Why does a light object appear lighter in your peripheral vision when it's dark? So, I am not sure I can reproduce it via images, but the steps are:

1) At night, open a window and have a look at the surface of the earth

2) Suppose there's an object that reflects a tiny amount of light

3) When you actually try to focus your eyes at this object, you either don't see anything (depends on the amount of light it reflects) or you can hardly see it

4) When you focus your eyes on something that is 3-10 metres away, you can easily see this object with your ambient vision. Not the details, but it seems that it reflects more light.

Why does it happen?

Short answer
Peripheral vision is more light-sensitive than central vision.

Background
When you look directly at an object the image is projected onto the fovea. The fovea has maximal visual acuity (high resolution) and a high density of cones, which are specialized photoreceptors to sense colors. However, cones are not very sensitive to light.

Here is a picture showing the foveal field of view:

Source: Pinhole Eyeglasses

If you look at the same object using peripheral vision, the image is formed more eccentrically on the retina. Here, cones are sparse, but high densities of rods are present. Rods do not detect color, but are much more sensitive to light than cones. In fact, they can faithfully detect a single photon! (Webvision) Moreover, many rods converge onto a single ganglion cell, and rod responses are therefore summated. This spatial  summation further increases light sensitivity in the periphery, but degrades spatial resolution.

Here is an image on rod and cone distributions on the retina, showing a high cone-density in the fovea and a high rod density more eccentrically:

Source: Webvision

And here is an image showing the higher light sensitivity of rods over cones:

Source: Webvision

Hence, peripheral vision is more light sensitive because: (1) there are more rods in the peripheral retina; (2) rods are more light sensitive; and (3) eccentric retinal rod circuitry further amplifies the rod responses. However, color perception and spatial resolution are better developed in the central field of view.

Further reading (Cognitive Sciences.SE)

Rod and cone distributions: "Why can we not see around our point of focus of our eyes?"
Visual acuity as a function of retinal eccentricity: "Visual acuity and offset stimuli"


Is it possible to increase lifespan through controlled evolution? A few years back when I was reading The Selfish Gene by Richard Dawkins, there's this short passage where he theorizes about a way to achieve an increased lifespan through controlled evolution.

The theory goes like this: we don't tend to have medical problems until after 30 because we all tend to reproduce before that age.  Thus, people who tended to die before 30 never passed on their dying-prone genes.

So, if you didn't let people reproduce before a age X (where X starts at 30) and then slowly move that age up, you could use evolution to increase lifespan.

The ethical issues notwithstanding, is there any reason why this wouldn't work?  If it would work, how long do you think you would need to sit at each value of X?  How far apart do you think each value could be?  Finally, how many generations, using this technique, would it take before someone would live to be 1000 naturally?

I think this would probably work.  The grandmother effect, which is one of the main theories for human longevity after fertility might indicate that human lifespan would increase if the children come later.

Just have to disclaim here: We will never do this.  Many unthinkable consequences would result...

If you simply forbid anyone to have children before they are 40 or 45 (fertility doesn't drop until age 35 or so), forbid invitro fertilization and medical assistance to conception we would probably be looking at a prolonged lifespan.  Infertility rates in women at age 40 are not clear, but one estimate is that 40% of women can have children at 40 years of age.  If we want to seen an effect early, we would push the age up a year or two.  Forbidding in vitro fertilization and other medical assistance to offspring we could look like a 80-90% cut of people - lots of people would never have children.  This might make people unhappy an destabilize the social fabric.

Its not clear how long this would take.  The generation time would go to 40 years from about 20 now - 40 to get to childbearing age, but results would take 80 years - when we find out how the children would fare.  Given the C elegans longevity experiments and the fact that we are starting with 8 billion people, we probably would find some great late age breeders who may also live long.  But for the longevity phenotype to set in it would take several generations as we are looking for an indirect effect: later breeding causing longevity.  The Belyaev experiments which produced domesticated foxes by strong selective breeding took some 30ish generations to complete though they saw a significant effect in just 10.  It could take a similar numbers of selection rounds in this cse.  4-500 years. Ethical issues aside, this is why most geneticists study flies.

There would also be a lot of other negative socioeconomic consequences to this thought experiment.  One good thing is that the population of the earth would plummet - many people would be eliminated from the gene pool, though eldercare would be a major part of the world workforce.  Lots of work, not clear who is going to pay for it, but low unemployment and low low wages may result.

So you see Mister President, this is quite a distinct possibility, though some sacrifices would have to be made.

The science of human eugenics is not scientifically wrong, but selective animal breeding and lab experiments don't usually evaluate or care about the consequences of large peturbations in the gene pool.

You would also have a lot more autism and Downs syndrome and other congenital defects which tend to show up in offspring of older parents. These issues might improve with application of biotechnology which screens weak sperm and eggs without ruining the effect you are looking for, maybe not.

Since we are selecting against fecundity, the human race could be dogged by fertility problems or chronic genetic diseases which the genetic contribution of some of the more robust people in the gene pool being removed and the tendency to such age-related birth defects might not go away given the drastic selection pressure we are putting on the gene pool.

Other consequences you might not expect; some physical traits associated with longevity and prolonged fertility would cause us to look more alike and not necessarily in a good way.   Browse the internet; its probable that we would get shorter and possibly uglier?

There are many more direct ways to increase the human lifespan - better diet, exercise, the elimination of poverty, vaccinations, proper medical care, access to clean drinking water and a lower birth rate (fewer children not later) all are known to directly effect longevity, having more than doubled the human life expectancy in the past few hundred years.


Is it true that it is mostly impossible, for any kind of antibiotic, to succeed in killing off every bacteria in a very rich environment? It is commonly believed that the resistance to antibiotics by micro-organisms is truly evolution at work, and that the recent surge in superbugs may very well be attributed to it.

When we refer to a bacteria's ability to "evolve" into resisting this antibiotic, I assume we mean that when we introduce antibiotics into the environment, a lot of bacteria die but some who by mere chance and luck didn't do so and that these lucky bacteria go on to survive and multiply, thus aiding in the creation of so-called superbugs, or rather, bacterial resistance to sophisticated drugs.

This whole situation already suggests to us, or at least to me, that there's much inherent complexity in these organisms and indeed a certain uniqueness to each.

I have, however, been troubled recently by the following question: is it truly impossible, for any kind of wholly new antibiotic which was not used before (no matter how complex), to succeed in killing off every single bacteria in any rich habitat/environment (no matter how populous)? And that there'll always be some bacteria on whom this shall not work apparently due to uniqueness in something of their structure?

Yes. It is down to mutations. DNA replication is not 100% accurate, there will be mistakes that are not corrected in the progeny produced.

Antibiotics works like a bit of gunk wedging itself into the machine of a bacteria cell but avoids jamming a human cell due to that very same shape. Gunk that wedges into both human and bacteria machines is just a really bad poison. So that gunk has a very special shape.

Resistance can be acquired by recognizing gunk of that particular shape and removing it (not something easy to evolve but very effective when it does) or just change the shape of the machine so the gunk cannot stick. Usually the altered machine doesn't work as efficiently as it can but in an environment polluted by fouling gunk, it works well enough.

And a rich environment means there are many bacteria.

So if your chances of mutating the right part of the bacteria machine to gain resistance is 1 in million, a rich environment with 10 million cells will have 10 such mutates.

Of course in reality we are talking about trillions (a million million) of bacteria cells per human (actually 39 trillion bacteria per human) and we are talking about billions of humans.  And we are not even counting the number of bacteria in the soil and in farm animals.  And it takes a few years for resistance to evolve.

When you look at the numbers involved , it is very difficult not to imagine resistances evolving. Even if the chances of that happening is 1 in hundred of trillions. It just takes a single bacteria cell to mutate and so gain resistance for it to spread and pass that resistance to other bacteria.


Do mRNA vaccines cause transfected cells to be killed by cytotoxic T cells? Based on my research on how mRNA vaccines (specifically for COVID-19) work:
An mRNA sequence, that contains the sequence of the coronavirus spike protein, is absorbed by some cells. These cells now produce foreign coronavirus spike protein. These cells then present some of the produced foreign spike protein on their surface via MHC I complexes so that they can activate a cytotoxic T cell and cause it to produce lots of copies of itself (cell-mediated immune response). Some of the foreign spike proteins are also released from the transfected cells which allow for B cells to activate a humoral immune response and for professional antigen-presenting cells to present the foreign spike protein on MHC II complexes to activate helper T cells.
My Question:
As far as I understand it, once a cytotoxic T cell encounters a cell that has a foreign protein presented on an MHC I complex, the T cell kills the cell that has presented the foreign protein before it leaves. This means the cells transfected with mRNA through the COVID-19 vaccine (even though a coronavirus hasn't actually hijacked them) will eventually be killed by cytotoxic T cells that encounter them since they are presenting foreign spike proteins on their surface. Is this not toxic for the body since it is killing your own cells? Or does the fact that the mRNA sequences are not self-replicating contain these cell deaths to only the transfected cells and only a few cells die in this process so that the vaccine is not toxic overall?

There is a question on stackexchange that is not only related
Why cytotoxic T cells don't kill dendritic cells when they present antigen?
Your question refers to "some cells" (explanatory text) and "transfected cells". Thus, any cell that takes up the m-RNA-vaccine is referred to. However, any answer must be based on the different types of cells involved in immunization, vaccination and - in killing infected cells, in the end. There are the immune cells which present antigen, there are, as well, the body cells which present.
The explanatory text of your question speaks of "presentation".  The very first paragraph of Wikipedia on "Antigen presentation https://en.wikipedia.org/wiki/Antigen_presentation seems to even limit the term  "presentation" to presentation by immune cells, which would exclude any body cells, like muscle cells transfected with vaccine antigen.  This might illustrate that immune cells are different from body cells in respect of presentation of antigen that becomes target of cytotoxic t-cells.
Both immune and body cells  take up antigene, however the immune cells, by presenting prime naive T-cells, i.e. activate the T-cells. The related question  cited asks about the fate of the immune cells.
As for  the fate of body cells like muscle cells you refer to  in  the last paragraph of your question the video message you link to in your own answer seems to refer to those body cells: transfected cells will simply be killed, but not enough of them to cause harm.
Here are additional remarks, enjoy: I think  it is an open question if the transfection as such would lead to cell death (assuming some failure of cytotoxic T-cells, not doing their job). Think of vaccination that transfects with "attenuated", if not live virus: even if the virus is incapable of - natural - replication  it is unlikely that the host cell whose ribosome machinery has been usurped can keep up its metabolism. I would like to be allowed to mark the following as a new thought of mine: the fact that the antigen is being presented speaks in favour of the cell not being able to survive - which is counterintuitively (how can a cell infected by virus still be able to digest, process, transport and present antigen on its MHCs, at all? Looks like it will stay alive.)
From the very fact of antigen presentation it is possible to infere, in my opinion, that the cell will not survive transfection. Host cells may  have their  own, inner defence mechanisms which are able to beat infection without any presentation of antigen - think of "interferon", but also, nowadays, of double stranded RNA, dsRNA.  A cell that is successful in defeating the virus without engaging the adaptive immune response would cancel out its survival by presenting and attracting cytotoxic t-cells. So it is a possibility that cells in spite of being transfected by mRnA vaccine do not die.  However, that would be considered a vaccine failure.
So with effective vaccination transfected body cells will die.
Caveat: from my reading of textbooks it is a possibility that vaccination might be effective even if body cells are not transfected, but that is beyond your question. Premise of your question is that a cell is being transfected (then what happens?).
A reference on the  possibility  that a "transfected cell" might survive by self defence  would be  "RNA interference",
https://en.wikipedia.org/wiki/RNA_interference
Last not least - see  the video you linked to - there is "B cell immunity".
To my mind it is a possibility that B-cells become transfected by mRNA vaccine - if so, they should present the antigen as an endogenous on to cytotoxic T-cells which makes your question very relevant in respect to B-cells, in my opinion. However, B-cells produce antibodies, considered most important in vaccination. This speaks in favour of B-cells taking up antigen via their B-Cell receptor that should be among cell debris of transfected cells that died - for instance few muscle cells transfected by vaccine. What you need here, in respect of B-cells is authority on either cross-presentation of endogenous antigen by B-cells (if mRNA is being uptaken through membrane, if B cells are transfected) or, authority on B-cells "only cleaning" up dead cell's antigen as part of dead cells, killed by virus or immune cells.
My answer is in line with the answer you already gave -  elaborating on what is in fact causing the cell's death:
"Do mRNA vaccines cause transfected cells to be killed by cytotoxic T cells?"
Yes,  mRNA vaccines cause transfected cells to die.


Are cells guaranteed to get at least one mitochondrion when they divide? If mitochondria exist at random within a cell, isn't there a possibility that cell division will result in a daughter cell with no mitochondria?  If not, what is the process for guaranteeing at least one is present in each daughter cell?  If so, what happens to that cell?

Isn't there a possibility that cell division will result in a daughter
  cell with no mitochondria?

Yes, there is always the possibility. However, there must be a strong negative selection pressure against eukaryotic life that cannot achieve the proper partitioning of mitochondria, so you can imagine that there are mechanisms in place to prevent this case.

Mitochondria are both passively and actively partitioned to daughter cells. This is understood to occur through the cytoskeleton and with the control of mitochondrial fusion and fission at key stages of the cell cycle, prior to mitosis and cytokinesis!

Here is a great review from several years ago that addresses your question well.


3D models of adult male brain in the Blender software? Any open-sourced version for research? I am trying to find 3D model of brains. I am particularly interested in adult-male -brains in Blender-model. I could find such 3D models of brains for sale here but because I am researching I would like to use some open-sourced candidate so anyone could preview things. So does there exist 3D models of brains in Blender?

There is a model of an adult, male, real human brain here:
http://brainder.org/download/brain-for-blender/

It can be imported into Blender or any other 3D application that can read Wavefront OBJ or Stanford PLY formats.


What does self-perpetuating mean? From Wikipedia

  The community begins with relatively few pioneering plants and animals and develops through increasing complexity until it becomes stable or self-perpetuating as a climax community.

From Wikipedia again,

  Self-perpetuation, the capability of something to cause itself to continue to exist, is one of the main characteristics of life.

What I  don't understand is every organism has the capability to perpetuate (except the sterile ones, which are not under consideration) even a seral community does then why is climax community specifically labeled self-perpetuating?

The key here is to recognize the distinction between a community as a whole and the individual species within that community. Just because individuals have the capability to self-perpetuate, doesn't mean that a community as a whole does.

For example, imagine an island with a whole bunch of caterpillars. Now imagine that you introduce a non-native caterpillar-infesting wasp. On the mainland, the caterpillars have evolved resistance to this wasp and so can fight off the infestation. But on the island, they never evolved that resistance, and rapidly succumb. Upon introduction of the wasp, you have a "community" of wasps and caterpillars. The caterpillars can reproduce, as they have been, so they're self-perpetuating within their species. The wasps can also reproduce by laying their eggs in the caterpillars, so their species is self-perpetuating. But the wasp infestation is killing caterpillars faster than they can reproduce, so the community is unstable. Over time, the population of both wasps and caterpillars will crash as all the caterpillars die off. Each species can self-perpetuate, but the wasp/caterpillar community, taken as a whole, does not.

That, in a slightly more complex way, is what happens with non-climax communities. The pioneer species change the environment in a way that permits other species to grab a toe-hold. These species are more suited to the changed environment, and thus push the pioneer species out.

For example, species which can survive in nutrient-poor soil grow and die in that soil, enriching it with nutrients. Now that the soil is no longer nutrient poor, faster-growing plants can grow in the soil, and push out those species which started there. Each individual plant can reproduce, but the community as a whole is changing from one which favors the nutrient-poor adapted plants to the nutrient-rich adapted ones.

It's only in a climax community where the members of the climax community create/maintain an environment which is most conducive to the climax community species. This is why it (the climax community) is being called "self-perpetuating". The community as a whole is maintaining an environment which favors those species which make up that community.

Wipe out the climax community species (e.g. through a forest fire), and you no longer have an environment which favors the climax community species. A new set of species comes in, changing the environment, which then allows other species to come in, changing the environment further, which then ...


How does the color of henna fade? Henna contain lawsone pigment that attaches to the proteins of the skin,hair,etc.But after a few weeks the color fades?

How does the color fade?

Is the pigment volatile or it is degraded by the body?

It doesn't become volatile nor is it degraded. Neither is really possible because the dye (lawsone) forms very strong bonds with protein molecules and also penetrates the skin quite well [source: here].

Henna fades with time via exfoliation. In other words, it fades progressively as additional layers of skin die and fall (or "slough") off.


Is working with (nitrile) gloves around a bunsen burner safe? Recently I have started in a new microbiology lab, and with a new lab come new habits. When I was working with my bacterial (liquid) culture next to the flame (Bunsen burner) wearing nitrile gloves, my colleague warned me to not wear gloves close to the flame. Personally, I never experienced any problems with them and I think that wearing them provides better sterility.

Is it more dangerous to work with gloves close to the Bunsen burner than without?

new microbiology lab

What're the entry requirements for your lab? If you're working in BSL-2 or greater, the appropriate PPE ensemble is listed and required at all times while you're in there. Likewise, gloves are required whenever you're in contact with potentially infectious materials (OSHA 29CFR1910.1030). There shouldn't be leeway to decide when and when not to wear your PPE ensemble.

As bunsen burners do present a burn hazard, your work with a bunsen burner should be preceded by general lab safety training, and subject to work practice controls. It's safe to wear nitrile gloves working with an open flame, and your gloves are not readily combustible. Burns will typically result from a failure to exercise universal precaution and/or use the burner properly.

If you're working dangerously close to an open flame or with heated materials, consider controlling for injury with thermal gloves, tongs, or engineer out the burner with a biosafety cabinet.


Why are the shells of birds' eggs fragile but not those of other creatures? In my limited  understanding, eggs of oviparous creatures other than birds have a flexible outer membrane.
Is there any obvious reason that bird eggs should have fragile shells?

Notes

I'm asking why birds seem to be a special case. If all other oviparians manage perfectly well without shells, what is it about being a bird that requires the extra resources to form a shell?

I believe birds are considered to be modern-day dinosaurs. Didn't dinosaurs have leathery eggs?

Your question is, I think, based upon a false presumption: that avian eggs are more fragile than those of other oviparous animals.
The paper Evolution of the Cleidoic Egg Among Reptilian Antecedents of Birds1 suggests that increased calcification of the avian eggshell is an evolutionary response to protect against predation and microorganisms, particularly in soil. The trade off was less permeability and water absorption. To offset that "cost," birds' eggs evolved the albumen or "egg white" which adds liquid content.
This is discussed more (and referenced) in Frank B. Gill's Ornithology2, which goes on to further explain that the shells additionally protect eggs from the weight of incubating parents.
Other functions, such as that of oxygen exchange, are permitted by the calcium shell due to microscopic pores. Also, crystalline calcite (the main ingredient of the shell) can be used by the embryo to form calcium in development of its bones.
1 Evolution of the Cleidoic Egg Among Reptilian Antecedents of Birds by Gary C Packard and Mary J Packard; American Zoologist, Volume 20, Issue 2, May 1980, Pages 351–362
2 Gill, Frank B.. Ornithology. United Kingdom: W. H. Freeman, 2007.


Meaning of "Domain with function to find" (FIIND) From NALPs: a novel protein family involved in inflammation.

FIIND - Domain with Function to Find.

What is the meaning of this name? Does it mean "Domain with an unknown function"?
I'm translating an article in which this domain is mentioned, and I found three different translations of the term into Russian: "Domain with an unknown function", "Domain with a search function", "Domain with identification function".
I think the first translation is the most logical one, but I'm asking just in case, because I'm not an expert in this field.

The NALP subfamily. Finally, a large subfamily of the CATERPILLAR proteins is composed of 14 NALPs (also called PANs36 or PYPAFs37; FIG 2.) and is characterized by the presence of an amino-terminal PYD. This modular architecture is found in NALPs 2–14 (short NALPs), whereas NALP1 contains an additional domain — which our group has designated FIIND (function to find) — and a CARD, forming a carboxy-terminal extension. With two notable exceptions (NALP1 and NALP3), the NALP genes are located in two clusters on human chromosomes 11p15 (NALPs 6, 10 and 14) and 19q13.4 (NALPs 2, 4, 5, 7, 8, 9, 11, 12 and 13) (TABLE 1). Interestingly, the 11p15.5 region is an important IMPRINTED region and has been implicated in the imprinting disorder Beckwith-Wiedemann syndrome and in various human cancers, including Wilm's tumour38.

I was pretty certain @David's comment was spot on, that this was some one-use funny acronym from just this paper, but a search of Google Scholar suggests that it has indeed been propagated sufficiently to have meaning beyond this paper, while also originating, as these things do, in some clumsy one-off usage.

One of them gives a clear definition that is consistent with what you supposed:

  The acronym FIIND (domain with function to find) was coined several years ago to indicate a highly conserved protein region with unknown function[4]

D'Osualdo, A., Weichenberger, C. X., Wagner, R. N., Godzik, A., Wooley, J., & Reed, J. C. (2011). CARD8 and NLRP1 undergo autoproteolytic processing through a ZU5-like domain. PloS one, 6(11).

The paper they cite (reference 4 in the previous quote) is in fact this one:

Tschopp, J., Martinon, F., & Burns, K. (2003). NALPs: a novel protein family involved in inflammation. Nature reviews Molecular cell biology, 4(2), 95-104.

...which probably looks familiar since it is in fact the paper you started from. Importantly, though, this is not a generic term for a domain with unknown function, it's a specific domain which was known to be highly conserved (and since found in several other proteins) - it's just that it's specific function was at the time unknown.

This paper is a recent review of NLRP1 that may also be useful and has some discussions of what has been found of the functions of the FIIND:

Mitchell, P. S., Sandstrom, A., & Vance, R. E. (2019). The NLRP1 inflammasome: new mechanistic insights and unresolved mysteries. Current opinion in immunology, 60, 37-45.


What's the mechanism for being mentally tired? I notice that after long tests, or long periods of critical thinking, my body and mind feel noticeably tired. Why does this happen? Are the neurons in my head not firing as quickly, or is there just a perceived lack of mental concentration?

What exactly is the mechanism that makes my brain feel worn out, or at least gives me the perception of my brain being worn out?

There is ongoing research on this topic, but there is a theory known as inhibition theory. It has been defined as:

  Inhibition theory is based on the basic assumption that during the performance of any mental task requiring a minimum of mental effort, the subject actually goes through a series of alternating latent states of distraction (non-work 0) and attention (work 1) which cannot be observed and are completely imperceptible to the subject.

For a more in-depth explanation, see this paragraph from Wikipedia:

  Directed attention fatigue occurs when a particular part of the brain’s global inhibitory system is overworked due to the suppression of increasing numbers of stimuli. This temporary condition is not a clinical illness or a personality disorder. It is rather a temporary fatigue of the inhibitory mechanisms in the brain. According to inhibition theory, it is natural for one to alternate between periods of attention and distraction. Although one’s efforts may involve very different tasks, each incoming stimulus calls upon the same directed attention mechanism.

or this paragraph from NCBI:

  Recently, it has been shown that the neural mechanisms of mental fatigue related to cognitive task performance are more complex than previously thought and that mental fatigue is not caused only by impaired activity in task-related brain regions. There is accumulating evidence supporting the existence of mental facilitation and inhibition systems. These systems are involved in the neural mechanisms of mental fatigue, modulating the activity of task-related brain regions to regulate cognitive task performance.

In short, it is now believed that the brain contains mental facilitation and inhibition systems, which control mental freshness and fatigue. Basically, when you concentrate, you actually stop all distractions from taking over (and not give more focus to the main point). This mechanism is governed by the inhibitory system of the brain. After some time, this system stops working ('it gets tired') and you become unable to pay attention towards anything. That's  why it is advised that after some time of concentration, you need to distract yourself (to refresh your inhibitory system); like, say, while preparing for exams, you should have a break of 5-10 minutes after studying for about 45 minutes.

Now, why mental tiredness causes physical fatigue can be (I think) summarized by the diagram below from here:

The exact process at this part is rather very interesting. Here, the neurons are not firing as quickly as they do normally. See this Wikipedia page:

  Physical fatigue can be caused by a lack of energy in the muscle, by a decrease of the efficiency of the neuro-muscular junction or by a reduction of the drive originating from the central nervous system. The central component of fatigue is triggered by an increase of the level of serotonin in the central nervous system. During motor activity, serotonin released in synapses that contact motor neurons promotes muscle contraction. During high level of motor activity, the amount of serotonin released increases and a spillover occurs. Serotonin binds to extrasynaptic receptors located on the axon initial segment of motor neurons with the result that nerve impulse initiation and thereby muscle contraction are inhibited.

The same might happen in the case of mental fatigue i.e. the excess serotonin released from frontal or parietal lobes, or even the inhibition system itself, can cause the same effect i.e. inhibition of muscle contraction.

References:

Inhibition theory
Directed Attention Fatigue
Neural mechanisms of mental tiredness
Mechanism of physical fatigue from mental tiredness
Fatigue


Can fructose take multiple forms ? Which of these structures of fructose is correct? When I look up the structure of fructose I get various different structures
Which of them is correct ?
Are these all just isomers of fructose ?

The two structures on the left are correct; the one on the upper left is the alpha-D-fructofuranose form, while the one on the lower left is the beta-D-fructofuranose form.
Fructose is a ketohexose (a six-carbon sugar with its carbonyl group present as a ketone group in the molecule's open-chain form); the carbonyl carbon (the 2-carbon, to be precise) is optically inactive in open-chain fructose, as the oxygen and two carbons bonded to it adopt a flat trigonal planar geometry, but, when the carbonyl group is attacked by the 5-carbon's hydroxyl group to form the cyclic fructofuranose (fructose in a five-membered ring) configuration, the 2-carbon changes from being part of a (trigonal planar) carbonyl to being part of a (tetrahedral) hemiketal, introducing an additional stereogenic center that wasn't present in the linear form.  The arrangement of the substituents around this new stereogenic center is essentially a random crapshoot, with half of the new fructofuranoses having the hydroxyl pointing in direction 1 and the hydroxymethyl pointing in direction 2 (the alpha form), and the other half having the hydroxymethyl pointing in direction 1 and the hydroxyl pointing in direction 2 (the beta form).
There are, by the way, eight other configurations that fructose can take; three of them (plus the two you've already drawn) are for D-fructose (the naturally-occurring-in-the-vast-majority-of-naturally-occurring-fructoses form), while the remaining five are for L-fructose (which occurs only very rarely in nature and is essentially useless for most living organisms), which has the hydroxyls on the 3-, 4-, and 5-carbons pointing in the opposite direction.1

The alpha-D-fructopyranose and beta-D-fructopyranose forms have a six-membered pyranose ring, rather than the five-membered furanose ring; these are formed when the hydroxyl group attacking the carbonyl is that attached to the 6-carbon, rather than the 5-carbon, and are actually energetically much more favourable than the fructofuranose forms, making up essentially 100% of crystalline fructose and 70% of fructose in aqueous solution.
The open-chain D-fructose form is acyclic, with the 2-carbon actually being part of a carbonyl group rather than a hemiketal.  It is present in only minuscule concentrations in aqueous solution, but serves as the intermediate between all of the various cyclic forms of D-fructose.
L-fructose can adopt the alpha-L-fructofuranose, beta-L-fructofuranose, alpha-L-fructopyranose, beta-L-fructopyranose, or open-chain L-fructose forms, which are essentially equivalent to their D-fructose equivalents apart from their opposite chirality.

1: In the L-fructofuranose configurations, this takes the form of the hydroxymethyl group hanging off the 5-carbon pointing down rather than up.


Does Goryaev's chamber have the same grid layout as the conventional counting chamber used in the West? I'm translating a Russian biotec text where some cell counting operations are mentioned. The piece of equipment the authors mention in this context is "Goryaev's chamber" (камера Горяева):

  We discarded the supernatant, washed the cells with DPBS twice (suspended and centrifuged them for 10 min at 200 g), then diluted with 10 ml of ADCC assay medium and assessed the concentration and viability of the cells in a Goryaev's chamber.

Is a Goryaev's chamber any different in terms of its counting grid layout from the conventional hemocytometer chamber described in Wikipedia?

I would like to translate the phrase simply as "using a cell counting chamber" or "using a hemocytometer". The Multitran dictionary does offer these words as possible translations, but it occurred to me that Goryaev's chamber might differ somewhat.

From the description at http://cldtest.ru/hdbk/chamber

It appears to be functionally the same device, except the only the smallest square are marked (0.25 nL and 4 nL), and the total capacity is 90 nL instead of 100 nL. A hemocytometer could be used in place of a Goryaev's chamber (though not necessarily the reverse).


Why is this Cuscuta compacta purple? I was recently browsing the web and came across this site abut the compact dodder.

https://gobotany.nativeplanttrust.org/species/cuscuta/compacta/
The image used to identify the plant shows it as purple. This struck me as odd, as those are usually a greenish-yellow. Why is this plant purple? Is it a special sub species? Is it perhaps another type of dodder entirely, and gobotany simply messed up? I think this image might actually show the Cuscuta glomerata, but I'm not sure. Please explain this discoloration. Thanks in advance!

the Genus Cuscuta has over 200 species varying in color from yellow, to orange, and purple (sometimes but rarely can also be green).
The organism in the photo is not likely to be a subspecies of the usual dodders you find in your area, instead it is likely to be a different species entirely (while still belonging to the same genus).
The rope dodder (Cuscuta compacta) is very possibly the species you are looking at. However, I am also convinced that Cuscuta europea is a possible candidate, particularly due to this photo of the species that I got from the European Nature Information System (EUNIS) web site:

I must admit that I do not know nor have access to photos of all the different species of the Cuscuta genus to make a truly objective analysis of your image however I hope this information as a minimum leads to some new insight on the matter.


Are glycoproteins and glycolipids present only on the cell surface membrane? I haven't read this being stated explicitly, however whenever I read about proteins and glycoproteins this seems to be implied. For example, in this Wikipedia article,

  Lipid and proteins on the cell membrane surface often have short carbohydrate chains protruding out from the cell surface, known as glycolipids and glycoproteins.

My question is, is this the case? And if so, why would they only be present on the cell surface/plasma membrane. Would they not be useful elsewhere in the cell for example for vesicle trafficing as receptors for targetting sequences?

One idea I have is that, to the best of my knowledge, the enzymes for glycosylation are present in the endoplasmic reticulum and Golgi lumens (oligosaccharyl transferase in ER, etc) so glycosylation would only occur on the part of the protein/lipid that is topologically outside of the cell, however this brings up more questions:

This does not exclude glycoproteins from sticking into certain organelles (i.e. on the other side of the membrane to the cytosol) which is also topologically equivalent to the cell exterior.
Why would there not be glycosylation enzymes on the cytosolic side?

Since you asked three questions, I'll answer them one by one.

Are glycoproteins and glycolipids present only on the cell surface membrane?

No, glycoproteins have many functions and are certainly not restricted to cell membranes.

Some examples of glycoproteins in blood include fibrinogen, antibodies, miraculin, etc. See this:

  Fibrinogen (factor I) is a glycoprotein in vertebrates that helps in the formation of blood clots.

For a more detailed list of glycoproteins, see this wikipedia article.

On the other hand, glycolipids are found only on cell membranes. See this:

  Glycolipids are lipids with a carbohydrate attached by a glycosidic bond. Their role is to maintain stability of the membrane and to facilitate cellular recognition. The carbohydrates are found on the outer surface of all eukaryotic cell membranes.

This does not exclude glycoproteins from sticking into certain organelles (i.e. on the other side of the membrane to the cytosol) which is also topologically equivalent to the cell exterior.

Glycoproteins, or any proteins, after they are completely processed , don't just float around in the cell and reach their appropriate place. Its obviously not that proteins 'know' where to go, but they are actually taken to their appropriate places. This is known as protein targeting. See this:

  Protein targeting or protein sorting is the biological mechanism by which proteins are transported to the appropriate destinations in the cell or outside of it. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion. This delivery process is carried out based on information contained in the protein itself. Correct sorting is crucial for the cell; errors can lead to diseases.

There are differences between cell membrane and organelle membrane, which makes them distinguishable for targeting factors.

Why would there not be glycosylation enzymes on the cytosolic side?

Glycosylation is a post-translational modification or proteins.

  Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins during or after protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product.

Only certain proteins require glycosylation, that is why they are translated by ribosomes connected to golgi apparatus or endoplasmic reticulum. If glycosylation enzymes are present everywhere in the cell, then every protein that encounters them would get modified and, possibly, non-functional. Thus, there are special compartments in the cell for such purposes.

EDIT: To answer the questions you asked in comments:

are there any glycoproteins found elsewhere inside the cell? For example in the mitochondria?

We aren't sure about that yet. There have been a couple of studies to find out whether there could be glycoproteins in mitochondria, one of which is this:

  Isolated intact mitochondria selectively incorporate monosaccharides from nucleotide diphosphate monosaccharides into protein. Fucose, mannose, glucose, and galactose were incorporated by the mitochondria into glycoprotein; xylose was not. Structural integrity of the mitochondria was not necessary for the incorporation of monosaccharide into glycoprotein; mitochondria broken by homogenization also incorporated monosaccharide. The monosaccharides incorporated into glycoprotein were localized in the inner mitochondrial membranes, the same membranes which contain the protein into which leucine is incorporated by the isolated mitochondria.

If there are glycoproteins in mitochondria, they could be at many other places too inside a cell.

does the cell not sometimes need glycosylated proteins inside of its cytoplasm? How would it get these proteins in its cytoplasm?

Glycoproteins are not required inside cell (I, or maybe nobody, knows why). Their main function is as receptors or secreted products, thus they are not found inside a cell. However, glycosyltransferases can behave as dynamic glycoproteins and hence are found inside cells. See this:

  Glycosyltransferases (GTFs, Gtfs) are enzymes (EC 2.4) that establish natural glycosidic linkages. They catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as the "glycosyl donor") to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen- carbon-, nitrogen-, or sulfur-based.


Transcription and translation of prokaryotic operons I'm taking a molecular genetics course, and we're currently discussing prokaryotic operons. The lacZ operon came up frequently for me as an undergraduate as an example for teaching regulatory control of transcription, and the focus was always on determining whether the operon was transcribed under certain conditions (mutations, nutrients, etc). I don't remember much discussion about what happens after transcription. Today, however, I noticed something I had never seen before: three of the genes in the lacZ operon are transcribed simultaneously on the same transcript--I don't know how I missed this before!

My question is what happens post-transcription. Obviously there are 3 protein products. How are these products derived from the transcript? Is the transcript broken into 3 pieces, or does a single ribosome translate all 3 proteins from a single transcript substrate, or do ribosomes translate a single protein from a single transcript substrate at a time? Where could I find the relevant literature that elucidated the translation process?

As you pointed out, the repressor gene lacI is transcribed as a one mRNA, and three structural genes: lacZ, lacY and lacA are transcribed into a single polycistronic mRNA. The two mRNAs are translated independently of one another.

The polycisronic mRNA is not broken into pieces. Rather, it is translated by ribosomes (at least three, explanation below), giving rise to three individual proteins.

How from one mRNA three protein products are translated? The polycistronic DNA consists of a promotor (Plac), which ensures that transcription will be initiated, and three open reading frames (ORFs) for for lacZ, lacY, and lacA. Upstream of each of the ORFs, ribosome binding sites (RBSs) are located. Translation is initiated by the binding of the ribosome with both the RBS and the start codon. Thus, multiple ribosomes can bind upstream of the three ORFs and thus resulting into three proteins.

There is not very thorough literature on the translation of polycistronic RNA in prokaryotes, mainly because the condition which is necessary for translation is the RBS and there is nothing specific for polycistronic translation. A brief overview on the subject can be found in several places, as I recommend the following:

Ralston, A. (2008) Operons and prokaryotic gene regulation. Nature Education
From Genes to Genomes: Concepts and Applications of DNA Technology
Molecular cell biology
Analysis of Genes and Genomes


Why is Aorta sometimes called Compression chamber? I find this statement that Aorta is called Compression Chamber in my study materials.

Aorta can

it keeps blood flowing
it can accumulate potential energy for bumping and compression

However, why aorta is called chamber and particularly compression chamber?
I heard this term today first time.

The aorta is a compression chamber because it is an important drive for diastolic perfusion. To keep the blood flowing constantly, and not only during systole (as would be the case with a rigid aorta), the high elasticity of the aortic walls allows it to dilate as a consequence of the high systolic pressure. This allows the aorta to accumulate blood in its proximal part, which is then propelled by the passive elastic contraction of the aorta during diastole.


How to seek for available genetic data relevant to ecology and evolution? I had a quick look online. There seems to exist many different website of database archiving. Some data might be free of charge while some others might not be. I found things such as Dryad, TreeBase, DataOne or GeneBank. I think that several journals (American Naturalist, Molecular Ecology, Science and Nature for examples) force their authors to make their data available

General Question

Can you make a short review of what different database exist, what are their properties (what kind of data, what license and fees) and how to seek for data (are datasets associated to keywords or do we have to look for a paper and then look for their data).

Case study

Imagine for example, you are looking for SNP data of a spatially explicit population that recently underwent a range expansion (might be too accurate, you may want to drop down some specifications). How would you go about to look for this kind of data? (No need to pull out data but only to describe a procedure).

As a bioinformatician, one of my tasks is quite often to get information from databases or find the correct database to compare to. There are several big databases around, but even those are way too many for any single person to know.
There are databases specialising on genetic data, some specialising on taxonomic information, some on ecological information and then there are species specific databases which collect all kinds of data from a given species, genus or clade.

For me the biggest source of generalised information would be the NCBI databases, including GenBank for nucleotide sequence, their Protein database and maybe dbSNP for, well, SNPs. Then there are multiple 16S databases I have used, there is UCSC for the basic data about the human genome, flyBase for Drosophila,... I think the point should be clear. And those are only the ones that just sprang to my mind.

If you don't have a very exact question to answer like "Is there a gene similar to gene x from Drosophila present in any Bacteria?" it can be very hard to both choose the correct database and also find the important information in it efficiently.

Then there is the problem of metadata. I might be able to find sequencing data from the gut microbiome of a human treated with antibiotics quite easily. If I am looking for a specific antibiotic given over a minimal time of seven days to a different healthy humans, preferably including at least one breastfed child and it's mother (which was the one taking the antibiotics, not the child), then it's getting complicated. Here it is generally way easier to scan PubMed for some relevant publications on the matter and find out if they used published datasets or published their own.


Identifying a creature that appears to be a worm wrapped in a cocoon This creature was found on a bed. At first, I thought it was a piece of lint, but then it suddenly moved. I picked it up in a paper towel and put it in an eye cream containers, which it is currently in. I believe this means that it is pretty strong, since it appeared to have pulled itself all the way up from the floor, to the top of the bed, then across to the other side of a King-sized mattress.

It appears to be a worm wrapped in a cocoon. It is pretty short, being small enough to fit inside an eye cream container.

The creature is a pale yellow-white/cream, with brownish-red tips on each end (unless it can somehow turn around without exiting its casing). It looks from the side as if it has a rather flat face, one that comes to a slight bump at the bottom, but is pretty much flat. The casing is light grey, with some small portions that appear to be almost the same color as the organism, just slightly darker. There is an opening at each end of the casing, which the organism uses to slide slightly out. It has never fully come out of the casing. The edges of the openings at each end are white. The casing seems to either be made out of or covered in dust.

It can create a substance that is sticky and strong enough to support its weight. I cannot tell if the substance is created by the 'worm', or the 'cocoon'. A thread at each end of the casing is connected to the side of the container by the substance. When I accidentally detached one end of the casing, the entire thing began to shake violently when held so that one end was hanging. It wouldn't stop until I had turned it so that both ends were touching the side of the container. Within minutes, though, it had reattached the broken end. Minutes. Not hours, but one minute.

The holes at each end of the cocoon can either grow or shrink closed. I believe this allows us to tell which opening is in use. If it is nearly shut, it will come out the other end.

It appears to be nocturnal, since it doesn't move during the day, but it is very active at night. It also appears to react to light. If some is put on it, it will poke out to look around.

It has survived for four days straight without food, as far as we know. We put a small piece of lettuce in with it. However, there are two small, brownish things on the bottom of the container. This may be its excrement.

The creature moves by reaching out with its 'tentacle/worm', grabbing onto something (including the ground), and pulling itself forward.

I cannot tell if the creature is attaching to the container's side to climb, or because it is morphing. If that is the case, then the outer shell may be a cocoon. It did detach itself from the side of the container, and first hid under a ledge of lettuce, but now has wrapped itself in lettuce.

To summarize: can someone please help me identify this creature?

I think it's just a case bearing moth larva (Tinea pellionella).

Source: http://www.hantsmoths.org.uk/


Have novel interactions or pathways been predicted by GRN or PPI data and later confirmed by experiment? I've been learning about the gene regulatory network (GRN) and protein-protein interaction network (PPI) recently.
I've found a huge amount of extremely interesting papers about how biological network data is accumulated and how it can be studied.

However, what I haven't found is any examples where the network data was used to make a novel prediction which was later experimentally shown to actually exist.  What are some of the cases where this has happened?

There is very interesting work in this regard done by Ed Marcotte. An overview of the "machine" and its conservation across species is here. The point here is the machine or network is conserved, but used in different ways in different organisms. Hence, the phenotypes of mutants might be different, but they'd be consistent across many variants in the components of the machine.

One paper of his describes a tool, which uses well developed guilt-by-association principles upon a human gene network to identify associations of gene sets. This is available at www.functionalnet.org/RIDDLE.

Look at their approach to prioritizing candidate disease genes by network-based boosting of genome-wide association data.

Some specific examples of the conserved "machine" are given in this elegant PNAS paper. It is nice how they tested the genes in Xenopus embryos.


How much energy does a cell expend maintaining its contents? In software engineering, an analogy is sometimes made using biological cells. I would like to know whether it has basis in fact.

People say (Alan Kay was first) that "objects" in software should be like cells: separate from one another, communicating by passing messages. This separateness has been argued by saying that a cell spends much of its metabolic energy keeping its insides in and its outsides out. The implication is that programmers should likewise spend significant effort maintaining boundaries between parts of a system.

Is this actually true? What percentage of its energy does a cell generally spend maintaining its contents?

(My guess is that the answer varies wildly depending on the cell and its environment, but some ballpark example numbers would be nice.)

I'm going to take a stab at this.  Its a difficult question to get right, just to put is in the right mood here.

Lets leave energy out of this as the proper term is structure.  The cell is designed to compartmentalize itself to differentiate its own living tissue from other cells.

In this regard Alan Kay's analogy is pretty good.  In multicellular organisms, individual cells (mostly) each maintain their own DNA and energy storage, though they get their nutrients and energy from outside.  They create the organism as a whole by differentiation; each cell changes to take on a specialized role and depends on other cells to support it. E.g. in animals some cells/organs digest the food and distribute nutrients to the rest, others form the lung and help distribute oxygen and others scrub the blood of waste.

This is somewhat like good code design where functions are partitioned out into specialized parts of the software for the sake of maintainability and organization.

Somewhere after this point I think the analogy breaks down since after all the point of good coding practice is to organize the code for understanding within reasonable human conceptual limits.  The cells and how they organize themselves are still plenty mysterious to us as they have their own definition of roles and function much of which is still being discovered today.  For instance the many kinds of neurons in the brain and the sorts of structures they form are extremely diverse.  We have few organizing principles for predicting how many cell types would exist in a system and these only create partial answers.

After all its just an analogy...

getting close to an answer?


Is there a minimum load below which an infectious agent will not cause disease? Suppose a single smallpox virus is injected in an human adult's body. Will it cause disease in the host? Is there a minimum microbial load below which it will not cause disease?

It depends on the pathogen, delivery method, environment, etc. In most cases, a single pathogen is not enough to cause disease -- it may need many millions or billions -- but there are some cases where it does seem that a single pathogen can consistently cause infection. For example

  The minimum infectious dose of ASFV in liquid was 100 [i.e 1] 50% tissue culture infectious dose (TCID50), compared with 104 TCID50 in feed. The median infectious dose was 101.0 TCID50 for liquid and 106.8 TCID50 for feed.

--Infectious Dose of African Swine Fever Virus When Consumed Naturally in Liquid or Feed

If you're asking specifically about smallpox, I don't think anyone has done the experiment (the natural and most susceptible host being humans, I think you'd have some trouble finding volunteers to find to lethal dose). A single virus of the related ectromelia (mouse pox) virus can cause death in particularly susceptible mouse strains:

  The intranasal lethal mousepox model employing the A/Ncr mouse strain is used to evaluate anti-orthopoxvirus therapies. These infections mimic large droplet transmission and result in 100% mortality within 7-10 days with as little as 1 PFU [plaque-forming unit] of ectromelia virus.

--Mousepox in the C57BL/6 strain provides an improved model for evaluating anti-poxvirus therapies

As a side note, the notion of what a "single virus" actually is, is more fuzzy than you might think, but that's a more complicated question; to a rough approximation a single TCID50 or PFU can be considered to be a single virus.


Why aren't 'exons' named 'introns'? Why are introns called 'introns' when they are the actual ones who are getting spliced out from the pre-mRNA. Shouldn't exons be named introns as they are the ones that are 'in' and are not 'exiting'? On what criteria were they named like this?

The terms intron and exon were coined by Walter Gilbert in a renowned 'News and Views' article, Why Genes in Pieces, published in the journal Nature in 1978.

Introns are the intragenic regions and exons are the regions which are expressed.

This is the relevant passage in full:

  The notion of the cistron, the genetic unit of function that one thought corresponded to a polypeptide chain, now must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger - which I suggest we call introns (for intragenic regions) - alternating with regions which will be expressed - exons. The gene is a mosaic: expressed sequences held in a matrix of silent DNA, an intronic matrix.


What might a supposed “tree enzyme” be — injected into a Morton Bay Fig tree? I was recently visiting Fremantle in Western Australia and noticed a large Morton Bay Fig tree in Kings square in the centre. Apparently the health of this tree had been declining, but they hope that recent treatment will lead to an improvement.

The notice by the tree said this was by “injection of a tree enzyme”. I also found the following quote on the City of Fremantle FB page:

  To improve the tree’s absorption of nutrients which will help it grow stronger, the bioscientist has given it a ‘booster’ enzyme injection. This enzyme naturally occurs in trees and is an additional boost that will hopefully help the fig tree recover and flourish again this spring.

Well trees have enzymes like any other living thing, but I find it difficult to imagine what enzyme injected into a tree would get transported through its system and help it heal. Is there anyone in silviculture (or WA) who has any idea what this was?

So eventually I decided to email the City of Fremantle, who put me in contact with their Parks Department, who gave me the name of the company who had handled the tree, who replied with a most informative letter.
And the answer is…

Glutathione

Most animal biochemists, like me, will be more familiar with the importance of glutathione (reducing sulphydryl group highlighted in yellow, above) as a reducing agent in erythrocytes, the constituents of which are subject to oxidation damage.
What was wrong with the tree?

“…the figs in Kings Square… had quite elevated levels of heavy metals Cd, Cr, and metalloids Hg and As.
We traced this back to the colonial past, where in the 1830s – 1840s, when gold had been discovered south east of Fremantle, a battery operated (by the Crown) in Fremantle. In those days, gold was commonly lixiviated using mercury. Kings Square had a pit cut earlier for mining limestone. A good place to dispose of battery mullock is a pit.The earliest gold deposits were mafic ores, so often contained Cd and Cr.”

Why use glutathione to treat the trees?

“Firstly, it stimulates the jasmonate pathway, thereby alters transpiration and root growth.
Secondly, it assists in the isolation and immobilisation of heavy metals.
Thirdly, if assists in the breakdown of triazine herbicides by ring cleavage…”

And my correspondent kindly provided a review by Hossain et al. in the Journal of Botany, which elaborates on the second point.
And why the “tree enzyme” business?
This did not come from the company that handled the treatment, but from someone (unknown or nameless) who was handling the public relations, and who wished to provide reassurance that the treatment was ‘natural’:

“I guess in the world of snake oil, “enzymes” are benign, natural things, rather than usually ephemeral catalytic proteins.”


Feedback affecting myocyte metabolism in humans I understand that there are several reserves available to muscle that can be tapped for ATP, and that each reserve is being used to some degree at all times.

Are these reaction rates purely due to the presence of reactants which are products of myocyte activity?

Or are there other controlling reactants involved that determine the rate at which each reserve is consumed?

Well, ATP is replenished from three energy sources, namely:
1. phosphagen system (very fast, but quickly deprived)
2. glycolysis (fast, but slower deprived)
3. oxidative system (slow, 'impossible' to deprive)

When ATP is used, for example for muscle contraction, ADP is formed. The formed ADP can be rephosphorylated to ATP by the enzym creatine kinase, which also requires creatinephosphate (the phosphate attached to the creatine provides the phosphate group for ADP to form ATP). Additionally, ATP can be formed out of 2 ADP molecules by adenylate kinase. The phosphagen system is largely driven by the law of mass action, i.e. the direction of the enzymatic reaction is controlled by the concentration of the products and substrates. In other words; when ATP is low, and ADP is high, the generation of ATP is favored and vice versa. The energy from the phosphagen system is depleted rather quickly tho.

The second system, glycolysis, simply refers to the breakdown of carbohydrates (e.g. glucose) to resynthesize ATP from the energy stored in those carbohydrates. Your muscles contain a buffer of glycogen, approx. 300~ gr for the average Joe (give or take). The glycogen can be broken down to glucose-6-phosphate, which can then enter glycolysis. The glucose-6-phosphate is broken down to 2 pyruvate and yields 3 ATP netto (2 when derived from glucose, rather than glycogen, due to a first enzymatic step which requires 1 ATP). The enzymatic steps of glycolysis are controlled by ATP, AMP, ADP and other factors, factually integrating the energy status of the muscle (primarly through allosteric regulation of enzymes, especially phosphofructokinase).

The third system, the oxidative system, refers to the breakdown of carbohydrates and fatty acids, requiring oxygen to 'burn' them (citric acid cycle). The yield of this is much higher than for glycolysis, but the process is way slower.

In essence, all are regulated by the concentration of substrates and products, as well as through allosteric regulation (binding of a molecule at a different site, inhibiting or activating the enzyme, often by intermediates of the pathways themselves). Additionally, there is some long-term regulation through gene expression (e.g. up- or down-regulating expression of genes involved in these pathways), mostly by hormones.

Edit:
Well, I guess this is described in any basic biochemistry book (I'm very fund of the book 'Fundamentals of Biochemistry: Life at the Molecular Level'). If you want to see a description of these energy systems in a more exercise related context (since you were aiming at myocytes) I suggest reading Strength and Condition: Biological Principles and Practical Applications from Marco Cardinale et al., and the NSCA book Essentials of Strength and Conditioning.


How does the helicase enzyme break the hydrogen bonds between the strands of DNA? I know helicase breaks the hydrogen bonds between the strands of a DNA, but how is this done?

Does it put an ion between the strands of the nucleic acid so that the bond breaks apart itself or is there some other mechanism?

Im not sure if there is a decided helicase mechanism but the ‘backbone stepping motor’ model has been proposed for
helicase translocation and unwinding. Helicases contain two domains that are analogous to a set of ‘pincers’ (motor domain), when ATP is present, there is only a distance of two nucleotides between the
pincers and so they are closed, whereas when ATP is absent, there is a distance of three nucleotides between the pincers and so they are open. The motor domains interact with the
nucleic acid through contacts between threonine residues on the pincer terminus and phosphoryl oxygen on the nucleic acid. ATP binding weakens these interactions, allowing a pincer to move one nucleotide closer to the second pincer. A third domain (D3), that is part of the helicase but not involved in the binding of ATP, also interacts with the nucleic acid using a threonine residue. As the motor domains move along, tension builds up between the motor domain and D3 and after the motor domain has moved three base pairs, the protein contracts like a spring, pulling D3 toward the motor domains, disrupting the DNA in between. The structures responsible for prying apart the DNA are called “pins” or wedges”, which act as a physical barrier between the two strands of nucleic acid, prying apart its structure. The single
stranded regions are stabilised by helicases as well as other proteins such as single stranded DNA binding proteins, which prevent the reformation of the double stranded nucleic acid.

For more information and good images see: “Translocation and unwinding mechanisms of RNA and DNA helicase”


Explain a gene network to a first year undergrad I have an adjacency matrix with list of genes connected to each other which signifies the gene network. How do you get this information that one gene is connected to other in the first place. Is it that you do a microarray analysis and find genes that are upregulated and downregulated and assume that all the genes that are upregulated, regulate each other. Kindly explain.

P.S The microarray example is what I assumed. Doesn't mean that it should be the way that a gene network is deduced. My network is an undirected one.

There is no single answer, because networks (or graphs, as they are called in discrete mathematics) are flexible tools that can be used to model all sorts of relationships between genes, transcripts, proteins, or other entities in biology. (And networks are useful models in many other disciplines too, like sociology.) Depending on the type of network you're considering, there are various experimental methods for determining connections. I give only a couple of examples below. For general information on networks as abstract models, look into graph theory.

Gene regulatory networks

A gene regulatory network is a directed graph where one gene (A) regulates another (B). In this case, the connections between genes are directional and can be represented by arrows A $\rightarrow$ B. Depending on exactly how you define "regulation", a connection A $\rightarrow$ B can mean different things, for example:

Gene A encodes a transcription factor that binds to gene B. In this case, evidence for A $\rightarrow$ B comes from assays of proteins binding to DNA, such as chromatin immunoprecipitation (ChIP). Large collections of such data are available in databases like Transfac.
Expression of gene A causes regulation of gene B, by any mechanism (possibly indirectly). In this case, data for an interaction can come from experiments where gene A is induced (forcibly expressed) or suppressed/deleted and the resulting changes in other genes are measured, for example by microarrays or RNA sequencing. A famous early example of this is the "Rosetta" data set on yeast deletion mutants.

Inference of gene regulatory networks is a large and complicated topic that I cannot cover here. It depends on many factors, such as how you model the time dimension (do you have steady state or transient data), and how you parameterize the network to model expression data quantitatively. The review suggested by @CMosychuk looks like a good place to start.

Coexpression networks

This type of network represents coexpression between genes (or more accurately, between mRNAs or proteins). This is typically a representation of pairwise correlations between genes across some set of conditions, so the data source can be any collection of mRNA or protein level expression data. (Here is one example.) Because correlations are symmetric, connections in this type of network have no direction, and can be represented simply as a link A$-$B (not an arrow). Partial correlations are sometimes used to filter out indirect associations, but still these networks contain no causality information, and should not be confused with the directed type.

Protein-protein interaction networks

These are undirected network models where a link A$-$B means that two proteins interact physically. Data supporting such connections come from various biochemical assays for protein interaction, such as the two-hybrid assay or immunoprecipitation. There are large databases collecting protein-protein interaction data that can be used to build these network models, for example BioGRID.

There are many other types of networks, but this is already a long answer :) As you can see, it's important to be clear on what type of network you are working with. Often the data you have available will determine what network model is suitable --- for example, if you have only a collection of unrelated transcriptome profiles and no causality information, a coexpression network might be the best model.


How does the number of chromosomes evolve through generations? Mitosis is a complex mechanism that, through mutations and crossover, determines how a chromosome is composed. But at that point, the number of chromosomes is already determined: how can this number evolve through generations? What mechanism is involved?

A mutation is a general term referring to any alteration of a nucleotidic sequence. It includes small mutations like indels (insertion or deletion of a single nucleotide) and substitutions, or bigger mutations such as e.g. chromosome fusions, whole chromosome duplications, Robertsonian translocation, whole genome duplications and gene deletions. Some of these bigger mutations can affect the number of chromosomes (and ploidy number).

Such of these mutations can typically be caused by the non-disjunction of homologous chromosomes during meiosis.

Most of these mutations are deleterious but some aren't and might eventually fix (fixation = reach a frequency of 1.0) in the population.

A very common example of such mutations in humans is the mutation that is causing the Down syndrome.


Can a person die from over exposure to rain? Is it possible to die from being over exposed to rain? For example, if outside for a long amount of time (days) in a continuous storm?

I searched online but didn't find anything immediately. To me, maybe a really long exposure to rain (water) would cause skin tissue issues, which might then have potentially more serious effects on other body organs/systems.

Rain per se? No. But when you are wet, your body looses heat more quickly. If it's near freezing, windy, and raining you are in much more danger of developing hypothermia, or low body temperature. If your body temperature falls low enough, you can die. You may hear references to death from exposure, which is shorthand for "exposure to the elements", but the actual problem is hypothermia. If your feet are continuously wet for days and day, you may develop immersion foot, also called trench foot:

  Trench foot is a medical condition caused by prolonged exposure of the
  feet to damp, unsanitary, and cold conditions. The use of the word
  trench in the name of this condition is a reference to trench warfare,
  mainly associated with World War I. Affected feet may become numb,
  affected by erythrosis (turning red) or cyanosis (turning blue) as a
  result of poor vascular supply, and feet may begin to have a decaying
  odour due to the possibility of the early stages of necrosis setting
  in. As the condition worsens, feet may also begin to swell. Advanced
  trench foot often involves blisters and open sores, which lead to
  fungal infections; this is sometimes called tropical ulcer (jungle
  rot).


What is the non-local impact of a large-scale destruction of coral reefs? I'm reading today that the "bleaching" of coral reefs is progressing with unanticipated speed. Bleaching is occurring at a scale which was previously believed to be decades in the future.

Bleached corals, according to the article in the New York Times1, have shed their symbiotic algae in order to protect themselves from toxins the algae produce when the water temperature rises above a certain threshold. If cooler temperatures are not restored quickly, the corals will die. This has happened with many affected reefs in the past and seems likely with the latest wave of bleaching too, given the apparent long-term increase in global water temperatures.

Even if the article does not say so directly it appears to me a distinct possibility that most coral reefs will simply disappear from the planet within just a few decades.

What impact will the disappearing of the coral reefs have on the oceans and the life in them, and ultimately on the whole planet? We know that reefs are the core of a complex and rich ecosystem. Which plants and animals outside the immediately affected areas depend on it? Are there migratory species who lose the reefs as a seasonal base? Which food chains will be interrupted, or over-provided? Do coral reefs have other functions like filtering, causing or reducing turbulence, influencing currents? Have there been studies or simulations which try to assess the global consequences?

[Edit]: I know the question is very broad. I'd be happy about answers to just one aspect. Specifically I'm interested in effects which are not obvious and/or have not been broadly publicized. Links to scientific publications would be awesome. Maybe somebody is working in the field, or knows somebody?

For example, affecting migratory species (fish or birds) may have unexpected consequences in otherwise unrelated parts of the world, similar to the effect of disappearing wetlands on migratory birds.

I also think it's possible that non-reef fish which are important food sources directly or indirectly depend on coral reefs. Are there specific examples?

I'm less interested in answers concerning species just living around the reef because cause and effect (though significant) are obvious.

1Which refers to the original study in this nature article.

Disclaimer: the question is too broad and speculative to some extent, and thus less likely to get complete answer (at least in a single post).

As is already known, thousands (or millions) of species are dependent on coral reefs for their survival and are likely to get extinct (unless they adapt) because of destruction of coral reefs. A short list includes fishes, turtles, sharks, eels, crabs, shrimps, urchins, sponges, algae, and so on1. Now, telling which of them will be immediately affected will be largely speculation, yet the first 5 species to lose the race, as per a speculation, are2:

Butterfly Fish: Species of fish that are obligate corallivores, such as many butterfly fishes (Chaetodontidae), feed exclusively on coral polyps. Obviously, survival would not look good for these fish if their food source disappeared.  Like parrotfish, butterflyfish assist in keeping algae from smothering corals.

Spiny Lobsters: Spiny lobsters rely on coral reefs for protection, especially during their vulnerable molting episodes. These lobsters have a significant role in maintaining a balanced ecosystem. Like sea otters, spiny lobsters are predators of sea urchins, which feed on kelp forests and can destroy them if populations are not predator-controlled. Kelp is important for many reasons, including those listed on OGP’s kelp recipes.

Whales (and dolphins): Many scientific studies have substantiated that dolphins and whales have extreme emotional intelligence. Sadly, their intellect won’t be enough to help these animals if coral reefs are destroyed. Dolphins and most whales (cetaceans) are predatory animals and they are all carnivorous. It’s a fish eat fish world and many fish survive by consuming fish that rely on coral reef habitats. Every species lost will affect another…and another…and many others. So, these come under the indirect adverse effects of coral depletion, since they themselves don't rely on corals.

Whale Sharks: Whale sharks are an important indicator of marine productivity and have a role in the conservation of other marine organisms. Although there has not been adequate research to understand why whale sharks are dependent on coral reefs, it has been shown that decreases in whale shark populations in the late 1980’s and early 1990’s may have been linked to increased rates of coral destruction.

Hawksbill Sea Turtles: Although all sea turtles would be affected by the loss of corals, Hawksbill sea turtles have become critically endangered species and are highly dependent on coral reefs for their food sources, mainly consisting of sponges. Sea turtles play significant roles in their ecosystems in that they help with nutrient cycling from ocean to land, maintaining healthy sea grass beds, and balancing food webs.

Coral reef fishes are in general rather sedentary and territoriality and home range behavior patterns are highly developed. However, many species migrate, often relatively long distances compared to body size and often with spectacular precision. Migrations in reef fishes may be associated with3:

Life history: movements of
planktonic larval stages to reefs or movements of juveniles from nursery areas to reefs
Seasons: precisely timed spawning aggregations drawing fishes to particular locations from wide areas of the reef
Diel patterns: movements to and from feeding or resting areas associated with dawn and dusk.

Another species, which is to be affected, though not immediately, by destruction of corals, is humans(!). As per experts4, coral depletion will bring threat to not only income and economic stability, but also to survival by causing depletion of food and increased risk of coastal disasters, which are likely to kill millions.

Coral reefs also serve many purposes, a few of which are5:

protect coastlines from the damaging effects of wave action and tropical storms
provide habitats and shelter for many marine organisms
are the source of nitrogen and other essential nutrients for marine food chains
assist in carbon and nitrogen fixing
help with nutrient recycling.

Finally, I suppose most of the species will be affected because of depletion of source of food rather than more-than-sufficient amount of something. Also, I was unable to find any simulations of the global consequences of destruction of coral reefs. I hope this much would help!

EDIT: I did some online research, and found lack of research about this topic. But I found a paper regarding relationship between seagrass, mangroves and coral reefs6 regarding life cycle of migratory fishes. From the same:

  Coral reefs showed the highest mean fish species richness and were dominated by adult fish, while juvenile fish characterized seagrass beds and mangrove sites...Our results suggest that connectivity of seagrass, mangrove, and coral reef sites at a species and site levels, should be taken into consideration when implementing policy and conservation practices.

It becomes evident from this research that depletion of coral reefs would certainly affect life cycles of these fishes, which include Scarus iseri (Striped Parrotfish) and Lutjanus apodus (Schoolmaster Snapper), which will, in turn, affect biodiversity in seagrass beds and mangroves, leading to further break in food chain in more diverse areas.

Some researches have also suggested that seabirds might also be on a high rank in this list. Seabirds survive by eating fishes, and studies have shown that increasing water temperatures halt their growth while higher sea levels cause them problems in nesting. Now, it has also been suggested that due to coral bleaching, many fish species which live on corals might either die or move to other places, because of which seabirds could also face survival crisis7.

Another point regarding your demand I'm interested in effects which are not obvious and/or have not been broadly publicized, specifically not been broadly publicized, is that it has now become difficult to find such papers. This topic (climate change) has become so much publicized now that all related papers get attention immediately. So, it is quite difficult to find environmental research papers about climate change which hasn't gained much attention. Yet, I'll keeping on adding more research papers as I find some more.


Lentivector biosafety Lentivectors are widely used in molecular biology, most commonly to transduce in a stable way a desired gene. These vector system takes advantage from the ability of viruses to introduce their own genome in the host cell. Thus the lentivectors are transfected to a producer cell line (typically HEK) and there viruses are produced with the desired insert. Eventually this viruses will be harvested and the desired cell lines transduced.

For bio-safety reasons, this system is engineered in a way that that the risk posed by the "virus system" is reduced. Thus the viruses produced by this system are incapable of replication, meaning with this that, as far as I understood, the viruses that are formed are then unable to form more in the second host as the genes in charge are not recruited. Yet, apparently the plasmids used can recombine and pose a possibility to create a replicating capable virus. Yet as far as I found in the literature this has never been detected and stands as a theoretical possibility.

My first question, in actual numbers, what is the probability that such event would take place (the number of recombinations in the specific locations). In the case that this would happen, the lentivector system would be potentially dangerous, as this system is based in HIV most of the times. Additionally, this vectors use not the endogenous HIV envelope protein but rather VSV/G from vesicular stomatitis virus, in order to increase the tropism and stability.

Additionally, even though HIV derived, most of the HIV genes are taken away from the lentivectors, yet in my opinion the most important ones are there. Second question, taking into consideration all of this, this theoretical "created" virus would be able to eventually cause AIDS or other whatever adverse effect? it is noteworthy that now is able to infect almost all human cells due to the VSV protein, then is it correct to think that the disease would be much worse, and much more contagious than the original HIV? note that even the stability is increased.

Yet, I can additionally think that this recombinant new virus may be indeed destroyed by the immune system, despite the increased tropism, due to the fact that vesicular stomatitis virus does not cause pathologies in humans, and possibly this protein works as an antigen and can induce an enough immune response.

Last, would theoretical recombinant virus be detected by a standard HIV test?

To simplify things, I am referring to third generation lentivectors

How many recombinations are required to achieve an active virus?

The FDA has recognised the likelihood that lentivectors can be converted into actively replicating lentivirus if they undergo recombination with wild type HIV in a HIV positive patient. In this case, two recombination events are required to transfer the lentivector sequence into the HIV sequence (the mechanism of transfer is identical to the case of first-generation lentivectors).

This article from VCU describes another mechanism through which this can occur in first generation lentivector systems, which consists of two recombination events between the lentivector and the helper plasmid. Note that the 3 genes gag, pol and env are present on the same plasmid, and that plasmid is flanked by LTRs. Second generation lentivectors, such as the pLKO system, do not suffer from this problem and require wild type HIV to produce actively replicating lentivirus.

To reduce the likelihood of this happening, second and third-generation lentivector systems split the genes into multiple plasmids, which then requires more recombination events to produce replication competent viruses. Additionally, the polyA tail of the 3' LTR is replaced to reduce likelihood of recombination events occurring.

According to Addgene's article on lentivector biosafety, the gene of interest's transfer plasmid (both 2nd and 3rd generations) has a deletion in the 3' LTR region which prevents it from becoming replicatively active. Therefore, the only likelihood for the recombination to occur is for the cell line expressing the virus to undergo replication with an active, wild-type HIV strain. An example is this pLKO transfer plasmid, which contains a truncated 3' LTR, preventing the sequence from replicating outside of E. coli, which replicates it not using the LTR but instead using the plasmid origin of replication.

Are the active viruses produced by recombinations more dangerous in the wild than wild type HIV?

This is difficult to answer, since recombination only allows an active virus to form, but it does not guarantee that the virus will be dangerous. Dangerous viruses are theoretically possible, but require far more recombinations than the minimal 2 for replication competency in 2nd generation lentivector systems.

For example, lentivector systems generally do not encode for the viral proteins vpr, vif, nef and vpu. These proteins are necessary for increasing the infectivity of HIV in different types of tissues (but not cultured cells such as HEK293). The lack of these proteins in a hypothetical replication competent lentivector would significantly hamper its spread in the wild. Incorporation of these proteins is plausible but extremely unlikely, since more crossover recombination events will be required.

To use your example, the env protein coding for the VSV protein coat resides in the envelope plasmid. Since the replication competent lentivector formed by 2 recombination events will be a pseudotype containing only the HIV env proteins, it will need to further acquire the VSV gene to replace its env proteins, since these genes are not present on the same regions. There is no homology between the two DNA strands, which would significantly hamper the likelihood of the VSV gene somehow being incorporated into active HIV.

The addition of various chimeric proteins and LTR regions in 3rd generation lentivectors only complicates the matter.

Overall, I was unable to find any sources comparing the infectivity of these theoretical transgenic HIV versus the wild type. However, even though it is theoretically possible that a transgenic replication competent lentivector can have better tropism than HIV by acquiring the VSV gene, the likelihood of that occurring is far lower than that of it being produced in the first place.

Can a lentivector be detected by a HIV test?

Regarding the final question of whether a lentivector can be detected by a standard HIV test, the answer is that the detection is possible if the person who was infected with lentivectors, has obtained an immune response to the lentivector gag proteins, and the lentivector loads are high enough.

HIV tests are specific to different parts of the virus, but most of them target the viral protein p24, which is a component of the gag polyprotein.

PCR based HIV tests also exist, but these tests would depend on the specific primers produced and whether the RT-PCR would produce an amplicon given the specific sequence of the plasmids.

Since gag genes are encoded for in most lentivector systems, it is therefore very likely that anyone infected with a lentivector would therefore express antibodies towards p24, and therefore result in a positive for the ELISA as well as the Western blot tests assuming that the p24 and antibody quantities are high enough to reach the cutoff point.

I was unable to find publicly available cutoff levels for the ELISA and Western blot levels, but if (hypothetically speaking) a person was injected with a load of lentivectors, they would likely test positive for HIV. However, since the lentivector is not actively reproducing, it would quickly be cleared out by the immune system.


Why are peas in mendelian genetics different? In mendelian experiment, yellow seeds were seen to be dominant over green seeds. The peas I've seen are generally green and not yellow. Did he use a different variety of pea plant ?
The other trait that was seen was white or grey seed coat where grey is dominant over white.
Why are these results not consistent with the peas found in pea pods ?

You are confounding the concept of dominance with the one of high frequency. The dominant phenotype might be at lower frequency than the recessive phenotype.

Dominance

  Dominance in genetics is a relationship between alleles of one gene, in which the effect on phenotype of one allele masks the contribution of a second allele at the same locus

Trait frequency

Let's imagine a case where A is dominance and a recessive. Let, $f$ be the frequency of A alleles in the population. The frequency of individuals that have the dominant phenotype is the frequency of AA individuals plus the frequency of Aa individuals. Under Hard-Weinberg assumptions, the frequency of individuals having the dominant phenotype is therefore

$$f^2 + 2 f (1-f)$$

The frequency of individuals having the recessive phenotype is $(1-f)^2$.

If

$$f^2 + 2 f (1-f) < (1-f)^2$$

reorganizing the in-equation yield to

$$f < 1 - \frac{1}{\sqrt{2}}$$

So under the condition that $f < 1 - \frac{1}{\sqrt{2}}$, the dominant phenotype is present at lower frequency than the recessive phenotype.

If the calculations were unclear to you, then you should have a look at the wikipedia article of Hardy-Weinberg principle.


What are the visual, behavioral similarities and differences between Yellow Fever Mosquito (Aedes aegypti) and the Tiger Mosquito (Aedes albopictus)? The Tiger and Yellow Fever Mosquito visually look very similar.

Recognizing the difference is important for tracking and controlling the spread of Yellow Fever, Dengue fever and other diseases. Especially important, now that the range of the two have overlapped in the United States.

I have some questions about the commonalities of these mosquitoes.

Evolutionarily, How can the similarities be explained?

Why do they both have the black body with white stripes?

What is the best way to tell them apart?

A. aegypti, the Yellow Fever Mosquito

A. albopictus, the Tiger Mosquito

For the best way to tell them apart, see this guide: http://www.cdc.gov/dengue/resources/30Jan2012/comparisondenguevectors.pdf

Specifically, it seems that the silver pattern on the torso is different (lyre-shaped for Yellow Fever Mosquito, more linear for Asian Tiger Mosquito).  Location is probably also an important determinant.


Comprehensive biology or anatomy wordbank I teach A&P for bio non majors. I have a special needs student whose accommodation requires a word bank for any anatomy identification questions I have on the exam. I would like to present the student with a 'master wordbank' (presumably hundreds of words in length) that would act as a word bank for all the exams in the course. I'm surprised to be unable to find much of anything online. Has anyone seen something like this?

So I found a good list. Behold: wikipedia:

https://en.wikipedia.org/wiki/Glossary_of_biology


Recombination frequencies I have been learning about recombination frequencies, but an still getting a bit confused despite having gone over many of the links in Google regarding them. I was wondering if someone could verify whether the following is correct.

To calculate recombiation frequencies and thus create a genetic map from this, you have to have true breeding parents for two or more different genes.
You have to cross these parents, so that you have an F1 generation consisting only of heterozygotes
You then have to backcross the F1 individuals with either of the parents. If these genes are all located on different chromosomes you will just get independent chromosome segregation and therefore a 50/50 chance of each allele occuring with the other one in the progeny. Whereas if they occur on the same chromosome, then in the F1 heterozygotes the alleles from each parent will only segregate differently into the gametes if recombination occurs.
To calculate the recombination frequencies we therefore take the number of offspring for which the combination of these two alleles is different from that observed in the parents- we call these the recombinants.

Is this correct?

Yes that's how it works as far as I know

Because the theory part is pretty straightforward.of the genes are on the Same chromosome, the chance of them being separated in segregation during meiosis is lower

Consider a simple example

---------A--b--------------c----d-e---------------------------------f

Let this be a rope with 6 point a b c d e f
If I were to make a random cut anywhere here, the chance that a,b will get separated is much lower than a,f....because a and f are so far apart that any cut in the middle will ensure them to be separated.
If u look at it again...the chance of d,e to be separated is EXTREMELY low

This is the principle of LINKAGE

Now let me say gene a stands for tall, b for blue and f for bushy...(don't judge the characters)

Now if this is a part of a chromosome on the parent, and meiosis is taking place
We all know that crossing over too is a phenomenon involved here

Now during crossing over.....a and f are bound to get separated for sure, so they will be independently assorted, obeying the law of Mendel

But when we talk about a and b, they may or may not get separated in the various gametes

The closer they are, the lesser chance of them being separated and thereby, higher chance of them occurring in the same gamete and therefore, higher chance of them being expressed in the same offspring(assuming they are dominant)

lets assume we cross blue tall(dominant) with green dwarf(recessive)
As you know f1 will be blue tall(no incomplete or co dominance please)

Now if I take this blue tall and cross it with parental green dwarf

You will have very high number of blue tall and green dwarf(remember, there are alleles of SAME GENE....AND OCCUPY SAME LOCI)(therefore.....high chance of both occurring together in the same gamete)

Therefore the number of recombinant you get will be very low(blue dwarf and green tall........as the chance of these characters entering different gametes is very low)

Therefore we can conclude that higher the number of recombination....higher the chance of the genes segregating which implies a greater distance between the genes)

Therefore a higher recombination frequency implies a higher distance between the 2 linked genes

I hope u have understood the concept and are not struggling to byheart it as a force
Thanks


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

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

Hi sorry i missed this one - not too hard for "biology"

If you look at a protein crystal (or any crystal really) in an x-ray beam, it scatters lots of spots (diffraction reflections).  If you look at a picture of crystalline diffraction, at larger angles from the center of the x-ray beam, the reflections get weaker and weaker and basically just stop, if the wavelength is short enough (in all crystallography labs its plenty short - from 1.5 to 0.9 Angstroms).

The resolution is marked by the angle of scattering to the last measurable spot (aesthetics can vary here, but there is little variance from personal judgement here).  Once you have the angle of scattering, you can calculate the resolution from the Bragg scattering equation:

lambda = 2d sin(theta)

which is rearranged to solve for 'd'

d = lambda / 2 * sin (theta)

where lambda is the wavelength of the incident radiation and theta is the scattering angle.
d = the apparent width of the 'slit' which caused this highest resolution reflection is called the 'resolution' of the X-ray scattering experiment.

There is one part that's a bit tricky as in the typical diagram, depicting Bragg reflection/scattering, you would take the incident x-ray beam as first beam and the scattered angle as the beam of the high resolution scattering, which is more easily measured as 180 - 2* theta.