Rust on kettle dangerous to consume? I recently traveled to Japan, where I picked up a cast-iron kettle known as a tetsubin. When I opened it up, I found that the inside was heavily rusted. Rust is a result of various combinations of $\ce{Fe^2+}$ and $\ce{Fe^3+}$ bonded to different combinations of oxygens and hydroxides. Would it be safe to drink water boiled in this kettle? I know that Iron is a dietary supplement, but I am not sure in what form our bodies can use iron. Are these oxidation states potentially harmful for the human body? Additionally, is there anything else (such as bacteria) that I should be worried about? I assume that bacteria would be killed since I am boiling the water, though. I am not sure if this question fits withing the scope of the biology stackexchange and if not, where should I post this question?

By the way, I will take full responsibility if I chose to implement any suggestion on this page. If I were to blame anyone else for their free advice, that would make me a jerk.

Background:

Iron exists in a wide range of oxidation states, −2 to +6, although +2 and +3 are the most common.

How is Iron Handled by the Body:

According to Wikipedia:

  After uptake in human cells, iron storage is carefully regulated; iron ions are never "free". This is because free iron ions have a high potential for biological toxicity.

Performed by the protein Transferrin that traps the Fe$^{3+}$ ions.

has such a high stability constant that it is very effective at taking up Fe3+ ions even from the most stable complexes.
At the bone marrow, transferrin is reduced from Fe$^{3+}$ and Fe$^{2+}$ and stored as ferritin to be incorporated into hemoglobin.

Dangers of Iron:

A number of sources reference toxicity and dangers of iron:

The Food and Nutrition Board of the U.S. Institute of Medicine indicates that Tolerable Upper Intake Levels (known as ULs) for iron is 45 mg/day. [Source].

Note: Tolerable upper intake level (UL) is the highest level of daily nutrient consumption that is considered to be safe for, and cause no side effects in, 97.5% of healthy individuals in each life-stage and sex group.

The World Health Organization (2003) suggests:

  The average lethal dose of iron is 200–250 mg/kg of body weight, but death has occurred following the ingestion of doses as low as 40 mg/kg of body weight

Of course, one can get iron poisoning due to an acute overload of Fe.

Toxic effects begin to occur at doses above 10–20 mg/kg of elemental iron.
Ingestions of more than 50 mg/kg of elemental iron are associated with severe toxicity
See Abhilash et al. (2013) for an example study examining fatail Fe overdoe in adults.

Note: inhalation of Iron Oxide dusts is complicated but potentially dangerous, but should be of no concern to you.

However, outside of trying to OD on iron supplements, it's not easy to consume that much iron. So even given all tose nasty numbers, I wouldn't be too concerned

According to 2 citations (Greentree & Hall 1995 and Goyer 1996) in The toxicity of iron, an essential element:

  Because iron must be ionized to be absorbed, metallic iron  and iron oxide (rust) are not generally of concern when they are ingested.

Even when iron is heated (and supposedly ionized) very little becomes available for ingestion:

This source cites a 1986 study that found that cooking in a cast iron skillet added typically 1-4 mg (though as high as 7 mg) of iron into the food (well below dangerous levels)
Besides, iron oxide is already present in most drinking water.

Concentrations of iron in drinking-water are normally less than 0.3 mg/L [source] and is seldom found at concentrations greater than 10 mg/L or 10 ppm [source].

Bacteria connection:

There are bacteria associated with rust:

Iron-oxidizing bacteria are chemotrophic bacteria that derive the energy by oxidizing dissolved ferrous iron

However, these species are aquatic, and are more likely to be found in ground water or well-water. (not living in your kettle).

What about Tetanus? From Wikipedia:

  Tetanus is often associated with rust, especially rusty nails. Although rust itself does not cause tetanus, objects that accumulate rust are often found outdoors or in places that harbour anaerobic bacteria. Additionally, the rough surface of rusty metal provides a prime habitat for C. tetani endospores to reside in (due to its high surface area), while a nail affords a means to puncture skin and deliver endospores deep within the body at the site of the wound.[21]

In other words, rust really has nothing directly to do with tetanus, a soil-dwelling species. One might just inconveniently find a sharp, rough rusty item in the soil to introduce the soil-living species into their bodies.(again, it shouldn't be a concern in your case).

Conclusion Would it be safe to drink water boiled in this kettle?

Almost certainly. But if you're concerned about it, just sand off the rust and  boil it to kill off anything that might be living there (more likely from old food/drink residues). Otherwise, get yourself a new kettle :p.

Citations

Goyer RA. (1996). Toxic effects of metals. In: Klaassen CD, ed. Casarett & Doull’s Toxicology: the basic science of poisons. 5th ed. New York City, NY: McGraw-Hill;715-716.
Greentree WF, Hall JO. (1995). Iron toxicosis. In:Bonagura JD, ed. Kirk’s Current therapy XII  small animal practice. Philadelphia, Pa: WB Saunders Co;240-242.
WHO. (2003).  ORIGINALLY PUBLISHED IN: Guidelines for drinking-water quality, 2nd ed. Vol. 2. Health criteria and other supporting information. World Health Organization, Geneva, 1996.


Prevent biofilm formation on moist surfaces I have an indoor fountain with lots of water. What are the most common microorganisms in this kind of moist environment, and what are the standard way to prevent biofilm formation by them? I thought of copper and/or salt as general cheap disinfectants so far.

You can use some antibiotics or germicide or alcohol...they prevent the formation by interfering with the attachment or adhesion and expansion of immature biofilms..


Why aren't more prostate glands just removed? Some 80-90% of men have some problem with their prostate gland as they get older. Beyond about age 60 it is unlikely that men will need the prostate to contribute to seminal fluid, so there seems little point in keeping this troublesome organ - yet a huge proportion of older men end up with either benign prostate hyperplasia and/or prostate cancer. So why isn't the standard treatment just to remove the prostate altogether?

Your question is along the lines of "Many women will develop breast cancer, especially later in life. Why don't they just remove their breasts after menopause, because they won't need them for breast feeding?" There are a lot of disadvantages and only questionable advantages.

Chief among the effects of removing the prostate are urinary incontinence and erectile dysfunction. That area of the body is very highly innervated, and it is nearly impossible to just remove the prostate without damaging anything else. While it is true that many men will develop prostate problems as they get older, they can frequently be treated medically, or just observed for any dangerous changes. Benign prostate hyperplasia is just that - benign - so there's no need to undergo a major operation with significant side effects. Additionally, many prostate cancers are so slow-growing that they never metastasize or pose any threat, so they are simply monitored and treated medically as needed.


What is this fish?! Is it even real? According to a guy in a Facebook group I belong to, this fish was caught in the Missouri River near Omaha, NE, US. I have never seen one like it in my life, not in person or photo or anywhere. What on earth is this fish?! Is it even real? I've not seen it in person, only the photo below, but he says its real.

Original Answer

It looks to me like a species of sculpin, for example, the "short-horned sculpin" Myoxocephalus scorpius.

http://www.luontoportti.com/suomi/en/kalat/short-horn-sculpin

Best answer

After some deliberation, and it appears the other very good answer was for some reason removed: the OP fish appears to be a northern sea robin Prionotus carolinus.

This conclusion comes from the aid of user chauxvive, so much thanks for the identification, though his answer is oddly gone. The conclusion is based off of (1) the morphology of the head and face plate, (2) the longer and tapered pectoral fins, (3) the distinguishing long feelers at the sides anterior to the pectoral fin, and (4) the more probable distribution.


Does applying sugar to the tongue taste buds releave sugar withdrawal symptoms? I found several online articles discussing sugar withdrawal symptoms that people experience after cutting back on large sugar intake.

http://healthyeating.sfgate.com/refined-sugar-withdrawal-symptoms-9911.html

http://www.growyouthful.com/remedy/sugar-addiction-recovery.php

One question that came to mind, was the following: If one experiences a sugar withdrawal, what happens if they apply sugar to the tongue, but do not digest it? Does that trick the brain into stopping the sugar withdrawal, or is it far more complicated than that?

Theoretically if you could somehow activate the G-protein-coupled receptors (GPCRs) corresponding to sweet stimuli without absorption of the sugar into the bloodstream than it may be possible to "trick" the brain. (See this review to learn more about how taste signaling works). However, the process of absorbing sugars into the blood stream begins in the mouth (see this question), so testing your idea would be nearly impossible.


LacZ' selection: blue colonies despite ligation of insert It has been suggested that bacteria transformed with pBlueScript vector, containing an insert in the middle of the lacZ' gene, can still give blue colour on X-gal, if the insert is small and ligated in-frame with the lacZ' gene (source: my course, ResearchGate).

I don't understand how it is possible that translation doesn't end at the stop codon encoded by the insert. Is this something to do with leaky termination? Moreover, even if leaky termination was possible, this would mean that there is ALWAYS a 1 in 3 chance of the insert being in-frame.

Most inserts will disrupt beta-gal expression (by shifting the reading
  frame and introducing stop codons) and therefore remove the enzymatic
  activity required to cleave X-gal and produce the blue color.

Your source is agreeing with you - inserting a stop codon will stop translation (not transcription) and keep the white color.


I want to know the name of this water plant? Above is an image of an unknown plant. It grows without any care.

This is a water-primrose Ludwigia, probably Ludwigia peploides but I am not sure about the species (also because you didn't provide a location). Luwigia peploides and L. grandiflora are native to South america. However, in the rest of the world they are considered invasive weeds. In the European union L. peploides and L. grandiflora are considered "Invasive alien species of Union concern" This means EU member states should take appropriate action against these species.

Water-primrose has a high variation in the shape of the leaves, especially between vegetative and flowering sprouts. On the picture in the question the leaves are almost round. However, on the ground just left of the hand, there are lanceolate leaves, almost willow-shaped. This is the same species and the reason it is also called floating primrose-willow.


if the load is removed from an eccentrically contracting muscle, will it start contracting concentrically? Geometrically speaking, a muscle contraction should exert a force between the two attachment sites. However, the actual effect of the force on the overall geometry of the body near the point of attachment may not match the direction the force pulls. For example, although the bicep contraction in principle would pull the forearm closer to the humerus, instead during eccentric lengthening the arm is actually extending due to how the rest of the system is configured. This is an example of where the direction of force exerted by the muscle doesn't coincide with the movement of the

My Question:

Can a muscle's net effect on the geometry of the system it acts on change mid-way through contraction?

For example, if my arm is eccentrically extending due to too heavy a weight in my hand and suddenly I drop the weight and now the bicep can contract. That's a simple example but I'm wondering how common it is for a the effect of a muscle's action to change midway through.

Yes, because net force is the only thing that matters. To address @Chris's comment, in an eccentric contraction and a concentric contraction, the muscle is applying force in the same direction. However, in an eccentric contraction, the muscle is not applying enough force to actually lift the load. A biceps curl is a good model:

SportScience

In the second image, the muscle is contracting but not exerting enough force to lift the weight--the net force causes a slow lowering of the weight.

  Rather than working to pull a joint in the direction of the muscle contraction, the muscle acts to decelerate the joint at the end of a movement or otherwise control the repositioning of a load. - Muscle contraction (Wikipedia)

It may be clearer with an actual force diagram:

University of Guelph

The only factor influencing which way the lever (your arm) moves is the net force. So yes, if you change the load (force F in the above image), the muscle could begin pulling your arm in the opposite direction. The muscle isn't really "changing action", it's exerting the same force, but now there's less force resisting it and the overall movement changes direction.

The question in the title and in the body are not really the same question, but the force is still exerted in the same direction as the muscle. You don't "see" movement in that direction because the forearm on which the force is being exerted is fixed at the elbow joint.


Are there animals which can see movements better than shapes or colors? I remember that in Michael Crichton's novel Jurassic Park, Tyrannosaurus Rex was supposed to have movement based vision. (Of course, that is a novel and not a scientific text.)

I have also noticed while feeding chickens, that they behave differently when they see me adding the food for them into the container as opposed to leaving it there for them when they cannot see me. (But this can be explained easily by different reasons, for example they are used to human as a source of their food, so they naturally go close to them.)

So my question is:

Are there some kinds of animals who have primarily movement based vision? If yes, which animals are examples for this?

The Michael Crichton's novel has been widely discussed online, I found for example this and several answers at Yahoo Answers. Frogs and reptiles are mentioned there.

I think "movement-based vision" is perhaps a bit of a misnomer. Ultimately, all vision is contrast-based, depending on integrating signals from ON and OFF bipolar cells. It seems that this notion of so-called "movement-based vision" is derived from work on toad vision and feature detection. In this case, it's more the downstream processing that results in different behavior based on the shape of the stimulus and the direction that it moves. The simple sensing of visual stimuli does not seem to be motion-based.

So, aside from evolutionary inference, we would have no way of knowing whether Tyranassaurus rex had such behavior. As for the chickens, it's possible but I would be skeptical of such a system discriminating between immobile food and hand pouring food. I would chalk that up to a simple behavior of associating seeing you with getting food.

One interesting note: many, many species have reflexive responses to moving visual stimuli. The first is called the optokinetic reflex, in which the eyes reflexively track contrast-based movement; and the second is the optomotor response, in which the head or even the whole body move in response to a moving stimulus. Thus it is safe to say that for many (most?) species, motion detection has a strong influence on the visual response...but again, I remain hesitant to use the phrase "motion-based vision".


Is the minicolumn the unit of the neocortex? There are many arguments for what the unit of the neocortex is. "Columns" seem to be the standard, but what exactly those are is extremely contradictory between individuals, cortical regions, and species. Often times, when a column is referred to, it's actually a functional column without any anatomical borders (such as Hubel and Wiesels ocular dominance columns). Sometimes, the "column" is semi anatomical, such as the rat barrel cortex. Other times, these functional columns are confabulated into anatomical units, without any evidence for a border.

So my question is, could Mountcastle's "minicolumns" be the actual anatomical unit of the cortex? I've heard arguments that they are mere developmental relics. But they seem like the only reliable and consistent unit in the cortex.

I am skipping the background information (I will amend my question later) for now.

So, what is known about minicolumn?

The term was coined by Ramon y Cajal who saw narrow stripes, running from white matter to the surface (reference) in his preparation with Nissl staining.
The hypothesis about minicolumns to be anatomical units was proposed by Mountcastle in 1957, known as "columnar hypothesis" in neuroscience (reference).
It has been shown that minicolumns grow from progenitor cells within the embryo (reference), and don't require brain functions to emerge.
Minicolumns  contain neurons within multiple layers of the cortex (reference).
One of the latest review on the topic (Buxhoeveden & Casanova, 2001) contains 121 references to experimental papers on this topic.

I wouldn't say that these columns are developmental relic, for there is a known heterogenity among these structures (like hypercolumns, macrocolumns and segregates) and it is rather improbable that all these types are relics.

So, as long as we stick to the term "anatomical unit", I see no problems why columns (with all possible types and sizes of them) should not be it.


The Origin of Mitochondria For a long time I've just accepted, because it is just what everyone told me, that mitochondria became organelles in the cell when they were "engulfed" by another cell which acted like it's host. This is the endosymbiotic hypothesis.

  "The endosymbiotic hypothesis suggests mitochondria were originally
  prokaryotic cells, capable of implementing oxidative mechanisms that
  were not possible to eukaryotic cells; they became endosymbionts
  living inside the eukaryote."

However, recently I looked at the wiki entry on mitochondria and saw there that it lists two main hypothesis, endosymbiotic and autogenous.

  "In the autogenous hypothesis, mitochondria were born by splitting off
  a portion of DNA from the nucleus of the eukaryotic cell at the time
  of divergence with the prokaryotes; this DNA portion would have been
  enclosed by membranes, which could not be crossed by proteins."

It also states that, given that mitochondria have some striking similarities to bacteria, the most parsimonious hypothesis for mitochondrial evolution is that of endosymbiosis. (This question here deals with some aspects of multiple-occurence/convergent endosymbiosis).

My questions are;

How strong is the evidence for either of these leading hypotheses (perhaps there is a review article)? Is there evidence that is overwhelmingly in favour of endosymbiosis?
Further, are there any other (plausible) hypotheses to explain the origins of mitochondria (with or without supporting evidence)?

This is one of the most intriguing questions of eukaryotic evolution. As far as I know and have read, the autogenous theory is not accepted. There are quite some reviews on this topic. Also there is a wonderful book by Nick Lane on mitochondria called Power Sex and Suicide. You would be interested to read it.

There are no sufficient evidences for the evolutionary transition from prokaryotes to eukaryotes which somewhat suggests that this was some kind of quantum jump. For example:

There are no microfossil records for the evolutionary intermediates
Almost all eukaryotic features including organelles, syngamy, nucleus etc emerged simultaneously

So to answer how it exactly happened is quite difficult.

As for the autogenous theory; it would have been impossible for the huge eukaryotic cell (the precursor of mitochondria) to meet its energy demands without an organelle like mitochondria i.e. a prokaryote as large as a eukayotic cell wouldn't survive. You may check this post.

There are eukaryotic cells that lack mitochondria (eg. Entamoeba histolytica ) or have one with reduced functionality. However, these are not intermediates in evolution but have lost the functionality in a retrograde manner.

There is one more evidence to support the endosymbiosis theory:
There is this observation that organelles that are less numerous in a cell have retained more of their genome compared to those with the organelles that are surplus numbers (eg. plastids vs mitochondria). This is called the Limited Transfer Window Hypothesis which reasons that the organelle to nuclear gene translocation would have happened because of organellar injury and the likelihood of a cell tolerating one is higher if there are more number of organelles.

This article suggests an alternative view that predatory bacteria like Bdellovibrio could have settled in a prokaryotic host. There are other cases of bacterial endosymbiont in a larger bacteria (I need some time to mine up the reference. Read it a while back) but these are not the the ancestors of eukaryotes.


Do all multiple sequence alignments employ global alignment algorithms? Multiple sequence alignments are usually done between sequences of similar length, which resembles best a global alignment. However, I'm not sure at all what the algorithmic background would be in such case. Is it essentially a global or a local alignment when one performs a multiple sequence alignment?

It is dangerous to generalize, as different multiple sequence alignment (MSA) programs may well employ different algorithms. However as the objective is to align many sequences along their whole length, and all MSA programs of which I am aware present the results as such, it is difficult to envisage anything other than global alignment being employed.

For the widely used Clustal W and X, this is certainly the case. Clustal employs a progressive alignment algorithm which involves the heuristic assumption that the most closely aligned sequences by pairwise alignment are a valid basis for the order in which progressive multiple alignment is performed. The initial pairwise alignments (which are used to produce a guide tree) use dynamic global alignment, as does each progressive alignment step, although this alignment is to a profile of previously aligned sequences, and uses context-dependent scoring.

There is an extensive Wikipedia article on MSA and one of the original Clustal papers is freely available on-line. The excellent book by Durbin et al., Biological Sequence Analysis, contains a chapter on the topic.


Is a species lifespan affected by meat consumption? I read a review-like article about the hypothesis of Caleb E. Finch  in a science magazine. The article of interest engages with the idea of Finch

  "[arguing] that immune functions and nutrition have been of major importance in the evolution of aging and longevity."

According to this, humans started to regularly consume meat. Meat itself, carrion or injuries during hunting have chances of getting infected and thereby causing death to humans. A strong defensive system against infections lets you survive and its coming into existence may be accompanied by an elongation of our lifespan.
I find myself now asking two questions:
(1) Because the whole article is only about the primate branch, I wonder, whether there are other omnivores that drifted apart concerning their eating habits and if now there is a more carnivorous, longer-living genus?
(2) Do carnivores, in general, have a long lifespan (or is their lifespan highly dependent on a healthy predator–prey equation)? I tried googling, but could not find a relevant scientific resource on this topic.

I don't think that the theory is very reasonable, because animals drink from stagnant ponds (i.e. savanna wells , forest puddles) and have lots of vectors of infection other than rotten meat: cuts and grazes, tract infections, parasites like mosquitoes and nematodes.

The olfactory sense is also very sharp in many carnivores and they can gage the decomposition state of meats. Even humans have a very strong sense of the age of meat using smell, although I can't find  research on it.

The fun thing is to see the age of other animals, i.e. birds and bears. The oldest zoo birds:

Flamingoes, seagulls, vultures, 50-70
parrots 90-120 years.

the oldest panda: 37
the oldest grizzly and polar bear: 40 and 42

Oldest reptiles:
lizards crocodiles and tortoises: 50-100 years
giant tortoise: 150-250 years.

Other herbivores with slow senescence: donkey 60, bison 50, gorilla 60...

research papers don't include any evidence to correlate carnivory and lifespan. It's mostly body mass and ecology, i.e. predation rate.

Carnivores have must stronger stomach acid also which mitigates some of the risk.


Cartilage regeneration Why can we not regenerate cartilage in our ear and nose, while bones and flesh can heal?

What makes it so resistant to regeneration. Can we artificially create it in the lab?

The reason that cartilage rarely is able to regenerate is that it is poorly vascularized and innervated. It doesn't have its own blood supply to deliver signaling molecules that promote regeneration and repair after injury.

There has been some recent progress on getting the body to repair and replace cartilage with lab created biogels detailed here.


Choosing viruses for influenza vaccine When scientists choose viruses for the influenza vaccine based on biological and clinical data, what indicates that a certain strain will circulate and likely be dominant in a certain season?

Does a low HI titer (meaning antigenic novelty) for a virus antigen relative to an antiserum of a virus that is currently prevalent mean that the new virus will likely dominate in the next season? OR is a high HI titer a better choice for the vaccine since it means the virus in question is very similar to currently circulating viruses?

Again, the full answer is too complex to answer here. The CDC has a broad explanation (Selecting Viruses for the Seasonal Influenza Vaccine) and the WHO has a presentation summarizing the process (The WHO Vaccine Strain Selection Process: Review of the Evidence).

The major factor for choosing a new vaccine virus is based on surveillance from the preceding season and from the opposite hemisphere's season. The surveillance data shows which virus groups are expanding or shrinking. Antigenic variation (high or low HI titers) is also a part of the decision, but every season has a number of viruses that have low HI titers to the current vaccine and the real question is whether those occasional outliers are just sporadic, or whether they're showing signs of becoming increasingly common.

Interpreting whether particular virus families are increasing or not requires a lot of familiarity with influenza behavior, genetics, and antigenicity. You can look at some of the data used in strain selection on the WHO site, e.g. Recommended composition of influenza virus vaccines for use in the 2018- 2019 northern hemisphere influenza season.


From an information perspective, are both strands of DNA necessary? I am learning about the genetic code, replication, and transcription, and I have a question about whether or not both strands of DNA are really "necessary".

In replication, at a high level, we are taking 2 strands of DNA and creating 4 of them. Part of my question is: suppose hypothetically that the genome only consisted of a single strand (instead of the double helix), couldn't replication just as well occur by turning 1 strand into 2 (instead of 2 into 4)? I suppose this could be done by taking advantage of complementary base pairing as usual, and then splitting the two strands?

In transcription, I believe only one strand of a gene is read by RNA polymerase, so I don't think think the second strand is "necessary" here.

Can someone shed some light on this for me? I realize this is pretty speculative, and DNA is what it is, and does what it does. but I think this sort of question will allow me to see deeper into tits finer workings.

From a strictly information theoretical perspective, no, a second strand does not provide any additional information that cannot be inferred from the complementary strand. But as many comments have pointed out, there are many practical reasons for DNA's double strandedness.

DNA is biochemically more stable in a double stranded state.
The redundancy of two strands allows for maintenance and repair mechanisms to ensure the integrity of the genome.
Proteins that bind to DNA can only recognize the sequence of that strand, so even though the complementary strand can always be reconstructed from the primary strand, DNA binding proteins cannot target that complementary strand unless it physically exists. In some cases, a DNA binding site encompasses both strands simultaneously.
Proteins (such as polymerases) traverse DNA in the 5' to 3' direction, so if information from the complementary strand was required it would have to be read "backwards".


Is NADH found in all type of cell in human body? Is NADH found in all kinds of cell in the human body? I am curious about microglia specifically.

As NAD+/NADH is involved in both glycolysis and in the tricarboxylic acid cycle it is difficult to imagine any cell capable of generating energy not having some NADH. (Are there any cells that are not capable of this? Calcified cells such as bone?)

A quick internet search for ‘microglia’ and ‘metabolism’ indicates that microglia have energy metabolism and so I would expect them to have NADH. How much (compared to NAD+) would depend on their metabolic state.


If the haploid prothallium of a fern fertilizes itself into a diploid sporophyte, does this make all ferns clones? From what I understand in the alternation of generations in ferns, mature spores germinate into a haploid prothallium. But how does this gametophyte produce recombinant gametes if it itself develops mitotically from a haploid spore? And if the gametophyte produces its own (haploid?) eggs and sperm, how does it ultimately produce a diploid sporophyte with the same number of chromosomes as its parent? If the haploid prothallium fertilizes itself, that means it possesses two identical copies of its parent's chromosomes, which themselves are identical - there is no outcrossing between plants. So are all ferns genetic clones? Why even bother with meiosis if you don't have a recombinant mixing of alleles? Or do I have this totally confused?

No, it would not be accurate to label them clones, and the organism still goes through sexual reproduction even if they are selfed. Selfed offspring would get two copies of the "same" chromosome (when selfed within the same prothallus), when the parent might have two chromosomes of different origins, and there will also be recombination during meiosis (during spore production in the sporangia), which will alter the chromosomes. And even if all selfed offspring from the same prothallus will carry that same chromosomes, different prothalli from the same parent will carry different chromosomes, which means that all offspring will not be identical. So to label selfed ferns as clones wouldn't be accurate, since the offspring wouldn't be genetically identical to their parents and offspring from different prothalli would also not be genetically identical. The situation is similar to e.g. monoecious plants that lack self-incompatibility (especially those pollinated by wind), where selfing will be common. The difference in ferns is that all gametes on the same prothallus will carry the same chromosomes.

Also note that some ferns have mechanisms to avoid self-fertilization, and that many species have a mixed mating strategy that allow both selfing and outcrossing, usually with higher fitness in outcrossed individuals.


How does salt concentration affect chromatin compaction? I've read that the primary obstacle to the compaction of chromatin is the negative charge on the DNA phosphate-sugar backbone. This negative charge is slightly stabilized by the positive charges on histone proteins. In solutions with high salt concentrations, chromatin adopts a more condensed state, whereas in solutions of low salt concentration, chromatin is less condensed. The explanation I found was that cations from the salt help provide additional stabilization to the negative charges on the DNA molecules—thus, solutions with higher cation concentration promote greater condensation of chromatin.

But what about the anions in the solution? A solution must be electrically neutral; when salt concentration increases, the concentrations of both cations and anions increase. Even if the salt cations stabilize the DNA's negative charge, won't this be perfectly offset by electrostatic repulsions between the DNA and the salt anions?

I think the 'whereas' part is excessive and misleading - I'd say "Higher concentration results to more condensed state".
So charge of DNA + solution will be the same but it will be distributed differently:

$$ D^{-} + nK^{+} + nA^{-} \rightarrow (D^{-}+mK^{+}) + (n-m)K^{+} +nA^{-} $$


Problems with SDS-PAGE, no separation - what could be the problem? I work in a lab were we have a common stock of 30% Acrylamide, TEMED, TRIS-HCl (pH6.8 and pH 8.8.) and a 10% (w/v) SDS solution pH 7.2.

We use the recipe for loading buffer (which we of course mix with BME before use):

3.15 mL MilliQ water
1.25 mL 0.5M Tris-HCl
2.9 mL 85% Glycerol
2 mL 10% SDS
0.4 mL 0.5% (w/v) bromophenol blue

Our problem is that there is no separation.

I have tried making 2 gels because I though I might have mixed the separating and the stacking gel, but I made sure i did not do this the second time. Then I asked someone else to make the gel, and it did not work for them either (nothing on the gel, no samples no ladder).

Then I remade the 10% SDS solution and both the TRIS buffers, but again something strange is going on as we get nothing on the gel.

The gels are obviously polymerized as its a solid gel when you take out to stain and destain, and I dont understand how the loading buffer can do this even if you mess it up (because you should see something on the gel as long as your sample in the well, even without denaturing). We obviously remade the loading dye and tried again, but this does not work.

I know there is protein in the samples, as I am putting cell pellet and purified protein (which I have tested the catalytic activity of) on the same gel.

Does anyone have a rational explanation for this, or suggestions of what can typically be wrong.

Bellow is a picture of the gel as it looks when its almost done running at 200V (80mAmp) for approx 40min. When we stain and destain there is nothing on the gel. Also I think the color (bromophenol blue) looks as if its running a bit strange on the gel, not as it normally should, see picture below, but perhaps I'm getting a bit paranoid.

After readjusting the pH of everything and making new running buffer with new SDS solution the separation seems to be back.


Names for effects of sleep deprivation on the brain & body When staying awake for a long period (3 or 4 days), some weird phenomena can occur. In my experience, it was always triggered by thinking too deeply and has in other occasions too.

Do these things have names at all?

During extreme sleep deprivation you can briefly fall asleep, this is known as a microsleep. The disorientation that you experienced can be referred to as  Hypogogia.

Hypogogia covers a range of effects including visual and aural hallucinations as well as having thoughts that are experienced as seeming logical during the microsleep but illogical once you're awake.


layman inquiry into mechanics of evolution Consider a species. Without some particular mutation, its members have quality A. Suppose that quality B is better for the survival of any individual member of the species. If one member possesses quality B, natural selection could take over.

What if B is preferable to A, but the intermediary stages are not preferable to either A or B? Can a species go from A to B?

Say an organism has 4 legs but having 6 would be advantageous. Could it get to 6 without some disadvantaged intermediate forms? Or is there a way for a single genetic mutation to result in a one step change? Also, if no organism has ever made such a transition then I suppose it can go without explanation. But then maybe something went from 6 legs to 4, or something.

I hope this isn't too rambling. Kindly,

The question is a very deep one, and the answer is 'it depends'. Organisms can in general only evolve by taking rather short steps through genome space, where each step is better than the last. This could mean one or two nearby basepairs change, or one or two segments of DNA get duplicated, inverted, deleted, etc. It's the DNA that evolution acts on, not the organism's 'qualities', or as we call them, it's phenotype.

In your example, there might be a single piece of DNA which when duplicated, causes the organism's number of legs to go from 4 to 6. In this case the mutation can happen and be selected for and extra legs can evolve. If however the evolution of new legs requires a lot of mutations, non of which are individually useful, then the trait won't arise before the intermediate mutations are selected away.

What may happen instead is something more complicated. E.g. the many mutations for the new legs could initially arise because they are doing something different, and then gradually get selected for other purposes.

In general though the problem of how organisms' move from one peak in the 'fitness landscape' to another is an ongoing topic of research.


How does the sensitive plant detect vibrations? The sensitive plant (Mimosa pudica) is a remarkable little plant whose characteristic feature is its ability to droop its leaves when disturbed:

Apparently, this ability to droop rests on the cells in the leaves of the sensitive plant being able to draw water out of themselves through changes in intracellular ion concentrations, which makes the leaves less turgid.

What I'm hazy about is how the plant "senses" vibrations. Plants don't really have a nervous system to speak of; how then does the sensitive plant "know" to droop when disturbed?

In fact, the idea of a plant nervous system is quite serious and constantly developing; of course those are rather local, simple signal pathways rather than an "animalian" centralized global network, but they use similar mechanisms -- depolarisation waves, neurotransmitter-like compounds, specialized cells... Here is a review paper by Brenner et al.

In the case of Mimosa, there is a good paper summing up Takao Sibaoka's long research of the topic.

In short, it seems that its petioles' phloem has cells which have polarized membranes and can trigger depolarization due to a mechanical stimulation. The signal then propagates to the corresponding pulvinus by a mixture of electrical and Cl- depolarization waves.

In the pulvinus, this signal triggers a second depolarization which coordinates the pulvinus' cells to trigger water pumping responsible for the leaf drop.

The transmission to the adjacent leaves is most likely mechanical, i.e. the movement of one dropping leaf excites another.

References:

 Brenner ED, Stahlberg R, Mancuso S, Vivanco J, Baluska F, Van Volkenburgh E. 2006. Plant neurobiology: an integrated view of plant signaling. Trends in plant science 11: 413–9.
 Sibaoka T. 1991. Rapid plant movements triggered by action potentials. The Botanical Magazine Tokyo 104: 73–95.


How does glucose uptake happen in the various tissues of the body? I know that the GLUT4 transporter allows for insulin-dependent uptake of glucose in skeletal muscle, liver and adipocytes. I also know that GLUT2 transporters are present in the liver and allow it to absorb glucose in the absence of insulin, and GLUT1/GLUT3 allow glucose to cross the blood-brain barrier and enter neurons.
However in my research I could not find the mechanism for glucose uptake in the remaining tissues of the body (Ex. epithelial tissue, connective tissue). Are there other types of transporters for glucose in these tissues? Surely these other cells also need glucose to survive.

As far as I am aware, all tissues have glucose transporters, but there are many different types with varying tissue distribution. A short review in Biophysical Reviews (2016) by Navale and Paranjapei is freely available and provides a summary with links to original papers.
In short, there are two types of glucose transporter, those involving sodium symport (SGLTs) and those operating by facilitative diffusion (GLUTs). The review lists six SGLTs and mentions thirteen GLUTs, belonging to three different structural classes.
The tissues specifically mentioned in relation to one or more of these transporters include:
For SGLTs — small intestinal cells, proximal tubule of nephron, intestine, testes, uterus, lung, brain, thyroid, kidney, liver, uterus, pancreas.
For GLUTs — pancreatic beta cells, liver, kidney, brain, heart, skeletal muscle, adipose tissue, small intestine, testes, placenta.
I reproduce below a table from Chapter 6, Insulin and Sugars, in Gerald Litwack
Human Biochemistry (2018). The chapter is available if you belong to an institution with a subscription to Springer publications.


Do babies conceived naturally or artificially have any differences in long-term health? Are there any long-term differences in children conceived via artificial insemination or sexual intercourse, pending that the mother successfully delivers the child?

A review paper on children born by the advent of assisted reproductive technologies (ART) and frozen sperm (Lansac & Royere, 2001) concludes that ART children, as compared to the general population:

Have normal weight;
Do not suffer increased occurrence of premature births;
Do not have increased rates in stillbirths;
Have equivalent sex ratios;
Show no increased occurence of birth defects and no chromosomal abnormalities;
Have normal overall health.
Have normal psychosocial development, at least up to 8-9 years of age, but the available data is scant in this area.
However, the rate of multiple pregnancies was higher in the ART group. This may be caused by excessive hormonal treatments during artificial insemination therapy, or by ovulation induction treatments and embryo transfer policies (multiple embryos implanted) that may increase the rate of multiple pregnancies.

The authors do conclude that larger and longer studies are needed to support these findings more conclusively, given that their review paper was based on just two studies. It deserves note, however, that both of these studies were prospective in design and included a large population of subjects.

Reference
- Lansac & Royere, Hum Reprod Update (2001); 7(1): 33-7


When infected with malaria, how many parasites are within a human host? When infected with malaria, how many P. falciparum cells are within a human host? And how does this compare with the average infection parasitemia of A. gambiae? I can't seem to find a reliable source to guide me on this question.

The uninucleate sporozoites are injected by the mosquito into a human host. They mature in the liver parenchymal cells in schizonts. Each schizont releases into the blood flow 2,000 to 40,000 uninucleate merozoites. Each of them can infect a red blood cell. Here, a merozoite can release other 10 to 36 merozoites [1].

The numer of injected sporozites depends on the bite and the number of bites [2]. And it seems that a parasitemia greater than 5000/microliters which is usually achieved by 10 infective bites during a 28-day period triggers the signs and symptoms [3].

I couldn't find any data on the mosquito parasitemia. It has been found that the infected mosquito and the parasite mutually benefit each other and thereby promote transmission of the infection. The Plasmodium-infected mosquitoes have a better survival and show an increased rate of blood-feeding, particularly from an infected host [4].

References:

James M. Crutcher and Stephen L. Hoffman. Medical Microbiology. 4th edition. 1996, The University of Texas Medical Branch at Galveston.
Garrett-Jones C, Shidrawi GR. Malaria vectorial capacity of a population of Anopheles gambiae: an exercise in epidemiological entomology. Bull. World Health Organ. 1969 Apr;40(4):531-45. PubMed PMID: 5306719.
McElroy PD, Beier JC, Oster CN, Beadle C, Sherwood JA, Oloo AJ, Hoffman SL. Predicting outcome in malaria: correlation between rate of exposure to infected mosquitoes and level of Plasmodium falciparum parasitemia. Am. J. Trop. Med. Hyg. 1994 Nov;51(5):523-32. PubMed PMID: 7985743.
Dr. B.S. Kakkilaya's Malaria Web Site. Life Cycle of Malaria.


Resting stage of primary oocytes In my biology textbook, I read that the primary oocyte gets arrested in the early stages of meiosis in prophase I (diplotene stage). I wanted to know why this is so. I searched google, and this phenomenon is known as dictyate. Furthermore the source was talking about translational arrest after transcription. Why does it occur during cell division? Moreover, what's so necessary about this phenomenon?

I am not sure if I can answer the question of why the primary oocyte gets arrested during meiosis (and finishes after fertilization), but the stage of growth the egg is arrested at does vary widely between species; it's not always primary oocyte. This might suggest that the reason is species-dependent.

In sea urchins, it's the fully mature ovum that gets fertilized.
In humans, it's the secondary oocyte (arrested during this stage of meiosis) that gets fertilized.
In the majority of mammals (dogs, etc.), it's the primary oocyte that gets fertilized. In both of these last two, the oocyte finishes meiosis after fertilization & the entry of the sperm nucleus into the egg.

The translational arrest of the egg you mentioned is because the egg is in a "dormant" state until it is fertilized, and it is "activated" by fertilization. Until fertilization, the mRNA's are present in the cytoplasm, but cannot be translated because they are missing poly-A tails (translational arrest); free levels of calcium in the cytoplasm are low; and respiration and oxygen levels are low. This is because the egg is "primed" for the explosion of activity necessary during early development (taking place after fertilization); the mRNA's code for proteins that are used at that time, but they are not translated until fertilization.

Source: http://www.ncbi.nlm.nih.gov/books/NBK10029/ (see the second paragraph under "Late Responses")


Are there organisms that have incorporated plastic into their lives? Are there organisms that have incorporated (manmade) plastic into their lives in any way? Either in their diet, or as a part of their body?

Biodegradable waste is a type of waste which can be broken down, in a
  reasonable amount of time, into its base compounds by micro-organisms
  and other living things, regardless of what those compounds may be.

from wikipedia

So yes, there are microbes which are capable of biodegradating manmade plastic. It depends on plastic types.

If you meant creating new pathways to biodegradate non-biodegradable plastics, then I don't think so. My opinion that by some of those plastics there are theoretical barriers (e.g. energy barriers or toxic byproducts), and by some of them evolution might create a pathway in time (I don't think in our lifetime, but nothing is impossible).

There are microbes which build plastics to store energy. They are just polymers like starch or cellulose (sugar polymers), with different building stones... Afaik the first biodegradable plastics came from here, but so they were very expensive. Nowadays we don't need microbes in the polymerization process, e.g. we can create polylactic-acid without the presence of microbes.

edit:

I have found an interesting article in the topic.

  Now, for the first time, researchers have found detailed evidence that
  bacteria in an animal’s gut can safely biodegrade plastic and
  potentially help reduce the environmental impact of plastic in
  landfill and elsewhere. The animal in question? The humble mealworm –
  which turns out to be not so humble after all.

  Researchers led by Stanford University in US and Beihang University in
  China found that the mealworm – the larval form of the darkling beetle
  – can safely subsist on a diet of Styrofoam and other kinds of
  polystyrene, with bacteria in the worm’s gut biodegrading the plastic
  as part of its digestive process. The findings are significant because
  it was previously thought that these substances were non-biodegradable
  – meaning they ended up in landfill (or worse, our oceans, where
  they’d accumulate for decades).

ScienceAlert - Scientists find worms can safely eat the plastic in our garbage


How do you differentiate between SR protein and SR-like protein? What are the criteria that the researchers use to choose whether a protein is an SR protein or and SR-like protein?

Im not 100% certain. If something is called an x-like protein, it usually means it is homologous and has some sequence and / or structural similarity to x. However, there may not be enough biochemical evidence to say definitively that it is in family x. I came across this paper where they are speaking about an SR-like protein. They said:

  While budding yeast lack alternative splicing, they do have three SR-like proteins: Npl3, Gbp2, and Hrb1. However, these have been best characterized for their roles in mRNA export, leaving their potential roles in splicing largely unexplored.

So in this case the protein has a serine/arginine binding domain and an RNA binding domain (just like SR proteins) but most of the biochemistry points to them being involved RNA export, not splicing (splicing, of course is what SR proteins are known for). So, they get the name SR-like. It will vary though. There is not a unified protein naming system


Is this some sort of fungus? There is something strange growing straight out of the glass windows at work. They look like hairs, about half an inch long, and each have a white spot on the tip of them, slightly weighing them down. I first saw a few of them a week ago, and now there's about twice as many. They don't move, except when blown in the wind, etc.

Here's just a few of them, the first ones I discovered:

They haven't budged from this spot since I first discovered them, but more have appeared surrounding them. This is located in Louisville, KY, USA, and there has been some hot humid weather lately. This particular area where they're growing is in the shade and a partial roof, so these windows rarely ever get rained on.

A friend hinted that they might even be insect eggs.

What are these things? Fungus? If so, what kind?

These are lacewing eggs. Lacewings lay their eggs on stalks.

From wikipedia  :


Examples of creating a new animal species by humans So recently, I was arguing with my friend who happens to be creationist. As he does not believe in the "theory of evolution" I asked him how he can explain such a big diversity in the dog Canis familiaris sppecies. (The example taken from Charles Darwin's on the Origin of Species saying that humans made to dogs what mother nature has done to every species)

My friend replied something like:

  Well, having chihuahuas or huskies is one thing but, getting a tetrapod from a fish is a something which can never happen.

I realized that indeed the Darwin's example isn't perfect... Even though, due to size chihuahuas and hounds can't copulate efficiently their semens and ovaries can start a new life.

I can't give a counterexample of a species which was bred artificially by human for so long in a new direction that a new species (whose specimens by definition were not able to reproduce with the specimens of the base species) was created.

It's not that I am becoming creationist... but is there any exception from that rule for any artificially bred animal species?

[Edit]
This question has nothing to do with this
I am strictly asking about examples of an artificially bred animal species which got bred into two species.

[Edit 2]
Also to be exact, I am not interesed in specimens that can't reproduce due to various "external" circumstances like environment's temperature or size (chihuahuas&hound example). I am interested in specimens which come from the same base species and can't reproduce even with the help of in vitro fertilization (I know this is not exactly the definition of species). I just want to avoid getting answer similar to this.

There are indeed many examples of new species created by humans, and observed to arise by humans. Many via deliberate experimentation. You can find examples googling "examples of speciation", looking at the Wikipedia page for speciation or the Talk Origins one:

http://www.talkorigins.org/faqs/faq-speciation.html

http://www.talkorigins.org/faqs/speciation.html

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

The issue is that there are two events of interest in "the origin of species" that are related but not the same thing: there is speciation, and then there is overall change. And as far as change itself goes you can have genetic change and phenotypic change which themselves aren't perfectly correlated.

Speciation is a very important evolutionary event, as it's the point at which genetic material is no longer exchanged between two groups and so they start evolving independently, meaning differences will accumulate over time (steadily and inevitably for genetic differences, more variably for phenotypic ones as that depends on the environment). But you can have differences accumulating without speciation (especially not with your "in vitro fertilization" criterion, which allows gene flow to be stopped for a long time without "speciation" by that definition happening), and you can have speciation happen without much genetic or phenotypic change.

And so on our human timescale we'll tend to see three categories of events:

1) large phenotypic change without speciation (especially by the in-vitro definition), because natural selection can cause large phenotypic change but random mutation cannot be rushed and that genetic drift is usually what will make groups no longer inter-fertile,

2) Speciation without large phenotypic change, again because speciation is just the beginning and all you need for "speciation" is just enough change to make interbreeding impossible or difficult, and so many examples of observed speciation involve just that, and

3) Speciation with large phenotypic change, which will usually be single-generation events with hybridization and polyploidy. Those are the most likely to fit your criteria that in-vitro fertilization shouldn't work. And they are legitimate and important evolutionary processes; polyploidy has happened many times in our lineage, it's an important source of genetic diversity, and hybridization and polyploidy are a major mechanism in the evolution of plants in particular. But they're not the major mechanism for the evolution of large vertebrates, so it's easy for Creationists to dismiss them.

Still, looking at the links I gave you I see a few examples that involve genetic change sufficient to block even in-vitro fertilization. The second Talk Origins link in particular refers to examples where speciation was determined by the offspring being sterile. There is also an article in the notes of the Wikipedia page about a recent discovery about the kind of genetic changes that can lead to speciation:

https://www.scientificamerican.com/article/wandering-fly-gene-suppor/

The general problem with giving Creationists examples though, is that the examples they want don't exist (and would usually contradict the theory of evolution anyway) and the ones that do exist they're not satisfied by (because the change involved isn't dramatic enough, or IS dramatic but as a result makes the dramatic look trivial because it happened via a small gradual underlying change - which, you know, is how evolution is thought to work).

I notice in fact that you are the one asking about the speciation with in-vitro fertilization, not your friend; your friend apparently just said that huskies and chihuahuas are not comparable to fish vs tetrapods. If this is personal curiosity from you then that's fine; if you are looking for arguments for your friend specifically then it looks like you're on the wrong track, since no amount of lack-of-interbreeding will make flies any less flies, which is usually the issue for people who focus on "fish to tetrapod" as a scale of change.

You might have better luck figuring out exactly what claims your friend makes, where they set the boundaries of what they think is possible and what they think it isn't, and then find an example that breaks that specific boundary. So they say "speciation can't happen !", you reply "speciation happened in fruit flies", and they answer "so what, fish haven't become tetrapods" - but, what is it they meant by "speciation can't happen" ? What mechanism do they think makes it impossible, what do they think this "speciation" is that's impossible, where do they set the boundary for themselves between "ordinary change that can happen" and "stuff that can't happen so evolution is false" ? They probably don't know clearly themselves, but figuring it out and addressing it is a better way of moving forward, and you both can learn things. And it makes it a bit easier for you too - you don't have to worry about finding proof that fish can become tetrapods, you can be like "OK fish can't become tetrapods whatever, but you said that new species cannot arise through genetic change, but here is a paper saying that a gene transposition makes it impossible for those two flies to interbreed, wouldn't that be an example of speciation via genetic change ? What do you think ?"


Are sensory receptors neurons? Background

There are many receptor types in the body, with various functions and various mechanisms of transduction. Receptor cells are considered to be part of the peripheral nervous system, as they are the first step in conveying information from the periphery to the brain.

Many receptor cells do not fire action potentials. Action potentials are widely considered to be a key property of neurons. Instead, receptors often operate by graded responses. For example, upon illumination photoreceptors gradually hyperpolarize. Cochlear hair cells gadually depolarize when the stereocilia are bent into one direction and hyperpolarize when they go in the opposite direction. Hence, many receptors are in fact analog sensors, whereas spiking neurons can be considered to be operating in binary (all-or-nothing) mode.

Given their similarities and differences, are receptor cells classified as neurons?

Credits: This question was formulated after a discussion with @OneFace on the question "Relationship between nerves and axons"

Short answer

Receptor cells are specialized neurons

Background

There are, globally, three types of neurons (Eckert's Animal Physiology):

Sensory neurons: these cells transmit information from external stimuli (e.g., sound, light, pressure), or from internal stimuli (e.g., blood oxygen level or head orientation);
Interneurons: these cells connect other neurons within the central nervous system;
Motor neurons: these neurons carry effector signals to effector organs, causing contraction of muscles or secretion by gland cells.

To illustrate these classes of neurons let's consider the visual peripheral system. Fig. 1 shows a schematized representation of the retinal circuitry, connecting the photoreceptors to the ganglion cells of the optic nerve (interneurons):

Source: Instituto Balseiro

The photoreceptor's response is graded. Notably, the bipolar cell, being an interneuron has also a graded response. The bipolar cells convey the signal, in turn, to the ganglion cells that translate the analog, graded signals into a binary, neural spiking code that enters the optic nerve.

Receptor cells are considered neurons, but they are highly specialized. Although interneurons may come in various shapes and sizes, they are not so specialized as receptor cells. The photoreceptor, for example, has a highly specialized dendritic region containing the photosensitive pigment and membrane stacks that capture light.

Another receptor is the Pacinian corpuscle, a vibrotactile mechanoreceptor of the skin:

  Source: Pixgood

In this case, the receptor cell is in fact a myelinized and spiking neuron that functionally much resembles an interneuron. Just as the photoreceptor, the dendritic part does not connect to another neuron, but is highly specialized structure designed to sense a physical external stimulus. In case of the Painian corpuscle, it is an onion-like structure consisting of many lamina. These lamellar structures substantially change the receptor's response to mechanical stimuli. Specifically, it allows the corpuscle to respond rapidly to pressure changes and allow it to faithfully transmit vibratory stimuli.

Reference

Eckert, Animal Phsyiology:
 - Chapter 5 - The Physiological basis of Neuronal Function
 - Chapter 7 - Sensing the Environment


What do the variants on the PolyT sequence mean? My son has been diagnosed with Cystic Fibrosis.  I am not looking for medical advice regarding his condition, but I am very interested in understanding the genetic causes of his condition.

In addition to the common CF mutation Delta F508, my son's genetic testing revealed both 6T and 9T variants of the PolyT sequence.

If I understand it correctly, it seems that the variants (I have found repeated reference to 5T, 7T, and 9T variants, but almost nothing on 6T) are tied to errors in the RNA transcription of the CFTR protein, but I don't understand how, or what the difference between these variants are.

What does "variant of the PolyT sequence" mean in this context, what are the difference between 5T, 6T, 7T, and 9T, and how do they impact the production of the CFTR protein?

I haven't read too far into this, but from what I understand the variant PolyT sequence is the number of thymine bases in a short sequence within one of the introns of the CFTR gene. Introns and exons are both parts of a gene structure, but introns are spliced out of the final transcript before its converted to protein (for more information see this article on RNA splicing).   Studies have shown that the presence of a 5T sequence in this region may increasethe skipping of exon 9 in the CFTR gene (there is a nice picture showing what I mean here).  This exon skipping will alter the final protein product translated from the spliced RNA species.

I could not find a lot of information about the 6T allele that your son has, however, I found one short article about a patient with 6T and F508 in the European Journal of Genetics. It references another paper that talks about the length of an additional repeat sequence of GT bases and its affect on individuals the the 5T variant.


Genomic library preparation: Why does the restriction enzyme not cut into the gene? I am currently trying to understand creating a genomic library more profoundly. In most textbooks I read (as well as wikipedia), they mentioned that the genomic library is created by isolating the DNA and fragment it with a specific restriction enzyme that cuts approximately as many times as there are genes. However, that cannot really work, can it?
Let's say E. coli has 4000 genes with a 4,600,000 bps genome. That means I must generate fragments of more than 1150 bps in theory (if each gene is the same length and no other sequences are present). That would mean I need a restriction enzyme that cuts about 4000 times creating over 1150bps fragments. So I would either use a restriction enzyme with a recognition site of 5bps (cuts every 1024bps) or with 6bps (cuts every 4096), of course just if the base-pairs are random.
Now you already see, with the first restriction enzyme I will (even in theory) cut through many genes, while with the second I might get genes of the appropriate size but I will also fragment others.
Furthermore the genes, especially in more complex organisms are not spaced out equally, but may be concentrated in some areas, while in others just repetitive sequences are located.
So why does every textbook mention that I can create a full genomic library with one restriction enzyme? Wouldn't it make more sense to shear many copies of DNA randomly, just as it is done for shotgun sequencing, to get a higher coverage?
So my question is, how is a genomic library REALLY prepared without knowing anything about the sequence? Do you just take into account that much genes will be cut in the middle and hope for the best? It seems like a very weird strategy to amplify complete genes.
Thank you! :)

A genomic library is generated for the purpose of encapsulating the full genetic component of an organism.
You do this by fragmenting the genome with  restriction enzyme that cuts at its recognition sequence. These fragments are then taken and cloned into a plasmid, so that they can then be sequenced inside the plasmid using common sequences that are found on the plasmid but not (generally) in the organism itself. The sequencing would traditionally be performed by Sanger sequencing, which has a limit to how long a sequence you can do at once - really good sequencing will get you ~1000 bp, with sequence quality tailing off after about 600 bp.
The genomic library are not intended for expression - once genes are identified, they can be sub-cloned into an expression plasmid to see what they do. So for this purpose, cutting a gene into fragments isn't a problem, as you will find the rest on another plasmid and can re-construct the full-length gene by taking the two fragments and assembling them.
The reason you use the restriction enzyme is that the sequence that it cuts at is also used for inserting it into the plasmid.
So, at this point you might be asking yourself how do you match the ends of genes (or any sequence for that matter), when they are all cut by an identical sequence?
Well, the answer that is that you use multiple restriction enzymes, either by themselves or in combinations to generate a variety of fragments cut at different sites. This will mean that once you create the libraries from these different digestions, you can sequence through the different libraries and find where the fragments overlap, and then assemble all the sequences together into the original sequence.
For instance if you look at the picture below. If you imagine the the black boxes  are the same gene, and the in the top one is cut with restriction enzyme A and the bottom with B, you can see that the two restriction enzymes generate overlapping fragments, so if you sequence the fragments from both restriction enzymes, you can find where the ends in A match others in A, by looking at the fragments in B.


Why is triclosan not considered an antibiotic? Triclosan is a chemical often referred to as a "biocide" instead of an "antibiotic". However, its mode of action seems to suggest that it is an antibiotic.

  Triclosan binds to bacterial enoyl-acyl carrier protein reductase
  (ENR) enzyme, which is encoded by the gene FabI. This binding
  increases the enzyme's affinity for nicotinamide adenine dinucleotide
  (NAD+). This results in the formation of a stable, ternary complex of
  ENR-NAD+-triclosan, which is unable to participate in fatty acid
  synthesis.

This is nearly identical to the action of many other antibiotics, such as penicillins (inhibits cell wall synthesis enzymes), quinolones (inhibit DNA gyrase) or sulfonamides (inhibit folate synthesis).

In fact, this paper describes the mechanism of resistance to triclosan and notes that it is identical to many antibiotics. Why then, is triclosan not classified as an antibiotic and is still prophylatically used in so many places (such as hospitals)?

I agree with @Chris that this is mostly a matter of definitions -

Greenfacts defines biocides as:

  According to the Biocides Directive (98/8/EC), biocidal products are those that are intended to destroy, render harmless, prevent the action of, or otherwise exert a controlling effect on any harmful organism by chemical or biological means. Examples include disinfectants, preservatives, antiseptics, pesticides, herbicides, fungicides and insecticides.

and antibiotics as:

  Antibiotics are widely used as medication against disease-causing bacteria. However, bacteria can acquire resistance to particular antibiotics through mutation or gene transfer.

So the key difference is that antibiotics act more specific and may induce resistance. Antiseptics such as alcohol stay active, even after repeated use, because they act broadly. Now that triclosan is argued to have a specific molecular target, it may have to be re-defined from a general biocide to antibiotic. This means that its widespread use may be alarming, and I quote from your linked article (Schweizer, 2001):

  [Triclosan is used in a] multitude of health care and consumer products [and has] germicidal properties [and has] flooded the market in recent years in response to the public's fear of communicable bacteria.

Reference
- Schweizer, FEMS Microbiol Lett (2001); 202(1): 1-7


What is this yellowish insect? I found this insect inside of my shoe. It is approximately 1cm in length and less than half a centimetre wide. It was found in the Netherlands, in the province Gelderland.

Close shot

Distant shot

Upside down

What kind of insect is that?

Edit:

As @fileunderwater suggested: the question is "close" but not identical.
I think that the suggested duplicate will only provide an identification of the family of the insect, but nothing more precise and specific. Therefore, the answers for the 2 questions vary.

It is the larva of Harmonia axyridis (Asian lady beetle).

The image posted by timbernasley is more accurate because the larva you have shown is in its late instar ,a stage not an early as this one.

Here's the link: Wikipedia


When should you use a stringent plasmid? I was wondering if anyone had good examples of when you would want to use a stringent plasmid vs. a relaxed plasmid in a research setting.

The three general advantages are:

Lower expression. If your plasmid is expressing something toxic to cells at high levels, reducing the amount of DNA can reduce expression.
Lower plasmid burden. If you are concerned about the stress imposed by maintaining many copies of the plasmid, low-copy plasmids are helpful.
Population homogeneity. Relaxed plasmids tend to replicate such that there will be a wide distribution of # plasmid copies/cell. Meanwhile, stringent plasmid replication is tightly coupled to the cell cycle itself, so the number varies less. In certain cases it may be desirable to control the number of plasmids per cell.


Question regarding research project on indigenous ants during Eastern European winter I am by no means biologist (I'm a programmer), but I want to make an experiment that involve the participation of ants. So please excuse my ignorance on the subject and my potentially uninformed questions.

I need to find some ants, but it's fall/winter here in Eastern Europe, so it seems that I won't be able to find in the wild. So my questions are:

If I find a species that is local (meaning that it's used to live through winter - maybe entering some kind of lethargy?) is it just putting them in high temperature enough to get them out of this mode?
Probably depends on the species, but if I take just few individual workers without a queen, and provide them with food, is it possible for them to live without a queen? Clearly they won't reproduce so their "colony" will disappear, but are the individuals able to live for a while without a queen?

Do you have any specific reason for using a wild species? If not, you would have better using a lab lineage (or any ant farm). Breeding a wild species by yourself might be very tricky.

Taking care of an ant colony might not be as easy as you may expect. Your best chance is to target a species of interest based on past studies and visit a lab that is breeding this specific species.


What are these two fruit flies doing? When taking some pictures I accidentally captured two fruit flies doing this:

The photos are unfortunately blurry, but from what I can tell, one fly approaches the other from behind, and something is then retracted/pulled into the front fly's body. I'm guessing it has to do with reproduction, but it doesn't look like the fruit fly mating I've seen before.

Here are some stills from the sequence:

I've been working on fruit flies now for 7-8 years, including a lot of large mating and courtship assays. I believe what you are seeing is the male (identifiable by the black end of the abdomen and different shape) approaching a female. Judging by the extension of the male's right wing in the second still image, he is making a brief courtship attempt, but its very difficult to be certain of that from these images. The female then extends her ovipositor.

I believe that this could be one of two things:

A mate rejection behaviour by females - she actively made the movement to stop the males advances
The female was simply preparing herself for oviposition - the male just happened to approach her

I've seen it happen enough times both with females subject to courtship and females not subject to courtship to think that either of those is plausible for what is happening in your clip. Given the possible courtship by the male and the following text & videos from a recent paper I would say it is option 1, a mate rejection.

  "Recently mated females reject courting males through a variety of actions such as decamping, flicking their wings, kicking the approaching male, or extrusion of the ovipositor [8]. Thus, copulation switches female behavior from acceptance to rejection." - Kimura et al. 2015

and

  "Under natural conditions, the recently mated female occasionally extends the ovipositor straight along her body axis (anterior-posterior axis) toward the courting male (Fig 1A, S1 Movie), who usually positions himself behind the female [21]. During the ovipositor extension, the female abdomen was width-compressed throughout its entire length. We refer to the ovipositor extension as mating-type extrusion when it was protruded horizontally along the female body axis. A mated female that has found a suitable site for oviposition will lower and bend her abdomen downward and insert the ovipositor into the substrate before performing movements to expel an egg that is inserted into the substrate (Fig 1B, S2 Movie) [9]. Unlike the extrusion for rejection, the female narrowed the abdomen only at its posterior part." - Kimura et al. 2015

In figures S1 and S2 you can see those two behaviours very clearly in videos.

Note, I came to my answer before finding this Kimura paper so that's two lines of independent evidence (my experience and their paper). I hope it answers your question.


How to relate human metabolic model reactions and cancer drug targets / reactome items? Trying to find a way to take a cancer drug (from CancerDR, for instance) and infer the metabolic reactions that are affected by it in the Human Metabolic Model.

Essentially, I would like to know which HMM reactions are affected by a certain cancer therapy drug, especially the ones found in the Cancer Cell Line Encyclopedia.

Example:

Searching for the reactions that are associated with the HSP90 protein, which is targeted (to some extent) by the 17-AAG agent.  That way, I can trace back the relevant section of the HMM and mark it as 'affected' by that agent.

This could be a very broad or naïve question, but I am afraid I don't know enough to be able to determine that.

If someone can only provide some tip or guidance, that will be greatly appreciated as well.

Thanks very much!

Short answer:

For drugs with targets having a direct effect on reactions in the model:

Find the gene name for the target protein -> Find the Entrez Gene ID (or other gene identifier, depending on the model) -> Search the model file or database for reactions having a gene association with the gene identifier.

AND/OR:

Find the EC number for the target protein. -> Search the model file or database for reactions associated with the EC number (likely to miss many reactions or be imprecise).

EC numbers can be found in the UniProt database, while the HGNC database at http://www.genenames.org/ can be used to look up genes by name and find their Entrez Gene ID and other resources, including links to UniProt. Many other databases can also be used.

For drugs with targets having an indirect effect on reactions in the model:

Model/estimate in-direct metabolic effect yourself by using data on known regulatory effects to create new gene-reaction associations or modify the bounds on reactions affected by the drug.

Long answer:

To knock out or constrain a reaction based on data about a drug, you have to go from an entry in a drug database to an EC number or gene identifier consistent with the annotation in the model you are using. However, There is currently no standard annotation nomenclature for gene-protein-reaction (GPR) associations in metabolic models, and in general only direct GPR associations are encoded in model files.

Assuming that you have a metabolic model in SBML format (for example the RECON 2 model), reactions may have a gene association and/or be associated with an Enzyme Comission (EC) Number.1 However, several model reactions catalyzed by distinct isozymes (different enzymes catalyzing the same reaction) may be associated with the same EC number, and many reactions may not be annotated with an EC association. Therefore you might want to use the gene associations directly. Both gene associations and EC numbers are recorded in the "notes" tag for each reaction in the SBML file, and is not part of the SBML specification. (A proposal has been published for improving support for gene associations in the SBML format.2)

Using EC numbers:

Using EC numbers is the simplest, but not the most precise or possibly even usable solution. It is simpler than using gene associations, because genes may described using any of a number of identifiers depending on the database while any reaction is associated with at most one EC number. Once you know the target protein, you can look it up in the UniProt database, and find its EC number (if any) in the field "protein names". A simple example: The DrugBank entry for the cancer drug Fluorouracil (http://www.drugbank.ca/drugs/DB00544), links to the UniProt entry for one of its targets, Thymidylate synthase (http://www.uniprot.org/uniprot/P04818), where the EC number is given as 2.1.1.45. Searching the RECON 2 SBML file (or searching in BiGG at http://bigg.ucsd.edu/bigg/main.pl) for occurences of this number will show that it is associated with the "TMDS" reaction.

The IUPHAR database (http://www.iuphar-db.org/index.jsp) may also be useful.

Using Gene associations:

Genes are conceptually at least one step removed from the reactions their products catalyze, so one might argue that using EC numbers which actually correspond to reactions would be better. However, it is thinkable that a drug might affect only one of several enzymes which catalyze the same reaction and thus share an EC number. Furthermore,  annotation of reactions with EC numbers in metabolic models may be poor. Thus you may want to use gene associations to determine which reaction are affected by a drug.

Unfortunately, due to the large number of databases, a single gene may be described using many identifiers or symbols in different databases. You thus have to identify the gene coding for the product which is the target of the drug, and obtain the correct identifier for that gene which corresponds to the nomenclature used in the model.

Assuming again that you are using the RECON 2 model, it is an update of RECON1 which was made using the BiGG database3. Gene protein reaction (GPR) associations are therefore recorded using the gene names in BiGG. When ignoring the decimal and any following numbers, BiGG gene names appear to correspond to Gene IDs in the NCBI Gene database.5 A question on how to identify BiGG reactions  was also discussed at BioStar.6 However, you have the opposite problem: Finding a BiGG gene name from another gene identifier.

Using Fluorouracil as an example again, the DrugBank entry lists "Cytochrome P450 2C9" as a targeted enzyme, with the effect being inhibition. Following the link to the UniProt entry P11712 (http://www.uniprot.org/uniprot/P11712), we find that it has an EC number 1.14.13.- However, this EC number corresponds to a class of reactions (or rather, enzymes). There are also listed several additional EC number at the single reaction level, but as these may not cover or be associated with all relevant reactions, we'll use the gene association. Going back to the DrugBank entry (or just reading on the UniProt page), we find that the gene name is CYP2C9. Looking up this name at a suitable database, for example the HGNC database of human gene names at http://www.genenames.org/, we find the entry for CYP2C9 (http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=2623) and that its Entrez Gene ID is 1559. Searching for this gene identifier in the BiGG database, we find that four reactions are associated with this identifier (The actual association is to "1559.1"): P4502C9,P4502C92,P4502C93 and P4502C94. Note that none of these reactions have an associated EC number.

Defining your own GPR associations

Keep in mind that even in genome-scale metabolic models, a large number of reactions and processes are missing. While the term metabolism in its widest sense may be used to refer to all reactions occuring in a cell, metabolic models have so far been mostly limited to covering transport and inter-conversions of small metabolites. Processes involving signalling molecules and regulation of enzymes have been mostly or completely left out, along with critical processes such as DNA replication, DNA repair and apoptosis.  Because of the limited scope of the models, gene-protein-reaction (GPR) relations do not generally take regulatory effects into account, being limited to describing direct relations between one or more genes encoding (part of) a protein which directly catalyzes a reaction.

One could also model a very large number of indirect regulatory effects, but as current metabolic models generally do not specify these, you may have to construct them yourself. To find reactions in a metabolic model which are affected by a certain drug, you may have to "travel" several steps of interactions from the original target of the drug. You may consider using protein-protein-interaction network (PIN) data to help in this. You will have to consider the strength/importance of the interactions, something which may require a high degree of manual curation.

For example, if your drug affects HSP90, which is needed for correct folding of certain enzymes, you may consider creating a GPR stating that the gene for HSP90 (or rather, HSP90 itself) is needed for any reactions catalyzed by a specific enzyme to be active. This would be an indirect GPR, as HSP90 does not itself produce any part of the enzyme that catalyzes the reaction. As an alternative to on/off regulation through a GPR, you may consider searching for data on the ratio of correctly folded and misfolded enzymes in the presence and absence of HSP90, and apply bounds on reactions catalyzed by the affected enzyme to reflect this.


How does radiolabeling work? Protein turnover can be measured by calculating the "decay" or loss of radio-labeled proteins in the blood, for example, but I am confused at how this calculation works. Wouldn't the radioactive isotope that you're using be decaying due to being unstable and not just due to protein turnover? Would you have to account for that in your calculations?

Technically yes, but practically it depends on what the half-life of your isotope is relative to the half-life of your protein. For example, tritium has a half-life of a little over 12 years, but most protein labeling experiments take place over only a few days at most (it depends on your protein). So while technically the tritium is decaying during your experiment, the amount of decay will be below your detection limit, and therefore is negligible over the course of the experiment.

So basically it works best to choose an isotope that will not appreciably decay over the time course of your experiment so you don't have to worry about it. If this is not possible, then yes, you would need to correct for this.


I think evolution has goal Richard Dawkins says evolution doesn't have any goal. But I think evolution has one. At the end evolution creates intelligent being. If we find another earth like planet evolution sould have the same pattern. Evolution is not a chaotic event. Am I wrong?

Yes you are wrong I am afraid. Evolution is the process of change through time of species by inherited changes. Heritable differences mainly come about from random mutation in the genome. These genetic differences between individuals lead to fitness differences between individuals, ie one individual is better able to produce offspring, thus spreading more of its genes in to the following generation, than another individual. For example, environmental change causes selection for a dark body morph in moths, stabding genetic variation and new mutations affecting body colour is then more favored by selection, and those with the dark body genes survive and reproduce better.

There is no end or goal to evolution. It is often mistakenly said that humans have stopped evolving. This is wrong and to suggest we have is to suggest that evolution is directed and has an ultimate goal. As long as genetic fitness variation exists there will always be some level of evolution because there is a difference between individuals in selection coefficient. Selection is also very unstable, it can change drastically an rapidly, evolution could only then stop if selection was constant and favored one "ultimate genotype" over all others in which case all genetic variation would cease to exist.

If we found another planet which had the exact same conditions and time as earth we may find the same species, but it is not likely. It requires the same mutations and selection processes occurring. Analogous to this is the observation of "many solutions to one problem" where different species use different adaptations to deal with a common problem. For example, geting oxygen is difficult for water deelling species. Sea mammals like whales gather oxygen by going to the surface and breathing and then holding their breath. Fish have evolved gills, a different solution to the same problem, to harvest oxygen from the water. These solutions evolve from random changes with selection acting only on the results (those that could filter oxygen from the water or hold their breath the best survived and reproduce best).


What is the relationship between the e value reported by HMMER and BLAST? (Are they equivalent?) Both HMMER and BLAST report an e value for alignments.  Is it calculated in the same way and - assuming that default settings are used - can they be compared directly (are the equivalent)?  If not equivalent, what settings can be changed to make them equivalent?

They use very different algorithms so they should not have the same E-value. BLAST uses a position-independent substitution matrix (e.g. BLOSUM) while HMMER uses a position-dependent substitution matrix that is different for every profile. Check out the "Background and Brief History" section in the HMMER's user guide. It explains the conceptual differences at a very broad level.

Therefore, I don't think there's any way to make them equivalent.


What is the maximum potential sucrose concentration of plant sap? What keeps plants below this potential? I am interested in identifying the maximum potential dissolved sucrose (%w/w) that plant sap could have, and which (biological, physical, chemical) factors constrain the observed sucrose concentrations.

For example, sugar maple has one of the highest sucrose contents at 6%, and the solution also contains fructose, glucose, organic acids, minerals (K, Ca, Mn, Zn, Na, Cl), amino acids, volatile organic compounds, phenols, enzymes  (according to Wikipedia), and most sap flow occurs when temperatures cross the freezing point each day.

Is there a way that I can calculate this theoretical maximum from "first principles" of organic- or bio-chemistry, or is this a question better suited for empirical study?

this is a biological application of my question at physics.SE

As the concentration of sugars in the sap increases, so does viscosity. At high viscosity, the sap will not flow at a sufficient rate to provide nourishment to the different plant tissues.

In addition, there are limitations to concentrating the solutes in the sap. As the sap becomes more concentrated, the plant would be working against a osmotic gradient to further increase that concentration. That energy cost may be too great.


What is the significance and method behind Ramachandran plots? My PI showed a Ramachandran plot in class today with minimal explanation, but I'm interested in finding out more. I understand that the Ramachandran plot shows the relation between the omega phi and psi angleson either side of an amino acid alpha-carbon, but there are a few further points I'm confused about:

a.) What do these angles describe? Are they just dihedral angles that show translation around the bond-axis?

b.) Why are these angles important beyond the scope of identifying a secondary structure? Can they be used instead to identify the amino acid components, or only higher level structural units?

c.) What kind of instrument is used to collect the data and how are angles on either side of a single alpha-carbon correlated?

Ramachandran plots show the relationship between the phi and psi angles of a protein referring to dihedral angles between the N and the C-alpha and the C-alpha and the C-beta. As an aside, the omega angle between the C-beta and the N tends to be fixed due to pi-pi interactions.

Dihedral Angles

There are limits to possible distributions of phi and psi angles due to steric clashes between the side chains. Furthermore other limitations from higher order structure will result in the adoption of defined phi-psi angles. Using data from solved crystal structures, it can be seen that the dihedral angles will adopt specific conformations in a protein.

RAMACHANDRAN PLOT from Lovell et al.

Furthermore, it can be noted that some of these conformations relate to specific secondary structures. As seen above, peptides in alpha-helices and beta-sheets adopt a even more limited set of phi-psi angles. Certain amino acids like glycine and proline, which differ from from canonical amino acids have an unique Ramachandran plot.

The angles from a Ramachandran plot are useful not only for determining a amino acids' role in secondary structure but can also be used to verify the solution to a crystal structure. Furthermore, it assists with constraining structure prediction simulations and helps with defining energy functions.


Why human body cannot defend against HIV? Some says that HIV destroy IRF3, and some says HIV overruns T-cells.

There are two main components of the immune system that are involved: Antibodies and T-cells.

T-cells are responsible for activating white blood cells to help fight off infection. These are the cells the HIV infects. Antibodies bond to the HIV virus and try to neutralize them before they can infect more cells. Unfortunately as the HIV virus replicates, there is too much virus and not enough antibodies to neutralize.

When a T-cell becomes infected with HIV, the virus takes over and causes it to start replicating more HIV. This eventually causes the T-cell to die. So T-cells keep dying while HIV loads keep increasing. When enough T-cells die, the infected person is considered to have AIDS.

It is particularly difficult for the immune system to fight off HIV infection for a number of reasons, including the following:

HIV attacks the immune system itself, weakening its ability to fight back.
HIV replicates in large quantities that are more than the compromised immune system can handle.
HIV has the ability to mutate (change itself) very quickly, making it more difficult for the body to fight the infection.

So conclusion, our bodies can fight HIV for awhile. It's just a matter of time before the viral load outweighs the capabilities of our immune system.


Dinuclei cellular mechanism I am no biologist, but I have this question buzzing in my mind. It's a matter of curiosity

What happens when two nuclei occupy the same cell? Would we expect the embryo (if it lives) to have complex cells (assuming the nuclei are from different species, i.e., genetically incompatible with each other)?

It depends on the kind of organism.

When the cell with two nuclei will try to go through mitosis, the nuclear membranes will fragment, releasing all genetic material to the cytoplasm, where it will behave normally, as if it came from only one nucleus. The DNA will divide and move into two daughter cells, each of which will assemble its one nucleus from the membrane fragmnets. However, each daughter nucleus will have double the normal number of chromosomes - one whole set from each of the old nuclei.

(In fact, this is what happens in humans after fertilization - the male and female pronuclei never merge, they just copy their DNA and divide it simultaneously into two daughter cells. The pronuclei are haploid, so the resulting daughter cells are diploid.)

What happens later, to the tetraploidic cells from your question, when they try to develop into a full organism, may end better or worse.

For exapmple many plants will just grow normally, only form bigger plants (modern wheat is such an example - it may be tetra- or even hexaploidic, meaning it has up to 6 sets of chromosomes).

For animals this is usually fatal, but some, like the xenopus, seem to be unaffected.


Predicting and identifying microbes and enzymes DNA sequence with metabolic prediction Presently I am working on metagenomics of coal biomethenation by bacterial consortium.

I have got the sequence result (Illumina). The sequence is huge and I can't predict anything from the sequence.
I have gone through different database like Metacyc, Biocyc etc.
Please help me that how can I draw an inference towards the metabolic enzyme that are involved in biomethenation of coal.

The first step after sequencing is finding probable genes. After that, genes and their proteins can be classified to belong to protein classes. This is the most what you can do with completely unknown genes. It's possible nowadays to predict the final structure using contact maps (if there is no homologous structure known) but this will still leave you unclear on ligands in many cases. So, the final step is to clarify the function with biochemical lab methods.

So, if you are stuck with a huge sequence, first try to find the genes in it.

http://en.wikipedia.org/wiki/Gene_prediction

For subsequent annotation/classification, I recommend InterPro and PROSITE.

http://www.ebi.ac.uk/Tools/pfa/iprscan/

http://prosite.expasy.org/scanprosite/


Property of E.coli harboring F element From Genetics by Ursula Goodenough

  E.coli harboring an F element are endowed with a number of phenotypic
  traits :

  1.They are sensitive to infection by ssRNA phages and certain ssDNA phages.

  2.They resist the growth of female specific phages as T3 and T7.

What is the molecular mechanism behind this sensitivity and resistance ?

Some bacteriophages adsorb on the pili. So the individuals carrying the F-element will be susceptible to these.
F-plasmid encoded membrane protein PifA is responsible for the T7 resistance [See here]. The exact mechanism is not known

If you see the list of references in the textbook chapter you will be able to trace the reference for a certain quoted fact


Do cold blooded animals generate any heat? In explaining energy and work to an 8 year-old I said that all conversion of energy generates heat as a by-product.  For example, cars generate heat in their engines and running generates heat in our bodies.  Then the 8 year-old said, except for cold-blooded animals.

So my question is, do cold-blooded animals generate any heat in their conversion of stored energy (food, fat, etc) into motion?  If they generate heat, why are they cold-blooded?

They do generate heat. They just do not SPEND energy specifically on heating their bodies by raising their metabolisms. This is a form of energy conservation. The metabolic rate they need to live is not nearly enough to heat their bodies.

An example of spending energy to heat the body is seen in humans  shivering. Here muscle is activated not for its usual purpose, but to function as a furnace. "Warm-blooded" and "cold-blooded" is somewhat a misnomer. The correct way to think of it is...

Endotherm or ectotherm. Does the heat primarily come from within (endo) or from the surroundings (ecto). Endothermic animals include mammals. Most of their body heat is generated by their own metabolisms. Ectothermic animals include reptiles and insects. They absorb most of their body heat from the surroundings. This is not the same as saying they let their body temperature fluctuate with their surroundings, some avoid this by moving around to accomodate themselves.

Homeotherm or poikilotherm. Homeotherms want to maintain homeostasis for their body temperatures. They don't want it to change. Poikilotherms do not exhibit this behaviour, instead their body temperatures vary greatly with the environment.

We can have endotherm poikilotherms, such as squirrels, who let their body temperature drop while hibernating. Endotherm homeotherms, such as humans, where temperature is constant by means of complex thermoregulation. Ectotherm homeotherms, such as snakes (moving into shadow or into the sun to regulate temperature), and ectotherm poikilotherms, such as maggots.