text:
Is starch and glycogen digestion intra or extracellular?
Do humans have the enzyme for starch intracellular digestion?
Also, do plants have the ability to digest Glycogen? Intra or extracellular, or both?

DIGESTION IN THE MOUTH:
Starch digesting enzymes are extracellular in human beings.All starches and some glycogen are hydrolysed in the mouth by the time the food is swallowed due to the effect of ptyalin(alpha amylase)enzyme in our saliva.
DIGESTION IN THE DUODENUM OF SMALL INTESTINE:
Pancreatic juice containing pancreatic amylase promotes extracellular starch digestion.And almost all the starch in food is completely hydrolysed to maltose, limit dextrin and isomaltose in its effect.
The same enzyme pancreatic amylase also causes the total extracellular digestion of glycogen in the duodenum and forms maltose and other products like limit dextrin, isomaltose.
DIGESTION IN THE UPPER JEJUNUM OF SMALL INTESTINE:
Products like limit dextrin and isomaltose is digested extacellularly in the small intestine by the enzyme isomaltase and maltose by maltase in intestinal saccus entericus to form glucose.
NATUREOF INTERCONVERSION OF GLYCOGEN AND GLUCOSE IN HUMAN:
The principal glycogen storing organ in human is the liver and glycogen formation or hydrolysis in the organ is 'intracellular'.
NATURE OF INTERCONVERSION OF STARCH AND GLUCOSE IN PLANTS:
Similarly in starch storing organs in plants the hydrolysis or formation is 'intracellular'.
REFERENCES:
https://en.m.wikipedia.org/wiki/Starch
https://en.m.wikipedia.org/wiki/Glycogen
https://www.ncbi.nlm.nih.gov/books/NBK21190/
https://en.m.wikipedia.org/wiki/Carbohydrate_digestion
http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2004.01101.x/pdf

It seems like you're getting confused between starch and cellulose. Amylase digests starch, and is obviously found in humans.

xtremely sorry @ another'Homo sapien'.I 'll edit right away.And thank u really.

"Digestion in the pancreas" really?


text:
Enlargement of thyroid gland
Why does thyroid gland enlarge both in hypothyroidism and hyperthyroidism?
Hypothyroid goitre is due to lack of iodine in diet and hyperthyroid goitre (Exopthalmic goitre, Grave's disease) is due to oversecretion of thyroxine, or Thyroid stimulating Hormone. How does these two apparently opposite effects produce similar physical manifestation of the disorder (symptom) i.e is the enlargement of the thyroid gland?

Check  this out. It is a very similar question.

The primary activity of the thyroid gland is to concentrate iodine from the blood to make thyroid hormone. The gland cannot make enough thyroid hormone if it does not have enough iodine. Therefore, with iodine deficiency the individual will become hypothyroid. Consequently, the pituitary gland in the brain senses the thyroid hormone level is too low and sends a signal to the thyroid. This signal is called thyroid stimulating hormone (TSH). As the name implies, this hormone stimulates the thyroid to produce thyroid hormone and to grow in size.
In Graves' disease one’s immune system produces a protein, called thyroid stimulating immunoglobulin (TSI). As with TSH, TSI stimulates the thyroid gland to enlarge producing a goiter. However, TSI also stimulates the thyroid to make too much thyroid hormone (causes hyperthyroidism). Since the pituitary senses too much thyroid hormone, it stops secreting TSH. In spite of this the thyroid gland continues to grow and make thyroid hormone. Therefore, Graves’ disease produces a goiter and hyperthyroidism.

Source: American Thyroid Association. What is a Goiter - Causes

source: Stack Exchange

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sort: votes


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Why do our limbs and other body parts get numb/feelingless and then they start to tickle?
Why do our limbs (legs, arms) get numb/feelingless when they are under prolonged pressure or when one has crossed his/her leg while sitting for a long period?
After we move it to a more relaxed or natural position numbness goes away and we get the really strange and hard to bear tickles. Why does the numbness go away by doing this and why do why get these odd tickles?

This other post should answer your question (The question had been quite poorly asked I think but well answered!)

It doesn't elaborate the needle sensation and for another it not always happens because of apparent pressure, like I stated, if one keeps his/her legs crossed (like this) even than the foot on the top gets numb.

Keeping feet crossed like in your picture, involves pressure on nerves in both the legs. If one leg applies pressure on the other, it feels the same amount of pressure. (Newton's third law)

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RNA secondary structure comparison
Do you know any program which can compare two and more different RNA secondary structures? I need find some (dis)similarities between lots of predicted secondary structures. And create maybe common sec. structure/shape.

You can use R-coffee of the T-coffee suite of tools. In general, the *coffee tools are excellent and work very well if you can get over their author's self obsession1. R-coffee can align RNA sequences taking into account structural information:

1 The guy actually adds his name to the output of all his programs! Seriously, he does. Apart from being simply ridiculous, this also affects other programs you might want to pipe your data to. For example, I wanted to pipe t-coffee alignments to an alignment viewer and I had to parse out his effing name in order to be able to do it.

I was amused by your remark - but from what I can see, you'd only have to delete the second line of text.

@Superbest yes, isn't that enough? The default output of t-coffee is in clustal format, a standard and widely used format for alignments. Because of the author's self importance, I had to edit the output to remove his name before being able to view the alignment in another program. Just cause the guy likes to see his name written everywhere.

there a number of tools in the Vienna package (RNAalifold, RNALalifold):
http://www.tbi.univie.ac.at/~ronny/RNA/index.html
some other tools are available from Freiburg Univ. such as:
LocARNA or CARNA (http://rna.informatik.uni-freiburg.de/CARNA/Input.jsp)


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How to determine the actual flux in the human metabolic model of a cell line?
The problem to be solved is to determine what the flux values are for the different reactions in the human metabolic model.
As far as I understand, a good way to do that would be to use gene expression data to calculate a flux, but I am not sure that is a good idea or if it is even possible.  I am not very sure of what is the correct process to do this.
Thanks for any help or suggestions!

A metabolic flux is the rate at which a metabolite gets converted into another metabolite by an enzyme. Metabolites aren't coded for by genes, so gene expression data doesn't help determine metabolic flux, unless there is some feedback that will cause the concentrations of the various enzymes involved to change via gene expression. But that occurs on a timescale which is much slower than typical metabolic flux.

I am no expert on the field, but quantifying gene expression isn't a simple problem, although it is a possibility.
A solution I know to be used is using radioactive markers. See for example this review and particularly "The cell-cell lactate shuttle" section, which might give some insights.
This can include radioactive tracers (such as [14C]lactate), non-radioactive tracers (with [13C] or [2H]), "net exchange measurements" (I don't really know what this means here, perhaps the kind of exchange calculations they present here), and muscle biopsies (it is then possible to measure the metabolite concentration by enzymatic reaction or spectrophotometry for example).

Summary: Try one of the extensions of FBA which take gene regulation into account, but be aware of the limitations. See below for references.
Long answer:
There are two approaches to estimating internal metabolic fluxes: The (primarily) experimental and the (primarily) computational. I say primarily, because even for the experimental approach, a large amount of computation need to be done, and for the computational approach, experimental studies must be consulted in order to set realistic model parameters.
Experimental determination of internal metabolic fluxes has been centered around 13C-metabolic flux analysis (13C-MFA) performed through carbon-labelling experiments, as mentioned above. 13C-MFA is complicated and expensive, so there is a relative lack of experimental data, and most experiments cover only a few fluxes when compared to the number of possible reactions, typically several thousand in genome-scale metabolic models. In 13C-MFA, most experiments estimate the fluxes in a much smaller model (for example the central carbon metabolism), avoiding or ignoring other possible reactions, and the set of fluxes that are estimated varies between experiments.
Models which are used in computational approaches to flux analysis are typically larger than the models used in 13C-MFA experiments, and thus it is usually not possible to determine all the fluxes from experimental data alone. Thus, an approach called constraint-based modelling (COBRA) is mainly used. The basic assumption of most current flux analysis methods, both experimental and computational, is that metabolite concentrations are at steady state. Mathematically, this can be described by the equation
$S\overrightarrow v  = 0$
where $S$ is a stoichiometric matrix relating the metabolites and all possible reactions (basically a compact description of the metabolic model), and $\overrightarrow v$ is the flux vector containing all the flux values. In addition to the steady state requirement, constraints are typically applied to the uptake and excretion rates of various metabolites, limiting them to biologically realistic values. Other requirements, such as requirements for ATP maintenance consumption can also be applied.
Because there are typically many possible flux patterns that obey the above constraints, a principle is needed for selecting a biologically realistic solution from the solution space of feasible flux patterns. Assuming that cells optimize their metabolic patterns in some way, different objective functions are used that attempt to capture the metabolic behaviour for cells. Once an objective function is chosen, the set of possible solutions can be searched for the flux pattern that gives the highest objective value as a function of the flux vector. Given that the objective is linear (simply a weighed sum of fluxes), an optimal solution can be found rapidly. In general, many different optimal solutions may exist for a given objective function. The method of applying an objective function to a constrained metabolic model at steady state is called Flux Balance Analysis (FBA).
The most basic and a popular objective is maximization of biomass production. While useful for determining maximal growth rates, this objective is unlikely to be realistic when applied to human cells. FBA and related methods is generally well-suited to determining performance limits for single endpoints such as growth rate or production of a single metabolite, but not capable of precisely determining all internal metabolic fluxes. The point that many optimal solutions may exist for a single objective function is important in this regard.
As 13C-MFA and FBA are based on the same concept of metabolite balancing, they can be viewed as different ends of the same spectrum, from purely experimental to purely computational, with 13C-MFA constrained FBA (where 13C-MFA results is used to constrain the possible fluxes in a model before optimizing an objective function, or minimizing the difference between the experimental fluxes and the FBA solution, subject to additional constraints) in the middle.
For an introduction to Flux Balance Analysis, see  Orth, Thiele & Palsson: "What is flux balance analysis?" Nature Biotechnology 28 245-48 2010.
For performing Flux Balance Analysis, several software packages are available. One of the most used is the COBRA Toolbox for Matlab. A version for Python called CobraPy is also under development. Both are available at http://opencobra.sourceforge.net/openCOBRA/Welcome.html
Note that most gene-expression data only shows relative changes in expression between two conditions. Most methods are thus based on comparing two different conditions. More recently, RNA-sequencing (RNAseq) may also be used to obtain more direct measures of gene expression levels. Many extensions and variations on FBA have been published which take into account gene expression. Some of these are regulatory FBA (rFBA, Covert & Palsson: Journal of Biological Chemistry, 2002 277, 28058-28064), Metabolic Adjustment by Differential Expression (MADE, Jensen & Papin: Bioinformatics. 2011 Feb 15;27(4):541-7 ) and iMAT (Schlomi et al:  Bioinformatics (2010) 26 (24): 3140-3142.). For a more recent method, gx-FBA (gene expression-FBA), see *Navid & Almaas, BMC Systems Biology 2012, 6:150).
You may also want to read this article which deals with construction tissue-specific metabolic models: Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol. 2010 Sep 7;6:401. doi: 10.1038/msb.2010.56.
The problem with using FBA and related methods to estimate internal fluxes is that validation of the results is difficult because of the mentioned lack of experimental data. I wrote a project report on the topic during the last year of my Master's, which includes a basic description of 13C-MFA. It can be read at http://www.slideshare.net/jarlemag/rapport-31295058

This is a wonderfully complete answer.  Thank you very much!  I am actually on the path of using FBA to achieve this.  In our project, we have several cancer cell lines from the CCLE that we are trying to simulate through FBA.  However, we would like to "customize" the Human Metabolic Model to the characteristics of each cell line in order to get a better baseline for analysis.  The CCLE provides some gene expression data, so we'll definitely look into that.  Again, thank you!  If you have any other suggestions, I would gladly hear them :). +1.

Glad to be of help. It's a bit difficult to give suggestions without knowing more specifically what you want to do, but feel free to ask if you have any more questions. May I ask what software you will be using for the analysis?

Absolutely.  So far, I have chosen COBRAPy to run FBA (don't have access to MATLAB and I'm experienced with Python).  Perhaps the greatest aid I could get from you would be your opinion.  I have asked this about using the HMM, as well as this on where to get good HMM data.  In essence, I am trying to gauge what I need to do to predict the outcome of gene knockouts by cancer therapy drugs.

That's cool. I'm in the same situation, also using CobraPy. I like it better than the MATLAB Toolbox, but unfortunately it doesn't have as many modules available. I've been working on implementing some methods only published as MATLAB code (or not at all) for use with CobraPy, but they're not quite ready yet. I'll see what I can do for your other questions, although I haven't worked on any applications of FBA to human metabolism.


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How usable is the Human Metabolic Model to predict biomass?
In order to use the Human Metabolic Model for Flux Balance Analysis of specific cancer cell lines, we would like to know what sort of flux values have been determined for the Human Metabolic Model.
Basically, how usable is it to predict biomass production in humans (to some extent)?  If it is not very good for this, what other options are there?
Thanks very much!

Firstly, it is important to remember that Flux Balance Analysis computes theoretical performance limits, i.e, the theoretically optimal behaviour of the system with respect to the objective and constraints. When growing bacterial cells growing in culture evolve under selection pressure for biomass production, the theoretical limit on biomass production may indeed be approached, see for example Ibarra et al: Nature. 2002 Nov 14;420(6912):186-9. (http://www.ncbi.nlm.nih.gov/pubmed/12432395) and Fong & Palsson: Nat Genet. 2004 Oct;36(10):1056-8 (http://www.ncbi.nlm.nih.gov/pubmed/15448692).
How closely other systems can be expected to approach optimality should be considered on a case-by-case basis, and the constraints should be realistic. In humans, you would for example expect that the physiology of the persons (blood glucose levels, etc.) would greatly affect the growth rate of any cancer cells, in addition to the structure of the tumour (especially blood supply). For cells growing freely in culture, one might expect FBA to be easier to apply.
For HeLa cells growing in culture, the results of at least one study suggests agreement between experimental and FBA-predicted growth rates: See Resendis-Antonio et al: Modeling core metabolism in cancer cells: surveying the topology underlying the Warburg effect. PLoS ONE, 5 (2010), pp. 1–11 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012383)
Whether the precise biomass production rate is predicted or not may actually not be so important, and there has been considerable interest in applying FBA to studying various aspects of cancer metabolism. Here are some papers that may be of interest:
Ashwini Kumar Sharmaa, Rainer König. Metabolic network modeling approaches for investigating the “hungry cancer”. Seminars in Cancer Biology 23:4,2013, 227–234 (http://www.sciencedirect.com/science/article/pii/S1044579X13000436) (Review)
Shlomi et al.: Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect. PLoS Coputational Biology 2011 (http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002018).
Lewis & Abdel-Haleem. The evolution of genome-scale models of cancer metabolism. Front. Physiol., September 2013 (http://www.frontiersin.org/Journal/10.3389/fphys.2013.00237/full). (Review)
And a relevant Master's thesis: Computational Metabolic Modeling of
Cellular Growth: From Bacteria to Cancer. http://www.cs.tau.ac.il/thesis/thesis/Benyamini.pdf

As usual, awesome answer.  Thanks very much for your input!


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What are good data on the Human Metabolic Model and where can I get them?
Trying to get a good SBML representation of the Human Metabolic Model for use in Flux Balance Analysis and drug targetting (i.e. gene knockout) simulations.
What are good sources for these data?
Thanks very much!

As far as I know, there is no one model officially known as "the Human Metabolic Model", but the Recon 2 model, described as a "consensus" model and the most comprehensive to date in Thiele et al. 2013, A community-driven global reconstruction of human metabolism (http://www.nature.com/nbt/journal/v31/n5/full/nbt.2488.html) is available at http://humanmetabolism.org/?page_id=75
Tissue-specific models are also available. See for example  Wang et al.:  Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Systems Biology 2012, 6:153:

Interesting.  Yep, I have found Recon 2, but I am also having trouble matching the drug therapies against it (I assume I should do that through figuring out which genes are knocked out by each therapy and trying to match them with the model).  Tissue specific models sound interesting.  Thanks!


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Valid comparison of gene expression between several genes in several cell lines
We have gene expression data (Affimetrix mRNA gene expression results) for several cell lines, over a set of genes.  Our goal would be to be able to compare relative gene expression for genes over the different cell lines.
The method we have thought of so far involves calculating some sort of gene-based average (the expression of a particular gene over all the lines) and normalizing our expression data, grouped per gene, based on that.  However, we are not sure that this is a valid method for obtaining relative expression data from our data set, especially so that we can compare the data from several lines.
Does this seem like a valid strategy?  How is this normalization commonly done?  Should we do something differently to get a better comparison?
Thanks so much!

Perhaps a formal statistical test like ANOVA would be applicable.

If your data came from a single lab and a standard protocol gcrma normalisation is a good method to use (and comes with the affy R package); if the arrays are of U133A or HGU133plus2 types frozen RMA may be a good method to use. Finally you can check for and control for batch effects using ComBat and use the corrected expression data.

This is not an easy task, as there are many factors which you have to take in account. First there are intra-essay differences as slightly different conditions for each set of probes for the repetitions. Then, there are inter-assay differences, as differences in the array slides and so on, this paper ("Analysis of microarray gene expression data") goes into more details.
This articles might be helpful as well:

Multiple-laboratory comparison of microarray platforms
Increasing consistency of disease biomarker prediction across
datasets.
The curse of normalization.
Microarray probe expression measures, data normalization and
statistical validation.

What you could also do is go over the Researchgate, I think there are more people around with a lot of experience in this field.

Thanks a lot.  These are all great tips!  I'll look into the articles and probably head over to Researchgate.


text:
What is the difference between the basal membrane and the basal lamina?
I'm researching about the basal lamina in lung tissue and I'm not sure if the basal membrane is the same.
What is the difference between them?

The basal lamina is a specialised type of extracellular matrix. It is found on the basal side of all epithelial tissue but can also surround other cell types like myocytes and adipocytes. It is also called the basement membrane, although it is not the traditional plasma membrane that we have come to know and love. Rather, it is composed of proteins (often glycosylated) and polysaccharides.
The basal membrane is the actual plasma membrane on the basal side of an epithelial cell (adjacent to the basal lamina/basement membrane).


text:
How to safely sterilize urea-containing growth medium?
I'm using urea-containing growth medium for experiments with bacteria (1-2 l/day). After the experiment, the growth medium has to be sterilized and disposed. I did this so far by autoclaving, but our technician complained about the ammonia smell that develops (urea breaks down when heated, releasing ammonia).
I'm pretty sure the amount released into the air is not dangerous (I've emptied the autoclave several times), especially if you don't purposefully breathe in the first gust of air that comes out after opening, but I think it's useful to look into alternatives. Also I'm not sure if the autoclave might get damaged on the long run.
Does anyone have experience with this? Do you see a way to sterilize larger amounts of growth medium reliably without heating?

You can use chemical methods to sterilize the media - I have used cleaners which develop chlorine dioxide for this purpose. This is smelly as well as you will always smell some of the chlorine dioxide when emptying the vessels.

Is the bacteria potentially pathogenic? What bacteria is it basically?

It's Sporosarcina pasteurii, not pathogenic and not a GMO. I just wrote an email to our safety officer to inquire if sterilizing is absolutely necessary, but I guess I will have to. Also, I might use GMOs in future, and then it's a must.

Bacilli can form spores; I am not sure if this one can. Sometimes I use concentrated acid (H₂SO₄) to disinfect stuff, especially flasks that are long unwashed (with media still in it; they contain a variety of organisms). You can neutralize the acid after the treatment. It is a little dangerous though. Common disinfectants should work for you.

Autoclaving is the best way for sterilization. If your growth medium is large, how much chemical disinfectant do you think you would need to bring up to its working concentration?
Add some acid to your waste medium (so that it's only weakly acidic), not as disinfectant, but to suppress ammonia formation. Urea will still break down during autoclave, but ammonium ion (pKa~9) will generally stay in solution.

You should check with your institutions guidelines as different facilities have different regulations but generally it is acceptable to:
In a fume hood and in a ventilated (unsealed) container:
1.add liquid bleach to a final concentration of 20% (add 1 part bleach to 3 parts culture)
2.Let sit overnight
3.Dispose down drain with copious amounts of water


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Can the human body enter "Power Save" mode?
Once a year, I am fasting for 24 hours. No food or drink at all for whole 24 hours.
Recently I thought about what is happening to me during those 24 hours, and realized there might be something strange going on. I will try to describe the things I find strange:

I do not feel thirst or hunger at all. Not even after 20 hours.
I still urinate after 10, 15, and 20 hours, and unlike what I would expect from not drinking, the color is not very dark. (actually, same as when I drink normally)
I can still perform energy consuming tasks after 20 hours without eating or drinking anything. I'm not talking about running in the park or lifting weights, but I can walk, do house chores etc, and only after 20 hours or so the body starts to "protest" in the form of headache.

All of the above led me to think that maybe when knowing it's going to be deprived of energy, the body enters "Power Save" mode, allowing it to function as usual under those conditions? (to a limit of course, but still - I would expect hunger, thirst, and headaches to appear few hours into fasting)

I just voted to close, because I find it an anecdotal question. Maybe the headache is caused by a lack of coffee etc etc. It sounds all like a personal monologue on your experience.

@AliceD fair enough, wasn't sure if it fits here or not. Still giving it a chance to see if others find it off topic as well and in this case will delete. (for the record, the headache is really not the issue here)

Please leave the question as is, it is just a single vote - no harm done :) And I understand the headache is just a side note. I just took it as an example. If you could try to extend the horizon of your question to broaden its scope I'm happy to retract the vote. Btw: fasting = good, no liquids = nono afaik

Thanks @Alice, not going to delete yet. Any tips how to broaden the scope?

If you are performing the fast for ritualistic or spiritual purposes, then that mental state likely overcomes the feeling of thirst or hunger, especially if you are an otherwise healthy person.
As for the physiological aspects. The Human Body is made up of 2/3 water, and as your kidneys are still functional, they are constantly filtering, and creating urine. The body can last a few days without water.
As for food, the body has about a one day supply of sugar, assuming limited exertion, that it can consume before it begins to break down other substances. Then there are the fat reserves. The average person will likely have on the order of 7 to 15 kilograms of fat in reserve. There are 9 calories per gram of fat, so roughly 63 to 135 thousand calories worth of energy. Since the average adult will use about 2000 calories a day, then you can see that burning body fat alone would allow about a months worth of energy.
I am not saying that these are optimal conditions, but the body of a healthy human adult can easily withstand a 24 hour fast with no adverse effects. You would likely encounter more problems if you tried to go without sleep for the same period of time than if you refrained from food or water.

So in essence, in reply to the actual question of "Can the body enter power save mode" you say "No, it's just a mental state"?

I am saying that while feelings of thirst and hunger are sensations derived from physiological effects, they are experiences which are interpreted by the brain, and as such humans have developed the cognitive capacity to act against their instincts, and things such as meditation, prayer, repetitive ritualized behaviors can overcome the perceived sensations of the body. I said that if the reason for your fast was related to such a behavior it is likely that not experiencing the sensations of hunger and thirst has far more to do with the focus of your state of mind than the signals of your body

Some mammals hibernate, and in those cases, actual metabolic activity is drastically reduced. Humans didn't evolve to do this. The closest we come to this are situations of hypothermia. As far as power save... It is likely that if you have enough of a calorie deficit for a long enough period of time, you could end up needing more rest and not being able to exert yourself, also in the absence of food our body's metabolic processes are altered, but a single day isn't going to shut you down or alter your metabolism in any significant way, assuming again you are a health, non-pregnant, adult.

The human body can last several days without food and (to a lesser degree) water, and often had to. I myself and certainly many others have not had to experience that tho, as modern Western society has pretty good countermeasures against this.
After 24 hours, your body has still sufficient amounts of water, unless it was dehydrated earlier already. Contrary to what an American stereotype would suggest, a few hours without food won't do any harm.
When looking at longer times, however (which is closer to the core of your question!), this is not as easy anymore. Sadly I'm not familiar enough with this topic to give sensible intervals, but there are certainly many papers about this that could explain this in detail, if you're interested.


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Why human hair is losing its color over time?
Human hair is losing its color over time, that's a known fact.
I would like to know why, meaning what biological processes are involved in this?
Also, is it part of the DNA somehow, i.e. the exact rate of losing the color is known when one is born?

Human hair is losing its color over time, that's a known fact. Is it? I know plenty of elderly people who still have dark hair.

@Matt none that I know of, and even they can't retain the original color, just might lose less color. Unless you have a link to some official post about it?

@rg255 thanks, I searched for "hair" and "color" key words, that one doesn't contain any mention of "color".


text:
What exactly makes bananas go brown?
I know that often oxidation processes are mentioned when referring to the color change from yellow to brown in bananas (specifically: those that you get everywhere in supermarkets, with no seeds).
However, I am really interested if there is a specific oxidative pathway that is generally followed in this process, and whether it has been examined.

Note: When answering this question, please back up your claims with references to the scientific literature.
(This is not a homework question [although phrased like one] but arose purely from personal interest and lack of time to pursue it properly.)

As a sidenote: Ethylene is an hormone involved in fruit ripening.

Irrelevant to why bananas go brown, but the process is faster  in cold conditions than in warmer ones. So it's not worth putting bananas in a fridge.

The reason for this is the oxidation of phenol residues in the banana (for example in the yellow color) which get oxidized by the enzyme Polyphenol oxidase (PPO) to melanins. The scheme (the image is from this website on food browning) looks like this (you can of course also use more complicated substrates):

For further information, see these references:

Banana Polyphenoloxidase. Preparation and Properties.
Molecular cloning and characterisation of banana fruit polyphenol
oxidase

Polyphenol oxidases are widely found in fruits and cause most of the oxidative browning. See these articles:

Polyphenol oxidases in plants and fungi: going places? A review.
Enzymatic Browning, Polyphenol Oxidase Activity, and Polyphenols in
Four Apple Cultivars: Dynamics during Fruit Development

Could you explain how tyrosine gets in there? What is it that's being oxidized? I assume you mean free tyrosine molecules and not those incorporated into protein right? If I'm missing something obvious, please point it out, biochemistry was never my strong point and I haven't worked in a wet lab since university.

@terdon Tyrosine is a simple molecule used for demonstration. PPO's can oxidize quite a range of molecules, which have to contain phenyl groups. See this paper for some details.

I remember reading somewhere that PPO  has a role to play in the change in colour(to brown) of cut apples when exposed to air.

Ah OK, thanks. I thought you were suggesting that the oxidation of tyrosine molecules was responsible for the change of color.

@biogirl PPO's are present in almost any fruit. Appples, Bananas, they are responsible for the brown color of tea and cocoa, mangos and so on.


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Question about *Cryptosporidium hominis*
Cryptosporidium muris infects mostly rodents and it is usually found in gastric gladns. Cryptosporidium parvum infects humans and certain animals and it is found in the terminal ileum and colon.
There is also Cryptosporidium hominis that infects only humans. My question is

where exactly in the human gastrointestinal tract it resides?

This page seems to indicate that it adheres to the epithelium of different internal organs. They write:

The sporozoites are released and parasitize epithelial cells (b, c) of the gastrointestinal tract or other tissues such as the respiratory tract.

Here is the figure from that page:

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


text:
Encephalitozoon cuniculi
Can anyone advise me a literature supporting the claim that Encephalitozoon cuniculi is an aerobic organism? I have seen papers saying otherwise, but also I was told that this is not quite true.


text:
Question about flavodiiron protein
I came across an article about flavodiiron proteins that are responsible for reducing ${\rm O}_2$ to ${\rm H}_2{\rm O}$ thereby protecting the anaerobic prokaryotes and some eukaryotes from oxidative stress. However, I am confused about the structure of that protein and its relation to heme proteins. Is this a heme protein?
The article I am reading is:

Di Matteo et al., The O2-scavenging flavodiiron protein in the human parasite Giardia intestinalis. J Biol Chem. 2008 Feb 15;283(7):4061-8. Epub 2007 Dec 12.

No flavodiiron proteins are not haem proteins. See here for a simple depiction. Basically there is a flavin, and there are two iron atoms which go through a FeII/FeIII cycle during catalytic activity. These iron atoms are not held in  haem, but rather via carboxylate ligands.

No, Hemes are not proteins. They are porphyrins (large organic molecules) which are composed of four pyrrolic groups linked together. In the middle the coordinate the iron atom which is responsible for the activity. The combination of heme and iron is called a prosthetic group or co-factor. They are bound by the protein.

The image shows the Heme B from the Wikipedia.

Right, thank you. However I meant heme proteins in the sense of http://en.wikipedia.org/wiki/Hemeprotein
In other words, is flavodiiron protein a heme protein?


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Strange Exoskeleton Found in Maine: What is It?
There is a gall like object or exoskeleton attached to a plant stem I have found. At first I thought it was a cicada but it is not. The object cannot be identified by me. Attached are some pictures of it. Could you identify it?

It's a praying mantis egg case. It won't have "legs" until the eggs hatch. If you're lucky and watchful, you'll see a bunch of tiny praying mantises around it (if you put it back) and the shrubs around it in late spring.

It seems to me the ootheca of a mantis before larvae eclosion. You can read more about it here.

.jpg

There were no legs or anything.

Are they easy to find?

I used to find about a dozen egg cases a year on my property in PA, Sometimes more. Yet we only had three, maybe four adults active that I could find.


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Plant vs animal protein digestibility?
The protein scoring methodologies ( https://en.wikipedia.org/wiki/Protein_Digestibility_Corrected_Amino_Acid_Score) rate plant proteins of a lower quality than animal proteins. Now I can understand the reasoning that proteins have a lesser quantity of essential amino acids (allegedly) making them "lower quality" in terms of protein; but I don't see why there should be a difference in digestibility between plant and animal proteins (I can give links but it's common knowledge that plant proteins are less digestible). What is the basis for this difference in digestibility ? Whatever the amino acid composition, I don't see how that would affect digestion of proteins. So why are plant proteins considered less digestible ?

Anti-nutritional factors or antinutrients (wikipedia has a page about this) https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/anti-nutritional-factor


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CRISPR/Cas9: What are the main differences between sgRNA and the Cr:TracrRNA ?
So from what I understand, in gene editing, the CRISPR vector expresses a small RNA sequence comprised of a small guide-RNA that is complementary to your target sequence. The sgRNA comprises a 20 Bp CrRNA and a truncated (cut down) TracrRNA right ?
My main question is how does this truncation enable gene editing ? After all, the bacteria have a full TracrRNA and not a truncated one.

You are correct about the components of the sgRNA.
However the truncation of the tracrRNA does not enable gene editing. Rather it is all that is required.
In bacteria the crRNA and tracrRNA are distinct molecules which must pair through the complementary palindromic repeat sequences. This is not the case in gene-editing as the crRNA and tracrRNA have been fused with a synthetic stem loop. Thus the palindromic repeat sequence is not required and the tracrRNA is shorter.
Check out Cong et al. (2013) in Science.


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How can a coldblooded animal make an egg hatch?
I have chickens at home, and yesterday while removing the eggs I felt that they were quite warm. This seems to make sense, because the chicken has been brooding on it in order to make it hatch.
However now I wonder: next to chickens and/or other birds, there are other animals who are coldblooded and who are having eggs. Brooding on an egg means that the animal is delivering body temperature to the egg in order for the egg to grow and eventually produce a young animal. Now how can a coldblooded animal deliver body temperature if by definition, such an animal does not have body temperature?

Welcome to Biology.SE. The term cold-blooded is very misleading, you should have a look at this answer.


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carbohydrates and lipids as a source of energy? why?
Why carbohydrates and lipids basically used as a sources of energy? Why only proteins are used as building blocks of all the creations? Yes there are some parts of cells like cell walls in which carbohydrates are used but 98% portion of cell is made up of proteins? Why it so?

you are very wrong about only proteins being used, all your cell membranes are lipids (cell membranes are about 40% of your bodies non-water mass) and wood and chitin are both made of carbohydrates. vertebrates don't use carbohydrates for much structurally but lots of animals do.

First, it is a matter of the energy that food can provide. Here fat wins clearly (from the Wikipedia article on Food Energy):

Fat: 37 kJ/g
Ethanol (drinking alcohol): 29 kJ/g
Proteins: 17 kJ/g
Carbohydrates: 17 kJ/g
Organic acids: 13 kJ/g
Polyols (sugar alcohols, sweeteners): 10 kJ/g
Fiber: 8 kJ/g

Proteins and Carbohydrates have approximately the same energy content. But the advantage of carbohydrates (and especially glucose) is that is can be taken up by the body and the cells pretty fast, while proteins need to be digested and broken up, before they can metabolized further. Also plants make primarily sugars (or derivated polymers like starch), so carbohydrates are readily available in the food.
Fat and sugars are chosen for nutritional reasons, since they have a higher energy content and are available for it.
Structural components are build by proteins, since the 20 amino acids allow a much greater diversity in the protein chains than it would be possible for fats or carbohydrates. The building blocks are relatively small and simple but they all have the same basic structure (carbogroup, aminogroup and the sidechain) which allows linking via the functional group and the sidechain influencing their behavior (hydrophobic, hydrophilic, charged, etc.).

I am asking the reason that why lipids and carbohydrates are are choosen to get energy while proteins are choosen as building blocks to form the structural components of cells..?? Why not lipids and carbohydrates can be used to form structural components and proteins can be used to get energy..??

@katherinebridges Sorry, I answered only the first part of the question. I expanded my answer. Better now?

the reason we don't use carbohydrates for structural components is a quirk of history nothing more, vertebrates can't make cellulose or chitin.

There can be many reasons for why proteins are chosen as building blocks. Apart from what Chris said, I would add some points:

Amide bond in proteins is quite strong and thus provides a stable backbone
Because of different amino acids proteins can be versatile
Functionality comes first and then storage (assuming that initially there was just harvesting and no storage). Considering this and the composition of earth at that time, hydrophobic lipids don't seem to have been functional molecules in the aqueous solvent. Carbohydrates on the other are quite complex. You may argue that nucleotides have sugar backbone so sugar must have existed. I don't have an explanation of why polysaccharides could never be functional molecules: perhaps because they are more structurally complex than proteins but could not adopt stable structures such as helices etc.

But having chosen proteins as the functional molecules it won't be a nice idea to use them for energy storage unless there is extreme need (such as starvation). Fats being hydrophobic wont easily suffer attack from the regular reactive species in aqueous solvent; this makes them good storage molecules. Same case with carbohydrates, which arise from carbon fixation. Despite the existence several types of sugars the chemical spectrum is much less compared to amino acids.
And then there is the reason that Chris pointed out based on calorific value. But I would add a point on this regard: the energy in a food cannot be just measured by their absolute thermodynamic calorific value. For e.g. cellulose (which is present in fibers) has the same constitution as starch but provides practically no energy to humans because it cannot be digested. And in plants it plays a structural rather than functional role. So exceptions exist at least in the case of carbohydrates.


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Signaling through G protein Coupled Receptors?
There are two different cell lines but we do not know that these cell lines have Gs or Gi proteins, associated with their G-protein coupled receptors. If we wants to know about this. Can we design a experiment through which we would be able to identify specific Gs or Gi proteins in cell lines?

I have studied about Adrenergic Receptors. Beta Adrenergic receptrs and alpha2 Adrenergic receptors.. ?

Wat else do you know about your cell line? Are you sure that the two receptors are expressed in the cells in a mutual exclusive way?

I want to know that how can i distinguish between these two cell lines that whether they are Gs or Gi cell lines associated with the G protein coupled receptors..? Beta-Adrenergic receptor (epinephrine) is for Gs and alpha-adrenergenic receptor (acetylcholine) is for Gi.I have this information about the two cell lines..

Thats why I ask if you know if these proteins are expression mutual exclusive. If they are, you can do a simple RNA extraction, cDNA preparation and then do PCR (doesn't have to be realtime PCR) with specific primers to sort this problem.

Depends on if you've got antibodies for the associated subunits and the GPCR. If you do a pulldown (Immunoprecipitation) + western blotting would be a good way of checking.

EDITED ANSWER
Based on comments and responses my original answer to this question received I have decided to edit the answer and respond to some questions.
Since I work on proteins, I tend to favour protein based approaches specially when wondering about the presence of a protein. This is simply the case because protein is what is important functionally (purely talking about protein based problems/questions here and not talking about RNAi stuff here) so what I have experienced editors require for majority of papers, they want to see some sort of protein work. Now I'm aware that is not always possible since the antibody (Ab) might not be very specific or sensitive specially for low expressing proteins. If a protein is highly transient that makes the problem even worse, which is why many people resort to mRNA expression to make deductive reasoning for the presence of proteins although that makes a number of assumptions about how the mRNA is processed and whether the relationship between mRNA expression and protein expression level is linear but thats another discussion. So all I'm trying to say is that it's important check for the presence of a protein using Ab based techniques, which are immunohistochemistry (IHC) and western-blot (WB).
So my primary recommendation is to use Gi and Gs species specific (non-cross reactive) antibodies to check for the presence of your proteins of interest and always use Ab heavy chain control for IHC and a negative control for your WB using a sample that you know doesn't express your proteins of interest, if thats available. IHC also tells you some spatial information and whether Gs and Gi are both present in the same cell line or not and if they co-localise etc etc! Obviously check for Ab availability and if its compatible for IHC or WB procedures.
The other method that is feasible is if you know your two different cells express only one of the Gs or Gi exclusively, you can look at their specific inhibitors and add it to some of your cells and the chances are if the dose is high enough it will cause the cells to die since Gs or Gi are crucial for cell function. You can probably get away with an experiment like this using wells in a 24 well dish so you don't have to use that much media or drugs. But with stuff like this it might not work and you might get off-target effects so just do this as a complementary test. For your drug test always do a DMSO control since the chances are that's what the drugs are dissolved in and if not just use whatever solvent the drugs are dissolved in and add them to your cells in your control experiments.
Now the other possible and commonly used method to check for the gene expression of protein and subsequently infer its presence as a protein is to use a reverse transcription based PCR, such as RT-PCR although it doesn't have to be real-time as correctly mentioned in the comments. Please note that I'm not at all an expert in this and do check my answer in this section since I haven't personally done reverse transcription based PCR. As far as I'm aware, the basic procedure is to extract cellular mRNA, which can be performed using kits such as RNeasy or a similar product (I'm not promoting any products here and these are just what I have came across!). The protocols come with the kits and available online, and tells you exactly what min/max cell number/RNA levels should be present and how your cells should be (pelleted) before processing. Another method for RNA extraction is CsCl but thats pretty messy and complicated and requires high expertise to get it right but I know its inevitable for certain situations but for cell processing, a kit will do. At least RNeasy protocol states it enriches for mRNA and selectively exclude other types of RNA. Once you have your cellular mRNA you can proceed to reverse transcription using the appropriately designed primers for your gene of interest using a thermocycler. Again I'm not sure what tools to use for designing the primers for making cDNA from mRNA and what to look for (apart from the fact that make sure your primers are specific) as I only do regular PCR but would welcome any edits! Once you get from mRNA to cDNA, you can then run them on your (Ethidium Bromide or whatever DNA staining based) agarose gel and see if your amplicon is present and is the correct size (again based on the primers you have chosen you would know what the correct size is) and hence whether your gene is expressed or not. At least RNeasy kit says you do not need to use DNase digestion to get rid of any DNA before reverse transcribing your mRNA as most of it gets cleaned up when using the kit but you have that option. Now regarding the next-generation RNA sequencing I do not know anything about them so would again welcome any edits but seems unnecessary since you only want to know if the gene of interest is expressed so don't need any sequence info but thats an option too (although I imagine a little expensive?). Just to mention something very obvious, it's important that the species, which your lines have been generated from are sequenced or you have good sequence information about the Gs and Gi genes in your lines otherwise designing primers would be guess work. Its always best to see if anyone has done what you are trying to do and ask for their primers as most people are happy to share reagents.
Now you have probably noticed so far that my methods are quite biased towards molecular biology approaches and that's simply because that's what I know more about, however a great suggestion was to use cAMP levels as an indicator for Gs or Gi expression. Again I'm not an expert in this since I haven't ever analysed small molecules but I imagine that involves something like a HPLC, which you need to discuss with a chemist/biochemist how to extract and clean up your cells from everything and leave only the cAMP. There is probably a procedure/kit/biosensor for it but I will avoid getting into it as I know virtually nothing about this. However I have a note of caution for these types of indirect experiments. I have no idea what your cell lines are and how well they are characterised but since lines have all sorts of mutations and deletions and insertions in them, it's not a good idea to make inferences from cAMP levels. Since considering cAMP presence is quite important for cellular function, their absolute levels in a cell line is not necessarily a good indicator of whether one cAMP production regulator is present or not and I'm sure if you do something like this you open yourself to major criticism by any journal editor/referee. What will be a good idea though in any future experiments you do with these cells is to over express Gs or Gi and see their effects on cAMP production but I just don't recommend using cAMP levels as a sole indicator as to whether Gs or Gi is expressed or not.
If everything else fails and you got tired and wanted to wash your hands off this identification task, you can always lyse your cells and send them for mass spectrometry (MS) if there is such a facility at your institute. It's crucial that the species, which your lines originate from are characterised in terms of their global protein sequences since programs such as Mascot query the raw spectral data against databases such as UniProt to get protein coverage and subsequently protein hits. Also before you go ahead with you MS experiments, just speak to the facility manager and ask for guidance as to what lysis buffer is best to lyse your cells in and what components should not be in your lysis buffer and how sensitive their machines are and how likely you are to get detection and what your protein concentration should be. I think the best machine to use is Orbitrap and as a general rule, the higher the protein amount, the more likely you are to detect it. Since cell lysate is pretty messy and the MS machine columns can get saturated by abundant proteins such as actin, it would be best to run your lysates on an SDS-PAGE gel under reducing conditions (you can even do multiple loads by running your samples in the gel, switching off the WB machine, loading more samples and running them in the gel and continue doing this a few times. It works, I have done it myself but for pulled down samples which are a bit cleaner (less contaminants/unwanted proteins) in general). Once your gel runs through just cut the region of the gel corresponding to the molecular weights of Gs and Gi and send that for MS identification. This method (running your lysate through SDS-PAGE gel) gets rid of unwanted proteins that can interfere with the identification process. But MS is very expensive!
Again I would highly welcome any edits to my own edited reply! I'm here to help and learn.

As in G protein coupled receptors, the Gs protein is associated with adenylyl cyclase and thus increase the level of cAMP in the cell by activating adenylyl cyclase but when  Gi protein is associated with adenylyl cyclase it will inhibit the level of cAmp in the cell by inhibiting adenylyl cyclase, so is their any technique by which we are capable to detect the elevated presence or absence of cAMP in the cells.

based on your comment, you should edit your answer to describe making cDNA from mRNA and sequencing those, or using next-gen RNA sequencing protocols.  You are correct, 'genomic' sequencing won't address expression.

Ok, i have now extensively edited my original answer. hope the information are helpful.

@ Shigeta, thanks for the spelling corrections. My keyboard isn't working well for some reason. Just thought I point out it's not RNAeasy its RNeasy! But thanks to all anyways!


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Significance of lipids in biological membranes...?
Membranes are specifically designed by lipids to maintain internal hydrophilic environment in narrow range.There are hydrophobic amino acids among naturally occurring 20 amino acids and as well as there are also number of water insoluble polysaccharides like cellulose. These hydrophobic and water insoluble materials can also be used to build membranes but why not? Why lipids are only choice?

Membranes are built from a specific class of lipids, namely phospholipids, whose key property is that they are amphiphilic and so can self-organise to form bilayers. Not all amphiphiles do this, some prefer to adopt a micellar organisation. A bilayer composed of phospholipids produces the ideal combination of a hydrophobic barrier with a hydrophilic surface.
Although there are clearly amino acids with hydrophobic side chains, it is difficult to conceive of a proteinaceous barrier that would reproduce the properties of a phospholipid bilayer since it would not have a continuous hydrophobic phase.
Cellulose may be insoluble, but is full of polar groups so again would not create a hydrophobic barrier - I'm sure that ions can diffuse through a cellulose structure for example.
added later
@WYSIWYG raises an excellent point in the comments. Archeal membranes are composed of a different class of amphiphile in which the hydrocarbon tails (branched; derived from isoprenoids) are attached to glycerol by an ether linkage. It's instructive to note that the overall design principles are retained however, suggesting that the self-organising properties of these molecules was the key to the "invention" of biological membranes.

an addition.. archaeal membranes are not made of phospholipids but isoprenoids..


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Why does Hunger lead to the aggressive behavior?
I have observed that frequently when people are hungry; they tend to get angry more easily on pointless issues. Does this mean that our fight or flight response is more active when a person is hungry? What is a possible reason for this? Is this phenomenon linked with our cell signaling pathways? If it is, then what would be the pathway that leads to the aggressive behavior?

To summarize the question:
When a person is hungry and they get angry, is it due to a cell signaling pathway? If so, what pathway?

As I recall hypoglycaemia leads to a sympathetic response that can promote fight/flight behaviour.

I think a review should be offered to this post http://biology.stackexchange.com/questions/19515/effect-of-testosterone-hormone to answer this enough well. Testosterone in relation of hunger and aggressive behavior is a valid research topic.

Could you please tell me what u r missing in the answer that Cornelius has given for you have put up a bounty on this question?

I would say simply that when we are hungry, we feel a certain degree of pain and diminished emotional security. this puts us on the defensive and makes it harder for us to bear difficulty, so we snap out at those things (or people) which make our lives harder.

@TheLastWord from the answer,I got it that hypoglycemic condition leads to the Release of Epinephrine and nor epinephrine and activation of beta adrenergic receptors, but how the activation of this signalling pathway leads to aggressive behavior? Is their release of any hormone or secondary messenger in this pathway that effects behavior..?? wondering about this, can you explain me this point..please..???

Brain's main energy source is glucose. It uses about 20% of total glucose [1]. Brain hypoglycemia causes depressive-like behaviors in mice through adrenergic pathways [2].
When it comes to humans, here is a study that claims low glucose leads to increased aggression in married couples (see this too):

Self-control requires energy, part of which is provided by glucose. For 21 days, glucose levels were measured in 107 married couples. To measure aggressive impulses, each evening participants stuck between 0 and 51 pins into a voodoo doll that represented their spouse, depending how angry they were with their spouse. ... As expected, the lower the level of glucose in the blood, the greater number of pins participants stuck into the voodoo doll, and the higher intensity and longer duration of noise participants set for their spouse [3].

However, the conclusion is disputed:

Bushman et al.'s study does not demonstrate that fluctuations in blood glucose affect individuals' self-control abilities. As an important consequence, there is no reason to assume that giving couples a sugary “boost to their self-control energy” (p. 3) will reduce intimate partner violence. Because the glucose model of self-control lacks empirical foundation, it does not qualify as a framework for scientifically based intervention strategies [4].

What is sure, is that hypoglycemia activates sympathetic nervous system:

... the neurogenic symptoms of hypoglycemia are largely the result of sympathetic neural, rather than adrenomedullary, activation [5].
Hypoglycemia increases plasma levels of both epinephrine and norepinephrine. These catechols are released primarily from the adrenal medulla. However, it is well documented that hypoglycemic increases muscle sympathetic nerve activity, and that both alpha and beta adrenergic activity increase [6].

And this leads to behavioral changes (at least in animals):

Noradrenaline is involved in many different functions, which all are known to affect behaviour profoundly. ... Part of these effects may arise in indirect ways that are by no means specific to aggressive behaviour, however, they are functionally relevant to it. Other effects may affect brain mechanisms specifically involved in aggression. Hormonal catecholamines (adrenaline and noradrenaline) appear to be involved in metabolic preparations for the prospective fight; the sympathetic system ensures appropriate cardiovascular reaction, while the CNS noradrenergic system prepares the animal for the prospective fight. ... It appears that neurons bearing postsynaptic alpha2-adrenoceptors are responsible for the start and maintenance of aggression, while a situation-dependent fine-tuning is realised through neurons equipped with beta-adrenoceptors [7].

References:

Wikipedia contributors, "Human brain," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Human_brain&oldid=615456836 (accessed July 6, 2014).
Park MJ, Yoo SW, Choe BS, Dantzer R, Freund GG. Acute hypoglycemia causes depressive-like behaviors in mice. Metab. Clin. Exp. 2012 Feb;61(2):229-36. doi: 10.1016/j.metabol.2011.06.013. PubMed PMID: 21820138.
Bushman BJ, Dewall CN, Pond RS, Hanus MD. Low glucose relates to greater aggression in married couples. Proc. Natl. Acad. Sci. U.S.A. 2014 Apr 29;111(17):6254-7. doi: 10.1073/pnas.1400619111. PubMed PMID: 24733932.
Lange F and Kurzban R (2014) Sugar levels relate to aggression in couples without supporting the glucose model of self-control. Front. Psychol. 5:572. doi: 10.3389/fpsyg.2014.00572
DeRosa MA, Cryer PE. Hypoglycemia and the sympathoadrenal system: neurogenic symptoms are largely the result of sympathetic neural, rather than adrenomedullary, activation. Am. J. Physiol. Endocrinol. Metab. 2004 Jul;287(1):E32-41. doi: 10.1152/ajpendo.00539.2003. PubMed PMID: 14970007.
Hoffman RP. Sympathetic mechanisms of hypoglycemic counterregulation. Curr Diabetes Rev. 2007 Aug;3(3):185-93. PubMed PMID: 18220670.
Haller J, Makara GB, Kruk MR. Catecholaminergic involvement in the control of aggression: hormones, the peripheral sympathetic, and central noradrenergic systems. Neurosci Biobehav Rev. 1998;22(1):85-97. PubMed PMID: 9491941.

Ok... I got it that hypoglycemic condition leads to the Release of Epinephrine and nor epinephrine and activation of beta adrenergic receptors, but how the activation of this signalling pathway leads to aggressive behavior? Is their release of any hormone in this pathway that effects behavior..?? wondering about this, can you explain me this point please..???

@katherinebridges Those hormones activate sympaticus (fight-flight-response) - increased blood pressure, irritation, uneasiness when prolonged. Different people react to it differently (different genomics). Some become very aggressive, some are just silent and calm. Probably, testosterone and male gender have something to do with this. Men need more energy than female every day so they are exhausted faster. Link between hunger and testosterone can be one thing.

@Masi can you give me any reference for the involvement of testosterone hormone in developing aggressive behavior due to hunger..??

@Masi you have asked me to provide the reference for the link between testosterone hormone in developing aggressive behavior due to hunger..?

@katherinebridges I am working on this now. It will take some time because I have to study again some of the genetics and embryology related to this one. I try to find something until Saturday.

@katherinebridges I posted a short roadmap about the thing. I will update it when understand better this case. I did not manage to study my all notes in Embryology. I will update the post when I either remember my previous discussion about this thing in genetics or found my notes about this.

This is a short review about the issue and not complete.
This and the earlier answer are not proofs of the link between the two proceses.
To investigate this better, I think it would be much easier first to narrow the case to

testosterone and energy homeostasis (Embryology; or better formulated research case)
catabolism and anger
anger and aggressive behaviour.

Then, think about specific cases.
Think genes which are associated with aggressive behaviour and violence in catabolism (criminal studies).
Terms

Satiety
Appetite
Hunger

I was not sure in which specific area you are particularly interested.
At this stage, we cannot provide a proof between hunger and aggressive behaviour.
It depends so much on the individual (life style; genomics) what is the end result.
Here follows little general pieces of information:
Some cases

InsR/FoxO1 Signaling Curtails Hypothalamic POMC Neuron Number [1]: it's possible that the hormonal and nutrient milieu contributes to alterations in POMC neuron development.
Early-Life Exposure to Testosterone Programs the Hypothalamic
Melanocortin System [3].
Study about testosterone and basal metabolic rate [2].

Nuclei

hypothalamus lateral nucleus
hypothalamus tuberal medial perifornical nucleus [4]
hypothalamus arcuate nucleus (appetite and energy expenditure - POMC-CART; upregulative NPY AGRP)

Receptor

androgenic (NR3C4) (adipose tissue; more in visceral) (no link)

where I found no receptor existing directly between those two events - appetite and testosterone secretion by comparing the NCBI gene databases between those two processes.
It is much more easier to show the thing first in the embryologic studies and then by using the gene found in bigger studies.
At the moment, more work is needed in these studies in Embryology.
My initial clause is based on some of my notes in Embryology.
There are researches who are trying to show this link between studies in embryology.
The problem is at the moment in the development of hypothalamus and something else.
I will update this post when I remember about the situation better and when finding the right things from my notes.
Sources

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271107/#!po=14.0625
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402517/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060636/
John E. Hall. Guyton and Hall Textbook of Medical Physiology. 12Th edition.


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Formation of peptide bond..?
Proteins peptide bond is made by condensation process in which a molecule of water is released and according to this process it is not favorable in water systems than how peptide bond is formed by condensation in cytoplasm in the presence of water ?

The condensation is not done in water alone - the enzymatic function of the ribosome plays the essential part here. And in the active center of the ribosome where the formation of the peptide bond takes place, no water is present, only the growing peptide chain and the single amino acid (bound to the tRNA). See this schematic image from the Wikipedia:

If you make x-ray crystallography, this looks like this (from here). You can see that the tRNA with the unbound amino acid is actually inside the ribosome and protected from the outside:


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results of FgenesH and GenScan
Why FgenesH and Genscan don't give good results as I have prdicted number of genes of Chromosome 16 which according to NCBI are 86 but the results I have obtained are 57 genes predicted by FgenesH and only 47 genes predicted by GenScan. why they have done missed predictions. Kindly help me to know the reason?

You would be mistaken to assume that a computer program that is predicting, or classifying, the biological features in a nucleic acid or protein sequence is infallible.
Different programs use different algorithms and will have different parameters for their models of what a gene looks like. Typically they are tested on a learning or training set of features, and optimized to yield the highest score on that training set.  Then when you feed in your novel sequence and ask the program to predict where the genes are it will hopefully give you a list of predictions along with an estimated probability of the confidence of that prediction. However there will always be outliers, actual protein-coding genes that have atypical features not contained in the training set.
In other words, each program is only as reliable as its underlying model, and nobody has a perfect model.

Ok i get it that these methods are not reliable but my problem is that I was using Chicken Chromosome 16 for which FgenesH is trained so my question is that if its parameter is trained for chicken then why don't it give me missed prediction?


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How does air pass through when we breathe through the mouth?
When you sleep with your mouth open, does air pass through the nasal cavities? If not, how will you describe the air that enters the mouth?

Welcome to Biology.SE. I am not sure what you mean by [..] how will you describe the air that enters the mouth? Are you looking for a specific adjective to describe this air? I wrote a short answer, let me know if this was the kind of answer you were looking for.

The oral cavity and the nasal cavity merge into the trachea which yield to the lungs. As a consequence one can breath in and out through the nose or the mouth.

When you breathe, air follows the path of least resistance. Since the mouth (to pharynx to trachea) has a larger diameter than the nostrils, most of the air will pass through the mouth (unless obstructed by the tongue, etc.)
However, some will enter the nose and proceed towards the lungs by virtue of decreased air pressure in the nasal cavity while inhaling.


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How do plants grow year after year even though they die?
How do plants grow, die, and then grow again? For instance, when my plants die during the winter, how do they grow again next year? Does it have something to do with the root system? Or do they even die?

There are these things called seeds.

@TwistedGenes There's no need to be condescending.

It depends on the type of plant, but basically not all of the plant dies.  Plants have evolved a number of strategies for winter* dormancy.  These are common ones, but probably not an exhaustive list.
Deciduous trees and bushes simply drop their leaves in the fall, and so may look "dead" to the unskilled eye - though with practice, it's usually easy to distinguish between dead and dormant.  Then when the weather warms in the spring, new leaves grow.
Other perennial plants may lose some or all of their top growth, even dying back to ground level, but the roots will be alive, and will start growing when the ground warms.
Still other plants have developed specialized underground structures like bulbs & rhizomes - think daffodils, tulips, irises, and similar.  The rest of the plant dies, only to grow again from the bulb when conditions are right.
It's worth noting that most, if not all, of these are used for propagation as well, often naturally, and frequently with a bit of human help.  Bulbs and rhizomes multiply: the daffodil bulb you planted a few years ago may now be a dozen bulbs, each of which can be moved to grow new ones.  Many perennials can be increased by dividing the root mass into pieces, each of which will become a new plant.  And cuttings from many trees & bushes can be induced to form new root systems, and become new plants.

Or summer, dry season, &c.  For simplicity, I'll just say "winter".


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peritoneal dialysis Vs Hemodialysis?
Their are basically two types of dialysis: 1.peritoneal dialysis 2.hemodialysis, My Question is Why the peritoneal dialysis needs to be carried out on everyday BUT hemodialysis is carried out on only 3 days in a week?

Have you done any research on your own? Just googling the title of your question brings up lots of relevant results.

No I did not find the proper reason, just find out the pros and cons of both types of dialysis but I can't understand the proper reason.

Which type is more efficient at eliminating wastes may be the major factor.


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Separation of sister chromatids diring anaphase without Centrosomes in plant cell during mitosis
As in animal cell during mitosis sister chromatids are separated from each other during Anaphase by the pulling of kinetochore fibers toward their originating poles of centrosomes but as we know that Plant cells lack centrosome or centrioles then how sister chromatids are separated in plant cells from each other?


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Fate of Acetyl CoA in well fed state?
When we have eaten well and take fat rich diet then in this condition Acetyl CoA produced from fatty acid breakdown will be gone to storage in adipose tissue or not? If it will go for storage then why and if not go for storage then what will be reason?

It may not be compulsory to store it. It should be converted into CO2 to yield energy. I don't think a few more ATP in the cell would hurt.

But if cell has enough ATP then what will be fate of Acetyl CoA?

respiration-related processes is not my field of research, so I'd just give a guess that yes, it'd be converted back to fatty acid & then stored. But, I don't think humans have ability to do so, so I'm not sure on this.

This is either a trivial question, to which the answer is "If energy is needed then it will be used to generate ATP (in the liver) through the Krebs TCA cycle, if not it will be used to synthesize triglyceride (in the liver) which will be transported to the adipose tissue for storage. Why? because use or storage are the only options (other than excretion)." If you want biochemical details of the regulation then your question is too broad to be answered here. You need to read an account of fat metabolism in a biochemistry text book.

I don't think your premise is correct. Acetyl-CoA is not produced at all unless needed, because there is a limited pool of Coenzyme A, which limits Acetyl-CoA abundance. If there is an excess of fat, it is not catabolized to acetyl-CoA at all, but simply stored away until needed. Adipose tissue is capable of taking up fatty acids directly and esterifying them into triacylglycerides (fat).

As Roland mentioned in the comments, in the well fed state, not all of the Acyl coA is converted to Acetyl coA. This picture from Harper's Biochemistry, 29th, should come handy.
It is the CPT-1 gateway that regulates the amount of acyl-coA (from FFA) that enters into the mitochondria to form acetyl-coA.
In the Fed state, the CPT gateway is shutdown (regulation by malonyl-CoA) - allowing esterification by sending them back as VLDLs. In the starved state, the gates open, leading to beta oxidation giving acetyl-CoA.
The acetyl coA then can enter the Kreb's cycle to get completely oxidised and give ATP + CO2 (this ATP the liver readily utilises). Or, the acetyl-CoA can be channeled into ketogenesis, where this energy can be used by other tissues (since liver lacks the enzyme thiolase and hence can't metabolise ketone bodies). How the liver distributes the acetyl-coA for ketogenesis/Kreb's cycle is a different story altogether.


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Protein tertiary Structure formation
As we know that coils and loops are evolutionary variable regions where mutations,deletions, and insertions frequently occur. So does it mean that they don't have much role in the structure of protein? If it so then what are the factors for the protein core structure formation?

I think it would be useful in this case to look into instrinsic disordered proteins. Not to say that coil or loop regions have no role in the structure of a protein, but in avoiding the expression of a completely broken construct, protein domains including disordered or linker regions can tolerate mutations of specific types that don't 100% inactivate a critical region. For example, amphipathic residue substitution to another amphipathic residue. The reason we don't see functional valine -> lysine mutations, for example, is they seriously mess up the protein, even from a coil domain.

This is a really big question. Are you asking specifically "How and why do disordered loop regions pack the way they do in protein structure"?

Solving the 3D structure of a protein is complex problem. There are multiple layer of informations that come into play.
The first level of organization comes from secondary structure, which is in turn dictated by the AminoAcid sequence. There are common secondary structure motifs such as alpha-elices and beta-sheets. The combination of several 2nd structure motifs will give rise to more complex motifs and eventually to a local 3d structure. This local 3D structure is called a "domain" and is a minimal independent functional unit of a protein, which means it can often be cut out from the rest and retain its function.
Given this overview, the first layer of selection comes from creating 2nd structures which depends on the charge and size of amino acidic residues.
Mutations that destroy the creation of these secondary structure motifs will ultimately have an effect on the final 3d structure.
Loops in a way connect these more rigid motifs and therefore they are less likely to be subjected to evolutionary selection.
However in the end it all ties down to function. If you have a loop within a catalytic site inside a protein, the sequence in the loop will be greatly preserved because size and charge will strongly dictate its interaction with substrates.
Hope this helps.


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Choice of Molecular markers to carry out molecular phylogenetics
For evolutionary analysis of different individuals within a population, the preferable molecular markers are non-coding regions of mitochondrial DNA. My question is that why they are used what is the logic behind that and why specifically mitochondrial non-coding region is taken for evolutionary analysis between them?

The molecular markers need have an appropriate amount of divergence to resolve the phylogeny at the desired scale. If the markers are too conserved, there will not be enough characters differing between taxa. On the contrary, if the markers are too divergent, the sequences may be somewhat randomized, there may be misleading convergences between distant taxa...
Non-coding regions are usually less constrained than coding regions, so they can accumulate more mutations. This makes them more suitable for studies at small evolutionary scale.


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

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

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

Click on send and then complete record

Click create file and you are ready to go !

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

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


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Stabilizing forces between the protein sequences?
we know that Protein structures from secondary to Quaternary are maintained by noncovalent or weak interactions including electrostatic interactions,van der Waals forces & hydrogen bonding. What is the significance of these weak interactions why they are preferred by nature rather then strong covalent interactions?

Proteins often undergo conformational changes. The activation energy required to undergo a conformational change in a protein with only covalent interactions would be much higher compared to that of a protein with weaker bonding forces. An example of a conformational change seen in enzymes is the change in conformation during allosteric regulation, in which an effector molecule binds a site on the enzyme distant from the enzymes active site. The binding of the effector molecule induces a conformational change that exposes the active site of the enzyme. Another example of conformational change is the change in conformation seen in Toll-Like-Receptors (TLRs). Additionally, many proteins change their conformation in response to pH. These changes would likely not occur if the protein only contained covalent bonds, and the ability of proteins to undergo such changes makes them responsive to the environment, as well as allowing them to carry out their enzymatic actions, if such actions exist for that particular protein.
Here is the wiki on allosteric regulation https://en.wikipedia.org/wiki/Allosteric_regulation
Here is a figure on conformational changes in TLRs http://www.nature.com/ni/journal/v8/n7/fig_tab/ni0707-675_F1.html
And here is the wiki on activation energy, a concept used in chemistry (see section on catalysis and Gibbs free energy) https://en.wikipedia.org/wiki/Activation_energy

There are examples of covalent interactions that influence tertiary structure. One such example is a disulfide bridge. Check out this figure, where the two yellow balls constitute a disulfide bridge and influence tert structure https://i.ytimg.com/vi/ysPt1lIllcs/hqdefault.jpg

I know that one of the covalent interaction exist such as disulfide bridge my question was that majority of stabilizing forces are non covalent and what is significance behind this.

Please see my answer above. I believe it is what you are looking for. The non-covalent interactions allow the protein to easily change conformation. This makes the protein dynamic and responsive.

Conversely, if the protein only contained covalent bonds, its structure would be rigid, and it would require much higher activation energies to change conformation (compare the changes in enthlapy between breaking a covalent bond and breaking a hydrogen bond).

yes, I find it useful..

The word DonJulian uses for proteins — "dynamic" — is very well chosen. Life is dynamic, proteins underpin living things, and their dynamic properties help convey dynamism to life.


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What is an isolated beta bridge?
DSSP gives the letter B for a "residue in isolated β-bridge (single pair β-sheet hydrogen bond formation)", according to Wikipedias page for secondary structure (and various other proper sources). Can somebody please explain what this is in some more detail please? If I google it all that comes up is pretty much the same as what wikipedia gives.

http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.2b.html

@rg255 Thanks for the link. This seems to describe beta sheets (which I am familiar with). A quick cntrl+f of "bridge" doesn't return any results? I will have a proper read in the morning if you think it will help.

In Kabash and Sander's paper related to DSSP (Biopolymers 1983 vol. 22 (12) pp. 2577-637) the following appears in the abstract:
We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.”
It seems from this that they are using the term bridge to mean one hydrogen bond of the type found in a beta-sheet, ladder as two protein strands joined by many hydrogen bonds, and sheets as beta-sheets — more than two protein strands joined by many hydrogen bonds. The term beta-bridge in the DSSP documentation (http://www.cmbi.ru.nl/dssp.html) is presumably equivalent to a bridge in the paper
In the DSSP files residues that are in ladders or beta-sheets are designated E, and B is used for instances where there is a single hydrogen bond. The former are very common, wheres the latter are quite rare — some proteins have none. I have prepared an image of an example for residues 74 and 79 (side-chains omitted for clarity) in a loop in the protein 1PPR.pdb (a light-harvesting protein). The other loop residues 75-78 are designated as T (turn) in the DSSP file, whereas residues 73 and 78 have no structure designation. Hence the hydrogen bond between Ser-74 and Val-79 is an isolated singleton and designated B.

Thanks for this answer David. I agree with you're reasons and I think you're correct. I appreciate you tackling the literature better than I had and the example!

You're welcome. The DSSP nomenclature is not straight-forward and some protein chemists are not too enthusiastic about some of the designations of rarer structures.


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

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

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

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

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

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

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

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


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Resting and action membrane potential..?
In the resting membrane potential of neurons the inside of membrane is kept negative and outside of membrane is kept positive by the utilization of energy through Na-K Atpase pump, While during action membrane potential through the opening of specific gated ion channels inside of membrane is made positive while outside is made negative, What is the significance of specific charges across the membrane, does these specific charges across the membrane play any role in the passage of neurotransmitters ? or these charges are just arbitrary ?does this can happen that during resting membrane potential the inside will become positive and outside will become negative and vice versa, I want to know that what is the significance of these specific charges across the membrane ..?

I'm not sure how far back your confusion goes.

A membrane potential is defined as the difference in charge across the memb. Do you understand that?
The charge diff is not just the NaK Pump, but leaky K channel. Do you know that?
Have you looked at youtube videos of action potentials leading to neurotransmitter release? What part confuses you?

I m not confused about the points that you have written above, I m clear about these points, I just want to know the significance of These specific charges across the membrane..? That why there is need to maintain negative membrane potential by using Atp..?What is Significance of Negative membrane potential?

Just wanted to point out that the K channel open near the resting potential isn't "leaky". Like all other ion channels, it allows a passive flow of ions so it's not actively pumping but just allowing things to happen. If you like, you can call that "leakage" but then you'd also have the leaky sodium current, leaky calcium current etc. What's more, there are already things called "leak currents" which are currents caused by ions slowly permeating the membrane through other means than the main pump, exchanger or ion channel currents.

I've tried to split this into the answer to three questions:

Why does a membrane potential arise at all?
Why does it happen to be around -80mV
How does the cell use its membrane potential

(1) You've indicated that you know this one already, but I'd still like to point a few things out: The NaK pump not only creates a negative resting potential, it also seriously unbalances the Sodium and Potassium concentrations on each side of the cell. Even without any voltage, diffusion forces would cause an inward sodium current and an outward potassium current if you made holes in the membrane. The NaK pump (and the other active pumps/exchangers) are much slower than the passive currents through ion channels when they open.
(2) The resting potential is a dynamical equilibrium. This means that the potential you end up with is simply the one where all the opposing forces are equal. If you were designing a new cell from scratch you could put it at other values than around -80mV without too much trouble. In the cells we have, there's this region around -80mV where sodium and calcium channels are closed but a particular Potassium channel is wide open. Because there is much more Potassium inside the cell than out, diffusion drives Potassium out of the channel. However, because K+ has a positive charge the negative potential drives the K+ right back in. These two forces are able to balance each other out at around -80mV.
(3) A cell uses its membrane potential in two important ways: Firstly, when you trigger an action potential (AP) in one cell, it almost immediately triggers an AP in its neighbours. This allows rapid communication between neurons in your brain, but also allows for the coordinated contraction of your heart. Secondly, the action potential opens up Calcium channels which let Calcium flow into the cell. The free calcium concentration within a cell acts as a second messenger initiating all sorts of actions. For example, in muscles the increased Calcium triggers a contraction: muscle cells contract during their AP. In neurons, the presence of Ca2+ in a cell strongly increases the release of neurotransmitters.

Answering the question: "Why is a negative membrane potential important?"
I don't think cells have strong feelings about being slightly negative inside its membrane. I'm guessing these are the driving factors:

the cell membrane is nonpolar, so charged particles can only pass via transport proteins. This makes ion gradients an easy way to maintain a source of (literally, in the physics sense) potential energy.
the cell needs to control its environment and send signals to other cells. The particle gradient (sodium, for example), allows it to accomplish these tasks: bring in glucose by co-transporting with sodium, send an action potential by triggering voltage-gated ion channels.
Therefore, the Na/K pump is a way to "charge" the ability of the cell to perform various types of work in the future.

To risk an analogy, a cell having a membrane potential is like you charging your cell in the morning. You aren't quite sure what exactly you'll be doing with your phone all day, but it will be many different tasks and all will be doable because you've got a controlled energy source.


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Significance of synthesis of D-glucose in plants..?
why plants can only synthesize D-glucose why not L-glucose along with D glucose. I know it very well that plants have only enzymes which can synthesize D-glucose but Why not they have enzymes which can also manufacture L-glucose. So that we could have mixture of L and D glucose molecules? What is the significance of synthesis of only D-glucose by the plants ?

You need only one set of enzymes to make and to metabolize glucose when you choose one isoform. This saves energy for making the enzymes.

@Chris has explained the advantage of using one isomer - why do you think that it would be advantageous to synthesise and use both?

Synthesis from chemicals in organisms is fundamentally different from laboratory synthesis of chemicals. In the latter, more than one chemical species or other unwanted byproducts are usually formed, whist living organisms use enzymes, that are often stereo-specific. This means that they usually can bind, in the case, produce, only one stereo-isomer.
To produce both forms they would need double sets of enzymes.
It makes sense for animals, bacteria, protozoa, etc. to digest whatever comes, so less specific enzyme, but since plants will only access the glucose they themselves formed use of a stereo-specific enzymatic pathway probably enables a more efficient metabolism.

D-Glucose and L-Glucose have similar names only because we humans decided that's how we should name sugars; they have as much in common as, for example, D-Glucose and D-Allose (one chiral bond is different).
So, in essence, organisms don't synthesize L-Glucose for the same reason they don't synthesize D-Allose: they have no use for it. Its similarity to Glucose is only coincidental, it is different enough that, biologically speaking, it's a totally different molecule.


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Specificity of Protein Kinases in Signaling Pathways..?
In most of the signaling pathways the activated receptor when activates Protein Kinase through the action of secondary messenger, then these protein kinases almost always phosphorylate on the specific Serine, Threonine, or Tyrosine amino acid residues? what is the reason of phosphorylating specifically these amino acid residues. why not other than these amino acid residues are choosen for phosphorylation ?

Phosphorylation requires a nucleophile and hydroxyl oxygen acts like one. Serine, theronine and tyrosine get phosphorylated on the free OH group in their side chains.
Nitrogen, in some cases also can act as a nucleophile. In case of histidine, the imidazole nitrogen is phosphorylated during bacterial chemotaxis signaling. As far as I know eukaryotes do not have an enzyme for histidine phosphorylation.
Carboxylic groups in glutamate and aspartate can technically be phosphorylated as it happens in case of phosphoglycerate. Glutamate is phosphorylatyed by the enzyme glutamine synthase during the synthesis of glutamine. Same happens in the case of aspartate during aspargine synthesis. However, this is a reactive intermediate and the phosphorylation is not stable like that of hydroxyls.
Other amino acids do not have such nucleophilic groups to render an attack on the phosphorous atom in phosphate- so they are not phosphorylated.

This is mostly because of the nature of the amino acids. You need to have a Hydroxy-group in the sidechain of the amino acid which is the point where the phosphogroup is attached. Since this process needs to be reversible, this can only happen here. See the image below (from here) about the chemical structure:

In eukaryotes not only these three are phosphorylated, histidine phosphorylation also occurs (and happens more frequently than tyrosine phosphorylation, see this article:"Phosphorylation of basic amino acid residues in proteins: important but easily missed.").

Those residues are phosphorylated because they have a free hydroxyl group available to be bonded to a phosphate.  Many other resides can be modified, like acetylation of lysines, but only those residues are chemically compatible with reversible phosphorylation.

those are phosphorylated because they are the present in consensus sequences and enzyme are specific to phosphorylate the specific target that's why other are not phosphorylated and also because of the OH group of these amino acids


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Structure of biological membranes?
Integral membrane proteins have functional asymmetry i.e. they have two different domains of proteins performing different functions. these proteins have Tyr and Trp amino acid residues at the interface between the lipid and water.Because these amino acids have dual nature that their side chains can interact with both extracellular aqueous environment as well as hydrophobic lipid phase and another generalization about amino acid location relative to bilayer is described by "positive inside rule": The positively charged Lys,His, and Arg residues of membrane proteins occur more commonly on the cytoplasmic phase of membranes.My question is that why only positively charged amino acids are faced towards cytoplasm why not negatively charged amino acids or other amino acids are favoured here?

Yes, I have a reference for this claim.from the Lehninger Principles of Biochemistry Chapter 11 Biological membranes and Transport. and Sorry for the late acceptance of answers because it did not know it actually how to accept answers by using green trick but know i became familiar with this so i accepted the answers. @Chris

Some thoughts on this. First of all, the positive-inside rule, proposed by Gunnar von Heijne, is an empirical rule based upon observations, not one derived from theoretical considerations, so any explanation is simply an attempt at a rationalisation.
Having said that, here are three of those rationalisations:

the membrane potential is usually negative inside. This will create an electrostatic tendency for basic amino acid side chains to stay inside.
most phospholipid head groups are either neutral or anionic (phosphatidylserine, when the phosphate is included). Again an electrostatic force favouring basic residues inside since to move them out would require overcoming their interaction with the negatively-charged membrane surface
the pK values of the basic side chains (lysine and arginine) are much further from 7 than are those of the acidic side chains, so,  since charged residues must be neutralised to get them through the bilayer, it is more energetically unfavourable to deprotonate basic side chains than it is to protonate acidic ones.

The environment inside the cell is reducing.

@biogirl yes, it is, but acid-base equilibria are not redox reactions. I don't understand what your point is.

I thought reducing environment would lead to addition of protons.