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Identification of this species of Toad
I found a short video on the Internet of a toad and I wonder if anybody could identify it?
It was posted on a social-media/blogging website called 'Tumblr',

so I don't know much about it (e.g., where the video took place).

EDIT: The original link is no longer active. Here's an alternate link.

Useful for hearing the specimen's "squeak"/scream.

EDIT 2: Here's a gif of some frames from the video for permanence on this site:

P.s. I think it's a toad. Please, don't hesitate to correct me/edit my question, if i'm mistaken.

Do you know where the animal is from?

In all honesty, I'm not sure. Although i would Initially suspect it was filmed in North America. I presume, that the person in the video is keeping it as a pet too, so, it could be sourced far from there... Sorry, I'm not too helpful on this one :(

@p.s.w.g thanks for the update, but your link also doesn't seem to work :/

@theforestecologist whoops... copy/paste error. I've corrected the link (but will need to be reviewed)

This indeed looks like a species of "Pacman Frog."
Specifically, this specimen most resembles the terrestrial Ceratophrys cranwelli (Cranwell's horned frog or Chacoan horned frog).

 © 2014 James H. Harding
Facts:

8-13 cm long; can weigh up to 0.5 kg.
Origin: endemic to dry Gran Chaco region of Argentina, Bolivia, Paraguay and Brazil.
Cranwell's are very popular as pets.
Their common name comes from their large mouths. According to Wikipedia:

Like most members of the genus Ceratophrys, they are often considered Pacman frogs because of their resemblance to the popular video game character of the same name.

Like most reptiles/amphibians traded worldwide as pets, a fair amount of interbreeding between captive species (and even speciation as a result of captivity) result in various hybrids and color schemes.
I couldn't find any reputable sources describing the sound the frog makes in the video, but Valetti et al. (2013) studied their calls in the wild.
Closely related Ceratophrys ornata is both larger and typically much greener compared to C. cranwelli.

It looks to me like it's a Pacman frog or Ornate Horned frog, a common pet frog. The specific species, by googling pet websites, my guess is Ceratophrys Cranwelli (common name Brown Pacman frog).

They most certainly do look very similar! I'll look into it, now. Thank you for your contribution. +1. I'll mark your post as the answer, if so.

It is almost certainly a toad, not a frog as the name of the video suggests. It probably belongs to the familie Pseudepidalea, aka the green toads. The live in Europe, Asia and North-America. Wikipedia
I don't know the species, as I am.not familiar with the North-American species. This animal has relative large and few spots. That may help in identification, but may also be intra-species variation.
I can't see the video, only the opening still.

I apologise for the issues with the video, I'm not sure if I'm able to suggest any "work-around", for it neither. Your contribution to this question is much appreciated, however. Thank you for your time. +1


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What do leafcutter ants do with the leaves?
I have seen pictures of leafcutter ants carrying off leaves. What do they do with them? Make a house?

c'mon...https://en.wikipedia.org/wiki/Leafcutter_ant maybe?

Trivial questions about basic biological concepts are off-topic on Biology unless you have shown your attempt at an answer.

I'm voting to close this question as off-topic because it is an underresearched trivia

As in the Wikipedia article, these ants have a mutualistic relationship with a fungus. They feed their leaves to the fungus and in return the fungus makes pellets of food to feed it to the ant larvae. Along with that, the fungus provides defense to the ants.
Ants and many other animals cannot fully digest leaves as they contain cellulose which can only be digested by certain fungi and bacteria.

@AliceD I have added some extra information.

source: Stack Exchange

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sort: votes


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Why do mice have a higher metabolic rate than humans?
Mice and other small animals have higher metabolic rate than humans.
How does that happen on cellular level, if we look on one cell in the mouse body?
What is it in this cell that will be different?
How is that regulated inside mouse cell?

I have changed the title. "higher" in  the original title is meaningless without a comparator. Let's keep science precise please.

In endothermic and ectothermic animals, ie. warm and cold blooded animals, metabolic rates are inversely proportional to size of the organism.

Quoting from https://www.biog1445.org/demo/04/metabolicrate.html
This is because smaller animals have a higher surface-to-volume ratio,
  thus a larger relative heat loss to the environment per unit time. To
  maintain a constant body temperature despite rapid heat loss across a
  body surface, a small animal must oxidize food at a high rate. Because
  the relative amount of food consumed and the pace of digestion,
  respiration, and so on must rise with decreasing body size, there is a
  lower limit on the size of endotherms. The smallest mammals are
  shrews, which weigh only about 4 grams. They must eat nearly their own
  body weight of food every day, and starve to death is just a few hours
  if deprived of food.

This is shows that smaller animals, like mice have a much faster metabolic rate than that of larger animals like humans or elephants.
When talking of within the cell, the mitochondrial content of a muscle cell of a mouse would be increased to produce more energy from one feeding than that of a human. This is because cells themselves increase the number of mitochondria based on the requirement of the body, thus a muscle cell of a human has more mitochondria than a neuron, since muscle cells have to utilize much more ATP to function. This phenomenon, known as mitochondrial biogenesis would be observed in mice vs human cells.
In mice, having more mitochondria would be an evolutionary advantage, as only those producing the optimal amount of energy would be able to survive the loss of energy to the surroundings and the process of natural selection would leave mice with relatively larger numbers of mitochondria in their cells.
(For more info)
https://en.wikipedia.org/wiki/Metabolic_theory_of_ecology
http://www.sciencedirect.com/science/article/pii/S0378111900005825

This basically re-states the background of the question, without actually answering it.  The question asks if the difference in metabolism extends to intracellular processes.

I'm sorry, I didn't quite pick up on that. I will do some more research then edit this answer

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Examples of prey predator interactions where density of predator is very low and prey form groups when the predator attacks the prey for food

Examples of prey predator interactions where density of predator is very low (has a threat of extinction) and prey form groups when the predator attacks the prey for food.

I have searched this in net but not get examples. Please help me to supply some examples with a brief interaction of type discussed above.
EDIT
Specialty of predator:
Predator population has a threat of extinction due to their low population. They have the difficulties in locating acceptable mating partners for sexual reproduction during their receptive period due to low population densities.

This sounds like a homework question. Look up bait fish ball.  Use what you learn there to guide other searches.

@akaDrHouse Thanks. In that case which one is the engendered predator mostly feeds on the bait fish. Please provide me more such examples of prey and predator pairs having such interaction.

Homework questions are off-topic on Biology.SE.

This post might help you to understand how prey-predator interactions affect population size. The post does not contain examples though as it focuses on the theoretical aspect.

@Remi.b This is not a home work question.

@Remi.b I am not interested to understand "how prey-predator interactions affect population size". I know this. But I am in need of a very special type of interaction that I have discussed above. Please don't think this search is for solving a homework question or homework-type question.

@user1942348 If it's not homework, can you then provide a better background? Describe your problem, what you know, what kind or interaction you are interested in and why? By doing so, you are much more liklely to get useful answers.

Are you asking for cases where the flocking behaviour is used specifically against low-density predators, or flocking against predators in general? At the moment, it's unclear why are asking specifically about low-density predators,and bring the risk of extinction of the predator into the equation.

@fileunderwater I am asking examples about group defending behaviour is used by prey against engendered predator (who have the risk of extinction due to low breeding or mating for their low density).

@fileunderwater Please reply if my question is not clear.

You are only restating exactly the same thing that is already in the question. Why is it important that the predator is potentially endangered? The flocking behaviour will probably have been selected for when the predator was more common. And as I wrote earlier, add more information and background to your problem. Why are you interested in this?

@fileunderwater I have to study about the feeding behavior of engendered predators.  This is required for my higher studies. I got some information. But I am in dark if the prey are of special type for example prey tries to defend the predator in group. If I get this information, then I can study further. I have to collect all information for engendered predator only, as my topic is for engendered predators.

The endangered Canadian Lynx interaction with Snowshoe hare.

A low predator density is not synonym with "threat of extinction". Of course large predators are more prone to extinction because of lower numbers, but they usually exist in lower densities than prey (look, for instance, Lotka-Volterra equations and graphics, and also biomass and food pyramids). The risk of extinction is usually caused by fragmentation of habitat, that reduces population and gene flow.
Many preys form groups to avoid predation. That happens with schools of fish, caterpillars that walk as a multi-organism mass, grasshoppers that change behavior into locusts, bovids and related mammals, that make a circle with the horns to the outside to defend against predators.
So, it's not clear what you're asking. Is there any special case of low density of predator/modified prey behavior?

EDIT: If you want a more concrete answer, it will depend of the geographic region. But everywhere the largest predators are usually the most endangered. They usually prey on large mammals (but not only, since a jaguar can eat an anaconda or an alligator, etc.).
Here is an example from Alaska:
http://www.nps.gov/gaar/learn/nature/muskox-circle-defense.htm

If there is one predator—a lone wolf for example—the defense strategy
  is to form a line. If a wolf pack surrounds the group, the muskoxen
  will form a tight circle, all facing outward, forming a phalanx of
  heads and horns.

https://www.youtube.com/watch?v=pb6Rke7jiTc
http://www.iucnredlist.org/details/3746/0
Although IUCN has no data about the subspecies Canis lupus arctos, they say:

Originally, the Grey Wolf [Canis lupus] was the world's most widely
  distributed mammal. It has become extinct in much of Western Europe,
  in Mexico and much of the USA, and their present distribution is more
  restricted; wolves occur primarily but not exclusively in wilderness
  and remote areas. Their original worldwide range has been reduced by
  about one-third by deliberate persecution due to depredation on
  livestock and fear of attacks on humans.

It may not be the case in Alaska, though.
Another example from Africa are zebras. There are many species from two different subgenera, but if Equus zebra is endangered, what we may think about their predators! Lions, for instance. They flock in groups so the stripes may confuse the predators about where one individual ends and the next begins - making a successful attack more difficult.
http://animals.howstuffworks.com/mammals/zebra-stripes.htm/printable

"Is there any special case of low density of predator" - Answer is yes. Special case is predator population has a threat of extinction due to their low population. They have the difficulties in locating acceptable mating
partners for sexual reproduction during their receptive period due to low population densities.

Not sure if its a "special case" or just a usual low-density predator worsened by other causes of extinction, such as deforestation. Still, not clear what the question is.

Ok. It may be just a usual low-density predator worsened by other causes of extinction, such as deforestation. Only thing is that predator should have threat of extinction.

May I get more concrete answer that I need?

In any example given you can add a theoretical extinction risk.  That's very common nowadays.  You can look at iucnredlist.org, for instance.

Many species of animals use flocking/ schooling/ shoaling/ etc as a mechanism to confuse predators. A few examples are tuna, starlings, goldband fusiliers. tuna and goldband fusiliers use their reflective scales to blind and confuse the predator, whereas starlings use sheer numbers to overpower and throw off their predator. The large groups tend to scare away far away predators.
The act of grouping is not dependent on whether or not the predator is endangered or not, but there would be cases where both the predator is endangered and the prey uses grouping. For example, several species of owl are endangered, which prey on starlings.
https://en.wikipedia.org/wiki/Collective_animal_behavior#Protection_from_predators
http://www.fcps.edu/islandcreekes/ecology/european_starling.htm
http://rsif.royalsocietypublishing.org/content/10/85/20130305


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When performing mutagenesis for an assay, how do you decide on the sample size of individuals to be mutated such that all genes are covered?
If I want to study, say, gustatory response of salmons to a bile acid, I need to mutagenize a sample of salmon males. However, given that there are many genes involved in this response, what is minimum no. of salmons I should mutagenize, such that ALL the genes involved have some mutations?
I have searched quite a lot for some statistical method that tells me this, but to my surprise I haven't found any.

Don't think about mutagenized animals, think about mutagenized genomes. Depending on when the mutagenesis is carried out, and how efficient it is, a very small number of males could give rise to thousands of mutagenized F1 progeny, each carrying a uniquely mutagenized genome. That is the number to focus on. Typically, in fruit flies and soil nematodes the animals are hit "pretty hard" such that each F1 is carrying hundreds, if not thousands, of mutated sites, randomly throughout the genome. The trade-off is to not mutagenize them so much that they suffer a drastic decrease in fertility or viability, while at the same time minimizing the number of F2 homozygotes you have to screen for phenotypes.
In C. elegans exposed to 50 mM ethylmethane sulfonate for 4 hr, you might reasonably hope to recover 1 loss-of-function mutation after screening 2,000 mutagenized F1 genomes.
Are there good genetic markers along all of the salmon chromosomes?  If you are only interested in recovering dominant mutations then you can screen the F1 directly (however dominant alleles tend to be much rarer than recessive alleles, and interpretation of dominant phenotypes is challenging without lots of good genetic tools, like duplications and deficiencies). Otherwise you will have to mate the F1 to obtain male and female F2 and then set up brother-sister matings so that you can score the F3 for phenotypes of interest.
None of these numbers would apply to salmon because the genome is much larger, and unless someone has already done a dose-response curve on the optimal mutagenic dose for salmon, you would need to do that first.


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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.


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Data Retrival from the GenBank?
When I go to NCBI & Select nucleotide option there and in search box write For Example CNGA3 gene the page shows that there are 553 items.I know the method of downloading or retrieving the One item's or record's FASTA format but "if I have to download the FASTA Format of all the 553 items simultaneously without opening each link then what options should I use..?" If you know it then please help me.. ?

It is easy and possible. I will use steps which you already used and add additional steps to answer your question.

Go to Pubmed
Select nucleaotide from list
Enter gene of interest
In format option choose 'FASTA'

Click on send and then complete record

Click create file and you are ready to go !

I think that using NCBI Gene would be a better option here:

Go to NCBI Gene http://www.ncbi.nlm.nih.gov/gene/
Enter your gene of interest, in this case CNGA3 (and optionally the species)
Click the species of interest (I'm assuming you are looking for human, the first search result)
On the information page scroll down and click on FASTA which will provide the sequence for the gene of interest.


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Do endosymbiotic organelles have Latin classification?
Do endosymbiotic organelles such as chloroplasts or mitochondria have Latin classification?

You might find this article interesting Mitochondrial Evolution

As any other organelle, endosymbiotic organelles do not have a systematic name. However, their descendant prokaryotic organisms do have a genus name.


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Is there a web tool for species identification?
I know this stack exchange provides the ability to post photographs of animals/plants for species identification, but is there a web resource that can automatically identify a plant/animal using image processing/correlation tools - so the user doesn't have to painstakingly work with keys?

Try searching "species identification website" and there are many websites for species identification. Therefore I have flagged as too broad. Also, you haven't showed much research effort. A simple search gives you so many results.

I recommend using iNaturalist and their mobile app. That is very useful community in species identifications.

Encyclopedia of Life is also a good database for species identification but it does not have "automated tools" to do the search. Any kind of image search would work reasonably well if the training set is big+diverse enough or the query is unambiguous. This is a machine learning problem. Yes the user has to take pains and that is why there are biology courses on these topics.

Quality of images, variety in organism physical traits, and institutional motivation & coordination, or lack thereof, are the primary reasons why a tool like this doesn't exist. To automate species IDs, extremely specific images would need to be provided; e.g., high image resolution & quality (TIFF files), region(s) of organism depicted (ex. reproductive organs), age of organism, size/distance away from organism, etc. All of these parameters would need to be standardized, and then strictly followed.

Scientists are only beginning to develop robust techniques using DNA markers and NIR spectroscopy, for instance. For automated systems based on photographs there are some tests too, but usually restricted to very narrow taxonomic groups.


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How to determine the relationship of competition or cooperation?
I am currently studying the interaction of Twitter memes (two or many), such as competition and cooperation. Is there any model or method in biology that can identify the types of the relationship, such as competition or cooperation?
I have heard the Lotka–Volterra equations, but when I begin to dig deep, I found that it is still not suitable.

Welcome to Biology.SE. By identify, are you referring to methodologies of identification of to definition. In other words, are you asking for comonly accepted definitions or for methodologies to detect a concept that you have already defined (in which case, can you please your definitions).

@Remi.b Yes. I want to know the commonly accepted/acknowledged methods to define competition and cooperation between specifies.

I am not sure what you mean by "methods to define". Either just "definition" or "methods to detect"would make more sense to me. I wrote an answer to provide some info about the definitions of the different biological interactions (and not about the methods to detect them).

Species interactions
Generalities
Species interact. Species actually interact a lot. One can classify species interactions into categories based on the effect that the interaction has on their fitness (≈ reproductive success). Here is a table of possible biological interactions (comes from [wiki][1]), where a + indicates "beneficial", a - indicates "detrimental" and a 0 indicates it has no effect on fitness.

Different terms exist for a given relationship. Typically, antagonism is often called parasitism.
Note about symbiosis
Different authors use the word symbiosis differently. From wikipedia:

The definition of symbiosis is controversial among scientists. Some believe symbiosis should only refer to persistent mutualisms, while others believe it should apply to any type of persistent biological interaction (i.e. mutualistic, commensalistic, or parasitic).[6] After 130+ years of debate,[7] current biology and ecology textbooks now use the latter "de Bary" definition or an even broader definition (i.e. symbiosis = all species interactions), with the restrictive definition no longer used (i.e. symbiosis = mutualism)

Blurry limits
Generalities
It may seem pretty obvious that two species should have either one type or another type of interaction. However, the reality is often more complicated than that. An interaction might fall in one category under one set of environmental conditions and fall under another category under another set of environmental conditions. In addition to that, it is not uncommon that due to selection on the host genes due to the presence of a parasite, the host evolve so to tolerate the presence of the parasite up to the point of actually having a lower fitness in the absence of the parasite.
Example of environment-dependent interaction type
Consider an animal that is host to an algea. The host is providing shelter to the algea while the algea is providing sugar (produced through photosynthesis). If there is no light or if the enviroment is loaded with sugar, then the host has no gain of hosting the algea. In such case, the algea may even be parasitic. If, however, there plenty of light and there is few nutrients in the environment, then the algea and the host have a mutualist relationship.
Example of the evolution of a parasitic interaction
Consider for example a snail which is infected by a parasite. Let's assume (I think it is a real world example but I am too lazy to find out a reference) that the parasite need the snail to be eaten in order to reproduce in the body of the predator. In order to improve the chance of its host to be eaten the parasite is selected so to diminish the thickness of the snail's shell. In response to that, there is selection (which intensity depend also on the proportion of infected snails in the population) for having thicker shells. But now, snails that are not infected have shells that are so thick that the can't move as fast as they'd need to forage. So, by the end infected snails may have a higher fitness than non-infected snails. And therefore the interaction between the snail and its parasite is not a parasitic interaction anymore but a mutualistic interaction.

Is there a mathematical model or analysis that can determine the types of interaction based on the specifies' population growth curve?

Not that I am aware of. You might want to ask further questions on CrossValidated.SE and eventually use dummy data and ask how can one investigate this question knowing that there is a delay between the change in size of one population and its affect on the other population.


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How are steroid hormones secreted?
Peptide hormones for example tend to be secreted by Ca2+ mediated exocytosis following depolarisation and are secreted in vesicles. How are steroid hormones secreted and what stimulates their secretion? Please leave references if possible.

Homework questions and trivial questions about basic biological concepts are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy. "Homework" is interpreted to mean any academic or other assignment, test preparation, or task given in relation to a class, educational setting, or self-learning.


text:
Query from a ppt slide
I came across this slide:

Now I haven't understood what the last two grey colored lines mean. Can't ORFS be of any size? What is overlapping frames here?

Can't ORFS be of any size?
I think the point being made is that in a random sequence of 64 amino acids, on average 3 out of 64 should be stop codons, because there are three possible nucleotide sequences for stop codons (UAA, UAG, UGA). ORFs could theoretically be any size but the longer the sequence the more likely you are to come across a stop codon purely due to probability.
What is overlapping frames here?
An example of overlapping frames is shown in the slide:

For instance, you can see that the first "CU" in the first frame produces an alanine (as GCU), while the "CU" in the second frame produces a leucine (as CUU).
They have the same nucleotide sequence, but are offset to produce different amino acids. Viruses have very "condensed" genomes and often can use the same nucleotide sequence for different genes, just starting at different points in that nucleotide sequence. This means they have functional overlapping frames.

"but the longer the sequence the more likely you are to come across a stop codon purely due to probability." what does this line mean

so they have considered the frame size to be 3 here

@Rishika A reading frame is always 3 nucleotides. All I am saying is that in a random sequence of nucleotides, if you select any three at random you should come across a stop codon 3 out of 64 times. Think of it like driving down a road, where there are traffic lights every few blocks. You might get lucky and have a green light for 5 lights in a row, but it is statistically unlikely that you can avoid a red light for a very long distance. Think of the stop codon like a red light.


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ChIP-seq data Analysis Database
Where can i find already analyzed ChIP-Seq Data? Is there any database or any web tool that takes ChIP-seq raw data and automatically analyzes them? Or is there any database that provides some API to analyze the raw data it provides. I am new to ChIP-seq data analysis and i really need these to create a web-based platform for mapping ChIP-seq data. Thanks in advance.
I found some interesting data in genome.edu. Is there another database?

do you mean UCSC genome browser by genome.edu? It actually incorporates data from the ENCODE ChIP-seq experiments.

The largest database of curated ChIP-seq data is currently Encode and it supports an API.  You can use JSON to get at all tracks.
That page will have a link to Getting Started that should get you going. You can visualize raw data, normalized data, and processed data tracks in genome browsers that load in ENCODE data.  My favorite genome browser is:
WashU Epigenome browser


text:
What is the difference between Amino acids from blood and urine?
I would like to understand the difference between different tests for Amino Acids. Any blood laboratory offers amino acids tests using 3-4 methods

Blood serum
Urine Random
Urine 24 hour (all the urine samples collected in the last 24 hours)

After having tried Google and coming up empty, I have the following questions that I would like answered.

What would be the difference between testing it via each of the above methods?
What's the purpose of each of these different test methods?
Is one method better than the other? If so why?

Thank you.
Disclaimer: This question is for general knowledge purposes only. Please don't use the question or answers given as personal health advice.

Detecting protein and elevated levels of amino acids in the urine is generally a bad thing and is usually indicative of an underlying disease.
Kidneys are supposed to filter out waste products and retain metabolites that your body needs. There are many possible diseases that can cause amino acids to be detected in the urine, some as innocuous as overexertion or exposure to temperature extremes, and some as serious as Hodgkin's lymphoma, Amyloidosis, Malaria, Lupus, etc. For a more complete list see this Mayo Clinic page.
As for the blood, there are certain normal levels of amino acids found naturally in the blood. The reason for testing these levels is that certain imbalances can be indicative of different medical conditions. A doctor can use these levels to help to identify a problem that may not be noticed or may use it to diagnose a disease that you are seeking treatment for. This MedlinePlus page, has information.
Testing of Blood and Urine amino acids can and will be done in conjunction with one another in order to help narrow down the possible diagnoses that are likely.
Disclaimer: Personal medical questions and health advice are off-topic on Biology SE. We cannot safely answer questions for your specific situation and you should always consult a doctor for medical advice.

Edit to address comments
"Also, based on your answer and the Mayo Clinic link, what I understand is in a healthy individual - testing amino acids from urine might give false positives?"
I think that your concept of false positive here is incorrect. A false positive for this test would be indicating higher levels of amino acid in a sample than the sensitivity and standard error for the test would allow for.
That there is a laundry list of reasons why one might find abnormal levels of amino acids only goes to the fact that the kidneys "see" the results of several metabolic processes (normal or abnormal) and urinalysis is only a single datapoint from a spectrum of data for a clinician to begin to recognize a pattern and formulate a diagnosis.
As for greater accuracy, when comparing "Urine Random" to "Urine 24 hour" I would say that the "Urine 24 hour" test is more accurate strictly from a perspective of statistics. The larger the sample size for any test, the greater the level of confidence that the results observed are not due to random chance, error, or outliers in the data.
But this is the same concept for a political poll, marketing research analysis, or medicine; larger sample size gives you a clearer picture, but it does so at an increased cost. So the single screen is there just to look for issues, possibly based on a complaint that brought you into the doctor's office, or a way of monitoring a previously diagnosed condition and/or treatment, while the time courses are done to provide a clearer understanding of what is representative for the levels in that individual.
The single test has a number of reasons why it might be anomalous. Maybe the elevator from the underground parking garage was out of order and you had to walk up several flights of stairs to the office where they were collecting the sample, so it would show an elevated result due to exertion. Or maybe your drank a liter of water before the exam and your urine is dilute, causing a false negative. So to mitigate those anomalies, you run the time course, but usually only if there is a problem suspected because of the fact that it is an increased and unnecessary cost if all other indications are that the person is healthy or the result is easily explainable due to other data collected.

"I also understand that at times they would be used in conjunction - which seems logical. What I am trying to understand is which would give more accurate 'picture'. If one is not more accurate than the other, then what would be the difference between the 'picture' acquired from a blood test and the urine test."
Each test has its own parameters and give you an independent picture, that can be used to put together a more complete whole. Their accuracy will be based on their own sensitivities and built in standard errors and one will not be more accurate than the other because comparing free amino acids in the blood versus in the urine are two different pictures with different normal outcomes.
More samples, i.e. "Urine 24 Hours" or multiple blood draws over a time course is really the only way that you will improve on the accuracy of the individual tests, for the reasons I gave above.
They also have different baselines. Blood you expect to find free amino acids and there are ranges of normal results that you would expect to find in the blood. Here, too much or too little amino acid would be an indicator of a possible problem. For urine on the other hand, one would not expect to see elevated levels of amino acids, so here, a test that indicates elevated levels of amino acids indicates that more follow up is needed.
Think of it in terms of an analogy about astronomical observation. The electromagnetic spectrum is far broader than any one instrument can detect, so astronomers/astrophysicists use different sensors; visible light, radio waves, infrared, x-ray, etc. telescopes to detect many of these different pieces of data coming from the same object to gain a better understanding of what they are studying as a whole. Each gives slightly (or very) different views of the object, all of which contribute to a more complete picture of the object as a whole.

The first sentence is incorrect. Normal urine contains a small amount of protein. Of course an excess of protein in the urine (proteinuria) could have a number of underlying causes, some of which are "bad". Though I wouldn't necessarily call a transient proteinuria from strenuous exercise a "bad thing".

@AMR - Thanks for the answer, this is not a personal health advice question. I just want to understand as a clinician (I am not a clinician) which would be more helpful. I also understand that at times they would be used in conjunction - which seems logical. What I am trying to understand is which would give more accurate 'picture'. If one is not more accurate than the other, then what would be the difference between the 'picture' acquired from a blood test and the urine test.

@AMR - Also, based on your answer and the Mayo Clinic link, what I understand is in a healthy individual - testing amino acids from urine might give false positives?

@AMR - Finally, if my question is off-topic on Biology SE, please advise where to post the question for it to be safely answered. As I mentioned this is not for 'my specific condition'. It's a general question to understand why do different tests exist to test for a the same amino acids. I have the same question for glucose (which can be tested via blood AND urine). I would like to understand the difference.

@andthereitgoes I didn't necessarily think that your question was related to a personal medical question per se, however as this question / answer may be referenced by someone trying to understand their own medical condition, I think it is better to consult with their physician than use my answer as a basis to calm their fears or fuel their concerns.

@AMR Yes, makes perfect sense. I have edited my question to display a disclaimer for the same. Thanks.


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Which of the two chromosomes in a pair is expressed?
I have completely dummy question.
I have 23 pairs of chromosomes in the cells 23 single coming from my mother and 23 single from my father. So how my cell choose which chromosome, mother's or father's to use to synthesize peptides?

Actually, both sets of chromosomes are used to synthesize proteins. This is true for most proteins, ignoring things like imprinting and X-inactivation, which is a bit more advanced to grasp.

I dont find it a dummy question. Article "gene expression" on wikipedia does not provide a solution to this question.

The majority of normal autosomal genes have biallelic expression, i.e. the alleles on both chromosomes are used to make protein. This is why mutations in a gene which cause non-function of the product can be silent if the mutation is heterozygous (only found on one of the alleles), because the effect is masked by the second, fully-functional, copy of the gene. In other cases heterozygous mutations may cause slight phenotypes, because half of the protein produced is non-functional.
A small minority of autosomal genes have monoallelic expression, through a process called imprinting. This is where one of the alleles of the gene is modified by methylation of the DNA, or of histones (the proteins which are used to package and condense DNA). This imprinting switches off the expression of that allele, so that protein is only made from the other allele of the gene. Usually in this case, which allele is switched off depends on which parent it came from.
Things are slightly more complicated in the case of genes on X or Y chromosomes. Men have only a single X chromosome, and a single Y chromosome. This means that any mutation on X or Y which causes a phenotype will always present itself, because there is no second copy to mask it.
In the case of women, who have two X chromosomes and no Y, something similar to imprinting happens, where one of the X chromosomes is chosen to be inactivated. This X-inactivation process occurs very early in development, and the inactive X chromosome is kept that way for the rest of that person's life. In this case, however, the choice of which chromosome is inactivated is not dependent on which parent the chromosome came from, and is entirely random.
Some further reading:
http://www.nature.com/scitable/topicpage/monoallelic-expression-8813275
http://www.nature.com/scitable/topicpage/genetic-imprinting-and-x-inactivation-1066

According to some moderators you need to go into the intricacies of monoallelic expression in detail or else this is an incomplete answer.

@OmarMourad how is it now? thanks for the feedback, this is the first question I've answered on SE

I considered this to be an extremely clear and thorough answer.


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how body doesn't make antibodies against adjuvants of vaccine?
we know that all antigenic molecules don't have PRR on phagocytes and so they use an adjuvant that has a receptor for pattern recognation and fuse it with in order to phagocyte the antigen-adjuvant complex and present it on MHC II molecules for antibody syntheses now the question arises the phagocytes don't know which molecule is antigen and which is adjuvant then why MHC II molecules don't present the adjuvants for antibody syntheses and make the body sensitive against adjuvant and future vaccination should not be successful because the antibody recognises the adjuvant binds with it and not letting the vaccine to be processed?

Some adjuvants are not immunogenic. See this article.

Basically, this is what is happening when you receive a vaccine.

Immunoglobulins are being made agains protein adjuvants such as flagellin
Some of the adjuvants based on endotoxins such a lipopolysaccharides are not proteins. While there are some immunoglobulins produced that detect these molecules, the majority detect proteins
Most antibodies are produced against the functional conformation of the protein, so its tertiary or quaternary structure. When polypeptides are loaded into MHC II, it is a small piece of the primary sequence of amino acids. This is used to activate CD4+ helper T-Cells.
Vaccine is given in one of three ways; subcutaneously, intramuscularly, or orally (including nasally). Most antibodies circulate in the blood until they leak out of the blood vessels at the site of an infection. Also free antibody have half-lives of between 7 to 21 days, so even if there had been IgG in the tissue from a prior inoculation, it is unlikely that any will be at the site of the new inoculation without an inflammatory response taking place.

Oral vaccines will encounter IgA molecules in the mucus, so if they were made from a prior immunization, they could opsonize the vaccine, however, it is likely given in a high enough dose that some of the vaccine will reach the antigen presenting cells.
When delivered subcutaneously or intramuscularly, the vaccine will first be encountered by the innate immune system, even if adaptive immune cells were activated in previous rounds of vaccination. It is very unlikely that IgG will be encountered at the site of the inoculation, as IgG circulates in the blood and only ever really gets into the site of inoculation or infection after the innate immune cells have initiated an inflammatory response leading to the permeabilization of the blood vessels, allowing other immune cells and immunoproteins access to the site of the infection. Either way, APCs will be taking up the vaccine before the antibodies against them can neutralize them.
It is also likely a good thing that there are CD4+ cells in circulation that recognize a sequence of the adjuvant. If the B cell phagocytoses the vaccine and adjuvant, such as with a flagellin fusion vaccine, because there was specificity for an epitope on the target protein (vaccine), then even though the B cell is not making an antibody to the adjuvant, putting the adjuvant sequence on the MHC II means that it can be activated by a helper T-cell that recognized the adjuvant polypeptide, even if there is no T-cells that recognize the vaccine.

a lot of this is "common knowledge" for those of us familiar with vaccines an the immune response.. but can you list some sources?

@VanceLAlbaugh That is going to take me a while. The answer was written completely from memory and I did not refer to any sources when writing it. That being said, that knowledge is based on extensive study and reading on immunology.

A general source would be Janeway's Immunobiology, 8th Edition. But basically one would need to read the entire book and make the various connections to how the different systems play a role in the response to Pathogen Associated Molecular Patterns, Cytokines, Antigen presentation, etc. The answer is a summary of all of that information and how it is interconnected to one another.

@VanceLAlbaugh Are you okay with Janeway... This popped up again, and I don't know whether to work on it or just delete. Also WYSIWYG is right in that there are non-organic compounds used as adjuvants...

I'm completely fine with Janeway - he was a great immunologist and had a great book - used it in my graduate immunology course. I like your answer - a good compact explanation  - nice work


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Could someone please identify this species?
I have come across these insects a lot more lately, as far as I can tell, they can sustain a hover state in flight. I'm actually quite interested to know what these are, seeing they look like a cross between a bumblebee and a common housefly...

For species ID questions, it is very useful to know where and when you saw the animal, and it can be useful to know details such as weather conditions. Could you provide some of these extra details?

Easily done, lower Blue Mountains, Bew South Wales in Australia, about 4pm AEST, overcast conditions...

Based on location, behaviour, and markings, I'd go with some sort of hoverfly (https://en.wikipedia.org/wiki/Hoverfly). I can't offer positive ID, but I would hazard a guess at https://en.wikipedia.org/wiki/Melangyna_viridiceps based on the all-black thorax and the fact that this species is relatively common.

New South Wales*

It's definitely a hoverfly (Syrphidae), but I don't you will get a certain identification to the species level based on that single photograph.

@bshane, in the few pics I've seen, Melangyna stands with the wings folded, while Eupeodes stands with the wings spread apart. But don't know if this is a useful taxonomic trait for that group.

Looks very similar to Eupeodes corollae (Syrphidae). But only a specialist in the group will tell you if its the same species, genus or family. And not with that low-resolution photograph (sometimes they need to take the genitals off for proper identification).

the photo was the best I could I at short notice... I'll see if I can update the photo at a later time.

Better talk to a specialist. Depending on the group, you can only know the species by capturing an individual. And sometimes, only knowing the place and the flower it's in, is enough for the identification.


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What is the molecular mechanism of odorant transduction signaling pathway?
I have read a few papers on the topic of odorant signaling pathway. The following papers are listed as examples. However, I found that there is not a clear pathway representation of the odorant signaling pathway, through which the involved genes and regulations should be known. Is there any paper I have missed?

Menzel, R. and P. Benjamin (2013). Invertebrate learning and memory,
Academic Press.
Leal WS: Odorant reception in insects: roles of
receptors, binding proteins, and degrading enzymes. Annu Rev Entomol
2013, 58:373-391.
Kaupp, U. B. (2010). "Olfactory signalling in
vertebrates and insects: differences and commonalities." Nat Rev
Neurosci 11(3): 188-200.
Vosshall, L. B. and R. F. Stocker (2007).
"Molecular architecture of smell and taste in Drosophila." Annu Rev
Neurosci 30: 505-533.

Information available on this is huge. I will pin point main points. Generally this signalling will involve four components viz. receptors, transduction machinery, perireceptor processes and downstream processing of chemosensory information.
Receptors
First step is to receive signal (here odorant or chemicals). Following figure shows comparison between primary chemoreceptor neurons in vertebrates, insects, and nematodes.

These neurons constantly undergoes birth-maturation-death and process is well studied in many model systems.
Signal transduction
After stimulus is received, it needs to be transfer inside cell for further processing. In this case, generally transduction happens via GPCR signalling. These neurons use two widely used signalling cascades. Following figure shows main components in this signalling ( (a):vertebrate olfactory receptor neurons (b): lobster olfactory receptor neurons),

Perireceptor Processes
These process are important for receptor activation and transduction. They can be any type like mechanical or biochemical.
Downstream processing
There is huge information available at the level of pathway. Following figure represents main components in two model systems.

For finding genes, you have to search in specific part of this process (like this is good example of receptor genes in human).
I would strongly recommend reading chapter 4 of "The Senses - Comprehensive Reference". All above information is taken from this book. Another good open source reference is The Neurobiology of Olfaction, this reference has all things you need for free.

thank you for your comprehensive answer. I will peruse the references.


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How to do multiple sequence alignment?
I have a DNA sequence that makes protein 1. but now I have asked to:

compare the amino acid sequence of protein 1 with nine homologous proteins and make a multi sequence alignment (MSA) of the sequences.
Determine a consensus sequence for the proteins based on the MSA.
Find any specific parts of the proteins that are conserved, then explain why these parts are conserved.

Hint : http://www.bioinformatics.org/wiki/Multiple_sequence_alignment

A good start would be to load your sequence into an alignment tool/software. I would suggest using MUSCLE (http://www.drive5.com/muscle/). It is relatively easy to use.

MSA Tools

compare the amino acid sequence of protein 1 with nine homologous proteins and make a multi-alignment of the sequences.

EBI have a portal for many MSA tools and there are also other MSA tools available elsewhere.
In research, it's good practice to use several alignment techniques and look at which generates sensible indels. Usually, this is the lowest number of indel events.
Clustal Omega is probably the most sophisticated MSA tool hosted on the EBI site, however, it is relatively new and isn't as established as T-coffee or MUSCLE.
Note that these tools are updated fairly regularly. This question and top answer about "cutting edge" MSA tools from 2014 refer to a paper from 2011 that attempts to benchmark MSA tools. As you can imagine the state-of-the-art tools change rapidly (for example, clustal-w2 was released, and now clustal omega since that benchmarking paper). For most researchers though, it's a personal preference, and different MSA tools are "better" for different situations (speed of computation, number of alignments, similarity of sequences, complexity of secondary structure, local vs global alignments etc.).
Consensus sequence

Determine a consensus sequence for the proteins based on the
multialignment.

This depends entirely on the information from your alignment.
A common way to make a consensus sequence is to just take the most abundant residue at each position in the MSA. I don't like this approach because it heightens the significance of abundant residues, and diminishes the appearance of less abundant residues. This distorts the biochemistry and can easily lead to sequences that would be impossible or useless in biology. I would always rather see a raw alignment.
Conservation amongst alignments

Find any specific parts of the proteins that are conserved, then explain why these parts are conserved.

Conservation usually implies function, and hopefully you'll have a homologue that has a categorised function. Perhaps in your case one could attribute this function to a conserved sequence in the other homologues.
One brilliant tool is called consurf.

You can upload your MSA file to it and it will colour code regions of conservation from purple to blue. A purple region implies an evolutionary selection to not change that region, implying that it is a "functional" region.
Consurf works better with more sequences, so perhaps it isn't appropriate for this project. Instead try loading the alignment in Jalview and show "sequence conservation".

Caution.
When performing an MSA remember that the algorithm assumes that the sequence is homologous and that assumption can produce errors. If it looks wrong, it probably is!


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Do eukaryote cells contain DNA that isn't part of a chromosome or located in the mitochondria?
I specify eukaryote in the title, but I'm also interested if this question isn't applicable to eukaryote cells in general but is to humans. I was reading "RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays" (John Marioni 2008).
In the results it states
"By these criteria, 40% of reads mapped uniquely to a genomic location, and of these, 65% mapped to autosomal or sex chromosomes (the remainder mapped almost exclusively to mitochondrial DNA)."
I couldn't help but notice the "almost exclusively to mitochondrial DNA". Almost exclusively? Can DNA be found in places other than chromosones or mitochondria? Perhaps I'm interpreting the sentence wrong. Any pointers would be appreciated
Thanks

In plants, chloroplasts and other plastids contain DNA, but I suppose you are more interested in humans. Quoting from wikipedia,

In many cells cytoplasmic DNA is also found, which is different from
  nuclear DNA, both in methylation levels (cytoplasmic has less), and in
  sequence. EccDNA or extrachromosomal circular DNA is present in all
  eukaryotic cells, derived from genomic DNA and consists of repetitive
  sequences of DNA found in both coding and non-coding regions of
  chromosomes. EccDNA can vary in size from less than 2000 more than
  20,000 base pairs. In animals, eccDNA molecules have been shown to
  contain repetitive sequences that are seen in satellite DNA, 5S
  ribosomal DNA and telomere DNA. The function of eccDNA has not been widely studied, but it has been proposed that the production of elements of eccDNA from genomic DNA sequences adds to the plasticity of the eukaryotic genome and can influence genome stability, cell aging and the evolution of chromosomes

You should 'quote' with reference if you are copy pasting from external source.

I'm sorry! I'm new to Biology SE, and will keep that in mind while answering future questions.

Sure, no problem. It is not just for SE, in general in science you should practice that :)

In some reference genomes, D. melanogaster comes to mind, there are chromosomes designated as 'U' that contain sequenced genomic contigs of nuclear DNA that have not been physically mapped to one of the genetic linkage maps, or cytogenetic chromosomes.
These segments are probably flanked by long regions of repetitive DNA, and the sequencing techniques cannot unambiguously link these contigs up to the other huge contigs.

That is true, but this is still in the nucleus. The question was about DNA in the cytosol.


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yeast protein secondary structure
i have a fasta file of yeast orfs (from the SGD database) and i need to find out(predicted) secondary structure/classification for all of them (so ~6K queries and doing this by hand on numerous available websites is not an option). is CATH database a place that can give me this info? (so far i struggle to recover anything that can help me from the website but perhaps i am missing something), if not what's the best way/software to go about it? surely, these predictions have been done before and there is a databse somewhere -- yeast is too much of an important organism, with a lot of information about its genome.

Lot of resources are available online, choose depending on your requirement and protein of interest.

@Dexter, thank you. i am well aware of this site and others but i need the procedure automated: i have ~6k ORFs and i need to run all of them through the algorithm to obtain secondary structure.

Then you need little bit programming with server queries. Alternately, search for server which accept batch sequences.

@Dexter unfortunately this is not something i am able to do, so i was more after either a piece of code (R/python) or a relatively easy to use software. i am struggling with installing and running s2D (whose server version i've tried and approved) at the moment and it's a nightmare.

From comments I understood that you need to predictions in bulk. You can use API based system of JPred. They allow you to submit more than 1000 jobs per user per day. You can go through instructions step by step from their documentation. It looks simple !
Another hit I got while searching is Phyre2. I am sure there are many such servers.

Phyre2 took a non-trivial amount of time for me to get a model back. I don't know if their batch processing is any quicker, though.

@canadianer I haven't checked any of these sites. API integration sounds interesting. My personal choice will be submit to ExPASY server through python queries but OP is not (or don't want to be) a programmer I guess.

@Dexter like you said JPred was very easy to set up and use, thank you again. and i am programming myself, however i am not very experienced in python and i don't have much time to learn how to submit queries etc in python at the moment

No problem. Go with whatever you find easier. At the end only thing matter is to get your job done.

in addition to Dexter's answer i found that the s2D does exactly what i need. setting up might be a bit tricky and is certainly more involved than setting JPred up but using it is easy and the output is in a nicer format.


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Have there been any "chopstick gene" mistakes in genetics?
I've heard of the "chopstick gene" fallacy - wrongly assuming an association between genetics and some characteristic, confounded by non-genetic factors.
Has this fallacy happened in real life?
I'm not really interested in cases deliberately focusing on race, where people have argued that there's an innate difference between people of different races based on certain genetic differences, such as the putative "warrior gene" ("warrior allele"?) being described as more common in Maori people. As far as I can tell, the "chopstick gene" isn't about arguing that Asian people are better with chopsticks because of genetic differences between Asians and non-Asians.
I'm more interested in research that was done in good faith, which ignored the possibility of genetic variations having different frequencies in different groups, that produced erroneous conclusions.

If something is a fallacy, then how, by definition, could it actually have occurred? If you are asking if there are examples of genetic differences that separates ethnicities based on physically performable traits, then there are some examples. Sherpa's are able to live normally a very high altitudes and is related to genetic traits that were selected for because they were an isolated population in a selective environment. http://news.sciencemag.org/archaeology/2014/07/tibetans-inherited-high-altitude-gene-ancient-human

@AMR I was thinking of a scenario where a scientist publishes something, then either they or someone else notices this problem.

Have a look at this time article from a couple years ago.
A concept that you should think about is nature vs nurture. You can think of nature (your genetics) as controlling part of the potential of what you could become (for example, many long distance athletes have genetics that are beneficial for their sport) where as nurture encapsulates the environment that you grow up in (a nutritionally deficient child will not reach maximum potential height that you might predict based on genetics alone).
When scientists are studying a gene in relation to a phenotype, they statistical methods to determine how much a genotype contributes to a phenotype. This process would minimize these types of fallacies since different alleles in different populations would be considered. However, sampling biases can occur and most human variation studies are done on people of european, asian, and african descent.


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Exhaled air and lung capacity
I wonder if there is any connection between exhaled air and lung capacity. I need to implement some algorithm in my game to calculate points of how much time you blow and compare it maybe with some sportsman.

First of all nice idea! Secondly, wikipedia has very nice graph to answer your question (Image courtesy: wikimedia commons)

Look at the caption below figure in wikipedia for specific details. You will get all values you want plus how to calculations.
[Note: Sorry, I am not able to interpret why X axis is sinusoidal]

[It's sinusoidal because the x-axis is time and it's a graph of a person breathing]

Thanks! I thought so, but what's up with sudden bump ?

They're taking a really deep breath.

There is.
At a first approximation the total lung capacity is the anatomical dead space(the volume of your trachea, more or less) + the tidal volume(the volume of each breath). It's slightly more complicated than that based on the differences in how deep you breathe and how often you can breathe, but at a first approximation exhaled air + half a liter(plusminus) = lung capacity.

The way this is worded is confusing. The exhaled air you are referring to is from a maximal inspiration to a maximal expiration, also known as FVC or forced vital capacity.  FVC + another 1/2 liter is a good good approximation of total lung volume.

Is is, but I figured I'd gloss over most of it given the precision implicit in the question. If the speed of expiration isn't being measured "how much time you blow" won't give you an accurate representation of FVC at all. And the total lung volume is only first-order related to the VO2max, which you could meaningfully compare to athletes.


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What is the name of cellular respiration that Prokayotic cells use?
Eukaryotic cells use mitochondria using anaerobic or aerobic respiration. Prokayotic cells lack mitochondria but are bacteria. Mitochondria originated from bacteria and can be used in the same way. Bacteria produce ATP the same way that Mitochondria do.
So, what is that kind of cellular respiration called?

"Prokayotic cells lack mitochondria but use bacteria instead" ??

@Dexter Yes. Here's some extra info.  http://biology.stackexchange.com/questions/5430/how-do-prokaryotes-perform-cellular-respiration-without-membrane-bound-organelle

Prokaryotic cells don't 'use' bacteria. Bacteria are prokaryotic cells. Is it some wrong formation of sentence ?

@Dexter I fixed it.

Check this.

I think I figured it out from someone else

Prokayotic cells use anaerobic respiration.
Glycolysis is the only stage of cellular respiration that does not occur in mitochondria.
The glycolysis process does not need oxygen and uses anaerobic respiration. The other stages require oxygen and use aerobic respiration.


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Permeability of Plasma Membrane
I’m having trouble grasping why small polar molecules can cross the hydrophobic region of the membrane and not ions. Won’t the polar molecules be attracted to the watery extracellular medium and not be inclined to move through the hydrophobic region? (This is my reasoning for why ions won’t go through.)
Also, why do lipid-soluble particles go through the membrane? I understand they have an affinity for the hydrophobic region, but won’t they want to stay there, sandwiched between the two watery layers? Isn’t that the point of the orientation of the bilayer? Why would the lipid-soluble particles move from the hydrophobic region into the watery interior of the cell? Furthermore, why are lipid molecules not repelled by the hydrophilic heads on the exterior of the membrane?

Polar does not equal charged. Polar molecules have dipole moments, but they do not carry a charge. Ions on the other hand are charged particles. There is a difference between trying to get something polar through the membrane and something that is charged through the membrane.

Passive diffusion.
This question specifically refers to passive diffusion.
Ill reiterate and clarify what was mentioned in the question.
Passive diffusion involves a molecule dissolving into the membrane, diffusing across it, and then dissolves in the aqueous solution on the other side.
The second part of your question can be answered briefly: this diffusion event occurs from time to time, and often at a high rate.

Importantly only small, relatively hydrophobic molecules are able to diffuse across a phospholipid bilayer at significant rates. Thus, gases (such as O2 and CO2), hydrophobic molecules (such as benzene), and small polar but uncharged molecules (such as H2O and ethanol) are able to diffuse across the plasma membrane. Other biological molecules, however, are unable to dissolve in the hydrophobic interior of the phospholipid bilayer. Consequently, larger uncharged polar molecules such as glucose are unable to cross the plasma membrane by passive diffusion, as are charged molecules of any size (including small ions such as H+, Na+, K+, and Cl-).
-Cooper, 2000

Hydrophobic fatty acids repel charge.
The additional or missing electron gives the ion its charge. The hydrophilic head groups of the bilayer are charged, but the fatty acid chains are not, and these repel charge.
There are also repulsive forces between hydrophobic and polar residues (hence the bilayer exists in water), however polarity is essentially a spectrum. A small relatively non-polar polar molecule will not experience enough repulsion to stop diffusion, but a larger, or more polar molecule might.
Active and passive transport.
Although not mentioned in the question, these ions and other molecules can permeate the membrane via protein channels that allow, often with great specificity, ions and large molecules to traverse the membrane.

In the structure of the bilayer, there are proteins sticking out through the membrane as either transmembrane (through the whole membrane), extrinsic (on the outside) or intrinsic (on the inside) proteins. These act as gates or channels to allow polar, water soluble substances through. This process is known as facilitated diffusion. Check out page 11 of this article
Some ions are allowed in but this is a mediated process of active transport, where ion channels or gates regulate it. This is seen in neurons during the movement of the electrochemical signal along the axon, however, this does not happen automatically, unlike facilitated diffusion.
As for the second part of your question i feel like you can check out this question here


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Differences on biological classification?
Why we use the term phylum for kingdom animali but for kingdom planti ,fungi and prokaryota we use them division?                         What difference between phylum and division ?

Phylum and division are both listed under the same taxonomic ranks. The wikipedia page for phylum states that

Traditionally, in botany the term division was used instead of
  "phylum", although from 1993 the International Code of Nomenclature
  for algae, fungi, and plants accepted the designation "phylum".

What you have to keep in mind is that the scientists categorizing plants and animals worked in isolation for a long time and only recently have they come together to build a tree of life for all organisms (rather than just working separately on plants / animals / bacteria)

Is it just for a tradition ???

probably for that and legacy purposes to not confuse the people already in the field


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Access and decay time of long-term memory
As for STM (short-term memory), access time is 70 ms and decay time is 200 ms.
Is there any calculated time for LTM (long-term memory) also?
And does LTM really decay with the passage of time?


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Plasmid addiction system in high-copy number plasmids
Are there high-copy number plasmids that utilize a plasmid-addiction system?

According to the review by Kroll J, Klinter S, Schneider C, Voß I, Steinbüchel A. Plasmid addiction systems: perspectives and applications in biotechnology. Microbial biotechnology. 2010;3(6):634-657. doi:10.1111/j.1751-7915.2010.00170.x., there are high-copy-number Plasmid Addiction Systems (PAS), "specifically the addiction system depending on plasmid‐borne ORT utilizing the lac repressor."

The lac repressor protein (LacI) binds to the lac operator (lacO) and therefore represses the expression of the kanamycin resistance gene. When IPTG is available as an inducer, LacI is titrated by lacO, and the E. coli cells were able to grow in media containing kanamycin due to expression of the corresponding resistance gene. The same result was obtained when high‐copy‐number plasmids harbouring lacO were used for ORT. In this case the plasmid was stably maintained over 72 generations (Williams et al., 1998).

ORT = operator repressor titration
ORT is one of the three main groups of PAS.


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Why is chromatin not condensed during interphase but is in prophase
Cell cycle goes through three processes:

Interphase
Mitosis
Cytokinesis

Why are chromatins not condensed during interphase but instead condensed at prophase of mitosis? What makes them condense at prophase?

What resolution answer are you looking for here? Chromatin is complicated. If it was condensed during interphase, how would it be used? It would be folded up and inaccessible.

but then why is it condensed in prophase? and I still don't understand why are they condensed at prophase?

So that it can be partitioned neatly into daughter cells. If I understand correctly, your question boils down to "why is chromatin condensed at all?" ?

exactly. Also what makes them not condensed at Interphase?

This question is far too broad. From What types of questions should I avoid asking? in the [help]: "If you can imagine an entire book that answers your question, you’re asking too much." I suggest reading the Wikipedia article on chromatin and the linked articles on, for example, the structure of DNA.

is there a brief explanation of the causes that lead to this process?

Here's an image that explains the cell cycle:

And here's one that explains Mitosis as a subcategory of the cell cycle:

Chromosomes condense on the metaphase plate before they are pulled apart by kinetochore microtubules in a Tug-of-war. Chromosome condensation is not yet fully understood, but nucleosome structure is hypothesized to play a role. This is a very good question and is definitely not too broad.


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Which metazoans host anaerobes to aid in digestion? Do any host oxic digestive tracts?
Many metazoans (e.g., mammals, insects, earthworms) have anoxic digestive tracts that are colonized by anaerobic microbes that perform portions of digestion of food for the host.  Some other metazoans (e.g., porifera/sponges) rely on intracellular digestion.
I'm wondering, which metazoan taxa (I suppose we can keep it at phyla level) host digestion that is aided by anaerobic microbes, which do not, and are there any that have digestive tracts that host aerobic microbes instead (though that seems unlikely since they'd likely completely consume the food for themselves)?
We could start by addressing a partial list of the most well described metazoan phyla (plus a few of particular interest to me).  Perhaps no one will have the knowledge/expertise for each of these phyla - in which case we could have a community answer that is built on over time.

porifera- sponges
cnidarea - jellyfish, corals and sea animals
platyhelminthes- flatworms
nematoda- round worms
rotifera- worm-like animals
bryozoa- small aquatic animals
brachiopoda- lamp shells
phoronida- tubeworms
anelida- segmented worms
mollusca- soft bodied animals including chitons, snails
arthropoda- insects and others with hard, segmented bodies
echinodermata- starfish
hemichordata- acorn worms
chordata- primarily vertebrates
placozoa - simplest non-parasitic multi-cellular animals
Ctenophora - comb jellies
tardigrada - water bears
loricifera - tiny shelled sediment dwelling animals

Too broad... should be closed.

I have added a list of specific phyla to make the question more narrow.  It may require multiple answers over some time to fully answer this question and I plan to help by researching and adding answers for some of the phyla.  I could open a separate question for each phyla, but that seems inefficient.


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Why doesn't the ambient lighting condition change the perception of colors we see on a monitor?
Suppose that I take a picture of an object illuminated by an incandescent light bulb and I choose the daylight white balance setting. The picture I then get will display a white object as looking yellow, which is how the object would look had my brain not processed the image according to the ambient lighting conditions.
The question is then why the way the picture looks doesn't change depending on the ambient lighting conditions. If a white piece of paper continues to look white when illuminated by an incandescent light bulb, then why would that same piece of paper displayed on a computer monitor look yellow when I'm viewing it in a room illuminated by incandescent light bulbs?

Because actual reality and our ability to perceive reality are very different. Or brain is predictive and will predict white for a piece of paper under variable light color temperatures. But the context of the paper on the screen is different, as that is transmitted light and not reflected light. Your brain hasn't predicted that paper color by adjusting to the ambient light in the room. I would however say that you can perceive the differences in the reflected light coming off a piece of paper when you change the light source.

@AMR Can you please not answer questions in the comments section?

@Chris, but that isn't an answer. An answer would either from the standpoint of providing expert knowledge, i.e. in my field of study, or would be well referenced, neither of which my comments are. This reflects a comment, based on my general understanding that I feel adds to the discussion but does not rise to the standards of an answer.

The best ever answer is here: https://www.robotbutt.com/wp-content/uploads/2017/03/Calvin-Hobbes-Strip.png - that's a pity I have to keep it as a comment only :)

The phenomenon you are referring to is color constancy: The apparent hue of a reflective surface remains constant even when changes in the spectral power distribution of the illuminant alter the wavelengths reflected from it (Mather, 2008). In other words, despite substantial changes in illumination, we usually experience the color of an object as being constant.
The spectrum of wavelengths that enter our eyes is jointly determined by 1) the spectrum of the illuminating source (a variable), and 2) The spectral reflectance properties of the object (a constant).
To achieve color constancy, an object's spectral reflectance is the constant color parameter that needs to be evaluated.
Any information that better characterizes an object's spectral reflectance is a cue to colour constancy. This includes (Mather, 2008):

Local color contrast. Cone excitation levels of one surface relative to another remains constant when both surfaces experience the same change in illumination. Relative cone excitation levels are invariant ratios useful for achieving colour constancy.
Color adaptation. Adaptation reduces the contribution from the source illumination by lowering activity in the most highly active cone classes.
Global contrast. Global spectral changes generally represent changes in the illuminant; localised differences usually correspond to reflectance differences.
Luminance highlights. Glossy surfaces offer near-perfect reflections of the illuminant, which can then be factored from the rest of the scene.
Mutual reflections. The pattern of reflections that arise from different surfaces, under the same illumination, carries valuable information about the reflectance properties of each surface.
Range of reflected spectrum. This gives an indication of the breadth of the illuminating spectrum.

A graphical example of the effect of lighting conditions is found below (Fig. 1.)

Bowl of fruit photographed under artificial daylight (left), hazy day light (middle) and clear blue skies (right. Source: Mather (2008)
The most powerful cue to constancy is thought to be local color contrast (Mather, 2008). In other words, the relative contribution of the different cone classes stays constant, despite differences in the spectrum of the illuminant.
In your example, the object (paper) is not represented by a reflectance, but as an image; a representation taken out of its context, and it will appear yellow. Even if the ambient lighting is the same, as in your example, the monitor displays a 'real' yellow color, which has a different spectrum, because it is not a reflectance, but it is generated by a light source: your monitor; as mentioned in the excellent comment of @AMR. The real sheet of paper will have a different reflectance spectrum. Hence, both photo and real sheet will be interpreted as a function of ambient lighting by your visual system and they will appear different.
Even when your image was printed as a photo, the color is obviously different from the white sheet of paper. So the ambient light has a different effect on the reflectance spectrum of the photo and the real sheet.
Also the global contrast is different: the photo with a different spectral content than the real sheet is re-placed into the context of ambient lighting. Hence, the photo it is out of context and will be re-interpreted.
Reference
- Mather, Foundations of perception and sensation 2nd ed. Psychology Press 2008


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What do "reduced antipredator defense" and "reduced antipredator vigilance" mean?
The book BIOMAT 2010 (International Symposium on Mathematical and Computational Biology, edited by Rubem P. Mondaini) mentions the terms reduced antipredator defense and reduced antipredator vigilance.
Can you help me to make sense of them?

Do you mean "What is the definition of RAD? and What is the definition of RAV?"?

@Remi.b Yes. Where they are seen and what are those effects.

Where did you first encounter these terms? In the book you're citing? Does the book attempt at defining these terms at all?

@Remi.b Yes, in the book. Not defined those terms.

I edited your question. Feel free to rollback (or to further edit) if you don't like my edits. I would suggest that you make an attempt of what you understand of these terms so far. I personally have never encountered them before but I am not an ecologist.

A quote placing terminology into context is helpful

When groups of prey use certain mechanisms to defend against predators, those mechanisms are known as antipredator defenses. For example, groups of tuna and starlings flock together to confuse predators. A reduction in this defense would be 'reduced antipredator defense'.
Groups of prey also exhibit shared antipredator vigilance, as in certain members of a group will look out for predators to protect the group. This is seen most predominantly in meerkats. A reduction is said vigilance would be a 'reduced antipredator vigilance'.
With reference to the Allee effect, which is what you appear to be reading about, this reduced antipredator defense and vigilance can significantly effect the population and the population growth.
Some related links:

On the ecological mechanism of the Allee effect.
Vigilance, predation risk, and the Allee effect in desert Bighorn sheep, a recent research paper.

Please explain in more details the term reduced antipredator vigilance. I understand the term 'reduced antipredator defense'

I think it's a good answer, but basing questions entirely on Wikipedia is not preferred, given its dynamic contents. Your info used may be gone from your link tomorrow.

Alright, I will find different sites to validate this information. Thanks!

@user1942348 Reduced antipredator vigilance would mean that the group of prey would not be able to detect the predator as well as earlier. This can be due to increased ability of the predator to hide and camouflage or isolation of prey from the predator for some time
Here is a link you might want to look at : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559846/

@malharkhushu Thanks a lot. Would you please give some examples where it is seen?

If (hypothetically) meerkats are taken to islands without predators for many generations, they would eventually forget to be vigilant about predators. When put back into a normal condition, they would not be able to detect and avoid predators. This was also seen in dodos, who could not survive when external predators were brought onto their isolated islands. There are quite a few more examples, but I can't remember any off hand. If I remember more, I will be sure to tell you


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Why are lipid-soluble substances harder to excrete?
I understand why water-soluble substances can be excreted. However, why are they easier to excrete than lipid-soluble substances? Why can’t lipid-soluble substance be excreted just as easily in the kidneys?

Short answer
If you understand why hydrophylic compounds can be excreted, than it's kind of straightforward why hydrophobic ones can't - because they are not hydrophylic.
Background
The kidneys, through the production and excretion of urine, are the major gateway of clearing the body from toxins. Some toxins absorbed in the gastrointestinal tract can be excreted by the liver through the gall system.
Urine is watery and kidney's excrete water through ion homeostasis. Hydrophobic compounds do not dissolve in water and hence cannot be excreted by the kidneys. The liver has an important role in making hydrophobic toxins water-soluble. Often hydrophilic groups are attached to it in the liver, making them hydrophilic. If that can be achieved, they can be excreted through the kidneys. Hydrophobic compounds that are resistant to chemical modification tend to accumulate in the body in fatty tissues like the nervous system, for example the notorious polychlorinated biphenyls (PCBs).
Reference
- Chen. Activation and Detoxification Enzymes: Functions and Implications, Springer Science+Business Media (2012)

I guess what I’m wondering more about is what happens to those hydrophobic compounds that can’t be excreted. (Even if this doesn’t happen and the body makes sure they’re made more water-soluble, let’s say hypothetically it happens.) What happens to these substances then, if they aren’t dissolved in the urine?

I should add that by my previous comment, I meant what happens to them as they pass through the nephrons of the kidney. They still move through the nephrons, right? Then what happens, if they aren’t flushed out?

They accumulate, as said above

@lightweaver -They are, as AliceD stated, changed into more hydrophilic substances in the liver, then excreted, often through the biliary tract or the kidney.

@AliceD I understand they accumulate as fatty tissue in other places of the body. But I’m just not seeing how they end up as fatty tissue elsewhere if there isn’t a mechanism by which they are saved from being excreted in the kidney, so to speak. What happens to the fat-soluble compounds as they move through the nephrons? Accumulate within the kidney? (And if this entire scenario doesn’t happen, then hypothetically what would happen if it did?)

If I've interpreted your question right then I think this is the answer..
You have both lipid-solule and water-soluble in the filtrate.
Lipid-soluble substances can easily cross the phospholipid bilayer of cells lining the tubules and so are extensively reabsorbed by passive diffusion. Thus the kidney cannot actively excrete lipid-soluble substances. This means the kidneys cannot alter the plasma concentration of these substances.
Water-soluble substances are effetively trapped in the tubules. This means the kidneys can selectively secrete or reabsorb water-soluble substances via channels etc. So the kidneys can only control the excretion of (and actively concentrate in the urine) water-soluble substances.
Sorry I don't have a reference for you but you've probably already found an answer anyway since this was originally posted a year ago.

You need to understand how renal ultrafiltration works to answer this question.
In the glomerulus, hydrostatic pressure forces fluid (filtrate) across 3 barriers into the collecting tubule. The first is the membrane of the glomerular capillary, which has fenestrations (pores) which are about 8um wide; only molecules smaller than 8um and\or molecules that can diffuse across a lipid bilayer will pass this membrane.
Next, they must pass the glomerular basement membrane, which has a slight negative charge. Any negatively charged molecules will be repelled and not excreted.
Last, they must pass through the filtration slits formed by the interdigitations of podocytes that are applied to the glomerular basement membrane. This is also a very narrow passage and has a slight negative charge.
Now, none of those seems to immediately preclude hydrophobic molecules from passing through the glomerulus... but how do they get there? They have to be dissolved in blood! But that's impossible if they're hydrophobic- physiologically hydrophobic molecules are usually bound by proteins, which are hydrophilic but often have hydrophobic regions. Albumin is the classic example, and albumin is just slightly too large to pass through the filter. There is no carrier system that allows hydrophobic molecules to be shuttled to the glomerulus and then dumped off to be filtered.

Brian thanks for your effort on this answer - please add some references so that other users that are unfamiliar can understand what you're talking about and can read further if necessary


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Proteases in the blood
I’m reading on hormones and the book talks about how peptide or amine hormones are easily broken down by proteases present in the blood plasma. This has led me to question the interactions between these proteases and the blood proteins of the blood (such as albumins and globulins). Does having proteases in the blood mean the blood proteins are constantly broken down? How do the blood proteins get anything done then? And what good do binding proteins do in protecting hormones during vascular transit when the binding proteins are also susceptible to blood proteases?
Edit: I’ve been requested to provide some quotes and references.

Because water-soluble hormones can dissolve in blood, many circulate as free hormones, meaning that most of them dissolve directly into the blood and are delivered to their target tissue without binding to a binding protein.

The book goes on to say

Water-soluble hormones, such as proteins, peptides, and amino acid derivatives, have relatively short half-lives because they are rapidly degraded by enzymes, called proteases, within the bloodstream. The kidneys then remove the hormone breakdown products from the blood.

These quotes were from Seeley’s Anatomy and Physiology, 10th edition.

When asking a question like this, it is usually best to cite the source that gave rise to the question. Also making a direct quote and attributing it to the reference makes it easier to determine the context of the assertion.

@AMR I have added some.

Basically it is that you are dealing with textbook vague. They don't define for you what relatively short half-lives is or the enzymes that are in circulation. IgG, which is the major immunoglobulin circulating in the blood has a half-live of between 11-21 days, depending on its subclass. Also the proteases may have certain specificities but not others. Certain proteins may not contain the moieties that the enzymes need to bind and catalyze the reactions and this acts to "protect" the protein from degradation. Without them providing the specifics of what they are referring to, its hard to say.

So is 11-21 days relatively short in the authors' estimations or are they referring to half-lifes on the order of minutes to hours? Unless they define it for you, it is difficult to say.

@AMR Can you give an example of a protein that does not contain a moiety to which enzymes can bind?

Well I don't know if this counts as this is an abhorrent form of a wild-type protein, but prions (PrP^Sc or PrP^TSE) are highly resistant to enzymatic degradation, even from Proteinase K. [Human Serum Albumin] (https://en.wikipedia.org/wiki/Human_serum_albumin) has a half-life of 20 days, and if I had to guess is much longer than what the authors of your text had in mind by saying "relatively short," so I would go out on a limb and say that those and Immunoglobulins are also resistant to serum proteases. If your text book gave a better definition than it would be easier to answer.

I think that you also have to remember that hormones are generally signaling molecules that induce transcriptional activity in the cells that receive them. They tend to be released based on certain stimuli, and most of the time, you only want them on for short periods of time, i.e., different stages of development, fight or flight, respond to changes that cause an imbalance in homeostasis, repair damages to cells and tissues. So you would want enzymes that can quickly degrade these molecules, in matters of minutes or hours, so that you don't over-respond to the stimulus.


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How do crocodiles stay fit?
My 8 year old son asked me a question I could not answer (and Google, at least in so far as we tried, was no help either).
We were watching a documentary about Salt Water Crocodiles in Northern Australia.
The crocodiles seem very energy efficient: they barely move if they don't absolutely need to (and when they do, it is mostly to eat). Particularly, they hardly ever run, but when they do they are very fast and powerful.
So the question he asked me was: how can crocodiles remain so fit if they don't do any exercise?
If humans just sat around and moved only to eat, ran only when they absolutely had to, our muscles would atrophy. Other mammals seem to be in a similar boat to us humans.
Why not crocs? What distinguishes animals that need to exercise to be strong from animals that don't?
This is the closest question I could find here, but I don't think it assists in answering this question: Do insects' muscles become stronger with exercise?

Imagine their strength and speed if they would exercise.  In other words: what make you think they are currently at their maximum potential?

It is a good point and the proposed answer below seems to suggest there is some truth to that. But still mammals seem to have a lot more built-in 'inefficiencies' (presumably for training) than do crocs. By inefficiencies I mean tendency to exercise without the direct outcome being food: whether play and hunting against long odds (or in the case of humans straight up exercise). And we seem to need those 'inefficiencies' to survive. Why do some species rely on external stimulation to reach fitness while others (apparently) much less so?

Let us start with difference between humans and crocodiles. There are lot of differences but the one which matters in current discussion is thermophysiology.
Unlike humans, crocodiles are cold blooded animals (more specifically ectotherms). These animals needs to get heat from environmental sources to maintain their body temperature. As contrast to humans who can get heat from internal metabolism. That is the precise reason crocodiles are seen always not moving and basking in sun light when it is cold (while go to shade or water if it is hot). Read this for more elaborate strategies they use. If you want scientific reference, you can check this, this or this.
On your exercise point, there are few reports which suggest exercise can enhances aerobic capacity in young crocodiles. In this study they actually put crocodiles on treadmill and checked affect on their respiration. This report suggest  crocodile uses 3 different kinds of muscle mechanisms for lung ventilation. These three act differently in different conditions (means one acts during rest while other during high metabolism). However I couldn't find any information regarding atrophy.

how can crocodiles remain so fit if they don't do any exercise? What distinguishes animals that need to exercise to be strong from animals that don't?

Short answer: Their body metabolism.
Their body metabolism is different from human's. Although doing exercise  might help in their aerobic capacity as mentioned in reference above.

Great answer. Thank you. Though I don't quite understand it as it pertains to strength and adaptation. Humans and mammals seem to need to stimulate muscles in order to develop them to their potential. Superficially, it appears that crocodiles do not. I understand that the distinction you draw (which makes more sense) is between cold/warm blooded (as opposed to crocodiles/mammals), but what I am missing is (a) whether the lay observation that they don't need exercise as much as mammals is true and (b) if true, why?

@rafraf Not the case for all mammals I think, for example the bears that hibernate do not lose nearly as much muscle mass as humans would during the same period of not doing any physical activity

rafraf : your questions are right. Unfortunately, I couldn't find any good studies related to muscle atrophy in crocodiles. On other hand @Zavior is also correct.


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Loss of appetite during fever
It is a well-known phenomenon that sickness like the common flu is often accompanied by reduced appetite. Why do sick people stop eating?

@AliceD answered this eloquently and scientifically. The very simplified version is: if you were still hungry, you'd have to get up and do something about it. Today, that might be doable. But before food became so easy to obtain, the price metabolically of going out to forage/hunt while sick would be far too high.

@anongoodnurse - thanks for adding the reason why! I added a line with a reference of the merits of loss of appetite.

The psychologic and behavioral components of sickness represent a highly organized strategy of the organism to fight infection. Sickness is generally accompanied by fatigue, numbness, coldness, muscle and joint aches, and reduced appetite. These symptoms are not simply an effect caused by the pathogen. Instead, it now believed to be an active defense strategy of the body, referred to as “sickness behavior”. Sickness behavior is thought to be an adaptive response that enhances recovery by conserving energy to combat acute inflammation (Maes et al. 2012). It is triggered by the proinflammatory cytokines produced by activated cells of the innate immune system due to the presence of pathogens. These cytokines include mainly interleukin (IL) 1 (IL-1α and IL-1β), IL-6, and tumor necrosis factor α (TNF-α) (Dantzer, 2009; Plata-Salamán, 1998).
One of the sickness behaviors is a loss of appetite. Among a host of other effects, cytokines are believed to inhibit feeding by their actions in the hypothalamus. The hypothalamus is an important neural center that regulates food intake (Plata-Salamán, 1998; Meister, 2000).
I refer you to Maes et al (2012), Plata-Salamán (1998) and Dantzer (2009) for backgrounds and further reading, as cytokine immunology is highly complex and this answer is anything but complete.
References
- Dantzer, Immunol Allergy Clin North Am (2009); 29(2): 247–64
- Maes et al, BMJ (2012); 10: 66
- Meister, Vitam Horm (2000); 59: 265-304
- Plata-Salamán, Semin Oncol (1998); 25(1 Suppl 1):64-72


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What is the difference between conditional and inducible activation?
In the modern genetically modified animal models, there are not only constitutive mutations which start producing proteins already in the embryo, but also mutations which can be turned on later. I've seen the terms "conditional activation" and "inducible activation" used, especially in the context of Cre-Lox recombination.
Are they used interchangeably, or is there a difference? If they are different, what is the difference?
If I'm looking at a mouse name, like K-Ras+/G12V;Elas-tTA/tetO-Cre;p16Ink4a/19Arflox/lox, how can I recognize which of the two it is?

I think that there is a slight distinction. Conditional activation of Cre-Lox can occur simply when Cre is expressed. It could be that you have the Cre gene under the control of a liver promoter, so the recombination will only take place in liver cells. Inducible activation usually means that you add something to the system to induce the recombination event. So if you feed the animals Tamoxifen or G418, then the addition of that chemical will turn on Cre expression leading to recombination. This is probably used when the recombination would be developmentally lethal.

I guess you could say that inducible activation is a subset of conditional activation.

In my opinion the terms inducible and conditional are synonyms. Together with the term constitutive they refer to how transcription takes place, that is, the second phase in the central dogma that states that genetic information is propagated from replication to transcription to translation. The proteins that are produced during translation by ribosomes can have a feedback effect on replication and transcription.
When proteins bind to the promoter region of genes, they can induce or inhibit transcription. If a gene is preceded by a promoter region that always promotes transcription, it is said that the gene has a constitutive promoter. If the gene is transcribed conditionally, it may refer to proteins having to bind to the promoter region so that transcription can take place. There could be inverse situations and I believe the Cre/Lox technology is an example of such a situation.
Take the following as an example. A gene could be lethal meaning that if the protein it encodes is expressed it will kill the cell. It could have a promoter that promotes expression if a protein with an inhibitory effect is not bound to the promoter. Suppose I have these cells in a culture plate and I add some compound to the culture plate. The compound diffuses into the cells and binds to the inhibitory protein that is bound to the promoter region. With this binding of the compound to the protein that is in turn bound to the promoter region, the protein loses its ability to bind to the promoter region and inhibition of transcription is uplifted. Transcription then continues and expression of the lethal protein takes place after which the cell dies.
This could be used in practice as follow: if you were selling seeds to farmers, you would want them to buy seeds next year again, so you want the plant not to be able to produce viable seeds.
Coming back to your question, if you want to know more about the mice in question, you should contact the breeder as nomenclatures differ. See this article on interpreting mouse genetic nomenclature:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039125/

It seems that your third paragraph is describing inducible transcription, but is not identified as such. Also while inducible transcription is inherently conditional, conditional transcription need not be inducible, in the sense that the transcription can occur in a given cell type without the addition of an inducer molecule. One need only place the gene under the control of a tissue specific promoter (in recombinant technology) or a gene need only be under the control of that promoter to drive transcription conditionally only in that cell type, with no other action (induction) needed.