Interlocus Contest Evolution means suicide? I was reading Matt Ridley's "Genome" book. I am trying to understand the Interlocus Contest Evolution in his X-Y chapter. I do not understand why the X and Y chromosome would want to kill each other. Wouldn't that cause the death of the species (actually, have any species died that way?).

Can someone shed light on the issue?

X and Y chromosomes don't "want" anything-they are not conscious. I know that sounds obnoxious, but it's very important in evolutionary biology to understand that there is no agency and no intended final product for natural selection. I think the best way to think about it is like this: let's say there's a mutation on the X chromosome that happens to make females more fit at the expense of making males less fit. It seems possible that the evolutionary arms race that this establishes (i.e., males bearing a mutation that compensates or overcompensates for the new expense of the mutation that, say, their successful mom gave them, would then start to sweep to fixation in the population, and so on and so on) could result in population collapse. Apparently, there's theory out there that confirms this: http://www.els.net/WileyCDA/ElsArticle/refId-a0003669.html. Also, I vaguely remember a paper about toxic sperm (vs. female mating behavior) in Drosophila melanogaster suggesting that populations could collapse. As Bonduriansky mentions in the link, though, one resolution to the arms race would be the evolution of genes that get expressed very differently between the sexes (i.e., a gene that is good for a female but terrible for a male would evolve to only be turned on when it's found in a female). I hope that helps?


Is There An Initiative To Sequence The Genomes Of Critically Endangered Species? I realize that there are many isolated efforts to sequence the genome of a particular endangered species such as the orangutan or the snow leopard. However is there a concerted effort to sequence the genomes of every species on the brink of extinction? Also, is there an effort to sequence the genetic diversity of the surviving populations, since it would be very difficult to re-create alleles that would be needed if the species were to ever be resurrected.

The seedbank terdon mentions is the Norwegian Svalbard Global Seed Vault located at Spitsbergen island:

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

However, the closest thing to a concerted initiative for sequencing animals I know of is the Genome 10K project:

http://genome10k.soe.ucsc.edu/

Their list of first 101 vertebrata proposed for sequencing contains 29 species with status RED from the red list. Most of them are only proposed, but the sequencing of the following are already in progress:

crested ibis (Nipponia nippon)
Amur tiger (Panthera tigris altaica)
cheetah (Acynonyx jubatus)
lion (Panthera leo)
domestic yak (Bos grunniens)
bactrian camel (Camelus bactrianus)

and that of the Chinese softshell turtle (Trionyx sinensis) has funding secured. Already complete are the giant panda, the chiru, and the polar bear.

And some surprising fact: where the funding is secured it is/was funded by the Beijing Genome Institute. A shame if this would remain the only one.


Could someone explain the join in the SARS-cov-2 genome at location 13468? I am having trouble understanding the reference sequence for sars-cov-2, NC_045512.2

Three nucleotides equals one amino acid, right? But the nucleotide at position 13468 seems to be used twice, so the sequence starting at 13463 reads:

tta aac ggg ttt ... which translates to LNGF

However, according to the reference, the translation is LNRV, so it's read as tta aac cgg gtt etc - like the c is repeated.

The reference says "join(266..13468,13468..21555)" but how does this work and why?

In the reference genome browser, it seems you are looking at the first Coding Sequence (CDS) line, YP_009724389.1, which shows the translation to LNRV...:

If you look lower down, you'll see a line for CDS YP_009725295.1, which shows translation to LNGF... as you expected.

So, these are two different interpretations of possible translations for this area of the genome.  Why does the first have the weird peptide sequence?  If you hover over the CDS line, the browser will pop up more information about it.  For the top CDS, that includes this comment: "pp1ab; translated by -1 ribosomal frameshift".  This suggests that someone believes that sometimes the ribosome translating the RNA glitches at that point and advances only 2 nucleotides instead of 3 after the "N" codon.  This shifts the interpretation frame as if there were another C present.

If you search for "pp1ab", you'll see it's mentioned in the Feb. Nature article on the sequence.


How did palaeontologists discover the age of the Tyrannosaurus rex named Sue? I'm trying to understand how they discovered or speculated the age of Sue the Tyrannosaurus rex to be about 28–29 years old. How do they know exactly the age of Sue? Could it be wrong? Could it be possible that she is older then they thought — maybe 35 years old?

Dinosaur bones contain rings, similar to a tree, that can be counted to determine age. SUE was 28 when she died, making her the most geriatric Tyrannosaurus yet found. Her bones show signs of wear and even disease, including arthritis.
Paleontologists can make micron slices of bone and view the rings through polarized light, even on a microscope at 5-10x, similar to geologist mineral ID's.
https://mistralmtn.blogspot.fr/2013/03/bone-growth-rings.html

Wiki: Growth lines may be deposited in synchrony with endogenous biorhythms. For example, captive crocodilians exposed to constant temperature, diet, and photoperiod, still exhibit the periodic and cyclical skeletal growth banding of their wild counterparts.[4] Consequently, it is assumed by many paleontologists that the growth lines of dinosaurs reflect annual rhythms, and that they may be used to determine individual ages. However, in the large and long bones of many dinosaurian taxa, resorption of internal and external bone proceeds even as new cortical bone continues to be deposited, so that growth lines deposited early in development may need to be inferred.
http://tbrnewsmedia.com/wp-content/uploads/2015/05/Dinosaur-Growth-Rate-w.jpg


Clarification about taxon (plural taxa) If i am right, then any category placed at any rank in the taxonomical hierarchy is a taxon. For example Panthera, Mammalia, Solanaceae etc. But are general group of organism (casual groups which are not biologically defined like Birds, Cats, Fishes) also regarded as taxa? Please clarify.

Definition of taxon (From ICZN glossary):

  A taxonomic unit, whether named or not: i.e. a population, or group of
  populations of organisms which are usually inferred to be
  phylogenetically related and which have characters in common which
  differentiate (q.v.) the unit (e.g. a geographic population, a genus,
  a family, an order) from other such units. A taxon encompasses all
  included taxa of lower rank (q.v.) and individual organisms. The Code
  fully regulates the names of taxa only between and including the ranks
  of superfamily and subspecies.

Birds are called Aves and that is a taxon. Cats come under Felidae. If you are asking - "Is a colloquial/vernacular name considered a taxon". Perhaps the group of organisms can be referred to by a colloquial name when they are not given any scientific name but in this case these taxa are well defined by a standard scientific name (according to the nomenclature codes such as ICBN, ICZN, etc).

So "cat" is not a taxon, but cats fall under the taxon called "Felidae".

In some cases certain groups are not even actual clades. A clade is a monophyletic group i.e. all its members have a common ancestor. The group — reptiles, is not a clade.


Effect of doubling volumes of PCR reagents We ran PCR with a positive control and two lanes of sample. We used the same sample, but in one PCR mixture we used a total volume of 50μL (25μL Taq, 5μL forward&reverse primer each, 10μL sample, 5μL dH2O) while in the other we halved each volume to a total of 25μL. Pipetting was done by the same person.

The positive control and the 25μL total volume lane gave nice and clear bands, but the 50μL sample showed nothing. How could this be explained?

Edit: We only ran one PCR with all the samples simultaneously, so no second thermocycler or different temperatures or anything. Didn't even consider that option!

Edit 2: In case it's relevant, we were using this: http://www.chemheritage.org/discover/collections/collection-items/scientific-instruments/perkin-elmer-cetus-model-480-dna-thermal-cycler.aspx

The thermal cycler adjusts sample temperature based on the volume of the sample. So if you run samples of different volumes side by side, not all of them will cycle through the optimal temperatures of each step. If you were working with a "hot start" polymerase this is even more critical, as the Taq won't be able to amplify at all unless the sample is heated up to a specific temperature.


Why can silicone reduce keloid? I heard people use silicone sheet for reducing raised scars (i.e., keloids). I was wondering what is the rational behind it, and whether it actually works.

I cannot say the mechanism, but I can confirm it works, and can say that is generally accepted as working, not as some weird dubious treatment. I had surgery to install a rod in my leg after a broken bone. On the advice of my physical therapist, I purchased "Scar Away" brand silicone oil with roller applicator. Placing a thin layer and massaging with the applicator twice a day for four weeks turned my giant cheloids into small sections of skin which were distinguishable only by their smoothness and lack of hair, not color. He said he used to work for some basketball team and it was common practice to be used in professional basketball.


Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis? Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an area around the match area for structure prediction.

In one paper, I found that ~70 flanking nt of match area was taken as pre-miRNA for structural analysis while in this paper ~100 flanking nt of the match area was taken for pre-miRNA structure prediction. Any idea why so?

There is no hard and fast rule for how many nucleotides you have to select. If your miRNA is ~20nt and you take 70nt from both sides (average length of hairpins is ~84nt in humans), your total length will be 160nt. The point of taking $\pm70nt$ is that you don't know if your read is -3p or -5p. So take 70nt from both sides.

The maximum length of a human miRNA hairpin is 180nt for mir-3648 (90nt per half hairpin). In such cases you may take more flanking residues. But these cases are rare.


What causes goose bumps? What is the actual process and reflexes that cause the goose bumps? Why is it an evolutionary advantage to have goose bumps in the first place?

We get goose bumps because of the flight or fight response or because of cool temperature. The process is that whenever our body experiences such stimuli, the arrector muscles contract and thus the hair follicles straight out. As per the evolutionary point of view, mammals possessed this feature to portray the enemy our response ( in fight). Given photo will tell you the arrector muscle's position so that u can understand how the follicles straight up.
And the thing about cool temperature, the goose bumps appear so that they can form an insulation sort of thing to prevent us from losing our body heat to the surroundings.


Is there any example of living beings destroying their environment? I had an argument with someone about mankind being the only being destroying its own environment. I don't think this is true, yet, I cannot provide any example of significant importance.

Are there any examples of a living being destroying its own environment, making it uninhabitable to them? (Bonus point if this event led to an environmental catastrophe or to their extinction.)

Species don't live in isolation
As simple as the question seems, it actually contains some issue in the conceptualization of a species in isolation that affect or does not affect its environment.
Species do not exist in isolation from others. Many species have very important impact on their environment. These transformations would yield the environment to be unsuitable for the survival of the species over time if there were no other species to interact with. But by the existence of other species creating a cycle of, say oxygen for example, the transformation that the species is bringing to their environment is not seen as destroying the environment. In fact, if they were to disappear that could be an important problem. Let's go through examples
Example 1: Cyanobacteria and the Great Oxygenation Event
In the history of our planet, about 2.45 billions years ago, some species started to produce oxygen. Before that the oxygen level on earth was very low. We refer to this rise in oxygen as the Great Oxygenation Event. At the time, there was very few species that were performing respiration (breaking up oxygen and producing carbonic gas). Oxygen is a very reactive molecule and the rise in oxygen level was actually a MASSIVE environmental impact (arguably the most important life-induced environmental that had ever happen on Earth). It lead to an event of mass extinction.
The main contributors to this rise in oxygen were cyanobacteria. Cyanobacteria were most definitely destroying their environment. However, today, while modern cyanobaceteria are still producing loads of oxygen, we don't consider they are threatening the environment. In fact, they are fixing quite a bit of carbonic gas, which we rather tend to see as beneficial.
Example 2: Ants
I will not develop this example too much... Ants are greatly affecting forests of the world. Without ants, forests would be pretty different (see this non-peer reviewed source of information).
Ants are typically considered indicator of a "healthy" forest (see Segat et al. 2017; Lawes et al. 2017 and the book Gorb and Gorb 2003). Howe ver ants can also be invasive species that cause massive "destruction" on their habitat (Tsutsui and Suarez 2003; Lach 2003; Ness and Bronstein 2004).
"Destruction" is context specific
So, wether a species is "destroying" it's environment depends upon what other species are around. It also depends upon what you are aiming for (species diversity vs stable communities vs ...) but I won't go into these details.
Instead of asking

What species destroy their environment

it would not be 'more wrong' to ask

What species are present in ecosystem that are not adapted to their presence

or even (although that is a little of a stretch and some may argue on it)

What species have recently been introduced in a new ecosystem? / What species have recently changed their environmental impacts?

Always keep in mind, that no species can live sustainably on its own alone.
Do humans destroy their environment?
What do we mean when we say that humans destroy the environment, then? Human activities have changed drastically very recently. This is caused for two main reasons 1) our technology and, consequently our needs and therefore consumption have changed drastically ever since the industrial era. 2) we went through a demographic explosion.

So, yes we are pumping lots of carbon dioxide in the atmosphere. We get this carbon from forests we cut down, from large carbon reserves that have accumulated over millions of years (petrol, gas, peat and others). This change in our environmental impact is often seen (and for rather good reasons) as destructive.
Other modern species that destroy their own environment
Pretty much any invasive species would qualify as an example of a species that destroys its environment in a way that is not sustainable for itself over the long term. Among the invasive species that have important environmental impact that are seen as highly destructive, I can think of

Emerald ash borer (North America)
European starling (North America)
Feral hogs (North America)
Brown tree snake (North America)
grey squirrel (North America)
Zebra mussel (Europe and North America)
Japanese knotweed (Europe)
Cane toad (Australia and Latin Amercia)
Northern Pacific seastar (Australia)
Common wasp (Australia)
Rabbits (Australia and New Zealand)
Crown-of-thorns starfish (Indo-pacific and Australia)
Water hyacinth (global)
black wattle (global)
Argentine ant (global)

Many of these examples are from western countries because 1) that's what we tend to have most data on 2) because that's what I know having only lived in Europe, North America (and a little bit in Indonesia) 3) There are many examples from Australia and New Zealand because they are the world champions in invasive species and in bad policies concerning these invasive species!
Some readers will probably complain (and some with good reasons) about the species listed as what we mean by "destroy" is very subjective and my list is not intended to show the species that are considered "most destructive". Also, the locations of where these species are invasive might be inaccurate and I welcome anyone to edit them.
You can also consider any predator (incl. herbivores) and parasitic species that is leading it's prey / host to extinction such as

The experimental case with lizards in the carribean (Schoener et al. 2001)
The atlantic salmons leading shrimps to extinction (with the help of human activities) in the baltic sea
The red foxes affecting (with the help of human activities) hares population in Europe.

Coming back to the question

Is there any example of living beings destroying their environment?

Yes... other species than humans are "destroying" their environment. Estimating how much they are destroying their environment is really hard to both define and measure. Without a good working definition and without looking at actual data, I would personally be happy to consider humans as being the species that "destroys" the most today.


Etymology of vimentin What is the etymology of the intermediate filament , Vimentin?

According to this paper:

  From the Latin word vimentum, used to describe arrays of flexible rods,both ordered ones (e.g.,latices,filigres,and wicker-work) and non-ordered ones (e.g.,brushwood).

Vimentin:

Filigree art:


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

Now, my question:

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

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

One of the main points of contention in the study of virus evolution is whether or not they appear before the last universal cellular ancestor (LUCA) or afterwards (commonly accepted: genes that "escaped" from host organisms aka the escape hypothesis or vagrancy hypothesis).  Basically though, the LUCA is the most recent ancestor that all organisms living on Earth are derived from.

Increasing evidence support that ancestry of viruses may predate the LUCA, for example an idea is that there "was an 'ancient virus world' of primordial replicators that existed before any cellular organisms and that both RNA (first) and DNA (later) viruses originated at this time, donating some features to the first cellular organisms.  However, "a competing theory is that RNA cells existed before the LUCA and that RNA viruses were parasites on these RNA cells that later evolved DNA as a way of escaping host cell responses."

So basically, some theories support the pre-LUCA ancient virus origin and some support post-LUCA.  Because it's impossible to replicate conditions from billions of years ago, several approaches using evolutionary genetics and probability models are recommended by the author of the paper, referenced below.  He also discusses the specific supporting criteria for the theories that you can read in greater detail.

Holmes, E. C. (2011). "What does virus evolution tell us about virus origins?" J Virol 85(11): 5247-5251.


Why is water flavorless? I read recently that humans have an innate preference for sweet-tasting foods. That seems feasible since carbohydrates are necessary for cells to undergo cellular respiration, but why then is water not similarly good-tasting? The thirst mechanism is a very long, multi-step process that ensures that humans intake a sufficient amount of water, and it can be really satisfying to drink water when you're really thirsty, but why is it flavorless if it's so vital to life?

Consumer water is not flavorless. Sources of flavor include (1) the chemical and microbial content, which is most influenced by geology and ecology; (2) chemicals added or removed during water treatment, and (3) inputs and reactions that occur during distribution and storage (Dietrich, 2006).

Two examples of ecology-related flavors are geosmin and 2-methylisoborneol, which are respectively responsible for earthy and musty odors, produced by cyanobacteria and actinomycetes (Izaguirre et al, 1982). Humans detect these earthy and musty odors at concentrations of only a few ng/l. The ability to smell geosmin and 2-methylisoborneol is affected by other factors, such as the presence of chlorine, which masks odors (Dietrich, 2006).

The capability of organisms to detect microorganisms like cyanobacteria is not trivial, as cyanobacteria produce toxic microcystins with hepatotoxic and neurotoxic properties that can cause illness and even death (Blaha et al, 2009).

In my opinion, from an evolutionary perspective, it would be more important for survival to taste pollutants in the water than to mask these components by generating a taste to water that could potentially make the detection of toxins less effective.

References
- Blaha et al., Interdiscip Toxicol (2009); 2(2): 36–41
- Dietrich, J Water and Health (2006); 4(Suppl 1): 11-6
- Izaguirre et al., Appl Environ Microbiol (1982); 43(3): 708–14


Is hands-only CPR as effective as traditional CPR? Is hands-only CPR as effective as traditional CPR ? Wouldn't 30 chest compressions + 2 rescue breaths be more effective if the person doesn't have a pulse AND not breathing?

From my understanding (correct me if I'm wrong) by doing chest compression you manually make the blood continue to circulate the body in order to deliver oxygen to the organs (and most importantly, to the brain), but after some time (several minutes?) all the oxygen from the blood will be used up, and if the person is not breathing, that means that no new oxygen is entering the bloodstream, so that would mean that chest compressions alone won't provide oxygen to the brain anymore, so they would be useless... am I wrong?

The wikipedia page for CPR actually goes into some detail on this, going to block quote the section here for ease of access,

Compression-only (hands-only or cardiocerebral resuscitation) CPR is a technique that involves chest compressions without artificial respiration. It is recommended as the method of choice for the untrained rescuer or those who are not proficient because it is easier to perform and instructions are easier to give over a phone. In adults with out-of-hospital cardiac arrest, compression-only CPR by the lay public has a higher success rate than standard CPR. The exceptions are cases of drownings, drug overdose and arrest in children. Children who receive compression-only CPR have the same outcomes as those having received no CPR. The method of delivering chest compressions remains the same, as does the rate (at least 100 per minute). It is hoped that the use of compression-only delivery will increase the chances of the lay public delivering CPR. As per the American Heart Association, the beat of the Bee Gees song "Stayin' Alive" provides an ideal rhythm in terms of beats per minute to use for hands-only CPR. One can also hum Queen's "Another One Bites The Dust", which is exactly 100 beats-per-minute and contains a memorable repeating drum pattern. For those with non cardiac arrest and people less than 20 years of age, standard CPR is superior to compression-only CPR.

The American Heart Association has assembled some efficacy testing studies in the following review article, Hands-Only (Compression-Only) Cardiopulmonary Resuscitation: A Call to Action for Bystander Response to Adults Who Experience Out-of-Hospital Sudden Cardiac Arrest. Importantly, the human clinical studies reported no significant difference between those who received conventional cpr and those who received compression-only CPR. Some animal efficacy studies are noted, and with respect conventional CPR, the animals that didn't receive "rescue breaths" experienced a lower survival rate. In the end they note some limitations to hands-only CPR:

"...raised concerns about the possibility that recommending hands-only CPR for witnessed sudden cardiac arrest will, in fact, increase the complexity of decision-making for bystanders or that unresponsive victims of noncardiac medical emergencies (eg, drowning, drug overdose) will not receive rescue breathing."
"There may be situations in which ventilation alone could be life-saving but is not provided. There may be an interval after cardiac arrest when ventilations become absolutely critical for survival."

And as to the content in the second paragraph of the original post,

"It is important to acknowledge that during cardiac arrest without lung inflation and ventilation, there is a continuous decrement of blood oxygen saturation. At some point in time, the possible hemodynamic advantage conferred by continuous chest compressions (without ventilations) will be offset by this reduction in oxygen saturation, and the ultimate result will be a compromise in oxygen delivery. One porcine cardiac arrest study (3 minutes of untreated ventricular fibrillation, then 12 minutes of CPR) suggests that after 4 minutes of continuous chest compressions without rescue breathing, the delivery of 2 rescue breaths every 100 compressions provides a survival advantage over chest compressions alone."

The paradigm, again, is that hand-only CPR provides opportunity to get some help, other than no help at all, but the review also notes that more clinical data is needed on all fronts.


Skin color explanation? I do not understand how skin color in humans work, even after taking a basic genetics course and reading some on wikipedia.

From what I understand, skin is color based on multiple genes that control melanin and other products that affect appearance of skin. So then their are multiple alleles for "skin color" and also some of these alleles can be varying in their expression/inheritance? based on the other alleles presence?(epistasis)

So then a black person and a white person could have various skin colors (phenotypes?) And the offspring of these children could then have varying offspring as well?

Diagrams would help me maybe in explaining the concept.

The genetics of pigmentation is relatively complicated, as the pathway for the pigmentation (regulation of the pigment production, ratio between the melanins, maturation, trafficking and distribution of the melanins from the melanocytes to other cells) is quite long and also subject to different regulations. All the mutations found to date (at least to my knowledge) affect single parts of this long process (so for example MC1R mutations are affecting whether eumelanin is made, while Rab7 and Rab27a is most likely involved in the distribution of the melanosomes). Not all gene functions in this network have been understood so far.

Population studies have shown that the three main ethnic subgroups (west-africans, asians and europeans) have developed independently from a common ancestor with different (and independent) mutations in each arm. See the figure from reference 1 as an illustration, it also shows the genes involved in each arm:

Pigmentation is a protection against UV light, so there is a strong selection against mutations in areas with high UV light (west africa for example). The general theory is that in areas with less UV light the skin got lighter to allow the production of vitamin D (for which you need UV light). If you want to go through the single genes and their influence on pigmentation, please have a look at this Wikipedia page, which gives a good explanation. Also have a look at the references.

References:

Unpacking Human Evolution to Find the Genetic Determinants of Human
Skin Pigmentation
The genetics of pigmentation: from fancy genes to complex traits.
Molecular genetics of human pigmentation diversity
Human pigmentation genetics: the difference is only skin deep
The etiology and molecular genetics of human pigmentation disorders


Does the creation of memory involve mRNAs crossing the synaptic gap? There is a diagram from a book titled "Teaching with the brain in mind". The diagram shows

The diagram appears to show that the "creation of memory" involves "messages coded by RNA" moving through an axon and being released into the synaptic gap, whereupon they presumably bind to the receptors on the other side of the synapse.

Unfortunately the book does not seem to provide any sources for this and I have not been able to find any sources corroborating this claim. Can anyone provide any references?

I have never heard of this pathway. Memory is usually assoiciated with synaptic plasticity by ‘Long-term potentiation’ (LTP), which has glutamate as a neurotransmitter. Neuroscience Exploring the brain (Bear, et al,. 2007), has a pretty good explanation of this process, if you're interrested. Motor patterns have more mechanisms than LTP, and are not as well understood.


Can anyone identify this? Found on Cape Cod MA near a fresh water pond with a muddy bottom. Strange looking creature with a suction cup single "foot" with a mouth opening on opposite end, no limbs, mouth ridges inside mouth, spiral rings of tissue up entire body. Any idea what it is? I thought it might be a tunicate of some kind but I can't find a match anywhere.

It is a artificial fishing lure.specifically a soft worm T-tail, there are hundreds of variations.


Do animals with crypsis know where they should stay to save their lives? For example, would a green lizard know it need to stay on a leaf, and avoid creeping on ground? Or in general, would animals with crypsis know what color they are and then hide on suitable place? Or they don't planned to do it and just be unlucky if they leave their suitable place and be seen by predators?

I think you can break this down into two sub-questions:

Will natural selection select animals whose crypsis and behavior align with each other? The answer here is definitely yes, but with a few caveats:

Crypsis might not be the best strategy in a particular situation: a green lizard crawling on a leaf might be outcompeted with a red-and-blue lizard that is poisonous, for instance.
Either behavior or crypsis might be easier to change over evolutionary time: you might see your green lizard evolving to spend more time in leaves (particularly if it's herbivorous or eats plant-dwelling insects), or you might see it evolving brown pigmentation to hide on the ground.
Natural selection isn't going to be concerned with individual actions but overall behavior. So a lizard might fall off a bush, get spotted on the ground and eaten. But it might dash from bush to bush without getting caught. But if a lizard spends most of its time on leaves, there might be selection towards it being well-camouflaged on leaves.

Does this require a conscious decision on the animal's part? I think the answer here is no, consciousness isn't necessary. Very simple animals show responses to their environment, such as bacteria swimming towards food. Your green lizard might be staying close to leaves that it feeds on, or near the insects it feeds on that itself feed on the leaves, and so stay near the green leaves that camouflage it by accident. Or its brain might be programmed to carry out a complex action to hide it better. Perhaps the most sophisticated examples of this is animals that reconfigure their body to match their surroundings, such as octopuses, cuttlefish (but not, interestingly enough, chameleons!)

This doesn't mean that the animals don't have consciousness or are not deliberately hiding by finding surroundings that match themselves. It just means that that's not necessary to explain why we find green lizards hanging out on leaves.


I have a black tiny bug crawling all over the house This bug is crawling all around the house it stays within the shadows and moves very very slow, i have never seen it jump or run, it just moves very slowly

P.S. those bugs as u can see are smaller than 1mm so it's hard to take better pictures but i will get better ones tomorrow

P.S. the hairs are not hairs they are wool from the carpets, i just got married in october 2014 and everything in the house is new, including the flat, it was built in january 2014.

Bug pictures with a 1 mm thick pencil refill

it is very similar to what's in this picture, but i couldn't take a picture of it because it's tooo tiny

I really need to know what it is so I can deal with it :(

Edit: once i found a very little few under the carpet but it generally stays away from the carpets and stays on the tiles and I don't think it is a termite because I don't find any piles of eaten wood

EDIT 2:
More pictures:

-- Stage 1 --

-- Stage 2 --

-- Video for stage 2 --

I don't know what it is but I know that there is ones young in age i call them stage 1 they are unable to move

and there are ones I call stage 2 older in age and bigger in size and they can move and I think they can bite too

-- Insect 2 -- 5mm by 5mm

I found this one across the hall from the others and I do't know if it's related, i found it dead but I haven't sprayed that side with insecticides i sprayed the other side so it's possible that it was with the others but ran and died far from them.

EDIT: More photos

P.S. I found those moving in daylight (now)

when i blew a little air i think i turned it

Insect 1 is a:

Booklice
Introduction
Booklice, also called psocids, are not true lice. While they resemble lice in size and shape, booklice feed only on fungi or mold. If you find them in grain or other stored food products, it is an indication of high humidity which encourages mold growth. In addition to food products, psocids may be found under wallpaper, in furniture, along the sides of windows or on window sills around potted plants. Booklice do not bite, transmit disease, or damage food or fabric, but they can be very annoying when present in large numbers.
Biology

Booklice found inside homes are wingless and very tiny: less than 1/16 of an inch long. While their back legs are thicker than the other four, and resemble the legs found in jumping insects, booklice do not jump, but run about rather quickly.
Adult booklice range in color from translucent white to gray or brown. Females can produce about 60 eggs during the warm summer months and their life cycle (from egg to adult) can be completed in less than one month. When cool temperatures prevail, female booklice produce fewer eggs and the time required to complete their life cycle is over three months. Females deposit their eggs singly and often conceal them by covering with debris. Booklice undergo simple metamorphosis, that is their nymphs look just like adults except that they are much smaller and sexually immature. The common house-infesting booklice normally have four nymphal stages.
Injury
Booklice feed on molds and will overrun cereals and similar materials that support mold growth. Their presence, therefore, is a nuisance and can render some foods unfit. The starchy paste of wallpaper and books also can support mold growth or may be attacked directly by booklice. Outside of annoyance, their damage is insignificant.
Management
The best way to control booklice is to eliminate moist environmental conditions. Reducing the humidity in your home will eliminate the mold on which the booklice feed. Lowering the relative humidity to less than 50% will prevent their development. An air space under potted plants on windowsills will help keep the humidity down and reduce mold growth. Throw away any infested food material and make sure other foods are kept dry. Pesticides are not normally necessary to control booklice in homes.
Warning
Pesticides are poisonous. Read and follow directions and safety precautions on labels. Handle carefully and store in original labeled containers out of the reach of children, pets, and livestock. Dispose of empty containers right away, in a safe manner and place. Do not contaminate forage, streams, or ponds.

Source: Penn State, Entomology: Booklice


Testing monophyly from per site log-likelihoods without optimising branch lengths How can I obtain per site log-likelihoods for a topology against an alignment without optimising branch lengths? (which software can I use to do this)

Per site log-likelihoods can be used for various tests of whether a topology fits the data in a multiple sequence alignment well using e.g. the Shimodaira-Hasagawa test, the AU test etc.

RAxML, Garli and FastTree and other software packages can calculate per site log-likelihoods given a tree, alignment and substitution model but all will automatically optimise branch lengths first.

I would like to test a tree in which a pair of sequences (A and B) are monophyletic, where in the maximum likelihood topology they are not. My problem is that when I infer a tree with a constraint requiring A and B to be monophyletic, the edge length is set to the minimum within the allowed precision. But having an edge length so close to zero does not make biological sense if the tree is describing a monophyletic clade for A and B: the minimum length of the edge must be equivalent to one substitution or character change, else A and B are in a polytomy containing clade with other sequences which is not the biological scenario I'd like to test (in that case there would be ambiguity regarding the relationship of A and B to other groups emerging from that polytomy).

So . . . I'd like to edit my constrained tree and increase the edge length to the A and B clade to the minimum one substitution length, then perform the AU test against the per site log likelihoods for that topology. But the above software optimises the edge lengths, resetting the edge length to A and B to effectively 0!

thanks

If you have the budget for it, I highly recommend Geneious for topology work.  It was a real saver for me on an epi paper last year.

Anyway, they allow for testing per-log likelihood without adjusting edge length.  If you want to throw up some dummy data somewhere I can throw up an example.
I have no connection or stake with the company, just happy with it.


Is it possible to reduce maturity time of plants with biotechnology? I've heard of speed breeding which makes use of optimal circumstances in glasshouses and growth chambers. Is it also possible to shorten a plant's maturity time (i.e. the time it needs from being planted until the time its yield can be harvested) using genetic modifications?

Perhaps investigate the families of YUC genes that synthesize the growth hormone auxin (ncbi.nlm.nih.gov/pmc/articles/PMC6941117) and ARF genes (ncbi.nlm.nih.gov/pmc/articles/PMC4737911) that respond to auxin. Auxin overproduction or changes to ARFs might speed growth. But some herbicides are synthetic auxins (e.g. 2,4-D) and work by exhausting and killing weeds (en.wikipedia.org/wiki/2,4-Dichlorophenoxyacetic_acid), so modifying these pathways may have unwanted side effects, depending on the crop.


What happens to the cut-out introns from a pre-mRNA? Once the spliceosome has cut out the introns from a pre-mRNA they are said to be degraded. What does that mean and is that happening in the cytosol? Can the nucleotides be used for something else within the cell?

Yes. Ribonucleases (RNAses) break down the spliced RNA strands back into mononucleotides, and these building blocks can be reused.

They will be broken down into nucleotide monophosphates, so they will have to be re-phosphorylated to triphosphates before they can be reused for transcription.

Here are a couple of reasonable reviews of the mechanisms:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177198

Note: this one also mentions that sometimes introns are not fully degraded to single nucleotides, but instead can serve as signaling molecules.

http://www.sciencedirect.com/science/article/pii/S0092867409000671


What do bats do if played ultra sound? If there are bats flying in the cave, and I play the same pitch they use to echolocate from a speaker, what would the bats do?

Depends completely on how good ultrasound you are producing.

Will they interpret your signal as an obstacle ?

Not really until you produce signals exactly calculated for the distance and speed of bat from obstacle. Here something known as dopler effect will come into play which will make bats understand probably thats not their sound. Otherwise every bat would have made a noise to divert another bat.

Is just making sound good for dislocating

Well, till this date we don't know what humans are speaking from their sound waves what you can guess for bat for what they did just speak. If you listen closely to bat sound you will find amplitude variation at non-constant duration.

Here is a detail of what else bats use . Its harmonics that takes sleep of physicists.


Lipid packing defect I have been trying to understand the phenomenon of lipid packing defect, but the resources in this subject are very limited. Well, I did find some papers, but before reading papers, I want to have some intuitive knowledge about it. Can anyone explain to me lipid packing defect in brief. Thanks

It would help if you could delimit in which cellular of molecular context you would like to understand packing defect, for exemple during vesicular budding or lipid droplet biogenesis.

In the larger context of cellular membranes lipid packing defect occurs when there are transient "holes" made in the phophosolipid bilayer.

These packing defects can be caused by the chemical nature of the phospholipids present in the membrane. A phospholipid is chemically defined as an amphiphilic molecule: it contains a hydrophilic head and an hydrophobic tail.
The head size can vary a lot between the different possibles groups (serine, choline, ethanolamine, etc).
The size of the hydrophobic tail which is composed of long carbon chains can vary in length (typically 16-18 carbon atoms) and saturation. The saturation is very important because insaturated lipids (16:1, 18:1) tends to have to be kinked where the insaturation is.

Thus depending on the lipid composition of the membrane, it is possible to have micro domains (previously named lipid rafts) composed of only a specific lipid or group of lipid with a defined molecular composition. Packaging defects which called be name "holes" or imperfections in the membrane might occur at the boundaries of these microdomains because of the difference of the head size, length of the fatty acid chain, and saturation.

Many people also think that proteins can be responsible for the segregation of chemically defined lipids in the membrane and cause packaging defects for exemple proteins with an hairpin structure instead of a transmembrane domain, or proteins which interact with membranes with an amphipathic helix.

I hope this helps!


Can someone help me interpret these charts on fluorescent polarization? I have to present an article about binding designed proteins to fentanyl for my biochem class; I understand everything except how to interpret these charts on fluorescence at the very top of Figure 2a: https://elifesciences.org/articles/28909#fig2

It seems fentanyl was tagged with PE and the proteins (Fen49 and 2QZ3) were tagged with FITC. Fen49 binds with fentanyl and 2QZ3 doesn't but I don't know what about these charts tells me that. Is it the blue specks scattered all over 2QZ3's graph? I'm also confused about the bar graph next to it representing mean fluorescence - does it represent the binding affinities of these proteins/mutations to fentanyl?

These charts are flow cytometry graphs, something not explicitly stated in the figure description, but obvious to everyone who has seen similar graphs before (and I assume it's at least mentioned in the method section of the paper, I didn't read that though).

Each dot in a flow cytometry graph represents a single cell and, as you correctly identified, the PE & FITC flourescence corresponds to fentanyl and the respective proteins of interest. (The labelling was done somewhat indirectly and as is typical for flow cytometry with antibodies but that doesn't matter for the interpretation.). The dots are coloured according to their density: blue indicates only single dots and warmer colors show increased number of overlapping dots (with red being the highest).
It is also important to note that all the axes in these graphs have logarithmic scales, so the shifts you see in the graph represent shifts in orders of magnitude.

The combination of the logarithmic scale with per cell data points means, that you also see 'negative cells' on each axis: along the FITC axis (which represents expression of the protein) you can make out two groups of points. The lower one of these groups has cells that don't express the protein (meaning the florescence detected is just background from staining), while the higher groups contains cells that do express the protein (the staining for the protein is significantly above background).

If you now compare the two proteins you can see that high (protein expressing) group for Fen49 also has an increased signal for PE (which represents fentanyl), meaning that these cells bind fentanyl. In contrast with that for 2QZ3 the fentanyl signal is independent of whether the cells have a low signal or high signal for protein expression.

The bar graph on the right gives the average PE (fentanyl) levels for other additional protein variants. The figure description doesn't explicitly say whether this is the average of all cells or only the ones expressing the corresponding protein at above background levels.


Can there be forced evolution Can we force a species to evolve through a mixture of natural and artificial selection in a closed environment?

Selection (whether natural or artificial) is one of the force causing evolution. So yes, artificial selection is one way to 'force' evolution to happen in a specific way. One could select trees for bigger fruits or dogs for longer fur for example. One cannot force "Natural Selection", as "forced natural selection" is defined as "artificial selection".

You might want to have a look at an intro to evolutionary biology such as Understanding Evolution by UC Berkeley for example


Does urea at different concentrations (5 or 0.5M) have different effects on proteins? The problem is to explain why each additive gives rise to the distribution of the protein (RMAS) as shown in the Western blow below:

In each case, the homogenates were subjected to high-speed centrifugation and the supernatant/pellet fractions were resolved separately by SDS-polyacrylamide gel electrophoresis. The gels were blotted and probed with an antibody raised against RMAS.

I am specifically stuck on explaining the effect of the 0.5M urea vs 5M urea on the soluble and insoluble proteins represented by the pellet and supernatant respectively. My thinking is that at low urea concentrations (0.5M) the pellet protein is destabilised by urea and solubility increases showing a band. However, soluble proteins are denatured and show no band. However, at 5M urea, the pellet proteins are reversibly soluble and therefore do not show as a band whereas the soluble proteins are OK and so show a 'normal' band. I don't know if this is the right explanation, so could someone please explain it to me??

What you need to do is compare the relative amounts of the protein in the insoluble (pellet) fraction to the soluble (supernatant) one. This way you can determine how soluble the RMAS has become through the effect of the indicated compound.

DTT breaks disulfide bonds, but does nothing else to solublize the protein, so it's all in the pellet, with none detectable in the supe. NaCl is a salt that increases the ionic "strength" of the lysis buffer, but doesn't really do anything to solublize the protein, so again all of the target stays in the pellet. On the other hand, detergents like Triton and SDS free the protein from the insoluble fraction and move most of it into the supernatant, leading to the pattern you see for them. Depending on the exact subcellular localization of the protein of interest, and the amount and combination of detergent(s) used, you may see essentially no protein at all in the pellet, as it has all been solublized.

Urea and guanidinium hydrochloride are chaotropic agents, disrupting hydrogen bonding, van der Waals forces, and weakening hydrophobic associations, causing the protein to denature and separate from other proteins in the pellet, thereby putting it into the supe. This effect is generally seen at relatively high molarities (e.g. GuHCl is often used in the 6-8 M range), which explains the difference in effect seen with 0.5 and 5 M urea. At low concentrations, there is just not enough urea present to effectively denature the protein. I am a little surprised that nothing showed up in the 0.5 M lane, however, this is just a simulated Western showing ideal results - in real life things are almost never quite this cut-and-dried.


Why is there more variation in proteins than genes? The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular).
How do you account for the presence of more variation among of proteins than there are in genes?

The simple answer would be "there are more proteins than genes", but I'm more interested in why. Is it sufficient to say that during gene expression a single gene codes for multiple proteins (Alternative Splicing) and ribosomes translating mRNA to polypeptide chains (Posttranslational modification)? Could someone expand more on this?

There are several concepts to understand:

Alternative splicing

From one gene, several proteins can be constructed depending on which introns are spliced.

Tissue-specific genetic expression

Genes are differentially expressed (and differentially spliced) depending on the tissue.

Post-transcriptional modifications

Those are modifications that are made directly on the proteins (in opposition with alternative splicing which are modifications made on the RNA)

Structure of the proteins

Proteins may fold (to what we call primary, secondary, tertiary and quaternary structures) differently in different environment.

Therefore there is variance in proteome between cells although there is no variance in genome between cells (except mutations and red blood cells). Moreover, one gene sequence can give rise to many different proteins due to the processes of alternative splicing and PMT.


Writing methods section on PCR amplication in a paper Considering that I am writing a paper for a journal, could the following phrase be understood? or should I put the 'step-by-step' way by giving numbers?

PCR Amplification and sequencing

PCR reaction for sequencing with universal primer  ITS5: F: (5’TCCTCCGCTTATTGATATGC3’ and ITS4:R: (5'TCCGTAGGTGAACCTGCG
C3'), including 5,8S rDNA region (White et al 1990). Amplification condition  was performed in a 25 ml reaction volume and consisting of 10 µL nuclease free water, 12.5 µL Tag green master mix, 0,5 µL forward primer, 0,5 µL reverse primer, 0,5 µLDMSO, 1 µL template. Mixture solution  was amplified by PCR machine (Biorad). Thermal cycle programmed for 90 seconds at 95°C as initial denaturation, followed by 35 cycles of 30 sec at 95°C for denaturation, 30 sec at 55 °C as annealing, 90 sec at 72 °C for extension, and final extension at 72 °C for 5 min. PCR products were examined by electrophoresis  at 100 V for 30 minutes in a 1% (w/v) agarose gel in 1 x TAE buffer. The marker used DNA ladder 1 kb.  Electrophoresis gel was soaked in ethidium bromide for 30 minutes then visualized in UV light.

Here's my take, just a few minor changes which are shown in bold (I have also changed ,to . for decimal numbers and added a few spaces where needed):

  PCR Amplification and sequencing

  A PCR reaction for sequencing was performed using universal primers ITS5: F:
  (5’TCCTCCGCTTATTGATATGC3’) and ITS4:R: (5'TCCGTAGGTGAACCTGCG C3'),
  including 5.8 S rRNA region (White et al. 1990). Amplification condition
  was performed in a 25 ml reaction volume and consisting of 10 µL
  nuclease free water, 12.5 µL Taq green master mix, 0.5 µL forward
  primer, 0.5 µL reverse primer, 0.5 µL DMSO, 1µL template. PCR was performed using a Biorad PCR machine. The thermal cycle was
  programmed for 90 s at 95 °C for initial denaturation, followed by
  35 cycles of 30 s at 95 °C for denaturation, 30 s at 55 °C for
  annealing, 90 s at 72 °C for extension, and 5 min at 72 °C for the final extension.
  PCR products were examined by electrophoresis at 100 V for
  30 min in a 1% (w/v) agarose gel in 1 x TAE buffer. The marker
  used a 1 kb DNA ladder. The electrophoresis gel was soaked in ethidium
  bromide for 30 min then examined in UV light.


What test to apply to detect genomic signatures of selection? I would like to ask you for your sugestions for selecting a test to detect signatures of selection in the following mouse model:

We have three groups: animals exhibiting trait A, trait B and controls. These animals were selected over the last 4 decades (controls were mated randomly and do not show any of the traits). That is total 170 generations (~4 generations per year).

We want to detect the genomic signatures of selection for trait A and B.

I am new in population genomics, but according to this paper (http://www.ncbi.nlm.nih.gov/pubmed/21218185), showing a desition tree (fig 1). I should apply a the Fst and a Linckage 'Desequilibrium test, given that the time scale would be short (40 years, 170 generations) and there are multiple populations.

Could you corroborate if this is the correct approach?

Thanks

I am assuming in this answer that you do not have any information about what environment is affecting the selection pressure so that methods like Bayenv2 can't be used.

The standard algorithms are:

Lewontin-Krakauer test
fdist
BayeScan
FLK
PCAdapt

Whitlock and Lotterhos 2014 showed that most often FLK and Bayenv2 perform better than the the three others. A number of articles (Meirmans 2012, Bierne et al 2013, De Mita et al 2013 and Fourcade et al 2013) have also shown that fdist and BayeScan suffer from high false positive rate. I would therefore recommend to go with FLK but I am probably not good enough to give very good advice.

Note that you should learn a bit about how these algorithms work and not using them blindly.


To get Standard ECG from PhysioNet? I am trying to get standard ECG by using PhysioNet's ATM with parameters

but I get

It should be something like

How can you get complete standard 12-lead ECG out of Physionet database?

I don't think that all leads are available.

I looked at the Signals combobox for different databases. This combobox seems to be the list of all available leads.

For example, take a look at iafdb (Intracardiac Atrial Fibrillation Database). It will plot you an ECG containing leads II, V1 and aVF and some other leads.

Another example is the EEG database eegmmidb (EEG Motor Movement/Image Dataset) which contains many leads.

Look also at the mimic2wdb/39 (MIMIC II waveform database, version 3 part 9) which contains 4 ECG leads and some other parameters like breath rate.


How does formaldehyde cause protein-DNA crosslinking? How does formaldehyde cause protein-DNA crosslinking?  I would guess it's because the strongly polar water molecule interacts strongly with polar residues on a protein-DNA complex, and adding a less polar solvent causes the DNA and protein to pull more tightly on each other than their pull on the solvent, but I haven't been able to find an answer online.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866014/

In this work they find that formaldehyde crosslinking happens by formation of a methylol adduct (due to nucleophilic attack by N or S in case of proteins) in protein which then attacks the DNA or vice-versa.
The final crosslink is by a methylene bridge

Formaldehyde can react to amino groups in nucleotides and proteins and form a schiff's base, but i dont have a clue how this is involved in crosslinking


What kind of insect is this? (seen in Goma, Democratic Republic of the Congo) We recently (in November) saw this insect in Goma, DRC.

I would appreciate help identifying it.

Common name is "Giant Water bug". These are hemipterans, in the family Belostomatidae. Images can be found here: https://bugguide.net/node/view/12796


Are there echolocating insects? Echolocation is the ability to obtain spatial information of the surroundings from echos generated by the animal. There are bats and other vertebrates that naturally use it.

I was wondering if this is limited to vertebrates, or if there are examples among the invertebrate, especially insects.

Some moth actually do use clicks for their own echolocation: "Noctuid moths (Noctuidae) are the only group of invertebrates for whom echolocation was
demonstrated":

Lapshin & Vorontsov 1998
Lapshin et al 1994.


What makes DNA sequences most different/recognizable from a biological perspective? We can pretty easily quantify the amount difference between two different strings/sequences of characters. For example, if we take the words trebuchet and trebucket, we can say they have a Levenshtein distance of 1 (only one character-edit's worth of difference).

From a linguistic perspective, that distance is very noticeable, whereas the difference between compliment and complement is much less so. Even though both pairs are only one edit apart (respectively), not all differences are equally distinguishable.

What is the biological equivalent of this when it comes to DNA binding proteins and RNAs? How do I identify which DNA sequences are more recognizably distinct from each other? For example, if we took a DNA binding protein that recognizes the sequence TGCCTCGAA, is it more likely to misrecognize AGCCTGGAA than TGCCAGGAA (or vice versa) as its target sequence?

This isn't a question with a really well accepted answer yet, and comes up quite a lot in e.g. studies of population variation in transcription factor motifs.

Usually, we approximate the sequence preferences of a DNA-binding protein with a position weight matrix. A weight matrix will given you a score for two sequences,  so the simplest means of quantifying the relative binding strengths for two sequences is compare these scores. You could also, say, compare the relative chances of getting the scores under some background distribution of scores, which would arguably be more comparable between different factors.

The PWM score (and other means of describing sequence specificity) are only an approximation to what you're really interested though, which is the binding energy associated with the interaction. If you have detailed experimental evidence about how the protein binds, you might use that, and there are some papers that build models for approximating it from PWM scores as well. However the reality is that you can only ever roughly approximate what's happening in the cell, because of molecular crowding, and the many other factors that will be present on the chromatin fibre, so the difference in PWM scores is often what gets used.

Predicting the impact of a given change to a non coding DNA sequence is a hard problem. Sometimes you'll get a decent approximation, but in the end you're trying to do biochemistry from first principles, and we aren't there yet.


How can you improve solubility of colloidally dispersed substances? If you solve collidally dispersed substances then the particles can form large colloids. This may block narrow passages and diffusion into dense structures may become completely impossible.

What can you do to improve the solubility of such substances?

In my case, three-four rounds of sonication greatly helps in having smaller and more homogeneous hydrophobic particles dispersed in water.


Why do dragonflies lose all of their coloration once they die? At 06:43 in The Secrets of Nature video Sky Hunters, The World of the Dragonfly - The Secrets of Nature the narrator says:

Scientists have been collecting dragonflies since the eighteenth century, but there’s always been a difficulty. Dragonflies quickly become deathly pale, they lose all their color. That’s why collectors have usually preferred to concentrate on butterflies...

and an image of rows and rows of uncolored dragonflies pinned to a display are show.
Question: Why do dragonflies lose all of their coloration once they die?
 click screen shots for full size

This is probably because the color in dragon fly wing is due to chitin crystal and which is protected by some secretion over the entire wing something like cuticle upon leaves and when dragon fly dies that secreted substance upon wing washes away when not maintained resulting in shredding off of the color from wing. Sorry I can't comment (<50 reputation) so I did answer even tho im not clear with it.
Try reading this you might find something useful maybe Insect Wing
Also this journal said that while studying the wing of dragonflies they killed and kept them in lab it didnt mention that wing lost color Mechanism of the wing colouration in the dragonfly Zenithoptera lanei (Odonata: Libellulidae) and its role in intraspecific communication
So it might be possible that the video shows dragonflies after some long time maybe a week after death and body is intact because of chitin layer but wings bleached away in sun or degraded in environment.
Also wings have supply of veins so something related with continuous production might be cause of that thing too.


What is an simple way to burn glucose for visible effect? I want to make a partially working model of the digestive system that could digest complex carbohydrates. My ultimate goal is to be able to cut up some bread, put it into the model, operate it, and eventually see some effect equivelent to glucose being used in a muscle. I obviously have a very limited buget. How could I simulate glucose being burned in some way that has a visible effect?

Edit: I'm specifically looking for some way glucose can be used to achieve some visible effect that makes sense as a metaphor for combustion, without dangerous/expensive chemicals.

You could combine the demonstration that glucose can be burned with the principle of catalysis: a sugar cube won't burn by itself if you hold a match at it. Using a bit of MnO2 or even simple ash on the cube will make it inflammable through catalysis: the MnO2 acts as catalysator (is not used up).

MnO2 (manganese(IV) oxide), a dark powder, is a safe chemical that only reacts with acids, and is insoluble in water.


Can cysteine alone change pigmentation? According to this graph (from here):

cysteine contributes to pheomelanogenesis, and having a high enough concentration of cysteine makes the shift towards pheomelanin instead of eumelanin. So my question is: theoretically, let's say I would feed my dog a cysteine supplement daily, would that change its coat color over time? If yes, how, and if no, then why not? What am I missing in this process?

Disclaimer: this is just an example, of course I do NOT intend to feed my dog anything at all, it's just a hypothesis. What I want to know is that raising cysteine/glutathione levels can really contribute to pheomelanin production? I know that theoretically, in lab tests a higher cysteine concentration means a higher pheomelanin production, but I am interested in actual living things. If this is possible, it can be a huge breakthrough. If you have the opinion that cysteine alone won't make the difference, than what will? According to the graph attached, that's the only thing making the difference.

Surprisingly, it is indeed possible! But, the fact is that the actual process is a bit more complex and might actually require more compounds along with cysteine to give such effects in living beings. First of all, see this image1:

As is clear from the diagram, GSH (glutathione) is also a factor for pheomelanin production, along with cysteine. Another factor on which one might not pay heed is Tyrosinase protein expression. High amount of L-cysteine is thought to decrease the expression of tyrosinase in cells2 (but since I found just one article, I'd suggest to not pay much attention on this point).

Apart from gene expression, cysteine affects tyrosinase itself too. High concentrations of cysteine and glutathione have been shown to inactivate tyrosinase in cells, and the cause has been suggested to be the thiol-group of GSH and cysteine, which somehow generates oxygen radicals and inactivates tyrosinase3. A concentration of 10mM cysteine is sufficient to inhibit tyrosinase activity in cells4. It is because of these kinds of effects that GSH and cysteine are now being used in cosmetics as skin whitening agents as they, in higher concentrations, inhibit tyrosinase activity and hence, melanin production in skin cells5.

Just to add, when it comes to gene regulation, then it seems that cysteine has some more effects too. As pointed out by @Chris, eumelanin production in skin is stimulated by a cascade which involves a receptor known as melanocortin-1 receptor (or MC1R). When activated by one of the variants of MSH, typically $\alpha$-MSH, MC1R initiates a complex signaling cascade that leads to the production of the brown or black pigment eumelanin6. Now, a research has concluded that 0.07 mg/ml concentration of L-cysteine greatly reduces expression of MC1R gene, thus literally leaving no way (not really) for eumelanin production7!

Thus, in short, it is not as simple as "Hey, you want a red skin tone? Here is some cysteine for you!" Cysteine, and other related compounds like GSH, have more complex effect on melanin production than just promoting production of pheomelanin over eumelanin. You can also have a look at this answer (by @Chris) for some more information.

EDIT: To tell where you're going wrong, I'll make two reaction flowcharts. First, this is (IMO) what you're expecting as an answer:

But this is what is actually happening:

The red line is what we're interested in. But as you can see, the diagram is already quite complicated (and expected to get more complicated as more factors are discovered). So, giving a simpler explanation than this would be, very much, impractical or impossible.

References:

Malathi M, Thappa DM. Systemic skin whitening/lightening agents: What is the evidence?. Indian J Dermatol Venereol Leprol 2013;79:842-6
The Inhibition Effect of L-cysteine on Melanogenesis in B16F10 Mouse Melanoma Cells; In-Sook An, Ji-Hye Kim, Hoe-sook Yoo, Rui Zhang, Sang-Mo Kang, Tae-Boo Choe, Tae-Jong Kwon, Sung-kwan An, Gi-Yeon Kim
The effect of catalase on the inactivation of tyrosinase by ascorbic acid and by cysteine or glutathione; Lindbladh C, Rorsman H, Rosengren E.
Inactivation of human tyrosinase by cysteine. Protection by dopa and tyrosine.
Jergil B, Lindbladh C, Rorsman H, Rosengren E.
Mechanisms Regulating Skin Pigmentation: The Rise and Fall of Complexion Coloration; Jody P. Ebanks, R. Randall Wickett, and Raymond E. Boissy
Melanocortin 1 receptor - Wikipedia
Substantial Effect of Melanin Influencing Factors on in vitro Melanogenesis in Muzzle Melanocytes of Differently Colored Hanwoo; Touseef Amna, Kyoung Mi Park, In-Kyung Cho, Tae Jeong Choi, Seung Soo Lee, Kang-Seok Seo, and Inho Hwang


"Spontaneous Immortalization" HaCaT keratinocytes are described as "spontaneously immortalized "(see paper below) due to aneuploidy or chromosomal alteration.
From the paper I get that this is a literal term, that the cells just continued growing (?) in vitro and never went into senescence without any "human-induced" transformation.
Is this a common procedure for cell immortalization or a rather rare example?

[http://jcb.rupress.org/content/106/3/761.long][1]

It depends how you define it. Many early cell lines (as well as some modern ones) were derived from tumors. Tumors are spontaneously immortalized cells which became immortalized in vivo. If you're asking how often researchers collect primary cells (non immortalized) and grow them with the hopes they will become immortal the answer is pretty much never.


Difference between null and recessive allele? I get that in a single gene locus, an individual can have RR, Rr, or rr as the two alleles for that gene. R is "wild type" because it is the allele occurring most frequently. r is the allele that is not WT.

RR and Rr show dominant phenotypes, whereas rr shows the recessive phenotype.

But what's the difference between r and a null allele (allele generated by a loss of function mutation outputting the complete loss of the WT phenotype)? Where _ is a null allele, my questions are below:

R _ would produce the same as Rr, correct or not?
r _ would produce the same as rr, correct or not?
_ _ would produce the same as rr, correct or not?

To add to Remi b's answer - this question is confusing because 'null' and 'recessive' are terms emerging from two very different levels of analysis. The concept of 'recessive' existed before we knew what genes were, or how they worked. It just describes the patterns of inheritance you see in a gene's effects.

The concept of a 'null' allele however came later, and explicitly describes how an allele works - by destroying gene activity. So 'null' is molecular concept, 'recessive' is an abstract genetic concept. It so happens that null alleles are very often recessive, because usually one working copy of a gene is fine. But the two terms are describing genetics at very different levels.


Catabolic and Anabolic Reactions How do we differenciate between catabolic and anabolic reactions?

According to my researches;

Catabolic Reactions

  Catabolic reactions (also called “catabolism”) break down larger, more complex molecules into smaller molecules and release energy in the process. The smaller end products of a catabolic reaction may be released as waste or they may be fed into other reactions. The energy that is released by catabolic reactions can be captured and used in many ways. Some of the energy is released as heat and increases the temperature of the cell. Sometimes the energy is stored in the chemical bonds of another molecule. And sometimes it can be used to do work, such as movement of cellular machinery to power the active transport of materials across cell membranes. Catabolic reactions are central to biological processes such as cellular respiration and the digestion of food molecules.

Anabolic Reactions

  Anabolic reactions (also referred to as "anabolism") use energy to build more complex molecules from relatively simple raw materials. “Anabolic” and “catabolic” sound similar but are opposites. To remember the difference, it may help to think about how “anabolic steroids” promote the buildup of muscle mass. All of the complex molecules of life — carbohydrates, lipids, proteins, nucleic acids — are generated by anabolic reactions. Anabolic reactions are central to processes like photosynthesis, protein synthesis, and DNA replication.

Here are my questions

Is there water in every chemical reaction?
Do i just need to look at water ($H_{2}O$)?

Regards

Starting of with the basics, reactions are the breaking of bonds in the reactants and the forming of bonds in the products.

To answer your questions about water, there is not always H2O present, although most of the times there is water. You are referring to the hydrolysis and dehydration synthesis reactions, in which water is added or removed, to break down and combine molecules, respectively.

Catabolic reactions are more defined as the net release of energy in the reaction. They break down bigger molecules to smaller molecules. There is a need for energy input to begin the reaction and break the bonds of the reactants, however, the release of energy when the bonds of the products form are far greater, resulting in a net release of energy.

Anabolic reactions are essentially the opposite, where smaller molecules are combined and built up to larger macromolecules, many times with the removal of H2O. This results in a net decrease in free energy, as energy is absorbed/stored in the larger molecule. Energy inputted to break bonds of the reactants are far greater than the small energy released as bonds form.

As you will learn soon, these reactions can be characterized by exergonic/exothermic, and endergonic/endothermic reactions. They can be considered synonymous in many cases.


Why Hfr cells are called high frequency recombination cells? I understand that Hfr cells are formed when fragment of bacterial plasmid integrates itself in another bacteria's (host) genome through homologous recombination but my question is why do we call these cells as "high frequency recombination cells". Where is the term high frequency coming from?

According to Luca Cavalli-Sforza, the scientist who coined the acronym Hfr:

  Recombination as observed at the beginning had a very low frequency. It stopped being rare when I found a mutant strain which I called Hfr for “high frequency of recombination.” I found it accidentally in 1949 while I was selecting mutations resistant to nitrogen mustard and radiation. The first two resistant mutants, which had undergone a rather heavy treatment in the process of selecting for resistance to nitrogen mustard, proved to be exceptional in their mating behavior. One was Hfr and it showed immediately its remarkable mating ability, which was higher than that of normal crosses by a factor of 1000 or more. I repeated the experiment two more times before believing it. The other mutation, as I later proved, was an F- (self-sterile) mutation of an F+
  (fertile) strain. (emphases mine)

Source: Forty Years Ago in GENETICS: The Unorthodox Mating Behavior of Bacteria


What is this insect that showed up after I left food out? How can I get rid of it? These bugs showed up after I left some food out. I noticed a significant reduction after I cleaned up my place, but now they're back again. They're pretty small, but can you guys help me identify these bugs. I need to look up how to get rid of them.

I live in the Midwest.

I realize the quality is not the best.

It is likely a fruit fly, a Drosophila melanogaster.

I've tried different methods to trap then but the most effective way I found is this. You need a container (pan, jar, bowl, whatever), vinegar (I use any type), a drop of dish soap, and plastic wrap over the top with holes poked in. Then the flies cannot stand on top of the liquid but also have issues escaping through the holes in the plastic wrap.


Don't understand figures in this citizen-science mosquito ID project The Citizen-based mosquito monitoring system is a Citizen-Science vector tracking project that involves using any of a wide variety of cell phones to capture "sound bites" (sorry!) of mosquitos. These are collected and analyzed in order to gain some insight into the distribution of different species of mosquitos at different times and locations. Attention is paid to ensure the system works with older model phones that are distributed more widely.
While a positive identification of a single insect form a single recording is not likely this way, over time a statistical analysis is expected to give meaningful information. I believe the idea is that similar sounding species are expected to not be in similar places at similar times so often that it muddles the identification too much. This is citizen-science; imperfection is not a deal-breaker.
I was happy to see that there is a BioRvix paper. In fact, I was surprised to see there is such at thing as BioRvix in the first place!
The principle is illustrated in Figure 5, and some of the argument behind species differentiation is illustrated in Figure 7, and screenshots of both are shown below.
I think there is a lot of information densely packed within the figures, and I'd like to understand more of it. In the second figure below, which is Figure 7 in the paper, what does the color scale and color coding represent?
There seems to be some suggestion of time of day as well, but I don't understand exactly how. What about time of year - that should also play a major role.

Some may recognize Manu Prakash as "Foldscope guy".

In the second figure –
  What does the color scale and color coding represent?

Each color is an individual mosquito species,
arranged the same from top to bottom on all plots.
Here, on the left, all species are gathered on one plot,
with the y-axis now labeled “Species.”

The sounds of many mosquitoes apparently have statistical profiles
similar to each other,
so the individual plots
demonstrate how additional factors help distinguish species
in some such cases.

In the plot for “Time” (C),
the sun and moon merely accompany the species
whose differing circadian habits they illustrate.
It is only a coincidence
that the daytime species is plotted higher.

Just to complete the picture,
here is how these plots mark statistical profiles.


Why are some menstrual cycles irregular? A friend of mine asked me this today, and I didn't know. I remember studying the menstrual cycle a few years ago, but I can't remember the details (other than it was very hormone-related), and so I don't have a good base in the matter anyhow.

What makes some women have irregular periods? Why?

There's two phases of a menstrual cycle, before ovulation known as the follicular phase and after ovulation known as the luteal phase. The second phase is not very variable, it's the same length almost always as it is governed by how long the corpus luteum (remnants of the follicles after the ovum bursts out) survives. The first part is variable and is what causes periods to be irregular. In this phase the eggs mature. The body picks several eggs to mature but only one will "win". However, how fast it wins changes. It all depends on how fast it grows and much it manages to suppress growth of the other eggs and that in turn depends on the quality of the egg. But then this also branches out, as it is controlled by levels of hormones this is heavily affected by stress and diet among other things.

It's unfortunate that the first phase is variable otherwise knowing which day you were going to ovulate would be easy.


How does the NAD+/NADH ratio affect lifespan in vertebrates? Here's the proximate physical implication of the ratio (from the Wikipedia article on NADH).

  The balance between the oxidized and reduced forms of nicotinamide
  adenine dinucleotide is called the NAD+/NADH ratio. This ratio is an
  important component of what is called the redox state of a cell, a
  measurement that reflects both the metabolic activities and the health
  of cells. The effects of the NAD+/NADH ratio are complex,
  controlling the activity of several key enzymes, including
  glyceraldehyde 3-phosphate dehydrogenase and pyruvate dehydrogenase.
  In healthy mammalian tissues, estimates of the ratio between free NAD+
  and NADH in the cytoplasm typically lie around 700; the ratio is thus
  favourable for oxidative reactions. The ratio of total
  NAD+/NADH is much lower, with estimates ranging from 0.05 to 4. In
  contrast, the NADP+/NADPH ratio is normally about 0.005, so NADPH is
  the dominant form of this coenzyme. These different ratios are key
  to the different metabolic roles of NADH and NADPH.

So here's my question: how does this manifest in vertebrate aging? Is it something that's simply the resultant of other aging processes, or can the ratio also contribute to aging in a certain way?

This study found a statistically significant decline in NAD+:NADH ratios and in intracellular NAD+ with age in the organs of rats.

They discuss that the activation of  PARP - the  NAD-dependent enzyme Poly(ADP-ribose) polymerase-1 instrumental in DNA repair - increases in aging organs (heart, liver, kidneys). This depletes cellular NAD+ levels via poly(ADP-ribosylation) of proteins. This reduced cellular  NAD+ then reduces the effectiveness of Sirtuins (Sirt1) which can deacetylate tumor-suppressor proteins such as p53.

Here's schematic showing the basic idea from their figure 10:

So, the inference is that oxidative stress in vertebrates increases with age due to lowered cellular NAD+ - i.e.,  consistent with the free-radical theory of aging.  This could mean that lowered cellular NAD+, NAD+/NADH in any given individual may well decrease said individuals lifespan.

The authors of the first study (Braidy et al 2011) suggest that therapies involved in maintaining high NAD+ levels may alleviate age-associated disorders.

Braidy N, Guillemin GJ, Mansour H, Chan-Ling T, Poljak A, et al. (2011) Age Related Changes in NAD+ Metabolism Oxidative Stress and Sirt1 Activity in Wistar Rats. PLoS ONE 6(4)
Smith, J., (2002) Human Sir2 and the 'silencing' of p53 activity, Traneds, Cell Biol. 12, 404


What makes drosophila eyes red? and is it stable? I have Drosophila melanogaster which I am doing an eye pigmentation assay on in the future. To do this I will dissolve the heads, 10 of them removed from frozen whole flies, in acidified ethanol for at least 48 hours (in the dark at 25 degrees) and then measure the colour of the liquid using a nanodrop. Specifically, this measures how well the liquid reflects red light, quantifying how much red pigment is in there.

I would like to know what causes the red colour in the eye and if leaving it dissolving for extended periods of time will (or is likely to) result in changes of what I measure? (ie is the material causing the redness in the eye susceptible to deterioration, which would change the colour of the liquid it is dissolving in over time)

Have any methods type papers tested this by comparing those dissolved for longer periods to those over shorter periods?

There's been a fair amount of work on this subject but a lot of it is old - see for example this 1945 paper and this 1948 paper.  That latter one in particular goes into some good stuff: color in the wildtype is due to red and brown pigments, which the authors separated by using acidic ethanol (after grinding up the flies).  Here's a 1961 paper from JSTOR that goes into a bit more detail on some of the red pigments (drosopterin, and isodrosopterin, and neodrosopterin) and looks like a good reference for some other, more basic work on Dmel eye pigmentation.  More to the point, here's a 2013 minireview on the chemical synthesis of drosopterins, which is useful mainly for referencing a lot of other work, in particular this overly detailed chapter from 1970.  That last one has tons of info about some of these pigment-causing proteins in insects.

The only particular reference to stability I could find was from that chapter, on page 144:

  The simple pterines (group 2) are chemically stable under normal physiological conditions, while the substituted (groups I and 3) and conjugated pterines are unstable. Light catalysed oxydation of the polyhydroxy side chain at C-6 is a normal phenomenon. The hydrogenated pterines are extremely unstable, especially at pH 7. Tetrahydrobiopterin, for instance, is oxidized within seconds in the light, but more slowly in the dark. [sic]


Identity and similarity for Multiple Sequence Alignment (MSA) of proteins I have to do homology modeling for a transmembrane protein (sodium channel) and right now I am in the process of aligning the sequences of the template with the homologous proteins I have found. I am using T-Coffee to do the alignment. I would like to have some numerical descriptors of the different sequences and I have been told to include the percentage of similarity and identity. How can I compute them? Is there an on-line tools to do this? Thank you.

I've never used T-Coffee but it looks like the web-server version gives you a total score as well as a score for each individual sequence; do you know if those numbers are related to the numerical descriptors you need?
A good place to start would be to read the documentation. Another good place to look would be the Google Groups page for T-Coffee.


What makes synaptic vesicle release probabilistic? The fusion of synaptic vesicles (SVs) with the plasma membrane of the active zone (AZ) upon arrival of an action potential (AP) at the presynaptic compartment is a tightly regulated probabilistic process crucial for information transfer (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773589). In a typical forebrain synapse, only ~15% of APs arriving at the presynaptic terminal cause fusion of a synaptic vesicle.

My question is, what factors make this process probabilistic? What happens at the molecular/cellular level that an action potential can lead to the fusion of synaptic vesicles one time and not another time? Is it due to some differences between different synaptic vesicles, how the vesicles are positioned inside the synapse, variations in the synapse's environment, differences between action potentials, etc?

From the source you provided, the answers seem to be outlined well from the authors' sentence that states:

  The Pr [release probability] of SVs [synaptic vesicles] at the AZ [active zone] is set by a complex interplay of different presynaptic properties including the availability of release-ready SVs, the location of the SVs relative to the voltage-gated calcium channels (VGCCs) at the AZ, the magnitude of calcium influx upon arrival of the AP, the buffering of calcium ions as well as the identity and sensitivity of the calcium sensor. These properties are not only interconnected, but can also be regulated dynamically to match the requirements of activity patterns mediated by the synapse.

Below, I use an analogy to provide a framework for understanding how these factors come together to mediate Pr as a whole, but you can read a scientific review on that here:  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059705/.  However, the actual molecular/proteinaceous machinery that underlie these phenomena are pretty well explained in your source (particularly in the sections "SV Proteins Regulating Pr" and "Recruitment of Calcium Channels to the AZ").

To use an analogy, think about the presynatpic terminal as the 100 meter dash at the Olympics.  The track only has so much space, so not everyone can run the race at the same time.  That's why there are multiple heats of the race.  The first point from the authors is availability of release-ready SVs, which your source discusses as part of the readily releasable pool (RRP) of vesicles.  Think of those SVs as the runners in a heat, lined up in the start position waiting for the gun to go off.  Their equipment is ready (starting blocks set, shoes tied, proper uniform and tag on, etc.). They're all in position, awaiting the signal, and they will take off as soon as they get that signal.  Therefore, the more SVs you have in that position with equipment/molecular machinery prepared to "go" in response to a signal, the more likely you are to have SV release.  The second point is location of the SVs relative to VGCCs.  In our example, this would be equivalent to having a lane closer to the person shooting the start pistol.  The closer a runner is to that, the more likely they are to hear the pistol go off and start the race.  Conversely if the person with the start pistol is at the finish line, it's possible less runners will hear it go off and miss their cue to start running. Since SVs require calcium to undergo membrane fusion and release their contents into the extracellular space, the closer these vesicles are to calcium channels the more likely they are to get that necessary substance for fusion/release. Third, the magnitude of calcium influx upon arrival of the AP, which we can think of as the volume of the start pistol.  If the start pistol is loud (a high volume of calcium comes into the cell), it's more likely the runners will hear the shot go off and start running (SVs will fuse to the membrane).  However, a very quiet start pistol (low influx of calcium) is less likely to be heard by the runners (less likely to bind SV proteins important for fusion). Lastly, they list buffering of calcium ions as well as the identity of the calcium sensor.  What's important to remember about the process of SV fusion is that it requires free calcium that can bind to the necessary vesicle proteins, so any other proteins (calmodulin, calbindin, the list goes on forever) that bind free calcium and make it unavailable to the vesicle will decrease the likelihood of successful vesicle fusion and neurotransmitter release.  This would be like someone giving the runners ear plugs before the race, which dampens the sound of the start pistol and decreases the likelihood of runners hearing their cue to start.  Again, there are nuances not covered in this analogy, but I'd recommend going through your source again with this framework in mind to pick up where those nuances come in.


Freezing after restriction digest Brief question:

I have performed a double digest with heat inactivated restriction enzymes with no star activity. I usually purify the DNA (PCR inserts and linearised vector) using a kit or gel electrophoresis but today I don't have time for it.

Is it okay to freeze (-20*C) the PCR inserts and linearised vector following heat inactivation of the enzymes? After a week, I will thaw, purify and perform ligation on these products.

Thanks!

From my experience I would say that it is no problem to freeze the digested DNA, when the enzyme is inactivated (even when not, for this time period I wouldn't expect much damage).

However, if possible, I would rather opt to freeze the PCR product and make the digest fresh, since the overhanging ends are kind of sensitive to hydrolytic degradation. I have also frozen linearized vectors without problems.


when does osmosis stop I have a question about osmosis that goes a bit deeper than most basic textbooks so I cannot find the answer.Here's the problem:

Imagine an animal cell, say a red blood cell, in a slightly hypotonic solution.
The water starts to flow in osmotically.
The concentration of solute in the cell decreases.
The cell slowly starts to swell but does not burst.

The question is:
Does this water entering increases the pressure on the membrane (similar to turgor in plant cells only less, because the cell can increase in volume - comparable to elastic energy that must be overcome when blowing a baloon...) and does this cause osmosis to stop BEFORE the concentrations come to equilibrum (meaning that cytoplasm still has a bit more solute concentration than outside of cell) or do the concentrations perfectly match?

Thanx in advance.

It doesn't

As long as liquid water is present osmosis will never stop, the closest you can get is a point at which it happens at equal rates in both directions, called equilibrium.

Plant cells will help you understand as osmosis will create immense internal pressure as water enters the cell even though the cell cannot expand thanks to the cell wall. the amount of water inside the cell will keep rising until it reaches equilibrium, this also makes the cell more rigid.


Is any known plant magnetic? Is there a plant (not a microscopic type but one that is visible to the naked eye) that has so much iron (or magnetite), cobalt, or nickel in its body that it can attract a magnet?

In this case "attract" would mean that a person holding a small magnet next to the plant can feel a small attraction between the magnet and the plant.

There was a 2011 study where they used a sensitive atomic magnetometer to try to detect a plant's magnetic field. They stated that:

  To our knowledge, no one has yet detected the magnetic
  field from a plant. Biochemical processes, in the form of ionic
  flows and time varying ionic distributions, generate electrical
  currents and time-varying electric fields, both of which produce
  a magnetic field. However, contrasted to muscle contraction
  and brain processes, which have a characteristic time
  scale shorter than one second, plant bioprocesses span several
  minutes to several days and the expected magnetic field from
  such processes is correspondingly smaller.

  Measurements with a sensitive atomic magnetometer were performed on the Titan arum
  (Amorphophallus titanum) inflorescence, known for its fast biochemical processes while blooming.
  We find that the magnetic field from these processes, projected along the Earth’s magnetic field,
  and measured at the surface of the plant, is <
   0.6 lG.

So according to this, no, you wouldn't be able to sense the magnetic field from a plant with a magnet.


Is the Opah a warm blooded fish? In 2015 many sources, including USA TODAY, Discover Magazine, and National Geographic, ran stories about the Opah fish (Lampris guttatus) being warm blooded.

Image Source: http://discovermagazine.com/2016/janfeb/58-meet-the-first-warmblooded-fish

Headline from USA TODAY 5/14/2015:  First warm-blooded fish identified

  In a discovery that defies conventional biology, a big fish that lives
  deep in the Pacific Ocean has been found to be warm blooded, like
  humans, other mammals and birds.

Article from National Geographic 5/14/2015: Meet the Comical Opah, the Only Truly Warm-Blooded Fish

  The opah’s wonderful nets are in its gills, and that makes all the
  difference. The blood vessels carrying warm blood from heart to gills
  flows next to those carrying cold blood from the gills to the rest of
  the body, warming them up. So, while a tuna or shark might isolate its
  warm muscles from the rest of its cold body, the opah flips this
  arrangement. It isolates the cold bits—the gills—from everything else.

  This allows its huge pectoral muscles, which generate most of its
  heat, to continuously warm the rest of its body. It also keeps that
  heat with the help of thick layers of fat, which insulate the heart
  from the gills, and the pectoral muscles (which produce most of the
  animal’s heat) from the surrounding water.

According to the Merriam-Webster Dictionary warm blooded is defined as:

  having warm blood; specifically : having a relatively high and
  constant internally regulated body temperature relatively independent
  of the surroundings

This definition seems to agree with the stories about the Opah fish being warm-blooded.  However, it seems different from humans, mammals, and birds which generate and maintain body heat when muscles are at rest too.  Are there different definitions of warm-bloodedness that would fit the Opah fish that is different from humans, mammals, and birds?

Did you say warm-blooded?

Despite the definition you cite from Merriam-Webstre Dictionnary, the term warm-blood is very unclear. The correct terms are endo-, exo-, poikilo- and homeo- therm. In short…

Source of heat

endo = inside
exo = outside

Variation in inside temperature

Poikilo = varies
homeo = does not vary

Please note, that these terms refer to extreme cases. There are organism which temperature are extremely constant (homeotherm), organisms which temperature are extremely variable (poikilotherm) and anything in between.

Any combination of these two axes exist. For example: If the temperature in the environment never varies you can be homeotherm without needing to be endotherm. Also, some organisms manage to keep a quasi constant body temperature via behavioural actions (moving to the sun when cold, going into the water when it's hot). A fun example (although debated to what I've heard) are the large dinosaurs that are thought to be homeotherms because their metabolism produce some heat and they are so large that they remain warm thanks to this heat source. However, they were probably not able to regulate actively their temperature. Therefore, I would tend to qualify dinosaurs as homeo-exo-therm but I wouldn't be surprised if someone prefers to call large dinosaur homeo-endo-therm individuals.

Opah fish

From what your second quote, it sounds like the Opah fish is endotherm. It is unclear from the quotes whether Opah fish are homeothermic.

Wegner et al. (2015) is a great read on the subject. Below is their abstract but I recommend reading the whole paper, it is easy to read and is very short (3 pages).

  Endothermy (the metabolic production and retention of heat to warm body temperature above ambient) enhances physiological function, and whole-body endothermy generally sets mammals and birds apart from other animals. Here, we describe a whole-body form of endothermy in a fish, the opah (Lampris guttatus), that produces heat through the constant “flapping” of wing-like pectoral fins and minimizes heat loss through a series of counter-current heat exchangers within its gills. Unlike other fish, opah distribute warmed blood throughout the body, including to the heart, enhancing physiological performance and buffering internal organ function while foraging in the cold, nutrient-rich waters below the ocean thermocline.

In the whole, paper, I could not find a mention of how much variation in body temperature there is. They highlight however that the point of such adaptation is for foraging in cold waters suggesting that they would just make a boost of temperature in extreme cases but not necessarily actively maintained a constant temperature otherwise. I would tend to think that Opah fish are much more variable than birds or mammals. To reinforce my believes, in the wikipedia > Opah fish it is written (without reference unfortunately) "The opah is not homeothermic like birds and mammals".

FYI, this answer was written by partially recycling this other answer of mine.