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What is the difference between a predator and a parasite?
A human encountering a tiger or a malaria plasmodium is likely to suffer, and the tiger/plasmodium is likely to gain from the transaction. Not necessarily a good example, and I am aware that a successful parasite avoids prematurely killing its host, but I can't see any fundamental difference.
Of course it's like pornography: "we know it when we see it". But is there a formal, generally-accepted distinction?

An even better comparison might be between humans and plants: do humans parasitise apple tree when we eat its fruits?

Good question.
There is no fundamental difference between parasites and predators.
Ecological Interaction
In terms of ecological interaction, they are both defined as an interaction where one species benefits and the other suffers from the interaction.
Intuition parasite vs predator

In general predation is viewed as a big individual eating a smaller one while parasitism is when a small individual eats a bigger one. These general intuition however fails to consider a number of cases. Here some cases I can think of
Examples when intuition don't match the above picture
Generally considered as predation but does not fit the above picture-based definition:

social animals attacking in groups preys that are much larger than themselves - non-social animal attacking prey larger than themselves
herbivores browsing on large trees

Generally considered as parasitism but does not fit the above picture-based definition:

indirect effect of habitat modification that would rather be considered as parasitism.
Species that take advantage of parental care of another species by mimicking babies (but being larger)
Individuals of large species stealing the habitat built by a smaller species
Batesian mimicry (see this post; Thank you @WYSIWYG and @NL_Derek for the comments)

Population culture vs science literature
In the popular culture, some people call parasites only endoparasites. This concept is also misleading and not so much in accordance with the general literature in biology.

As we had discussed in another post, Batesian mimicry has also been considered a parasitic interaction.

Thanks Remi; it seems that there is a continuum parasite-predator and no real dividing line. @JordiZambrino's answer was also excellent (therefore +1 from me) but as kevbonham pointed out only tangentially relevant.

Parasitism – a parasite that lives on or in an host, obtaining food from the host and harming it.
Example: Ixodes ticks use white tailed deer as a host

Parasite is smaller and weaker than the host
Parasite may feed over the host from outside or inside
In parasite-host relationship a weaker organism is benefitted
Host specificity is more common
The host is most likely alive when nourished on

Predation – predators benefit as they feed on prey; predation affects numbers and behaviour of prey
Example: Coyotes are predators of white tailed deer

Predators are generally larger than their prey
There is progressive development of characters or evolution
In predator-prey relationship the stronger organism is benefitted
Prey specificity is not very common
Predator usually feeds on prey from the "outside"
The prey is usually dead when consumed

This is a great answer, but doesn't directly address the stated question (what's the distinction?). I think the living vs dead is probably the most consistent. I can't think of any predator/prey relationship where the prey stays alive for very long, nor any parasite that immediately kills its host.

It seems like the difference is that predators feed on most or all of their prey individual, whereas parasites feed on a fraction of the resources of their host.  This distinction explains a lot of the six distinctions given in the above answer.  e.g., predators are larger and therefore require a greater portion of energy of their prey; prey specificity is less common because a fraction of prey does not suffice; the prey cannot survive having most of its resources consumed.  Question:  What do you mean by "progressive development of characters or evolution"??

Previous answers to the question seem to originate from one misunderstanding.  Of course, the large-small distinction between predators and parasites is easily observed by anyone, like the fact that predators kill their prey while parasites only sap the strength of their hosts.
But parasites do not actually attack a host.  Parasites attack only a TINY component of the host. The parasite and that tiny component then develop what is fundamentally a predator-prey relationship.  Whether the host is significantly affected or not depends upon the role of the component in the host’s overall health, and the size of the infection or wound.  Exactly the same could be said about an attack by a predator on its prey.  The actual significance of the attack comes down to the size of the wound and the significance of the wounded body part to the health of the prey.
To sum this up in a few words, the methods and logic of a parasite are the same as those of a predator. Their size difference is not critical; not all parasites are small, and not all predators are large.  The size of the host or prey is not the critical issue, either.
I think the biggest PRACTICAL difference between predators and parasites are the methods used to defeat them. Weapons like spears and guns for predators; nutrition, soap and science for parasites.  Avoidance — aided by brainpower— is the best defense of all

Most definitions of predator/parasite rely on quite subjective (or not exactly precise) characteristics. That being said, I like Ricklefs' definition (Ricklefs, 2009), which is simple and straightforward:
It can be summarised like this:

Predatism: a consumer-resource interaction in which the consumer (predator) removes the resource from the resource population.
Parasitism: a consumer-resource interaction in which the consumer (parasite) does not remove the resource from the resource population.

Of course not everything is black or white, and there are situations in which applying the above definition is quite complicated, such as parasitoids or cases of parasitism that end up killing the host. However, it can be used for most of interactions.
Let's see some (counter-intuitive) examples:
This is a parasite:

A cow grazing doesn't kill the grass plant: it only eats parts of the leaves, not the whole plant. Therefore, the resource (plant) is not removed from the resource population.
This example is interesting because we, normally, tend to imagine the parasite smaller than the host. However, as you can see, a cow (the parasite) is some orders of magnitude heavier/bigger than the grass plant (the host).
This is a predator:

Pigs (sometimes, not always) like to pull up the root, eating the whole plant and, therefore, killing it. Thus, the resource (plant) is removed from the resource population, that changes from N to N - 1.

Source: Ricklefs, R. (2009). The economy of nature. Vancouver, B.C.: Langara College.

A parasite may or may not kill the host. It's basic motive is to constantly derive nutrition from the host. More a sort of one time investment and as an interest you keep getting the nutrition.
Whereas a predator's motive is to kill the host to satisfy it's hunger. One kill and eat can be a taken as a case of consideration here.


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Moss Transportation System
In my biology textbook, it says that mosses are avasculer and do not have xylem like spermatophytes. So by what means do mosses transport nutrients ?

I am not sure if this answers your question, but mosses also have no roots (just rhizomes that do not take up nutrients). Mosses take up nutrients directly with there leafs. So many they have no need for a transportation system?

Mosses are able to transport water and nutrients internally through intercellular voids and cell-to-cell connections involving exchanges of cytoplasm, as well as externally across their surface. Labeling mosses as nonvascular plants is misleading because mosses in the Polytrichales order have highly specialized water and nutrient conducting systems which are reminiscent of xylem and phloem. But in general, a moss's main vascular system can be said to be its outer surface which is carefully designed to store and conduct water across the plant.
External Conduction
Moss cells absorb water and nutrients directly from their environment, so many of their nutritional needs can be met simply by ensuring water and its dissolved nutrients can spread across the entire surface of the moss plant. The water is able to spread through capillary action, aided by a carefully designed surface. Moss leaves are frequently appressed to the stem and have sheathed bases which create small places for water to climb along a stem. The leaves may also be covered in small bumps (papillae) which create capillary spaces. Rhizoids, which are somewhat like roots except typically only 1 cell thick, can also make good paths for water to flow across. Some mosses have their stems covered in rhizoids or paraphyllia to help conduct water. Sphagnum mosses have large cells across their leaves which exist mainly to absorb water like a sponge, and Leucobryum mosses have a layer of water holding cells on both sides of their leaves. Colonies of mosses often form compact mounds that allow for water to flow across the entire mound.
As far as I know, moss cells do not deliberately dump nutrients into the film of water on their surface in the hopes that it will be absorbed by other cells of the plant that need it more. But, when dessicated moss is rehydrated, solutes in the protoplasm may leak into the external film of water. These contents might be able to be reabsorbed by other cells of the moss, forming an incidental external nutrient transport pathway.
Internal Conduction
Water and nutrients are also able to flow through cells or spaces between cells from inside the moss. Experiments have shown that nutrients are relocated from old growth to new growth using cytoplasm-linked pathways in Sphagnum and Polytrichaceae mosses. Many moss stems and almost all seta (the stalk connecting a spore capsule to the main body of the parent moss plant) have special nutrient conducting parenchyma cells surrounding water conducting cells called hydroids. The central ribs of moss leaves also often show a similar pattern. Sometimes these chains of nutrient conducting cells in the leaves connect to the main conducting strands in the stem, but usually the leaf conducting strands come to an end somewhere in the stem cortex without connecting.
Mosses in the Polytrichales order have the most specialized nutrient and water conducting cells of all mosses. The nutrient conducting cells for mosses in this order are different enough from other mosses to be given a special name--leptoids. The vascular system in these mosses are not evolutionarily homologous to xylem and phloem, but serve the same basic transport purpose. In Polytrichum moss, water has been measured to flow 200 cm/h through the stem and organic compounds at 32 cm/h. These specialized hydroids and leptoids are what enables the tallest moss, Dawsonia superba, to grow up to 70 cm.
The water and nutrient transport architecture for mosses outside the Polytrichales is more variable and less specialized. Andreaeopsida, Andreaeobryopsida, and Sphagnopsida completely lack hydroids. Takkakia's hydroids are unique in that they are short instead of tall and transfer water through pores formed from plasmodesmata at their ends. Sphagnum has nutrient conducting cells, but they are not homologous to the nutrient transferring parenchyma cells of other mosses. Some mosses in families which typically have central conducting strands have lost that feature over time, and mosses which would normally have hydroids may fail to develop them if grown underwater.
Outside of the usual stem, seta, and leaf midrib conducting cells, it has been suggested that rhizoids and caulonemal cells also conduct nutrients due to similarities in cell organization to the nutrient conducting parenchyma cells. The cells that form the interface between the parent gametophyte and the sporophyte foot also transfer nutrients.
Sources
Chopra, R. N. Biology of Bryophytes. 2005. Chapter 11 "Conduction in Bryophytes".
Goffinet, B., and A. J. Shaw. Bryophyte Biology. 2009. Pages 60-70, 83, 301.
Ligrone, Duckett, and Renzaglia. Conducting tissues and phyletic relationships of bryophytes. 2000.

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miRNA_ID to GENE_SYMBOL conversion
I have a list of miRNA IDs and a list of mRNA IDs and they are from Mus musculus species. I have converted the list of mRNA IDs to gene symbols by a list of data that was exist in NCBI and miRNA IDs list to gene symbols using Diana but I got in trouble because gene symbols on NCBI didn't match with the gene symbols that exist in Diana site. I think the problem is that naming of gene symbols doesn't follow a specific rule in different databases and are not standardized. Can anyone tell me a good way to transform both mRNA & miRNA lists to a platform for example unigene that would be unique in all kinds of databases?

As far as I know, the gene names also in NCBI changes often. Did you have a look on the synonyms listed in NCBI? This may help you. You can also look here. Here you can search for your NCBI number and the species and also get a variety of synonyms for this gene.

For mouse gene names and other details you should refer to the mouse genome informatics database (it is a standard organism-specific database like flybase [Drosophila], SGD [yeast], etc).
However, it is much better to work with RefSeq IDs. Moreover, miRNAs are seldom referred to, using their gene names. Always stick to the miRNA naming convention that is described in miRbase.
I am not sure what you are actually interested in. If you intend to map miRNAs to their targets then you can use one of the standard gene names along with the RefSeq ID. If you are using miRanda or TargetScan to predict the targets then these programs return different identifiers for the target gene including its official gene name.
In general, for ID conversion, I would prefer BioMart.

Can you please tell me how can I use BioMart for mapping miRNAs to their targets ?  I used Diana but It returned me Ensemble gene ID and their own gene symbol and not Refseq ID, How can I convert miRNAs to their targets as refseq ID ?@WYSIWYG

@minoo Sorry for the late reply. BioMart cannot be used for mapping miRNA to their targets. Use the abovementioned tools for that. If you want a different ID corresponding to the one that miRNA target prediction tools return, then use BioMart for ID conversion.

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why is the cleavage in frogs holoblastic and not meroblastic?
background information
The cleavage of the frog embryo during the embryo development is holoblastic (complete cleavage). However when we look at yolk-rich eggs we see a cleavage pattern which is meroblastic (partial cleavage).
Question
But the frog eggs are also yolk rich right? So why do frog embryo's use holoblastic cleavage?

Because:

Frog eggs are not yolk-rich. They are mesolecithal, they have an intermediate amount of yolk.
Yolk is concentrated within vegetal pole of the egg. That is why yolk-packed macromeres divide much slower than micromeres on the vegetal pole, which barely contain any yolk.

My sources:

https://kjcscientific.wordpress.com/project-excalibur/
Gilbert's Developmental Biology (2009)


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Effect of HIV on T-cells
When HIV infects macrophages, it doesn't kill or destroy them immediately, but once it infects T-cells, they're destroyed. Why is that? As in why does it destroy T-cells and not macrophages or other cells.

This process does not destroy the macrophages.
  Unlike macrophages, helper T cells are destroyed.

I think HIV can destroy macrophages, since just by virtue of the infected cell accumulating the virons and the cell lysing due to so much accumulation no? Is this not one of the ways the virus spreads throughout the body?

No, it doesn't destroy macrophages, or so my book says. It does destroy T-cells though ; @RoSiv

Can you provide a quotation from (or better, photo of) the book so we can understand the context? As written, this question is rather unclear.

PLEASE DO NOT POST TEXT AS IMAGES. Copy and paste the text into your question. Images are not searchable, and can not be interpreted by screen readers for those with visual impairments. Use the [edit] link to modify your question.

From this article:

Researchers found that when the virus productively infects the few permissive CD4 T cells present, death occurs through apoptosis mediated by an enzyme called caspase-3. But when HIV abortively infects nonpermissive CD4 T cells, death occurs by pyroptosis, which depends on the activation of caspase-1. It turns out that the vast majority—roughly 95 percent—of CD4 T cell death in lymphoid tissues is driven by caspase-1-mediated pyroptosis.

When it comes to macrophages, however:

macrophages are much more resistant to cytopathic effects of lentiviral replication than for example activated CD4+ T cells [23, 24, 25], and HIV-1 has evolved sophisticated mechanisms to prolong the life span of infected macrophages [24, 26]. Especially long-lived macrophages may therefore harbor the virus for long time periods, thus constituting HIV-1 reservoirs and posing a major obstacle to virus eradication from infected individuals.

Source


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What's the name of this insect?
Here's a picture:

That's pretty much it, besides that it was found in Vienna, Austria.
Edit: Thanks to Magne Flåten; it's called Hausmutter in German.

This is probably a large yellow underwing not finished pumping up its wings: https://en.wikipedia.org/wiki/Large_yellow_underwing


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Has anyone done a GCTA of leg length?
There is extensive genomic research on height, but nobody seems to have done a gcta of leg length.

What do you mean by "doing GCTA of leg length"?

Do you mean "do we know the QTL for leg length?"

I don't and only few people visited this post yet, so saying "nobody" sounds a bit extreme. I googled the thing a few times and found Genome-Wide Complex Trait Analysis. It seems to be a recent technic that has been only used a few times only and it seems to always be about height. There is therefore probably nothing on leg length. Seems not surprising if I (and others) don't know its meaning.

If a concept is likely to not be understood, please link to its definition (or even better, include a definition) and indicate what does the abbreviation stand for. I let you make the edit. Thanks.

I am a PhD candidate in population genetics and I find your comment (now deleted) offensive :) You should just add a link and definition to save everyone's time.

Voting to close as "homework" because it's extremely trivial: a Google scholar search is the service you need for this. You could also look at the articles citing the original methods paper. As far as I know there's nothing published specific to leg length (and I doubt it will happen soon - it's a fairly uninteresting thing to measure).

GCTA is not a well known term. I myself have worked a bit on genomics but I was not aware. Providing context and explanation is not only important for explaining your question but is also useful for users who refer to the post to learn some facts.

I am assuming you are referring to the use of the software GTCA (which stands for Genome-Wide Complex Trait Analysis). Original paper: Yang et al. (2011).
I looked to the papers who cited Yang et al. (2011) and quickly scanned through looking for "leg". I did not find anything on it. So my best guess is: No, nobody ever applied GTCA to leg length.


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What is the effect of TSH on the calcitonin?
I know that TSH is released from the pituitary gland and it motivates the thyroid gland to release thyroxine, and calcitonin is released when the calcium level is high in the blood, but is calcitonin affected by TSH or not, I didn't find a specific answer on google, could you help me please?

I found a paper, where it is postulated that TSH secretion is inhibited by calcitonin. However, the paper is quite old (1984) and I'm not sure if there are any more actual paper.


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What is the difference between a human being, a Homo sapiens, and a Neanderthal?
I know that the Neanderthals were part of the genus Homo. How do they relate to other members of the genus, such as Homo sapiens?

Homo sapiens / Homo sapiens sapiens
Human being, in the popular culture generally refers to modern humans, called either Homo sapiens or Homo sapiens sapiens. The existence of the two names will make sense when talking about the Neanderthals. In the term Homo sapiens, Homo indicates the genus and sapiens indicates the species. In the term Homo sapiens sapiens, the second sapiens refers to the subspecies.
Homo neanderthalis / Homo sapiens neanderthalis
Neanderthals (or Neandertals) is sometimes referred to as a species in the same genus (Homo) as H. sapiens and sometimes as a subspecies of H. sapiens. When considered as a different species then, they are called Homo neanderthalensis. When Neanderthals are considered as the same species as H. sapiens but different subspecies, then they are called Homo sapiens neanderthalensis and modern humans are then called Homo sapiens sapiens.
Related Post
The post How-could-humans-have-interbred-with-neanderthals-if-were-a-different-species will probably be of interest to you.

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A 10mm long creature in the California dust

I observed this tiny creature burrowing through the dusty soil of Cachuma Lake Recreation Area in Santa Barbara County, California, on June 8, 2014, about 7 a.m. I have really no clue what it could be, other than an annelid, or newly hatched type of legless lizard or snake. But it seems too tiny for the latter. Yet, I would think an annelid would need more moisture, or different soil. Do worms live in dust? I watched it for about five minutes, maybe more. Burrowing under and re-emerging. So that seemed to be its normal environment.
Here's a closeup, and a link to a Youtube page I put up for it. Video on Youtube of animal's movement

The creatures movement (youtube) is NOT that of an annalid. They contract and expand rather than zigzagging like this creature does. Zigzagging is a snakelike movement. Unfortunately, I am by no means an expert an Californian fauna.

Thank you! I couldn't put my finger on it, but yes, that's it - it doesn't move like a worm, which is why I'm very curious what this is. Thanks for helping clarify that in my mind.

could it be an enchytraeidae?

@Jordi_Zambrino Aren't all enchytraeidae aquatic?

Just found here that the worlds smallest snake is still four inches. That makes a snake very unlikely. Hmm confused now.

http://www.agpix.com/view_caption.php?image_id=590425

@Jordi Sorry, still getting used to how this site works. Spent too long editing ...  What I meant to say was: Thanks for the reference to enchytraeidae. At least per the Wikipedia page, there are some terrestrial species, known as potworms.  And, I have to say, the creature in the image on this page looks pretty similar. But ... they tend to live in much wetter environments. This was dry and dusty, and it looked very much at home. You can also find videos of potworms in compost bins, and they move similarly to this.

Also, I did run this by a curator of reptiles, who also said it was not a snake (I thought it might be a juvenile Brahminy Blind Snake, an invasive species). He thought it might be a beetle larva but, while I'm not a professional entomologist, I've seen and handled a fair number of larvae, and this just doesn't scream "grub" to me.

Well, maybe I stand corrected: BugGuide.net has a similar picture of a Stiletto Fly larva found in Santa Barbara County. And The Clueless Gardener blog has some comments on behavior - says they're very strong, and move very fast.

I'm going to answer this question and close it. Based on the location, the environment, its appearance and behavior, I'm 90% sure that this creature was a Stiletto Fly (Therevid) larva. Most likely an Acrosathe sp., as those tend to be very common in the area. Thanks to all for your help in clarifying and narrowing it down for me.

You are probably right. Unless you can find an expert on Californian flies, it's unlikely you will ever be 100% sure.


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Why are sarcomas rare compared to carcinomas?

A sarcoma (from the Greek σάρξ sarx meaning "flesh") is a cancer that
  arises from transformed cells of mesenchymal origin. Thus, malignant
  tumors made of cancellous bone, cartilage, fat, muscle, vascular, or
  hematopoietic tissues are, by definition, considered sarcomas. This is
  in contrast to a malignant tumor originating from epithelial cells,
  which are termed carcinoma. Human sarcomas are quite rare. Common
  malignancies, such as breast, colon, and lung cancer, are almost
  always carcinoma.

ref: https://en.wikipedia.org/wiki/Sarcoma

I was wondering why most of the tumors come from epithelial cells?

https://clinicaltrials.gov/ct2/show/NCT00029991 I have found something interesting. "These cells, known as endothelial cells, are susceptible to damage by blood cholesterol, smoking or high blood pressure and, when damaged, will allow cholesterol to deposit in arteries. Antioxidants can prevent the endothelial cell damage" - So antioxidants might prevent cancer by protecting endothelial cells from being damaged by carcinogens. If so, then atherosclerosis and high LDL cholesterol should be a risk factor of cancer. I don't remember reading of such a connection...

According to many articles and wikipedia as well obesity is linked to cancer. http://cancerpreventionresearch.aacrjournals.org/content/3/11/1451.short http://link.springer.com/article/10.1007/s11912-010-0139-7 http://www.sciencedirect.com/science/article/pii/S014067360860269X According to this article fat on its own is not the cause of the cancer but changed metabolic state might be. http://cancerres.aacrjournals.org/content/67/6/2391.short

So the previous articles indirectly support that endothelial damage causes cancer.
Another interesting topic is: https://en.wikipedia.org/wiki/Surface-area-to-volume_ratio The endothelial tissue has a high surface/volume ratio, so it might come in contact with potentially damaging compounds more often than other tissue, since these compounds tend to travel through blood. However I don't feel this a complete explanation. I think endothelial tissue is more prone to cancer somehow genetically. Probably cancers caused by ionizing radiation support this somehow, because they are not blood related.

Note that epithelial and endothelial cells are two different lineages. Carcinomas derive from epithelium. Tumors originating from endothelium are considered sarcomas, and they are rare. See https://en.wikipedia.org/wiki/Angiosarcoma


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Why do emperor penguins breed during the antarctic winter?
No land animal, and I think no sea animals either, stay in the antarctic during winter - except for one: The emperor penguin. These penguins not only stay there, but their prolonged stay involves 4 months of harsh winter, averaging -70$^o$C, no sunlight and no food for that period of time. And if that wasn't enough, then it's during that time that the emperor penguin male incubates the egg alone, left by his female mate. The male emperor penguins gather together to endure the antarctic winter.
My question thus becomes very obvious: Why does the emperor penguin stay in Antarctica during winter at all, and moreover, breed there during that time and incubates a precious egg in the harshest conditions on earth, while all other animals flee for their lives?

It could be that Antarctica is their niche, land that they don't have to compete with or worry about other animals stealing their eggs as much. Also when they incubate over the winter, the chicks will hatch and grow and be fed during the more productive summer.

Scroll down to "why do emperor penguins breed in such severe conditions"   http://www.coolantarctica.com/Antarctica%20fact%20file/wildlife/Emperor-penguins.php

They breed during the arctic winter because they are large enough to get their own food during the summer.

Because that's when they're 'cool' !

From my experience working on sheep farms in Australia, it could very well be for similar reasons to why farmers breed their sheep at specific times in the year - they breed their sheep, so that by the time winter hits the lambs are large enough and have enough wool to make it through. The penguins lay their eggs in the dead of winter, but they then incubate for 65-75 days, by this time winter will have largely passed, and the chicks will be growing in the spring and then summer. By laying in the winter, the penguins avoid exposing their young to a winter for as long as possible.
Another point to consider: As you said, Antartica is largely devoid of other life during the winter. To me, what I hear is: There will be no predators to feed on the eggs, or attack the vulnerable penguins incubating their eggs.
Reference: http://www.antarctica.gov.au/about-antarctica/wildlife/animals/penguins/emperor-penguins/breeding-cycle


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What do arranging and assigning mean in sequence annotation?
Please could someone explain these lines to me in a simple way

These sequences were then arranged based on some overlapping regions present in them. This required generation of overlapping fragments for sequencing. These sequences were subsequently annotated and assigned to each chromosome

What do "arranging" and "assigning" mean in this context?
Source: NCERT class 12 (This text in in reference to the method developed by Frederick Sanger)

I edited the post to improve its format. Feel free to roll back if you don't like it. Would be great if you could link to the source.

Word "arranged" means simply alignment of sequence based on overlapping regions in two sequences. For example:
Seq1: AGTGTCCGTCGTAAGTCA

Seq2:GTCGTAAGTCATCGAGATACC

leading to:
Seq12: AGTGTCCGTCGTAAGTCATCGAGATACC

Maybe he used the word "arrange" as overlapping determines the direction of resultant sequence (for which word alignment is sufficient)
Assignment: Is simply dividing the genome's sequence down as per chromosomes of the species. Like for example, if it's human genome sequence and first chromosome is 2,50,000bp long (just assumption - I don't remember exact figure), then first 2,50,000 nucleotides in the sequence will be "assigned" to chromosome 1. From 2,50,001 onwards to chromosome 2 and so on..

@Felix_17 Pleasure! :)


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Relationship between genetic diversity within and between species
Here is a quote from Wagner (2008)

A second line of evidence [against neutralism] comes from the relationship between the mean number of polymorphic differences between alleles within a species, $\pi$, and the number of fixed differences between genes in two species, $d$. For neutral mutations, a positive association between $\pi$ and $d$ should exist, because the neutral theory predicts that both quantities are linearly proportional to the rate at which neutral mutations arise. Recent genome-scale data shows instead that this association is in fact negative.

What do "the mean number of polymorphic differences between alleles within a species" and "the number of fixed differences between genes in two species" have to do with each other?  Why should there be any relationship at all?  And by "two species", are they talking about Eastern Yellowback Whooping Finches versus Western Yellowback Whooping Finches, or any arbitrary two species, like E. Coli versus Muskrats?
I found this related question, but it doesn't say anything about different species.

Good question +1. I edited your post to get rid of what I thought was unnecessary information. Feel free to roll back if you don't like the edit.

Assuming everyone else here has the necessary background, it's fine.  I'm not a biologist, so the neutralism/selectionism theories were news to me.

Metrics of interest
The two metrics you are interested in are

$\pi$ - the mean number of differences between two randomly sampled (with replacement) alleles in a population
$d$ - the mean number of differences between two randomly sampled (with replacement) alleles coming from two different species

Consider two sequences

ATCGTCAAT
ATAGTTAAT

There are 2 pairwise differences between these two sequences (positions 3 and 6).
The whole point here is to understand that two individuals in the same population coalesce at a given time in the past just like two individuals coming from two different species. The number of pairwise differences is just equal to the rate at which mutations accumulate multiplied by the coalescence time. Let me develop this idea with a few equations below.
Neutral Expectations
Let's do the math! We will do two important assumptions below.

Every mutation makes a new allele (it is an infinite allele model)
All mutations are substitutions (no indels, no gene duplication, etc...)

Intro to Coalescence Theory
Let's first make sure you understand the concept of coalescence. Imagine you were to look at an evolving population backward in time. A coalescent event, is an event by which two lineages become one (looking backward in time). For simplicity consider a case of an asexual population (but future calculations don't do this assumption). In an asexual population, two siblings coalesced the previous generation, as in the previous generation the genes they are carrying were in a single individual (their parent).
We will see below how to calculate coalescence time between two randomly drawn individual from a population and how we can make inference about genetic diversity from this coalescent time.
Rate of accumulation of neutral mutations
The rate of accumulation of neutral mutation is also called the fixation rate of neutral mutations. Let $fix$ be this fixation rate. Consider a panmictic diploid population of constant size $N$. At a given locus of interest, the mutation rate is $\mu$. The number of mutations occurring every generation in this population is $2N\mu$ (The $2$ comes from the fact that in a diploid population, there are two homologous copies of every gene in each cell). If the mutation is neutral, then every single individual in the population has the same probability to end up being the parent of the whole population in a long time in the future. In other words, starting to look at this problem from the future and looking backward in time, any individual in a distance far enough in the future descends from a single individual in the present. As a consequence, the probability of a new mutation to reach fixation is $\frac{1}{2N}$. Multiplying the probability of fixation by the rate at which mutations occur in the whole population we obtain $\frac{1}{2N} 2N\mu = \mu$. In other words the rate of fixation of new neutral mutations is simply equal to the rate at which mutation occur.
Key equation:
$$fix=\frac{1}{2N} 2N\mu = \mu$$
$d$ - number of pairwise differences between randomly sampled (with replacement) alleles coming from different species
Consider two species which common ancestor lived $T$ generations ago. Each lineage accumulated mutations at rate $\mu$ (and explained above) and therefore the expected (average) total number of pairwise differences is $\bar d=2\mu T$. The probability of having exactly $d$ pairwise differences comes from a Poisson distribution with rate $2\mu T$ ($P(D=d) = Poisson(2\mu T)$).
Key equation: $$\bar d=2\mu T$$
$\pi$ - number of pairwise differences between randomly sampled (with replacement) alleles coming from the same population
Here the calculations follows the same logic as above $\pi = 2 \mu T$. The whole issue is that $T$ (the coalescence time) is unknown for the moment and we need to calculate it.
Let $P(T)$ be the probability that two randomly sampled (with replacement) individuals from a diploid panmictic population coalesce exactly $T$ generations ago. The probability of coalescing in a given generation is simply the probability for drawing the same individual, that is $\frac{1}{2N}$ and the probability of not coalescing in any subsequent generation is $1-\frac{1}{2N}$. Iterating over the generations we obtain
$$P(T) = \frac{1}{2N} \left( 1-\frac{1}{2N} \right)^T \approx \frac{1}{2N}e^{-\frac{T}{2N}}$$
, where $e \approx 2.7$ is Euler's number. The above approximation is accurate for large $N$ (say larger than 100). In case you are interest, you will find on this Math.SE post, an explanation for this approximation.
The expected value (average) $\bar T$ of this distribution is $\bar T=2N$ (and the variance is $var(T) = 4N^2$). As a consequence the expected number of pairwise differences between these two individuals is $\pi = 2 \mu 2 N = 4N\mu$
Quickly speaking, these calculations can be extended to calculate the coalescent time between $k$ randomly sampled alleles. The expected coalescent time is then $\bar T = \frac{4N}{k(k-1)}$ and therefore some algebra shows that the total expected time (along all branches) is $4 N \sum_{i=1}^{k-1}\frac{1}{i}$ and the expected number of segregating sites is $4 N \mu \sum_{i=1}^{k-1}\frac{1}{i}$.
Key equation: $$\pi = 4N\mu$$
Conclusion
It is clear from the above that $\pi = 4N\mu$ and $d=2\mu T$ are correlated as they are both linearly related to the mutation rate. As it is said in your quote

For neutral mutations, a positive association between $\pi$ and $d$ should exist, because the neutral theory predicts that both quantities are linearly proportional to the rate at which neutral mutations arise

The quote goes one saying

Recent genome-scale data shows instead that this association is in fact negative.

Such negative relationship between $d$ and $\pi$ cannot be caused by neutral processes. Therefore selection must be involved somehow.
Imagine for example that two species are both selected at different optima (opposite selection pressures). In such case, you would see purifying selection within species reducing the probability of a new mutation to reach fixation to a value lower than $\frac{1}{2N}$ and therefore reducing the rate of fixation $fix$ so that $fix<\mu$. However, such opposite selection pressure among species will yield the species to diverge more than expected by random processes that is $\pi > 4N\mu$. Such selective pattern could explain the observed negative relationship.
More information
This post offers book recommendation on the subject (population genetics).

when you say "mean number of differences", how is this quantified?  Number of differing base pairs?

Yes exactly. There are two assumptions (I forgot about in my answer but I will add them) 1. All mutations are substitutions (no indel, no whole chromosome duplication etc..) and 2. every mutation makes a new allele (infinite-allele model)

Are those assumptions specific to neutral theory?  I guess this is supposed to be a proof by contradiction, so I want to see which specific premises are leading us to the contradiction.

Those are very common assumptions found in the neutral theory literature and more globally in the literature on genetic drift. The concept of proof by contradiction applies to math but not to empirical sciences (isn't it?). We just have a null prediction (model without selection) and if the data don't match these then something else must be going on. (Thanks for the edit)


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Why is aconitase classified as a lyase?
Aconitase in the TCA (tricarboxylic acid) cycle isomerizes citric acid to isocitric acid via cis-aconitic acid intermediate. Since overall it functions as an isomerase, why it does not belong to isomerases? Why does it belongs to lyases even though it involves hydrolysis of water in second step? Should not it belong to hydrolases in this way?
So how it can be justified that it is lyase?

The mechanism of aconitase classifies it as a lyase, even if (under most physiological conditions), the relative concentrations of substrates results in it catalysing the conversion of citrate to isocitrate. In short, it is not an isomerase because the substrate is released after each step.

As the mechanism of aconitase shows, it catalyses the conversion of either citrate or isocitrate to aconitate as well as the reverse reaction. This is similar to the reaction catalysed by fumarase, which is the reversible addition or removal of water.

Because the physiological concentrations of citrate is much larger than the concentration of isocitrate, aconitate overall catalyses the reaction from citrate to isocitrate, and does so via catalysing two lyase reactions.
Regarding the other part of your question, hydrolases are a completely different group of enzymes, and none of the reactions involved are related to hydrolases in any way.
While water is in fact involved in the reaction, it is not used in the process of hydrolysis. To be specific, hydrolysis (in its enzymatic/organic, and not chemical sense) requires that water be a substrate required to break apart a molecule A-B into A and B. Since the addition of water does not result in citrate/isocitrate being broken down into two smaller organic molecules, aconitase is not a hydrolase.

@JM97 Updated answer to clarify what is and what is not a hydrolase.


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What is this crawling next to my house?
I just found this outside my house while walking the dog. I was thinking it's some kind of slug? It's been raining a lot lately and today, so maybe that has something to do with it being on the pavement. I live in South Central Indiana, US. When it wasn't stretched out, I'd say it was 2-3 inches long.

It's definitely some sort of slug. I would suggest you link the images directly in the post using the image tags. I would edit it for you if I knew the direct URL for the images, not just the imgur links. I would also suggest you posted your approximate location so we can narrow down options for specific species of slugs. Since I'm not a slugologist, I can't help much more than that.

@user137 The precise term is a malacologist

You'll actually find them, or their tracks, quite commonly on the sidewalk or pavement in the early morning just before sunrise. I imagine if it was raining it might have gotten washed onto the pavement or it may have gotten there searching for higher ground. In the US they are generally considered a pest and can consume crop plants very quickly. I don't actively treat my lawn for them but if I find them I take the opportunity to not let it back into my yard.

It could help if you were to say what country / region you're in ...

Based on another post, the OP is in Indiana.  Or at least was 2 years ago...

It looks as though it has a keel along it's back (the area behind the mantle shield.)
If so (and I think it is), it would be a keelback slug, the coloration strongly suggesting a leopard slug (Limax maximus):

Coloration varies but the general pattern is a spotted spotted mantle sheild about a third of its length in size, with a striped tail.
The major doubt I have is the size. It looks smallish in the photo. Leopard slugs are very large. Perhaps it's a juvenile.

I suspect the keel is just an artifact of the way ansarob took the photo. If ansarob is in the Midwest USA, that's almost certainly a leopard slug. It's hard to tell scale from the image but it looks as if it's retracted into a defensive posture which might explain its lack of length.

+1; definitely looks like a leopard slug to me and as @RobertKaucher says above I think the apparently small size is an artefact of the camera angle.

Yes, this is the leopard slug. It's native and relatively common in my country, but it has been introduced to North America.


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EC number classification of synthase?
It is quoted in wikipedia that:

Following the EC number classification, they belong to the group of ligases , with lyases catalysing the reverse reaction.

And we all know that enzymes are biocatalysts which catalyses reaction in both forward and backward directions.
So my question is that how can the reaction in one direction catalysed by one enzyme and in reverse direction catalysed by other enzyme? If we assume that they are telling that one direction synthase acts as ligase and in other direction it acts as lyase then how can lyases have more than one substrate for reaction? Because products(more than one) of ligase acts substrate for reverse
reaction.(taking for example a ligase, glutamine synthetase as synthase)
It is also quoted from wikipedia

Lyases differ from other enzymes in that they require only one substrate for the reaction in one direction, but two substrates for the reverse reaction.

I am a bit confused here by your first statement, because not all enzymes are bidirectional. Most reactions which involve the breakage of an ATP or other energy molecules are not bidirectional for the same enzyme. Or even if they are it involves some sort of modulation. Next, a ligase may be a synthase but not all synthase are ligase. For me a ligase quiet literally relates to a class of enzyme related to DNA/RNA polymerization. The last question sort of relates to my statement on modulation, that if an enzyme was able to catalyze a bidirectional reaction then a checkpoint would be required...

so that the enzyme does not catalyze the back reaction immediately after creating the product....so the enzyme attaches to the substrate using the lock and key model, it catalyzes the reaction, lets go of the product because  the motif doesnt fit, then when the product is present in sufficient concentration it attaches to another site on the enzyme changing the binding motif so that the product is accomodated and then the back reaction is catalyzed..

Remember that Wikipedia is only as good as its contributors. It does not claim to be correct, only to be correctable. Like anyone else, I could just go in and change the entry, but I have initiated a discussion about the lyase/hydrolase question I raised in my answer, in order to try to obtain consensus before making a correction.

A reasonable question, but it contains a fallacy. This is because what are referred to as the forward and reverse reactions being catalysed by different enzymes are generally not, in fact, the same overall reaction.
Consider the relationship between DNA and its constituents (or RNA or Protein or fatty acid). You may be thinking of this as:

DNA ⇌ DNA constituents

But in fact, because hydrolysis (actually a hydrolase reaction) is thermodynamically favoured, synthesis of DNA (a ligase reaction) needs to be coupled to the hydrolysis of ‘high group-transfer’ deoxynucleotide triphosphates in order to shift the equilibrium in its direction. So the two reactions are (somewhat simplistically):

DNA → n dNMP (catalysed by DNases)

and

n dNTP → DNA + n pyrophosphate (catalysed by DNA polymerases)

Although in certain circumstances you can force reactions of this sort into reverse, in the cell they tend to be unidirectional, and are classified accordingly.
(In this sort of ligase reaction in the cell there is a further factor affecting the observed direction. That is the presence of pyrophosphatases that catalyse the thermodynamically favourable hydrolysis of pyrophosphate to orthophosphate, removing the former.)
Coda: Is the reaction in the reverse direction from a ligase necessarily catalysed by a lyase?
Although not affecting the principle expressed in my answer, I think that the latter part of the statement quoted from the Wikipedia page that “(synthases)...belong to the group of ligases, with lyases catalysing the reverse reaction” is not generally true. As mentioned above, the enzymes catalysing the reactions in the reverse direction from ligases involved in ‘polymerization’ are generally hydrolases (EC 3.1...), not lyases (EC 4...). I couldn’t immediately find an example of a lyase that fitted this description. You can peruse the links on this authoritative page if you wish to follow this up.

@ Koustav Pal — I see you have commented in a similar vein while I was composing this.

So, the could the summary be: Certain reactions are essentially unidirectional because of unfavourable thermodynamics in the other direction (for e.g., ATP hydrolysis or other entropic effects) or non-uniform reactant concentrations leading to skewed equilibrium?

@WYSIWYG — Yes. Probably better to add something like "especially lyase and ligase reactions)".

Just added a coda about the Wiki statement on lyases, questioning whether it should be hydrolases. Contributions welcome.


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Does depolymerisation take place at the minus end of microtubule?
Wikipedia says that

Dynamic instability refers to the coexistence of assembly and disassembly at the 'ends' of a microtubule.

but Karp's Cell Biology, 7th edition says

Dynamic instability is an inherent property of microtubule itself, more specifically, of the plus end of the microtubule.

I was of the opinion that the GTP bound to the minus end does not hydrolyse and so no depolymerisation take place at the minus end.
But again from The Cell: A Molecular Approach. 2nd edition I found that

treadmilling is a dynamic behavior in which tubulin molecules bound to GDP are continually lost from the minus end and replaced by the addition of tubulin molecules bound to GTP to the plus end of the same microtubule.

The concept I have developed so far is completely shattered by this treadmilling thing. Can somebody explain,
i) Whether GTP remains attached to the minus end?
ii) Whether depolymerisation occurs at the minus end?
iii) If depolymerisation does not occur, then is treadmilling a special condition?

I think the reason why the literature contain these contradictions is that all these phenomena do happen, but in most conditions the dynamics is strongly dominated by the plus-end dynamics (growth and catastrophies), leading most research to disregard minus ends completely.

Treadmilling, AFAIK, happens in actin filaments not tubulin.

@WYSIWYG no, it happens in microtubules. See this.

@MattDMo Interesting. The textbook that I used to read never mentioned that even though the article you mention is quite old. I found a more recent article on this topic. Thanks for correcting me.

@WYSIWYG no problem. I found that article while researching an answer I've decided not to write - seems the idea of treadmilling has been around for a long time.

Often microtubule (MT) dynamics and actin dynamics are taught side by side, which can be quite confusing as MTs display unique characteristics relative to actin filaments. Indeed, treadmilling is an in vivo behavior primarily associated with actin, while dynamic instability characterizes MT growth. But why?
Both actin filaments and MTs are "sided" (polar), with actin having barbed- and pointed-ends and MTs having plus- and minus-ends. This polarity emerges from two properties: 1) the energetic state of the individual monomers that make up the filament and 2) the rate of growth.
For actin, the barbed-end is compromised mostly of ATP-actin (high energy), while the pointed-end is made up of ADP-actin (low energy). This composition preferentially adds new ATP-monomers to the ATP-rich barbed-end, yielding a faster rate of growth than at the pointed-end. Disassembly at the pointed-end occurs more readily as ATP-actin is converted to lower energy ADP-actin. Treadmilling occurs when the rate of assembly at the barbed-end is equal to the rate of disassembly at the pointed-end (Pollard and Borisy, 2003).
Similarly to actin filaments, MTs are polar, with their plus-ends made up of GTP-tubulin monomers and GDP-tubulin concentrated at their minus-ends (Desai and Mitchison, 1997). Unlike actin filaments, which can form sporadically almost anywhere in the cell (Pollard and Borisy, 2003), MTs are initiated at what we call a microtubule organizing center, or MTOC (Kollman, 2011).
The bulk of MTs within the cell are attached to the MTOC through their minus-ends, though there are unattached sub-populations. Both in vivo and in vitro data indicate that growth and shrinkage at the minus-ends does occur, but that the rates are slow relative to those occurring at the plus-ends (Hendershott, 2014). In these instances, MTs can undergo treadmilling in a manner similar to that as actin and this behavior is readily observed in vitro (Waterman-Storer, 1997). Recent studies have suggested that MT minus-ends are under tight regulation in vivo, likely limiting their dynamics (Akhmanova, 2015). Therefore, MT growth and shrinkage primarily occurs at thee plus-ends. Enter dynamic instability.
MT plus-ends undergo a cyclical process of growth and shrinkage known as dynamic instability (Mitchison and Kirschner, 1984). The key to this process is the difference in shape between GDP-tubulin and GTP-tubulin (Buey, 2006). One can imagine GTP-tubulin as a rectangle, with perfectly straight lines connecting its angles. On the other hand, GDP-tubulin has a small bend in the center of one of its long ends.
As a MT grows, GTP-tubulin is added to the plus-end forming a "GTP cap." The role of this cap is to counteract the inherent desire of GDP-tubulin to bend outward, thereby forming a straight filament and ensuring continued growth of the MT (Desai and Mitchison, 1997). However, the MT will lose its cap when the rate of GTP-tubulin addition drops below the rate of GTP to GDP conversion, thereby exposing GDP-tubulin. This event characterizes the "catastrophe" stage of dynamic instability (Mitchison and Kirschner, 1984). The shape of GDP-tubulin is no longer constrained in this stage, and instead, bends outward causing rapid disassembly of the MT. Because the cell is chock full of GTP-tubulin, recovery of the GTP cap rapidly occurs and the MT re-enters productive growth. This cycle of growth-catastrophe-recovery is the hallmark of MT dynamic instability.

Answer is mostly fine, but, as per the earlier comments on the original post, MTs can become detached from the MTOC, and then undergo treadmilling.


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Does Cas9 require a nuclear localization signal (NLS) for it to work in a Eukaryote?
I'm trying to establish if it's required to add a NLS to Cas9 when expressed (or transfected) in a Eukaryotic cell.   Several papers report using a viral NLS, but is it absolutely necessary?   Could Cas9 be trafficked to nucleus without addition of a NLS?

As far as I know it should be needed because it can not enter the nucleus otherwise.

Most of the Cas9 genes you buy for mammalian gene editing experiments will contain at least one copy of the SV40 NLS sequence.

The transport from cytoplasm to nucleus is mediated by importin family. Importion family recognize NLS and transport proteins such as transcription factors into nucleus. So, NLS is necessary for cas9 to be transported into nucleus.

can you add some references to your answer? it always helps for others on the site to have further reading and substantiate claims.

Yes, it does.
In general, proteins required in the nucleus must be directed there by some mechanism. https://en.wikipedia.org/wiki/Nuclear_localization_sequence
Adding a nuclear localization sequence to the N-term of a protein is a very efficient and established way to accomplish this.
Also, as a supporting fact, you can notice that any CRISPR/Cas expression plasmids for mammalian cells on Addgene (here an example http://www.addgene.org/48138/ ) contains one or more NLS at the N-term of the Cas sequence.
Here some links for further reading:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1083765/
https://www.ncbi.nlm.nih.gov/pubmed/27126810
https://www.ncbi.nlm.nih.gov/pubmed/26173234


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Amino acids in human cancer cells expose dextrorotation?
I would like to know if the amino acids in the human cancer cells are dextrorotatory or levorotatory.
I mean the majority of them.
They expose levorotation just like the amino acids in the normal cells or they are different?
I mean in general. Maybe some particular types of cancer are significantly different from the rest.
I'll try to make the question more on-topic: The amino acids in cancer cells are also levorotatory, just like the amino acids in the normal cells?
This book: Breaking the Cancer Code: A Revolutionary Approach to Reversing Cancer says "We know that tumor cells grow in dextrorotation" - so I wonder where the author(s) know that from. They must be speaking about amino acids inside tumor cells, when they say "tumor cells"

what makes you think there is more R in tumors? Is this a wild guess? If yes, this question is off topic

What brings you to this conclusion? Where should this amino acids come from? Can you please add some references about it?

No idea where they can come from, but I remember reading this in a science magazine a long time ago. How can I make the question more on topic?

I took a 30 second look at the book you mentioned. The authors just made this up, just like 95% of the book.
The authors are not wrong, they didn't want to write something useful and made a mistake, they're just bullshitting: They're making stuff up, letting it sound a tiny bit scientific and try to sell a lot of books.
If you want to know more about something, usually Wikipedia is a good place to start, and if you're not sure how to distinguish between science and pseudoscience it might be a good idea to read a bit about recognizing pseudoscience.
Now to answer your question: cancer cells are almost the same as normal cells, and they contain mostly levorotatory amino acids. The main difference between a cancer cell and a normal cell is that the cancer cell has one or more mutations that cause it to divide a lot more than normal cells. The DNA, proteins and small molecules in the cells are mostly the same as in normal cells, that's why it's so hard to specifically kill cancer cells.

I can't vote yet, but thanks for the answer. I think it's much better to talk about pseudoscience and debunk it's myths than to pretend it doesn't exist. Therefore such questions and answers are highly valuable. Just my 2 cents.


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How would cloning affect conservation of rare species?
Many species are at risk of extinction, and cloning could be seen as a relatively quick method to produce large numbers of members of the species to aid in conservation efforts, especially if the species involved has low fecundity (such as the giant panda).
However, cloning results in the reduction of genetic diversity, which may lead to significant issues due to inbreeding and susceptibility to diseases. This can most clearly be observed in the Gros Michel banana cultivar, which was nearly wiped out by Panama disease due to the cloned banana cultivar not having any resistance to the disease.
What are the main positive and negative aspects of cloning when applied to conservation of rare species?
(This question is based in part on this question, which was closed for having not done any research, but has an interesting premise that I wish to see answered on this site.)

Cloning become an important method for conservation genetics. However, it is not a magical solution and doesn't solve all of the the problems. There are two key considerations with conservation: short term issues which are causing the immediate threat such as poaching, habitat destruction etc. and long term issues of genetic variation. Genetic variation is critical to the long term survival of a species because low genetic variation results in inbreeding depression (reduced ability to survive and reproduce resulting from higher expression frequencies of deleterious mutations) and reduced potential for adaptation. The rate of adaptation is determined by the strength of selection and the volume of genetic variation; without genetic variation there can be no adaptive evolution. Therefore, genetic variation is key to the long term success of a species.
Where cloning can come in is it can be used to increase the gene pool, sometimes quite substantially. Consider the meta-population of a species, this could be allowed to include all of the wild sub-populations and all captive or managed (semi-captive) populations. For example, there are ~3900 wild tigers in the world, and ~5000 in captivity. Among all of those, only a subset contribute offspring to the next generation of wild animals, reducing the effective population size, and increase rates of inbreeding and genetic drift. For example, often very few males fertilise the females of a population with strong effects on the effective population size. What cloning could be used for (to various levels, depending on the specifics of the method) is to allow other individuals to contribute. For example, by cloning the members of a wild population that were unable to secure mates during a reproductive season (there is often high variance in mating success which reduces effective population), conservation managers can artificially re-inflate the effective population size to more closely resemble the census population size. In other cases, conservation managers may chose to clone particularly viable/fertile individuals that are approaching old age or nearing death, and are therefore at risk of being lost from the population. Conservation programs could use cloning of (semi-)captive individuals and introducing clones from (semi-)captive populations in to wild populations allowing genetic variation to be drawn from the gene pool of (semi-)captives in to the wild populations. Increasing the variance in the gene pool will increase the adaptive potential of the wild population. Another option is to clone wild animals in threatened areas (e.g. where populations are in decline as a result of poaching) and to put the clones in to safer areas such as national parks, or even zoos, to preserve genetic variation while conservation managers try to bring the other issues under control. Effectively this would act a bit like a seed bank.
However, there are some issues to consider, and this is a non-exhaustive overview. What if there was a good reason for some individuals not mating? The action of selection, which causes adaptation, is to induce variance in reproductive success as a result of the genes an individual carries: in principle selection reduces genetic variation and allows the "better" variants to prosper. So if we clone a wild individual that produced no offspring in the reproductive season we may just be maintaining genes in the population that selection would otherwise be removing. In other words, cloning efforts could be counter-productive to the long-term success of the species and make conservation more difficult. What if we reintroduce bad genetic variance to the wild population? Captive populations have adapted to some degree to the environment that they are in, this may have selected genes out of those populations that are more beneficial in the wild. For an extreme example, dogs are descended from wolves and have adapted to an enormously different environment, so it would probably be very counter-productive to start cloning chihuahuas and introducing them to wild wolf populations as a conservation strategy to get genetic variation from captive "wolf" populations (but maybe the chihuahuas would be a good food source at least). Can clones be effectively, and efficiently, reared and introduced to wild populations? It will be extremely hard to actually get to the point where clones can be successfully introduced to wild populations. Resources (including money), are extremely limited in conservation, so there may be better ways to use those resources. Are populations under remaining threat from short term issues such as poaching and habitat loss? If there is continued extrinsic threat to the wild population then there is not much use in cloning, because clones will also be threatened by the same issues. Many places are still under serious threat from poaching. Adding some clones would be like trying to stop a ship from sinking and using a tiny bucket to bail out the water; you need to plug the hole first or use a really big bucket (can cloning be a big enough bucket?).
Bonus: You could read here about the issues faced in the Isle Royale system of wolves and moose, where wolves are on the verge of extinction, and the impacts it will have on the ecolsystem.

The Isle Royale wolf conservation paper is really interesting, thanks for the great read.


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Why must DNA be packed into chromosomes during mitotic phase?
Why does DNA have to be packed into chromosomes? Why can't DNA just divide itself evenly?

They don't pack into chromosomes. Chromosomes are made of DNA and during the metaphase, the chromosomes packed and look like the standard x-shaped(-ish) representation of chromosomes that we are all used to.

You have some misconception here: Chromosomes are an organisation unit for the DNA.

So is my concept of what chromosomes are is that they are basically DNA but condensed into the x-shaped representation correct ?(correct me if my concept is wrong)

A chromosome is simply a length or segment of DNA. Bacteria have few structural proteins on their DNA, and they have one circular chromosome. In humans, before DNA replication, the nucleus contains 46 strands of DNA, i.e. chromosomes (22 chromosomes in two copies and usually two X or one X and one Y for males and females, respectively). All chromosomes are DNA that is bound by histone proteins that are organised in nucleosomes, approximately every 147 base pairs.
What you are referring to is a condensed chromosome in metaphase, which confusingly in humans is actually an X shape consisting of 2 identical chromatids, structurally condensed and joined at the centromere to form a duplicated chromosome.
The duplicated chromosomes must condense and join before the cell can divide because a tangle of 96 chromosomes as chromatin would be almost impossible to organise and separate properly. The joining of identical chromosomes and compacting process allows all the 46 compacted and duplicated chromosomes (i.e. 96 chromatids) to simply align along the spindle apparatus that forms in centre of the cell during mitosis, and have separation of the chromatids during anaphase so that each of the new cells has a full set of 46 chromosomes.

If you mean to say why DNA is in the form of chromosomes, then obviously answer is simple: For Compression and Packaging - Around 2metre long DNA must be compressed (at an unbelievably high ratio) to let it fit in the tiny nucleus (order of micrometers)


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Estimated protein size using CDs data
The number of amino acids in a protein is important to predict their size. I used coding DNA sequence (CDs) to predict the average of the protein size of E.coli k12 from a sample provided by the seqinr R package. The size of each sequence is stored in variable x.
I used two histograms to fit the distribution of this variable and their logarithm.

I suggest that the log linear distribution is more reasonable.The average E can be calculated then:
E1=mean(x)/3

E2=exp(mean(log(x)))/3

Which average do I have to use?
Is there a correlation between the base composition and the predicted average?

You seem to have two questions but I don't really understand them. Here is my try to rephrase your questions. 1) What standard theoretical distribution best fit the observed distribution? This is a question of statistics, not biology. 2) Is there a correlation between GC skew and protein length? This question has little to do with the rest of the post.

Which average do I have to use? They are both the same, since you're using the exact same data. It's only the presentation that's different, as you're comparing a linear plot to a log plot.

@MattDMo Not necessarily. OP might want average log weight which is not the same as log of average weight.

Can you elaborate your question? I am having a hard time understanding what you are exactly asking for.


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Is it possible to remove one strand of double stranded DNA in vivo?
Assume we do have a double stranded DNA sequence in human cells, say
...ATCGATATCGATATTGCAGAGCATAGCTATAA...
...TAGCTATAGCTATAAGCTCTCGTATCGATATT...

Now I want to cleave one strand, such that I do have
...ATC..........................TAA...
...TAGCTATAGCTATAAGCTCTCGTATCGATATT...

The distance is not so important to me, so it can be 20 bp I remove or 1000s. Hence, if I need some PAM or so and it is not nearby the target deletion site, I will simply move in 5' resp. 3' direction until I find it and cleave there, as long it is ensured that I have the target site single stranded then.
I would be very grateful I you could help me here!

I don't understand what your question is - why are you trying to remove a single strand in vivo? What is PAM in this context? Please [edit] your question to add additional explanations and details.

Both TALEN and ZFN gene editing technologies use a pair of single-strand endonucleases that ultimately lead to a double strand break. Cas9 in CRISPR-Cas technology, however, cuts both the DNA strands (there are some Cas enzymes in certain bacterial species that cut only a single strand [ref]).

Image courtesy: http://www.xenbase.org/other/static/CRISPr.jsp

So, if you use a single unit of the pair, you can cut one strand of the DNA. You can use another nuclease to impart a cut at another site in the same strand. This will still not lead to the removal of the DNA sequence between the two cut sites. There is no available technology that can do this in-vivo. Possibly (a wild guess), you can use a modified oligonucleotide (or even an IVT synthesized RNA) that can bind to this stretch of sequence and break its interaction with the other DNA strand. In any case, a stretch of ssDNA would not be stable and be repaired quickly by polymerase.

Many thanks for your reply. Another thing that would be sufficient for my project would be that on a specific site the DNA gets unwinded in vivo (perhaps by some CAS enzyme like dCas9, though others might be better suited here). Then one of the strands might be "hidden" by the machinery, but the other one should be accessible to toy around with it. Is such a thing possible?

@tobias Possibilities are infinite but we should go with the one that is simplest in principle and is easy to implement.

Sure :). What would you suggest for it?

@tobias I don't think such a protein has been engineered yet. That would be a research project in itself and you would have to do many experimental try-outs. So, I cannot suggest much regarding that- you would have to try it. What I said in the answer (the guess) would be the first thing that I would try because it is easy.

Many thanks for your reply. Regarding the second question, where I try to have a large strand of ssDNA, could I fuse dCAS9 to a helicase, such that the dCAS9 bind in sequence-specific manner to the dsDNA, opens the DNA and the helicase opens it for, say several tens of bps. Is that realistic?

@tobias Sounds good but as I said, it may be a research project in itself. Sometimes even the most perfect designs on paper may not work out in the lab (happened to me three times). There is always some risk with designing a new tool. It may or may not work. If you wish, then you can try. Moreover, even the design step would involve a lot of thinking (how to fuse the proteins, how will the domains interact etc).


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Difference between null and recessive allele?
I get that in a single gene locus, an individual can have RR, Rr, or rr as the two alleles for that gene. R is "wild type" because it is the allele occurring most frequently. r is the allele that is not WT.
RR and Rr show dominant phenotypes, whereas rr shows the recessive phenotype.
But what's the difference between r and a null allele (allele generated by a loss of function mutation outputting the complete loss of the WT phenotype)? Where _ is a null allele, my questions are below:

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

Good question +1. Unfortunately, the mechanisms by which dominance work is relatively poorly understood and it is likely that the mechanism differs from one locus to another.
You might want to have a look at the posts

Why are some genes dominant over others? What is the mechanism behind it?
Evolution of dominance

or some papers such as

Llaurens et al. (2009)

I don't think one can make any general prediction about the phenotype of R_, r_ or __ without having a priori knowledge of the biological pathway (incl. allele interaction (see Llaurens et al. (2009)) and gene interaction network) by which this particular locus is affecting the phenotype. It is tempting to say that R_ is alike Rr or RR, and r_ is alike rr but this is not necessarily true.

To add to Remi b's answer - this question is confusing because 'null' and 'recessive' are terms emerging from two very different levels of analysis. The concept of 'recessive' existed before we knew what genes were, or how they worked. It just describes the patterns of inheritance you see in a gene's effects.
The concept of a 'null' allele however came later, and explicitly describes how an allele works - by destroying gene activity. So 'null' is molecular concept, 'recessive' is an abstract genetic concept. It so happens that null alleles are very often recessive, because usually one working copy of a gene is fine. But the two terms are describing genetics at very different levels.

That makes sense. Why scientists don't change the nomenclature?

Because both levels of genetics are still very much in use. We often want to talk about molecules, but if we have a family tree, or an association study, or a mathematical model of inheritance, we also want to talk about the effects of mutations while remaining agnostic about the molecules.

Basically, a recessive allele leads to formation of a product that has a low activity or no activity, which is complemented in the presence of the dominant allele (there can be effects related to dosage, in some cases). This can be easily understood in terms of an enzyme; a dominant allele would code for an enzyme with full activity whereas the recessive allele codes for one with a reduced activity. There are further complexities but this is a simple example.
A null allele however results in zero activity of the gene. This may be because of many reasons:

The allele may produce a non-functional protein (for e.g. an enzyme
with mutated active site such that it cannot carry out the catalysis)
The geneic region of the allele may be transcribed but not translated (loss of ORF)
There may be no transcription at all (deletion of DNA sequences
critical for transcription)

In cases where there is no dosage effect, a null allele is always recessive but the converse is not true.

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

The first two these assumptions are true for a simplistic case (no dosage effects). Since, r is a hypomorphic allele (by assumption) i.e. it has a reduced activity whereas _ has zero activity, _ _ may not have the same phenotype as rr. Only in cases where there is a threshold on the activity leading to phenotype, can a low activity allele/genotype (activity below threshold) lead to same phenotype as the null allele.
If we add further complexities, R _ or r _ may not be functionally equivalent to Rr or rr respectively. Even RR may behave functionally different than Rr. This would happen because of altered gene dosage (expression level) and reduced expression level of the functional product can cause a change in the net activity. (Also see: Can difference in the expression potential of alleles lead to dominance?)

It is not true that a null allele is always recessive. R_ can have a different phenotype from RR if gene dosage matters.

@JackAidley True. I have mentioned gene dosage. I also clarified that when dosage matters then even heterozygotes would behave differently from the homozygotes. Basically the concept of dominant/recessive alleles somewhat breaks down when dosage is important. I have clarified all these exceptions. However, the null allele may still be considered recessive because the presence of R will at least partially complement it. I added a statement to explicitly mention this.


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Why do some macaques have redder faces than others?
I'm watching Monkey Kingdom, and I noticed some of the macaques have redder faces than others.
Specifically the females, and as the social ladder increases, so does the redness.
An alpha female:

Does the redness-hierarchy correlation have something to do with attractiveness or aggressiveness? (These seem to be leading factors in defining hierarchy otherwise.)

Aggressiveness, seems more likely, on first thought. Heightened Aggression, leading to stress, causing High blood pressure or an increase in vascularity, maybe? Inferring the reason for the colour? A good start would be to find out why, their faces are red in the first place, and then hypothesise from there onwards.

@user19679 That's part of my question. What causes the redness, and does what cause the redness also increase a certain kind neuro connection or hormonal release, etc., that's also correlated with aggressiveness or some other dominant trait.

@user19679 increased vascularity may be part of it, yes. But from seeing the monkeys at different angles, it looked like more a pigmentation. I was hoping there'd be a wildlife vet (or something along those lines) who could speak to it.


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Does any specific property decide which DNA strand acts as leading strand template?
Of the two strands of DNA, the one that unwinds in the 3' to 5' direction constitutes the leading strand template, with the other strand of course acting as the lagging strand template. Is there any specific property - such as a specific base pair sequence present on one of the strands - which decides that that strand shall be the leading strand template - whereas the second strand with the complimentary sequence will be the lagging strand template? What decides, in other words, which of the two strands will be unwound in the 3' to 5' direction (effectively rendering it the leading strand template and the second strand the lagging strand template)?

Basically, the orientation of the origin of replication sequence decides that. I'll read up a bit on that and give you a full answer.


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Is there any clear relationship between physical characteristics and patterns in the genome?
Given that for example humans have five fingers on each hand, is there a region in the genome with a sequence of five similar subregions, one for each finger? Is the region on the genome that encodes for the right hand near another region that encodes for the left hand?

This kind of question is what developmental genetics is all about. The answer turns out to be, in general, 'no'. There is no neat mapping between spatial dimensions of an organism and its genome. (There is one exception to this in some organisms called the Hox cluster, but they are kind of a freak case).
The reason for this is that in general you should think of the genome as being a recipe for a developmental process, rather than a description of the end product. You might have, say, a specific set of genes which is active in all limb buds, which are the structures that become limbs and fingers etc. These genes would be active at different levels, at different times and places, in your different fingers. E.g. length of time one gene is on could control how long the finger grows for and thus how long it gets.
There are some genes which are only active in specific parts of the body, but you don't necessarily need a particular set of genes for each distinct finger/limb etc. And these genes certainly don't need to be in the same place in the genome. Your left and right hand are going to have identical gene expression for instance.

Thanks. I am in general interested in how close software is to the recipe you mention and if modern software approaches are very different whether we can adapt what we learn about genetics to developing software.

In general I would say, software code is very, very different from the genetic code, because it has an intelligence behind it. Consider the difference between a road from a mountaintop to the sea, and a river making the same journey. The road's path will be far simpler and more efficient, because the stream can only follow local minima, whereas the road is designed by an intelligence that can consider the whole problem at once. Evolution can be used to generate code, but expect the results to be... different, from what a human mind would produce.

i think there are some deep questions here. but as i said, even if very different or because it is, we might learn from it.

Possibly - presumably you're aware of evolutionary algorithms. It's an active topic of research.

Yes but this may end up being very different than a programming language that uses "approaches" that nature uses to build/regulate organisms.

Fair. I guess taking natures approaches and improving on them is something we've been doing for a while. If you're interested in the nitty gritty of how gene regulation works in development, this  is a classic text on the topic.


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What exactly is the time constant of an ion channel gating?
Let's take a channel that does not get inactivated, but is only in open and closed states. I understand what m (activation variable) represents. It's the fraction of the gates open.
But what does $\tau$ (tau) , the time constant represent? Does it mean the time taken to open the gate? If tau is higher then it mean more time taken to open the gate?
I'm slightly confused.

It totally depends on what the model is. Can you please add the model equation?

Let's say can you describe the time constant for the activation gate of a sodium channel?

@WYSIWYG Could you please answer?

I need more information. Can you put your model equation in the question? The time constant can mean anything.

Although the membrane time constant is very important in neuroscience, the time constant described in the original question is about ion channel gating rather than the rate of change of membrane voltage.
The "tau" when referring to ion channel gating is indeed referring to how long it takes to open/close.
When the membrane voltage changes, there is a new equilibrium value for the probability of the channel to be open versus closed (note: there can be other states for channels too, but for this explanation I will stick to open/closed). The rate at which this equilibrium is approached from the previous open probability is described by an exponential function, with "tau" as the time constant of that approach. A small value of tau means that the new equilibrium is reached very quickly. This site has a good explanation of the terminology and gating process, as do many others.
Time constants are involved in any system described by an exponential (these are called "linear time invariant" processes), whether decay or increase, and it is equal to the time it takes to progress approximately 63.2% of the way to the equilibrium. The cool thing about time constants (and linear time invariant processes in general) is that it doesn't matter what your starting point is or how far into the process you are, the time constant stays constant and every time "tau" passes you are now 63.2% closer to equilibrium than you were at time t-tau.

According to Wikipedia

In physics and engineering, the time constant, usually denoted by the Greek letter τ (tau), is the parameter characterizing the response to a step input of a first-order, linear time-invariant (LTI) system.

In Neuroscience:
The time constant, $\tau$, characterizes how rapidly current flow changes the membrane potential. $\tau$ is calculated as:
$$\tau = r_mc_m$$
where r$_m$ and c$_m$ are the resistance and capacitance, respectively, of the plasma membrane.

The resistance across the membrane is a function of the number of open ion channels and the capacitance is a function of the properties of the lipid bilayer

Note: the time constant is a "passive property" of membranes because they are intrinsic properties of all biological membranes. [Source].
My guess is that you are referring to some equation reference from Hodgkin-Huxley Model for the Generation of Action Potentials, but without further information about your specific equation, I cannot comment about Tau's specific role in your equation.
Example Application:
This constant can be applied to one of a few equations describing changes in membrane voltage. For example, a fall in membrane voltage is modeled as:
$$V(t) = V_{max}e^{-t/\tau}$$
where voltage is in millivolts, time is in seconds, and $\tau$  is in seconds.

You can read more about the mathematics behind this and passive membrane properties in general here and here.

Again, From Wikipedia:

The larger a time constant is, the slower the rise or fall of the potential of a neuron. A long time constant can result in temporal summation, or the algebraic summation of repeated potentials. A short time constant rather produces a coincidence detector through spatial summation.

Hey, nice answer, but this wasn't the question: the question was about time constants in ion channel gating which is better thought of with equations describing binding or reaction rates, not the membrane time constant, it is a completely separate concept.

@BryanKrause Hmm so it is. Thanks for pointing this out! I wasn't quite sure what the OP was referring to when I first read it. Because of my uncertainty, I tried answering first broadly and then regarding the only tau I knew in this general area of biology. Your answer appears to be the correct answer in this case, though (and thus I gave you a +1).

I Understand that you are referring to the 2-state model of ion channels. In this case, the transition from one steady-state to another is modeled as an exponential decay.
$$
\tau * dm/dt = (m_\inf - m)
$$
The so called "fast" channels have $\tau$ of a few milliseconds, "slow" ion channels have time constants of hundreds of milliseconds or more.
Of course, the 2-state model is a simplified mathematical model of ion channels, but for many phenomenological purposes, it is good enough.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
How to interpret Percent identity matrix created by Clustal Omega?
I did a multiple sequence alignment using Clustal omega. checked similarity for 3 protein sequences : aspartyl aminopeptidase [Homo sapiens], aminopeptidase P (APP) [Plasmodium falciparum 3D7], yeast aminopeptidase (S000001586)APE1. I got Percent identity matrix as
Percent Identity  Matrix - created by Clustal2.1
 1: PF3D7_1454400              100.00   16.18   20.35
 2: gi|5902181|gb|AAD01211.2|   16.18  100.00   29.66
 3: S000001586                  20.35   29.66  100.00

My doubts:

I would like to know how to interpret this matrix result
Coming back to sequence alignments results, when I click on 'Show colors', the alignment summary is colored in 4 colors - red, green, blue and pink. Can anyone help me in decoding the color reference of alignment summary?

Thanks

        Gene-1   Gene-2    Gene-3
Gene-1  100.00    16.18     20.35
Gene-2  16.18    100.00     29.66
Gene-3  20.35     29.66    100.00

Gene-1 and Gene-1 have 100% similarity (and all the other diagonal elements). Gene-1 and Gene-2 have 16.15% similarity, and so on. Therefore the matrix is symmetric M(i,j) = M(j,i).
You can also show just the upper triangular part of this matrix and that would be sufficient.
        Gene-1   Gene-2    Gene-3
Gene-1  100.00    16.18     20.35
Gene-2           100.00     29.66
Gene-3                     100.00

The colours basically denote the type (molecular nature) of residue. Have a look at this and this.


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Best method to cure cancer as of now?
I am not talking about chemotherapy or radiotherapy. So, if it exists, what is the best biological technique to cure cancer as of now?

why rule out chemo/radiotherapies... they may be the "best". Also what is the meaning of best in this context; something may cure cancer excellently, but cause heart attacks as a side effect, be ridiculously expensive and involve unethical methods to develop and manufacture it, while something else might cure 2% of cancers and have no side effects and minimal financial and ethical costs.

@rg255 I don't know why chemo, but radiotherapy is ruled out because the OP wants to know only biological methods. And best might mean, of course, something that cures cancer most effectively, has least side effects, be ridiculously cheap, follows ethics to develop & manufacture i.e. more utopian in scientific terms :)

Oncolytic viruses are a potential cure as of this ted talk I came across

There is no general therapy for cancer - as there is no general cancer. Cancer is the umbrella term for a disease where you have body cells growing without control, leading eventually to death. But since there is a wide variety of cells in the body, there is also a very wide variety of different cancers.
To treat these, surgery is often the first line of therapy. For some cancers this is already sufficient to cure the patient, examples are skin cancers (not only melanoma but the other forms as well) where you can cure a very high potion of the patients. This only works for early forms of the cancers when there are no metatases present.
Besides this, additional therapies are used - as you said yourself chemotherapy in the different forms as well as radiation therapy. Chemotherapy is given systemically and targets fast growing cells (cancer cells have these properties) and causes mutations or other problems which let the cancer cells eventually die. Radiation works with the same principle, but is more focussed.
Relatively new therapies are the targeted therapies where the treatment uses the occurance of certain common mutations. An example would be the mutated BRAF kinase in melanoma (and also in a number of other cancers) which can be specifically inhibited with an inhibitor. This avoids a lot of problems general adverse effects of the drugs. Additionally immune therapies are also new which use antibodies against surface receptors of T cells to prevent their inactivation. These T cells then attack the tumor.
These are all non-biological treatments. More biological ones are modified oncolytic viruses. In this therapy you inject genetically modified viruses which preferrably infect the tumor and then destroy it. These are relatively new, but an interesting option. See references 1 and 2.
An old method is the usage of bacteria to treat tumors - the first obervations on this where done in the late 19th century, see reference 3 for more information and a lot of further references.
A number of the chemotherapeutic drugs used today are originated from nature, but are today synthesized and used in a pure form and not isolated from their origin anymore. Examples would be vincristine, irinotecan, etoposide, and paclitaxel. See references 4 and 5 for details.
Besides this, there are no effective "natural" cancer cures, despite the claims of several "alternative medicine people". These are either based on wrong assumptions of biology or wrong ideas like Homeopathy.
References:

Advertisement Oncolytic Viruses and Their Application to Cancer
Immunotherapy
Oncolytic viruses: a new class of immunotherapy drugs
Strategies using bacteria to target tumors
Anti-inflammatory and anticancer drugs from nature.
Drugs From Nature, Then and Now

I'd like to vouch for adoptive cell transfer therapy, ACT, using tumor-infiltrating lymphocytes, TIL (Lee & Margolin, 2012). While the therapy is currently geared largely for metastatic melanoma, there are investigative studies involving TIL ACT in other cancers such as head/neck, cervical, ovarian, breast, etc. I want to note immediately that this is not a cure but rather a promising treatment.
The idea is that T cells have recognized a tumor antigen and become activated toward the tumor. They extravasate to the tumor and attempt to kill it, but they become overwhelmed by evasive tumor mechanisms and the tumor environment. So they're just kind of there, with the tumor, ready to fight but too tired to finish the job. Hence, tumor-infiltrating lymphocytes.
The patient will have an accessible tumor excised by a surgeon, where a technician will cut the tumor into small fragments. The fragments are incubated with media and IL-2 in a way that skews the growth toward lymphocytes. And so from the same patient we'll take some blood, and separate the PBMCs, and then irradiate them. The irradiated "feeder" cells provide to the lymphocytes co-stimulatory signals that promote their growth. We also incubate the T cells with an agonistic monoclonal antibody OKT-3 that activates CD3 on the T cells. And so with this, the T cells rapidly expand over the course of a couple of weeks to several billion cells. Importantly, we should have a good population of CD8+ T cells that are tumor-reactive.
The patient, before re-infusion of their own T cells, undergoes lymphodepletion with the drugs cyclophosphamide and fludarabine. The point is that immune responses are heavily regulated, and so you want to get rid of T-regs, and other immune regulatory cells that might blunt the effectiveness of the TIL. You also figure, you're infusing several billion cells, you need to make room for these extra immune cells. The T cells should then in theory find every tumor with the antigen they were programmed for initially and kill them with granzymes, perforins, etc.
There are some barriers to the treatment, the first being that it's largely exploratory and thus not widely available. Due to the complexity of the treatment, it's also very expensive (at the NIH, $500,000 USD perhaps?). You must also consider that while we're growing these TIL, there's a patient dying on the other end that may not make it to the treatment phase. There are stochastic issues that also prevent the treatment from reaching it's maximum potential.
The first is the tumor: they exhaust the T cells quite a bit, and in T cell exhaustion you get an abrogation of the T cell mechanisms, and so our fight becomes bringing these TIL back from the dead:

Source: T Cell Exhaustion
For example: The presence of the T cells also sometimes cause the tumor to begin expressing PD-1L, ligand to a programmed death receptor PD-1 that T cells up-regulate in exhaustion. Through SHP-2, PD-1 blocks stimulatory signal 1 to T cell activation at ZAP70. The tumor microenvironment is also very acidic, and the T cells take issue with this and it blunts development. Because of this, when you're growing T cells out of the tumor fragments, sometimes you get a bad yield, and the way you actually cut the fragments, or how the surgeon excised the original tumor play a part in manufacturing the cancer treatment. You can have a patient that might respond well to TIL, but end up they just don't grow out of the tumor.
And so research is focused on getting the T cells to grow better, making the tumor less stubborn, and reducing the noise caused by these stochastic effects that aren't at the moment in much control of the scientist. You can also make note that while TIL ACT is largely a biological therapy, you still need chemo as a crutch to achieve optimum efficacy, hence the cyclophosphamide/fludarabine immunodepletion.
PS I tried to cover everything but we can go deeper and deeper with this therapy so I wanted to keep it brief, but this means I may also miss some critical notes, so I'm available to clarify things if need be.


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How do I know whether or not a nuclear gene is single copy?
As a part of a phylogenetic study, I need to find a nuclear gene that meets the following requirements:

Single copy gene;
Highly variable gene;
Gene longer than 400 bps;
Gene that gives information at the species/genus level in Gastropoda.

My candidate genes are the following: 5.8S, 18S, 28S, ACT, APN54, EF-1alpha, endo-1,4-beta-glucanase, GSTM, GSTO, GSTP, H3, ITS1, ITS2, MCP, MYO.
However, I do not know where to find whether or not they are single copy.

Even simpler: If you are lucky and your target Gastropoda is in Ensembl (http://ensemblgenomes.org/) you can just introduce the gene ID and see if it has any paralogs. A lot of other info is available for each gene.

The simple way to do this is to use blast to search the genomes your interested in for sequences similar to your gene. If there's another copy it'll turn up in the blast results (so will orthologous genes - but they'll have lower scores than an actual copy). That relies on the annotation and genome being correct, of course.