text:
Does "Garbage Enzyme cleaner" contain cleaning enzymes?
There are many recipes which call for using fruit peel fermentation process to make a concentrated enzyme cleaner solution, some variations call to add bakers yeast. So the question arises that does this recipe really have those cleaning  enzymes and how are they generated?
This says that it may not have the cleaning enzymes, but maybe some other cleaning agents like vinegar or alcohol.
A discussion from two independent researchers on this topic give contrasting positions
Moreover if fruits  like Pineapple and papaya are used does it make the solution more potent?

The discussion you linked (here) shows that both researchers agree that 'garbage enzymes' are mostly acetic acid or vinegar, with a low pH(3-4). Fresh papayas contain papain, but roughly 2% of the enzyme self-digests per day in aqueous solution. Bromelain from pineapples is still active at acidic pH. Like most other proteases, it self-digests much more rapidly than papain. As a result, any digestive enzymes present when the mixture was made would destroy themselves by the time the mixture matured.
((Those among you quick at math will note that perhaps 1/5 of the papain activity would remain after ninety days. While true, there's evidence yeast cultures eat gluten for sustenance, and if they can digest gluten they'll digest papain. There's no reason to expect yeast to leave a delicious protein source unused.))
If the solution acquired proteases somehow, they would self-digest under the conditions the 'garbage enzyme' solution is stored at(room temperature, aqueous solution, nothing exotic like formaldehyde, months). The yeast itself by the time the fermentation is complete has died, destroyed by the acetic acid(or ethanol, depending) they created. Any digestive enzymes used by the yeast to dissolve proteins destroy themselves as the mixture matures and the yeast die off.
If the mixture starts with no digestive enzymes, there's no mechanism to get appreciable amounts active digestive enzymes. If the mixture does start with digestive enzymes(papaya or pineapple), either the yeast will eat them and then die or they will digest themselves and the yeast will eat the byproducts. Finally, the yeast will die.
It's a vinegar/alcohol blend, depending on how much oxygen is available during the fermentation, and it smells like whatever you put in it. If you used orange peels, it probably smells pretty okay. That's why it cleans.
If you are anxious to use real live proteases, there are powdered papaya/pineapple/etc powders you could reconstitute in water right before use. They are usually sold as meat tenderizer among other things. There are also blends of enzymes sold for pet urine deodorizing, and general purpose cleaning fluid with bacterial and enzymatic action. Formulating those at home is going to be fairly involved, but if you wanted an enzymatic cleaner you made yourself that's how to do it.

Just for the sake of curiosity how do we prevent self-digest happening by laundry detergents? E.g. in the stomach pepsinogen is activated by pH lower than 3 (HCl secretion), and it activates the other proteolytic enzymes after that.

I think you answered your own question with respect to stomach enzymes, but most laundry detergents are just detergents and have no proteolytic activity, as far as I'm aware. I will admit I'm not keeping tabs on laundry science advancements, however.

thanks , but what about the intra cellular enzymes of dead yeast?

What about them? Few people recommend a lambic beer or yogurt as a cleaning agent, even though both contain intracellular enzymes. The fraction of intracellular proteins that are digestive or proteolytic in nature is extremely small. If it's intracellular proteins from yeast that you're after, mix brewer's yeast with a little dish soap to destroy the cell membranes and enjoy the intracellular protein soup. No need to let them ferment for three months, and what you save on time you can spend on more yeast.

"but most laundry detergents are just detergents and have no proteolytic activity" - just the opposite. if you just want a detergent you can use soap, or horse chestnut (saponin), etc... proteolytic activity is important to clear stains like grass, blood, chocolate, etc...

The stain-fighting ability of laundry detergent is due to oxidizers unless you have 'bio' detergent(I don't, but you can buy them) with proteases, amylases, lipases to break down proteins, carbohydrates, and fats respectively. The pigments in grass stains for example(mostly chlorophyll) will not be attacked by proteases, because they're not proteins.

so how to actually measure enzymes in the output

also is it possible to multiply the enzymes?

@JeremyKemball Afaik most of the pigments are bound to proteins and are in cells organs. Proteases (and other enzymes) degrade cells and pigment-protein complexes, so the pigment will be easier to wash out. (Oxidizers do something similar.) Btw there can be pigment degrading enzymes in the detergents as well, e.g. chlorophyllase. This bio detergent term is not used in my country, I guess it is a marketing term, because my laundry detergent (and basicly all laundry detergents I can by in the shop) contains enzymes. (Next time please use @ if you want to answer my comment.)

@Bioguy We usually measure enzyme activity and not enzyme content. You need something you can measure and the enzyme can degrade, and you can measure the decreasing concentration of that thing.

@JeremyKemball It is possible to change the pH, salt content, temperature, etc... in order to prevent self-digestion. I guess most of the detergents use the same solution. So when the detergent is diluted in water and warmed up by the wash machine, then the enzymes become active... Btw. only proteases self-digest, so there can be amylases, lipases, etc... in these garbage enzyme cleaners.

There could indeed be those things, and pH changes are how the stomach(for example) avoids self-digesting. And there is certainly some amount of amylase/lipase/etc present. Nearly all living things have some amylase around at all times. 'Garbage enzyme' cleaners do not have a plausible source of large quantities of enzymes, and the very inconsistency of the conditions given means that even if under very specific circumstances you had a magical recipe that provided a lot of lipase or something, most garbage enzyme formulations will not have enough enzymes to actually achieve anything.

There is some evidence that garbage enzymes have significant enzyme activity, so they really work.

The decomposable waste thrown into the environment can be used to
  produce value added bio-product which in turn reduces the production
  of greenhouse gas. Garbage enzyme is one such value added product
  produced by fermentation of organic solid waste. In the present study
  enzyme activity and disinfectant potential of garbage enzyme was
  evaluated and its influence on reduction of total solids, suspended
  solids and pathogens in dairy waste activated sludge were studied. The
  result showed the garbage enzyme possesses protease, amylase and
  lipase activity and reduced 37.2% of total solids, 38.6% of suspended
  solids and 99% of pathogens in dairy waste activated sludge. This
  significant result may be helpful for researchers to compare the
  effectiveness of earth-friendly garbage enzyme treatment of industrial
  sludge with various physical and chemical pre-treatment methods to
  improve the bio gas production from the sludge digestion unit.

2014 - INVESTIGATION OF BIO CATALYTIC POTENTIAL OF GARBAGE ENZYME AND ITS INFLUENCE ON STABILIZATION OF INDUSTRIAL WASTE ACTIVATED SLUDGE
2011 - A Study of the Garbage Enzyme’s Effects in
Domestic Wastewater

This study was conducted to explore the feasibility of using Garbage
  Enzyme to treat sullage. The enzyme was prepared from fruits dregs,
  kitchen waste, molasses and water and capable of having reinforcing
  and cleaning function to work with nature. In this study, sullage was
  collected at open drainage at Arked Meranti, Arked Cengal and Kolej 9
  cafeteria?s and enzyme dosage determinations were done at laboratory
  scale. Sullage collected were analysed for BOD, COD, TSS and oil and
  grease. From the result obtained all samples treated using garbage
  enzyme prepared shows removal of BOD was 60% , COD and oil and grease
  almost 90%, then TSS was 80% after 7 days of treatment with different
  dosage of enzyme.

2010 - Garbage enzyme as an alternative method in treatment of sullage - pdf

To answer your questions:

So the question arises that does this recipe really have those
  cleaning enzymes and how are they generated?

Fruits, biological garbage etc... all contains cells, and those cells contain enzymes. By the fermentation process the cells are breaking down (lysis) and they release their enzymes.

Moreover if fruits like Pineapple and papaya are used does it make the
  solution more potent?

Pineapple and papaya contain proteases (e.g. bromelain). Enzymes are proteins, so these proteases can degrade them as well. (I think these proteases can be inhibited safely, but this would require a lot of research.) So I think it is not a good idea to ferment pineapple or papaya, because the result will be a significant loss of enzyme activity.


text:
How does a Plasmodium move?
Plasmodium sp. does not have any locomotory organs. So, how does it move? What biochemical process allows it to move?

Short answer: Only some stages of plasmodium are motile.  These use "gliding motility".
Gliding motility relies on actin filaments, which enable the organism to deform it's shape, facilitating movement.
This video provides a good visual representation of the filament-based motility.

"Gametocytes develop into gametes in the insect midgut, and then fertilize each other to form motile zygotes, which escape the gut."

The ookinete and sporozoite are motile.  The merozoite is non-motile.
Then of course there is the circulatory system of the host.
Source:
https://en.wikipedia.org/wiki/Plasmodium
http://www.sciencedirect.com/science/article/pii/S0092867400812817

You did not answer the OP's question.

What makes the sporozoite and ookinete motile? Are there any filaments responsible for cell movement?

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

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text:
Why do bacteria die in a high sugar content environment?
I was reading some questions in the test bank. Then in Chapter 27, I wonder why the answer is A. (undergo death by plasmolysis). Is the high concentration of sugar that kills them or the effects of sugar on bacteria?

Reece et al. Campbell Biology Test Bank. 9th ed. Boston: Benjamin Cummings / Pearson, 2011: 563.

Have you read about osmosis?

@Joseph http://classes.midlandstech.edu/carterp/courses/bio225/chap06/Slide4.JPG

@WYSIWYG yep, i read about it. Actually this question came from a biology textbook (Reece Campbell Biology 9th ed.).

Related: http://biology.stackexchange.com/q/19744/5198

In (very) short: enzymes are necessary for life. Cytoplasm is necessary for enzymes to function. Water is necessary for cytoplasm to exist. Cells have osmotic membranes.
Given a cell in a solution (even a goopy one, like jam) with a very high concentration of sugar, water will move along a gradient of low to high sugar concentration, in other words, water will move out of the cell and into the jam, thus stopping all major activity in the bacterium (basically stopping it from reproducing, if not exactly killing it. The killing actually comes from heating the jam and canning it while still hot enough to kill most bacteria.)
Plasmolysis: The shrinking of protoplasm away from the cell wall of a plant or bacterium due to water loss from osmosis.

In short our environment always tries to maintain an equilibrium, a stable state.
When microbes encounter a surrounding like a high concentrated sugar state or solution (hypertonic), water diffuses out of the permeable cellular membrane of the microbe to its outer environment with high sugar concentration causing dehydration of the microbe and it leads to shrinking of cell. As water is necessary for chemical reactions inside the cell, the natural metabolism is hindered.The phenomenon of contraction of a cell as a result of water loss is called plasmolysis and the food preservation technique is called sugar curing. Actually we can say a different environment created for microorganism (here for the purpose of food preservation)  with high sugar concentration has effect of plasmolysis in microbe resulting inhibition of its natural metabolic activity that results its destruction.

Actually, it doesn't kill them. As far as I am aware people with weak immune responses shouldn't eat honey or jams because of risk of fungal or bacterial infections.
Resource:
http://www.mayoclinic.org/drugs-supplements/honey/evidence/hrb-20059618

I can't find anything in your source about people with weak immune response and a risk of bacterial infection from honey.  Can you point to where it supports that?

In the side effect section, it is mentioned that spore producing microorganisms like Clostridium botolinum have a chance to grow in it.and also I did some research and the reason many microorganisms can't live in high sugar concentration is low water activity level because of sugar molecules which is needed for microorganisms' activity.but it is not simply the case for all microorganisms.

@ShayanKabiri - While you're correct that immunocompromised people should avoid many foods, jams, jelly, syrups (refrigerated after opening) are allowed; raw or unpasteurized honey - and raw soft berries - usually are not, though. See, for example, Diet for Immunosuppressed and other sources.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Which factors may affect a choice of an oviposition place in nocturnal moths?
Winter Moth (Operophtera brumata) is a small brachypterous (females have stunned wings - unable to fly) moth which places eggs on thick branches.
I would like to know which abiotic and biotic factors may play a role in selection of place for oviposition. Taking into account that level of humidity is probably the same on whole tree (and probably whole forest) and the branches are so thick that they are not distinguishionable from surrounding environment (and there is no accumulated heat to identify their orientation (south, north etc.)
What other factors may play a role?

The winter moth's preferred host plants are mainly deciduous trees, oak being the main food plant and also many fruit trees, birch and hazel. Females generally deposit eggs in bark crevices, under bark scales, bark snags and under lichen along tree trunks of host species. Eggs are initially small and green but gradually change colour to orange and then red before hatching (reference 1 and reference 2).
Though the oak is preferred,

There does not seem to be much discrimination in selection of host
  plant or oviposition site by the female (Wint 1983), as the choice of
  larval food plant depends on the female's pupation site and the
  direction she takes on emerging, as she just climbs up the nearest
  tree. So it might be fair to say that the larvae contribute more to
  host plant choice than the adults, as the larvae can balloon if the
  host plant is unsuitable. However there is the possibility that year
  after year each generation of females will climb up the same tree as
  their mother, and oaks (one of the most common host plants) can be
  hundreds of years old, so there could have been hundreds of
  generations of winter moth on the same tree (reference).

So that in effect means, that the thickness of branches or being indistinguishable should not be a factor. Regarding abiotic and biotic condition, the main abiotic conditions are precipitation, temperature and photoperiod.
An increase in temperature leads to more activity and a faster metabolism (reference) Since leaf buds open faster, there is a chance for eggs to be laid faster according because the larva needs to burrow into the buds before the leaf opens (bud-burst) Hatching is temperature dependant but I do not think that it effects the number of eggs much. Biotic factors like the presence of parasitic predators reduce population but does not seem to reduce the number of eggs.. (reference)


text:
Increasing/decreasing signal intensity in Western blotting
So I was in class and my professor was explaining western blotting. It seems as though there's more than one way to increase or decrease the signal intensity. He presented us the challenge to discover different ways this can happen. As hard as I look all I can find on the internet or even in google scholar is just certain chemicals like 'signal enhancer' and that's it, nothing remotely specific. Legitimately I do not propose this as actual homework, in fact it's just a curiosity I have. Therefore I ask the scientific community what, if any, are conditions that one could increase or decrease the signal intensity in western blotting? I understand what western blotting is, anyone can find this on wikipedia, but conditions that could increase or decrease signal intensity?

There are several different places in a typical Western blotting protocol where conditions can be altered to modulate signal intensity. The first is the amount of protein loaded - more protein will give a stronger signal, less will give a weaker signal. However, too much protein can result in indistinct bands, increased background, lane distortion, and other issues.
The next condition to change is the amount of primary antibody and the incubation buffer. More primary may lead to an increased signal, but too much can give higher background. Some antibodies give a better signal when diluted in BSA, others when diluted in nonfat dry milk. Generally, milk will give you a cleaner blot, but may reduce the signal. Incubation time can also affect specificity and signal intensity - some antibodies will fully bind with a 1-2 hour incubation at room temperature, others require an overnight incubation at 4°C.
The third condition to alter is the amount and type of secondary antibody. Increasing the amount of secondary may increase signal, but again may result in increased background. There are also different types of secondaries, depending on your detection system - HRP for chemiluminescent detection, AP for colorimetric, fluorescent tags for imaging systems, etc. These have different sensitivities, but can also result in increased background, depending on the other conditions of the protocol.
Finally, the type of detection system can affect sensitivity. For example, when using standard HRP-conjugated secondaries, there are numerous different ECL substrates with widely varying sensitivities. Here is a list of different systems available from Thermo/Pierce, ranging from standard ECL to Femto.
So, while Western blotting seems like a fairly straightforward procedure, there are many places to optimize the conditions to get the results you're looking for.

Wow I was sort of close with some of this yet so far away.  That is amazing, you must work with western blot on a regular basis?  Curiously, could I get a reference from you as to where or how you got this?

@Fistula I worked for an antibody company for over 6 years doing antibody preparation, QC, and tech support, so this answer is just a quick distillation of my knowledge. I can talk for hours about Westerns, if you're so inclined :)

This is a good answer @Fistula

One thing that others have not mentioned yet is that the time of the wash can affect the signal. If its washed longer than the usually required 5 minute three time wash, this could result in a reduced (decreased) signal.
Reference:
http://www.cellsignal.com/common/content/content.jsp?id=western-trouble

Additionally to the points in the answer @mattdmo has given, it is possible to enrich the protein of choice before the gel run. This can either be done by using tagged proteins (possibly with the cleavage of the tag before loading) or by doing an immunoprecipitation of your protein. The later is interesting when you have only low concentrations of your protein present in the cell. What you basically do is to bind an antibody to the protein, the bind the protein-antibody-complex to a column or beads, wash away (in theory, practically you are not getting all the other proteins away) and then load the sample. Depending on the enrichment, you will be able to see a band, where this is not possible without immunoprecipitation.
Then washing and blocking of the blot plays an important role. Usually you use milk powder to prepare the blocking solution, as this is quite cheap and works pretty well. But it can give quite a high background and make problems with phosphoproteins (not necessarily though). Sometimes it's better to use more expensive solutions like BSA for blocking the membrane. The washing is also critical, depending on how stringent you wash, you will loose signal and influence the background. Here you can play with different concentrations of detergents as well as with different detergents.
Additionally you can get a lot of different signals in the detection. For chemolumincence based detection you can either use x-ray films (which are rather unsensitive) and have problems with strong bands outshining neighbouring weak ones. They are also harder to quantify, as the linear range in which more intensity corresponds with more signal is limited. With chemoluminescence you can also use special highly sensitive CCD-cameras (which are more sensitive and have a much higher linear detection range) or phospho-imager plates (special plates, which store the chemoluminecent signal on a light sensitive plate and which are read out with a special scanner).
The latest development in the detection technology are infrared scanners for which you use secondary antibodies coupled to a dye which fluoresces at infrared wavelength. These scanner are extremely sensitive and also allow the usage of two differently labelled secondary antibodies at the same time, which can be very handy in analyzing protein interactions. You will need primary antibodies from different species, though. The modern detection techniques also have the advantage of delivering digital files, while films need to be scanned before further use in publications.

Also a good answer @Fistula


text:
Where to find E.coli gene expression data?
I am searching E.coli whole genome expression data with different conditions, any suggestion is appreciated. Condition could be for example different growth temperature, different medias, etc.
I have tried GEO but it only gives a list and one should read all pages and samples one by one to see which conditions were used.

What do you mean with "different condition"? GEO is a database which holds gene expression data, so it is not the place to look for whole genomes. If you look for gene expression data instead, please adapt your question. Information about different complete E.coli genomes can be found here

@Chris  I modified my question

Are you looking for something that would give you a list of what genes are expressed under specific conditions?

you can run an automated GEO query and fetch GEO accession numbers for the ones that match your keywords.

If you are interested in sequencing data then search NCBI-SRA

@WYSIWYG can you please give me an example how to run it and how to get them?

@Nemo see here. You have to construct a search based on your keywords and mention the database. Then you have to mine the retrieved list of information to select which ones you actually require. You can then download the data corresponding to these experiments in a similar manner. See this too. If you have specific doubts about this then post them as new questions.

There are some databases in which you can search for E.coli gene expression data:

GenExpDB: E. coli Gene Expression Database
Many Microbe Microarrays Database (M3D): A resource of microbial
gene expression data
Stanford MicroArray Database (use the search tool to find relevant organisms)
Colombos (COLlection Of Microarrays for Bacterial OrganismS)
ArrayExpress

To find out about the purpose and the conditions of the experiments behind this data sets you will have to read the respective publications.

can you please post some example papers done for E coli gene expression data if you are aware  of any

@Nemo http://lmgtfy.com/?q=e.coli+gene+expression+studies


text:
Which information can be obtained from a list of gene names?
Lets say I only have a list of gene names. I know they are up regulated and I know they are related to cancer.
What information can I obtain from having only the names of genes? For example is there any way to find a gene-gene interaction, or anything else? Is it possible to retrieve any information by having only the name of the genes?

The info you have is the gene name, nothing more, nothing less. You need info about each gene to draw any conclusions.

@MattDMo thanks for your message. how can I get info about each gene , do you know any way to do it? should i search one by one in google and see what comes up ?

I don't really understand what you're asking. With a gene's name, you can find out anything about it that's ever been published

@canadianer Yes when it comes to only one gene but when you have a list of them, how they interact with each other or anything else related to a set and not one gene alone

In light of your comments, you might be interested in Gene-set enrichment analysis (GSEA).

@cagliari2005 GSEA is when you want to find a score for your genes and you should definitely have two sets of genes like healthy and diseased but in my case I have only a list of gene names and I already know they are up regulated , so , I don't need to do GSEA

You can do a GSEA using 1 set, the other one coming from reference databases such as MSigDB (see here). You can categorize your list by gene families for example.

@cagliari2005 that is very interesting FOR SURE!!! thank you. do you know how to map such outputs for example overlaps or any other things can be obtain from there?

How many genes do you have in your list? You can get an idea of what cellular process is the most impacted by the genes in your list and from there try to reach some conclusions but just as a warning, what you are attempting is not trivial at all. It will be hard to reach valid conclusions from a simple list of genes as correlation does not mean causation (i.e. is the gene up regulated because of cancer or is it provoking the cancer?).

@cagliari2005 I kept only 20 up regulated , it can simply be perform but visualisation is difficult :-)

I would suggest searching the name in any trusted genetics database such as NCBI's GenBank (http://www.ncbi.nlm.nih.gov/genbank/). You can just Google search it, but it may take a little longer to find useful information that way.
I hope this helps and good luck with your research,
CDB

NCBI also hosts OMIM, which is a good place to find a link between a gene name and a disease occurring of the gene is mutated. You can select OMIM by following the link above and then selecting OMIM from the drop-down menu by the search box. Then search the gene name.

Was getting long in the comments.
In light of your comments, you might be interested in Gene-set enrichment analysis (GSEA). You can do a GSEA using your set, the other one coming from reference databases such as MSigDB (see here). You can categorize your list by gene families using this technique for example.
You can get an idea of what cellular process is the most impacted by the genes in your list and from there try to reach some conclusions but just as a warning, what you are attempting is not trivial at all. It will be hard to reach valid conclusions from a simple list of genes as correlation does not mean causation (i.e. is the gene up regulated because of cancer or is it provoking the cancer?)
To visualize pathways you might want to look at this post on Biostars. Several software are available for this purpose.

It depends; what species are the genes from? Some organisms have extensively annotated genomes, and actively curated species-specific databases, while other species may not even have a reference genome sequence available.  By itself, a priori, if you were lucky, about all you list would tell you was how to spell the names of those genes--if you're lucky. But to a skilled Bioinformatician said list could be a gateway to a discovery, or a patent, or a publication, or a grant, although none of these is very likely.

I know already the genes are human genes

Also try putting the list through Reactome or String DB to see if you see mapping to certain pathways. http://string-db.org/
You can also put lists through ConceptGen to carry out ontology based analyses
http://portal.ncibi.org/gateway/conceptgen.html

Assuming each gene symbol represents a unique gene or protein (this may not be true; see for gene name aliases in e.g. NCBI Entrez gene) you can get a lot of information programmatically. Below is an example using R and Bioconductor resources.
Define your list of genes:
# list of gene symbols, here we focus on one.
> genes <- "KRAS"

Load the annotation package org.Hs.eg.db and retrieve basic information including Gene Ontology ids:
# annotation package for human genes.
> library(org.Hs.eg.db)

# query Entrez gene id, description (GENENAME) and Gene Ontology id (GO)
> info <- select(org.Hs.eg.db, keys = genes, keytype = "SYMBOL", columns = c("ENTREZID", "GENENAME", "GO"))
> head(info)
  SYMBOL ENTREZID                                   GENENAME         GO EVIDENCE
1   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0000165      TAS
2   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0000186      TAS
3   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0001934      IMP
4   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005515      IPI
5   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005525      IEA
6   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005737      IDA
  ONTOLOGY
1       BP
2       BP
3       BP
4       MF
5       MF
6       CC

Load the GO.db package and retrieve the term associated with the GO ids (this gives info about putative function):
> library(GO.db)
> info$Term <- Term(GOTERM[info$GO])
> head(info)
  SYMBOL ENTREZID                                   GENENAME         GO EVIDENCE
1   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0000165      TAS
2   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0000186      TAS
3   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0001934      IMP
4   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005515      IPI
5   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005525      IEA
6   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005737      IDA
  ONTOLOGY                                           Term
1       BP                                   MAPK cascade
2       BP                   activation of MAPKK activity
3       BP positive regulation of protein phosphorylation
4       MF                                protein binding
5       MF                                    GTP binding
6       CC

Load the RefNet package and get information about interacting proteins:
> library(RefNet)
> refnet <- RefNet() # this step downloads from AnnotationHub and may take some time.
> int <- interactions(refnet, species = "9606", id = genes, provider = "BioGrid")
# create data.frame with Entrez id of proteins.
> d <- int[,1:2]
> d$A <- sub(".*locuslink:(.*)\\|.*", "\\1", d$A)
> d$B <- sub(".*locuslink:(.*)\\|.*", "\\1", d$B)
> head(d)
      A    B
1  3065 3845
2  8841 3845
3 23411 3845
4  1994 3845
5  3845 9770
6  9770 3845

Use the igraph package to visualize the interacting proteins.
> library(igraph)
> g <- igraph::simplify(graph.data.frame(d, directed = FALSE))

# annotate the nodes with the symbol.
> V(g)$label <- select(org.Hs.eg.db, keys = V(g)$name, columns = c("SYMBOL"), )$SYMBOL
> plot(g)

Then you could repeat the cycle with the interacting partners. There are many other things you can do, starting from a list of symbols; this is just a brief example. More detailed examples and workflows can be found here.

take the gene names and copy all of them, next open an online tool called gene mania. paste all your genes on the window. you will get their interaction and other related genes.
Now go to a database called gene cards and type in all the gene you got from gene mania and paste it one after the other to get useful information about the individual genes. some of which are restriction site information's, transcription factors etc.

It would be helpful if you provided, at least, the URL of the tool you recommend.


text:
Possible genotypes for blood types?
If I am blood type B, what are all the possible genotypes that could be expressed by my parents?
I think it might be 16 but I was reading online and saw this:

Similarly, someone who is blood type B could have a genotype of either
  BB or BO.

So if someone can help me answer this, that would be great.

Parent 1 and 2 have each 5 possible genotypes (OO, AO, BB, BO and AB).
Here a Punnett square with each possibilities. I highlighted the possible parent genotypes.

The total number of possible crosses is exactly 21. Note that here A = Ia, B = Ib and O = i.

OOxBB,OOxBO,OOxAB
AOxBB,AOxBO,AOxAB
BBxOO,BBxAO,BBxBB,BBxBO,BBxAB
BOxOO,BOxBB,BOxAO,BOxBO,BOxAB
ABxOO,ABxAO,ABxBB,ABxBO,ABxAB

This is starting from the information based on your blood type only (i.e. no information about your genotype).
Some background information. Antigen expressing alleles (here referred as Ia or A and Ib or B) are dominant. Not expressing an allele is notated i or O. Being of blood type O is when you don't express both alleles so it is a recessive trait (only possible genotype is ii or OO genotype).

You probably shouldn't call an AB individual homozygous.

@canadianer thanks for pointing that out. Modified the table.

Your answer is better, so I'll just delete mine to avoid confusion.

@poka.nandor was getting messy without a table ;)

@cagliari2005 yeah I should have done the same to avoid missing possible crossings. I feel bad about it... I mean not about you having a better answer, but about me being careless.

21 crosses could be many more if you considered minor types as A2, A3, B3 or hybrid alleles as Ax, Bx or chimera AB alleles as cis-AB, B(A). These rare phenotypes break standard 4 type rules, for example, Ax/O genotype could be both type A or type O. It depends if you talk about genetcis or blood compatibility.


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How to do Sliding 80mer Window search against a database with fasta
I know how to do a 80-mer window search against a single protein
fasta35 -k 0 -w 80 -a -m 9 -C 20 -Q -3 -E10 -d20 -B tempQuery:0-80

FASTAbyGI15/378405189
fasta35 -k 0 -w 80 -a -m 9 -C 20 -Q -3 -E10 -d20 -B tempQuery:1-81 FASTAbyGI15/378405189
fasta35 -k 0 -w 80 -a -m 9 -C 20 -Q -3 -E10 -d20 -B tempQuery:2-82 FASTAbyGI15/378405189

....

This will give me the detailed results but I want to do the search against a database in Fasta like this website:
http://www.allermatch.org/allermatch.py/form
Can anyone help me?

Fasta utilizes a k-tuple method to fasten up the search. You could try and set the default ktup parameter to 80 ( you might have to recompile from source to do that). Or you could try brute force and manually chop your input to 80 amino acid windows and call fasta search for each, and then collect all the results and filter out those that are above the threshold.

I don't think fasta is the tool you want use, because the speed of a fasta search against a database involves a step where each record in the database is chopped up into shorter substrings, e.g. 3-mers or 4-mers, and that pre-compute step takes awhile. Then, for each search your query sequence is similarly chopped up into a list/table when you submit the job. Your query runs quite fast (yes that is how they named it) compared to the classical hamming distance calculation, because the best hits are targets with the largest number of k-mer matches (that is a slight simplification).

Yeah, what @poka.nandor said. I was going to add that classical textbook dynamic programming would be another approach to explore


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What is the impact of stress on the human body?
Can stress trigger any changes in the human body? I'd like to know more about things less commonly known than, for example: sweating and tiredness. What are the long term risks of chronic stress? Do stressful people have higher chance of having heart-diseases or affected by hair-loss, for example?
I'm also interested in how can an emotion induce physiological changes in our body?

Welcome to Biology SE! Could you be more specific on your question, please? In this form I'm afraid this is too broad. Please visit http://biology.stackexchange.com/tour or http://biology.stackexchange.com/help sites for help on asking on-topic questions.

@I don't know - After your editing the question got better, yet I thought it's still too borad / unclear, so I took the liberty and reformulated so I can be reopened. I did this because in my opinion the question itself hold potential. To be honest I tried to keep as much of the original meaning / intention as possible, and it may still qualify as too broad. You can undo my editing if you wish to revert it back to your original edited form. I'm also voting for reopening this question.

Stress is the reaction, which our body reacts against the pressure or tension. There are many impact of stress on the human body, which includes

Emotional:  Moodiness, short temper, agitation, inability to relax, feeling lonely and always depressed.
Cognitive:  Memory problems, unable to concentrate, very poor judgment, negative thoughts, always anxious and worrying
Physical: Frequently suffering from pains and aches
Behavior: Addiction toward drugs, alcohol or cigarettes for relief, nervous, being alone, insomnia.
Other problems like headache, muscle pain, chest pain, fatigue, etc.

Hello Ravi. Can you add some references to support your answer?


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Hardy-Weinberg Color-blind
In a city, 4% of male population have color blindness. How many of the female are (a) color blind carrier, (b) color blind? Suppose the city holds Hardy Weinberg equilibrium.
My progress: 4% of male have color blind => $p=F(cb~allele)=0.04$ and therefore $q=F(not~cb)=0.96$. Since HW equilibrium stand, we get the allele frequency among female is the same as among male. Then (a) $2pq=2*0.04*0.96=0.0768=7.68\%$ and (b) $q^2=0.9216=92.16\%$.
Am I correct?

http://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle#Sex_linkage

Are you given any other data, total population, sex population, genotype of colorblind allele ?

@Macedon93 you don't need more data... HWE assumes organisms are diploid, only sexual reproduction occurs, generations are non overlapping, random mating, infinite population size, allele frequencies are equal in the sexes and there is no migration, mutation or selection. Color blindness is a trait known to be X-linked and recessive.

A: wild-type allele / a: color blind allele
Because color blindness is recessive and X-linked your assumption $p=F(a)=4\%$ is correct as men do only have one copy of the allele. Subsequently $F(A)=q=1-p=0.96$ is also correct. Therefore:
a) $F(Aa)=2pq=7.68\%$ is correct and b) is wrong, a is the color blind allele and $F(a)=0.04$ therefore it's $p^2=0.04^2=0.0016=0.16\%$.
92% color blind among females seems a bit high :).

Thanks @cagliari2005 haha, it totally slipped my mind :)


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Location of embryo development in angiosperms
What floral organ does the development of the embryos of angiosperms occurs in? Is it the ovary? The pollen tube grows down through the style and double fertilization occurs and the embryo begins to develop in the megasporangium.


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How to define drug-resistant or -sensitive cell line when knowing the IC50 values?
I have got the IC50 data for a drug on different cell lines. How to define if the cell line is sensitive or resistant towards this drug?
Could anyone tell me how to define this?

A low IC50 marks a sensitive cell line, a high a resistant.

From this post.
The IC50 is the concentration of inhibitor required to reduce the activity of a molecule/protein by one-half. It is the inverse of EC50. Usually inhibition curves looks sigmoidal so the IC50 is the middle point of the S curve. Here an example. (Note that the Y-axis can be pretty much anything, like enzyme activity and the X-axis is the concentration in a logarithmic scale).

Now for your actual question. The IC50 you got is by plotting a measure of the cell death rate vs the concentration of the drug. IC50 is expressed as a concentration so the higher the concentration of drug needed to kill the cell line the more resistant that cell line is. If the IC50 is very low then the concentration (or amount) of drug needed to kill the cell line is also very low which means the cell line is more sensitive.


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Understanding conclusions that functional regions are under negative selection?
I am reading in notes for a comparative annotation lecture that :

all DNA is subject to mutations
most functional regions are under negative selection (ie., mutations are often deleterious)

The conclusion was:

that pieces of DNA with specific functions (especially genes) tend to be conserved against mutation more strongly than a DNA region with no specific function.

So if i understand it properly, since all DNA can accumulate mutations, the regions of genes that provide some fitness benefits avoid the negative selection of random mutations and are preserved (conserved?).
Also, the author placed in parentheses, (especially genes), therefore are there non coding regions that can provide benefits? Is he referring to "Selfish DNA" like Transposable elements that can have regulatory functions (or so i have heard).

Your second to last paragraph is worded wrong. Deleterious mutations are negatively selected against.

Lets assume for simplicity that DNA is globally subjected to the same mutation rate (which is probably not a fully correct assumption).
Now let take a DNA region which is functional (what you meant by giving a fitness benefit), mutations in this region will occur as anywhere else in the genome. Some mutations will be deleterious and reduce the fitness of (or kill) the cell therefore, on the long run, cells that do not carry those deleterious mutations will propagate. This means that now if you look at the genome in the cell that propagated, certain genomic regions will contain less mutations than other because of the negative selection. They were "protected" against deleterious mutation.
Similarly, In multicellular organisms any mutations that reduces the fitness of the germline cells will be negatively selected (again functional regions will be more conserved).
The author was likely referring to regulatory regions. These are regions that do not encode proteins but are very important for gene regulations. Regulatory regions include enhancers, silencers, insulators and locus control regions (Maston GA, 2006). These regions will also be more conserved as deleterious mutations in regulatory elements could reduce the fitness of the cell/germline.


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Is it possible to express a mutant gene only in a specific tissue?
Imagine that someone tries to develop a knockout mouse for a gene, but this result in lethality for the homozygous.
Is it possible to express that mutant gene only in a specific tissue of interest to get a idea of which phenotype it produces? Does someone know an experiment which used this idea or something similar?

its possible, but it usually is unclear how to do it.

@shigeta can you expand?

I would like to comment on the language. You start by saying "express a mutant gene only in specific tissue". Then you mention specific mutation: KO. KO-gene is lack of gene expression. At the end you again say "express that mutant gene". I suppose you meant conditional KO.

While eliminating a gene is at least understood pretty well, tissue specific expression is difficult because the DNA sequences that encode the logic in animals as to when these genes are active are poorly understood.  Its been worked out only for a small number of cases I believe.

@shigeta You mean that you can gene-trap tissue markers, but we don't know how certain tissue is being form or what it consists of?

@aandreev  sorry i'm so swamped I can't do a proper job, but tissue specific promoters may only express a gene for a moment in development (and never again), or not be entirely specific for a given organ.  since we can't look at the DNA sequence and predict what the pattern of gene transcription will be, you would have to watch the rest of the organs over an entire lifetime to be sure (or several lifetimes).  a lot of work!

It is called conditional mutation.
You flox (put lox sites around) gene of interest and express Cre recombinase driven by tissue-of-interest-specific promoter.
Illustration from here:

Using chemically-activatable variant of Cre recombinase (cre-ER) you can create knock-out in some cells of tissue of interest, not every.
Addition: a bit weird but still useful method is to produce KO by means of CRISPR/Cas9 system. Tissue-specific expression of Cas9 protein together with gene-specific sgRNA will likely produce KO in mosaic fashion. One of positive sides is that such approach requires only one transgenic line, e.g. Tg(promoter:Cas9;sgRNA)
Addition: (via WYSIWYG's suggestion) you can express shRNA or other gene transcription-interfering product from promoter that only active in specific tissue/specific period of time. And beauty of genetic/bioengineering is that you can combine several methods for additional control, robustness, efficiency etc.
Taken from here:

Inducible and sell-specific gene KO with shRNA
For further reading:
http://cre.jax.org/introduction.html
http://link.springer.com/protocol/10.1385/1-59259-065-9:477#page-1
Update
I re-read OP question and, as commented to it, feel some confusion. So I would like to mention as well way to express mutated gene in specific tissue that, when expressed constitutively (all the time, everywhere), is lethal. Imagine some very strong oncogene. Or something like cell-toxic protein, e.g. chemically-activatable nitroreductase or light-activatable Killer-red. Or it might be mutated version of your favourite synaptic protein that, when expressed in all neurons, causes severe lethal phenotype.
What you do, is create transgenic animal with transgene-GFP fusion (nitroreductase, KillerRed, etc) that has floxed stop-codons in front, and cross that animal with transgenic with tissue-specific CreER (for example). What you get is animal that, when injected with tamoxifen, start to express mutated gene/toxic protein in tissue of interest. Then you are sure that only GFP-positive cells express that gene. That is how you "express that mutant gene only in a specific tissue of interest to get a idea of which phenotype it produces".

Additional info: For knockdowns, shRNA can be expressed in the desired cell type

Note that to get a knockout with Cre/LoxP system requires one further cross since F1 is heterozygous for the floxed gene. You need to cross your Cre +/0; target +/flox mice from F1 with the target flox/flox of F0 to generate Cre +/0; target flox/flox in F2.

yup, that is laborious


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What are the programming languages important to learn for a geneticist or bioinformatician?
I am interested in learning more about both genomics and bioinformatics, with emphasis on genomics. I was told after taking an introductory course of genomics that the programming language "R" and "python" are widely used. However having asked about learning genomics before on this fourm, I was suggested alot of books for learning genomics with "Perl". I was also told anecdotally that "perl" is falling "out of favor" and "Python" and "R" are desired.
To give background on my coding skills, I flunked out of computer science due to poor coding skills and poor math skills. I still had an interest in the field and therefore started studying genomics and biology instead.
I would categorize my self as a beginner in java and python in terms of skills.
I was also told anecdotally that the best way to learn coding is by having a project. But I feel incompetent in my coding skills to even attempt anything.
I tried to learn Python via "Codecademy" and their 13 hour course for python. Having completed it I felt lost enough to make this post, looking for further guidance. I tried to read a bioinformatics book based in Python, but I missed the handholding and directed exercises that Codecademy gave me.
Should one interested in genomics learn the coding language, R or Perl? Also what would be the best ways to learn these for one who does "not excel" in coding?
If this post seems opinion based mods feel free to delete it or move it, I just was not sure how to phrase my concerns adequately.

Which language do you prefer? Our lab uses fortran, bash/shell, python, perl, a bit of ruby, R, VBA (excel) etc. I've found python to be the most re-applicable language. These days it has 90% of the functionality of R too. I like discussions on this sort of thing, but it is off topic for the site. Perhaps browse around on the bioinformatics or biology subreddit.

Python bioinformatics learning opportunities that might be up your alley: http://rosalind.info/problems/locations/

Matlab! Nothing else ;-)

@InactionPotential    This sounds very cool !! Thanks.

@GoodGravy      I figured it was offtopic, but I cant resist the vast amounts of knowledgeable people on this site. To answer your question, I guess I am use to Java, but Python seems very strong and simple.

Also, not to be rude, but doing meaningful work in bioinformatics requires an excellent understanding of the underlying biology, the underlying computer science and mathematics, or, ideally, both. Sometimes life issues can make keeping up with difficult, but if you don't feel like you could make it through the fundamentals of CS and upper level statistics (and or linear algebra, differential equations). You are not likely to succeed as a bioinformatician. (Not to discourage your exploration, but I wouldn't quit my day job).

flagged for closure as opinion-based

@RoSiv Java is overkill IMO, but ultimately it's more about using a tool to understand the biology. If you find that by using Java you spend your time getting data, not debugging, then go for it using Java!

Bash and Python are the most used those day. If you want to do more data analysis/statistics, then R is a good choice as well. Perl is also quite common in the field.

this question is like asking what language to learn. There are bunch of people in china, so is in france or germany. As well as jobs and opportunities.

I have found that this chapter by Lincoln Stein is a very easy, accessible, and useful introduction to writing a Perl script: Using Perl to facilitate biological analysis. It is Chapter 18 in "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins" 3rd edition, by Baxevanis and Ouellette.  I use Perl and bash for almost everything, but most of my co-workers prefer Python.  I only use R when I need to.  One software engineer I know swears by Ruby.  As long as your scripting language has lots of useful libraries I don't know if it makes a big difference which one you select.

Comparing some commonly used languages in bioinformatics
I think that indeed Perl is losing users but there are still quite a lot of people using it. Bash (or other shell) is essential. While one can replace Python with C or Java and eventually replace R by Python or Julia, I find Bash to be really necessary. To compare Python to R, Python is much faster. If you are a purist, you'll like Python much more than R. R is a weird language, I use it a lot but you always have to deal with very special kind of objects. The big advantage of R is its community; There are tons and tons of functions. Typically, for any task you you want to do and related to statistics or to phylogenetics, you'll find an already existing package that will do the job for you. C is nice and very popular. It is super fast but it is not super handy for most tasks. Moreover, C doesn't have an interpreter which is always kinda annoying when you're use to high level languages such as R typically. I know nobody who uses Ruby and I don't code in Ruby but it is an important language. Some may use it for bioinformatics and it is very much used in many other disciplines (unlike R, which only statisticians know).
What I personally use
Personally, I use mostly R, Python, C/C++ and Bash. Bash to organize stuff, modify files and manage processes on my machine and on remote machines. R for data analysis. Python when R is too slow (to analyze more data such as sequence data for example) and C/C++ to run individual based simulation. I happen to use some other languages for my work but not as often.
How to learn
Nobody excels at coding to start with. Actually, after my first class of programming I had in mind that programming was not meant for me. Now, I don't excel, I am just a biologist who codes a bit and not a computer scientist but I spend the majority of time coding and I love that. I learn a lot everyday but ever since I started to feel a bit confident, I found that I could do much with this knowledge. You'll probably realize after some time that few people are really good at coding and you can already do much with only a few days of training. Don't be afraid. I think that indeed one of the best way to learn a language is to use it for a project. Here are a bunch of things you could do:

Go on Dryad.com, get some data and analyze them. You can redo the analysis they did on the original paper for example. Or, better you could try to discover something by yourself by combining some existing data.
individual-based (OOP) simulations in population genetics

simulate genetic drift in populations. Try to estimate the probability of a new mutation to fix and the time it takes to get fixed.
Simulate the process of selective sweep with defining chromosomes.
You'd basically have to have a function that creates a list of objects of type individuals. Each individual has two objects called chromosomes. You have a function that simulate reproduction (without selection, recombination nor mutations to start with). And you need a function to print the statistics you need on a file. I think you could do a simple individual-based simulation in a few days only and then you'd feel more comfortable with the language and you would also have a better grasp on how one can numerically simulate a population through time.

I particularly like the idea of practicing on real datasets from Dryad.


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What are the animals in these pictures?
I recently found some pictures of animals' skeletons. Does anyone know what species they are?

The pictures appear to be computationally generated or computationally enhanced visualizations (e.g.: change in color rather than in polygons around joints). Did the source perhaps include further images?

@tsttst Seems to be animal under X-ray.

@aircraft - They are not xrays. Just dramatically lit/shaded, maybe even computer generated, but not xrays.

The first, as @John said, is a water mammal: a seal, sea lion, something along those lines. The teeth are consistent with the Australian fur seal. The second, I have no clue. It's very light, fast, (I thought maybe a flying squirrel, but the 'hands' are wrong.) Seeing the teeth would help.

The top is some kind of seal (the flippers give it away) and the bottom is some kind of lemur (the long thin limbs and tail with the narrow skull) but that is the best I can do from just those photos. It might be a flying lemur but again from just the one photo without scale is difficult to say for certain.

the lemur's tail is longer than its trunk.

@aircraft There are many species of lemur with vastly different tail lengths, and we cant see how long the tail in the image is that well. Also your link is broken.


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Is there a biological determinant for right- or left-handedness?
When I was very young, I was sent by parents to examination where I was told both my hands are dominant in the same way. My parents preferred to make my life easier and chose to focus on my right hand development.
However, all my life I find myself naturally using my left hand - with a knife, to lift things, etc. Yesterday something happened that really twisted my perspective - I was playing bowling and I really sucked at it. And then, the moment I started playing with my left hand, I got perfect strikes.
I use my delicate motor abilities a lot with my right hand (drawing for instance), and now I wonder - how can I tell if I used the correct hand all my life?

This question ends with a question about the poster's personal life history. There is a biological question in the title, but it is never mentioned in the question itself. After five years, surely it is time to dump this question as completely off-topic.

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


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Using Jpred to predict secondary structure
I'm trying to use Jpred to predict secondary structure for a protein sequence. When I run J-pred, I get a bunch of hits from PDB. I've also noticed these 'hits' are the same name as the templates i use when using Swiss mod. How do i interpret these hits, do I just ignore them and force jpred to predict structure anyway?

That depends on what your are trying to do. Apparently your query sequence is similar to that of proteins with a known 3D-structure. As it says on Jpred's result page (and help), in this case it might be worth looking at these homologues with experimentally determined structures for information on secondary structure. Most likely it will be more accurate than Jpred's prediction.
How much of the secondary structure you can use from the 3D-structure also depends on which parts align between your sequence and the ones in the PDB. You can show the alignments on Jpred's result page by clicking the button below 'Alignment of PDB hits to your sequence'. However, if you are going with annotations from the 3D-structure, it would probably be better to use SWISS-MODEL directly.
If you don't want to see those hits and just force a Jpred prediction, you can tick 'Skip searching PDB before prediction' in the advanced options before submitting your prediction. The hits are shown merely as a convenience, ignoring them doesn't change anything about Jpred's prediction.

Thank you! So chou &Fasman, Gor, etc are just alternative alogrithms to Jpred? Do you think it would be worth comparing the results of multiple alogrithms or would one be sufficient?

@Ksims Yes, those are all secondary structure prediction methods, albeit of varying age: Chou-Fasman is one of the early methods from the 70s, GOR should also fall around that time, while Jpred still seems to be under development (at least until 2000). Wikipedia has a small list of secondary structure prediction methods which you can try out. I do think it is worthwhile to look at a few more results, although the consensus isn't necessarily always right.

awesome, I appreciate your help!

authors: ปัณรสี สิลตระกูล


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Which infectious disease would increase global life expectancy the most if eradicated
In the 1700s it was estimated, by Daniel Bernoulli, that wiping out smallpox would increase global life expectancy by over three years. If we could wipe out one infectious disease today, which would produce the largest increase in global life expectancy and by how much would life expectancy change?

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


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Swapping genes?
So, gene therapy is to take out a gene, correct its mutation, and put the corrected one back into the organism, right?
Is it also possible to take out a gene from an organism and put in a totally different one?
I read about this study where a scientist found four genes seemingly responsible for creating high, medium, low pan sensitivities.
Genes: COMT, DRD2, DRD1 and OPRK1.
DRD1 - more common among people with low pain perception.
COMT and OPRK genes were seen more, for those with moderate pain.
DRD2 gene variant was more common among those with a high pain perception.
So for example, can we take out a DRD2 gene from a person who has high pain sensitivity and put DRD1 in him/her so that he/she can have low pain sensitivity?
Is that technically possible?

First off we don't have yet the technology to perform gene therapy in human. Will be possible in the near future and the most likely candidate is the CRISPR/Cas9 technology. For your actual question, there are a couple of approaches, for mutation correction the idea would be to directly corrected the mutation without "swapping" genes. For your question with pain, the problem is that it is very hard to predict what will happen by taking a gene "off" and putting a new one "in".

Therefore gene therapy, at least at the beginning will be used on major genetic diseases (like the Prader-Willi syndrome or Huntington's disease) rather than playing with sensitivities.

@cagliari2005 I wouldn't say we can't do gene therapy in humans yet, but it's obviously in the early stages, glybera has been approved. And CRISPR/Cas9 would only be appropriate for certain gene therapies, such as repairing point mutations. Fixing large deletions or inversions requires delivery of whole genes.

@user137 you are right. Was thinking more along the lines of the question and for actual targeted genomic modifications. Good point though.

@user137 While gene therapy to treat a fully developed human has many obstacles and technical chances, CRISPR/Cas9 can be used for targeted gene replacement through homology directed repair https://www.addgene.org/crispr/zhang/faq/#HR

It's been possible for a long time now. Take a look at this article related to trials with retroviral vectors used for gene therapy trials. A single child developed leukemia, and following that trials across the world were suspended.
The article although notes that many countries decided to proceed with trials, since as they say "for the greater good". But mainstream media articles tend to glorify the actual reasons behind such decisions, because such questions are governed by much more complex ethical considerations.
But moving on this recognised the need for targeted gene therapies, so one of the most promising techniques right now is the Crispr/Cas9 technique as noted by the comments above above.
So do we have the technology? Yes we do.
Should we go forward with it?
I would say no. But, I would also say yes.
Why such a division in opinion?
There is much that we do not understand. Until a few years ago, the non-coding part of the genome was just junk. Now, it's an essential regulatory partner. Even more recently, the understanding of chromosome architecture was not understood, now we know that Chromosome architecture has a role to play in gene expression. In 2002 epigenomics was in it's infancy, we believed "central dogma" to be a dogma, non-coding RNAs were just some junk that you tended to pick up because the transcription machinery did not know what it was doing, and chromosome architecture? that hardly mattered in the grander scheme of the cell. All in all the cell was a much simpler place. Now we know more than we did yesterday and less than we will know tomorrow, so if I was a person whose entire life is a prolonged episode of suffering I would take my current options. If I was a person who could live with a mild discomfort I would work around it.

+1 as I agree in general - but the specific example of the non coding genome being thought of as junk I think is wrong. We've known there was a lot of noncoding regulatory DNA since at least the late 90s. And the ENCODE project's 'it's all functional' line was just marketing.

When you ask:

Is it possible to take out a gene from an organism and put in a totally different one?

The answer is yes. Gene knockout technologies are available in experimental scientific fields. You can destroy your target gene by swapping the gene with a drug resistant gene.
You can swapping genes using culturing cells, however it would be almost impossible to swap genes in cells of an animal body. But there is still hope. iPS cells can be generated from human and other animals. Then the technology can be applied to culturing iPS cells. Transplantation of differentiated iPS cells may be possible to replace tissues having a problems if anatomical structures allow you to do so.
I do not know details of pain perception, but it may be not that simple. You can classified genes by sensitivities of pain, but at biochemical level, the mechanisms to gain sensitivities may be different. I might check on this, although I might not able to draw the conclusion.

It is possible to insert a new gene in another organism.
The technique is very new. I know I have done it at school where we had a colony of bacteria, and we did some things to them that some of those bacteria would 'adopt' a gene that would make them able to live on a different pertium dish.
If you are intrested in these subjects you should try to google on "Genetically modified bacteria".
Also here is a site that shows with a few images what technigue is actualy used: Link
Edit:
As for the cutting of the DNA, for some bacteria (like E-coli) there whole genetic structure is known. So there are markers available that cut the DNA of the bacteria right at a certain place.

This does not answer the question, as the question is about higher organisms and nötig bacteria. Modifying bacteria is not a really new technique, it is done for about 40 years.


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Can reptiles digest grains?
As a caretaker of a turtle, I sometimes struggle understanding the logic behind the inclusion of corn, soybean, and wheat meals in reptile food, such ingredients seem truly aberrant from what a reptile would naturally be exposed to. Nevertheless I am aware of the biological and chemical similarity between most organisms, so I wonder whether that will help reptiles, especially omnivores with an eclectic digestive ability, to digest these compounds.
I'm looking for legitimate studies on reptile digestibility; anecdotal experience or advice is supplementary if present.

This is not a yes / no question. Many tortoise eat plants (veggies and fruits) while some turtles eat fish too. Snakes are basically predators and do not dwell on plants neither do most of the lizards. I think if a reptile is capable of digesting plant food in general, then it should be able to digest preprocessed grains as well.
Edit:  As for whole intact grains I'm unsure, as canadianer pointed out in comments section, intact grains are hard(er) to digest. /end of edit/
I found this article where scientist fed alligators with a mixed diet in various setup. The diet included corn too and the 'gators responded well in terms that they could use carbon-hydrates.

Recently, we (3) have demonstrated that hatchling alligators benefit from and apparently do utilize some dietary carbohydrate.

Don't make the assumption that being able to digest some plant material means that the organism can digest all plant material. Whole grain is notoriously hard to digest for many animals.

Yes that is true, but the OP asked about wheat in reptile food which I assume is preprocessed and as such can be digested. Nevertheless you're absolutely right in your comment, I did not express exactly what I meant to write / say. My bad, I'll edit my answer.

Ah yes, you make a good point. The original question did in fact specify wheat meal, meaning it has been processed.


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Do changes in an organism's cell modify the genetic information it uses for reproduction?
What I'm actually interested about is whether a modification in one cell during the life of an asexually reproducing organism affects its genetic information? Which cell's genetic information is used during reproduction like budding, for example in the case of Hydra.
Or does the incidental advantage it could have given rise to disappear with the death of the organism?

What kind of organism? Multicellular or unicellular? If the former, what cell? A random cell of a multicellular organism? A gamete?

In multicellular organisms there are specialised cells called gametes that are responsible for sexual reproduction (sperm/ egg cells). Mutations occurring in these cells can be passed on to offspring (germ line mutations). Mutations occurring in others cells affect only the given individual (somatic mutations).
Edit:
For unicellular organisms it is pretty straight forward, the daughter cells formed through fission are identical. As for multicellular organisms here are many forms of asexual reproduction, and even these may involve the formation of specialized cells (eg. spores). So my answer is: it depends on the type of asexual reproduction and the actual cell(s) that accumulate mutation(s). For example in parthenogenesis - where the unfertilized egg cell develops into a new individual - , a mutation can be inherited if it occurs in the germ line cells generating the egg cell, but any somatic mutation would stay in the parent. You can find detailed info on asexual reproduction with details on each form on this wiki page

Thx for editing my typos,.I wrote my answer on a phone.

I'm sorry for undoing the acceptance of your answer, even though it was correct for the previous question, but I realised that what I asked was wrong to begin with.

@FloriOn - No worries :) Since my answer does not fit to the question I shall edit it.

@FloriOn - I hope my edit helps a little bit.

Yes, it certainly does. But aren't the cells used for budding somatic ones? Or do they change into germline cells before reproduction, in which case they might integrate the mutation they might have experienced during their "somatic life"?

@FloriOn - Well, some sharks are know to be able to reproduce through parthenogenesis (at least in captivity there are known cases), so in their case the actual egg cell comes from the germ line cells. On the other hand many plants can be reproduced by digging a branch in the ground and all of those are somatic cells... So I still say it depends on the actual case.

Would something like CRISPR fit your criteria? CRISPR is essentially an adaptive immune system for bacteria. When a bacteria encounters foreign DNA (usually from an invading bacteriophage), it can cut it up and insert part of it in between palindromic repeats called CRISPRs. This small piece of DNA can be transcribed and then used as a template to recognize other copies of the foreign DNA. When a match is found, the foreign DNA is degraded, impairing the invading virus. Because a record of this foreign DNA is stored in the bacterial chromosome, it is transmitted to daughter cells, which will now have some protection against the offending virus in the future.
In the same vein, when certain bacteriophages invade bacteria, they integrate their viral genomes into the host bacterial genome---phage lambda is the classic example. At this juncture, the phage can choose between two lifestyles: lysis, in which the virus replicates like crazy, killing the host cell and spreading to other cells; or lysogeny, in which the virus lies dormant, allowing its genome to hitch a ride in the host genome, getting replicated and passed on to daughter cells just like any other piece of chromosomal DNA. When the time is right, the virus can switch back to lysis, proliferate, and infect new cells. Thus viral invasion of an asexually reproducing organism can lead to heritable changes in the host genome.
I'm sure you've heard of epigenetics, in which environmental factors can cause heritable changes to an organism without specifically mutating genes. While typically appreciated in eukaryotic organisms, asexually reproducing bacteria also have epigenetic mechanisms (1).
(1): Casadesus J and Low D. (2006). Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev. 70(3): 830-56.

Just saw your restriction to multicellular organisms. Less familiar with that, I'll let someone else answer that then!


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How detachment/separation works in biology?
It might be a strange question, but I'm interested in the mechanics of separation/detachment during asexual reproduction, for example when an organism reproduces by budding (I don't mean cellular budding like baker's yeast). When the newly formed body is fully matured it detaches itself from the parent / original body.
It might not be caused by a specific tissue, as animals with not so differentiated bodies are (also) capable of such, but I could easily be wrong. Is this (the detachment) triggered by changes in the cell membrane? I can't really think of other explanations.

can you bring an example?  I think mechanism is about as complicated as cellular division, in principle. Also, apoptosis (programmed cell death) might help separate "mother" and "daughter" tissues from each other

I find this unclear and you should specify what organisms you are interested in, since this will probably differ between organism types.

What got me thinking was the Hyra's budding

@FloriOn You can make this question a specific case of hydra. Worms do not bud off; they can regenerate and that is a different mechanism

@WYSIWYG I'm sorry, I didn't realise that someone has edited my question and put that sentence about worms their. It definitely not what I wanted to ask.

@FloriOn Then add to the question that you are most interested in Hydras (and other Cnidaria?), to narrow its scope, and include what you know from before about detachment in Hydras.

Reproductive budding and what you call 'cellular budding' are really highly related processes. Budding as a form of reproduction essentially partitions protein aggregates and damaged cellular components into the host or mother and builds fresh or 'young' cells on the opposite side of a partition. To begin understanding this look at Saccharomyces cerevisiae (budding yeast) which forms protein rings (from the septin proteins) at the membrane, around the bud neck which separates the mother and daughter cells Hartwell 1971. This ring acts a partition that in part, withholds protein aggregates and certain proteins from diffusing from the mother to the daughter. This protein ring is an example of how cells limit diffusion of proteins and cellular components to the daughter cell. Another good example that comes to mind is Linder 2007, though it is done in E Coli, not budding yeast, where mother cells maintain protein aggregates and age, while the daughter cells are given fresh components and are therefore more fresh and 'young'.
Now like you mention, imagine this process in a multicellular organism to be fundamentally the same. At some point the multicellular organism will start an outgrowth of cells, while restricting what materials are given to the daughter cells to maintain their youth. And eventually a new organism will have been created. Some of the details will be different, but the fundamental process is is quite similar. In that you start with an old cell that creates a new cell from scratch, but rather than splitting all cellular components equally between mother and daughter, the daughter cells is made in peak condition while the mother cell retains much of the cell 'junk' like protein aggregates.
Hopefully that starts to answer your question.

You should expand more on the budding in multicellular organisms. It seems that you are speculating that multicellular budding is similar to the unicellular form without having supported this argument with any fact.

Yeah I can do that. I just couldn't remember any papers offhand.


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How does an organism know when to stop growing, whether it is already on the outermost layer?
When a multicellular organism is under its development how does the current outermost layer of cells "know" that they should not divide furthermore, as their bodyplan coded into DNA is already achieved. Is it because of morphogens or something else's work is in the background?
If it is entirely controlled by morpogens, than it would mean, that injecting a given morphogen to the outermost cells, would result in further increase in the organism's size?

I don't understand your question.

Could you please expand your question because in this form it is unclear what you're asking and I do not really understand your question either.

@FloriOn - I think it's ok for me, I think I get what you're asking

@FloriOn - It is your sole decision :)

It is not the outermost layer of cells that determine tissue expansion. For example, during development the skull shapes itself to the expanding brain. I vote for question closure as it is badly researched. It definitely holds potential, and I encourage FloriOn to edit, but it does needs work.

@AliceD You are right, I have missed some important steps. But before the brain starts its development, the skull should be already in some place, for which it should have known the outer limit to its growing. I hope I am being clear here, as I am not sure about it.


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Is the "concept of time" coded into the genome?
What I'm interested about is whether environmental changes' effects are coded into the genome, like metamorphosis, deciduous plants. Can it be explained by morphogens, or it's something completely different?

I tried to narrow it a bit. I'm sorry, if I was not successful enough.

Do you know about epigenetic?

Something you might be interested in is circadian clocks, which are literally genetically encoded timekeeping devices. Although they can be entrained by environment, they can also "free run" in constant conditions cycling in the absence of light/dark cues. The core circadian clock in photosynthesizing bacteria called cyanobacteria consists of just three proteins. You can isolate them from the rest of the cell, and just like a watch taken from your wrist, these proteins will continue to oscillate in a 24-hour cycle. If that isn't a genetically encoded "concept of time," I don't know what is!


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Are these termites?
These are outside a window in Phoenix, Arizona. I looked on the internet for pictures and these guys looked very similar to winged termites.

Do you have any shots from above?

@Oreotrephes no, unfortunately not, they're just sitting on the glass

Based on the pinched waist, I'd say these are hymenopterans, not termites.

They could be halictid bees, possibly Agapostemon splendens.
Yours looks very similar to this picture

(by Bob Peterson)
Compare also with this one on bugguide and to the pictures of Agapostemon species in this National Geographic article.
Compare the metallic head and thorax (that's the middle segment), the striped abdomen (the last segment), the apparent large size of eyes and place of antennae attachment, and the 'buff' hindlegs.


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How do genetic chimeras with different blood types not die?
If a person is a chimera and has two different blood types in his veins, how does he not die? Shouldn't the immune system attack one of the blood types?

In 1953 a human chimera was reported in the British Medical Journal. A
  woman was found to have blood containing two different blood types.
  Apparently this resulted from her twin brother's cells living in her
  body. More recently, a study found that such blood group chimerism
  is not rare.

Can you please give a reference for this happening?

This is particularly true for the marmoset. Recent research shows most marmosets are chimeras, sharing DNA with their fraternal twins.[5] 95% of Marmoset fraternal twins trade blood through chorionic fusions, making them hematopoietic chimeras.[6][7]

@Chris Taken from wiki page for chimerism

If they have both antigens from the beginning, they won't develop antibodies to them.

That's like people who have bloodgroup AB - if they have this from the beginning, they develop no antibodies.

Since these cells are there by the development of the immune system, the immune cells recognize them as self. By blood transfusion with incompatible blood type, the immune system recognizes the blood cells with different histocompatibility antigens (A,B,Rh etc...) as non-self, that's why it attacks them.


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If eating 100% fat 2 times more worth the energy I spend during the day, will I store body fat?
So in theory, insulin hormone is the one that tells the body "eat more. don't burn body fat". Alongside with glucose blood level regulation and turning excessive glucose into liver (which later goes into muscles as glycogen or into fat cells). Fats are the only thing that do not provoke insulin secretion. 0 glycemic index.
So in theory, if I eat 2 or 3 times more worth the energy I spend during the day, I'll never store body fat because of 0 glycemic index?
Or will I still gain because such huge fat intake will make liver into making glucose from fats & proteins?
Surely u'll never find a sustainable product to eat that is 100% fat, but just a few examples are butter, lard, heavy cream. This is just a theoretical question, where the proteins/carbs intake is so low that it is not count.
Could you please clarify it since I got lost.

Interesting question! I would guess adipose fatty uptake and esterification would increase with higher fat ingestion, regardless of insulin levels, simply because there is more fat around. The body cannot make glucose from fat, so fat accumulation via glucose is not a possible. (Which is also a reason why such a diet would be lethal.)

@Roland how come it can't? It can. https://en.wikipedia.org/wiki/Gluconeogenesis

@Roland and also I can't consider "simply because there is more fat around" a legit argument. I am really curious about this and my local dietitians can't seem to satisfy my interest. Something has to tell the body to start storing the fat. If it's not insulin (that is significantly elevats due to carbs/protein intake), then what else can tell the body to store the fat? Btw what about "lethality" of this diet. I eat about 80% fat and 10% protein from calories. Other - from leafy greens. Also intake a lot of fiber and electrolytes. Not dead yet. Even more. I cycle 60k+ day at high speeds.

Gluconeogensis from fat doesn't work due to stoichiometric problems. With only acetyl-CoA from fatty acids, the TCA cycle cannot function, because oxaloacetate used for gluconeogenesis cannot be replenished. Organisms that can turn fat to sugar use something called the glyoxylate cycle, which doesn't exist in humans. See any major biochemistry textbook, like Stryer's.

I meant that there is likely a basal rate of fat uptake by adipose tissue even if you don't get a glucose-induced insulin peak. And adipose fat storage probably is faster at higher plasma fatty acid levels (I'm guessing). Also, note that in the presence of glucose, fatty acids do increase plasma insulin (see for example http://www.ncbi.nlm.nih.gov/pubmed/15929861), and animals and people on high fat diets are known to have higher insulin.

As for "lethality". 80% energy from fat (which sounds like a lot to me) corresponds to 65% fat in your diet (by weight). So you are still taking in 35% carbs and protein. Your hypothetical 100% fat diet would be more like drinking oil and eating nothing else.

"is the one that tells the body" sounds like a strange way to say it. The response to food is regulated by many more hormones and neurotransmitters. For example, gut cells secrete GLP-1 in response to both fat and carbohydrates. I don't know all pathways involved but I'd be very surprised if insulin is the only mechanism involved in telling the body to store fat. And then there is the theory that the trouble behind metabolic disorders doesn't come from storing too much fat, but  from storing too little fat - the overconsumed but unstored fat would wreak havoc in different tissues.

Agree with @Roland - any basic biochemistry textbook (i.e. Stryer) will tell you that you can't make sugar from fat. That is, you can't make glucose from fatty acids because the reaction catalyzed by pyruvate dehydrogenase is irreversible. When someone goes on a high fat diet (i.e. Atkins diet), they force themselves to become ketotic - which means the body begins making a significant amount of ketone bodies from the breakdown of fatty acids. The body is trying to 'hold on' to its glucose reserves by burning ketone bodies, which can cross the blood brain barrier for brain energy metabolism.

There are a couple of reasons why this approach doesn't work quite as well as you might hope.
First, insulin doesn't go away after a high-fat meal. This paper reports changes in serum insulin following pure-sugar and pure-fat meals. Although there is much less of an increase in insulin following the pure-fat versus the pure-sugar meal, you will notice in Figure 1 that the insulin levels following the pure-fat meals (panel A) are higher than the levels during a fast (panel B). So even if high insulin were the only signal for fat storage, your dream of eliminating insulin with a high-fat meal is not realistic.
Second, when a high-fat diet is designed for medical purposes, a good deal of care is required to avoid significant potential adverse effects. Adequate protein intake is still required, and amino acids from the protein can be converted to glucose. Furthermore, ketoacids are produced when fatty acids from ingested fat are in excess. (As noted in comments, humans do not convert fatty acids to glucose.) Although ketoacids can be excreted in the urine (admittedly, heading toward your goal of not storing all the calories you consume), the net metabolic effect on the body when you excrete ketoacids is increased acidification, which in turn can lead to difficulties with potassium regulation and thus, in severe cases, with heart function. In the extreme if this were continued for a long time, you may face a problem of life-threatening ketoacidosis as occurs in type-1 diabetics (low/no insulin) whose disease is not being managed.
That said, your basic idea is similar to the arguments for low-carbohydrate diets. How well they work and, if they do, through what mechanisms are still somewhat controversial, as I understand. Insofar as they work through excreting some of the ingested fat through urinary loss of ketoacids, however, the associated risks need to be considered.


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Why are clementines easier to peel than oranges?
In my experience, clementines have been significantly easier to peel by hand than and orange.  The skin of the orange seems to cling to the rest of the orange much more so than the skin of the clementine does.
What causes this?  Wikipedia (Clementine) merely mentions that they are easy to peel, but leaves it there. What is different between the way the skins are attached?

I think it all comes down to the thickness of the skin and how it's attached to the fruit itself.  For me, it depends on the variety of oranges and/or clementines, mandarins, etc. that I'm peeling.  Usually fruits with thick, hard skin are easier to peel whereas fruits with softer more delicate skin are harder to peel off in one piece.  Factors like growth climate and ripeness effect the skin quality.
If you roll the fruit on a hard surface under your palm before peeling, it makes the skin easier to peel off in one piece.

I'm not as concerned with getting everything off in one piece, but I feel like I really have to put a lot of effort to get the skin of an orange to separate.  Do you know more about how the different skins are attached? (And should I add that to the intent of my question?)

@BrianJ the ultimate arbiter of the way the skin 'attaches' (really it 'forms') is the genes of the plant.  Citrus fruit skins' all form by the same process of  cell differentiation and growth, which are controlled by the genes of the plant, which are in tern controlled by other genes, hormones, environmental factors, etc.  So, the oranges' genes may code to produce more fiber between the flesh and fruit, making the 'pull' easier or harder.


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I have a black tiny bug crawling all over the house
This bug is crawling all around the house it stays within the shadows and moves very very slow, i have never seen it jump or run, it just moves very slowly

P.S. those bugs as u can see are smaller than 1mm so it's hard to take better pictures but i will get better ones tomorrow
P.S. the hairs are not hairs they are wool from the carpets, i just got married in october 2014 and everything in the house is new, including the flat, it was built in january 2014.
Bug pictures with a 1 mm thick pencil refill
it is very similar to what's in this picture, but i couldn't take a picture of it because it's tooo tiny
I really need to know what it is so I can deal with it :(
Edit: once i found a very little few under the carpet but it generally stays away from the carpets and stays on the tiles and I don't think it is a termite because I don't find any piles of eaten wood
EDIT 2:
More pictures:
-- Stage 1 --

-- Stage 2 --

-- Video for stage 2 --
I don't know what it is but I know that there is ones young in age i call them stage 1 they are unable to move
and there are ones I call stage 2 older in age and bigger in size and they can move and I think they can bite too
-- Insect 2 -- 5mm by 5mm

I found this one across the hall from the others and I do't know if it's related, i found it dead but I haven't sprayed that side with insecticides i sprayed the other side so it's possible that it was with the others but ran and died far from them.
EDIT: More photos
P.S. I found those moving in daylight (now)

when i blew a little air i think i turned it

What region of the world are you located in?

The pictures are too blurry to make a certain species determination. To me, termites seems likely though. Can you see a clear waist? Do they have 6 legs?

@MattDMo I am from Egypt

Those photos dont provide enough detail--at least to me.

Added more photos the sources are at the dropbox folder cropped versions are in the question, PLEASE HELP!

I have added more photos please look at them, thanks

You write: "once i found a very little few under the carpet but it generally stays away from the carpets and stays on the tiles".
Could it be that they are simply less visible when in the carpet as when on the tiles ?

yes, it definitely could, if my tiles weren't whitish i would have never seen them, if they were on the carpets there is no way to see them

Can you keep some "stage 1" isolated in a jar with some dust and a tiny drop of water (just guessing what they might feed on) and see if they actually turn into "stage 2" ?

It seems from some of the photos that the "stage 2" have quite thin and long antennae, unlike what I've seen in termite images. Besides, the size is very small, so I wouldn't bet they are termites.

Let's hope it's not an insect that does irreversible damage like termites :(

Insect 1 is a:

Booklice
Introduction
Booklice, also called psocids, are not true lice. While they resemble lice in size and shape, booklice feed only on fungi or mold. If you find them in grain or other stored food products, it is an indication of high humidity which encourages mold growth. In addition to food products, psocids may be found under wallpaper, in furniture, along the sides of windows or on window sills around potted plants. Booklice do not bite, transmit disease, or damage food or fabric, but they can be very annoying when present in large numbers.
Biology

Booklice found inside homes are wingless and very tiny: less than 1/16 of an inch long. While their back legs are thicker than the other four, and resemble the legs found in jumping insects, booklice do not jump, but run about rather quickly.
Adult booklice range in color from translucent white to gray or brown. Females can produce about 60 eggs during the warm summer months and their life cycle (from egg to adult) can be completed in less than one month. When cool temperatures prevail, female booklice produce fewer eggs and the time required to complete their life cycle is over three months. Females deposit their eggs singly and often conceal them by covering with debris. Booklice undergo simple metamorphosis, that is their nymphs look just like adults except that they are much smaller and sexually immature. The common house-infesting booklice normally have four nymphal stages.
Injury
Booklice feed on molds and will overrun cereals and similar materials that support mold growth. Their presence, therefore, is a nuisance and can render some foods unfit. The starchy paste of wallpaper and books also can support mold growth or may be attacked directly by booklice. Outside of annoyance, their damage is insignificant.
Management
The best way to control booklice is to eliminate moist environmental conditions. Reducing the humidity in your home will eliminate the mold on which the booklice feed. Lowering the relative humidity to less than 50% will prevent their development. An air space under potted plants on windowsills will help keep the humidity down and reduce mold growth. Throw away any infested food material and make sure other foods are kept dry. Pesticides are not normally necessary to control booklice in homes.
Warning
Pesticides are poisonous. Read and follow directions and safety precautions on labels. Handle carefully and store in original labeled containers out of the reach of children, pets, and livestock. Dispose of empty containers right away, in a safe manner and place. Do not contaminate forage, streams, or ponds.

Source: Penn State, Entomology: Booklice

Nice find and great that you added an answer. Clearer pictures would have eliminated my termite guess at a much earlier stage.

Also, you should try to summarize information from sources, and not copy them directly. And if you do copy passages, you must show clearly that the text is a direct quote. I have reformatted your answer to reflect this.

Update: This is an incorrect answer. From the poster's comment above: "Clearer pictures would have eliminated my termite guess at a much earlier stage."

The organism you call 'stage 2' looks like a termite to me, and the movement pattern shown in the video also fits well. They are mostly nocturnal, which also fits your observations. Your 'insect 2' is some sort of Isopod (an anthropod but not an insect), and unrelated to other organism. However, 1 mm is really small for a termite from what I know, but there are many different species and some can probably be that small. You should try to see if they have strait, beaded antennas and no narrow waist (which ants have) - both these characters are used to separate termites from ants.
Here is another useful page on termites from Texas A&M university, which includes more pictures and information on how to deal with infestations.
This picture shows soldiers (large jaws) and workers (pale heads) of the Formosan subterranean termite (Coptotermes formosanus).

(public domain picture from wikipedia)
Another possibility would be springtails (which are generally smaller than termites), but they are mostly found in moist soil, wood and similar environments, and they can jump.

Thanks for your answer, what about stage one, is it some sort of larva ?

Do the ones you call 'stage 1' move at all, or are they just dead? Termites naturally have eggs and nymph stages, but there shouldn't be any immobile stages outside of the nest. I still think the pictures are too blurry to really say, but termites (or ants) should be most likely. Can you see what their antenna looks like or if they have a narrow ant-waist (found in the suborder Apocrita)?

The small stage 1 they are immobile and they are not even standing on their legs because they have no resistance to air what so ever, they move when i blow slightly even if they blow while i am standing

I just had a call with my uncle he had a termite attack a few years ago, he asked me a question about any winged creatures, a month back we did have something that we thought are butterflies, I will mark you answer as correct simply because i think it's termites in very very very early stages and those stage 1 are yount termite nymphes

Insect 1 i not a termite, it's an insect that feeds on natural materials like cotton and wool ...etc, But the exterminator didn't now the english name

@ShereefMarzouk Do you mean insect 1 or stage 1 (or both)? Did he say what type of insect (moth, beetle etc)? Maybe a beetle from Dermestidae? 1mm seems small for a Dermestidae beetle though.

http://biology.stackexchange.com/a/31790/15476

Insect #2 is not an insect, it seems to be a woodlouse species. It's a small harmless detritivorous crustacean that likes dark and damp places. They are not uncommon in houses, but though they usually live outside. They probably died from waterloss after entering your house.