text:
When do plasmids replicate relative to its host cell cycle?
For plasmids is so much shorter than their host cell's genome (about 1/1000 in my case), it will take only 1/1000 time for it to replicate.
With respect to cell cycle, when will that replication occur?

Description of the situation I'm facing:
I have a low copy number plasmids (pSC101) in E.coli, and I'm measuring a fluorescence protein expression level. The problem is, even if the plasmid copy number is known (N), depending on when it is replicated, the number of plasmid in my cell can vary. Therefore, I cannot directly infer expression level per plasmid. Higher expression level might just result from higher number of plasmids.
For instance, if it is replicated right after cell division, I will have 2N plasmids for the most of my cell cycle.
If on the other hand, it gets replicated right before cell division (and partitioning machinery delivers exactly half the number to each daughter cell), I will have N plasmids per cell for the most my my cell cycle.

So, when do plasmids get replicated?
I could not find a similar question here with search.
Thank you very much in advance.

I've found a nice review that has many details on plasmid replication in general, and several papers about pSC101 in detail, and I'll try to extract the key information from these papers.
First of all your plasmid as an ori region that contains so called iteron:

In many cases, the origin of replication contains directly repeated sequences, termed iterons, which are the binding sites for the plasmid-encoded Rep proteins and which have control properties. (...)iterons have been described for several replicons like P1, F, pSC101 (...).

pSC101 plasmid has three of these iterons present, along with a protein called rep that is necessary for replication. Besides these there are sequences that provide binding sites for host proteins such as DnaA and integration host factor (IHF).
Details of these can be found in this and this paper, both provides details on replication and the function of ori region in your plasmid.
As stated in this other paper, plasmid copy number is controlled by the plasmids themselves, that may vary on host type and growth conditions but:

At steady state, the 1 number of replications per plasmid copy is exactly
  one per cell generation. This defines the steady state as shown in Figure 1. It should be stressed that while this is true for the population, it is not for individual plasmids-these are selected randomly for replication.

So not all plasmid copies are replicated once per cell cycle rather random ones are selected and they replicate to maintain the desired number.
When your plasmid has reached its target copy number it will adjust its replication frequency to maintain this number. This is achieved by negative control loops. There are many ways to do this (repressor proteins, anti-sense RNA) or in your case iterons. These sequence along with the rep protein may inhibit replication if too much plasmid is present by a phenomenon called  “steric hindrance" or “handcuffing”. This happens because the rep protein is capable to bind two iteron, simultaneously.
At low copy numbers saturation of iteron sequences by rep proteins initiate replication, but at high copy number rep proteins tend to interact with each other and plasmids pair up through rep-rep interactions therefore cannot replicate. See figure below:

So, long story short: plasmid replication in part depends on host factors but plasmids have means to control their copy number, and once target has been reached they maintain this number in a stable form. I know this answer does not provide solution to the when part of your question, but it provides an answer to the practical part of your problem namely: plasmid numbers are quite stable after the target number has been reached. I hope this helps
EDIT: I've found this article http://www.ncbi.nlm.nih.gov/pmc/articles/PMC210920/pdf/jbacter00181-0364.pdf that says:

In all experiments, plasmids pSG21 (oriS only), F'lac (oriS oriV),pBR322,
  and pSC101 were capable of replicating at all stages of the division cycle,
  with no detectable differences in the patterns.

So bad news for you, because according to the paper above you cannot tell when your plasmid actually replicates. Yet still as the average copy number is quite stable due to reasons described above this may not pose a big problem. Keep in mind even if you have an extra plasmid for a short time that may still not cause problem, because transcription of your riporter gene, folding, etc takes time under which previously synthesized proteins might degrade.
However this paper says the F+ plasmid replication is cell-cycle specific, you may wan to give it a try.

Thank you so much for this help! Great to know the detailed mechanism of copy number control of pSC101 plasmids (iterons). Great papers, too. It will be great if I can also know when the replication happens, too. I have to estimate expression level per cell per plasmid and when I see twice as much fluorescence, I'd like to know whether expression level per plasmid actually went up or it's staying the same while there's just another copy of that plasmid. But thank you so much for this nice explanations!

@Neil - I did some editing, does this help you?

Yes, it is helping me greatly! Thank you so much. I'm trying my best to understand the new paper better to see if I should conclude the thought here or not.


text:
Y Chromosome in Ovary Cancer Data
I have been analyzing TCGA Ovary Cancer data. In Somatic Mutation data, there is data of mutations in all the chromosomes (1-22 and X), but amazingly, I have found one (just one) row of Y Chromosome mutation as well. What can it mean?
For Reference, I have pasted that row below:
icgc_mutation_id icgc_donor_id project_code chromosome chromosome_start
MU42454          DO28056       OV-US        Y          13500742

chromosome_end chromosome_strand mutation_type
13500742       1                 single base substitution

reference_genome_allele mutated_from_allele mutated_to_allele
G                       G                   A

consequence_type aa_mutation cds_mutation gene_affected   transcript_affected
stop_gained      R194*       580C>T       ENSG00000183704 ENST00000331172

In just one individual you mean? It means that there was a rare recombination event I guess in the father (or grand-father or grand-grand...-father)

Yeah it is for one individual and only one entry: Individual is a 76yo female (deceased)

Does it correspond to a region the is close to the PAR?

Just to expand on what @Remi.b said, there is the possibility that at some point in the past, in a male ancestor, a rare event occurred where a portion of the Y chromosome somehow ended up grafted to an X chromosome (or possibly any one of the others), but didn't cause enough issues/abnormalities to be an issue, or at least noted.

You can find the positions of the PAR on wiki

Its not in PAR of either X or Y

This question was asked more than six years ago.  Since then, the dataset in question has been updated.  I accessed the OV-US project dataset from the ICGC Data Portal, specifically simple_somatic_mutation.open.OV-US.tsv.gz. The 9th field of this file is chromosome.  Counting the occurrence of each chromosome, we see that Y is not represented:
awk -F$'\t' '{print $9}' simple_somatic_mutation.open.OV-US.tsv | sed '1d' | sort -n | uniq -c

  13171 X
  39564 1
  31363 2
  24657 3
  11021 4
  16849 5
  18643 6
  19492 7
  13067 8
  11133 9
  12090 10
  24980 11
  25608 12
   3947 13
  12728 14
  12123 15
  17554 16
  30315 17
   5669 18
  29571 19
   9054 20
   3639 21
   7084 22

Note that icgc_mutation_id MU42454 is only associated with acute myeloid leukaemia in a single donor. Moreover, the search scheme "Donor IS DO28056 AND Mutation Location IS ChrY" yields zero results from the ICGC data browser.
So, it seems that the inclusion of a Y chromosome mutation in the TCGA Ovary Cancer data was a mistake that has since been corrected.

Nice to see the correction

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text:
Is RNA polymerase affected by proteins bound to the coding sequence of a gene?
I am designing a synthetic gene construct to express genes in E. coli driven by either Ptet or PLacO. The construct would look like:
-Ptet-(Gene1)-PLacO-(Gene2)-
I want to express each gene using either aTc or IPTG, but I want to make sure that the transcription of each gene can be controlled independently.
Let say I only add aTc and transcription is initiated at the Ptet location, would RNA polymerase bump into LacI bound to the PLacO promoter and stop transcribing? Or would it knock-off LacI transcribe (Gene 2)? I am not sure whether or not need to include terminator sequence to make sure the expression of each gene is decoupled.

Nice question!
First of all make sure that you have multiple transcription stop / terminator sequences at the end of your first gene . This is quite standard procedure. Also in your case the phenomenon called transcription interference (TI) comes handy. Here's a review on TI. In short:

the term TI usually refers to the direct negative impact of one transcriptional activity on a second transcriptional activity in cis.

Although TI is mostly defined as two transcription events affecting each other, at the low level the basis of it is that two proteins bound to the DNA affect each other's activity. Now since LacI's function is to inhibit transcription, thus it is strongly bound to the DNA and I'd say even if a polymerase somehow slips through the polyA signals at the end of the first gene it is likely to be stopped by the LacI already bound at the second promoter.
Alternatively you could put a weak promoter opposing the first gene and drive its expression, so it would collide with the oncoming polymerase from the first gene thus stopping it before reaching the second gene. Also here is another article on TI, that proposes a gene regulation network based on TI.

PolyA addition occurs in eukaryotic nuclei, but E. coli is a prokaryote.  I think what @poka.nandor is referring to are transcriptional terminators, which are very well characterized in E. coli and its viruses.

Oh, right, my bad. I got my head wrapped around TI and stuff we work with. I 'll edit my answer immediately. Thx for point that out!

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text:
What is the difference between influenza A and B viruses that causes their distinct seasonal patterns?
I recently learned from an answer at health.SE* that influenza B tends to occur later in the season compared to influenza A. According to the graph in that answer, during this year’s flu season the peak for influenza B was mid-March, compared to late December for influenza A. I’m wondering why this is. What are the virological factors that account for this difference?

*Now public!

Regrettably, I don't believe we know - we don't actually know why influenza is a seasonal disease in the first place. There are a number of possible theories, discussed in this review, but none of them are compelling enough to be a definitive causal explanation
In terms of the difference between Influenza A and B, B mutates at a much lower rate, which may explain the slower rate of dramatic antigenic shifts, but that isn't enough to disrupt the seasonal cycle by a few months at most.


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Do acetyl-CoA, acetyl-CoA carboxylase and acetyl-glutamate carry any charge?
Do the following compounds have any charge? If not, then why? If yes, is there any database that would give me this information if the compound is negatively or positively charged?
The compounds are as follows:
Acetyl-CoA
Acetyl-CoA carboxylase
Acetyl-glutamate
I have searched and somehow I am getting more confused.

chemicalize.org is a good utility for predicting many molecular properties such as pKa, pI and charge. The Human Metabolome Database uses the same underlying software but tabulates some of the data (eg charge is explicitly stated).
Acetyl-CoA, for example, has a pI of 1.32 and charge of -4 at pH=7.4.

Your second link is to a portion of an enzyme (a serine residue that gets phosphorylated). Prediction of protein properties can be done with ProtParam.
Human Acetyl-CoA Carboxylase 1, for example, has a pI of 5.95 and charge of -39.

what is the difference between these compounds and lipids?

The first compound you mention is acetyl-co-enzyme A (acetyl-CoA) (first picture, left panel). The acetyl group is uncharged, but the co-enzyme A (CoA) group (Fig. 1, right panel) does carry charge through its phosphate groups. In normal physiologic environments these phosphate groups will donate one or more protons, leaving the molecule negatively charged, as shown in Fig. 1, right panel below:

Fig. 1 Acetyl-CoA (left) and the co-enzyme A group (right).
The second compound is an enzyme, namely acetyl-CoA carboxylase. Consisting of many, many amino-acids it will carry many, many charges under physiological conditions. Some of these will be negative, some positive.
The third compound you mention is acetyl-glutamate:

Acetyl-Glutamate
This compound carries two carboxyl groups, which makes the compound acidic and negatively charged under physiological conditions, as it will donate one or two protons to the environment, dependent on the pH.
PS: For an in-depth answer on the basic chemistry and pKa values I would ask this at Chemistry.SE :)


text:
How is haemophilia dominant in human females?

In human females one X chromosome is inactivated forming a Barr Body. Then how is it that haemophilia is dominant?

Suppose a female has one normal X chromosome and one chromosome with the haemophilia gene. Now suppose that the normal X chromosome is inactivated — will the female show haemophilia?

X-linked Hemophilia is caused by the lack of production of the clotting factors VIII or IX. It is not inherited dominantly, but instead inherited in an X-linked recessive manner.
These proteins are produced in multiple regions around the body. In a female heterozygous for the gene coding for Factor VIII or IX, X-inactivation would randomly prevent one of the chromosomes from expressing its allele. Therefore, the production of active Factor VIII or IX would only occur in half the cells which have the faulty allele inactivated.
However, half the production of the relevant factor results in a close to normal phenotype, as the hemophilic phenotype would not manifest unless the clotting factor activity levels are very low.
This Medscape article on hemophilia states that:

Normal values for FVIII assays are 50-150%. Values in hemophilia are as follows:
Mild: >5%
Moderate: 1-5%
Severe: < 1%

Therefore, despite X-inactivation reducing the production of clotting factors by 50%, the heterozygous female still displays the healthy, non-hemophilic phenotype.
While the clotting factor concentration can only be reduced to approximately 50% of normal, it is still possible for heterozygotes to suffer from mild hemophilia. This is because other genetic factors may also affect the hemophilia phenotype.
For example, the gene encoding FVIII may have point mutations which reduce the effectiveness of the protease, therefore reducing activity levels below the expected 50%. Mutations in regulatory elements or interacting proteins may also result in hemophilia due to the regulatory elements downregulating the expression or activity of the protein.

Approximately 40% of cases of severe FVIII deficiency arise from a large inversion that disrupts the FVIII gene. Deletions, insertions, and point mutations account for the remaining 50-60% of the F8C defects that cause hemophilia A.
Low FVIII levels may arise from defects outside the FVIII gene, as in type IIN von Willebrand disease, in which the molecular defect resides in the FVIII-binding domain of von Willebrand factor.

Note that X-inactivation is a random process. Therefore not all indivduals will have 50% cells lacking the healthy allele (as you write). This is a process known as skewing. One heterozygotic could have no cells with the faulty allele, all cells with the faulty, or any other intermediate form (this follows a Gaussian distribution in the population). Thus heterozygotes display asymptomatic - mild - severe phenotypes.

@Wolgast While this is true and the percentage of cells with inactivation of the faulty allele does in fact follow a Gaussian distribution, the law of large numbers makes it extremely unlikely that the deviation from 50% would be very large. Answer was updated to account for these factors.

@Wolgast. Also not all genes on Barr bodies are inactivated. There are some regions where you will see a small amount of expression. As March Ho pointed out, hemophilia appears to be a dosage dependent disease and as long as enough Megakaryocytes are expressing the functional allele, then the disease will be masked in heterozygous females.


text:
Are stem cell lines cryogenically preserved or commercially available like HeLa cells are?
There are HeLa cells, which were taken from sick cancer patient and now is growing worldwide in different laboratories for experiments. HeLa cells can be kept because they are immortal and so they are an instance of immortal cell line.
What about stem cells? They are also immortal. Such cells can be taken from normal healthy person and also kept forever. Do scientists do this? Why don't we hear about it then? For example, they are distinguished in Wikipedia article, referred above.
Are there some special properties of stem cell lines, making them different? For example, being low differentiated they may be useless for experiments.

Firstly they are not cancererous as other cell lines. Secondly under the right circumstances (cell niche, growth factors etc.) you would have an unlimited supply of normal healthy cells. Also because they are undifferentiated they are used for unravelling the components necessary for differentiation commitment to certain lineages.

This is too long for a comment, so I have to write it in here:
Mostly this is because other cell lines are more practical in the lab.
Stem cells are much more tricky to maintain - especially if you want to keep their stem cell properties. They only grow very slow, tend to differentiate when they get too much stress, cellular signals and so on and need special media (these need to be defined, so that they are not containing factors which promote differentiation for example).
For everyday experiments (like expression profiles, experiments on the effects of certain substances on the growth, gene expression or whatever of cells) "normal" cell lines are much more suited as these are much easier to keep in the lab using standard media. Additionally,experiments can be more easily repeated and reproduced, since these cells should behave always the same.

I would the to stress the 'should' in your last sentence, as it not uncommon for cell lines to be contaminated, mislabelled or wrongly annotated. (see article in Nature last week: http://www.nature.com/nature/journal/v520/n7547/full/nature14397.html)

This is written under the premise that the cell lines are identified by suitable methods and that this identity is controlled regulary.

Thanks. But from my point of view, keeping stem cells are of specific interest. For example, we can observe the process of aging, since some of aging theories say about stem cells depletion or damage. What if stem cell cultures live no more than 100 yrs? This would discover explicit lifetime limit hidden somewhere inside them...

There is a limit for normal somatic cells - it's called the Hayflick limit which happens due to the fact that the telomeres get shorter with every division and at some point active genetic regions will be shortened. However, this does not apply to stem cells (at least to current knowledge which is pretty solid here) as these cells have an active telomerase.


text:
Why do some proteins "use" a beta barrel structure instead of alpha helices in transmembrane space?
Most proteins are fixed in the membrane by alpha helices. But some use beta barrels.
Wikipedia describes beta barrels as used for porins, preprotein translocases, and lipocalins. To me, a coiled coil alpha helix structure could surely perform the same functions and given the vast number of proteins using alpha helices there might be some out there.
So my question is twofold:

Are these functions exclusive to beta barrels?
If so, what about alpha helices makes them unsuitable for those functions?

As you can see on the wikipedia page you linked yourself that beta barrels have far larger diameters (in some cases up to 40 angstroms as stated in this paper) depending on the numbers of beta sheets that make up the barrel, compared to the diameter of an alpha helix (that is fixed) of 6 angstroms. (source http://www.chem.uwec.edu/Modeling/GGProteinStructures/Pages/alpha_helix/helix.html). Alpha helices are good to anchor proteins into the membrane, or forming small holes that is suitable for compounds like ions, while with beta barrels larger compounds such as sugars, or various drugs can be transported.
There's a good list of proteins with different functions for both types on wikipedia


text:
Are all protein composed of all the amino acid (in animal) or are there less diverse protein?
I have a question about amino acid composition of proteins: Are there proteins in animals that are made up only from a small subset of amino acids? So instead of all 20 amino acids let's say only 6-14 ( or any arbitrarily small subset) amino acids are used in a particular protein. Could you give me an example (or maybe a few examples) of such protein(s).

Welcome to Biology SE! I took the liberty to reformulate the body of your question. You can revert to your original version at any time if you wish.

This may interest you: http://www.nature.com/srep/2013/131010/srep02919/full/srep02919.html

Trp-Cage is a protein found in Gila monsters, and it is only 20 amino acids long and there are plenty of repeated amino acids so this does not use all 20. But there must be plenty of other examples, there is no reason why physically a protein must use all available amino acids.


text:
What's a good simple test for cDNA library quality?
How do I assess the quality of a cDNA library?
I want to clone CDS copies of genes from a library, but I don't know what's a typical expectation of getting a full length clone even for a shorter gene (~1000 bp).  I know it doesn't have to be composed of full length cDNA for sequencing, but I'd imagine quality of starting materials is important there too.
Are there some common transcripts I can try to obtain from PCR that will tell me how fragmented the sequences are in there?
What's a typical result from a commercial cDNA library - are there any QC tests that are quick to run in the lab?

From what kind of cells do you have your library? I think the answer heavily depends on that info.

did you try googling? actin seems to be useful probe target: http://www.ncbi.nlm.nih.gov/pubmed/3273856

@poka.nandor interesting - human testis or spleen - does that help?

quite a lot! At least we know what genes should be expressed, however there are housekeeping genes that expressed in most or all cell types like actin as aandreev suggested.

Is this library for sequencing? What is your experimental setup?  Did you perform reverse transcription and you want to check how well it went? I deleted my answer as when I tried to work on it it raised more questions on the post.

You would usually run you library into a Bioanalyzer and check that the fragment distribution looks something like you expect. From there you can look at housekeeping genes to make sure those are present in the library. The expected fragment length distribution largely depends on the kit, the experimental approach and the sample type you are using so it is pretty much impossible to tell you exactly what you should expect with no information on that. Also the library depends on what kind of sequencer you want to use, you don't want the same library for say Sanger sequencing or a MiSeq run.

I was hoping for something more like this @caligari2005.  how can I tell if the cDNA is fragmented or full length.  I'll change the question.


text:
What is the difference between intrinsic and extrinsic apoptosis?
Hello my Professor has been teaching about apoptosis and sometimes makes the distinction between extrinsic and intrinsic. I am not sure if I know for sure what this means. Does this just refer to intrinsic is a cell doing itself while extrinsic refers to Fas ligand? Thanks.

In both pathways 'the cell does itself' the difference is in the reason.
In short:
Intrinsic apoptosis is a response to 'internal damage' eg. damaged DNA, chromosom rearrangement, hang ups in division, hypoxia, etc. that the cell senses itself and 'decides to commit suicide'. This is done by the mitochondrial pathway - release of cytochrome C from the mitochondria activates the caspase cascade that results in programmed cell death. This is like "I'm too damaged, I must die".
In the extrinsic pathway as you have mentioned is indeed related to the FAS ligand (and Fas/FasL being the main pathway for apoptosis), but that is not the only external signal as TNF (also known as TNA-alpha) binding to TNF-R1 (tumor necrosis factor receptor 1) may also lead to apoptosis. These pathways are usually activated by the immune system for example in cellular immune response. This is like "You're abnormal / dangerous / infected, you must die".
Both pathways activates the caspase cascade at some point that results in apoptosis. Either way the actual process of apoptosis is carried out by the cell itself in a programmed, regulated manner.
Source: http://en.wikipedia.org/wiki/Apoptosis
This papaer offers a great review on the topic, including both pathways:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2117903/
I'd like to quote few  important parts to support my answer:

The extrinsic, intrinsic, and granzyme B pathways converge on the same terminal, or execution pathway. This pathway is initiated by the cleavage of caspase-3 and results in DNA fragmentation, degradation of cytoskeletal and nuclear proteins, cross-linking of proteins, formation of apoptotic bodies, expression of ligands for phagocytic cell receptors and finally uptake by phagocytic cells.

(...)

The extrinsic signaling pathways that initiate apoptosis involve transmembrane receptor-mediated interactions. These involve death receptors that are members of the tumor necrosis factor (TNF) receptor gene superfamily

(...)

The intrinsic signaling pathways that initiate apoptosis involve a diverse array of non-receptor-mediated stimuli that produce intracellular signals that act directly on targets within the cell and are mitochondrial-initiated events.

Note that the TNFR superfamily is quite large - in this Cell paper from 2001 (sorry, not open access), it lists 26 known receptors binding to at least 18 known ligands.

Absolutely true, I've added that TNF-alpha bindig to the TNF-R1 may lead to apoptosis. The quote is there to justify the general idea that some members of the TNF superfamily play role in apoptosis. Thank you for your remark!

I would actually change the example to Fas/FasL, as that interaction almost always leads to apoptosis. While TNFα is pro-apoptotic in some circumstances, there are many cases where it isn't, as it is mostly regarded as a pro-inflammatory cytokine, helping to activate cells responding to infection. However, when cytotoxic cells express FasL and bind to a target cell expressing Fas (the receptor), that (almost) always leads directly to the induction of apoptosis. I just think it would be a more clear-cut example. Your choice, though :)

I wnated to point out that not only Fas/FasL can induce apoptosis, but I'll emphasize that Fas/FasL is the main component.


text:
Why does mint oil feel cold on the skin?
When putting (japanese) mintoil on the skin it produces a cool feeling.
You can experience this, when adding it to your bath or using a spray with mint oil on your skin. The cool feeling occures even if the actual temperature of the spray or bath is quite warm.
Where does this sensoric impression come from?

Anything related to mint usually contains menthol. What does it do? It triggers the TRPM8 ion channels, causing your skin's cold receptor to become sensitive, and causing it to overfire.
This causes the brain (receiving cold signals from skin) to feel cold, and that's why you feel cold.
I have summarised it in a few sentences, but as with any scientific discovery, it took quite a few years to fully understand what was going on. NCBI have summarised this quite nicely over here (http://www.ncbi.nlm.nih.gov/books/NBK5238/)


text:
Why are 2 electrons transported from photosystem II at the same time?
I only know that electrons are captured by the primary electron acceptor and then go through the electron transport chain, ultimately ending up at photosystem I. But why do 2 leave photosystem II in the first place? I thought the oxygen-evolving complex only replenishes the electron hole one-by-one?

So refer to the following diagram,

In the photosystem II complex, water is decomposed into oxygen and protons. That's two electrons liberated from each water molecule. Plastoquinone accepts two protons from the stroma by coupling it to the two electrons it receives from the photosystem complex. In this manner, the protons are transported to the lumen, and the electrons are sent into the electron transport chain. So PQ binds in a QB site in the D1 protein, and it's not released until it's double reduced/protonated. Another PQ binds in it's place when PQH2 leaves the binding site. Source
Short answer: Two electrons are liberated in splitting water, and that mechanism feeds into asymmetric lumen/stroma H+ concentrations and movement of electrons through the ETC.


text:
Is blood regarded as an organ?
It consist approximately 7 percent of body weight.
By definition organ is composed of multiple tissues. Blood is a fluid, a circulating tissue.
Therefore can we call this fluid system a liquid organ?

I think , blood is an organ due to the composed of different tissues

Hmm... Blood(a connective tissue) in my own opinion qualifies to be called an organ, if we are going by the definition which states that " Organ is a group of different tissues coming together to perform a specific function".
And we know tissue is basically a group of similar cells performing one function. So group of red blood cells in the blood is one tissue, group of white blood cells in there is another tissue,etc. So I think with these two different tissues coming together (with others) to make up the blood, automatically makes the blood an Organ.

Blood is considered a type of connective tissue (sometimes). However, an organ is formed of multiple different tissues. Thus, blood is a tissue, not an organ.

Would it be fair to say that a counter to blood not being an organ is that blood has multiple cell types? But what is key to remember is that tissues are organised structures of different tissues. Blood has very little organisation due to its fluidity.

@Good Gravy I suspect that the fact that blood lacks structure is a reason why not everyone considers it to be a tissue. As far as I know, the multiple cell types themselves are not considered to be separate tissues by anyone (for instance, we don't consider blood to be composed of red blood cell tissue and white blood cell tissue), but then again this is not my area of expertise so I wouldn't be able to say for sure

organs have to be solid or gelatinous to be organs OR tissues in my opinion. otherwise, they are just juices. blood is not a tissue, it is a juice! tissues are called tissues because they are meaty. your brain is tissue. your blood is merely liquid.

While organs are generally considered to have a single, specified function (or perhaps a group of closely-related functions), blood (the fluid inside the vessels, not the vessels themselves) has many different functions:

deliver $O_2$ from lungs to cells
remove waste $CO_2$ from cells to lungs
respond to injury by clotting
carry multiple different types of nutrients by multiple different means (free-floating, carrier protein-associated, lipid particles, etc.)
provide transport for the immune system, which in itself has diverse functions
transport waste products to liver and kidneys
move regulatory molecules around the body (hormones, chemokines, cytokines, antibodies, etc.)
regulate heat in the body
maintain $pH$ and $H_2O$ balance
and probably more I haven't thought of

So, I don't think blood should be classified as an organ, just because of its multitude of uses. Instead, it is vital for the proper functioning of pretty much all the organs in the body, and allows for connections among them.

Any reason for the downvote?

Sorry for the late update. I don't think multitude of functionality is an criterion of being an organ or not. Organs like the liver also have a multitude of uses which are not necessarily related. One could also argue that the functions you listed are also a group of closely related functions (transport and dissipation).


text:
Does the palate truly house the sense of taste?

Source: Your “palate” is the roof of your mouth, and by extension, your sense of taste.

I was reading Etymonline's entry for palatable {adj.}, which cites and derives from palate {noun}:

... Popularly considered the seat of taste, hence transferred meaning "sense of taste" (late 14c.), which also was in classical Latin. ...

Are the quotes above factually right about mouth anatomy (I ask NOT about language here)? Or was this an outdated wrong idea?
Footnote: Did the etymology become corrupt? I heed the Etymological Fallacy.

Anatomically speaking, the palate is the roof of the mouth, separating the oral cavity (mouth) from the nasal cavity (inner nose). While the palate may be sensitive to heat and spiciness (via the capsaicin receptor, for example), it does not contain any taste buds, which are located on the tongue, and are part of the taste-sensing system. The other part of this system, olfactory receptors, are responsible for sensing odors, and are mainly located in the nasal cavity, as well as partway down the back of the throat.
So, unfortunately, while your palate is figuratively the center of your sense of taste, in reality it has almost nothing to do with it.

There ARE palatal taste buds! See Simpson's (2018) chapter in Fundamental Neuroscience for Basic & Clinical Applications (5th Ed) and Nilsson 1979. From Simpson: "taste buds are located on the human soft palate, oral & laryngeal pharynx, larynx, & upper esophagus. Extralingual taste buds are not located in papillae but rather are situated in the epithelium. Palatal taste buds are located at the juncture of the hard & soft palates & on the soft palate"

Although @MattDMo's post rightfully suggests that gustatory senses are achieved primarily by lingual taste buds and olfactory nerves, he has actually missed that there ARE in-fact palatal taste buds.
See Simpson's (2018) chapter in Fundamental Neuroscience for Basic and Clinical Applications (5th Ed).

Additional taste buds are located on the human soft palate, oral and laryngeal pharynx, larynx, and upper esophagus. Extralingual taste buds are not located in papillae but rather are situated in the epithelium. Palatal taste buds are located at the juncture of the hard and soft palates and on the soft palate

See Nilsson 1979.

There is some uncertainty in the literature as to the existence of taste buds in the palate of the human adult. In those histologic studies in which the ages of the individuals have been reported, taste buds have not been found in the palates of adults, but have been found in fetuses or newborn. However, clinical studies have demonstrated taste perception in the palate of the human adult. Thus, the aim of the present study was to attempt to find taste buds in the human palate in subjects of different ages. In serial sections of selected areas of the palatal mucosa from autopsy material from individuals 0–80 years of age no taste buds could be demonstrated. However, in four of seven subjects aged 25–44 years, one or two taste buds were found in biopsis from areas of the soft palate where taste perception had been demonstrated clinically just prior to excision. Thus the present study indicates that scattered taste buds exist also in the soft palate of human adults.

That's very interesting. I stand corrected.

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


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How to use swiss-mod to predict the secondary structure and 3D structure of a protein?
I'm trying to predict the protein secondary and 3-D structure for the sequence [Q1NN20] and need some help getting the ball rolling.
I'm getting confused with how and when to use Jpred, swiss-mod, and PDB. So far, I got the sequence from scanprosite, put it into swiss-mod, but what next? When does jpred come in?

I've tried to provide a general answer, but could you provide more specifics about the type of protein you have, and why you want to model it. Why are you using swiss model and jpred?

3D structure.
Use the PDB to identify structures that are similar to the one you have found (you can use BLAST to search the PDB). A 30% match or above is usually acceptable, and multiple alignments are of course useful at lower match scores. If structures exist that are similar enough, you can use homology modelling to generate a 3D structure (this is what the SWISS-MODEL server does, and I think it automates the BLAST alignments from PDB). If there are no similar structures, you can resort to ab initio modelling if you have a reasonably straight forward globular domain, otherwise you might need to draw in additional expertise.
There are so many specific factors that need to be taken into account for a project like this. Depending on what the model will be used for, different questions are relevant.
Secondary structure.
You will need a few different secondary structure predictors to make it convincing and then you will need to check that your secondary consensus matches your 3D structure. If they don't match you need to think about "why not?"
If there is a difference it usually indicates that some 3D interaction is involved in the folding, so your 3D model usually trumps the sequence structure predictions, but do check your 3D structure against the secondary structure predictions.
Secondary structure prediction is more useful when a 3D structure is not available and modelling one is not an option.

Metaserver runs several methods for you and runs consensus analysis (and a bunch of other stuff). I'd start there.

That's a good one to start with, but ultimately will still be "trumped" by modelling (from a good alignment).

Swiss model is an online tool for modelling protein tertiary and Quaternary structure using evolutionary information. J-pred and Swiss model both are pretty straight forward tools which requires only the sequence. Swiss model requires searching for a template and based on which the protein will be modeled further.J=pred is exclusively used for secondary structure prediction.

So when i'm using Jpred, I get a bunch of 'hits' from pdb. what are these, just very similar sequences?

Do those hits come with a score?


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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.


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Are there human cells, apart from red blood cells and platelets, without a nucleus?
I know that blood platelets and erythrocytes do not have a nucleus. Are there more cells in the human body without a nucleus, such as pancreas, cartilage, or lung cells?

My lecturer told me that only red blood cells and platelets lack nucleus in humans

Short answer
As far as I know, red blood cells and blood platelets are the only human cells in our body without a nucleus.
Background
Erythrocytes and thrombocytes are the only human cells without a nucleus, as far as I know. However, if you count the gut as being part of the human body (in essence it is a continuation of the skin and as such it can be considered to be on our outside), then we are loaded with cells lacking a nucleus, namely all the bacteria that live in our intestines such as E. coli. Bacteria, being prokaryotes, lack a nucleus. In fact, there are ten times more bacteria than human cells in our gut (Wenner, 2007).
Reference
Wenner, Sci Am 2007

There are a couple of them more if I am not wrong.

Wanted to give a one line answer some day!!
Lens fiber cells and keratinocytes.

That's two lines :) +1 nonetheless, interesting finds!

What do lens fiber cells and keratinocytes do? Thanks for the help, but I just wanted to know of all the common known cells, like cells of organs.

@Ace lens fiber cells differentiate to form the lens of your eye and keratinocytes form skin and hair.

@WYSIWYG Wonderful findings.

Most keratinocyte types have a nucleus. A small subtraction of keratinocytes, namely corneocytes , https://en.wikipedia.org/wiki/Corneocyte , lack a nucleus.


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How can we create a living dinosaur using DNA technology?
I'm wondering what would we need to do to create a living dinosaur using DNA technology? If it is not possible with current technology, will it ever be feasible?
In the movie Jurassic Park, scientists extract dinosaur DNA from a mosquito which was preserved in amber, and which has sucked blood from a dinosaur. The DNA is incomplete, so the scientists splice it with frog DNA. The DNA is then inserted into a crocodile ova and an embryo is created, and so on.
The Jurrassic park method is dubious. Although dinosaur DNA has been found and isolated, it was too damaged to restore it to its original form using current technology. It's not clear that splicing with frog DNA would work. Let's for the moment forget about how you would get the dinosaur embryo to develop and the eggs to incubate and hatch. I want to know how would we fully sequence the genome of some dinosaur?

Check this TED talk from Jack Horner: Building a dinosaur from a chicken. Quite interesting.

Jurassic Park approach is more or less correct. We can gather many DNA fragments and reconstruct entire chain by overlapping. Modern beings also can be used.

If birds evolved from dinosaurs, birds are a subset of dinosaurs. This makes birds dinosaurs. Technically we don't need DNA technology to make birds, Tyson Foods does it on industrial scale every day so you can get your dinosaur mcnuggets.

It is widely accepted that birds are in fact dinosaurs. Cladistically speaking, no DNA technology is required to create a living dinosaur, as they already exist.
Assuming you want to do the same to a non-avian dinosaur (a paraphyletic group), however, a better idea would be to ask on World Building SE, as there have been little to no scientific research on the topic, and speculative answers are generally considered off topic here.

Comparing back to related DNA is how it has been done in the past with the woolly mammoth. So it might be a mater of extracting enough and finding close enough relatives to do this. But from what I have read, the DNA is so heavily fragmented that is is relatively impossible to map even to close relatives. You can understand this as the more heavily fragmented the DNA the smaller the pieces. So if you have a strand like this:
ACTGATCGTACGTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTACTACTAGCT

It is long and may map to only one or two locations on a relative's genome. But if you have heavily fragmented strands that are much shorter like this:
AGTC

You can imagine that would map to millions of different locations. So putting these in order would essentially be impossible.
We have to also put these things on a timeline to really understand the difficulty, Woolly Mammoths lived 500,000 years ago, dinosaurs were like 60 million years ago.

So will it ever be possible to create a dinosaur?

I hate saying things are impossible in biology, but this seems pretty close to impossible.

Unless someday we fully understand how to 'program' from scratch designer organisms and create one from scratch. Obviously quite the challenge.

Woolly mammoths were around a lot more recently than that. According to Wikipedia, they diverged from the steppe mammoth around 400,000 years ago and didn't start going extinct until around 40,000 years ago. Isolated populations of woolly mammoths are believed to have existed 4,000-7,000 years ago.


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Quantitative Trait Locus process?
I do not seem to understand the concept of Quantitative Trait Loci(QTL's), can anyone explain it to me in detail? Reading the wikipedia article helped somewhat, but I do not understand it well.
What I understand:
-quantitative traits = a number(quantity) of phenotypes(traits) that vary
-To "make" a QTL, one must "map" the phenotypical traits to the genes that they are believed to propagate.
-This is done by AFLP-PCR, or Amplified fragment length polymorphism, according to wikipedia at least. This process cuts the genomic DNA into pieces and then amplifies the target region with primers via PCR. Then it is visualized using some type of gel technique?
-I am not sure how this gel data then allows the mapping of phenotypes to genes. I know gel electrophoresis can help to identify the length of a gene or region of a gene if using a ladder to compare.

I would disagree with your definition of "quantitative traits" and instead describe it as traits that are quantiative instead of qualitative. Eg, height is a quantitative trait whereas presence or absence of hairs is a qualitative trait

When we say that something is a genetic marker we mean that we can establish its linkage to a chromosome AND that we have some way of discerning, or detecting, how the marker has segregated after meiotic recombination (this definition is only valid for diploid species that undergo sexual reproduction).
So, for example, in the fruit fly, Drosphila melanogaster, the white gene is linked to the X chromosome. Wild-type flies have red eyes, a mutation in the white gene yields flies with white eyes.  You can use genetic crosses (matings) to (a) show that the white gene is linked to only one of the four fly chromosomes, and (b) if you have other genetic markers on that chromosome you might be able to construct a genetic map showing the order and distance of the linked genes.
You can also use a DNA fragment from a chromosome as a genetic marker--if you have an assay that lets you track the fragment after meiotic recombination.  A Southern blot, using a labeled probe is one way to accomplish this (e.g. a Restriction Fragment Length Polymorphism or RFLP).  PCR that lets you detect a RFLP or a SNP serves the same function, and is much quicker than a Southern Blot (and requires less DNA starting material).
A QTL is just one of these "molecular" genetic markers that shows linkage to the trait you are assaying. So, for example, if you had RFLPs or SNPs sprinkled all along the human chromosomes, and if you had a way to detect the segregation of all those markers after meiotic recombination, then you could use DNA from a family with lots of kids of varying heights, where one parent was tall, and the other parent was short, to see if any of your genetic markers were segregating, or linked to the phenotype of height in the children (this example assumes that height in humans is a quantitative trait).

If I may paraphrase you a bit, so the concept of a genetic marker is valid only for organisms that can do crossing over, or meiosis, since crossing over events allow for exchange of genetic material, and the closer a gene for a trait lies on a chromosome, the tighter the linkage will be. This means then that when looking for a genetic marker, we are looking at linkage? And also, therefore QTL's are simply a type of genetic marker, an gene in the chromosome to be studied for linkage to a chromosome? And then this is done by adding a probe that would fluoresce when examined?

Haploid organisms, like bacteria, and their viruses also have genes and DNA, and therefore have genetic markers. It is just that they don't have meiosis. You can still construct genetic maps, I was just trying to be precise. I think your understanding is correct. There are only two things to emphasize. The QTL is probably not the gene you are interested in, it is probably not even a gene, it is a proxy for the gene, because it is a hopefully tightly linked marker; you would still have to do further work to find the gene. Also you may want to ask how a Southern blot works.

Thank you, i think I know how a southern blot works, but do you have any suggestions for a image that would sum up the concept of QTL? I feel like learn better from images in general. Also as an aside, cant bacteria do some type of homologous recombination, i remember reading about it but maybe it was just my imagination.

@RoSiv Yes they can, for example a phage genome can be integrated in the bacterial genome through recombination. This is done through recombination att-loci (att for attachment). Of course this is only one example. http://en.wikipedia.org/wiki/Site-specific_recombination


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What is this frog?
(Man, there's a lot of 'What is this X?' questions here...)

I saw this while walking in Cyprus in early April. It was at about 100m altitude, in woodlands, sitting in the sun on a concrete step beside a muddy ditch; it's about 3cm long.
There appear to be three four types of frog in Cyprus, one of which is actually a toad, and this doesn't really look like any of them --- the closest is the Middle Eastern tree frog (http://en.wikipedia.org/wiki/Middle_East_tree_frog) but the colouring doesn't match and my frog is much more wrinkly and chunky-looking.
So what is it?

Looks to be a pretty good match for middle east tree frog... http://en.wikipedia.org/wiki/List_of_amphibians_of_Cyprus what specifically makes you think it is not that? remember that the wiki picture might not represent the variation that occurs in colouration and patterns etc

The mottled white patches on its back, the colour and shape of the waterline mark (although that could just be because it's in a different posture from the METF pictures I found), and the skin texture. The colour of the throat skin doesn't match either, although I don't have a good view of it here. I'm quite willing to believe it's a METF variation; I just don't know enough about frogs to know for sure, which is why I'm asking.

...I've discovered that most tree frogs look pretty similar.

Hyla arborea?

This patchy frog looks similar to one of the Gastrotheca species:
for example -
Gastrotheca pseustes -

It does looik similar --- thanks! But I suspect it's probably not, given that Gastrotheca appears to come from South America and I was in Cyprus. Unless it was very lost.

@DavidGiven Do you have other images of this frog?

@DavidGiven Perhaps an escaped pet?  Although the skin texture is quite different between the two pictures.

Since, frogs from the Hyla genus, look near enough exactly the same, it's fairly improbable to get an %100 accurate answer from a single picture. Not to mention, they change colour depending on their present surroundings and environmental conditions, making some of the more bold, distinguishable features in relation to visual appearance, that you could use as part of classification, no longer valid. However, the region of the frog helps in the process of elimination.
The frog and toad species with the greatest populations in Cyprus are; bufotes viridis; Hyla Savigyni; Pelophylax bedriagae. The toad Pelophylax cypriensis, is present too just not in as great populations.
In my opinion this frog in particular shows the greatest affinity to a mature Hyla Savigyni (Audouin) (shown below):

The frog in the picture you posted shares characteristics with the Pelophylax bedriagae, also found in cyprus:

More specifically, the dorsal spot distribution (although they're black in this picture); the dissolving white/cream border to lateral band and position; white "patches" on the legs etc. Notably, the nodules are of different size too; amongst the many other differences.
The size of the two species differs largely, as well.

You stated how the frog you captured in the image above had a rougher texture than the those you've seen. This could be due to the factuality that in some genus's, the males have rougher skin than the females. As well as the skin texture, sometimes male frogs have "thicker" and more muscular front limbs than their female counterpart! Considering this, you may now be able to spot one of the reasons towards the theory, of why female frogs are larger in overall size, than males. During mating, the male has to fully mount the female which, obviously would cause strain and possible injury. You can relate this to us as humans: if you were to mount (like a frog) your partner and you weigh more than her there's an increasing probability that she will get hurt; unless it's Ronda Roussey -  it would be you getting hurt. Incoherently, there are many variables to consider for example, muscle mass of "the one taking the weight".  This could be used to explain how some male mammals are more adapted to mating, by having a longer penis (male sex organ) e.g. a Horse.
Hence, the general rule: the larger the objects mass, the greater the resolved downwards force. To put it briefly. Providing you're on earth, and the force of gravity is equal to, 9.80665 NM, that is.

Presumably you used flash to capture the image on the camera, and this sometimes affects identification of the species since, it alters colours slightly and the appearance of certain features. Diverting the direction of the flash on your camera using a device can help avoid this - likewise with an attachment that alters the flash-effect. I have no idea what they're called, to be honest. Hopefully you know what I mean!

Despite my conclusion, I still have doubts. Did the frog make any noises that you can remember? That would help differentiate between members of the same genus.


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How long do the periods of systole and diastole last?
The background to this is i'm doing some work using ECGs for an animation of the heart and i'm having trouble defining the end points of these periods, particularly diastole. Currently, the only information the animation uses is the time (in seconds) when a R peak was detected in an ECG.
So i was wondering what the normal lengths of these periods are and what could affect the lengths of these periods.
I assume that the lengths of the periods is mainly affected by pressure/blood volume and not electrical activity so an ECG won't tell you how long these periods are (unless a heart beat is interrupted by another?). Is that assumption correct?
On a side note: what would happens to the heart physically if there is a large gap between beats. Does it sit relatively still during that period?
EDIT:
My original post could have worded better, so: I want to know specifically about long it takes for the ventricles to physical contract and relax. How would i determine the length of these two periods in seconds and where could i find the "normal" lengths of these periods? in the cause of relaxation, i'm wondering about what to do when there is a substantial gap between heart beats.

I've edited my answer, I hope it helps! If not please let me know, so I can refine to mach your needs.

I assume you are talking about humans?

The following image from wikipedia answer what you need. You can check corresponding page for details.

The top part shows the details of the different processes during a heart beat. Corresponding to these events the ECG reads are marked. As you can see the distance between the T wave ( the small bump after the QRS complex) and the next P wave corresponds to the diastole. As you can see the pressure changes correlate well with the electric reads from the heart. This wiki page has great descriptions of the features of the ECG and the corresponding events.
For example P to QRS corresponds to the conduction of stimulus from the sine node to AV node, or QRS depicts the rapid depolarization and repoliarization of the ventricles. This latter leads to strong muscle contraction and this causes intaventicular pressure rise, that is followed by aortic pressure change.
Edit: Sorry, for missing the key point, I totally misunderstood what you needed. I'll try to correct my mistake (I'll leave the previous info as it may be useful for others) The authors of this paper did a really nice work on modeling and measuring left ventricle contraction time and other things.
The reference: (Beyar and Sidman 1984)
Long story short: the contraction of the ventricle depends on the initial amount of blood (preload), aortic blood pressure at the end (afterload), and intial contractility. The results are summarized in three tables:

As you can see in the last columns, the ejection time varies with the parameters. The ejection time that is required for the ventricle to push the blood out to the aorta. Under normal circumstances a complete heart cycle is about 0.8s (or 800ms) this pie char shows the time ratio of main events. (Image taken from: tutorvista.com)

Note that complete cardiac diastole is when all the heart muscles are relaxed (this can be shortened if higher heart rate is required).
According to wikipedia

Isovolumic relaxation time (IVRT) is an interval in the cardiac cycle, from the aortic component of the second heart sound, that is, closure of the aortic valve, to onset of filling by opening of the mitral valve. A normal IVRT is about 70 ± 12 ms, and approximately 10 ms longer in people over forty years. In abnormal relaxation, IVRT is usually in excess of 110 ms.

Isovolumic relaxation is when the muscle relaxes, yet the volume of the ventricle remains the same, thus only the internal pressure changes (it is analogue to isovolumic contraction - when the volume is unchanged, but pressure is built up, this happens at early ventricle contraction).

Systole lasts about 3/8 and diastole 5/8 of a cardiac cycle.
Keep in mind though that such values vary with heart rate. The higher the heart rate, the shorter the fraction of diastolic time compared to the entire cardiac cycle.
That said, an ECG is not the best thing to look at if you wish to determine systolic and diastolic time intervals. What you would need is a heart ultrasound, so you can actually see the valves opening and closing. These events can be considered to happen in an instant. The potential you see on an ECG instead can vary with continuity and it would be a little harder to tell the exact timing.
So your assumption is correct.
Yes, a large gap between beats would show a heart expanding very slowly (this typically happens just before the atrial systole).
With substantial gaps between heart beats, consider those time intervals to belong to diastole.


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How Does NADPH Reduce 1,3-BPG?
If NADPH returns to being NADP+, then that means one proton and two electrons have been incorporated into 1,3-BPG. If only one proton and one electron were attached to the carbon in 1,3-BPG (removing phosphate), I’d understand, since there’s a single covalent bond between carbon and hydrogen which establishes stable octets. But there’s another electron hanging around. What happens to this one? Or am I totally mistaken about the whole process?
This is the chemical formula for G3P:

The Lewis diagram below shows the top part:

As stated, NADPH gave off 2 electrons, yet only one is needed to bond with carbon (orange). Where did the other electron disappear to?

NADPH is always accompanied by H+, and the electrons reduce as a pair. Otherwise, there will be no balance of charges.

And after NADPH reduces 1,3-BPG, it goes back to being NADP+. It loses two electrons. In 1,3-BPG, the hydrogen bonds with carbon, contributing one electron to the single covalent bond. My question is where the another electron has gone, if it’s not in 1,3-BPG and not in NADP+.

Sometimes the electrons react w/ oxygen to form superoxide, or react with surrounding hydrogen to form water

@Kendall So the electron does go elsewhere, and is not incorporated in G3P, correct?

Single covalent bond is a shared pair of electrons. For stable bond there should be 2 atoms with unfilled higher orbitals and at least a pair of electrons that is "distributed" among those slots.
UC Davis have hilarious page on that.

I have edited my question to show what I’m talking about better. A proton and one electron may be equivalent to a hydrogen atom, which can bond with a carbon atom. But there’s an extra electron that NADPH gives. What happens to it?


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How to analyse an ECG?
I have a project about extracting features from a homemade ECG. I need the PQRST points from the signal of the heart beat. The ECG I'm using has 3 electrodes that attach to the chest.
The problem is I don't know where I should define the PQRST points because the result does not look much like an ECG. I want to try to create a program later that can find those points.
Here are the raw ECG traces data taken from 3 subjects that were alcohol-intoxicated (0.2 to 0.3 promille):

I'm guessing the red and orange points here. And I'm pretty sure the green points are accurate located:

Green points is easy to locate but the orange is a little harder and the red ones are really hard to pin point out. Those points can be used to define the length of different complexes, intervals and segments of PQRST.
Which points is safe to extract? Where exactly are those points located in the graph?
Is the data too inaccurate for finding abnormalities?
Is there any other useful feature, beside heart rate, I can extract from my graph?

First bump is called P point, middle is QRS wave (as in Q-down, R-up, S-down), and last bump is T. Every feature is representation of electrical activity in certain region of heart. E.g. P bump is contraction of atrium. See more here. Bumps are P/QRS/T.
The reason why you see so many different recordings is that it was taken with many-lead ECG. Heart has very distinct shape, its atrium is on top of ventricle, it is a bit tilted to the right, etc. Your recording is a projection of electrical activity vector onto vector that connects two leads used for given recording. Pick two other electrodes and you will have different picture just because axis of projection changed.

via NIH
It seems to me that recording you show are from different pairs of electrodes, but it shouldn't matter. As you can see, different pairs of electrodes will "pick up" some processes better that the other.
Now, because ECG is electrical activity recording, heart rate is least useful information to extract from it. Measuring pulse will be less of a hassle and as accurate. But what you can do is estimate biophysicals properties of given heart. For example, distance between P and QRS (PR interval) complexes is time that it takes for heart to contract ventricle after atrial contraction. Any abnormalities will cause lengthening of PR or other change. Lengthening of PR interval often indicates 1st degree AV block (AV node is not conducting as usual).
There is bunch of information out there on ECG and abnormalities, you can find useful this page from U Utah with examples of many severe conduction abnormalities.

Can you please point out any algorithm/pseudocode which can find P / QRS / T in channels, please. I think there exist many of them but I would like to understand some basics how to do it.

@Masi what do you mean

Your answer is too generic. I would like to get some examples how you really analyse ECG with basic examples of false negatives etc QRS complexes with suspected PVCs in the immediate surrounding.

@masi well, then I would refer you to medical literature. Or some online knowledge bases, like http://www.ecglibrary.com/ecghome.php

The only abnormality which can be seen on the ECG curve is a prolonged PR Interval but only when acute alcohol poisoning has been done.
In the referenced paper the patient had consumed 3.7 g/l (3.7 per mille) which resulted in a PR prolongation of 200-300 ms. The normal PR interval is different for everybody but it normally is 0.12 to 0.20 seconds. A long PR interval will result in a first degree heart block. In your case (0.2 per mille) I doubt that you are going to see any abnormalities. But if the ECG sensor has a good sampling rate then maybe there is a chance.
The PR interval reference 1 is defined as shown here:

PR interval reference 2:

Further reading:

Normal ECG
Third-degree atrioventricular block in an
adolescent following acute alcohol intoxication. van Cleef AN1,
Schuurman MJ, Busari JO.

I think you should avoid the word only here. I would really like to see any pseudocode/software how you can detect those properies and waves in each basic ECG signals.

Beautiful work!
Whether the PR is prolonged depends on timescale om x axis (which i cannot find...).
I didn't really get the scope of this task. If you are attempting to create a computer automated interpretation of the crucial ECG intervals, waveforms and points, you are in for a very tough task (if you want it to be clinically safe). This is the subject of intense research with thousands of patents applying to it. There are also open-source software (i think MIT and Matlab has some resources on it.
Some good resources:
http://circep.ahajournals.org/content/6/1/2.full
http://circ.ahajournals.org/content/115/10/1306.abstract?ijkey=f624706cb1aa52e719908ba6fb39726f4434bcd9&keytype2=tf_ipsecsha
Www.lifeinthefastlane.com
www.ecgwaves.com (my site)
Www.bem.fi (good om electricity aspects).

This does not answer the question - answers are expected to stand alone and have links and references for further reading. Additionally one could see the promotion of your own website as critical.

you're right. i've modified the answer and included a reference to Kligfield et al which is a good starting point.

Please, no link-only answers without explaining specifically what you include. Your answer is pretty hard to read.

Additional resources for EKG tracings with analysis:
Practical Clinical Skills
EKG Academy  (my site)
Bill

This is not commercial as far as I see.

@Chris Isn't it considered spam.

@Mesentery I would simply avoid that - the cases where people post own websites are often spam...


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When is Water Produced During Photosynthesis?
The formula for photosynthesis is: $$6CO_2+12H_2O \rightarrow C_6H_{12}O_6+6O_2+6H_2O$$
I can count the carbons, the waters on the reactant side, the oxygens, and the glucose, but I cannot seem to locate where in either light or dark reaction 6 water molecules were produced again. Where and when were they produced?

why can't you just reduce $6H_2O$ on both sides? Do you have source of that equation?

@aandreev Googling photosynthesis formula "12h2o" gives multiple sources quoting the "12h2o" version. While it may not be correct, it is at least widely spread.

oh i love when biologists do physics/math

@aandreev  You can't think of this reaction as a math formula, the water on the right is actually produced by the reaction, it is not left over. While green plants use $H_{2}O$, some bacteria use $H_2S$ instead and they also produce water on the right. Also, this shows the net reaction which has many, many intermediate steps. The basic reaction is $CO_2+2H_2O \rightarrow (CH_{2}O)+O_2+H_2O$. However, to produce glucose ($C_6H_{12}O_6$), you need 12 water molecules and 6 of carbon dioxide. I love it when physicists try to do biology.

I realize that several steps are folded into one equation. And that is what the answer should contain, chemical equation where water appears as a product, or those where water is taken from environment.

Some of the water that's split is regenerated when the hydroxyl radicals (reactive oxygen species) are converted to hydrogen peroxide, water, etc. by superoxide dismutases and antioxidative mechanisms in the chloroplast (peroxisomes/catalases, etc. take care of this). There's also some evidence that the presence of mannitol, ascorbate and glutathione protect against ROS produced in chloroplasts as well. So you input water, and in an effort to avoid oxidative damage, you do get some water generated. However, the balanced equation doesn't reflect this because it's not an actual product of photosynthesis.
About ROS and protective elements
Extra Reading on ROS in photosynthetic systems
I think that's a very obscure fact, and despite the reality of things, it's actually difficult to query the literature. Good question.

So the water produced isn’t actually part of photosynthesis? Then wouldn’t the actual equation for photosynthesis be $6CO_2+12H_2O \rightarrow C_6H_{12}O_6+6O_2$? (Not balanced, but it reflects the reality of it, doesn’t it?)

In addition, when 18 ATP are hydrolyzed, should 18 water molecules also be included in the equation on the reactants side?

So you hydrolyzed 18 ATP, and if you look at the calvin cycle, for each CO2 that enters the cycle, you use up 2 ATP in the formation of G3P and 1 ATP in the regeneration of rubisco. So 18/3 = 6, and that would coincide with the entry of 6 CO2 into the cycle, or the normal photosynthesis equation. Someone correct me if I'm wrong!
As for convention, we'd say that yes 12 water molecules went into forming sugar and oxygen in reality, but had we not noted the regeneration of water somewhere in the formula, we'd have to assume the buildup of reactive oxygen species!

Short Answer
The short answer is the the six water molecules on the left-hand side come from CO2, as a by-product of reduction. That is, carbon dioxide may (formally) be though of as the source of the oxygen atoms in the six RHS water molecules (with the protons coming from 'the environment') 1†.
In photosynthesis, only half of the oxygen atoms of CO2 are lost to reduction.
The balanced equation given by the OP (Eqn 1 below) acknowledges this, and envisages that the other half remain as part of the synthesized hexose.
In photosynthesis, reduction of carbon dioxide is incomplete. If we reduce CO2 all the way to methane (an 8-electron reduction) both oxygen atoms are lost, and (in the simplest case) end up as water.
By inclusion of 12 water molecules on the left hand side, the balanced equation also acknowledges that the 12 reducing equivalents (24 electrons) required to make glucose from 6 CO2 all come from water and give rise to 6 dioxygen molecules (that is, oxygen is 'split').
In short, the six waters on the RHS result from the reduction of carbon dioxide, whereas the twelve LHS waters provide the necessary 12 reducing equivalents.
We need to add here that Eqn (1) applies to green-plant and cyanobacterial photosynthesis: not all photosynthetic organisms use water as electron donor, or produce O2 as a by-product.
Equations of Photosynthesis
The equation given by the OP (Eqn 1) is the overall balanced equation for green-plant and cyanobacterial photosynthesis (see Abeles, Frey & Jencks, 1992, p 635, for example) 2†:
$$\ce{6 CO2 + 12 H2O -> C6H12O6 + 6O2 + 6H2O \tag{1}}$$
We may summarize as follows:

12 reducing equivalents (24 electrons) are required to reduce 6 carbon dioxides to 1 glucose. These are supplied by water.
Water is the source of the oxygen released in green plant photosynthesis (not CO2)
In the reduction of CO2, six carbon-carbon and six carbon-hydrogen bonds are 'made' (thus accounting for the requirement of 12 reducing equivalents).
The reduction of 6 CO2 produces six water molecules as a by-product.
The reduction of 1 CO2 requires 2 reducing equivalents (four electrons). Or, 2 water molecules are required to reduce  1 CO2
CO2 is 'fixed'

In addition, we may add the following:

The reaction is thermodynamically unfavorable, where the free energy necessary (about 600 kcal/mol) being supplied by sunlight (Abeles, Frey & Jencks, 1992).

But green plants and cyanobacteria are not the only photosynthetic organisms, and  not all photosynthetic organisms use water as a source of electrons (or evolve oxygen).
Some photosynthetic bacteria use hydrogen sulfide (H2S) and 'make' elemental sulphur rather than oxygen.  The balanced equation may be written as follows:
$$\ce{6 CO2 + 12 H2S -> C6H12O6 + 12S + 6H2O \tag{2}}$$
It can be seen that although no water appears on the right-hand side of the equation, water is still produced as a result of CO2 reduction.
A balanced equation describing photosynthesis in general may now be given, where H2A is any substance that can be oxidized to A (Abeles, Frey & Jencks, 1992):
$$\ce{6 CO2 + 12 H2A -> C6H12O6 + 12A + 6H2O \tag{3}}$$
Other examples of H2A are H2, isopropanol and lactate.
The Reduction of a Single Carbon Dioxide
We may note first of all that the oxidation of two water molecules to a single O2 is a four electron (two reducing equivalent) oxidation.
$$\ce{H2O + H2O <=> O2 + 4e^- + 4H^+ \tag{4}}$$
The photosynthetic reduction of a single carbon dioxide may be represented as follows (Abeles, Frey & Jencks, 1992) and we may note that this is  a four-electron reduction:
$$\ce{CO2 + 2H2O^* ->[$hv$] (CH2O) + O2^* + H2O \tag{5}}$$
The asterisk indicates that if oxygen atom in water is labelled (using an isotope of oxygen, for example), the label is found in the oxygen 3†.
In green-plant photosynthesis, the (incomplete) reduction of 1 CO2 requires two reducing equivalents which are supplied by 2 H2O, and this four-electron results in the formation of 1 O2 and 1 H2O.
Oxidation and Reduction
I suspect that most readers of this post will know all of what follows in this section. Nevertheless, what is and isn't oxidation/reduction seems to sometimes cause confusion and some examples may help to clarify.
Oxidation is the loss of electrons. Reduction is the gain of electrons.  A hydration is neither an oxidation or a reduction, and neither is an ionization.
Some examples
The reaction shown in Eqn (6) is an oxidation (ethane is oxidized to ethanol). (Electronegative oxygen has 'taken' a pair of electrons from the second carbon atom, which is oxidized)
$$\ce{CH3-CH3 +\frac{1}{2} O2 -> CH3-CH2OH \tag{6}}$$
The  reaction shown in Eqn (7) is neither an oxidation nor a reduction, but a dehydration (the dehydration of ethanol to ethylene). The oxygen atom has not been  oxidized or reduced. It 'owns' the same number of electrons in ethanol as in water. (A good example of a hydration/dehydration reaction from the world of biochemistry is fumarase. The formation of malate from fumarate is not an oxido-reduction in any sense). This is an important one.
$$\ce{CH3-CH2OH  ->  CH2=CH2 + H2O \tag{7} }$$
The reaction in Eqn (8) is a reduction (the reduction of the carboxylate group of acetic acid to the aldehyde (acetaldehyde)), but note that the oxygen in water has not changed its oxidation state.  When water is eliminated, it leaves 'taking with it, in terms of electrons,  what is already owns'. But, unlike the previous example, the tetravalency of carbon is 'maintained' by the 'acquirement' of a pair of electrons (reduction).
An example from the world of biochemistry, is the aldehyde dehydrogenase reaction, where NAD+ acts as electron acceptor.
$$\ce{CH3-COOH + 2H+ + 2e- ->  CH3-CHO + H2O \tag{8} }$$
Eqn (9) is also a reduction (the reduction of acetaldehyde to ethanol). An example is the alcohol dehydrogenase reaction.
$$\ce{CH3-CHO + 2H+ + 2e- ->  CH3-CH2OH \tag{9} }$$
This final example (Eqn 10) is an ionization (the ionization of acetic acid), and may not under any circumstances be considered either an oxidation or a reduction (all the electrons 'stay put').
$$\ce{CH3-COOH ->  CH3COO- + H+ \tag{10} }$$
(When dealing with oxidation and reduction, protons are 'free'. We may add them in or take them out without changing the oxidation state).
Rant
Failure to distinguish between hydration/dehydration and oxidation/reduction has led to claims that water in the Krebs cycle is a source of reducing equivalents. Racker, for example, claimes in  A New Look at Mechanisms in Bioenergetics that electrons from water are transported down the respiratory redox chain, and Wieser claims that water provides 'the additional reducing equivalents needed to transform the chemical energy of one molecule of glucose into that of 36 molecules of ATP'. Both of these claims, IMO, are  nonsense (see here).
A Final Look at CO2 Reduction
Let's take a final look at the reduction of CO2 (where carbon is 'fully oxidized'), and reduce it by adding reducing equivalents (pairs of electrons) one-at-a-time until carbon is fully reduced, that is until we reach CH4. (We will also need to add a pair of protons at each step, but as far as oxidation and reduction is concerned, as stated above, these are 'free').
Adding a pair of electrons to CO2 gives formic acid, adding a further pair gives formaldehyde plus a molecule of water, adding another pair gives methanol, and adding a final pair gives methane plus another water molecule
This is summarized in Eqn (11).
$$\ce{CO2 ->[2H+, 2e-] {HCOOH}->[2H+, 2e-]{HCHO} + H2O->[2H+, 2e-]
 CH3OH->[2H+, 2e-]CH4 + H2O }\tag{11} $$
The oxygen atoms in the water molecules eliminated in steps 2 and 4 have not changed their oxidation state.
To fully reduce carbon dioxide to methane requires 8 electrons, and the two oxygen atoms are eliminated as water. To reduce six carbon dioxide to one gluc ose requires 12 reducing equivalents (24 electrons).  If nature had decided to make hexane ($\ce{CH3CH2CH2CH2CH2CH3}$) the photosynthetic storage product, this would have require 19 reducing equivalent (38 electrons), and if methane was the final photosynthetic product, then 4 reducing equivalents (eight electrons) per CO2 oxidized would have been required.
Footnotes

In the 'real world' of green-plant photosynthesis, the oxygen is 'lost' as phosphate, not water, in the glyceraldehyde-3-phosphate dehydrogenase reaction (see here), a key step in photosynthesis where reducing equivalents enter the carbon skeleton (see here). The electronegative atom (oxygen) 'eliminated' to 'accommodate' the incoming reducing equivalents does not  have to be part of a water molecule (or, in a more general sense, have to be oxygen at all).
In the case of aerobic respiration, the general equation may be given as follows, which emphasizes that 6 O2 atoms give rise to 12 H2O (six 4-electron reductions), and that (formally) 6 waters are consumed in the production of 6 CO2. Subtracting 6 waters from both sides, as is sometimes done (see here), only leads (IMO at least) to confusion.

$$\ce{C6H12O6 + 6O2 + 6H2O -> 6 CO2 + 12 H2O \tag{12}}$$

This experiment was done by Kamen and Ruben (1943), using 18O as tracer. Martin Kamin and Sam Ruben are credited with the co-discovery of  14C, that great gift to biochemistry and science as a whole. Sam Ruben died of phosgene poisoning, which he was preparing for the war effort during WW2. The story of his death is poignantly told by Martin Kamen in Radiant Science.

References
Abeles, R H.  Frey, P. A., Jencks, W. P. (1992) Biochemistry Jones and Bartlett
Kamin, M. D. (1985) Radiant Science, Dark Politics. A Memoir of the Nuclear Age.  University of California Press. Google Books


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Does the term "upper extremity" include hands?
I see on http://en.wikipedia.org/wiki/Upper_limb that the term "upper extremity" seem to include hands. However, in many hospitals, there is a "Hand & Upper Extremity Service", which would tend to indicate that the term "upper extremity" does not include hands.
Does the term "upper extremity" include hands?

Generally, upper extremities refers to arms (and everything attached to them), while lower extremities are the legs.

I suspect that "hand" is separated out because it is often a surgical subspeciality. Hands are complicated.

Interestingly, while hands include fingers with a lot of innervation, almost all muscles for hand are located in arm. 2OP: please accept answer if it is satisfactory

As far as I know, and the same is written on Farlex Free Dictionary, the upper extremity or superior limb includes:

the shoulder girdle
the arm
the forearm
the hand

Again, on this Dartmouth Medical School page, the upper limb bones are described and the article includes the bones of the hand.
So, anatomically speaking, the upper limb includes the hand.


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Why do flagella form a bundle only when they rotate counterclockwise during chemotaxis?
During Chemotaxis in bacteria with flagella, the flagellar rotation dictates how the cell moves. If the flagella rotate counterclockwise, then they form a bundle at one end of the cell (---O) and propel it forward in a coordinated fashion. However, if the flagella rotate clockwise, then each flagella acts independently to push the cell in many different directions.
My question is, why doesn't clockwise flagellar rotation simply cause the bundle to form on the opposite end of the cell? (O---)

In principle this can happen, but you have to read up on flagellar dynamics and polymorphic transitions (Real-Time Imaging of Fluorescent Flagellar Filaments, Turner et al. 2000).
From Howard Bergs lab page:

Runs can occur with filaments of any polymorphic form; although, the normal form predominates. For a cell to tumble, not every filament needs to change its direction of rotation. Different filaments can change directions at different times, or a tumble can result from the change in direction of only one.

If the whole bundle comes apart it can reform on either end of the cell body because E. coli has a random flagellation pattern (peritrichous) and thus no preferred direction of propagation of the cell body.
Also have  look here for some nice movies from the Berg lab.


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What is the connection between exercise and muscle growth
From a physiological perspective, all that is done during exercise is the expending of energy in the form of ATP to fuel muscle contraction and extension.
When I looked up why muscle grow due to exercise, there is the claim that recovery of micro lesions formed during exercise enables slight growth of muscle. I am not sure how micro lesions are formed and intuitively, these micro lesions should cause atrophy of the muscle rather than strengthening of the muscle fibers.
Further there is no logical connection as to why muscle fibers would be strengthened rather than just restored to its previous form during rest.
Can someone help me make the mental leap from the consumption of ATP through exercise to muscle growth?

Muscle growth and development is mediated by "trophic factors" not biochemical reactions (ATP) or muscle contraction directly. The best method of releasing tropic factors is exercise and not electrical stimulation or biochemical reactions (ATP) or biomechanical contraction.
Nerve ending release growth or tropic factors which stimulate muscle growth and for example if the nerves die off either due to injury or disease (ALS) the muscles will atrophy.
Not all of the tropic factors are as of yet known, but it is these tropic factors that stimulate muscle growth, not the biochemical or biomechanical reaction of the muscle (contraction). One can not as of yet stimulate muscle growth by delivering electrical energy to the muscle, for example (it has been tried to in an effort to maintain muscle mass in critically ill patients).
There is a review of the trophic factors here - http://neuromuscular.wustl.edu/lab/trophic.htm
And a review of electrical stimulation - http://www.medword.com/MedwordStore/PCP/EMS_truth.html
There are many claims of benefit for electrical stimulation, such as regeneration of the facial nerve in facial paralysis, such as Bell's palsy.
The "problem" is that the prognosis in Bell's palsy is very good, even without electrical stimulation, and so it is difficult to "prove" benefit with electrical stimulation:

With or without treatment, most individuals begin to get better within 2 weeks after the initial onset of symptoms and most recover completely, returning to normal function within 3 to 6 months.

http://www.ninds.nih.gov/disorders/bells/detail_bells.htm

Statistically, the natural history without treatment was described in a study of 1011 patients in 1982 [8]. One-third had an incomplete paralysis, and two-thirds had complete paralysis. Overall, 85 percent showed signs of recovery within three weeks, 71 percent had complete recovery, 13 percent had slight sequelae, and 16 percent had residual weakness, synkinesis and/or contracture. Patients with incomplete lesions had a 94 percent rate of return to normal function, while only 60 percent of those with clinically complete lesions returned to normal function.


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Are more molecules of ADP than inorganic phosphate returned to the light reaction in photosynthesis?
During the dark reaction, 9 molecules of ATP are consumed for every 3 carbon dioxide molecules, yet only 6 molecules of inorganic phosphate ultimately leave the cycle. Does that mean that there is a greater concentration of ADP than inorganic phosphate returning to the light reactions?

Not 6, but 9 molecules of Pi are formed in the Calvin cycle, from the conversion of 9 ATP to 9 ADP:

Source: Columbia University

I thought the inorganic phosphates were incorporated into phosphoglycerate to form DIphosphoglycerate, but then given off again in the formation of G3P. Then it is once again incorporated into glyceraldehyde phosphate to form ribulose BIsphosphate, but is not released anywhere else.

There's definitely some confusion. In the C3 cycle reactions, the conversion of 3-phospho-D-glycerate to diphosphoglycerate (DPG) actually affixes the inorganic phosphate from ATP to the DPG. The reaction that follows releases NADP+ and inorganic phosphate at a ratio of 2 per CO2 in the cycle, so for 3CO2 used in making one half a glucose, thats 6 inorganic phosphate liberated. If you're also considering the regeneration of rubisco, two inorganic phopsphate are liberated there for a total of 8 inorganic phosphate in the products per 3CO2.

And then, here's a link to a more detailed reaction schematic:
http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/polysacc/polygif/Calvin1.gif