested.


Can restriction enzymes (Type II) displace single-stranded binding proteins (SSB)? Many type II restriction enzymes have been shown to be able to cut ssDNA.
If single-stranded binding proteins are bound to single-stranded DNA (ssDNA), does this prevent restriction enzymes which cut ssDNA from scanning the ssDNA and interacting with the target cut site?
The NEB website says that using SSB's improve restriction enzyme digestion, so it doesn't seem to be the case that SSBs inhibit target site recognition. But it is unclear to me how a restriction enzyme could recognize the target sequence unless it can also displace SSB's while scanning.
edit: specified REs that cut ssDNA

This is an interesting point. In the case of typical restriction enzyme digestion, it is double stranded DNA that is being digested. So in this case the SSBs are presumably binding to the sticky ends after digestion, so there is no competition with the restriction enzyme.
If you are interested in a specific case where you are digesting ssDNA, and have decided to add in single strand binding proteins, the binding strength (rate constants) of the SSB and restriction enzyme would influence how much the enzyme can displace the binding protein.
Here's a paragraph from the NEB/T4 gene 32 page indicating many similar applications involving reverse transcriptases, polymerase etc.

"Recently, it has been shown to improve restriction enzyme digestion
(6), improve the yield and efficiency of reverse transcription (RT)
reactions during RT-PCR (7-9), enhance T4 DNA polymerase activity
(10-11), as well as increase the yield of PCR products (12)."

EDIT: Although the reference (6) cited by NEB does not have any evidence that proves the enhancement of restriction digestion with single strand binding protein 32. This chapter might be helpful? - Kowalczykowski et al., "21 single-stranded DNA binding proteins." The enzymes. Vol. 14. Academic Press, 1981. 373-444.
From their abstract, it looks like the mechanism of enhancement could be through prevention of ssDNA hairpins so that the endunuclease can access it's recognition site (I haven't read the full chapter). Another fact supporting this is that ref(6) mentions that other interacting enzymes can work alongside SSBs only when SSB's are not saturating all the DNA in the in-vitro reaction. In an in-vivo context, the chapter abstract states that intracellular SSBs are sufficiently abundant to saturate all ssDNA intermediates formed inside cells (I presume they are talking about E. coli)
Below is the supporting text from reference (6) mentioned by NEB - bolding is mine, for emphasis : Bittner, M., R. L. Burke, and B. M. Alberts. "Purification of the T4 gene 32 protein free from detectable deoxyribonuclease activities." Journal of Biological Chemistry 254.19 (1979): 9565-9572.

Nuclease Assays-The presence of both exo- and endo- deoxyribonuclease contaminants in the 32 protein fractions has been monitored carefully throughout these purification schemes. The results of exonuclease assays are presented in Table III, and the results of sensitive endonuclease assays are presented in Table IV. Note that, when such assays are designed to detect nuclease activities on single-stranded DNA, it is important to test 32 protein at subsaturating, rather than only at saturating, protein to DNA ratios. Otherwise, an activity which hydrolyzes only free (non-32 protein-com- plexed) single-stranded DNA will escape detection.


GWAS: matched-pairs and logistic regression Logistic regression is a common analysis tool used for GWAS when your response variable of interested is qualitative. It comes as one of the standard tools in most GWAS packages (e.g. PLINK).

Most logistic regression models for GWAS would be setup as:

$\log{\frac{P(Y=1)}{1-P(Y=1)}} = \beta_0 + \beta_1*X$

Where $X$ is number of copies of the minor allele for a particular SNP of interest and $Y$ is disease stuatus. However, suppose that my case-control data is matched (In my case matched by age, BMI, reported ethnicity, and distance to procurement site). I don't think standard logistic regression (as I have outlined above) is valid. What does everybody do? I don't see options for this in packages like PLINK.

I also posted this question on (http://www.biostars.org/p/81394/) before I realized they were no longer part of stackexchange.

My first thought was to suggest a mixed effects model, so I will describe that first. But having had a Google there are models known as "Conditional logistic regression" models in which you can include any data structure as a covariate, which may be more appropriate, but I cannot vouch for them as I haven't used them. I would suggest reading the documentation.

Mixed effects models

I only know how to do this in R (stats language - www.r-project.org), but if you're using PLINK (so presumably also UNIX) R is pretty straightforward.

There are a couple of packages available for mixed effects models, my personal preference is function lme in package nlme (CRAN link). This type of model allows you to specify 2 types of independent variable (e.g. age, BMI, ethnicity... in your case);

Fixed effects - such as age, sex (something that is a phenotype of the samples),
Random effects - such as batch or other "technical" consideration,

This means you can format a model as you would before, but include an additional "random effects" term for your "matched" variable;

model = lme( fixed= outcome ~ exposure + covariate1, random= 1|matched )

.

Conditional logistic regression models

In the survival package for R there is a function called clogit (CRAN link) which seems to do exactly what you want. Although I have never used it myself.

From what I can gather this allows you to run a logistic regression with an additional covariate strata(matched), so your model may look like

model = clogit( outcome ~ exposure + covariate1 + strata(matched) )

.

Disclaimer!

This may not be exactly what you are after, as I'm not familiar with your data, so I would suggest heading over to https://stats.stackexchange.com/ as well, and searching for questions about regression analysis and paired observations - if none answer your question then ask a fresh one.


Why does water stress lead to alkalinity of xylem sap in plants? I was reading this book: Plant Physiology and Development, Sixth Edition by Lincoln Taiz, Eduardo Zeiger, Ian M. Møller, and Angus Murphy when this doubt came to my mind. Abscisic acid, the stress hormone, works to prevent water loss from a plant. Its mechanism of action requires the xylem sap of the plant to be alkaline. I can't figure out how water stress in the plant body causes alkalinisation of the xylem sap. The section in the book stated as follows:-

  During the early stages of water stress,however, the pH of the xylem sap becomes more alkaline,increasing from about pH 6.3 to about pH 7.2.
  Stress-induced alkalinization of the apoplast favors formation of the dissociated form of abscisic acid, ABA–, which does not readily cross membranes. Hence, less ABA enters the mesophyll cells, and more reaches the guard cells via the transpiration stream.

I'd be grateful if anyone out there can help.

According to recent studies, drought stress does not consistently lead
to increases in the pH of xylem sap. One article which discusses
interspecies differences is Vit Gloser, et al., "The dynamics of
xylem sap pH under drought: a universal response in herbs?," Plant and
Soil 409, nos. 1-2 (2016): 259-272.

As to what may have prompted the textbook authors to assert this, see an
earlier article by two of the coauthors of the Gloser essay: Sally
Wilkinson and William J. Davies, "Xylem sap pH increase: a drought
signal received at the apoplastic face of the guard cell that involves
the suppression of saturable abscisic acid uptake by the epidermal
symplast," Plant Physiology 113 (1997): 559-573. Wilkinson and Davies
summarize an earlier study: "Hartung and Radin (1989) found that the pH
of xylem sap from water-stressed Phaseolus vulgaris roots increased
from control levels of 6.3 to 7.2." (560)


Why does cracking a joint make noise? What causes the noise when you crack a joint? Is joint cracking harmful?

The exact mechanism is unclear. Here are some possible causes:

rapid collapsing of cavities inside the joint [1];
rapid ligament stretching [1];
breaking of intra-articular adhesions [1];
escaping gases from synovial fluid [2];
movements of joints, tendons and ligaments [2];
mechanic interaction between rough surfaces [2], mostly in pathological situations like arthritis (and it is called crepitus [3]).

There are no known bad effects of joint cracking [1, 4].

  There are no long term sequelae of these noises, and they do not lead to future problems. There is no basis for the admonition to not crack your knuckles because it can lead to arthritis. There are no supplements or exercises to prevent these noises [4].

And no good effects either:

  Knuckle "cracking" has not been shown to be harmful or beneficial. More specifically, knuckle cracking does not cause arthritis [5].

References:

Wikipedia contributors, "Cracking joints," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Cracking_joints&oldid=617403659 (accessed July 22, 2014).
The Library of Congress. Everyday Mysteries. What causes the noise when you crack a joint? Available from http://www.loc.gov/rr/scitech/mysteries/joint.html (accessed 22.07.2014)
Wikipedia contributors, "Crepitus," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Crepitus&oldid=615557134 (accessed July 22, 2014).
Johns Hopkins Sports Medicine Patient Guide to Joint Cracking & Popping. Available from http://www.hopkinsortho.org/joint_cracking.html (accessed 22.07.2014)
WebMD, LLC. Will Joint Cracking Cause Osteoarthritis? Available from http://www.webmd.com/osteoarthritis/guide/joint-cracking-osteoarthritis (accessed 22.07.2014)


Why are excess amino acids toxic? While learning about deamination, I learnt that excess amino acids must be converted to urea and excreted, since the nitrogenous group can alter the pH and affect proteins. But shouldn't the pH stay the same since they have NH2 that becomes ammonia as well as a carboxyl group (weak base and acid). So why are amino acids deaminated?

Firstly excess amino acids are deaminated to form keto acids and not urea.
Urea is formed utilising the ammonium released as a consequence of deamination via Ornithine-Arginine cycle

Secondly the released ammonium is toxic because of two reasons:

1)pH changes in the tissues (as mentioned in the question)

2)disturbs the balance of K+-Na+ gradient between the intra and extracellular fluids.

  ammonium ions compete with potassium ions for inward transport, over the cytoplasmic membrane, via potassium transport proteins like the Na+/K(+)-ATPase and the Na+K+2Cl(-)-cotransporter.

This causes increased demand for maintenance energy, caused by the need to maintain ion gradients over the cytoplasmic membrane.That is why converting the ammonium to urea is neccessary.

why amino acids are deaminated:
to form glucose via gluconeogenesis or to form anaplerotic compounds

why acidic group of keto acids fail to neutralise the basicity of ammonia:
because they keep getting utilised for the energy expenditure that increases in the tissues as mentioned above.


How accurate are Illumina microarray chips for genotyping? What is the error rate for these machines in genotyping (like for 23&me)? What is the chance of a false positive or false negative?

23andme uses DNA microarrays ("chips") to perform genotyping. These methods only assay a set of previously known single nucleotide variants, so the probability of missing some specific variant (false negative) is high if that variant is not specifically assayed. It is not quite 100% as frequently known variants missing from the chip are closely associated with a variant that is on the chip, so you can sometimes impute missing data.

Sequencing-based methods will in theory pick up unanticipated variants, but they have their own foibles.

Generally both methods are quite good at single nucleotide variants (SNVs) but are bad to only ok at other kinds of variants. See for example (this paper (chosen somewhat at random, there are many similar papers) to see what the state of the art is for sequencing-based non-SNV calls.

Getting back to chips, these themselves depend somewhat on what version of the genotyping chip is used. For specific information on different versions of 23andme chips, I recommend this blog. For tech specs on the most recent Illumina chip used by 23andme, you can see their product sheet, and specifically Table 5. Their data claims that call rate among targeted variants is >99%, and among those the reproducibility is >99.9%. However things can be reproducibly wrong, so that's not exactly false positive that you requested.

Though it's somewhat old, this paper will give you a sense of both technologies in terms of variant ascertainment, claiming 89% sensitivity and 99.6% specificity (for European genotypes only) for either low coverage sequencing or a then-current chip.

To learn more about how these stats work for chips, specifically for false positives, this video may help.

Hope that helps.


Why would lethal genes evolve? I've been reading through 'The Selfish Gene' by Dawkins. At a few places in the book he states that incest is damaging because it would give a very high chance of lethal recessive genes becoming active due to the high probability of both children having the gene compared to one child and one stranger from the same species.

However, this leaves me with the question why lethal genes would evolve in the first place. The only reason I can think of is that these genes have some secondary purpose and survive natural selection because of that.

Is this simply the entire story or are there things that I'm missing? It seems to me that the having possibility of getting healthy offspring from incest is beneficial to a species, if only because finding a mate would be easier, so those secondary effects would have to be pretty good.

Also I'd be curious if any research has been done which has found examples of side effects of these lethal genes that would make them preferable.

Lethal genes evolve simply because of random deleterious mutations and absence of strong selection.

Recessive lethal genes

Random mutations can make a gene product non-functional or reduce its activity. However, in diploid organisms the other fully-functional copy of the gene can compensate for the non-functional allele.

Sometimes both the alleles can carry different mutations which can lead to complementation; this would not affect the gene activity. Also see:  Explain allelic complementation at molecular level. Let's not consider this case here.

So, the fitness of the heterozygotes would not be affected and they will continue to propagate. However, if both the alleles are affected then it would lead to lethality (or lets say reduced fitness). This can happen if two heterozygotes (with the same deleterious mutation) mate and give rise to a homozygote (with both the alleles affected). Since siblings (or other close kins) are genetically related, there is a good likelihood that both of them may be carrying a copy of a non-functional allele and homozygous offspring born out of such a mating may have reduced fitness.

Dominant lethal genes

There are some cases of dominant lethal alleles. Examples include the mutated genes responsible for Huntington's disease (or similar poly-Q disorders). Other examples include a mutant allele of a proto-oncogene that leads to its hyperactivity (and therefore cancer).

Dominant lethal alleles persist in the population primarily because of their late onset. In such cases an individual with such an allele would have already mated and produced offspring before the disease kills them.

Other reasons for the persistence of lethal genes

Another possibility (applicable to the case of cancer) is that the mutations are not in the germ cells and were acquired by somatic cells because of some external agent. These mutations would not be transmitted to the next generation.

Sometimes, the deleterious nature of the allele can exert its effect only under certain conditions. Let's say someone has a mutation that causes reduced immunity. Such a person would survive well if they remain in a sterile environment. In general, we can say that there is no strong selective pressure against the mutation.

Sometimes the reduced fitness because of a mutation under a certain condition can be overwhelmed by an increased fitness caused by it under some other condition. A very well known example is that of the haemoglobin allele that causes sickle-cell anaemia. However, the RBCs in the individuals affected by this disease are resistant to infection by the malarial parasite. The mortality due to malaria is much higher than that due to sickle cell anaemia. Therefore, in regions where malaria has high incidence (like Africa) this allele is positively selected.


codon optimization / enzyme active site improvement Does one necessarily have to use de novo synthesis of DNA when attempting protein expression improvement by codon optimization? Or are there other ways?

e.g. Say the gene coding for the enzyme needed to synthesize a certain secondary metabolite is known & sequenced already. The standard cloning approach is to extract mRNA from (say) plant tissue, then construct a cDNA library & express it in E Coli using a suitable plasmid.

Now if the neucleotide sequence needs to be modified (to increase expression) does one have to start de novo or is there easier ways that can start from the mRNA / cDNA?

A variant of the same question is when I'd want to modify the gene because a protein docking study shows some ways to modify the active site of the enzyme by changing a residue or two in the amino acid sequence.

Kind of an old post, I'm surprised it doesn't have an answer yet.
There's no reason why you couldn't modify the RNA or cDNA directly, you just have to splice the gene correctly to make the changes you want. You're absolutely right that even a single amino acid change can have a huge difference if it's in the right spot.


How does mad cow disease evade immune system? The mad cow disease is caused by prions right?

So how do prions avoid white blood cells and antibodies?

Prions are proteins that we produced but that are misfolded and affect the folding of other proteins. As we produce these proteins, we don't recognize them as antigens. If we were to recognize our own proteins as antigens, then the immune system would constantly be fighting against ourselves. This is what is called a autoimmune disease.

While this was a simple explanation, the reality on how the immune system interact with prions might be a little more complicated. Bradford and Mabbot (2012) might be a good place to start for further learning


Why does muscle blood flow decrease during exercise? My questions semi-relates to these two items: Where does extra blood come from to fill your muscles during exercise? , and Blood pressure during exercise .

While reading Exercise Physiology by Dr. Brooks, I've come to the following quote, which is a bit puzzling to me:

  Muscle blood flow increases exponentially with metabolism. At maximum exercise, some vasoconstriction occurs in active muscle in order to maintain blood pressure. Maximum muscle blood flow is largely determined by the amount of active muscle. The larger the portion of active muscle mass, the less total muscle blood flow.

Questions:

Why is it that the larger the active muscle mass, the lower the total muscle blood flow? I'd expect it to be greater.
Say that I am doing the bench press, does that qualify as an exercise with large active muscle mass?

I think there might be some missing context here leading to confusion of which muscles are being referred to in that passage.

During exercise, blood flow increases in active muscle due to local vasodilation. Cardiac output also increases, which ensures that total blood flow in the body is sufficient to meet the increased demand.

At higher levels of exercise, there is also systemic vasoconstriction. Systemic vasoconstriction acts to maintain blood pressure. You simply have too much total muscle for maximum cardiac output to supply all the muscle with full vasodilation plus the rest of the body without a loss of pressure. For an athlete with greater maximum cardiac output, it would be possible to fully perfuse more muscles at high effort than for someone untrained.

  At maximum exercise, some vasoconstriction occurs in active muscle in order to maintain blood pressure

Because vasoconstriction is systemic, it has an influence on all the muscles, including the active ones. You should think of this vasoconstriction as relative to already dilated vessels, not necessarily compared to rest.

  Maximum muscle blood flow is largely determined by the amount of active muscle.

This sentence could be rewritten as:

  Maximum blood flow through a given muscle is largely determined by how much muscle is active in the rest of the body.

That is, the maximum blood flow through an arm muscle would be greatest if your legs are resting.

  The larger the portion of active muscle mass, the less total muscle blood flow.

This is I think the most confusing sentence...I believe what they are referring to is the total muscle blood flow for a given muscle (total meaning over time rather than over space), which will be maximum when fewer other muscles are active at the same time.

Joyner and Casey 2015 explain all this in more detail; their Figure 8 is most directly related to the question but the rest of the background is also useful.

Joyner, M. J., & Casey, D. P. (2015). Regulation of increased blood flow (hyperemia) to muscles during exercise: a hierarchy of competing physiological needs. Physiological reviews, 95(2), 549-601.


Storing Taqman plates with polymerase in fridge before running I'm going to be running some Taqman assays on cDNA generated from RNA collected from various samples, and will end up running a bunch of plates (right now the setup is 1/2 a plate per sample, including controls etc.). Since our thermocycler can only handle one 96-well plate at a time, it has been suggested that I make up the mixes all together, aliquot them into the plates, then store the plates at 4°C (well wrapped in plastic or Parafilm) until ready to run. I would imagine that the plates would be in the fridge for just one day, at max overnight.

My question is about the polymerase - can I add it ahead of time, and just take the plate out of the fridge and pop it in the thermocycler, or should I add it just before use? I've been kind of out of the DNA/RNA field for over 10 years, and I seem to remember from before that polymerases could have residual activity even at 4°C. Is this still the case, or have they improved to only be active at 60+°C or whatever your temperature is?

Alternatively, is there another ingredient I should leave out until just before amplification? cDNA? Probes? Something else? Also, does the storage time make sense? Is overnight okay, or should I run them all the same day? Is over the weekend okay? I don't want this question to extend into a too-broad "How do I do qPCR?" question, but any tips you have would be very helpful. As far as I'm aware, all the reagents are from Life Technologies/Applied Biosystems.

The reason I ask is because it seems to me that it would be much more accurate and reproducible to prepare the master mix with polymerase already included, instead of adding 1 μL of polymerase to each well just before running the assay.

Not sure if this question is still valid, but it was marked as unanswered and frequently viewed, so here's a go :)

These days most polymerases (certainly for Real Time PCR) are so-called Hot Start enzymes (ask your manufacturer, because they save you a whole lot of trouble!). They are modified with a protein that prevents them from working until activated at 95 deg. Celsius. Be aware though that not all hot start enzymes require the same activation time at 95 deg. Celsius, and some enzymes lose activity when activated for 15 min. at 95*C instead of 2 min.

In my experience storing plates at 4 degrees (or room temperature) is not a problem at all, and most manufacturers advertise that the PCR mixes (including primers, probes and DNA) are stable at room temperature for 24 hours. You do however need to protect the mixtures from (sun)light because the probe might be damaged when exposed for longer times.

Personally, I would not recommend storing real-time PCR plates in the freezer, because condensate will most-likely form when you thaw your plates. This can influence the PCR, as real-time PCR uses light for the analysis of your samples.

If you want to save yourself some pipetting, but can't prepare plates in advance, you can prepare a primer-and-probe mix, which you can freeze in batches. In our lab, we keep a stock of primer-and-probe mix for every assay. Maybe this also works when you already add water and PCR mastermix, but I have never tried. I wonder how other people do this, so please leave a reply.

Hope this might help some people.


Why isn't the biological niche occupied by whales instead occupied by fishes? As by the title. Why aren't there many more, and larger, whale shark like creatures instead of the great mammalian swimmers? I'd assume fish have a benefit in doing the whole "being under water" thing on virtue of not having to get to the surface to breathe ever so often. Seems it's not that big of a benefit, but I still assume there must be something else about mammals that makes them good at being large swimmers and divers?

The "niche" of whales comprises much more than just being big. I would actually argue that this is just a byproduct of the marine lifestyle, since endotherms need to maintain their body temperature which is easier when you're big (lower surface/volume ratio). Some reasons for whales being very successful are:

1) Higher oxygen use efficiency:
AMR already mentioned the advantages of the mammal metabolism in the terms of oxygen intake. This allows whales to forage in great depths. Note that no fish could withstand such rapid pressure changes, since they need to dynamically adapt their swim bladder.

2) Intelligence:
Mammals are much more intelligent and therefore have access to resources that are not available for most other marine animals. E.g. hunting in groups requires a fair amount of intelligence and is much more efficient than hunting alone.

3) Acces to cold environments:
In contrast to fish, mammals can maintain high activity regardless of the ambient temperature. This gives them almost exclusive access to highly productive ecosystems like the antarctic and southern oceans.

4) Echolocation:
Toothed whales including dolphins use echolocation to communicate and sense objects. This is a very powerful ability for locating and tracking prey.


About radiation therapy With radiation therapy, could some of the radiation used cause new mutations in non-cancerous cells that are near the tumour that is being irradiated? If so could these new mutations lead to new cancerous cell colonies (which might later metastasize)?

Yes, this can happen, although the risk is low. The problem is that some tumors need to be irradiated since the cannot be operated (this is true for some brain tumors). Here the radiation therapy is the therapy of choice. The effect of the therapy is that the tumor cells get a high radiation dose which either kills them or drives them into apoptosis.

The problem the irradiation is that you will always affect healthy cells, of which most will die. This causes some of the negative effects of the radiation therapy, but it is also possible that a healthy cell receives a dose which is "only" damaging and causes a secondary tumor. Here a benefit analysis needs to be done to see if the benefit from the therapy is woth taking the risk of acquiring more damages. See the references for some more background.

References:

Long term side effects of brain tumour radiotherapy
Second Cancers Caused by Cancer Treatment
Therapy-Related Secondary Cancers


What are the most important differences between HSP70 and HSP90? Question originally asked on Quora. These proteins have many functional similarities, so why do cells need both to handle unfolded proteins?

Hsp70 and Hsp90 are not single proteins, but entire protein families. And those two protein families are not the only ones of their kind. There are different groups of heat shock proteins, Hsp70 and Hsp90 are molecular chaperones that assist in protein folding. There are five major families of molecular chaperones: Hsp100, Hsp90, Hsp70, Hsp60 and Hsps.

Hsp70 binds to nonnative, unstructured segments of proteins and helps folding them. Hsp90 doesn't bind to unfolded proteins, but to native-like proteins. Some substrates are also handed over to Hsp90 by Hsp70.

The whole area of chaperones and heat shock response is a very, very large and interesting field. I recommend to you to read the reviews below.

Vabulas, R. M., Raychaudhuri, S., Hayer-Hartl, M. & Hartl, F. U. Protein folding in the cytoplasm and the heat shock response. Cold Spring Harb Perspect Biol 2, (2010).
Richter, K., Haslbeck, M. & Buchner, J. The heat shock response: life on the verge of death. Mol. Cell 40, 253-266 (2010).


Creating a cell, not from another cell. Will it be possible? If some time in the future, we can know exactly what a cell (for example simple prokaryote bacteria) contains, (I mean, exactly which molecules, the shape of them, the density of each, everything), Then can we create a new cell (not from another cell)?

I mean, if we have such technology, then create a soup just like what that cell contains, and a DNA exactly same as that bacteria cell, and then put some of it inside a Cell membrane, will it start living?

Many of the parts of a cell, which perform its basic functions, such as transcription, translation, DNA replication, etc. have been already isolated and successfully recreated in a test tube. So if we obtain a complete list of all the parts we need and know how to make those parts and mix them together, we can make a cell from scratch.

However, this will probably be very time-consuming and costly and will serve no other purpose than showing that it can be done. It is much more time- and cost-efficient to create a genome only, transplant it into an existing cell, and wait for the cell to replicate and synthesize new molecules until it changes in a way that completely fits the new genome.


What is the purpose of Y-shaped adapters in Illumina sequencing? Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library.

The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary.

What are the advantages of this?

My take of this over having fully-complementary adapters (ADAPTER1 - - - - - ADAPTER1) is that:

-Upon primer annealing, the primer in turn would bind to the start AND end of the DNA fragment, and thus not allow synthesis to continue to until the end. Therefore, the next primer would not have a template to bind at the start of the fragment...

Y-shaped adapters also allow for paired-end sequencing. Fragments have a unique sequence on either end, which allows for the first "run" to sequence one side of all molecules, then synthesize the reverse and sequence that.

Am I on the right track?

Normally, when you need two unique adapters, say A & B, on either end of unknown insert sequences, cohesive-end ligation is difficult because the insert sequences are "unknown". So you have to do blunt-end adapter ligation, in a reaction containing Unknown Inserts + adapter A + adapter B. This can result in 3 possible versions of insert-ligated product: A-insert-A, B-insert-B and A-insert-B, among which only A-insert-B is the only desired product.

1) Ligation of A-tailed inserts with Y-adapters gives you 100% A-insert-B.

2) Lets now assign a directionality to the insert - say from base 1 to base 400. Following Y-adapter ligation, you will have 2 kinds of insert-ligated products per insert: A-Insert (1-->400)-B and A-Insert(400-->1)-B, both of which are very useful. Each will create a separate clonal cluster and you will get sequence information starting at both base 1 and base 400 of the insert, since in single-read sequencing, the instrument always sequences from Adapter A. However, to know that both these sequences belong to the same insert, one will need to do paired-end sequencing.


Features of phosphatase I was wondering if you would be able to help me with discovering what the main regulatory feature of a phosphatase is. I understand many have separate catalytic and regulatory subunits, however, so do kinases so I feel that there is a different answer that I am not understanding. Thank you,

Kinases phosphorylate, or add a phosphate group.

Phosphatases remove a phosphate group.

Beyond that, the concepts for regulating them are the same, though the precise factors of course are different.


Basener's ceiling and evolution There is a theorem in the Intelligent Design literature called Basener's ceiling.  It states that all evolutionary algorithms that attempt to optimize some fitness function will eventually reach a plateau where complexity no longer increases.  This is seen in practice when engineers and computer scientists try to use algorithmic forms of evolution.

  There are a number of standard models for the evolutionary process of
  mutation and selection as a mathematical dynamical system on a fitness
  space. We apply basic topology and dynamical systems results to prove
  that every such evolutionary dynamical system with a finite spatial
  domain is asymp- totic to a recurrent orbit; to an observer the system
  will appear to repeat a known state infinitely often. In a
  mathematical evolutionary dynamical system driven by increasing
  fitness, the system will reach a point after which there is not
  observable increase in fitness.

Biological evolution is the same as an evolutionary algorithm in the relevant aspects.  It is a search to optimize reproductive fitness, where the fitness function is just the fact of survival or lack thereof.

How then is evolution able to make organisms continually increase in complexity, as history shows, despite Basener's ceiling?

Four quick flaws:

1) Environments are always changing. The fitness space is dynamic, and includes both biological and non-biological players, the former which are also ever-changing. Given a sufficiently stable ecosystem, one would expect an equilibrium among species to develop (though it could be cyclical). However even if the environment stays constant, novel mutations could always increase the fitness of a given species, which could then affect the fitness of all the other species. Also, natural selection is not the only factor that influences evolution, and other factors can add dynamic instability.

2) You are conflating genetic algorithms with evolution. Genetic algorithms use selection to solve a minimization problem and are typically bounded within fairly rigid constraints. They are motivated by biology, not models for biology.

3) You are conflating complexity and fitness. Complexity can be more fit or it can be less fit. Evolution only selects for fitness, not for complexity.

4) Do organisms continually increase in complexity? Depending on how you define it, they may not. Thinking about humans as a "goal" of evolution or something like that is a feature of creationism or intelligent design, not biological evolution. Some of the most successful organisms on Earth in terms of number of individuals or even biomass are some of the simplest.

There may be others as well.


How do you break up cell clumps when passaging? I am working with HepG2 cells, and they really like to form clumps.  Pipetting up and down in TrypLE does not seem to be very effective in breaking them up.

I find that I only get clumps (with HeLa and similar cell types) if I leave them in Tryple too long. Generally I leave them in room-temp (not hot) Tryple for ~8 minutes, then I angle the dish, lid off, so that I can see the "sheen" of cells on the dish (this happens in the hood, of course). Then I blast the sheen with Tryple using a 1000ul pipetter, which de-adheres the cells. These are generally much less clumped than if I let the Tryple de-adhere the cells.


Why do bananas turn black after some time? Why do bananas turn black after some time? Please don't just give hypotheses but concrete references to experiments

Banana skin consists of plant cells and cellular tissue. This tissue contains phenolic compounds. On getting old, the cell membranes of the banana get weak. When the membranes weaken, the phenolic compounds mix with polyphenol oxidase (an enzyme present in the cells cytoplasm). As a result of this interaction, the phelonic compounds oxidize and produce a brown compound called melanin which results in the colour of the peel turning black. Also, the green skin of banana contains a gaseous plant hormone, ethylene, which diffuses into the fruit and hastens the process of ripening. It is yellow when the fruit is ripe and turns black with the production of more and more ethylene.


KRAS gene and K-Ras Mutations This question pertains to the KRAS wikipedia page, and I just want to double check and clarify my own understanding of how this mutation works in cancer.
It states:

K-Ras protein acts like a switch that is turned on and off by the GTP and GDP molecules.

So if K-Ras is a switch, does that mean that when there is K-Ras mutation, it functions defectively so that it does not shut off? So for example when it binds to GTP and converts it to GDP, KRAS does not shut off regardless of GTP is converted to GDP and this would lead to / cause cancer.
So I guess I have several questions to my reasoning above..

Why does excess conversion of GTP to GDP lead to cancer? Is it because this is specifically pertaining to the the RAS pathway?

When I referenced above "it" is the K-Ras binding event the K-Ras protein binding to GTP then converting to GDP caused by the K-RAS gene not being able to function correctly? I'm just confused if its the K-Ras gene causing the problem or the K-Ras protein being the problem, or is it both?

If K-Ras acts as a molecular switch, how to GEFs/GAPs effect K-Ras mutations? Because I know GEFS activate the conversion of of GTP to GDP, but what is its relationship to KRAS/K-Ras?

In the next line it states:

When the protein is bound to GDP, it does not relay signals to the cell's nucleus.

Is this saying when K-Ras is bound to GDP, that the conversion of GTP to GDP won't ever stop? I kind of just don't understand why this was written or what its relevance is. Or is it simply stating K-Ras can only turn on GTP to convert it in to GDP but not the other way around?

NRAS is indeed a molecular switch, as part of the MAP-Kinase signaltransduction pathway it acts in controling the signal which goes downstream and finally will cause the expression of genes. In the case of NRAS this includes genes for proliferation, which is important for tumors. In principle, this looks like shown on this figure (from here):

RAS (this is the same for all three RAS family members) needs to be activated so it can signal downstream, this happens, when GTP is bound to the protein. Since permanent activation is obviously not a good idea, RAS itself has an intrinsic, but slow GTPase activity, which is activated by GTPase-activating proteins (GAP) and will eventually cleave the terminal phosphate group group from the GTP to make GDP + P. GDP bound RAS is inactive. GDP stays bound to the RAS protein and needs to be exchanged against GTP by Nucleotide Exchange factors (NEF) to activate RAS again.

The general principle is shown in this figure (from here):

Mutations in RAS proteins occur in 98% of the time in three locations (see reference 1): In codons 12, 13 and 61. All three mutation affect the ability of the protein to break down GTP by abolishing the intrinsic GTPase activity by the GAP (see reference 2). This leads to the accumulation of RAS protein which is permanently bound to GTP and therefore activated, subsequently activation transcription of genes for proliferation (amongst others). This process can lead to the formation of cancer.

Your questions:

The conversation of GTP to GDP does not lead to cancer. This process stops the activation of RAS proteins. It is the permanent activation which causes the problems.
You have the mutation in the KRAS gene, which is the origin of the problem. The wrong activation is of course done by the KRAS protein.
GEFs facilitate the exchange of GDP to GTP, the break down of GTP is supported by the GAPs. The mutation hinders the GAP to fulfill their role, so they are useless in the mutated form of the protein.
The other way round. If RAS proteins are bound to GDP, they are rendered inactive, unless a GEF exchanges it again to GTP.

References:

RAS isoforms and mutations in cancer at a glance
Guanosine triphosphatase activating protein (GAP) interacts with the
p21 ras effector binding domain.