text:
Can I simply take the trend of heart rate amplitude to get breathing rate in an ECG?
I processed an ECG signal using findpeaks in Octave. Then, I plotted the amplitude of the "peaks" found by that function and got the followinge result (original unprocessed ECG signal on top, simple plot of "peaks" on bottom).

If I analyze the "peaks" signal, I get a frequency of about .07 Hz, which translates to about 14 events per minute. This correlates nicely with breathing rate. Is that really the breathing rate that I found, or am I jumping the gun? I've heard this may be referring to a "DC Drift"?


text:
How is output of DNA assembler measured?
I developed own DNA assembly pipeline. Input is set of reads and output is set of contigs.
Many papers measure own algorithms and compare it against each other. There are basic metrics like:

N50, N70..,
number of contigs,
genom coverage,
error rate

I download tool QUAST and there I can see metric N50, L50, where is easy to develop own computation. But how I can measure error rate of my output contigs? Is there any tool which can do it?
I searched in many papers but I cannot find way how they do it. I would like to compare with some assemblers with some general way. I found only hints that it should be done by aligning contigs to reference genomes but I do not know how and if it is right way.

This is just data parsing. You can use simple scripts for this.

Can you please describe more, or some example?

If you are interested on the topic of how to compare assemblers, have a look at assemblathon. That group has two papers and working on a third about comparing genome assembly algorithms.

source: Stack Exchange

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sort: votes


text:
why dna polymerase 3 requires a primer for replication
Why DNA polymerase 3 needs a primer to star replication.And whats happens when there is no AUG sequence on entire DNA.

You are confused among DNA replication, DNA transcrption, and RNA translation.
First, DNA replication happens during cell division, it create two exactly same daughter DNA.
Second, DNA transcription transcribes DNA sequence into RNA sequence, this RNA sequence may be used to synthesize protein, or RNA itself as signal, etc.
Third, RNA translation is the RNA sequence (codon) recognized by tRNA, and then synthesize protein sequence.
AUG is a codon in the RNA, the is recognized by tRNA, and then start translation. And please remember, DNA use A, G, C, T, but RNA use A, G, C, U, there is no U in DNA.
For DNA synthesis, why does it need primer? I have another answer for solving your question: https://biology.stackexchange.com/a/40954/17473

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text:
Why does agrose gel runs horizontally, and SDS-PAGE gel runs vertically?
It seems in electrophoresis, agrose gel always runs horizontally, and SDS-PAGE gel always runs vertically, why?

Be careful saying always, as in science you can rarely make an all-encompassing statement like that. Gels are traditionally run in those formats, but there are exceptions for a variety of reasons.

When you stand general agarose gel vertically, the gel is slippery coming out from the bottom; although, some run vertically.
To polymerize acrylamide, it is good idea to avoid air because oxygen inhibits polymerization of acrylamide. You would get an air tight condition, pouring acrylamide between glass plates, but how could you run gel made between glass plates. When you set such gel plates horizontally, how do you load samples? Then, it is easier to set gel plates vertically.

Yes, if you poured acrylamide into a horizontal slab mold it would take a very long time to polymerize, AND that top surface would dry out (unless you had a buffer layer on top of it, or plastic wrap, or similar).

Why does the agrose slippery out from the bottom if it runs vertically?

@sunboyharry Agarose does not adhere enough on glass plates to hold its position. I can not explain it via the physical and chemical properties, though.

Generally, one would want to run all the gels vertically to save the space. The gel slab has to either support itself or be enclosed in a supporting structure, like between glass plates. Simple agarose electrophoresis wouldn't benefit from enclosure into a precisely defined glass enclosure, and agarose is not strong enough to be run vertically - the slab will not support itself.
Thus PAGE gels are run vertically and agarose - horizontally.

To pour and run an agarose slab gel vertically the inner surface of the glass plates needs to be frosted (with microscopic imperfections).


text:
Why is Bcl2 a good target for cancer therapy?
Bcl2 is a family of proteins that are involved in the inhibition of apoptosis in cells. My question is that what makes this anti-apoptotic protein useful in cancer therapies as opposed to focusing on pro-apoptotic proteins? Are Bcl2 proteins simply easier to work with as opposed to the pro-apoptotic proteins? Or Bcl2 proteins have some sort of other characteristic that has allowed them for be the target for cancer therapies?

I don't have time for a full answer now, but the very quick explanation is that by inhibiting Bcl2 activity, you promote apoptosis. Bcl2 proteins are inhibitors, and by inhibiting the inhibitor you activate whatever process you're looking at.

Bcl2 is an anti-apoptosis protein, meaning that by inhibiting Bcl2 you will inhibit its anti-apoptotic effects. In other words, by inhibiting Bcl2 you actually induce apoptosis in cancer cells. This is one of those concepts in biology that can be hard to follow... that is, "by inhibiting an inhibitor you cause activation".
Cancer cells in particular seem to be resistant to the endogenous pathways in the cell leading to apoptosis, and the reasons for this phenomena are an area of active research. There are two major pathways of apoptosis within the cell, the extrinsic pathway the involves caspase proteins and the intrinsic pathway that involves Bcl2 and a number of other proteins associated with the mitochondria.
Bcl2 is part of a family of proteins that are involved in the intrinsic pathway of apoptosis - for a great and recent review see this recent review... or search on PubMed for a number of recent review articles.
Interestingly, cancer cells have a particular type of mitochondrial dysfunction that may be related to Bcl2, which is still incompletely understood. Cancer cells somehow inhibit the intrinsic apoptotic pathway, which involves the mitochondria. Additionally, cancer cells decrease aerobic metabolism by the mitochondria and preferentially use anaerobic metabolic processes instead - called the "Warburg Effect" by individuals in the metabolism and cancer fields. This was originally described by Otto Warburg almost 100 years ago - i.e. that cancer cells preferentially use anaerobic metabolism - but why this occurs is still unknown to present day.


text:
What causes fruit taste enhancement?
I'm not sure if this is a biology or chemistry question, maybe both? Some fruits, such as quince and quondong, taste of nothing when raw but have an extremely strong flavour when cooked. Why?

I am a little confused that does the word "cooked" means ripe？If yes, then the question will be easy to answer. Fruit has a kind of ripener, ethlyene. Ethlyene will help fructose break down and make up more glucose. That is why you may taste a strong flavour when fruit is cooked.

By cooking I mean literally heated with water in a saucepan. I'm not sure about glucose being the answer though. The 'flavour explosion' of cooked quince, in the mouth, seems to me to be far more than merely additional glucose.

So, when you cooked the quince (which means the quince got a higher temperature), the fructose would take a chemical reaction, polyreaction. And the fructose was transformed into amino acid. So you may taste sourer than before you cooked the quince. How do you think?


text:
Difference between PCR for linear template and a plasmid?
I believe PCR can be conducted both on a linear template and a plasmid, and I was wondering how these procedures differ in what enzymes are used, how the enzymes work on the template, primers used etc.

There's not much difference between them. The same enzyme and condition can be used whether the template is circular or linear.
You can amplify plasmids, but PCR intrinsically generates linear DNA fragments even if you use circular DNAs.


text:
Prader-Willi Syndrome and Angelman Syndrome?
On the website http://www.whatisepigenetics.com/fundamentals/2/ it states that

the imprint disorders Prader-Willi syndrome and Angelman syndrome, display an abnormal phenotype as a result of the absence of the paternal or maternal copy of a gene, respectively. In these imprint disorders, there is a genetic deletion in chromosome 15 in a majority of patients. The same gene on the corresponding chromosome cannot compensate for the deletion because it has been turned off by methylation, an epigenetic modification.  Genetic deletions inherited from the father result in Prader-Willi syndrome, and those inherited from the mother, Angelman syndrome.

To me it seems like this is suggesting the same problem in both Prader-Willi and Angelman sydrome- lack of expression of a particular gene. However in Prader-Willi syndrome it is the paternal chromosome that is missing and the maternal copy of this gene is silenced by methylation and the reverse applies for Angelman syndrome. Therefore it seems that in boh cases the problem is the lack of expression of this gene. Why, then, if both are caused by lack of expression of this gene, do these two illnesses have such different symptoms (constant hunger in Prader-Willi syndrome and mental disability and jerky movements in Angelman syndrome)?

I agree that one could read the passage and conclude that the authors are referring to the same " deletion in chromosome 15" but as @yingw explains in Prader-Willi Syndrome it is one region of Chr 15 and in Angelman Syndrome it is a different region of Chr 15.

In a wild-type human, you will inherit one paternal chromosome and one maternal chromosome, in this case, chromosome 15.
The paternal chromosome which is packaged into the sperm will be methylated in such a way that the Ubiqitin-Protein Ligase E3A (UBE3A) gene is silenced.
The maternal chromosome which is packaged into the oocyte will be methylated in such a way that the Small Nuclear Ribonucleoprotein Polypeptide N (SNRPN) and NECDIN (NDN) genes are silenced.
When the egg is fertilized, it has the paternal chromosome and the maternal chromosome, which complement each other (The same as a genetic complementation test would).
In a wild-time embryo, UBE3A is expressed off of the maternal chromosome, and SNRPN and NDN will be expressed from the paternal chromosome, and the wild-type phenotype will be rescued.
So in Prader-Willi Syndrome, at some point in time, the DNA that went into the male gamete sustained a deletion at 15q11, so the entire locus, with those three genes was lost. If that sperm then fertilizes an egg, the paternal chromosome no longer has SNRPN and NDN to rescue the wild-type phenotype. Because those genes are silenced on the maternal chromosome and deleted on the paternal chromosome, there is no allele available to express the relevant gene product. In effect, this embryo will be the equivalent of null/null for SNRPN and NDN.
Then in Angelman Syndrome, the opposite situation is in effect. The DNA that went into the female gamete sustained a deletion at 15q11, so the entire locus, with those three genes was lost. If that egg is fertilized, then the maternal chromosome will not be available to rescue the wild-type phenotype because the UBE3A is silenced on the paternal chromosome. In effect, this embryo will be the equivalent of null/null for UBE3A
So in effect Prader-Willi Syndrome is the phenotype for the SNRPN and NDN null/null mutant and Angelman Syndrome is the phenotype for the UBE3A null/null mutant.
Even though the genes are present on one of the alleles, the sex determined imprinting causes different genes to be silence, so that is why the same deletion is able to produce two different phenotypes, depending on which gamete that forms the embryo sustains the deletion.

Within that region, there are multiple genes.

Although the same gene may control imprinting for both disorders, the
  gene(s) causing their phenotypes differ. AS results from
  underexpression of a single gene, UBE3A, which codes for E6-AP, a
  protein that functions to transfer small ubiquitin molecules to
  certain target proteins, to enable their degradation. The genes
  responsible for PWS are not determined, although several maternally
  imprinted genes in 15q11-q13 are known. The most likely candidate is
  SNRPN

From this paper: http://www.ncbi.nlm.nih.gov/pubmed/11180221

Both Prader-Willi and Angelman syndrome can also occur as a result of having both members of the chromosome 15 pair derived from 1 parent, a condition known as uniparental disomy. Both can also result from a structural abnormality of the imprinting center, known as an imprinting mutation. In addition, Angelman syndrome can be caused by a mutation in the gene that causes it; a comparable cause is not present in Prader-Willi syndrome since it results from abnormality in more than 1 gene.
See details: https://thehealthbd.com/prader-willi-syndrome/

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text:
How much nucleoside triphosphate is required to form one peptide bond during protein synthesis?
I'm trying to find out how many molecules of nucleoside triphosphates (ATP, GTP, UTP and/or CTP) it takes to release enough energy to link two amino acid monomers together with a peptide bond, specifically during the process of mRNA translation.
I've tried to do some research online, but I could not find a reputable source that will say definitely how much energy is consumed in the process. The best answer I could find is formulated based on 'Molecular Biology of the Cell' 4th edition by Alberts B, Johnson A, Lewis J, et al., which is that at least one molecule of ATP is consumed for every peptide linkage. Is this correct?
I've also read on a science forum that the amount of ATP consumed during translation is different for every amino acid, but I could not find a reliable source to back up that claim. Is this true?

You might want to think a bit about the boundary of your question, which parts of the whole process do you want to include. Loading the tRNA uses ATP as well, do you want to include other aspects or just the peptide bond formation? I'm not sure if there's a single value here, as far as I remember there are also elongation factors and other proteins that require ATP/GTP for protein biosynthesis.

I'd agree with the explanation from Alberts et al from Molecular Biology of the Cell - it may see like a lot, but protein synthesis requires a TON of energy.

Duplicate of http://biology.stackexchange.com/questions/34783/atp-required-for-cell-processes

This is an old question, but as it has surfaced again I have cleaned up the title so it reflects the question better.

Although the question shows considerable effort to achieve clarity, the way it is phrased as:

How many molecules of nucleoside triphosphate… [does] it take to release enough energy

still allows ambiguity, as I would not really regard the NTPs involved in protein synthesis “releasing energy”. So let us consider two reformulations of the question, as the explanation of the answers is of more scientific interest than the actual answers.
1. How many molecules of NTP are hydrolysed in the reactions causing the formation of one peptide bond on the ribosome?

Answer = 3

Formation of each peptide bond involves a cycle consisting of the introduction of a single new aminoacyl-tRNA to the A site of a ribosome carrying a growing polypeptide chain (or initiator tRNA for the first peptide bond), the peptidyl transferase reaction, and than translocation of the extended peptidyl-tRNA from A- to P-site. (See, e.g. Berg et al. online — Ch. 29)
1 ATP is hydrolysed in the aminoacylation reaction:
                Amino Acid + tRNA + ATP → Aminoacyl-tRNA + AMP + PPi

1 GTP is hydrolysed in the aatRNA binding reaction catalysed by EF-Tu/EF1.
1 GTP is hydrolysed in the translocation reaction catalysed by EF-G/EF2
No NTP is consumed directly in the peptidyl transferase reaction — the energy for bond formation comes from the ‘activated’ aminoacyl-tRNA.

2. What is the total energetic cost in molecules of ATP for the formation of one peptide bond?
Here one might argue that:

Answer = 4+

The additional ATP occurs if one considers the total energetic cost of the aminoacylation reaction as 2 ATP, not 1 ATP. This arises from the fact that the ATP is hydrolysed to AMP (+PPi) and not ADP. Recycling of the AMP involves first the use of 1 molecule of ATP in the adenylate kinase reaction to produce ADP:
                                 ATP + AMP ⇄ 2ADP

followed by the energy (from membrane ATP synthase) to regenerate ATP from ADP:
                                 ADP + Pi ⇾ ATP

Why 4+? Certain amino acids (e.g. val and ile) are sufficiently similar to one another that the aminoacyl-tRNA synthetases have evolved a proof reading capacity, in which any incorrectly aminoacylated tRNA is hydrolysed. This only occurs for certain amino acids and at a rate that is difficult to determine, so the wastage of the ATP in this manner cannot be calculated precisely.

First, during the initiation of translation, a small ribosomal subunit binds to a molecule of mRNA. In a bacterial cell, the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon. An initiator tRNA, with the anticodon UAC, base-pairs with the start codon, AUG. This tRNA carries the amino acid methionine. And then, this process need one molecular GTP, and GTP--->GDP+Pi, which can provide energy for the assembly.
You can find more details in the book Campbell Biology, by Reece, Urry, et.al..

About 5 ATP molecules are required for the addition of a single amino aid to a growing peptide chain.
I found this answer in Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis by Piques et al.:

The addition of an amino acid to a growing peptide chain requires two ATP molecules for amino acid activation and another two ATP for peptide bond formation and ribosome translation, plus additional costs of about another ATP, for error correction and the synthesis of sequences that are removed during protein maturation.

This is plain wrong and phrased in meaningless terms, e.g. "peptide bond formation and ribosome translation". See the chapter on protein biosynthesis in any standard biochemistry text in the last 20 years.

Actually it depends on the question. Whether you mean to say: How many amino acids are required? Or proteins?
There is a characteristic difference between amino acids and proteins.
Hence the number. Of amino acids can be determined by the following-
If we consider a  protein composed of "n" number of amino acids,
it takes (4n)-1 number of ATP for the translation process.

You might want to add some reference to your answer. Just a simple answer without any citations wouldn't work.

4 ATP :
2 for activation amino acids to bind with specific tRNA.
1 for initiation
1 for elongation to push tRNA to the p site of ribosome

Please give some references and add some details for each step. A figure could really help clarify your answer.


text:
Why does HIV belong to a group of retroviruses called lentiviruses?
HIV is an enveloped retrovirus. Each virus particle contains two copies of an RNA genome. The virus also has a number of enzymes: reverse transcriptase, integrase and viral protease. But, once I also find that HIV also belongs to lentiviruses.
I am not very familiar with the relationship between retrovirus and lentiviruses. And does here have somebody know why HIV is a kind of lentivirus?

In Latin, lente means slow, so lentiviruses are retroviruses that are characterized by long periods of latency.

lentivirus A group of retroviruses that include human immunodeficiency virus, HIV-1. They cause disease after a long incubation period.
latency A state in which a virus infects a cell but does not replicate.

-Janeway's Immunobiolgy, 8th Edition, Kenneth M. Murphy
HIV-1 is characterized by long incubation periods. It can often take months before the virus is detectable on HIV tests.
It is also known that HIV reservoirs will exist in a patient, such that even if they have undetectable viral loads when on Antiretroviral Therapy, once they come off of the treatment, they will begin to produce virons again. The likely reason for that is that the immune cells that they infect can be very long lived, and as the viral genome has been incorporated into the host cells genomic DNA, it is incredibly stable. It will stay dormant for years until it is able to replicate again.

There're 6 genuses under the family"orthoretrovirinae": alpharetrovirus, betaretrovirus, gammaretrovirus, deltaretrovirus, epsilonretrovirus and lentivirus. So the question came down to the differences between lentiviruses and other retroviruses. Here are some major differences:
Lentiviruses have a cone shape capsid while other retroviruses have a icosahedral capsid.
Retroviruses share 3 common genes: gag, pol and env. While lentiviruses share 2 additional genes: tat and rev.
Lentiviruses have an overlap between gag and pol, and a gap between pol and env. While retroviruses have no overlap between gag and pol and an overlap between pol and env.
Retroviruses can only infect mitosis cells while lentiviruses are capable of infecting non dividing cells.
Pathogenesis of retroviruses and lentiviruses are also very different.


text:
What is enantiostasis?
I have searched around and read my textbook but I am failing to understand how enantiostasis is different to homeostasis. For reference, Wikipedia definition is as follows:

Enantiostasis is the ability of an open system, especially a living organism, to maintain and conserve its metabolic and physiological functions in response to variations in an unstable environment. Estuarine organisms typically undergo enantiostasis in order to survive with constantly changing salt concentrations.

http://www.hsc.csu.edu.au/biology/core/balance/9_2_3/923net.html towards the bottom of the page.

Welcome to Biology.SE. You are citing the wikipedia definition, not the Google definition

The Wikipedia page you're referring to more or less has the answer: "Enantiostasis is not a form of classical homeostasis, meaning "standing at a similar level," which focused on maintenance of internal body conditions such as pH, oxygen levels, and ion concentrations. Rather than maintaining homeostatic (stable ideal) conditions, enantiostasis involves maintaining only functionality in spite of external fluctuations"

Both are ways for an organism to adapt to the environment, but enantiostasis focuses on maintaining functionality while homeostasis focuses on maintaining a stable internal environment.
For example, if the organism has to deal with changing salt concentration in water, it can do it in two ways:

Homeostasis : the organism will adapt itself so that its internal conditions do not change despite the change in the external environment (the focus is on not changing these conditions). This could mean stopping or reducing other activities because of this adaptation, but, in this example, the internal conditions (salt concentration inside the organism) will not change.
Enantiostasis : the organism adapt itself so that its functionality is preserved, at the possible expanse of stable internal conditions. This could mean the salt concentration in the organism will change, but the organism's functions will not stop or be reduced because of it. Enantiostasis can be realized either by avoiding external changes (for example, absorbing more water when the salt concentration is high and less when it's low) or tolerating it with a wide range of possible conditions.

(Source : detailed explanation on this subject as a commentary on a university course)


text:
In DNA sequencing, is "mate pairs" synonymous with "paired ends"? If not, how do they differ?
By just looking at Roach et al's paper I get the impression that they are the same thing, and the Wikipedia URL for the former is a redirect to the latter.
However, I suspect they are not exactly the same - for starters, they wouldn't have two different words for the same thing, right?
Can anybody shed some light and suggest some references?
Thanks.

Paired-end is the name of the sequencing approach.
Mates refer to the read pairs that correspond to the same insert, but sequenced from opposite directions.


text:
In Sanger sequencing, why do we resort to cloning? Why doesn't PCR suffice?
I understand that in Sanger sequencing we can clone our fragments with the help of e.g. bacteria to make multiple copies of our fragments for further analysis.
I also understand cloning can be a bottleneck in Sanger sequencing - and partly prompted the development of NGS methods.
But doesn't PCR do just that, make multiple copies?
What am I missing?

Possible duplicate of Sequencing from PCR

@MarchHo: but... that question is not about Sanger :-|

In some cases, you do not know the sequence you are looking for--functional cloning, genome projects, cloning DNA/RNA binding to proteins you are interested in etc.

In addition, PCR can amplify any sequences having primer sequences at the both ends. Sometimes, you are not sure if you get a right sequence from crude DNA mixtures.

This is impossible to answer without knowing the context of what you are trying to sequence.  But as someone who has sequenced literally thousands of exons from genomic DNA, cloning is obviously not required for every single Sanger project.  I just used PCR to amplify the regions I cared about,.

You can use PCR products in Sanger sequencing; it is very common. Using PCR products instead of cloned genes does raise a set of problems that are less of a concern than with cloned sequences, such as the presence of incomplete or incorrect PCR products, but there are standard and simple solutions for most of these concerns.

And other minor issues like eventual need for cloning, possibility of using standardized sequencing primers post cloning (like T7) etc.

The error rate of PCR is still very high in comparison to natural bacteria DNA replication of its plasmids.
Natural bacteria DNA replication has an error rate of approximately 1 in 10 billion, and the best PCR polymerase commercially available (Q5 from NEB) has an error rate of approximately 1 in 1 million.
Therefore, cloning fragments into bacteria and sequencing the cloned plasmids ensures that you have the correct sequence for further downstream experiments, since the error rate of natural plasmid replication is far lower. With PCR, you are likely to have some errors introduced due to the higher error rates. This becomes more and more likely with increasing numbers of PCR cycles as well as increasing PCR amplicon lengths.
The fact that the PCR amplicon sequences correctly does not mean that DNA cloned from the PCR amplicon is correct. Therefore, if the PCR is intended for downstream experiments, it is best to sequence the cloned plasmid instead of the amplicon.
In addition, as WYSIWYG has pointed out in the comment, having the PCR amplicon cloned into a plasmid would also allow for the plasmid's regions flanking the cloning site to be used for sequencing. This allows standard sequencing primers on the plasmid to be used, instead of having to design new sequencing primers for each PCR amplicon.
Furthermore, since Sanger sequencing requires the primers to bind ~50-100bp upstream of the region to be sequenced, cloning the amplicon into a plasmid would also allow short amplicons to be sequenced in a single read, instead of requiring a forward and reverse read for sequencing a PCR amplicon.

This is not correct; or at least, it's only partly correct.  It's true that PCR has a much higher error rate than bacterial replication.  But that is not a major concern when sequencing pooled DNA from a PCR reaction, because while each amplified strand may have errors, the average of the amplification is still the original sequence, because only a tiny fraction of the strands have a specific error in a specific place.  However, if you first amplify the DNA with PCR, and then clone it and sequence it, you have the worst of both worlds, because you may well have errors in the piece you cloned.

@iayork While it is true that directly sequencing a PCR product is doable and is frequently done, the vast majority of cloning is done to transfer a piece of DNA into a vector for expression of some kind. If you sequence the PCR product before cloning it, you will need to sequence it again afterwards, since there is risk of the individual cloned fragment being incorrect. It makes more sense to sequence a known single clone instead. From what I know, PCR product sequencing is usually done either to check that the PCR has worked, or to sequence short stretches of DNA in long vectors.

I think you have a rather limited view of sequencing; I have been using PCR for sequencing purposes since 1992, and I am far from alone.  In any case, the original post wasn't asking how to clone, they were asking whether there was a technical reason for cloning with regard to Sanger sequencing.  There isn't one; sequencing from PCR gives highly accurate sequence, and your explanation of error rates is misleading.

@iayork I added a number of technical reasons for cloning. I would consider these to be good reasons to sequence a cloned plasmid instead of the PCR amplicon directly.

You have still not corrected your misleading comment about PCR error rates, though.

@iayork I don't consider the error rates misleading. The point is to show that PCR produces errors in a nontrivial proportion of amplicons, making it necessary to sequence a number of clones derived from the amplicon if you wish to obtain an error-free product for downstream experiments. Relevant to your own answer, one "standard and simple solution" to the issue of errors in PCR amplicons is to clone and sequence them.

Yeah, but you're missing the point.  Sequencing the PCR product doesn't show the errors.  It's only a problem if you want to clone the product.  The original question is whether you have to clone in order to sequence.  You're answer is saying "You have to clone because if you don't clone, then when you clone there are problems".  Seriously, this is very basic stuff.


text:
After doing brush I feel hungry?
Why I feel hungry after brushing my teeth in morning?
I usually have my dinner in between 9 to 10 at night and then I sleep at 12. Sometimes I wake up at 6 in morning and then I go to brush my teeth. After brushing my teeth I feel hungry. Why I feel hungry after brushing my teeth? And this hunger is gone even if I take few(about 5-10) biscuits.
Now one day I woke up at 6 am and then I have not brushed my teeth till 11 am and on this day I was not feeling hungry till 10 am.
So is there any chemical in toothpaste which triggers hunger? One thing which I can notice is that before doing brush there is saliva in mouth whereas just after doing brush there is no saliva or very less amount of saliva in mouth.
Even after chewing a gum for 30  min I feel the same hunger. So is there any relation between toothpaste and chewing gum?

Correlation does not imply causation. Furthermore, you have presented an anecdotal claim. Do you have any evidence this is a widely experienced event?

@Singh try to keep anecdotal experiences out of the questions - only if its a widely held belief or experience should you be asking the question

I think your daily pattern has made your brain associate brushing your teeth as a precursor of your breakfast. Skipping this step will confuse your brain into thinking it's not time for breakfast yet. Same goes for chewing gum, the toothpaste smell will trigger your brain's association of brushing teeth with the breakfast to come.

Sir I think you are right because when I was in school then my school timing was from 7 am to 12:30 pm but always I wake up at 6 am and after that I brush take bath then I get dressed and take my breakfast and then go to school. So the time in between my brushing and my breakfast is small and so I think you are correct. Thanks for your answer.


text:
Head transplant feasibility - Project HEAVEN-GEMINI
There is a news circulating that in the next two years, Dr. Sergio Canavero, of the Turin Advanced Neuromodulation Group (TANG) in Italy, will perform the world's first head transplantation. A procedure which will require

150 surgeons and nurses approximately 36 hours to complete

and after which the patient is held in coma during recovery

The recipient will be kept in a coma for around 3-4 weeks, says Dr. Canavero, during which time the spinal cord will be subject to electrical stimulation via implanted electrodes in order to boost the new nerve connections.

Is this even feasible? If it can be done, does that imply that humans can live for a long time, if they can find a compatible donor ? What requirements are there for compatibility?

Wouldn't that be a body transplant instead of a head transplant?

Well technically I guess so. But I doubt the body minds.

Related: http://skeptics.stackexchange.com/questions/20335/is-the-video-of-soviet-dog-revival-experiment-real/20337#20337

I have the impression that the MNT article is significantly over-stating the potential of this technique, at least with current technology. The mouse work by Xiaoping Ren (see this 2014 paper) seems to have a very steep death-curve post-surgery:

Forty Kunming mice and forty C57 wild type underwent the
  AHBR  procedure.  After  transplantation,  18  mice  survived
  for 3 h after the ventilator was disconnected.

There are no details in the paper about how long the most robust mouse survived for post-surgery. I would guess that it is not an impressive number, otherwise the authors would include it. Alternatively, the 18 surviving mice may have been euthanased after three hours - the paper does not make this clear, but it is common to have a predetermined time-limit for euthanasia in experiments where animals are expected to suffer from an irreversible treatment.

During these 3 h, the mice
  awakened and displayed normal cranial nerve function and
  characteristic responsiveness (blinking, whiskers moving, etc.).
  After the mice awoke, electroencephalogram (EEG) recordings
  were  made  directly  from  the  cortex  of  the  transplanted
  Cephalons (Figure 3). Because blood supply was maintained at
  an adequate level during surgery by anastomosing the donor
  and recipient carotid and jugular vessels, the intra- and post-
  operative EEG and ECG show electrophysiological activity.

This sounds a lot like a 'no' to 'can this technique be used to substantially extend human lifespans?', on current technology. If a human trial is approved, and is as successful as the mouse trials, the recipient will likely be dead within hours. If they survive for several hours, the level of motor control that can be expected in that time is likely restricted to unconscious motor tics (cf whisker twitching and blinking).


text:
How to best conserve a beetle inside a jar?
Few days ago a giant beetle appeared on my house. Well, it's dead now. Since it attracted some attention from my little girl, I'd like to preserve it inside some jar. What's the best way to do it? What products should I use?
I've researched a bit in the internet, and it's said not to use formaldehyde because the specimen would become too hard (that's not a problem to me, but I don't like using such strong products considering that a child will probably handle the jar).

The answer to this question depends on how you want to preserve it - as a pinned specimen (also dry preservation, most common) or in a liquid. If you want to pin it, placing it in a jar with a cottonball soaked with ethyl acetate (also used in killing jars) is good because it softens the muscles and makes the insect easier to pin and mount. Beetles are then usually pinned with a needle through the right elytra (wing cover), but there are also other ways to pin them. You can also glue the beetle to a piece of cardboard, which is then pinned. Gluing insects generally helps to protect them (so that legs and antennas dont fall of when handling them), but makes it more difficult to see the ventral side and it can also be cumbersome to have large glued beetles in a collection.
If you want to keep it in a liquid, 70-80% alcohol (ethanol) is a good choice, but not stronger (95% alcohol makes the insect stiff and brittle and might distort smaller insects). As you say, formaldehyde is generally not used since it's very toxic and it can also make the insect stiff.
Here are some more good tips on collecting and conserving insects from the University of Minnesota.


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Could drugs promoting angiogenesis be used as a treatment for burn victims?
From what I've learned from my textbooks and in class lecutures it seems that inducing angiogenesis for people with severe burns would be an excellent way to speed up the healing process. Is this already being done? If so or if not what are (if any) challenges that are presented to doctors and surgeons trying to use this self-healing method?

good question, interesting idea... obviously angiogenesis is necessary for skin grafts to grow to previously burned and debrided areas. It loos like angiogenesis is measured/quantified in research in this area, but I'm not aware of actual drugs/pharmaceuticals that act in this way directly.

A quick Google Scholar search yields a number of papers looking at this through a variety of angiogenic factors such as leptin, EPO, and dextran hydrogel scaffolds, mainly by topical application.


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Are non-coding RNAs introns?
I am slightly confused as to what part of the genome codes for non-coding RNAs. Is it the introns? This would make sense to me as to why they are not transcribed as the introns are not transcribed. Or is non-coding RNA actually exons which are simply not transcribed? If so, what are the introns actually for? I cannot seem to find a succinct answer to this. Wikipedia, for example, seems rather vague:

While introns do not encode protein products, they are integral to gene expression regulation. Some introns themselves encode functional RNAs through further processing after splicing to generate noncoding RNA molecules.[18] Alternative splicing is widely used to generate multiple proteins from a single gene. Furthermore, some introns play essential roles in a wide range of gene expression regulatory functions such as non-sense mediated decay[19] and mRNA export.[20]

In either case, does anyone also have any information as to why the ncRNA is not translated? What is the mechanism that prevents it from being translated? My guess is that, for some ncRNAs, it is a matter of them not being able to leave the nucleus as I understand many ncRNAs deal with post-transcriptional gene silencing, although tRNA and rRNA clearly do leave the nucleus...
I would be very grateful for any help about introns/exons/ncRNAs. Thank you :)

While Ankur's answer is correct, it must be noted that not all non-coding RNAs are introns.
An intron must be excised from an mRNA, which therefore means that any non-coding RNA that is not part of an mRNA cannot be an intron.
For example, rRNA and tRNA are all examples of non-coding RNAs that are not introns, since they are not part of mRNA. miRNA may in some instances be produced from introns, but when transcribed separately, they are not introns.
mRNA translation depends on many factors that bind to processed mRNA (a very long process). Other RNA do not undergo this process, and therefore are not reconised by ribosomes and are not translated.

You are correct. I would only say, as your answer is based on exact definitions, that for your third paragraph, it is probably more accurate to say not part of the precursor mRNA, as that implies that is the transcript that started from the TSS and includes all introns and exons prior to splicing.

A clarification on introns and exons.
While it is true that introns are not a part of the mRNA as March Ho said, they are essentially transcribed. This may seem trivial but it is important to note. So:

Both introns and exons arise from the transcribed region
Exons need not necessarily form the ORF (i.e. be translated to proteins)

Regarding intronic RNAs:
The community does not have a good definition of intronic RNAs. Most of these RNAs have been identified by sequencing and the sequencing experiment can only say which region of the genome a read maps to. It does not give any clue about how the RNA was produced.
So any read mapping to intron of another gene has been classified as intronic RNA which IMO is not fully correct. Only reads that truly arise from the intronic region of the nascent transcript (via RNA processing) are to be considered as intronic RNAs, and not merely based on their genomic overlap. Any independent transcript that overlaps with the intronic region is to be considered an overlapping gene. However, ascertaining the mechanism may not be that simple. miRNAs and some snoRNAs are known to be produced from processing of the intronic region.
A statement such as this (from the cited article [18] in your quotes):

Examining the data for intronic and exonic DNA from the human genome,
  piRNAs are significantly more likely than expected ($\chi^2_{1df}$ = 1353.2;
  P < 2.2 × 10−16) to reside in exons rather than introns, given that
  introns are on average, approximately 15 times larger than exons.
  […]
  we found 36 sequences with a perfect match to regions overlapping the
  exon–exon splice junctions of mRNA, suggesting that these piRNA are
  produced from mature mRNA.

may be misleading because it just talks about genomic overlap. Most piRNAs are synthesized as a long RNA that is exonucleolytically chopped from the 3' to yield the mature piRNA. Without further experimentation, making such a statement can be dangerous.

In either case, does anyone also have any information as to why the
  ncRNA is not translated? What is the mechanism that prevents it from
  being translated?

Apart from your reasoning on nuclear retention (many ncRNAs are cytoplasm-localized), there can be many other reasons, chiefly the absence of an intact ORF. Even if an ORF is present, translation initiation requires other features like Kozak consensus sequence etc. Having said that, some reads mapping to lncRNAs have been found to be associated with ribosomes (Guttman et al. 2013). Whether or not they translate is not really known.

Yup - in a lot of cases the transcription of non-coding RNAs is from introns. Some of them are within genes (intragenic) and others are intergenic (between genes). In humans, a large number of both have been documented http://www.nature.com/ng/journal/v47/n3/full/ng.3192.html
Coming to your question about why they are not transcribed - it again comes down to the same histone marks and promoters that regulate the transcription of coding genes; there is nothing fundamentally special about the transcription of ncRNA ; differences emerge later when mRNA is capped and polyadenylated, and therefore prone to less degradation.
Also, lots and lots of ncRNAs are transcribed , but are less abundant. Some of the interesting roles they play include interacting with chromatin modifying enzymes, regulating DNA methylation along with the traditionally known functions involving gene silencing by antisense transcripts or miRNA-driven suppression of expression.

Independent transcripts overlapping with intronic region of another RNA cannot be in true sense considered an intronic product. They are just called overlapping transcripts. The ncRNA has to come out of processing of an intron to be called an intronic RNA.

There is evidence for introns themselves giving rise to ncRNA though; not just in the sense of overlapping transcripts. http://www.sciencedirect.com/science/article/pii/S0888754308003042

Yes I agree but in many cases an overlapping transcript has also been called as intronic RNA and I just wanted to clarify on that point.


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How much energy would it cost to synthesize all cholesterol requirements de novo?
Imagine a scenario in which some person is unable to absorb any dietary cholesterol because of some intestinal mutation (for example). Thus, they have no cholesterol available from their diet for steroid hormone synthesis, bile acid synthesis, or any other process that requires cholesterol.
If that person had to synthesize all of their cholesterol requirements de novo (i.e. from acetyl-CoA), how much energy would that require on a daily basis? In biochemistry we talk about de novo cholesterol synthesis, but a lot of the time it is glanced over because it would be so energetically unfavorable to synthesize it when you can get it from your diet.
I'm curious to know... if we could somehow inhibit all cholesterol absorption and forced the body to make all its own cholesterol, then how much excess energy could we burn? Could we use that as a weight loss therapy?

You can easily figure this out by (1) counting up the stoichiometry of the cholesterol synthesis pathway and (2) multiplying by the amount of cholesterol lost each day by an average person.

@Roland how much cholesterol is lost each day by an "average person"? Are you sure that's fairly constant across adults?

@Roland I think the problem is trying to estimate the daily losses of cholesterol from conversion to "other substances" within the body - i.e. bile acids, steroid hormones, etc. I'm not sure how or what those estimates would be and if they would differ significantly between adults.

It's gonna be a ballpark estimate of course, as always with whole-body metabolism. This paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC297311 puts the loss of cholesterol at about 1g / day. Since cholesterol is not catabolized in the body, it should be a pretty good estimate of total cholesterol turnover. I think modifications like bile acid conjugation etc are minor in comparison to loss of the entire sterol backbone. Of course, you will see some variation between individuals, diets, etc.

@Roland that's a nice paper - the biggest sink for cholesterol is bile acid synthesis - of which the bile acid pool loses ~5% everyday - I will try to crunch some numbers and figure out an answer - thanks!

https://en.wikipedia.org/wiki/Mevalonate_pathway. Then it is Farnesyl pyrophosphate → squalene → oxidosqualene → lanosterol (http://www.genome.jp/kegg-bin/show_pathway?map00100)

Great, let us know what you come up with! Also, consider that the acetyl-CoA generated by sterol syntheis is a metabolic cost as well, as it could otherwise have been used to generate ATP.


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Question regarding research project on indigenous ants during Eastern European winter
I am by no means biologist (I'm a programmer), but I want to make an experiment that involve the participation of ants. So please excuse my ignorance on the subject and my potentially uninformed questions.
I need to find some ants, but it's fall/winter here in Eastern Europe, so it seems that I won't be able to find in the wild. So my questions are:

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

If that is enough for you, you can actually buy complete ant farms.

Do you have any specific reason for using a wild species? If not, you would have better using a lab lineage (or any ant farm). Breeding a wild species by yourself might be very tricky.
Taking care of an ant colony might not be as easy as you may expect. Your best chance is to target a species of interest based on past studies and visit a lab that is breeding this specific species.


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From STRUCTURE to FSTAT format
From numerical simulations I output a file that is input to STRUCTURE (Hubisz et al. 2009). I now realize that I would need to process my data with FSTAT (Goudet 1995). Both are text files.
Is there an extant algorithm that would reformat a file that is input to STRUCTURE into a .fstat format?

What kind of files are these? If they are text files then reformatting would be easy; in that case this question would be off topic.

Yes these are .txt files. My question is very specific to data format used in bioinformatics though and I am not asking for help to build my own algorithm to reformat but am asking for extant algorithm that would do the job. Does it make my question off-topic?

PGDSpider will do the trick.
PGDSpider is able to parse 31 and to write 35 different file formats including STRUCTURE and .fstat.


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Are there differences in energy of glucose isomers?
There are many isomers of glucose, including galactose and fructose. Do they have different chemical energy levels, and why? What makes galactose and fructose useful compared to glucose, and would they be more or less energy efficient at storing energy?
Basically, can isomers have more or less chemical energy than others?

The common hexoses do not differ much in energy content (meaning Gibb's energy of formation, $\Delta_f G$). But they have different structures and chemical properties. Glucose and galactose are aldehydes when present in linear form (they are tautomers), while fructose is a ketone, which gives somewhat different properties. They are also used in different macromolecules and other metabolic products. For example, galactose is a component of hemicellulose in plants, while glucose is used for glycoproteins in humans.
Glucose has evolved to be the main blood sugar in vertebrate animals, and other sugars from the diet are quickly converted into glucose. This arrangement is useful as it provides a "common currency" of carbohydrates that can be exchanged between cells of the body, and reduces the number of enzymes needed in central metabolism. The conversion of fructose and galactose into glucose has a small biochemical cost, so in this sense, these sugars afford slightly less energy to human cells than glucose. But again this is not because of an inherent difference in energy content, but rather due to how the metabolic network is structured, with glucose as a "central", preferred metabolite.
In general, though, isomers of chemical compounds can have different energy levels, because some configuration are more energetically favorable than others. The classic example is the difference between the trioses glyceraldehyde/dihydroxyacetone and their isomer lactate, which differ enough in energy to support the synthesis of 2 ATP in lower glycolysis.


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Is the problem of cryonics only the pressure?
According to the pop-sci sources which I drew on from, the only problem with freezing whole bodies its that you can't conserve it without freeze-damage.
If you were keeping a cold-blooded animal in a cold surrounding (well, before that removed the parasites somehow) and optimized the pressure in there so to make the cells not to collapse, could you stop all its functions and bring it back to life again later?

Lobsters sometimes wake up after being frozen alive...

@vervet wow...that seems like the problems are mostly about the parasites contained in water (that you should just drain out) - I really do not know anything about lobsters, but compared to other animals the main difference is outter skeleton (it could work as an antiinfective protective cover)...is it so?

"The parasites contained in water"? Could you elaborate? (I suspect part of the reason lobsters have an easier time is their semi-open circulatory systems. Lobsters can't die of internal bleeding.)

@Resonating Interesting indeed, I will look at that. About the parasites: Easier forms of life often survive harder conditions. But originally I wrote it because I said to myself that food in the fridge rot as well, but slower - that's not true for negative temperatures.

The major problem in cryonics is that when an organism is frozen, all of the organism starts freezing. The cell start expanding since ice expands too. The sharp edges of the ice crystals can destroy a lot. Also, your blood would freeze. Again, the sharp edges of the ice crystals would destroy major blood vessels. That is why currently, they have to insert antifreeze into the blood, but it still might not be effective.
Now, to answer your question, many cold-blooded organisms can survive freezing cold temperatures. Some frogs (like the wood frog), for example, have anti-freeze in their blood vessels! So some actually have special adaptations to survive freezing cold temperatures.
I hope this answered your question. Please ask in the comments if you want more information on this. I will gladly research up for you.

Thanks, that's about how I had imagined it. So is it so we really can handle all the other problems nowadays? And about the cold-blodded - they have some kind of salt to keep the blood liquid in colder temperatures, haven't they? (conifers and embryonal-cryonics definitely uses this technique)

@Probably yes,you are correct. Remember, if you like my answer, you can accept it


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Blosum matrix computation with X%
Why does the answers to the problem found in the referenced pdf, differ from my calculation below? I am trying to understand the math from this pdf from an online tutorial I am reading and my own math does not give the same result: Can someone help derive their answer or confirm mine?
http://www.cs.columbia.edu/4761/assignments/assignment1/reference1.pdf
On page 13, I am trying to figure out how the weighted values are determined:
For example C_LL: 2.33 means the construct is [L_1   (L_2a L_2b)  L] and the center block is being counted as 1/3 for each so we get 4*(1/3) + 1 = 2.33 but the L_2a to L_2b i.e., the inside the block is not counted that should make it 2.66 right?
For C_LV: here there is obviously 4*1/3+1 and now the internal would be 2*1/3 which sums to 3 not 3.33. And now the internal one is counted.
I am confused. Any help?


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What is the proper way to dispose of a medicinal substance?
Is there a protocol or a set of guidelines to safely dispose off a batch of expired drugs (as a manufacturer)? I guess the process may vary for different drugs. My specific question regarding the safe disposal of expired amlodipine; which is better — incineration or landfill or any other technique?

Usually you would return to the pharmacy of purchase for safe denaturing

@RoryM OP is asking from a manufacturer's point of view.

Chemically inactivating the drug (in a safe manner) is probably best - bleach, peroxide, other reactants that can themselves then be neutralized.


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Coefficient of Inbreeding - implementation issue
The formula for the coefficient of inbreeding is as follows...

I have a family tree going back 9 generations. Say I find a common ancestor X in the 4th generation on the mothers side and in the 5th generation on the fathers side. I can work out that constituent of F... but what do I do about all the ancestors of X (they will all also be common ancestors). Do I also work out their values and add them to F?... or do I ignore them? The descriptions of the COI I have seen do not make this clear.

The $F_i$ term is the term that accounts for inbreeding of your common ancestor X. If that common ancestor is not inbred then the term is 0 and the calculation is a little easier. Using the example you have given:
 X ─┬─ Y
    │
 ┌──┴──┐
GGGF  GGM
 │     │
GGF    │
 │    GM
GF     │
 │     │
 F ─┬─ M
    │
   Mick

In this case, the common ancestors are not inbred so the $F_i$ terms go away ($1+F_i = 1$). There are two paths of common ancestry (via X and Y), therefore the calculation of the two paths from the father (F) and mother (M) to X and Y is:
$F_{Mick} = \frac12^{n_{F,X}+n_{M,X}+1}(1+F_X)+\frac12^{n_{F,Y}+n_{M,Y}+1}(1+F_Y) $
$F_{Mick} = \frac12^{4+3+1}(1+0)+\frac12^{4+3+1}(1+0) $
$F_{Mick} = \frac{1}{256} + \frac{1}{256} = 0.0078 = 0.78\% $

In a more complex case, such as where ancestor X was inbred, $F_i$ cannot be ignored. In the following example, X's parents were first cousins:
  U ─┬─ V
     │
  ┌──┴──┐
 XGF   XGM
  │     |
  XF─┬─XM
     │
     X ─┬─ Y
        │
     ┌──┴──┐
    GGGF  GGM
     │     │
    GGF    │
     │    GM
    GF     │
     │     │
     F ─┬─ M
        │
       Mick

For this, we must first calculate $F_X$ (i.e. how inbred X is):
$F_X = \frac12^{n_{XF,U}+n_{XM,U}+1}(1+F_U)+\frac12^{n_{XF,V}+n_{XM,V}+1}(1+F_V) $
$F_X = \frac12^{2+2+1}(1+0)+\frac12^{2+2+1}(1+0)$
$F_X = \frac{1}{32} + \frac{1}{32} = 0.0625 = 6.25\% $
Then we can input this $F_X$ into the same calculation as done before for the simple case:
$F_{Mick} = \frac12^{n_{F,X}+n_{M,X}+1}(1+F_X)+\frac12^{n_{F,Y}+n_{M,Y}+1}(1+F_Y) $
$F_{Mick} = \frac12^{4+3+1}(1+0.0625)+\frac12^{4+3+1}(1+0)$
$F_{Mick} = 0.00415 + \frac{1}{256} = 0.0081 = 0.81\% $

A good explanation of these calculations with further examples can be found here: The Coefficient of Inbreeding (F) and its applications. The calculations can get quite complicated even with relatively simple inbreeding.

Thank you for your explanation - but I still don't think you've answered my question. Say we are considering child C and we find a common ancestor A in the family tree of both the mother and father of C. Let us say for simplicity that A is not itself inbred. I know how to calculate all the terms to the right of the sigma in the COI equation for A, so I can add that to the summation... but what about the mother (or father) of A? That will be a common ancestor too. Do I work out everything to the right of the sigma for that too and add that to our summation?

@Mick No, if A is not inbred, then you do not need to add anything for the mother or father of A (because the inbreeding coefficient for A is 0). This is what the first simple example in my answer illustrates (neither X nor Y are inbred).

Ok, I see. I will assume you are correct and give you the green tick. Thank you.


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Fur genetics - what are the causes of fur colour decision?
This Australian Shepherd puppy's father is a black-tri; mother is a blue merle. What would cause this dog to have so much white color?

Are there any general explanations as to why this might happen in nature? Other examples of this kind would also be greatly appreciated.

One of the reasons can be related to the migration of the neural crest cells that give rise to the pigmented cells. Many genes are involved in this process.


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Are gametes determined by the sex of an organism?
In the Wikipedia article for biological sex, I read the following sentence.

"The gametes produced by an organism are determined by its sex:..."

However, is it not through the gametes produced by an organism that "sex" is defined? Should this sentence be the other way around?

Please clarify, do you mean the type of gametes produced (i.e. eggs and sperm) are determined by the sex?

related: What's the difference between male and female?

Short version of the above link; sex is often determined by chomosomal makeup, but it can also be determined by other factors (e.g. environmental cues or sequential hermaphroditism). Sexes are defined in terms of Anisogamy (different-sized gametes).

The gametes produced by an organism are determined by the organism's sex - Thus, that statement from Wikipedia appears correct to me. In the case of humans, males have two different sex chromosomes. Thus, males produce gametes with either a Y-chromosome or an X-chromosome (XY). Female humans also have two sex chromosomes, but they are two different X chromosomes (XX). Thus, when females produce gametes they have a single copy of one of the X chromosomes in each gamete. In most cases, a fertilized embryo results and is either XX or XY - in the case of males the embryo gets the Y from Dad and the other sex chromosome is one of the two X's from Mom. In the case of a female the embryo gets the X chromosome from Dad and one of the two X's from Mom.

Here is an image describing what I said above with a link to the page to read more:

Here is a link from a basic genetics course from Dr. Young in the UK that has a more in-depth explanation.
Here is a link to another article from Nature Education that help explain how this works in humans as well as some other organisms that are slightly different.

No. You are confused. There are different types of chromosomal sex determination. If one sex is heterogametic (an example of one system like this are mammals, which have an X and a Y chromosome) then the sexual phenotype (male versus female) is determined by the presence (or absence) of the Y chromosome. If you have a Y you will develop testes,and the androgens produced by the testes will direct all of your secondary sexual characteristics to develop the male fates.
In the absence of a Y chromosome the default developmental pathway of the somatic gonads is to form ovaries. The ovaries produce estrogen which will direct all of your secondary sexual
characteristics to develop female fates.
Gametes are either sperm or eggs.  Early after fertilization some of the embryonic cells get sequestered away to form the primordial germ cells (PGCs). Later on these cells will mature in the somatic gonad to form the germline, giving rise to more sperm (or eggs).  These germline cells have no effect on the sex or gender of a mammal.  In some animals (like model organisms that can be subjected to genetic screens) you can isolate sexually transformed mutants where, for example  the XX animals develop as males and produce sperm, and the XY animals develop as females and produce oocytes.  There are other possible mutant situations as well where the male sex produces oocytes,  and the female sex produces sperm.

you're interpreting the question differently - the sex of the organism determines the gametes - males produce haploid sperm with either an X or Y sex chromosome, females produce ova that have one of two of the X chromosomes. I agree with you though - the way the sex is determined is not by the necessary presence of a particular chromosome though.

It looks like we need clarification from the person asking the question

In mammals carrying a strong loss-of-function mutation in the TDF (testis determining factor) gene, which is the only gene directly required for sex determination on the Y chromosome, both the XX and the XY individuals develop as fertile females. No TDF = no testes, no testes = no androgens, no androgens = default female developmental pathway. This shows that the Y is necessary for male fates. IF: you create an XX transgenic mouse carrying the TDF gene, THEN: it will develop as a fertile XX male. This shows that TDF (SRY or sry) is sufficient for male fates.

I agree with you - though the most common condition is that the sex of the organism determines the gametes – you're talking about a very rare type of anomaly - how rare is a strong loss of function mutation in the TDF?

We may me be addressing different sections of the original poster's query. I do not object to the edited title. My comments are replying to the body of the question: ". . . is it not through the gametes produced by an organism that 'sex' is defined?" To this I posted an answer that starts "No. You are confused." My gametes in no way influence or affect my sex or gender. The primary signals for mammalian sex determination are, as far as I know, chromosomal. It is the zygotic chromosomes that dictate and control the development of the embryos somatic and germline sex.


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importance of cDNA sequencing of a specific gene in different plants
i want to know what if i made a sequence of cDNA of a specific gene in different plants - what is the important from the sequence and can if found difference between plants , and can i use this sequence to determine cis regulating element

No, cDNAs are copies of spliced mRNAs, and typically contain a 5'-UTR (untranslated region), an open reading frame, or ORF, and a 3'-UTR.
The cis-regulatory information might be revealed by sequencing the genomic DNA upstream of the gene(s).  That is where one usually finds the promoter (although there are some rare exceptions, particularly for genes transcribed by RNA polymerase III).

ok , thanks alot however, how can i obtain the sequence of promoter of a specific gene with a simple method ( only primer and PCR)

The importance of sequencing
Sequence comparison is important because biologists tend to use prior knowledge to make inferences about the function of unknown entities.
Determing flanking sequences
You can use Genome Walking to isolate flanking regions of known sequences. It's a simple repetitive method. The amount of repeats will depend on how far you want to go upstream or downstream of your gene of interest.

One point is cDNA sequence encoding a specific protei, you will find differences in the coding sequence bewtween plants of different species and, within the same species, difference when you compare the genotypes
for promoter analysis you must use the genomic DNA, at leasst 1 kb upstream the ATG, or more (may be there are introns)


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Gel Electrophoresis
we add Etbr within the agarose gel but we do not add Etbr directly in native PAGE ?when we make agarose gel, we add Etbr before its solidification but we do not add Etbr when the native PAGE gel is in liquid form, why ?

The fact that EtBr is a potent mutagen is why it is not commonly used in liuquid solutions as it is hazardous. So this way it's in liuquid form for the least amount of time resulting in less human exposure.

Perhaps EtBr inhibits the polymerization reaction (by absorbing, or quenching, the free radicals required to initiate the reaction)? That is just a guess. While some people prefer to stain, and then destain the gel afterwards, since the EtBr is positively charged you can just add some to the running buffer in the anode chamber and the dye will enter the gel.

In the long PAGE runs, EtBr will run out of the gel.

Actually, my friend added EtBr to acrylamide solution and polymerized it. It was polymerized. In addition DNA was detectable. One of potential problems could be migration of EtBr opposite DNA. You could not detect DNA the bottom of gel unless you supply EtBr. And I guess a slight difference between gel and running buffer may cause shift of migration speed at the boundary. Because resolution in PAGE is higher than agarose, shift of migration speed might be problematic.


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How does membrane potential vary between intraceullar membranes and the cellular membrane?
Question
Does each type of membrane have a different membrane potential? I'm especially interested in answers that can cite academic papers that have attempted to measure membrane potentials.
Discussion
I've asked about the composition of membranes before , and although I recieved some information, I didn't get all the information I was after. This isn't a problem with our community but rather with the field at large: the popular thinking is membranes are membranes are membranes (mostly due to the difficulties in studying membrane biophysics experimentally).
This is how wikipedia defines membrane potential:

Membrane potential (also transmembrane potential or membrane voltage)
is the difference in electric potential between the interior and the
exterior of a biological cell. - Wikipedia

This isn't strictly true. Intracellular membranes also have membrane potentials as one can imagine, and there is some unverified information regarding compartmental pH values. This is why I am interested to find out if there have been studies attempting to quantify this across the cell membrane, and across different subcellular membranes.

Yes, various intracellular membranes do have potential differences, but as you can imagine they are more difficult to measure experimentally, so in general data on this is scarce.
Summary

Mitochondrial membrane: 150mV-180mV with negativity on the matrix side. Seth et al 2011
Endoplasmic reticulum membrane: 75-95mV with negativity in the ER. Qin et al 2011, Worley et al 1994
Golgi: No notable membrane potential. Schapiro & Grinstein 2000
Lysosomal: 20mV with more negativity on the cytosolic side. Koivusalo et al 2011

Discussion
The mitochondrial membrane potential is probably the best studied case. This is the potential difference over the inner mitochondrial membrane, between the mitochondrial matrix and the intermembrane space; it is about 150mV (more negative on the matrix side). There is also a potential difference between the mitochondrial cristae (folds of the inner membrane) and the matrix which is used to drive ATP synthesis; it is probably larger than 150mV, but this is still poorly understood I think. The outer membrane is permeable (has pores) so there should be no potential difference between the intermembrane space and the cytosol.
For the endoplasmic reticulum (ER), there is little data available I think, but there are some estimates based on measurements of ion transport, which gives a value of about 75 to 95 mV (more negative inside the ER). Probably this depends a lot on the situation, as the ER is involved in regulating ion homeostasis (notably Ca2+).
For the Golgi apparatus, this study found that no potential difference vs. the cytosol, based on the movements on H+ and counterions.
Lysosomal membrane potential has been measured directly, giving values of about 20mV (more positive inside).
For the nucleus I don't know of any data, but I would assume there is no potential difference here, given that the nuclear membrane has large pores.

Add plasma membrane? This will be most variable amongst all membranes.


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Do findings on promoter methylation of the serotonin transporter gene and amygdala activity contradict the established view of serotonergic function?
In this article http://www.nature.com/neuro/journal/v17/n9/full/nn.3778.html it states that

Increased promoter methylation of the serotonin transporter gene predicted increased threat related amygdala activity.

I'm finding this somewhat difficult to understand. Increased promoter methylation would imply that the serotonin transporter gene is less expressed, so less serotonin is taken up by the presynaptic neuron, leading to increased serotonin levels in the synaptic cleft. Surely the increased serotonin levels would lead to decreased amygdala response to threat? After all, selective serotonin reputable inhibitors (SSRIs) are used to treat anxiety disorders and depression by reducing uptake of serotonin and increasing serotonin levels as well. It seems like these two are suggesting two contrasting effects for the same cause?
I would be grateful if someone could point out where I have misunderstood. Thank you in advance :)

I don't think there is an obvious contradiction here.
(1) Mapping neuronal function to the perception of threat (or emotions in general) is often advertised as well-understood, but in fact it is not. Serotonin-concentration-based models (such as the monoaminergic theory of depression) are unavoidably imprecise because ”the brain is not soup”. Additionally, it is also impossible with current technology to measure actual serotonergic signalling in vivo with whole-brain comparability (though progress is being made, e.g. via: fMRI contrast-agents and stimulus-evoked opto-fMRI for monoaminergic systems).
(2) Numerous pharmacological interventions which increase signalling at the serotonergic synapse have been documented to cause widely varying effects (compare e.g. monoamine reuptake inhibitors, monoamine release agents, and monoamine receptor agonists). While selective serotonin reuptake inhibitors (SSRIs), such as fluoxetine and citalopram, are commonly reported to decrease anxiety, serotonin receptor agonists, such as LSD, are reported to induce acute anxiety (though interestingly small numbers of LSD administrations, in conjunction with psychotherapy, have also been reported to reduce anxiety in the long term).
The conclusions thus far would be: (1) we can't be entirely sure about how serotonin mediates or counterbalances anxiety (2) but the specific kinetics of activity at the serotonergic synapse seem to be just as relevant as the actual amount of signalling. You may think, however, that the effects of SSRIs are kinetically similar to reduced expression of the serotonin transporter, SERT. This is however not the case, as under SSRI treatment it is generally believed that chronic downregulation of 5-HT1A inhibitory autoreceptors is responsible for the therapeutic effect, rather than the acute increase of serotonin concentration in the synaptic cleft (this being in line with the fact that therapeutic SSRI effects are observed chronically rather than acutely). Further evidence corroborating the notion that constitutively reduced expression of the serotonin transporter increases anxiety can be found from studies on the 5-HTTLPR polymorphism. In these studies the short version of the allele, which leads to reduced expression of SERT, has also been reported (though afaik this effect is not very robust) to correlate with increased activity in the amygdala.

Excellent answer. To emphasize an important point that the OP may have missed, improvement of anxious/depressed symptoms don't occur until weeks after starting an SSRI (corresponding to the chronic effect of SSRIs). Serotonin levels in the synaptic cleft only increase in the short term (the acute effect). By the time you see symptom improvement, serotonin levels are no longer elevated. This is fairly complicated, and often glossed over, suggesting SSRIs work because of a simpler, but incorrect 'depression = not enough serotonin' mechanism.

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Pathogenesis of type IV hypersensitivity
In hypersensitivity, as I understand it, a normal immune response gets excessive, misdirected or wrongly regulated to cause tissue injury. The various types determine the various ways in which the tissue-causing responses are effected, at all times the ultimate cause being either excessive response (the normal amount being harmless), misdirection or wrong reglation. Hence, the ultimate cause beneath all hypersensitivities is some factor which just unleashes the immune machinery on normal tissues.
With this in mind, as Type IV Hypersensitivity is typically described under the headings of a granulomatous reaction, DTH (Delayed type hypersensitivity) or a contact dermatitis type response, involves the stimulation of $T_{h1}$ and $T_{h17}$ subsets of $T$ cells (along with $\text{CD8+}$ cells). What I fail to understand is that,
What goes wrong along the normal T-cell effector pathway to ultimately cause the injury?
(In type I, it is the IgE arsenal release on parasite mimicking allergen, in type II it is the self-antigen directed or hapten mediated self-tissue direction of Ab, and in type III it is the precipitation of immune complexes owing to the overburdening of the Ag-Ab response due to continued influx of Ag which cause the problem)
The events of stimulation, cytokine release and macrophage proliferation and activation is exactly what you would expect to be, in case the cells are doing what we want them to, to ward off a normal invader. But it ends up damaging the tissues.
Moreover, a lot of books say some variant of

"DTH is necessary to fight some specific pathogens"

Since hypersensitivity, (and hence DTH) by definition is immune-mediated tissue injury, do they mean that this tissue injury is indispensable in the fight against these pathogens (in which case, is worrying about DTH necessary?) or that the normal unaltered form of the pathway of immune response (the altered form of which results in DTH) is necessary for the fight (in which case there is a minor semantic error in the quoted statement)?

In some cases where your hypersensitivity reaction is due to autoreactivity it's cause for alarm. In other cases, though, nothing is going wrong with the development of the T cell response except for some reason they can't clear the infection in a reasonable amount of time or effort. The situation escalates as more effector cells are recruited, producing more and more cytokines/TNF-α/etc. as a part of their normal response. In fact, you end up with chronic DTH reactions when phagocytes uptake microbes but fail to get rid of them, such as Mycobacterium spp. that prevent lysophagosome formation.

@Kendall So, the tissue injury is just the result of a prolonged activation of the immune mechanisms or of pathogen-mediated misdirection of the system? Thanks. Can you also shed light on the questions following "Moreover, a lot of books....."

It's not 100% misdirection; while the pathogen remains the immune system is getting signalled "We need to clear this infection." So it's the normal response, just over an abnormal period of time and circumstance. I tried to answer that last part w/ the Mycobacterium spp. example. They infiltrate cells and are difficult to clear, so the DHT is actually an attempt to clear out the microbes by scuttling the infected tissue.


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Why does histamine release in Type I hypersensitivity help in case of parasites?
The IgE system exists because the same events which lead to often-life threatening complications of allergy, in presence of parasites are helpful in their elimination.
The tissue injury mediated via this hypersensitivity (type I) occurs due to the mediators released by mast cell degranulation due to IgE being synthesised in atopic individuals towards normal environmental particles. The effects are also due to further immune cells being recruited by the mediators. In case of parasites, this IgE is supposed to help in their elimination and not cause tissue injury, justifying its evolution as a defence mechanism.
How does this happen? If release of the mediators is a part of the pathway, even if the degranulation is localised in the vicinity of the
 parasite, the mediators will spread systemically or atleast in the
 nearby tissues with the same consequences as in the case of
 non-parasite activation of these events.
What then is the ultimate cause beneath there being tissue injury if the stimulation is unintended but there being none when the stimulation is directed and intended? Or is there some injury in the latter case also, in which case the classification of this response in absence of a parasite into hypersensitivity i only because there is no positive effect in this case, while there was some benefit accompanying the deleterious effects in the former case? Is the presence of a parasite and possible localised degranulation the only difference between these cases?

I think it does help in case of the intestinal parasites. By purging them out. I am not too sure about it though.

IgEs are generated by B-cells as a result of activation and antigen presentation. They associate with Fc receptors of mast cells and it is only when IgE is bound to antigen that the degranulation can occur . In the case of parasites, the antigen on the parasite would have generated those specific IgEs. It is the specific binding of the IgE to the surface of the parasite that causes the Mast cell to degranulate directly onto the parasite. There may be some diffusion, but most will find its target. In allergy, IgEs are produced against harmless compounds and mast cells respond in appropriately.

Also is your BlockQuote a direct quote, in which case, can you provide the citation, or is it to highlight your question, it which case you should probably just use Bold Text?

@AMR Can you elaborate on "Find its target". Is not the effect of these mediators on vasculature and musculature the part of their anti-parasite effect?

To answer the title: Histamine has a host of beneficial effects that assist the body in inhibiting and expelling parasites. Consider a parasite that's been ingested: (1) Histamine increases gastric H+ production, (2) promotes peristalsis, mucus production and vasodilation in the intestine. This causes bowel movements, diarrhea, and the mucus is a defense from the parasite. Of course, things tend to go overboard and mass degranulation does cause a lot of damage, but objectively the parasite is removed. The injury is largely unintended, or collateral damage.

it is just in terms of the fact that the Fab region of IgE's will attach to its epitope on the surface of the parasite while the Fc region associates with receptors on the surface of the mast cell, so the distance between the two will simply be the size of the complex. Degranulation will occur in that space and for the most part not much should diffuse away. This doesn't guarantee inappropriate response however. It is different when than when the IgE epitope is a soluble molecule that can trigger degranulation into the interstitial fluid where the target then becomes the hosts own cells.

@Kendall So, what you say is, this kind of degranulation injury is there also in case of parasite-removal, but then the condition is not considered hypersensitivity, since the damage is only a collateral of a positive effect. In case of wrongful stimulation, it is called hypersensitivity, since the deleterious effect is unnecessary? According to AMR, the anti parasite effect is due to histamine acting on the parasite and not on the somatic cells. Also, can you add a reference. Thanks anyways.

Hypersensitivity in itself is confounding of normal immune mechanisms. IgE and the like are extremely beneficial and specific when combatting helminthic infections (i.e. the Th2 immune response). What's weird is that some allergens have homology to helminthic proteins, and unlike helminths (broadly), allergens can be soluble and systemic (interesting read), hence allergic hypersensitivity. Against a helminth infection, we wouldn't consider it hypersensitivity as long as everything is responding normally.


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metabolic heat generation and exercise intensity
Is there a relationship between bio heat equation (found here) and exercise intensity as described here
That is I am trying to include the effect from exercises to the tempertaure variation in skin. I am trying include the term $Q_e$ which measures the heat generated from exercises,
 to the known bio heat equation

So that it would be modified as
.
So I would like to know if there is a relationship between metabolic heat generation and exercise intensity.


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How to obtain a tardigrade?
The tardigrade is often mentioned as one of the most "alien" lifeforms on Earth. This video speaks for itself:
 (from this article)
I have long wanted to see a tardigrade with my own eyes. I have a small microscope. How do I obtain a tardigrade? I know they inhabit mosses and lichen, but is there a concrete procedure an amateur can follow that will reliably net at least one specimen?

Tardigrades can be found in almost every habitat! The easiest way to find them is probably to look in lichens or mosses (although it depends where you live).
serc.careton.edu website suggests a procedure:

Collect a clump of moss or lichen (dry or wet) and place in a shallow dish, such as a Petri dish.
Soak in water (preferably rainwater or distilled water) for 3-24 hours.
Remove and discard excess water from the dish.
Shake or squeeze the moss/lichen clumps over another transparent dish to collect trapped water.
Starting on a low obejctive lens, examine the water using a stereo microscope.
Use a micropipette to transfer tardigrades to a slide, which can be observed with a higher power under a compound microscope.

Just FYI, the tardigrades are a sister clade to the Arthropoda (insects, spiders and others). You can find them there on tolweb.org

I have an idea, but it needs developing:
It is based on filtering out just the Tardigrades from a sample, by exploiting their property of being very robust creatures.

Collect the moss or lichen, see Remi.b's post.
Do one of the many things that kills everything except Tardigrades. Would a pressure cooker work? It's a sort of sealable saucepan that boils food at high pressure.
Perform an action that causes the plant matter to become unapealing to the tardigrades. This may involve a reaction, waiting for it to be eaten by the tardigrades, or to become too degenerate to be interesting to the tardigrades, introducing other small creatures that will then die out may speed this up.

I'm going to be calling those transparent squares used in microscopes to hold samples "slides", as I'm not familiar with the terminology.

Put a slide inside the container the tardigrades are in, with plant matter the tardigrades want to eat on a small part of the slide. Prepare the slide if required, if otherwise the tardigrades would slide (through lack of friction) around to much as soon as the slide is moved.
Carefully move the slide into the microscope and observe.


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How DNA programs the first cell in womb into a human
Sorry if you see me silly. I am just a programmer happens to be curious about biology...
So far I understand how DNA make protein, how cell divides, how one composed of cells->tissues-> organs.
But, still a piece is missing in my knowledge.. Given the sperm entering the egg creating the first cell, and the nutrients from the mother... how do that very first single  cell diversify , multiply, transform to a human of many different type of cells, tissue and organs ? Is this all the diversification and
specialization of cells directed just by the "child" DNA alone ?
Also, how does DNA (along with living condition ?) decide the course of my life  (making me 1m tall at 6 y.o , have my hair black, my life expectancy etc..)

I think the cyclin proteins ( https://en.wikipedia.org/wiki/Cyclin ) control the cell cycle, of which a part of is cell division. And I think the mothers DNA are used for the "embryogenesis" up until a certain point, and then the child's DNA is used.  ( https://en.wikipedia.org/wiki/Embryogenesis#Formation_of_the_gastrula ). I think this image gives a nice summary. ( https://upload.wikimedia.org/wikipedia/commons/8/8f/Human_embryogenesis.png ) . Sorry for giving a long comment instead of an answer, but i lack confidence in my biology.

Your question is a good one, but is unfortunately too broad for this forum as it encompasses the entire field of Developmental Biology. If you can narrow the focus of your question and ask a more specific question, then it is possible to get a good answer here.

@AMR             curiously, was there anything wrong with my line of thinking for my comment on this question? I feel I have been missing the mark for responses I give either due to my lack of experience or maybe general oversight.

@RoSiv Cyclins control the transitions from G1 through Mitosis/Meiosis, in any eukaryotic cell, throughout the organism's life, not just during dev. Your second sentence, has been shown fly development, though it is maternal mRNAs that are expressed before the embryo's. It has been shown in mouse eggs and it is possible that it occurs in human as well. Unlike fly development though, each duplication is marked with cell division. Flies go through several genomic divisions before they form distinct cells.

@RoSiv The point of my comment wasn't really about your comment, it is that human embryogenesis is extremely complex and no able to be fit in this forum. There are Master Regulators, Body Plan Genes, Signaling from the uterus, Quorum sensing, different stages of cell differentiation from different cell lineages, just to name a few... Timing also plays an extremely important role. Many of our genes are nearly identical to most mammals, but it is when and how much those genes are expressed that is the main reason that we have evolved into Humans and our other cousins are other species.

@RoSiv thanks for the reading materials, they will help me get closer to the answer.

@AMR : I know it is too broad but I don't have enough knowledge to narrow it down, maybe I could after reading articles from Ro Siv's suggestion. Thanks

The short answer is: "Nobody knows yet." The slightly longer answer is that different species use different mechanisms. In amphibians and insect the oocyte, or egg, produced by the mother, has a polarity such that some macromolecules are enriched in different regions of the egg. The best characterized examples are localized RNAs, but there could be other signals as well.  In nematodes the site of sperm entry at fertilization determines the polarity of the cells, which then leads to asymmetry, etc.
In mice, our closest approximation to humans, the early cells after fertilization all seem equivalent, but as the number of cells increases the cells on the inside of the ball and the cells on the outside start to choose different differentiation pathways. There can also be signals from the extraembryonic environment (i.e., the womb).

thanks! I hope it wont take too long for biologists/scientists to figure it out...


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Difference between micro RNA and short-interfering RNA and CRISPR Cas 9 system?
I read this article https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/ and am slightly puzzled as to why the CRISPR/Cas 9 system is seen as being so revolutionary. It seems like the very same thing that micro RNA and short interfering RNA does- cleaves synthesised mRNA strands by attaching to the complementary part of the mmRNA strand, and the restrictive enzymes combine to this RNA and cleave it. I don't see how the CRISPR system is any different or better...
Thank you in advance :)
EDIT: Also, does anyone know whether Cas 9 cuts both DNA strands at the same place, or whether it leaves 'sticky ends'? Thank you.

answer is that CRISPR targets DNA, while siRNA targets RNA. siRNA is incapable of creating mutations

@aaaaaa Thank you for your reply! I see why CRISPR is important in terms of it targeting DNA rather than RNA now! But I was wondering if you could elaborate on siRNA being incapable f creating mutations... From what I understand, CRISPR only cuts DNA at a specific location, and a different system has to be used to insert a new gene section...

@21joanna12 the CRISPR/Cas9 systems being used commercially and in academics have been cobbled together to cut the DNA and deliver a new template sequence into the cut, not only allowing for sections to be removed, but sections added or mutated as well. That is why it's so revolutionary - it's all based on the gRNA. Just change its sequence, and you change your target. (Hopefully)

The CRISPR Cas 9 system is used to introduce insertion or deletion in a genomic sequence not mRNA.
https://www.addgene.org/CRISPR/guide/

this is not an answer. CRISPR/Cas9 system originally is sort of immune response

@aaaaaa The article that 21joanna12 shows mentions the CRISPR/Cas9 system as a research tool to edit genomic DNA, doesn't it?

Whatever Cas9 is, it was and is never relevant to the cleaving of RNA, only DNA. This is a perfectly valid answer.

this is not high-quality answer


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Biological modeling languages - some basic issues
I am trying to get used to with couple of modeling languages in biological context like SBML, BioPAX, Kappa and BEL. Some basic issues came up to my mind that are unclear to me even after a lot of related studies I read.

Are there any causal reasoning algorithms available for SBML? If yes please give me the reference.
Which "framework" supports modeling and mining (e.g. candidate mechanism identification / identification of upstream controllers) in Kappa?

Anyone has any idea about these?
Thanks in advance!


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Can genes be expressed sequentially?
As I understand it, any gene on an exposed/unpacked region of a chromosome is continuously being expressed. Regulatory genes may increase or decrease the amount of protein synthesised due to its expression, but its expression is still fairly continuous.
Assuming I am correct, is there any regulatory framework by which genes are sequentially expressed. That is where the expression of one gene causes it to be turned off and another turned on?
For example, say some chromosome has genes A, B, and C. Is there a situation where gene A is expressed for some period, then gene B, and then gene C, but no more than one is ever expressed at once and they only are expressed in that order?
EDIT: I'll clarify that I don't expect genes which are suppressed to somehow still be accessible. Making them inaccessible is (as far as I know) how they are shut down. My point in mentioning how accessible genes are expressed is to highlight the uncontrolled nature of gene expression in relation to sequential gene expression and therefore to ask how the genetic machinery can get around this problem.

Herpesviruses are a good example of this. Upon entry the nucelocapsid, which is surrounded by this proteinaceous tegument, is translocated to the nucleus along with a tegument protein called VP16. VP16 induces transcription of immediate early phase α genes. These α genes tell host machinery to make ß genes that result in viral genome replication (in concert with α genes), after which you get robust transcription of late gamma genes. Described in part here, gamma genes code for structural elements that assemble before budding.

Although I'll add that for each phase, the genes aren't completely shut off, and still maintain some level of transcription.

I would say exposed/unpacked regions are ready to be expressed. https://www.bioscience.org/1998/v3/d/stein/d849-864.htm

Sequential expressions could be explained by expressions of transcriptional factors, which could bind to the enhancer regions of genes ready to be expressed.

@243 Wouldn't depending on the expression of transcriptional factors be pushing the problem back one level? Solving the question of how one set of genes are expressed sequentially by depending on the sequential expression of a different set?

Simple answer: yes, this happens all the time.
A couple of notes:
Firstly, pretty much everything in biology is continuous. If a gene is expressed at a level of 1 protein per million cells, everybody would say it's not expressed, even though I guess you could argue the point. And don't underestimate how much regulation can affect expression -- you can easily have thousand-fold or million-fold differences between tissues and conditions.
Now, regarding the expression cascade: This is exactly what happens during the cell cycle. As the cell grows, there are genes that can sense the availability of nutrients and all the other signals that control initiation of cell division. Those then can turn on the genes first phase of the cell division cycle. Other regulators can sense whether that phase completed, and turn on the next set of genes, and maybe degradation signals for the genes from the first phase. And this then continues through the cell cycle.
Here's a figure from a paper that looked at gene expression in synchronyzed yeast cells (http://www.pnas.org/content/104/43/16892.full):


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Why is it called Nematocyst "Battery"?
I was reading an article on Hydra where they mentioned Nematocyst Battery. I know that Hydra and other Cnidarians have nematocyst but why are they called Nematocyst 'Battery'?

Welcome to Bio. Can you add that reference?

sorry I cannot give you the reference right now. But i googled it and found this where the writer also called it the "Battery of Nematocyst" http://www.iaszoology.com/nematocysts/

Since cnidae are "single use" cells, and this costs a lot of energy, in order to regulate discharge, cnidocytes are connected as "batteries", containing several types of cnidocytes connected to supporting cells and neurons (from Wikipedia)

A battery generally refers to a series. E.g., a test battery is a (generally quite large) set of (related) tests. In this case you can replace "test" by "nematocyst" I guess. But I haven't looked at the link yet.

So it just means series and not related to energy source?


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What are the structural characteristics of a protein-protein interaction network
I am an researcher in computer science. I am interesting in the alignment problem of PPI networks of difference species. I know a PPI network is a graph in its nature. I want to know whether there are any structural characteristics or constraints of a protein-protein interaction network (such as, a certain kind of protein can only have certain kinds of interactions with other proteins, a certain kind of protein can appears in a PPI network at most certain times, and any thing like this). If a PPI network does't satisfy these structural characteristics or constraints, then people can know that this PPI network is not a valid one.

I have changed the problem's description according to your comments. Thanks.