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Why was not RNA completely replaced by DNA when the RNA world evolved into a DNA and protein world?
If DNA just has a slightly different chemical composition from RNA, why can't DNA act as a catalyst and why hasn't it replaced RNA? Here, I am talking in terms of evolution, shouldn't evolution just replace all the RNA with DNA?

Welcome to Biology.SE! One thing that needs to be made clear at once is that evolution doesn't work to make things perfect, if something works, it is okay even if it can be improved. Yes, DNA works as genetic material for higher organisms, but RNA is useful too for temporary things like transcription.

This is also an opinion-based question because it is asking about a hypothetical situation. From the [help/dont-ask], avoid asking subjective questions where … you are asking an open-ended, hypothetical question: “What if ______ happened?” We expect answers to be based on verifiable facts and references, along with subject-related expertise. While this is an interesting question, unfortunately it is off-topic.

DNA doesn't do much it is just the storage media for RNA information. RNA does all the work.

I don't know what this question was before editing, but it seems nothing to do with evolution and good traits and bad traits. It is about the chemistry of DNA and RNA and so is quite valid in that context. I shall edit out the traits stuff and ask you evoutionists to leave this as a molecular biochemistry question.

OK. That was a bit extreme. It is about evolution, but it is not speculative. You can look at the function of the molecules and analyse the chemical advantages of the different alternatives.

A related question is Why do some bad traits evolve, and good ones don't? Basically a strong selection pressure is necessary to filter out a trait.
Having said that, there is no strong argument in support of transcription being disadvantageous.
RNA has unique properties that makes it suitable for certain functions. RNA can adopt different secondary/tertiary structures that an equivalent ssDNA cannot. One of the reasons is that GU wobble pairs are stable in RNAs but not in DNA thereby allowing structural flexibility to the former. See https://chemistry.stackexchange.com/a/35224/5295
RNA also has a high turnover because of different RNAses. If there was DNA instead of RNA for carrying temporary messages and there were equivalent DNAses to increase the turnover of the "mDNAs", then the genomic DNA would also become susceptible to degradation by these DNAses, which would cause genomic instability. You can argue that protein synthesis could directly begin on DNA as a template instead of mRNA. I guess that it would crowd the DNA and clash with replication. Even transcription machinery clashes with the replication machinery; this is called Transcription Replication Conflict which leads to genomic instability. A hypothetical situation in which there are multiple ribosomes on a DNA, is likely to have higher chances of the conflicts with replication than transcription-replication conflicts, thereby causing higher degree of genomic instability. I am assuming so because a large number of ribosomes need to simultaneously be progressing through the gene in order to produce sufficient amount of corresponding protein (like in case of polysomes).
Another possibility is based on the RNA world hypothesis. If it is really true that RNA preceded DNA as a functional as well as a hereditary molecule then it is difficult to get rid of all RNAs that easily. Even if most of the functions of the archaic RNAs were taken over by DNA and proteins, they are still performing some vital functions. To replace RNA from these roles, an alternative should exist which performs much better than the RNAs.
These are just guesses. An absolute reason can not easily be attributed to many biological observations. This is because we do not know the actual evolutionary trajectory of how things happened. However, what is important to keep in mind is that evolution does to proceed towards some kind of global optimum. Evolution does not "aim" for perfection.

The argument in this question is based on the false premises that a slight difference between two macromolecular structures is an unimportant difference, and that any importance or lack of it for that difference will have the same weight for different functions.
The slight differences between DNA and RNA gave DNA certain advantages as genetic material — for example it is less subject to alkaline hydrolysis and therefore can make longer stable genomes. It will only replace DNA if its chemistry does the job better — for other functions of RNA, this is not generally so.
RNA was largely replaced as a catalyst — but by protein, not DNA, something one can rationalize chemically because there were a wider variety of groups for catalysis etc. in the 20 amino acid side-chains of proteins.
RNA was retained for functions in which either its extra sugar hydroyl group or acid lability conveys and advantage over DNA (e.g. mRNA), or replacement by DNA would seem to convey no advantage (e.g. ribosomes). I am not an expert on catalytic RNA, but I understand that the 2'-OH is involved in the acid–base catalysis.
In conclusion, if you talk about biological molecules, you need to think about how their chemistry affects their function. If you have no chemistry, go away and learn some or restrict yourself to some non-molecular area of biology.
Footnote
I have an answer to a related question here: Why don’t different organisms have nucleic acid genomes containing different bases and sugar?

There are actually DNA enzymes, but they are artificially created -> https://en.wikipedia.org/wiki/Deoxyribozyme


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Glycogen vs cellulose-curvature of glycogen molecule?
I was wondering if anyone knows what the degree of curvature is or bond angle between the $\alpha$ glucose molecules in glycogen is. I know that glycogen/amylose/amylopectin have a general curved backbone (as well as branches in glycogen and amylopectin). This is a consequence of the 1,4-glycosidic bond between $\alpha$ glucose molecules. On the other hand cellulose has straight molceules, which is a consequnce of the 1,4-glycosiodic bond between $\beta$ molecules with alternating orientation. However I cannot find anywhere what the degree of this curvature is in glycogen backbone, or the bond angle between molecules in $\alpha$ 1,4-glycosidic bond?

Interesting question. Here, the question actually comes down to how the bond actually looks vs how we depict the bond. In detail, see this image of maltose from here:

Pay attention to the geometry of the glycosidic bond. From how it is depicted, one would conclude that it is straight in geometry. But how it actually looks is like this:

Now, the obvious conclusion is that the glycosidic bond does have an angle.
Now, with introduction over, lets come to the main point. After searching a lot, I found the value of this angle. It is 109°, much closer to the general tetrahedral angle (109.5°) of sp3 hybridized oxygen atom (deviation could be due to steric hindrance). See this article:

300 alpha-glucose units, bonded by $\alpha$-1,4 glycosidic linkages, making a 109 degree angle between 2 C-O bonds
causing the polymer to twist into a helix. -OH group of C2 projects out into the middle and form H bonds with each other, stabilising the shape.

Yes, the glucose molecules in amylose form intermolecular hydrogen bonds which stabilize the molecule. See this article and in the diagram, notice that the hydrogen bond is formed between adjacent glucose units (to the left and right of the glycosidic oxygen atom):

Although the $\alpha$-(1$\rightarrow$4) links are capable of relatively free rotation around the ($\Phi$) phi and ($\Psi$) psi torsions, hydrogen bonding between the O3' and O2 oxygen atoms of sequential residues tends to encourage a helical conformation. These helical structures are relatively stiff and may present contiguous hydrophobic surfaces.

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why on hydrolysis ATP bond releases energy?
While studying respiration all i came across was that ultimately all that cell does is for the energy currency the ATP and some useful intermediates used in the cell building but i could not figure out how contrary to the notion of supplying energy to break a bond is energy released when the phosphate bonds in ATP are broken .

There are many many chemical reactions where breaking a bond releases energy, so this notion in your question is not correct; note that releasing energy isn't the same thing as having no activation energy, you still need to put a little in but you get a lot more out.

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conversion from cpm/mg to mg
I 've an essay about wheat sprout extract, there's a graph about protein content in first 4 day of wheat sprout. so under the graph there's this text

Phosporylation by endogenous kinases of the macromolecules contained
  in 1 g of the aqueous wheat sprouts extract. Results are expressed as
  cpm/mg of protein±SEM at 4 different days of germination. 0 are
  unsprouted seeds

so my problem is to know how many mg (milligrams?) is content for 1 g of protein
in few words I need how many mg of protein is content in 1g of products, a conversion from cpm/mg to mg ... is possible?
cpm = counts per minute

What is cpm (counts per minute)? It does not seem like a common abbreviation.

yes sorry counts per minute

I feel like the question isn't written very clearly, and you would get better answers if you can clarify a bit. Unfortunately I can't quite get what you are trying to accomplish so I'm not sure how to make helpful edits. The graph you are displaying is about phosphorylation levels, not content, so maybe that is part of the confusion? I.e., the graph seems to be already normalized to protein content, so from just this information you know nothing about the total protein content on various days, just the relative levels of phosphorylation.

yes, thanks for clarification, the problem is this:

yes, thanks for clarification, the problem is this: I found this info in a experiment sheets about content protein in a wheat sprout, so in the documents, that I found that I have to eat this sprouts during second day of germination because have the max level of proteins, but I can understand how many proteins of I have... If this comment is also unclear please write me thanks

Probably the graph is from this essay. However I fail to understand are you asking for the unit conversion 1000 miligram = 1 gram? or something else more complicated about enzyme and reaction-rate from the graph?

@LXG But that paper just shows there is more phosphorylation at day 2, nothing about the quantity of proteins.

So you're saying that with this data is just impossible to find the quantity of proteins for 1g or percentange ? and you're saing that the 4 day I have more proteins content that in the seconds ? thanks

E. Cpm to fmol/mg:  Enter the specific radioactivity as cpm/fmol, the number of cpm counted, and the protein content of the sample in mg. The result is the number of binding sites in fmol/mg protein.
here is a guide of conversions.
The measure is a relative measure, and it can't be very precise as a discrete measure without knowing the precise measurement conditions, i.e. is it mixed every 5 minutes or every 1 minute, is it dissolved in 1 liter or 100ml? CPM denotes the reactivity and not the weight. You are more likely to get a Mol/L rating associated with a CPM, and two vials with the same CPM rating can have different Mol/L and Mg/L depending on their reactivity.
So, if your paper gives you a comparative measurement, and if it gives you a specific measurement at some stage you should be able to multiply it and figure out the numbers for the various days.

ok i've tried but no luck I can't convert 299,000 cpm/mg in 1g to mg can U help me? thanks maybe this can help : Figure 2 shows the phosphorylation by endogenous
kinase of the macromolecules contained in
1 g of the aqueous wheat extract from seeds
sprouted for four days:
1day163900±17911 cpm/mg of protein;
2day 299,000±35,834 cpm/mg of protein;
3day 120530±11940 cpm/mg of protein; 4 day

Perhaps try a pharmacy forum perhaps, someone who has done a thesis in applied biochemistry can probably say it better. also the chemistry forum, i will have a go tomorrow if you send a comment, my eyes are blurry at the moment!


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What is inside the male’s body in the space where females have the ovaries and the uterus?
The male penis and scrotum are external, whereas the female sex organs are placed "inside" the body. As females have the bladder, rectum etc.  just like males, does this mean overall females have a larger volume of organs? Is this why females have wider hips — because the male penis and scrotum are external appendages just like female breasts?

The ovaries and uterus are pretty small except for the uterus during pregnancy. Just for comparison, think of how your intestines take up a significant fraction of the abdominal cavity, but the actual space they take up completely depends on how much food etc is in there - that variation from hour to hour is going to be a lot more than the volume of the female reproductive organs when not pregnant.

@BryanKrause I guess you could extend your comment (and use keywords like phenotypic plasticity) into an answer if you want to.

@Remi.b Not really my area besides a familiarity with abdominal anatomy necessary to pluck arteries out of an animal model, so I'll let someone else take a stab at it, just hoping to redirect the question asker a bit: probably the more interesting question to think about are the female specializations for pregnancy and delivery (humans and animals), rather than space for the organs generally.

You are asking multiple questions here. I would suggest that you restrict your question to the pelvic region, as your question title says. Each organ would have sex-based differences. We cannot cover all that in a single post.

Oh cool @WYSIWYG I'll make the second paragraph into a separate question.

Wider hips in females is not contributed because of large volume of organs.
Broadening of the hip bones happens as a feature of the female pubertal process, and estrogens (the overwhelming sex hormones in females) cause an enlarging of the pelvis as a piece of sexual separation. Consequently females for the most part have more extensive hips, allowing labor.
However, I found this article from International Business Times that states >>

Women have not evolved wider pelvises despite it being difficult and
  dangerous to give birth – yet they may have developed some physical
  features that help during labour.
Barbara Fischer, from the University of Oslo, has found a link between
  pelvis shape and statue and head circumference of both baby and
  mother.

There was, however, no sufficient evidence to back this article, but it is quite an interesting approach otherwise.
Males are not needed to have any extra organs, but females have just more space in the pelvis region. That space can be linked to idea of uterus expanding to hold the fetus during gestation as mentioned by @BryanKrause.

the article is a poor understanding of a study on the size of the birth canal portion of the pelvis, the pelvis as a whole is still wider. a big red flag is it is the an article in business times about evolutionary biology.

mostly nothing, males have narrower pelvises. The prostate, seminal vesicle, and basal anchorage of the penis do take up some space.

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Why do ribosomes associate with rough endoplasmic reticulum but not other membranes?
As far as I am aware, all eukaryotic membranes consist of a lipid bilayer. Smooth endoplasmic reticulum (ER) and rough ER are distinguished by the presence of ribosome on the rough ER surface, but are apparently otherwise similar. So what causes ribosomes to associate with the membrane of rough ER but not that of smooth ER. Or do ribosomes convert smooth ER to rough ER by binding to their membranes?

probably because there aren't ribosome translocation complexes on other membranes

there is a specific binding protein that attaches the ribosome to the rough ER. There are other such binding proteins for say the cell membrane. There are free floating ribosomes as well. But the RER is a specialized structure that produces the proteins in an controlled environment separate from the rest of the cell, reducing the potential damage by improper folding of the proteins and allowing for easier modification and transport of those proteins. the binding proteins also create an additional layer of control/regulation on protein synthesis.

@John — Please read the message that comes up when you click in the comment box and do what it says: "Use comments to ask for more information or suggest improvements. Avoid answering questions in commnets." This site has a particular modus operandum underpinned by a clear rationale that is explained when you join.

I think your question is good, but I made it more precise and compact because English is obviously not your mother tongue. If I have altered the meaning, do say so.

Thank you for refining my question. I have problem expressing ideas even in my mother tongue haha

Peptides that are destined to be either secreted or included in the cell membrane have a signal sequence that binds a protein called Signal Recognition Particle (SRP). The SRP will in turn bind to translocons--basically peptide tunnels in the RER membrane. You need to have this interaction between the translocon and the SRP in order to have stable ribosome attachment. That's why you won't have ribosomes attaching to other membranes. After attachment the ribosome will continue translating mRNA through the translocon into the RER lumen.
Now here's where things get a bit dicey. If the resulting structure in the RER lumen is largely hydrophilic then it will stay in the RER lumen where it will later be targeted to wherever it needs to go based on other signal sequences.
However, if there are large stretches of hydrophobic residues, then those don't like to be in the aqueous environment of the ER lumen. Ergo they will incorporate into the RER membrane. Thus they become transmembrane proteins. A good rule of thumb is that if you have 10 hydrophobic residues in a row, then there's a good chance that is going to get incorporated into a membrane.
Once protein transcription is complete the ribosome will no longer be associated with the RER and will re-enter the pool of free ribsomes (ready to pick up a new mRNA).
EDIT: In response to question in comments about why translocons are found in RER and not in other membranes
You can certainly ask the question, but you're getting close to falling into that beautiful genesis of basic science research: something I call the 'why-hole'. I searched around, and I don't think we have a full understanding of membrane organization throughout the cell, though I would defer to any cell biologists who have a better understanding. We do have some idea of the mechanisms. What follows is a stitching together of hypothesis and some facts I was able to find.
It stands to reason that since the translocon is a complex of transmembrane proteins, its parts were at some point synthesized by a ribosome through a previous translocon. That would get it into the RER membrane. Now in order for a piece of membrane (or anything within the ER lumen, for that matter) to get to its final destination it has to have another signal sequence. This signal sequence will be recognized by unique signal recognition protein. This will localize the protein to a part of the RER that has several proteins that will form a vesicle (one of which being clathrin) and a protein attached to it called a v(esicle)-SNARE. Once the vesicle buds off it will go through the cell until its v-SNARE runs into a t(arget)-SNARE. This interaction will ultimately lead to fusion of the vesicle into the target membrane (e.g. lysosome, plasma membrane, etc). I double checked all of my facts here, where you can read more about it.
All of this is to say that if a transmembrane protein doesn't have a signal sequence it won't get targeted for transport through this system and should stay in the endoplasmic reticulum.
At this point it would be good to remind everyone that the ER--both rough and smooth--is a continuous structure with the RER located closer to the nucleus and the SER closer to the cell membrane. So it would be reasonable to ask why translocons stay in the RER and doesn't diffuse into the SER. That's where we get into more emerging science. From what I gather there are many proteins that are involved in the strutrue and organization of the ER. You can look into "the ability of NDPK-B to form microdomains at the membrane level" or reticulon2, but I think there's still a fair amount of work to do in this field. I encourage you to look into these resources, and if this is something that you're interested in consider doing some research. There is some evidence that membrane dysfunction is associated with neuronal disease, so any advances would be well received.
As always, keep asking questions!

This seems quite a good answer, but it needs a supporting reference to the translocons, so people can check it independently. If you do that and it seeems correct, I'll upvote it. The other problem with your answer is that it goes off topic. The lipid raft thing is surely not relevant and therefore detracts from your answer. You would have done better to integrate your PS into the answer. Also, How about a spelling check?

Thanks for your feedback! I've adjusted the answer accordingly.

May I ask why the translocons are on the RER but not other membrane?

Of course, always! I've expanded my answer in response to your query. It seems that you're starting to get close to the limits of my (perhaps even science's) knowledge. But that just means that the area is ripe for further research in my opinion.

Ok, as I am aware that we're on the boundary of knowledge, your expanded answer has fulfilled my curiosity. Thank you very much for your effort. Accepted and upvoted.


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Why some traits are more desirable in the sexual selection?
For example, why do peacock females choose males with the biggest tail? If there is no advantage in such tail.

Have you done some work looking for an answer?

Wikipedia is often helpful....Have a look at Fisherian runaway and Zaahavi's handicap and eventually just at sexual selection.

Sexual selection is a big topic and while I am not quite an expert in this field, I doubt anyone would be able to really make a good summary of the possible reasons leading to sexual selection. It is even more true that there are big issues of semantic in the field (see the work of Hannah Kokko). Note however that reading the wiki article on Fisherian runaway will already bring you a long way.

Oh You should read about the sexy son hypothesis too

Also you can mark an answer as accepted.

There are two common explanations both are difficult to demonstrate. I personally favor the former but I will not claim it is the only explanation.

selection starts as either a random occurrence or as some initially beneficial trait (a slight increase in tail length may have been beneficial originally)
Then runaway selection takes over. Any increase also causes increased attraction because the evolved behavior of the desire in the females only functions as bigger is more attractive(or whatever=more attractive). This pushes further and further into absurdity becasue there is not behavioral regulation to say enough is enough. So any increase in the males increases attractiveness meaning any individual male with less can't reproduce in the current population of females no matter how beneficial to the individual male survival. Additionally no female will develop a favoring of smaller tail feathers becasue her smaller tailed offspring will not be able to find mates for the same reason. A positive feedback loop like this won't stop until it hits a point where the cost of tailfeather is more than the advantage of increased mating becasue the individual never lives long enough to mate.
By carrying a handicap the organisms shows it can withstand a greater burden and thus must be better.

so the desire of some trait can be transferred by genes ?

of course, most behavior is controlled by genes. The genes that control the structure of the brain control behavior. Even In humans a significant amount of our behavior is controlled by genes.

most behavior is controlled by genes is misleading and sounds like you might misunderstand the concept of heritability. You would at least need a reference for such claim.

I don't think that FIsher Runaway process (your first bullet point) necessarily require an initially beneficial trait under the sexy son hypothesis (but I am not 100% clear with all these concepts in sexual selection)

I said a beneficial trait or a random occurrence.

@remi. I think you are misunderstanding how many organisms exhibit behavior. Behavior is itself a poorly defined term. How much insect behavior do you think is learned?  but you also have the problem with what is considered controlled. language as an example the brain has a critical period for learning syntax, yet what language you speak is clearly learned so it both controlled and not controlled by genes.

My main issue was that "controlled by genes" is misleading. One can tell whether a behaviour is innate or learned or whether phenotypic variance is due to environment variance or genetic variance. When saying "controlled by genes", it makes me feel that you are stating that most of the variance in behaviour is explained by genetic variance (which I think would require a reference).

very few behaviors are one or the other, most complex behaviors are a mix of the two. But I perhaps, "Modulated by genes" would have been better. The massive gray area makes giving an exact number impossible. It is all about arbitrary categorization which makes it largely opinion.


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Photosynthesis in oxygen free enviornment
If a plant is grown in an oxygen free enviornment would it live longer in light or darkness?
It is evident that oxygen would compete with carbon dioxide during various processes like competing with carbon dioxide for reducing power, also oxygen quenches the excited electron of chlorophyll etc.
But all these effects to me don't give any sense of the extent of oxygen on these reactions. What does the absense of oxygen have on the system? Except ofcourse the plant not being able to respire properly.

So, what's your doubt here? Plants are dependent on oxygenic respiration for ATP because they evolved that way.

My doubt is which environment would the plant live longer, in light or in darkness?

If that "environment" is a closed vessel or bell-jar; certainly the plant would survive in light (when it simultaneously perform respiration and photosynthesis), and in darkness (when it can perform only the respiration) it would survive upto certain time due to the oxygen it accumulated. But should die at prolonged darkness when the plant would finish all the oxygen.
(as suggested by Priestley's classic 1870 experiment * there was enough oxygen to keep a mouse for certain time)

(image link)

However, if we look the effect of various concentration of O2 on photosynthesis rate without altering the CO2 concentration; yes the photosynthesis rate get affected; one known effect is called Warburg effect or Inhibition of photosynthesis by O2.
In this effect, photosynthesis rate only decrease if O2 concentration is increased. And in vice-versa, with O2 concentration decrease, photosynthesis rate only increase. (source: this, this, this and this)
This take place due to mainly 2 causes: 1. O2 work in  competitive way with CO2 for binding with the enzyme RuBisCO, the key enzyme for CO2 fixation in plants. 2. And that induces photorespiration (in C3 plants). (Wikipedia shows reference to here). (However this old paper also tells other hypotheses)

There are 2 type of responses in photosynthesis rate in at different O2 concentration in various plant species.
One group of plants ( known to bel C3 plants, those do not have any any CO2 concentrating mechanism) ), is remarkably affected by O2 concentration; i.e. affected by Warburg effect in true sense.
Another group of plants ( known to be C4 plants, those have a certain type of CO2 concentrating mechanism); does not significantly get affected by O2. I.e. doesn't show the Warburg effect.
(see also : table).

By the way, It seems photosynthesis would increase than normal  if we could make the environment "completely oxygen-free" but other parameters same. (due to elimination of O2inhibition) But I could not find any report about such "completely oxygen-free" conditions; and seemingly it is not possible because while doing photosynthesis; some  of the evolving oxygen molecules will pass through the cytoplasm; some will move in the intercellular space, and few molecules will stay diffused in atmosphere around the plant. We can only decrease the concentration of O2

Also; Warburg effect is completely about photosynthesis rate. It is not about plant's overall health. Removal of O2 increase photosynthesis rate... it does NOT mean the plant would live healthiest in oxygen deprived condition

Sources:

Fundamentals of Plant Physiology by Dr. V. K. Jain; revised edition; S. Chand Publications, New Delhi.
* Biochemistry/ Lubert Stryer/ 4th Edition/ W. H. Freeman and Co.


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Why are red blood cells preferred to study the structure of plasma membrane?
If we wanted to study the structure of a plasma membrane, why are red blood cells a more attractive cell type to work with than other cell types such as liver cells or kidney cells?

Did you try to find an explanation anywhere else before asking here? Why do you think that might be the best way to harvest cell membranes?

What is unsatisfactory about the explanation?

I would actually say they are all pretty terrible, unless you wanted something specific to look at in a cell type. The correct answer would be liposomes in a biophysical context, endosomes in a biological context, nanodiscs in a structural biology context (other answers of of course acceptable)! Whole cells are a nightmare unless you need some cell-specific information. Without knowing the explanation given, this question is unanswerable.

@James - I don't know if I could disagree with you more. The answer is really obvious.

@anongoodnurse Perhaps my comment was a little facetious, but I am trying to say that the question is missing a key point; some sort of testable hypothesis. The question remains unclear. If I want to study the PM structure relative to other bilayers structures, I don't need to work with specific cell types, rather many cell types (Sharpe et al 2010). If I want to compare the PM to other cell types, I need other cell types. If I wanted a crystal structure of how a particular protein sits in the PM, I need a nano-disc etc.

@anongoodnurse If I want to answer "If we wanted to study the structure of a plasma membrane, which of the following would be the best cell to do so?" My knee-jerk response is "It depends on what you want to know" regardless if there is an easy-to-handle option (and still, there are easier to handle options than RBCs).

@James - I understood that (believe it or not), and generally agree with your argument. However, the question was basic and non-specific; rbcs are basically just cell membranes surrounding an easily separable 'cytoplasm'. Lyse the cells, wash, and violà. Which cells would be easier? (I'm sincerely curious.)

@anongoodnurse I see your point and you've convinced me that the question has value. I've removed the homework-y-ness of the question and limited it to specifically whole cells making my comments redundant :P Until OP comes back with some research, the question still stands at risk of closure for lack of effort.

@James - Fair enough, and I've already VTC.

@James what are examples of "easier to handle options than RBCs"?

@AlwaysConfused Liposomes and endosomes are typically less messy when it comes to results analysis for many experiments, particularly for molecular biology. Whilst the RBCs are relatively simple cells, they still contain a lot of proteins that may interfere with your interpretation of the results. To reiterate, this depends on what you are wanting to know specifically, which the question is currently missing. After my edit, these options aren't viable since they're not complete cells, but rather bilayer models.

@James Thank you. Artificial-liposomes would best from viewpoint of purity and simplicity. But we don't have to 'prepare' any RBC with technologies like sonication etc. Also I assume (no experience) liposomes and similar naturally available structures like chylomicrons would be more difficult to handle due to small size. Also to isolate phagosomes we have to rupture the cell membrane, and separation task would be more difficult than RBC. so when high accuracy not reqd, RBC is easier.

Thanks for the help everyone. No, there is no explanation. I'm a junior in high school and came across this question in a biology practice book. That's all it stated, which cell would be the best for studying the structure of a plasma membrane? Only thing we have in our course is the fluid mosaic model and lipid bilayer so I guess it refers to that. The solution said RBC but didn't give any explanation, so i asked it here as I am curious to know why.

@AlwaysConfused I've only been involved in the biophysics end of molecular biology so I'm quite narrow minded about methods. RBCs are simple to a cell biologist, but those same cells might be too complex for a molecular biologist!

@James Me too never did experiments with rbc (except only viewing them under microscope) and did only very few experiments on cell-membranes in college and university botany courses. I've put the comments and answer from common sense.

Human RBCs are relatively simple in structure compared to the other cells in question; they contain no cell organelles (so far I knew; please correct me if there is any new theory) and therefore contain only one membrane.
RBCs do not have significant amount of extracellular matrix making them very easy to work only with the cell membrane. RBCs float in a fluidy medium (blood-plasma), so easy to collect, distribute in containers, keep into various solution. no need of maceration. Human RBCs are very uniform in shape and size, and do not divide. That makes it useful for various experiments like demonstrating plasmolysis and deplasmolysis as well as quantitative experiments on membrane biomolecules.
One classic example is Edwin Gorter and F. Grendel that first showed that cell membrane is bilayer; that is upon observation on RBC. They took known number of RBC, denatured the membrane, extracted the lipids and spread that as a lipid monolayer on water-air interface. They found that the monolayer is twice bigger than total surface area of taken RBC ! *

Source:  * The Cell/ Cooper/ 4th Edition/ASM-Press and Sinauer publication.

However this is not a reference-based answer, but these are the features more than enough to make me so lazy that I would choose only RBC and flyaway from any-other option.

I guess this explains it to me anyway.


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The effect of depth on net primary production in aquatic ecosystems
The figure shows the relationship between the water depth and net primary production (=P-R). I want to know why the production (P) initially increases with water depth near the surface? I have seen similar relationships from other sources but never seen a clear explanation.

Is the figure referring to gross primary production or primary production per capita?

Textbooks don't give details. At first, I thought the pattern of the productivity correlates with the abundance of phytoplankton. But because the rate of respiration is constant, now I think it is the per capita effect. If it is not the per capita effect, I like to know why the total respiration is constant.

But the texts in the figure (and other similar figuers from different sources) imply that the figure shows NPP = P - R. So I think it is probably not the per-capita effect. But this figure (http://www.jochemnet.de/fiu/Ink1.jpg) shows that the pattern does not emerge from difference in the concentration of phytoplankton.

Ok, a bit hard to answer if it is unclear whether the effect is per capita or the total productivity. For experts in the field I suspect it is obvious though (I'm not an aquatic ecologist). My initial guess was however that the graph showed total primary productivity (for the entire "ecosystem"), and that the dip towards the surface is related to the density of primary producers. Lower density at the surface could then be related to both turbulence (waves) and predator avoidance (among other things).

It looks like the result like the one shown in the figure is based on a controlled experiment using the dark/like bottle method (http://www.jochemnet.de/fiu/Ink1.jpg). Because the density of phytoplankton is controlled in each bottle, we can qualitatively interpret the result as the per-capita effect too. Because of this, the effect should be entirely based on physical factors (e.g., there are no predators in the bottles). Turbulence can still influence the bottles, though.

What book is the figure in the question from, and the figure you link to in the comments? This would be useful to know, so that people can read for themselves and get some context.

After a quick glance at the book "Light and Photosynthesis in Aquatic Ecosystems" by Kirk (2010), I think that the cause for the productivity dip towards the surface partially lies in photoinhibition, due to high light intensities at the surface. Here are a couple of relevant quotes from the book (Google books: p. 371):

In this light saturated state, the electron transport and/or CO2 fixing enzymes (most likely, the latter) are working as fast as they are capable, and so any additional absorbed quanta are not used for photosynthesis at all. From the end of the linear region through to the light-saturated region ([i.e. close to the surface, my addition]), since photosynthetic rate does not increase in proportion to irradiance, (P/Ed steadily falls, see Fig. 10.3) the quantum yield and conversion efficiency necessarily undergoes a progressive fall in value. This is accentuated further if, at even higher light intensities, photoinhibition sets in. If the cells contain photoprotective carotenoids, in which absorbed light energy is dissipated as heat rather than being transferred to the reaction centre...

However, the suspended bottle methods often used to estimate these depth gradients might be part of the problem, by overestimating the effect of photoinhibition, by forcing plancton to stay at the same depth (p 358):

Depth profiles of phytoplancton photosynthesis, such as those in Fig. 10.4, determined by the suspended bottle method, tend to overestimate the extent to which photoinhibition diminished primary production. In nature, the phytoplancton are not forced to remain at the same depth for prolonged periods. Some, such as dinoflagellates and blue-green algae, can migrate to a depth where light intensity is more suitable. Even non-motile algae will only remain at the same depth for extended periods under rather still conditions.

I hope I got the quotes right (quick manual retyping). There are many more relevant sections in the book as well, which seems to cover all kinds of aspects of aquatic photosynthetic efficiency and how this can be a function of depth.

I think it has to do with what wavelength of light is absorbed by photosynthetic organisms at what depth.
Ultraviolet light with short wavelength is absorbed closest to the surface. Red light (which is responsible for photosynthesis) is absorbed at a deeper point in aquatic systems by the primary producers like phytoplankton and metaphyta which increase the productivity of that particular depth.
[I'll include citations, references and diagrams as soon as I find enough time]

The amount of red light monotonically decreases with the depth. So it still does not explain the hump shaped productivity pattern.

Compared to the surface, slightly below the surface in the water column the availability of nutrients increases as winds and ocean currents cause increased mixing of nutrient rich deep water. The photic zone of the water column is quick to use up the macronutrients necessary to sustain primary production, however upwelling of nutrient rich deep water becomes a significant factor in determining an area's production.
[ I will provide citation later. ]

But according to this figure (http://www.jochemnet.de/fiu/Ink1.jpg), the result is based on controlled experiments (the dark/light bottle method). Therefore, the available nutrients are the same along the depth (even if they are naturally variable).

If this is the experiment I believe it is, then the bottles filled at different depths and returned to the same depth they were filled at. This would have a difference in available macronutrients. However this article about the experiment also details that primary production increases just deeper than the surface because "Primary production is usually suppressed just at the surface because the light is too strong there, but reaches a maximum just below the surface because this is where the light optimum occurs. Below the light optimum, production declines rapidly with light."

Article location: http://www-personal.umich.edu/~gwk/teaching/limno/lab/onlinemanual/primaryoxy.html


text:
Nutrient limitation in terrestrial and freshwater ecosystems
In terms of primary production, it is often described in textbooks that nitrogen is the most limiting nutrient in terrestrial ecosystems, while phosphorus is the most limiting nutrient in freshwater ecosystems. What creates this difference?

Can you provide references to these texts

Tropical terrestrial biomes can actually have more of a shortage of P vs N.

The traditional explanation for this is that nitrogen compounds are more mobile than phosphorus compounds. As a result, nitrogen is more likely to flow through terrestrial ecosystems and accumulate in freshwater ecosystems, making P relatively more limiting than N in freshwater.
Phosphorus compounds (e.g., phosphate) are more "sticky" and tend to bind/sorb to compounds in the soil and aquatic sediments, e.g., ferric compounds. Thus, most phosphorus gets bound up in terrestrial ecosystems because it's less mobile than nitrogen, or gets bound up in aquatic sediments. As a result, nitrogen becomes relatively more limiting than phosphorus in terrestrial ecosystems, and the phosphorus that does enter freshwater ecosystems often becomes inaccessible to biological organisms like primary producers.
Note that this paradigm is a generalization, and is dependent on many other factors. Lake pH and concentration ferric compounds can regulate whether the sediments are sources or sinks of P; anoxic conditions can lead to denitrification, a loss of N that could offset N inputs. Anthropogenic additions of N and P (either to the freshwater system directly or to the terrestrial ecosystem that drains into it) could dramatically perturb the natural balance between N and P limitation in terrestrial and aquatic ecosystems in a way that does not conform to the paradigm.
Some references you might find useful:
Elser, J. J., Bracken, M. E.S., Cleland, E. E., Gruner, D. S., Harpole, W. S., Hillebrand, H., Ngai, J. T., Seabloom, E. W., Shurin, J. B. and Smith, J. E. (2007), Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems. Ecology Letters, 10: 1135–1142.
Vitousek, P.M. & Howarth, R.W. Biogeochemistry (1991) 13: 87.

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


text:
How would one go about identifying unknown cell cycle checkpoint proteins (i.e., cyclins)?
No this is not 'homework'. I'm a PhD student, and this was something brought up at the end of a journal club recently, and one of the PIs posed this question and told us to think about it. It sounds simple, but it sort of has me baffled.

Western blot: No. Need a known antigen and so, since we don't know what we're after, this won't work.
Total protein gel: Collect cell lysates from different cell populations that are in different parts of the cell cycle, run it on a gel and observe any cyclic expression. This seems sort of ok but I feel like there are a few problems with it: 1) identifying the cell populations that are in the different cycle stages; 2) other proteins of same/similar size that cannot be differentiated.
Some sort of RNAi, knockdown, etc.: Like the western blot, we don't know what we're dealing with and so can't target anything.
Pulldown assay with mass spec: I don't know a lot about it aside from that it looks at protein-protein interactions. Unsure if it would be appropriate here.

As far as a model, I was thinking either yeast or some immortalized mammalian cell line.

One can fairly easily do genome-wide knockdown experiments nowadays, so don't discount RNAi/siRNA right off the bat. Which tool(s) you pick is going to be dependent on the model you're using. If it's yeast, you have many validated tools at your disposal, including mutants/knockouts for every single gene in the S. cerevisiae genome,  two-hybrid systems for looking at protein-protein interactions, reporter constructs that indicate by fluorescence or enzymatic activity when the gene of interest is being expressed, and others.

For yeast, people used to rely on mutants/knockouts which are supposedly easy to produce using HR, compared to other organisms. For animal cells people extensively use high throughput RNAi/CRISPR-Cas screens to identify the functions of a gene. If you have the protein sequence then you can express it and raise antibodies against it. With the antibodies, you can Co-IP-MS for identifying protein-protein interactions and ChIP-Seq (for TFs) or CLIP-RNAseq (for RBPs) to identify protein-DNA and protein-RNA interaction respectively. Overall, your question is quite broad. You should narrow it down.

I've actually been involved in a hunt for checkpoint proteins in diatoms (a type of eukaryotic algae), the cyclin family has been greatly expanded in these organisms and we were trying to figure what these extra cyclins were sensing/signalling[1].
In a nutshell, the first author looked at different conditions which were likely to affect cyclin expression. Most of these conditions prevented cell division (e.g. lack of nutrients, G2/M chemical inhibitors or light) and samples were taken before and after the blocking conditions were removed. Afterwards mRNA's were quantified of suspected cell cycle genes. As the checkpoint genes' mRNA and protein cycles extremely transiently this took some doing. Cyclins that reacted to the conditions were characterised using complementation assays and other techniques.
Afterwards yeast two hybrid assays were used to identify interacting proteins to build up the network[2]. In general, these experiments were not that straightforward and messing with essential genes causes a lot of trouble but it still nothing compared to the original yeast cyclin work where they were slogging through mountains of temperature sensitive mutants defective in their cell cycle (see the work of Lee Hartwell and Paul Nurse who got the Nobel prize for this in 2001 with Tim Hunt).


text:
How to keep activated sludge viable for a week?
I am working in biological waste water treatment and I need to collect some activated sludge samples and have them characterized through different methods. The characterization will take from a few days to a week. How do I keep the sludge viable in this time? How do I make sure the bacteria do not die?

What about cooling these samples to 4°C?

I though about that as well, but ... I do not know if it is enough. I was thinking about aerating them and feeding some... yeast extract now and then? I don't know. That;s why I am asking the experts. :D

@Pompilia activated sludge would have different kinds of microbes and the general yeast-extract based media may not be suitable for all the microbes. Therefore, I think 4°C cooling may be a better option.

@WYSIWYG It is also the simplest method, so I'm fine with that.
Let's see if someone suggests something else.
Thanks!

Have a look at this review: http://www.sciencedirect.com/science/book/9780123914538, it discusses the issue of mass-producing organisms in a more general sense (i.e. not just bacteria)


text:
Why do bacteria produce H₂O₂?
I recently read up that people with NADPH oxidase deficiency (Chronic granulomatous disease CGD) have a tendency to be infected by Catalase positive organisms. NADPH oxidase helps produce the $H_2O_2$ via superoxide that is required by other enzymes to kill the bacteria.
Case 1: In the phagoloysozome, when there is a deficiency of NADPH oxidase, catalase positives can clear off the $H_2O_2$ they produce, thereby stopping production of free radicals via Fenton and myeloperoxidase. The bacteria survives and hence causes symptomatic infection in CGD patients.
Case 2: On the other hand, since catalase negative organisms can't clear off the $H_2O_2$ they produce, they remain susceptible to the free radicals produced by other enzymes like Myeloperoxidase and Fenton reaction, which would still kill the bacteria. In short, the bacteria 'lend' the $H_2O_2$ which feeds into these reactions leading to its own death. Hence, CGD patients can fight off catalase negative organisms.
My question is, why do the bacteria produce $H_2O_2$ in the first place? Is it produced only by aerobic organisms? If so, why would there be organisms that produce $H_2O_2$ and still not have a catalase (as had happened in case 2)? Isn't $H_2O_2$ is harmful even in the absence of free radical producing enzymes since the Fenton reaction is a non-enzymatic reaction?

It is a by-product of oxygenic respiration which is basically toxic to the cell but it is also used by some organisms (I know of eukaryotes) for defence and some catabolic processes. Peroxidases can also clear H₂O₂. Also, catalase is present in almost all aerotolerant and aerobic organisms. Can you cite a counterexample?

@WYSIWYG yeah, catalase is present in aerobic/ facultative anaerobes. I get that. Why are catalase negatives also producing H2O2 then? Shouldn't they be able to handle it when they are producing it? As mentioned, catalase negatives can be killed even in CGD individuals.

Can you cite an example of a Catalase negative organism that produces H₂O₂?

@WYSIWYG I don't know. Well, that's what I find weird. In CGD patients, catalase negative organisms can be killed in the phagolysosome because, they 'lend' H2O2 which they are unable to clear off (unlike catalase positive organisms), to the downstream enzymes that can lyse the bacteria. This is why I posted this funda on top coz the confusion arose from this itself. The source is from a standard Hematology text, which I will quote once I get hold of it.

why does the bacteria produce H2O2 in the first place?
It is produced by all organisms as a byproduct of respiration. See this wikipedia article:

All living cells produce reactive oxygen species (ROS) as a byproduct of metabolism. ROS are reduced oxygen intermediates that include the superoxide radical ($O_2^•$) and the hydroxyl radical ($OH^•$), as well as the non-radical species hydrogen peroxide ($H_2O_2$)....The superoxide anion is formed directly from the one-electron reduction of molecular oxygen. Hydrogen peroxide is then formed from the disproportionation of the superoxide anion. This reaction occurs very quickly in seawater. Next, the reduction of hydrogen peroxide yields the hydroxyl radical, $H_2O_2 \xrightleftharpoons 2OH^•$, which can then get reduced to the hydroxyl ion and water.

 Source
But, it has some useful functions too! One of those, as you mention, is in immunity through NADPH oxidase, but there are some more! From the same above wikipedia article:

These ROS are important in the normal functioning of cells, playing a role in signal transduction and the expression of transcription factors.

For this line, wikipedia cites 3-4 articles, one of which is this:

The OxyR transcription factor is sensitive to oxidation and activates the expression of antioxidant genes in response to hydrogen peroxide in Escherichia coli. Genetic and biochemical studies revealed that OxyR is activated through the formation of a disulfide bond and is deactivated by enzymatic reduction with glutaredoxin 1 (Grx1). The gene encoding Grx1 is regulated by OxyR, thus providing a mechanism for autoregulation.

It is not produced by obligate anaerobic bacteria and that is why they are very sensitive to oxygen. See this article:

Obligate anaerobes are microorganisms killed by normal atmospheric concentrations of oxygen (20.95% $O_2$)...Because molecular oxygen contains two unpaired electrons in its outer orbital, it is readily reduced to superoxide ($O_2^−$) and hydrogen peroxide ($H_2O_2$) within cells. Aerobic organisms produce superoxide dismutase and catalase to detoxify these products, but obligate anaerobes produce these enzymes in very small quantities, or not at all.

If so, why would there be organisms that produce H2O2 and still not have a catalase (when the bacteria is outside, not in the phagosome)?
Logically, no. Producing $H_2O_2$ but not being able to handle it would be like suicide for any organism. Also, I could not find any example of bacteria which lack catalase but still produce hydrogen peroxide. However, if you talk about spontaneous formation of $H_2O_2$ from $O_2$ or spontaneous conversion of $H_2O_2$ to $OH^-$ or $H_2O$, then there could be many examples.
Isn't H2O2 is harmful even in the absence of free radical producing enzymes since the fenton reaction is a non-enzymatic reaction?
I think you have used some inappropriate words here; you probably mean free radical metabolizing enzymes (like catalase or superoxide dismutase) instead of free radical producing enzymes. And you probably want to say that $H_2O_2$ can also affect bacteria through fenton's reaction even in the presence of such enzymes (correct me if I'm wrong here).
You are partially correct. It should damage the bacteria, but, as you know, bacteria are ever-evolving and have already found a way to counteract this. First, lets see how fenton's reaction works. See this:

After addition of the iron and the hydrogen peroxide, they are going to react together to generate some hydroxyl radicals as it shows in the following equations:
$Fe^{2+} + H_2O_2 \rightarrow Fe^{3+} + OH^• + OH^-$
$Fe^{3+} + H_2O_2 \rightarrow Fe^{2+} + OOH^• + H^+$
The typical range for the iron dose is 1 part of Fe per 5-25 parts of H2O2.
After that the hydroxyl radicals are going to react with the pollutants to oxidize its. Actually the hydroxyl radicals can react according 4 kinds of reactions with the pollutants:
Addition: $OH^• + C_6H_6 \rightarrow (OH)C_6H_6$
Hydrogen Abstraction: $OH^• + CH_3OH \rightarrow CH_2OH^• + H_2O$
Electron Transfer: $OH^• + [Fe(CN)_6]^{4-} \rightarrow [Fe(CN)_6]^{3-} + OH^-$
Radical Interaction: $OH^• + OH^• \rightarrow H_2O_2$
During the Fenton's reaction all the parameters are adjusted to promote the two first kind of reaction between the pollutant and the hydroxyl radicals.

Now, lets see how the bacteria tackles this. See this:

While E. coli Dps can store iron, it prefers to use $H_2O_2$ rather than $O_2$ as an oxidant (Zhao et al., 2002). This suggests that the primary role of Dps in E. coli is to protect DNA against the potential damage of hydroxyl radical produced by the Fenton reaction, rather than an iron storage function. Although an iron storage Dps-like ferritin was found in the gram-negative bacterium Listeria innocua (Bozzi et al., 1997), recent studies have shown that it is indeed a Dps protein, which attenuates the production of hydroxyl radical by Fenton chemistry: DNA cleavage assays showed that the protein, while not binding to DNA itself, protects it against the deleterious combination of $Fe^{2+}$ and $H_2O_2$ (Su et al., 2005). It seems likely that the principle role of this family of proteins is a DNA protecting anti-redox agent (Chiancone et al., 2004).

EDIT: Now, as you asked in comments:
how catalase negative organisms manage with the H2o2 they produce
read the following paragraph from this article (emphasis mine):

Under different growth conditions we found that both L. plantarum ATCC 8014 and a catalase-positive strain, T-1403-5, were capable of utilizing $0_2$, particularly during the late stages of growth. This suggested the need for enzymes which would protect the lactobacilli
  from $H_20_2$ and $0_2$ which might be formed. Superoxide dismutase was present at low but constant levels in both catalase-positive and catalase-negative strains. NADH peroxidase was present in strain 8014 and this enzyme increased in specific activity as the cells aged and entered the period of increased $0_2$ uptake. The presence of this enzyme should protect the organism against toxic effects of $H_20_2$ in the absence of catalase production. In strain T-1403-5 this role can be performed by the very active atypical catalase, although this strain may also possess the peroxidase. When growth rates of the catalase-negative and catalase-positive strains were compared, the rates of the catalase-negative strains were greater than that of the catalase-positive strain. Therefore, it did not appear that the possession of catalase conferred any advantage on strain T-1403-5.

Or see another article on Streptococcus pneumoniae:

Aerobic growth of Streptococcus pneumoniae results in production of amounts of hydrogen peroxide ($H_20_2$) that may exceed 1 mM in the surrounding media...The mechanisms allowing S. pneumoniae, a catalase-deficient species, to survive endogenously generated concentrations of $H_20_2$ that are sufficient to kill other bacterial species is unknown. In the present study, pyruvate oxidase (SpxB), the enzyme responsible for endogenous $H_20_2$ production, was required for survival during exposure to high levels (20 mM) of exogenously added $H_20_2$...Thus, SpxB is required for resistance to the toxic by-product of its own activity. Although $H_20_2$-dependent hydroxyl radical production and the intracellular concentration of free iron were similar to that of Escherichia coli, killing by $H_20_2$ was unaffected by iron chelators, suggesting that S. pneumoniae has a novel mechanism to avoid the toxic effects of the Fenton reaction.

From the same article's Discussion heading (there are actually many points, so I recommend you read them yourself too, I'll add main points here):

The role of SpxB expression in resistance to killing by $H_20_2$ was confirmed by the demonstration that spxB mutants, which produces no detectable $H_20_2$, had a significant decrease in $H_20_2$ resistance and by demonstrating that complementation of the spxB gene fully restored both $H_20_2$ production both $H_20_2$ resistance. These results showed that SpxB expression is required for wild-type levels of resistance to $H_20_2$ rather than merely correlating with it.
when cultures of both strains were shifted from anaerobic to aerobic conditions with or without chloramphenicol, a protein synthesis inhibitor, $H_20_2$ resistance was not affected. This confirmed that de novo protein synthesis is not involved in the increase of $H_20_2$ resistance observed during aerobic growth, suggesting that an inducible response is not involved.
Furthermore, the addition of pyruvate to either mutant or wild-type cultures slightly decreased $H_20_2$-mediated killing, arguing that increased killing of spxB mutants is not due to toxic by-products resulting from the reaction of excess pyruvate and $H_20_2$. Together, this suggested that a product of SpxB activity other than $H_20_2$ acts to increase resistance
Furthermore, the ability of DF to eliminate the EPR signal caused by $OH^·$ in S. pneumoniae suggests that the inability of this iron chelator to increase $H_20_2$ resistance in S. pneumoniae is not merely due to a lack of permeability.

In the end, what I'd conclude is that different bacteria adopt different mechanisms to tackle this problem, and many of those mechanisms aren't known yet. So, there's no definite or exact answer to this question.
References:

ROS production in marine microalgae
NADPH oxidase
Activation of the OxyR Transcription factor by Reversible Disulfide Bond formation
Obligate Anaerobe
Catalase
Superoxide Dismutase
Iron Metabolism: From Molecular Mechanisms to Clinical Consequences - Robert Crichton
Oxygen metabolism of catalase-negative and catalase-positive strains of Lactobacillus plantarum.
Factors Contributing to Hydrogen Peroxide Resistance in Streptococcus pneumoniae Include Pyruvate Oxidase (SpxB) and Avoidance of the Toxic Effects of the Fenton Reaction

I'm sorry you're getting me wrong. I'll try editing my question a bit. Maybe the way I've asked it is causing some confusion. Thanks

So is there anything you still want to know? (I don't find any new question in it)

The main thing I would like to know how catalase negative organisms manage with the H2o2 they produce. The whole CGD thing I wrote is just to 'prove' that catalse negatives also produce H2O2.

Hey! I've come back to this answer after a long time. It finally says that there are mechanisms by which catalase negatives can handle the peroxide. Then the obvious question would be, why would CGD patients be susceptible to them? Wouldn't these bacteria survive by clearing of the peroxide with that mechanism.


text:
Will two Type IIS restriction sites cut if they are directly back-to-back?
I want to put two BbsI (or BsaI) restriction sites right next to each other, facing out, like this:
       \/ |BbsI||BbsI|  \/
CTCAAATGCGGTCTTCGAAGACGTTTTAGAG
   /\                      /\

Should I expect this to cut, or are the two restriction enzymes going to block each other?


text:
Whole Genome Sequencing vs Whole Exome Sequencing
I am working on a project where I want to discover causative genes for a certain disease I may have. I was wondering whether to get WGS or WES to perform this experiment:-
I am looking at SNP's and CNV's of my genes and I want to compare my data with that of normal and diseased individuals. For a gene I calculate the document distance for each group (normal and diseased) using this algorithm (https://math.stackexchange.com/questions/1080377/how-close-apart-are-two-message-document-distance-algorithm) as this will allow me to determine which genes I have that are abnormal or are "close" to being classified as abnormal and which genes are normal or "close" to being called normal per the algorithm and the data obtained from the two groups.
To perform this experiment I need to sequence my genome AND identify databases that would allow me to conduct my analysis. I wanted to know which is better for my experiment WGS or WES as publicly available data might also influence the decision.
Also, I believe alternative splicing adds a layer of complexity and wanted to know why WES is performed anyways.
Thanks in advance for your replies. Please do answer whatever you can. Thanks once again!

Hard to answer without knowing more about the disease. I think in many cases exome would be fine, since whatever disease you have is probably caused by a malfunctioning protein, but the mutation could also be in a splice site or regulatory sequence. With whole genome sequencing you'd get a LOT of crap, since we're all genetically dissimilar.

Possibly excepting some CNVs, a "distance" measure of genome sequence differences is unlikely to yield anything useful.  A single base difference can have huge consequences or have no consequence whatsoever despite having the same distance measure.

Thank you both for your replies! I have a list of candidate genes that were identified by GWA studies. I was thinking of profiling only those genes and looking for clues. As @mgkrebbs pointed out rightly that a single base difference can make all the difference or no difference whatsoever makes me question my method. Can you guys suggest alternatives?

If you have the money and decent computers then go for WGS. It is definitely more informative that WES. People do exome sequencing primarily to save resources.

@WYSIWYG it is also much, much easier to extract meaningful information from WES.

WES, almost certainly. First of all, the vast majority of phenotype-causing variants are found in exons. For most analyses that are looking into disease causing mutations, WGS is pointless. It only makes your analysis harder and doesn't actually add anything useful.
If you know you're interested in CNVs, that's different. CNV detection is hard in general but is particularly hard from WES data. Detecting CNVs in WGS data is much less error prone. However, you really should bear in mind that there are currently no 'good' methods to detect CNVs. This is a non-trivial problem and still in its infancy. While there are various methods that can detect CNVs, none of them find all (or even close to all). In fact, this is such a problem in the field that the currently accepted wisdom is that you should use multiple methods and combine the results. In fact, many recent CNV detectors do exactly that. And they still don't find all of them (especially not in WES data). Basically, CNV detection is not for the fainthearted and is certainly not for the non-expert.
The good news is that if you do have a disease causing mutation, it is very unlikely to be a CNV. It is far likelier that you're just looking for SNPs. Which brings us to the next issue. I'm afraid the algorithm you linked to, from what I can tell, won't help you at all. You're not trying to compare your gene to a list of healthy and unhealthy ones and figure out which group is most similar to what you have. First of all, because there are many differences (mutations) that don't actually have any effect whatsoever. These so-called synonymous mutations would still be counted by your algorithm but should be ignored. Second, because tiny differences can be enormously important. There are specific tools for what you want to do; don't try and apply broad, general mathematical approaches. You need algorithms that are specifically designed to deal with biological data and which take the underlying biology into consideration.
So, what you're looking for are programs called "Variant Callers". Two of the most popular ones are GATK and FreeBayes. These will read an input genome and compare it to a reference genome and give you a list of "variants", sites where the input differs from the reference. You then want to use resources like ClinVar or MutationTaster to check whether those variants are considered pathogenic. This is a bit of shameless self-promotion since I work for the company which created it, but VarSome, "The Human Genomic Variant Search Engine" is a new variant search engine that combines information from many different sources in a centralized and easy to search repository. I recommend it highly (and it is free).
However, before you get to finding your variants, you will need to align your genome to the reference. Basically, modern sequencing methods work by cutting the genome into many, many small pieces, copying each piece multiple times and then sequencing each piece. So the output of a sequencing run is a text file that looks like this:
@SN956:1934:H55WMBBXX:2:1101:0:15733 1:N:0:NTTACTCG
NCCCCAAGGAGACTTGCTGAGACCTTGAACAAGTGACACAATGTGAGCAGAACTTGTCTTGACAGAAAATGCTTTG
+
#AAAFJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJAJJJJFAJJJJJFJJ7
@SN956:1934:H55WMBBXX:2:1101:0:15743 1:N:0:NTTACTCG
NCTTCCTCACTAAAGTCCCATTTAGTGCTGATTGTGCTTTGGCTACTTCTCCTCTTGCCATTTTCCTGAACCCACG
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJF

This is usually several gigabytes (something like ~2-3G for WES and >80G for WGS). Therefore, the alignment of these sequences needs a powerful machine and you don't even want to try to align WGS sequences on your laptop. It will take weeks and will probably fail. Another reason why you should prefer WES over WGS for this. In my work, I routinely align WGS data to the reference genome and that can easily take >100GB of RAM.
The bottom line and what this rambling answer is trying to get across is that:

WES is better than WGS when searching for disease causing mutations. It is far easier to analyze the data and 99% of the cases you want are in exons. It is also much, much cheaper.
This isn't simple. You seem to think you can sort of waltz in and do it yourself. You can, but it is very far from trivial. It is also not cheap.

So, if you do actually have the money to pay for a WGS analysis (this costs several thousand euros/dollars, in case you didn't know), which is very surprising if you're just a private individual, instead of spending it on WGS, get a WES and spend your money on getting an expert to analyze your data for you. Seriously, this is what I do for a living, you really don't seem to have grasped quite how complicated it is. And no, I am not suggesting you hire me :). There are, however, companies that offer this sort of service. Use them, don't reinvent the wheel.
References
Useful review articles for CNV detection:

Zhao et al. BMC Bioinformatics, 2013, 14(Suppl 11):S1 (DOI: 10.1186/1471-2105-14-S11-S1, link)
Tattini L, D’Aurizio R and Magi A
Front. Bioeng. Biotechnol, 2015. 3:92. (DOI: 10.3389/fbioe.2015.00092, link)


text:
Aneuploidy in meiosis
I am quite confused about nondisjuction in anaphase II. If the double chromosome is not segregated, isn't it double. On pictures they are drawn as single but I don't understand why, and if they are double do they duplicate themselves in the S phase?

What is confusing me in picture above is cell (n+1) , why are all chromosomes single? I thought, after end of division in the third cell (labeled as n+1) there should be 3 chromosomes with single chromatid,  and 1 chromosome with 2 chromatid joined at centromeric region, as it is drawn in picture above that show nondisjunction in cell during anaphase ii . When and how do these 2 chromatids get physically separated?

can you add a little explanation about what is confusing? what pictures are you referring to? could you add them?

Hmm after your comment on  @ImtiazRaqib's answer it is now clear you are asking about when and how the centromeric region of 2 chromatids (of respective chromosome in respective cell division) get physically separated later-on if it skips the separation during metaphase-anaphase. Excellent question but original question too should contain diagram.

edit (addition) suggested

From Study.com >>
On the off chance that nondisjunction happens amid anaphase II of meiosis II, it implies that no less than one set of sister chromatids did not isolate.
In this situation, two cells will have the typical haploid number of chromosomes. Additionally, one cell will have an additional chromosome (n + 1) and one will miss a chromosome (n - 1) due to the nondisjunction of the chromosomes.
Here is a picture reference taken from Google.ca >>

In the image provided in the question, the chromosomes are not indicated clear and concisely, so it is very hard to follow through the logic of segregation of the daughter cells to (n + 1) and (n - 1) chromosomes.
As you can see from the updated image reference in the answer, we can notice that the cell that underwent nondisjunction in anaphase 2 gives rise to 2 daughter cells, in which, one cell receives the non-segregated chromosome plus one copy of a sister chromatid which makes it (n + 1) and the other daughter cell receives one segregated sister chromatid ONLY which makes it (n - 1).
On an additional note, from Biology Exams 4 U >>

Fusion of n+1 gamete with normal gamete (n) = 2n + 1 or Trisomic.
Fusion of n-1 gamete with normal gamete (n) = 2n - 1 or Monosomic.
In short, Nondisjuntion in meiosis II leads to trisomy (2n+1) or
  Monosomy (2n-1).

What is confusing me in picture above  is cell (n+1) , why are all chromosomes single. I thought there should be 3 single chromosomes and 1 double as it is drawn in picture above that show nondisjunction in cell during anaphase ii . I hope i am clear. :)

Look at the updated answer with a more clear and concise image. Hope it helps.


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What evolved to produce sweetness, plants or consumers?
I couldn't find an existing answer on this site, although I may be wrong.
What evolved to produce "sweetness", a pleasant reaction to the presence of sugar?
(A) Plants, using it to lure in consumers and spread seed
(B) Animals / consumers, which used sugar as a vital nutrient, to identify nutritious food, or
(C) Neither of the above; something else?

sounds like A and B could easily be answers - what do you think?

@VanceLAlbaugh I think either is plausible. I'm just wondering if there is one that can be proven or one that is widely accepted

@VanceLAlbaugh seems to be A and B both are correct but both are hypothetical/ speculative. Even if we have an established theory for only 1; the other seemingly could not be avoided as false. But it seems more to me that sweetness as indication of food was evolved earlier; and later-on plants 'applied' it for their benefit. So NOT a complete egg-or-chicken situation.

I don't understand the question. Is the question "do plants evolved sweetness first or did animals evolved attraction to sweetness first?". When reading a question of the type "What evolved for ...", it sounds like you are searching for a physiological explanation but the suggested answer don't go toward this direction.

@Remi.b I'm not exactly sure how to answer that, the idea of something evolving in response to something else seemed somewhat clear to me; answer however you think you can explain what occurred.

None of the above.
Seeking sugar evolved long before animals, before multicellular organisms even.
Plant evolved a strategy to exploit it much much later with the evolution of fruit and nectar.
Animals evolved to like the taste of sugar since it is the primary fuel almost all life metabolizes to live in an easy to digest form, literally a simple carbohydrate. plants use sugar substances as lures becasue that's what animals already wanted and plants were already making it. Also a lure is not going to evolve before the seeking behavior that would actually make it a lure. fruit and nectar are new sugar is one of the oldest metabolic compounds in existence.
Metabolizing glucose is one of the shared characteristics between Eukaryotes and Bacteria and is present in nearly all life,source. Meaning it is was likely present in their common ancestor. This means plants and animals have been eating sugars since before they diverged into plants and animals. . Chemotaxis  of motile bacteria towards glucose is well understood, and likely predates the existence of eukaryotes. source
The production of sugar by photosynthetic bacteria predates the merging of Eukaryotic cells and chloroplast ancestors. It was present in the Cyanobacteria that gave rise to chloroplasts, meaning sugars were produced long before plants existed. source the attractive aspect was only exploited later with evolution of nectar and fruit.

Plants have been making sugar since before they were plants and animals have been eating sugars since before they were animals... Perhaps you should clarify this statement (make it scientifically accurate so that it is not misleading).

Please add valid references (with links) to support your claims. Unsourced material may be disputed or deleted.


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Why are fish constantly in motion?
When I see fish in an aquarium, they never seem to stop swimming. This is in contrast to e.g. the penguins, who spend a lot more time just standing there.
Is this true in the wild or specific to aquariums for some reason? Is there a biological or evolutionary reason this is so? Is it a special case of some more general principle? (It occurs to me that fish are much smaller than penguins.)

I'm guessing it has to do with staying in one place - currents constantly move and change, so fish need to adjust with them - while penguins, for example, have their weight and the ability to lean if the wind blows.

Most sharks have to keep swimming in order to keep the gills supplied with oxygenated water. However, some can stay stationary. You can look up for a more convincing reference.

Wonderful question.

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A research, detailed in a 2012 issue of the journal PLoS Biology, suggests the fish do indeed take naps and can experience sleepless nights.
Another research with Pacific sand lance species, found them utilize a one of a kind methodology of tunneling into sand to rest and moderate vitality, and to maintain a strategic distance from predation.
Therefore, we can assume that fish sleep cannot be related to a terrestrial. As @Zxyrra has mentioned, with the currents being random in their direction, we can connect the reasoning of the continuous movement of the fishes as an effort to stabilize themselves.
On the aspect of any evolution or biological reasoning, fish sleep is still an ongoing research in marine biology. An interesting research have opened up a case in which through evolution, cavefishes have lost sleep. Information from this research could help you understand the evolutionary relationship of fish and sleep, in atleast, a broad scale.
UPDATE: Unique method of sleep in dolphins.
At the point when it's an ideal opportunity to rest, a dolphin will close down just a single side of the equator of its mind, and close the inverse eye (the left eye will be shut when the correct portion of the cerebrum dozes, and the other way around). Amid this time, the other portion of the cerebrum screens what's going in nature and controls breathing capacities. This process is termed as unihemispheric slow-wave sleep.

@WYSIWYG Here is an article that explains unihemispheric slow-wave sleep in dolphins.

Many fish do not sleep as we know it, most do however "sleep" while awake or sleep for very brief stretches of time. That alone means you are more likely to see them active than say a dog or rat.
Not all fish are in motion. Ambush predators can wait motionless for hours, but active hunter and foragers (aka most fish) will be in motion as long as they are not resting, becasue they are looking for food. Just like rats, mice, or other foragers.
Fish will drift if not in motion so most hide when resting or sleeping which makes them harder to notice. That means you will only see active fish. This simple observation bias is responsible for most of it.

I had to change this because recent studies have changed what we know about fish. This is why I love Stack Exchange, it makes me reseach things I never would otherwise. http://www.nature.com/news/2007/071016/full/news.2007.167.html

Do you have a citation on fish not sleeping? Pretty much every organism with a brain that has been tested sleeps, from fruit flies to whales.

@BryanKrause Apparently, some fish (or perhaps even cetaceans) keep one hemisphere active to keep swimming and put the other to rest. Then they switch them after a while. I remember reading this somewhere. I have to look up for a reference.

@WYSIWYG - yep, this is well known, and it is also known that other animals can also exhibit some sort of "local sleep" that doesn't cover the whole brain. That's a lot different than "never sleeping"

So you'd put most of it down to the observation bias, and the difference between fish + penguins is that penguins can get away with resting in the open because they won't get pushed around by the current?


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What animal/insect is this?
I saw this animal (probably insect) in my house in the Netherlands:

I have searched on the internet but was not able to find what this is, I first thought it was a kind of dragonfly, however there are only two wings which is not usual for a dragonfly. Any suggestions what this is?

I agree with the determination, though the picture is not this clear... Green lacewings have a good appetite for aphids and other plant parasites. I suggest you could try to rear and breed it, if you have several plants within your flat. Both larva and adults exert a regular and continuous control on phytoparasites, particularly Hemiptera...

It is an insect of family Chrysopidae under the order Neuroptera (net-winged insects).
The insects of this family are commonly called Green lacewings.
Neuropterans have large lateral compound eyes, four wings and a generalised pattern of veins.

(Source: Wikipedia)
Identifying morphological features:

Soft-bodied insects with copper-colored eyes, long thread-like antennae, and lacy wings.
Most species are green, but some are brown, especially overwintering adults of certain species

( Reference: Bugguide )
A similar family of lacewing, Hemerobiidae also exists which are brown, have rounded smaller wings and found throughout the world.
Here's a link to wikipedia showing the phylogeny of the Neuroptera as explored using mitochondrial DNA sequences: link .


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Do plants have cellulases?
I can't seem to find the answer to this. Not even Wikipedia could help- it mentioned bacteria and fungi that have cellulases but not plants. Using my own reasoning, I would think that

On the one hand it is better if plant cells do not have cellulases so that they do not break down the cell wall. Although maybe it doesn't matter because the cellulases would not reach the cell wall without being actively transported out of the plasma membrane.
Perhaps it might be useful for plants to have cellulase. I don't know if plants have any sort of immune system like humans, but plants also get bacterial and parasitic infections in their cells. Maybe plants should have some mechanism to destroy an unhealthy cell? In that case, the destroying cells would need to use cellulase, would they not?

https://www.ncbi.nlm.nih.gov/pubmed/16344110

@WYSIWYG Thank you for your reply! The article certainly answered my question, but the first sentence also confused me: "Many bacterial genomes contain a cellulose synthase operon together with a cellulase gene, indicating that cellulase is required for cellulose biosynthesis"        How does the fact that 'many bacterial genomes contain a cellulose synthase operon together with a cellulase gene' imply that 'cellulase is required for cellulose biosynthesis'? Would be grateful if anyone had any ideas about this!

I guess that these bacteria also produce cellulase for turnover of cellulose. Just the way all organisms have proteases to enable protein turnover. I did not get time to read that article in detail. I shall post an answer when I get time.

At least some plants have cellulases which can be used to cleave primers from mature cellulose chains.
Cellulose synthesis requires chain initiation and elongation (the two processes are separate). CesA glucosyltransferase initiates cellulose polymerization using a steroid primer and UDP-glucose. Cellulose synthase utilizes UDP-D-glucose precursors to elongate the growing cellulose chain. In some plants cellulase is then used to cleave the primer from the mature chain.
Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119035/


text:
Chemokines vs Chemoattractants
What differentiates chemokines from chemoattractants? They both are grouped by their chemotaxic function, but what features separate them.
What are examples of other chemoattractants that are not chemokines? Or examples that are not even proteins at all?

What research have you done on this subject? Simply reading the respective Wikipedia pages should tell you the difference (hint: read about chemotaxis and chemokine).

See also: http://biology.stackexchange.com/questions/8139/what-is-the-distinction-between-chemokines-cytokines-interferons-and-interleuk

@MattDMo I am not asking about chemotaxis vs chemokines or chemokines vs cytokines. Strictly the difference between two groups of chemotaxia inducing molecules. The link provided does not help answer this question. I will reword my question to make this more clear.

Did you read both of the suggested Wikipedia articles entirely? The chemotaxis article includes information on chemoattractants, as it doesn't have its own page. I know the question I linked doesn't completely address your question, which is why I didn't mark it as a duplicate. It was merely intended to provide some additional information.

@MattDMo Yes, the wikipedia article on chemtaxis mentioned chemokines once as a subgroup of chemoattractants, however there was no explanation on why this was. The article on chemokines also did not offer an explanation on my question.

And there is your answer. Chemoattractant is a general term to describe all molecules/atoms/ions, organic and inorganic, that induce cell motility. Chemokines are one type of chemoattractant, there are a number of others as well.

@MattDMo Ok thank you for helping me find this answer. I will need to improve my questions in the future. I was looking for what separates chemokines out from chemoattractants, which appears to be their four cysteine residues and approximate size of 8-10 kilodaltons. My confusion was from my professor's definition of chemokines as any protein that will induce chemotaxis.


text:
Why does the pH decrease, when adding pancreatin to different types of milk (cow milk, soy milk etc.)?
I'm experimentally observing how pancreatin affects the pH in different types of milk.
Why does the milk's pH decrease when I add an enzyme solution to different types of milk (e.g., cow milk, soy milk etc.)?
I am not sure how to explain this reaction.
Thank you for your help.

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

@Chris This is more of an experiment than homework.

From no-view a homework question. As well  Seeks visualization of what could actually going on there in chemical scale, which may require expertise on respective fields.

I have edited your question, removing the word level after pH. Also named the enzyme mixture in the title to make it specific, although this pancreatic preparation is so crude it hardly deserves a name.

Isn't it something to do with making cheese? That's what upsets vegetarians? Is it the same as the renet reaction? Try googling that.

the pancreatic fluid contains lipase which breaks down the fat in the milk in to fatty acids and glycerol. The fatty acids produce lower and create a more acidic pH.

Please don't answer questions when others have flagged lack of effort on the part of the poster. It is clearly a homework question, so that if she used your answer she would be getting undeserved credit. Fortunately the fact that she did not respond to the original comments suggests her deadline is long past and she has no further interest in the question. Which is why I would ban all homework questions if I had my way.

@David Which I'm glad you don't because some people don't have a teacher they can ask and the answer might not be in their textbook!

Please add some references! :)

@L.B. — l recognize my view is not list policy, and meta would be the place to discuss this, but there is no reason for not drawing attention to the characteristics of many homework posts.

@David There is that. And also I don't appreciate blatant homework questions. Just making the point that there are people like me who have questions regarding homework (and are either self studying or homeschooled and so don't have a teacher) who are afraid to ask for fear of a downvote and therefore, loosing reputation.

@L.B. — OK. I'll try to be more tolerant in future.


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What species of insect is this?
I saw this insect near a beach in Corsica France:

It's a mole cricket (in the family Gryllotalpidae).

Notice the cricket-like appearance of the posterior/abdominal portion of the insect, but the powerful, broad and flattened fore-legs that are designed for digging (reminiscent of a mole's digging legs). In fact, the family name literally means cricket-mole (from Latin, 'gryllus' = cricket and 'talpa' = mole).
Mole-cricket fore-legs:

Anterior mole legs:

The Gryllotalpidae are a monophyletic group in the order Orthoptera (grasshoppers, locusts and crickets). A 2015 paper by O. J. Cadena-Castañeda clarified/updated the phylogeny of this family using morphological characteristics.
The specific species is dependent on your location and morphological characteristics (and possiblly "song" differences too).
See here for a brief explanation and access to dichotomous keys to use to better ID the specific genus. Other keys exist here (SE USA), here, and likely via a google search. However, I couldn't quickly find a European key.
Here's an additional useful resource on these insects from University of Florida Entomology and Nematology Department.
Based on the OP's location in France, the European mole-cricket Gryllotalpa gryllotalpa (or one of it's closely related European allies in the Gryllotalpa genus) is probably a good initial guess at the OP's specific species. As seen from UC Berkeley's "CalPhotos" collection:

Note: to follow-up with a now deleted answer. The OP's insect is NOT an earwig. The confusion lies in the existence of posterior cerci. Though cerci are well known on earwigs (i.e., their "pincers"), many insects have a pair of posterior cerci (though typically they are functionless vestigial structures). Therefore, cerci are not strictly indicative of earwigs. Further, the enlarged and flattened fore-limbs of the OP's picture are not present in any species of earwig (which do not dig), but instead are the calling-card for the digging mole-crickets

I assumed the deleted answer (earwig) was incorrect and that's why I waited for more answers. Thanks for the detailed explanation!


text:
Source of blood glucose during starvation
During starvation there is many source for glucose such as pyruvate, lactate, amino acids (except leucine and lysine) and glycerol from triglycerides but what is the major source of blood glucose ?

Welcome to the Biology SE site. Please take the tour and carefully read through the help to learn more about the site, including what is on-topic and what is not, and how to ask a good question. Please ensure your post is formatted correctly as well.

Homework questions are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy.

It is not my homework its my question i am a medical student and we dont have homework ok?

@AhmetÖz you should at least show some attempt in order to answer your own question. This community is not a QandA forum.

I dont undetstand this rules i have a question about a subject and i want an answer . look my profile i asked a question about ldh reversiblity and it was my own question too . there is not any difference this two question for me .

@AhmetÖz there are some answers below, you should take a look at them, and then either comment with any clarification or elaboration that is necessary, or select one of them as an answer.

@AhmetÖz "Homework" is interpreted to mean any academic or other assignment, test preparation, or task given in relation to a class, educational setting, or self-learning. Just because you're a med student doesn't excuse you from doing some research before you ask here. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked, what you do know about the topic, and where exactly you still have questions.

I have been researching this question for 6 hours. Even I still cannot understand the mechanism of starvation.

@Ahmet Öz - if you want to be a good doctor, asking questions when you don't know something is important. But if you want to be a really good doctor, reading and researching are critical, as is good communication skills. People on this site gave you site guidelines and you responded very bluntly if not quite rudely. As a doc, I think I know a bit about this. Starvation is not a mystery by any means.

The (very) short answer is gluconeogenesis. When glucagon levels are high in response low glucose or low Insulin (perceived in the case of Insulin resistant DM Type II) key enzymes will be inhibited to prevent glycolysis and other enzymes will be activated to produce glucose from various substrates.
There are a few sources that can feed into the gluconeogensis machine. Two that are commonly used in short term fasting are lactate via the Cori Cycle and Alanine via the aptly named Alanine Cycle. Now when we get into long term fasting (i.e. starvation) things start to change a bit.
In starvation, glucose is conserved as much as possible and many tissues start using ketones (which are derived from Acetyl-CoA which are in turn usually derived from fatty acids) for energy. But even then, there is still a demand for at least a minimal level of glucose. This can be synthesized from a few sources. The backbone for triglycerides, glycerol, can be fed into gluconeogenesis. But that is not the main source for glucose during starvation. The main source is from gluogenic amino acids. These amino acids can be metabolized into pyruvate which can then enter into gluconeogensis.
This is one of the reasons you get muscle wasting during starvation but not in calorie restricted diets. During calorie restriction you have enough glucose to maintain adquete blood sugar between meals, and any energy deficits can be met through β-oxidation of fat. Thus you lose fat. However, when you enter starvation, the glycerol obtained from lipolysis (breaking down fat) isn't sufficient to maintain adequate blood glucose and you have to turn to muscle breakdown. This breakdown of muscle tissue is mediated by high levels of Cortisol, a hallmark of starvation that is not seen in calorie restricted diets. If you want to see the effects of starvation levels of Cortisol in a non-starving person, look into Cushing's Disease. You see similar breakdown in muscle that you would normally see in a starving person.

There are a couple of different levels of starvation, from fasting to malnourishment to long-term starvation.
Let's start from consumption of a carbohydrate-heavy meal. The carbs in this meal are readily converted into glucose, and blood sugar levels will increase. Assuming you're not diabetic, this will lead to increases in insulin production, which will lead to among other things, uptake of glucose by hepatocytes (liver cells) and conversion into glycogen for short-term storage. At some level, excess energy is also converted into fatty acids for more long-term storage. Other cells (like muscle, brain etc) will continue to use glucose for energy.
Say this was an evening meal, and you don't eat again until the morning. Over time, blood sugar levels will drop. This leads to decreased production of insulin and increased production of glucagon. As a result, hepatocytes reverse course, breaking down glycogen, turning it into glucose and secreting it from cells to raise blood sugar.
But let's say you miss the morning meal. Eventually, the liver's stores of glycogen will run low. At this point, the body can turn to stores of fat for energy. But most fatty acids cannot be converted into sugars. As a result, blood sugar levels do not rise. Instead, they are converted to molecules called ketone bodies, which can be released in the blood and used by most cells for energy.
However, some amount of sugar is still required to construct certain biological molecules. Also, certain cell types (particularly red blood cells) cannot use ketone bodies for energy. Even with abundant fat reserves, if no additional carbs are consumed, those sugars have to come from somewhere, and they can't come from fat. Instead, the body will begin to degrade cellular protein - some amino acids can be broken down to generate sugars. During long-term starvation, muscles, including those in the heart, begin to be consumed, and anemia is often an early symptom of starvation (since RBC's don't have sufficient energy).

Some of the information contained in this post requires additional references. Please [edit] to add citations to reliable sources that support the assertions made here. Unsourced material may be disputed or deleted.