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

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

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

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

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

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

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

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

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

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

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


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When contracting a muscle will the muscle spindle stretch or contract?
When you contract your muscle, will your muscle spindle stretch or contract? And why? I was always under the impression that it was contracting your muscle spindle, but now I am not sure.

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The muscle spindle normally stretches/contracts in concert with the muscle fibres in order to maintain detection of changes in length.
This image should demonstrate it clearly:

When the muscle spindle is stretched and excited it sends impulses to the spinal cord more rapidly (increased frequency). The sensory neurons synapse with alpha motor neurons in the spinal cord, which stimulate the extrafusal muscle fibers of the stretched muscle to contract and resist further stretching.
  Contraction of the muscle (extrafusal fibers) would cause the muscle spindle to become slack and stop transmitting impulses, however descending fibers of motor pathways synapse with both alpha and gamma motor neurons (alpha - gamma coactivation) so the ends of the intrafusal fibers contract and maintain muscle spindle sensitivity when the muscle contracts.

Further reading: here.

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Naming convention of miRNAs
I'm trying to understand naming convention of miRNAs. I've found the wikipedia article about it nomenclature Based on it, I try to figure out what is hsa-let-7a. As far as I understood, hsa refers to human but I expected a "mir" or "miR" after hsa but there is a word "let" .So my question is that hsa-let-7a is a name for a single mature miRNA or is it a name of a miRNA family(if there exists such a thing) ?

let-7 is a miRNA family (let stands for lethal). It was one of the first to be discovered, in fact (in C elegans). let-7a is a single member of the family. It seems rare in science that established names are changed to match newer nomenclature, though I don't know if that's the case here.

Another such example: There is an miRNA in Drosophila called bantam (Just bantam)

let-7 is a miRNA family (let stands for lethal) and, in fact, was one of the first to be discovered (in Caenorhabditis elegans). let-7a is but one of many members of the family, with orthologs in many species. It seems rare in biology that established names are changed to match newer nomenclature, though I can't say for sure if that is why many (but not all) of the let-7 family members don't follow the standard.
Edit: Coincidentally, I was just reading a review about miRNA and came cross this informative excerpt which should at least give some sense of legitimacy to my above speculation.
Ha M, Kim VN. 2014. Regulation of microRNA biogenesis. Nat Rev Mol Cell Bio 15(8):509-524

The nomenclature of miRNA genes is somewhat inconsistent. The genes found in early genetic studies were named after their phenotypes (for example, lin-4, let-7 and lsy-6), whereas most miRNAs found from cloning or sequencing received numerical names (for example, the lin-4 homologues in other species are called mir-125).

Roush S, Slack FJ. 2008. The let-7 family of microRNAs. Trends Cell Biol 18(10):505-516

The lethal-7 (let-7) gene was initially discovered as an essential developmental gene in C. elegans and, later, as one of the first miRNAs (Figure 1). Soon afterwards, a simple BLAST (basic local alignment search tool) search revealed exact matches to the mature let-7 miRNA sequence in the emerging Drosophila melanogaster and human genomes. It is now known that mature let-7 is highly conserved across animal species.
The let-7 family of miRNAs is often present in multiple copies in a genome (Table 1). To distinguish between multiple isoforms, a letter is placed after let-7 to indicate a let-7 with a slightly different sequence, and a number at the end denotes that the same sequence is present in multiple genomic locations. For example, humans have ten mature let-7-family sequences (Figure 3) that are produced from 13 precursor sequences (Figure 4). Three separate precursors produce the mature let-7a sequence (let-7a-1, let-7a-2 and let-7a-3) and precursors from two different genomic locations produce the let-7f (let-7f-1 and let-7f-2) sequence. However, the size of the family can differ between organisms. Drosophila (fly) has only one let-7, whereas the zebrafish Danio rerio has 11 mature sequences in 19 loci throughout its genome…

Early characterization of let-7:
Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901-906

Some general aspects about miRNA nomenclature in addition to canadianer's answer:

mir refers to the pre-miRNA whereas miR refers to the mature form
mir-x-y mir-x-z for example mir-1-1 and mir-1-2 refer to different precursors that give rise to same mature miRNA (i.e. miR-1). These different precursors can be regulated differently.
The mature miRNA resulting from the 5' arm of the precursor hairpin has a suffix of -5p; similarly the product from the 3' arm has the suffix of -3p. Previously, the lesser expressed/abundant (or unexpressed) of the two products was designated with an asterisk. For e.g. miR-124*. This convention is obsolete now. Any miRNA by default has the -5p/3p suffix. This is useful especially in case of let-7 because there is no uppercase notation to differentiate precursor from the mature miRNA. For example, the mature form is always denoted as hsa-let-7b-5p even though the -3p is never expressed.
A "family" consists of miRNAs with the same seed sequence (usually 2nd-9th residue). Sometimes it can be observed that one of the arms is less conserved than the other between different precursors. For example in the case of let-7 the -3p(s) do not have a conserved seed sequence, however, all -5p(s) have the same seed sequence.

And as mentioned in the other answer, the name let-7 just sticks around because of historical reasons.

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Is there a genomic code for nucleosome positioning?
What does a genomic code for nucleosome positioning in eukaryotes actually mean? By the code is it right to think that specific DNA sequences favour nucleosomes and others don't? I see that there for and against arguments on this topic. What is the current view on this topic?

Yes and no. Part of the issue is that there are different definitions for what a "genomic code" is and there are different definitions for what "nucleosome positioning" is. You may be interested in this review written by the two leading researchers involved in this debate: http://www.ncbi.nlm.nih.gov/pubmed/23463311

The genome is the complete set of DNA in an organism, including genes and non-gene sequences of base pairs (bp).1 Each codon of three base pairs in a DNA sequence specifies one of twenty different amino acids. There are four available bases in DNA; Adenine (A), Thymine (T), Guanine (G), and Cytosine (C).  Four letters taken three at a time (where order matters and repetition of a letter is permitted) gives 64 possible codes. There are only 20 amino acids necessary in most life on earth, so only 20 codes are needed from the 64 possible. One codon is also used as a start codon (start translation) and three codons are used as stop codons (stop translation). So there are 41 extra codons available. As it turns out, for most of the 20 amino acids several different codons can specify the same amino acid, but each codon only specifies a single, unique amino acid, so there is no ambiguity. The code is therefore said to be redundant or degenerate. This degeneracy allows the same protein (composed of amino acids) to be coded with different base pair sequences, which is important if one base pair sequence is better than another in its mechanical properties of bending DNA around a histone octamer to form a nucleosome.
If the DNA molecules in a typical human cell were lined up head to tail, they would form a string about 2 meters long. The diameter of a cell nucleus is only 5 μm (0.000005 meter), so the DNA really must be packaged or organized to fit. The packing solution eukaryotes developed is to coil DNA around histone proteins to form beadlike units called nucleosomes (packing the DNA also has implications for gene expression, but we will ignore that here).
Each nucleosome constains a 147 bp (base pair) stretch of DNA, which is sharply bent and tightly wrapped in a 1 and 3/4 turn (a left-handed superhelical turn to be exact) around the histone protein octamer. There are many of these nucleosome beads on each strand of DNA. Human chromosome 19, for example, has 58.6 million base pairs, so that makes for a lot of 147 base pair beads, even with streches of unwrapped linker DNA between the beads--about 75 – 90% of the base pairs end up wrapped in nucleosomes.
The bending of the DNA around the histone is made easier or more difficult depending on the geometrical and mechanical properties of the specific two base pairs or dinucleotides at the bend. This is not a trivial mechanical property: Some sequences may have a more than 1000 fold capacity to bend around the histone octamer compared with other sequences; we will say these sequences have an affinity for nucleosome positioning since they make it easy for the DNA to wrap. Conversely, some sequences are very "stiff" and are much more difficult to bend, e.g. poly dA:dT sequences. On average, high affinity sequences have more AA, TT and TA steps at positions where the minor groove faces inward towards the histone octamer, i.e., when more bendable di-nucleotides like AT and TA occur on the face of the helical repeat where it can directly interact with the histones (the helical repeat is about every 10 bp; see below).
What do we mean by "grooves?" Remember that DNA is a double stranded helix (as if you were twisting a flexible ladder) coiling two chains of sugar-phosphate "backbones" around the outside of the helix with the nitrogenous base pairs that connect the strands (with hydrogen bonds between base pairs) pointing toward the center of the helix (if you were twisting a flexible ladder into a helix the rungs would be the connected base pairs beween the two backbones). If you held up a screw you would see the threads as "grooves" in this similar helical structure. The backbones of the two strands are closer together on one side ("minor groove") of the double helix than the other ("major groove"). In undeformed β-DNA, the complementary base pairs of the "rungs" rise about 0.34 nm and twist ~36 degrees around the center axis of the "ladder" from each base pair rung to the next. A "helical repeat" will therefore occur every 10 bp's (10 x 36 = 360 degrees) as the helix completes a full turn around its axis. Don't confuse this helix with the wrapping of the DNA around a histone core; the DNA is a double stranded helix and that is in turn wound around the histone in a nucleosome.
But do nucleosomes in actual living organisms ("in vivo") actually tend to position themselves on sequences of DNA that wrap more easily around the histone core of the nucleosome, i.e., do nucleosomes in vivo actually show an affinity for specific DNA sequences?  If they do, then that could be considered to be a "genomic code  for nucleosome positioning." There are other factors (e.g., remodelling complexes which can move nucleosome positions) and related questions, e.g., do stiff sequences like poly dA:dT inhibit the formation of nucleosomes (and are nucleosome inhibitory sequences more common in DNA sequences like transcription start sites that should be exposed to facilitate interaction with trans proteins), but we will just consider simply the basic question.
By analogy, suppose I had a printer that could only print strips of paper a sentence high (vertical height of the strip sufficient to contain a 10 pitch character, say 0.1 inch high) but of arbitrary length. Imagine the printer is fed with a spool of this strip paper, like an old time printing calculator (or ATM receipt printer). If I printed this answer text page, out would come English sentences (at least I intend this to be recognizable English) on a long, thin strip. This sounds rather like a phylactery (tefillin) printer, now that I think of it, but that is a topic for comparative religion. If there are 66 lines of 7 inch long sentences on my page, then that is 38 feet of 0.1 inch paper strip to carry around for every page of text. I might find it more convenient to wind up portions of that long strip on little wooden dowels (like empty sewing thread spools for example) and then unwind them only when I wanted to read my article again (which I can never do enough). If DNA is kind of like this analogy (it is far more complex actually), then the spools are "histones" and when wrapped with paper strip become "nucleosomes." Does it makes sense that the letters I chose to construct the words in the sentences of my article were chosen to some extent based on some hypothetical capacity for some sequences of alphabetic characters to bend and coil around a spool (say some sequences had less cumulative stiff ink drying on the paper strip)? That gives you one angle on the controversy involving the idea of nucleosome positioning by genomic code. However, consider that, as in the case with degenerate DNA codons, I can choose different sequences of characters, i.e., words, to mean the same thing, so possibly I could still choose my words for meaning, but select synonyms that hypothetically bend easier, making it easier on average to coil my sentence strip up on spools.
A recent study, Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach, demonstrated that the local minima (the easy bending sequences) of a real gene could be repositioned (in computer simulation), that is, the nucleosome moved to another place in a real DNA gene sequence, by substituting equivalent base pairs (remember that a single amino acid can typically be defined by several different codons) to preserve the same protein encoding (a protein being a specific sequence of amino acids). This suggests that nucleosomes can at least theoretically be positioned anywhere on top of a gene, multiplexing the genetic information with the mechanical information as it were.
But do real genomes show any evidence of multiplexing genetic and mechanical information as described above? Experimentally mapped nucleosomes on top of genes do show strong signals in the probability for occurrence of mechanically favorable dinucleotides, but that does not prove the case (since shifting nucleosomes on random sequences may also demonstrate similar signals). The researchers in the study just cited then reasoned that if multiplexing is actually occuring, that is, if actual genomes have to balance the energy benefit of placing nucleosomes on DNA sequences where it is easier to bend the DNA into a coil around the histone, then it must be easier (and a more frequent occurrence therefore) to do that in non-coding sequences of DNA where only the "mechanical preference of the amino acids" need be considered (and not the necessity to maintain a specific sequence of amino acids to encode a particular protein).
Accordingly, they looked at the probability distribution for the amino acid threonine codons along nucleosomes on top of coding and non-coding regions of the S. cerevisiae and S. pombe genomes (high resolution nucleosome maps exist for both organisms). Both spectra showed a peak at the 10 bp (remember our earlier discussion of helical repeat), indicating that the codons for threonine display an overall rotational preference with respect to DNA bending within nucleosomes, but the non-coding peak was significantly higher for both organisms. When the 10 bp periodicity was plotted for all 20 amino acids for coding vs non-coding regions in both organisms the majority of points exhibited higher amplitude outside of genes, i.e., in non-coding regions where only the position preferences were a factor.
These findings (that the local minima, the easy bending sequences, of a real gene could be repositioned using degeneracy; that strong signals in the probability for occurrence of mechanically favorable dinucleotides are found in real genomes; and that the amplitude of 10 bp periodicity is higher in non-coding regions of actual genomes) at least suggest the possibility that nucleosome positions are the product of a mechanical evolution of DNA molecules, i.e., that there is a genomic code for nucleosome positioning in eukaryotes.

Welcome to BiologySE! Very comprehensive answer... If you are so inclined, you could add some links to terminology or other helpful resources to support individuals trying to follow your answer that aren't quite familiar with all the terms. It would only make your answer even better. Thanks for your effort on this answer.

Thanks, @VanceLAlbaugh. I had just worked through that paper and thought I would share what I learned. I really relied only on that paper, the link given by Bitwise in his answer earlier and an excellent Biology textbook at link for terminology and relevant concepts/context.

This is an outstanding answer

@Luigi Thanks for the tip of the hat (and Vance also). I hope this answer makes this topic more accessible to many. The OP question was in fact my own question, so I worked hard to understand.

There are definitely genomic DNA sequences that nucleosomes preferentially package in vitro. They are A/T rich and have a periodic structure that facilitates bending.  However such sequences would typically not be found on exons in vivo (because their protein-coding potential is reduced). Based on the accumulating literature, active promoters (and regions that will soon be activated) are usually Nucleosome-free, but I have yet to see evidence that this correlates with sequences that do not favour nucleosomes binding. These open areas are sensitive to DNase I, and the first nucleosomes downstream are phased.
For Epigenetic codes, people focus on the many post-translational modifications on the Histone tails.


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

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

Do you know about epigenetic?

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


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How to gauge the clinical significance of specific cell type presence?
How does one decide whether the presence of certain cell types is clinically important or negligible? Would the presence of certain cells in conjunction with other symptoms be enough, or should it be judged on relative proportions?
I have arrived at a diagnosis for a case study (and I know it is correct) and am just reviewing what I have included and am beginning to question myself. I fear that I am making unnecessary tenuous connections to further support my conclusions.
An example, to put this into context:

A peripheral blood film has all the hallmarks of acute myeloid
leukaemia (AML), however, the film alone is not enough to confirm.
In addition, have spotted definitely one, maybe two, dacrocytes (teardrop cell) on the film, these are not typically associated with AML as far as I am aware.
Dacryocytes are not diagnostically indicative of any specific
condition.
Dacrocytes are however present in several conditions that can
transform to AML.

So, in this scenario, I feel it would be worth mentioning considering the clinical setting but the numbers just seem so insignificant that I am concerned it would appear as grasping, or a bit through the grapevine.
Any guidance in general is appreciated, I'm not looking for an answer to the provided example per se.

one of probable answers is: through science and careful use of p-value


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What factors, other than its homochirality, make our "brand" of biology unique?
If humans were to discover organisms on another planet, it is supposed that (unless both we and they were seeded by the same source) we would have nothing to fear from alien pathogens, as they would likely be totally incompatible with our "brand" of life here on Earth. This is due to a set of fundamental particulars not inherent in all possible biologies (as apposed to physics, where characteristics are more omni-present). I know, for example, that the left-handed chirality of amino acids marks one such trait. There appears to be no reason why life could not arise with the opposite orientation. My question is, what other particulars make up this set?

Welcome to Biology S.E.! If you need/ want additional assistance, please visit The Help Center and take The Tour. I think you have a fascinating question here by the way!

I think the opposite list---what features of life might be reasonably expected to be the same elsewhere---would be much shorter. Nearly every feature of life on earth as I can think of it is arbitrary in the particular molecules.

DNA. Why only 4 bases? Why the bases that we have (ACTG)? Researchers are able to create organisms with expanded DNA alphabets even here on earth (1). Even if you believe that some form of molecular mechanism of heredity is a requirement for life, there is no reason it need be DNA. And while there has been plenty of controversy about arsenic-based life here on Earth, I don't see why there couldn't be arsenic-based life elsewhere.
Ribosomes. Why a combination of RNA and protein? There is a lot in the overall architecture of ribosomes that is locked in due to historical/evolutionary contingency, not any necessary feature of life.
The Central Dogma. Biology as we know it has certainly made great use of the ability to make temporary copies of messages, but I don't see why life orbiting Alpha Centauri would have to have arrived at a similar solution.
Phospholipid membranes. You could make the argument that some degree of compartmentalization is necessary for life to occur (to reduce complexity and allow evolution via drift and small-number effects to generate change), but I don't think they need to be phospholipids. I can also imagine all life on another planet contained within viral-like particles with purely protein (or some other alien polymer) coats.
Genes. Depending on the level one is arguing I can see this going either way. If a gene is just a modular set of instructions for a limited number of components, then perhaps this will show up everywhere---life on our planet is surprisingly modular, and it is hard to imagine life on another planet being able to get by without some modularity (though of course it is possible in principle). But certainly nothing is inevitable about the details of gene organization into promoters, coding regions (why a 3-base code?), introns and exons (I'm still surprised these exist on our own planet), operons, etc.

I think you get the idea. In fact, it's really hard to envision any feature of life on earth that doesn't smack of contingency in some way or other. Astrobiologists have held on to water as an essential ingredient for life as we know it, but still, that's "as we know it."
I am really tempted to make some sweeping speculative statement about what features I might expect to be "inherent in all possible biologies" (a fascinating idea to think about), but that is way out of my depth. Right now I find it hard to come up with good candidates.
(1): Malyshev D et al. (2014). A semi-synthetic organism with an expanded genetic alphabet. Nature 509: 385-8.


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Where is the aneurysm in this picture?
I'm a curious person, I've never had any medical training, but I wish to know some more about aneurysms. Aneurysms are basically weakened spots in the elastic artery wall. This can eventually result in a blood-filled balloon bulging from the artery wall due to the high blood pressure in these vessels. Aneurysms can rupture and this can lead to brain damage when it occurs in the brain. Aneurysms can be detected by injecting contrast material into the bloodstream and making an X-ray (called an angiogram). Now I was reading a wikipedia article about aneurysms where I saw the following picture of an angiogram where reportedly an aneurysm should be visble:

Now, as I said, I know nothing about biology so I would really appreciate it if someone could download the picture and reupload it with the aneurysm circled.
Is it the really dark spot or the big soft spot to the right? Thanks!

big blob just in the middle of picture

@aandreev Thanks so the black spot is normal?

I edited the question by adding some background info. this way other folks can more easily add answers if they wish.

Your image comes from the wiki page Aneurysm. The figure legend on the wiki page identifies it as:

Angiography of an aneurysm in a cerebral artery

I am not an MD so I chose to first dig up a similar appearing cerebral angiography with the aneurysm identified (dark protruding spot indicated by the arrow):
Source: WestJEM, UC Irvine
Taking into account the normal vasculature as seen on this graph from UC Irvine, and given the similarity between the identified aneurysm in this angiopgraph and your wiki angiograph, I tentatively have identified the red-encircled structure in your original image as an aneurysm:

Thanks! It looks like the one un the center of the wiki picture, as @aandrev said

Yes it does absolutely, but I found 'center' rather ambiguous

Exactly, that's why I asked for some circling or something haha, well, I guess my curiosity is satisfied, thanks!

I don't have enough reputation to comment, apparently, but I can answer that AliceD is correct. I'm a neuroradiologist, so I look at these images for a living.


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Serious question about a piece of meat

Does anyone know some scientific rigorous way to look at a slice of meat. I am not asking what kind of meat it is or which part of the animal it came from. I wonder what is the different lining on the meat, what is that huge white spot in the middle and what do the cells of that red part look like and what they are called.
If someone can provide a reference on that it would be great.

The white circle in the center is a bone, probably the femur. The muscles are covered with an external later of fascia, the epimysium (here's a question with some information). These layers separate muscles from each other, and often fat will also deposit in the spaces between muscles, which is what the white lines between muscle bellies are. There is also some cutaneous fat.
This is probably a section through the thigh, possibly a pig (though it looks a little too red). Regardless, the muscle will have the same basic layout as the image below of a pig thigh from pork.org, even if your image is from some other mammal.

You have to rotate your image clockwise about 45 degrees to get them to match up. The back of the thigh is at the top of the image.


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How to determine genotype?

In humans, the ability or inability to roll the tongue is a single
  gene trait.  The allele for tongue rolling (R) is dominant to the
  allele for not being able to roll the tongue (r).  Whether or not an
  individual can taste PTC is also an single gene trait.  The allele for
  being a taster (T) is dominants to the allele for not being able to
  taste PTC (t).

Claudia cannot roll her tongue but can taste PTC. Her mom also can taste PTC but her dad is not a taster. Claudia's grandparents were all unable to roll tongues.
1)  Based on the Info, what is Claudia's GENOTYPE?
I know she is "rr" because she cannot roll her tongue and it is recessive. However; I do not know the complete genotype for the PTC taster.  I know it for sure is a "T," but is it "TT" or "Tt?" How do we know? Do we have enough info to figure it out?

Claudia's dad is not a taster, so he is tt. He passes one allele on to his daughter. Since he is homozygous, he can only pass t. Claudia is a taster, so she must have the dominant allele from her mother, who is also a taster. Thus, Claudia is Tt.

Thank you canadianer. That makes perfect sense. I have one additional question.  What would the phenotypes be of Claudia's parents regarding tongue rolling? Because all the grandparents cannot does that mean both claudia's mom and dad cannot roll their tongues?

@Kyla Yes, that's a logical conclusion. All grandparents are homozygous recessive which means they can only pass on the recessive allele to their children. Thus, Claudia's parents are also homozygous recessive.


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Why are skin tactile receptors considered to be phasic receptors?
A phasic receptor by definition is one that quickly adapts to change. In terms of neuron firing, this means that it does not trigger another firing because the receptors are used to the stimulus.
But when I place my fingers on my arm, I continuously feel pressure. Does this mean that skin receptors are only phasic in the sense that it will fire as soon as it is touched and does not prolong this touching sensation?

Short answer
Slowly adapting mechanoreceptors in the skin mediate the perception of static pressure stimuli, while rapidly adapting skin receptors mediate swiftly changing (e.g., vibratory) stimuli.
Background
There are various skin receptors. Hairy skin, such as that encountered on the arm, contains at least four specialized mechanoreceptors, namely Pacinian corpuscles, hair follicle receptors, Ruffini endings and tactile discs. They can be roughly distinguished by their adaptation rates, namely fast adapting (Pacinian corpuscles and hair follicle receptors) and slowly adapting (Ruffini endings and tactile discs). Rapidly adapting receptors generate robust responses to vibratory stimuli, but respond weakly to static pressures. The opposite is true for slowly adapting receptors (Kaczmarek et al., 1991).
Hence, the static pressure is faithfully registered by static pressure receptors, while the phasic receptors are specialized in vibratory perceptions.
Static receptors fire a continuous train upon a continuous pressure stimulus, phasic receptors do so only at the start and the end of a static pressure stimulus. Hence, when there is a fast vibrating stimulus (say 200 Hz), then the phasic receptors will also fire action potentials each time at onset and offset of a pressure phase, thereby faithfully representing the stimulus. Here follows a picture of various skin receptors and their responses to a static pressure stimulus. Note that only the slowly adapting receptros show a rocust response:

Source: Michael Mann
Reference
Kaczmareck et al., IEEE Trans Biomed Eng 1991;38:1-16


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Blood Type/Punnett Square
Male: Blood type O   (Genotype written as: i^o i^o since O allele is recessive to the A and B alleles).
Female: Blood type AB
Draw a punnett square to show all of the possible offspring.
I got Ai^o,  Ai^o,  Bi^o,  Bi^o)
What are the possible phenotypes for the children?
I got...
Phenotypes: Blood type A
            Blood type B

What exactly is the question here? Do you want someone to clarify the answers you got?

yes please @iro

as far as simple punnet square is concerned your answer is correct.

A noble answer +1


text:
Risk of autosomal dominant disorder
What can you conclude about the risk (with each pregnancy) that a couple could have a child affected with an autosomal dominant disorder if...
One parent is affected (heterozygous) and the other parent is unaffected.
I did a punnet square and concluded it was 50 percent because half were Aa and half were aa.
But a classmate told me to line up Aa and aa and conclude that there is only a 25 percent chance that a child is affected because there is only one capital or dominant A and three are "a".  Which do I do?

Your classmate is forgetting that the child will have to inherit one allele (A or a) from each parent. Suppose the dad is affected---so his genotype is Aa. He has a 50% chance of passing the A on to his kid. That means the kid has a 50% chance of being affected.
If your classmate was right, then it would be possible for both the kid's alleles to come from just one parent. You have to pick one allele from each parent.

Agree with the answer by @A.Kennard. Here's a punnet square to clarify your answer further.


text:
Is there any way a human could whistle and be unable to speak?
Is there any situation anatomically, where a human could understand the speech of others perfectly, without any capabilities of speech themselves, but would retain the ability to whistle with a tune?
I was led to believe that the larynx is the most important thing for creating the sounds in speech, however I don't know if a damaged larynx would necessarily not allow someone to speak.
I would suggest someone who has no tongue cannot speak coherently, however I would imagine that the tongue is instrumental (pardon the pun) in creating a range of sounds whilst whistling.
Is there perhaps a part of the brain that could be affected in order to stop someone speaking? Or would this also mean the person could not understand speech either?

Thanks for splitting your questions - it is appreciated.

You can make a whistling sound by pushing air through your teeth.

Short answer(s)
Someone with a damaged larynx may still speak with the use of a speech aid (electronic larynx).
The ability to understand speech does not necessarily mean one can speak normally. There are neurological disorders where folks can understand speech, but have difficulty producing it.
Background
A full removal of the larynx (laryngectomy) prevents the patient to produce speech because the vocal chords are removed. However, with the use of a voice prosthesis this can be solved (Cancer Research UK).
There are neurological disorders where one can still understand speech, but has impaired ability to generate it, called apraxia. Apraxia can be acquired or congenital (developmental) (NIH). The developmental type is not well understood a the neural level (Dyspraxia Foundation UK). The acquired type is known to occur through damage to specific brain areas, for example due to trauma or stroke. One of these areas associated with acquired apraxia is Broca's area (Graff-Radford et al., 2014), which is a brain area intimately associated with the production of speech .

Broca's area. Source: UC Irvine
However, although damage to this area can result in pure apraxia (i.e., impaired speech but normal speech understanding), it can also result in Broca's aphasia, which means that language understanding is also impaired (American Heart Association). Moreover, regarding your specific question, apraxia is characterized by impaired speech, but not a total lack of speech production.
Reference
Graff-Radford et al. Brain & Language 2014;129:43–6

You can whisper without a larynx. "Patients who have undergone partial or full laryngectomy are typically unable to speak anything more than hoarse whispers, without the aid of prostheses or specialized speaking techniques." (source)
So the remainder of the vocal tract is capable of enough modulation to present typical human speech in many languages.
I expect, however, that the tongue, throat, jaw, and facial muscles figure very heavily into this modulation.
If these muscles become paralyzed or otherwise unusable, it's reasonable to assume that they may still be able to whistle with the use of the lungs and hands or fingers.
Hands free whistling, however, would require at least teeth and lips, or teeth and tongue, or lips and tongue - one surface to control the flow of air over the other surface that produces the whistle.  With control over just these few things, one could likely communicate to a reasonable degree in many languages.

Speech is generated by generating a frequency spectrum with the vocal folds, and then filtering it with the upper vocal tract.  Whistling is done by blowing air over shaped tongue and lips.
So, give someone a laryngectomy.  They still retain the upper vocal tract (and so can still whistle), but they cannot generate the source vibrations to speak.  Do it as an adult and they probably understand the speech of others.

It seems that speech can be recovered after total glossectomy, although it's not a short or an easy process.
Here's one case:

a case study, reporting the evaluation and evolution findings of the speech-language pathology rehabilitation of the swallowing and speech functions of a 58-year-old man submitted to total glossectomy in June 2009. After evaluation, the subject was diagnosed with severe mechanical oropharyngeal dysphagia and alteration in speech articulation. Speech rehabilitation used direct and indirect therapies. Indirect therapy focused on oral motor control, sensitivity, mobility, motricity, tonus and posture of the structures adjacent to the resected tongue. Direct therapy used the head back posture maneuver to help the ejection of food into the pharynx. The patient started exclusive oral feeding, except for solid foods, after ten months in treatment. Over-articulation, speed and rhythm exercises were used to improve speech intelligibility. Thus, the results of speech-language pathology intervention were considered positive, and the patient was discharged after a year in treatment.

Speech therapy in total glossectomy - case study, Vieira 2011


text:
Genes-of-interest analysis between organisms
I am interested in identifying the differential expression between several genes-of-interest of different organisms.
I am trying to assess the benefits of RNA sequencing over microarrays. Both techniques are a means to an end. With both of these two methods one can "count" the differences between two conditions, e.g. cell types, time points etc. They do use different technology to achieve it, but they both give a certain number 't' in the end, which can be looked at as the strength of the expression of a specific gene under a certain cellular condition. One can than compare the two (or more) conditions to get a picture of what is different in the cell due to the changes.
As I am new to this field, can someone tell me what the advantages are of RNA sequencing over micro arrays? Alternatively, information on comparisons between microarrays and RNA sequencing methods are welcome.

Welcome to Biology SE! What is GOI (G of interest)? Don't assume everyone's a molecular biologist and avoid technical acronyms and technical jargon. I've slightly type-edited your question. Please remove acronyms (RNA is fine)

No worries :)  - Aha genes of interest, that makes sense. Obviously, I am not able to answer your question (otherwise I would have known) but I'm just trying to polish up your question :)  Lastly, a bit more background may help you to get your question answered. I mean, sequencing and micro arrays are quite a different thing? The one is sequencing, the other one is expression profiling is it not?

Thanks for the excellent elaboration! Adding this to the question may be a good thing (At Biology.SE many questions are closed due to a lack of underlying research effort, that's why I am bugging you :-). +1 for your question. Good luck!

@AliceD RNA-seq is a gene expression profiling technique akin to microarrays. The sequencing step is just a technical detail.

Microarrays are pretty much dead. Go for a RNA-seq.

In RNA sequencing, total RNA is extracted, then mRNAs are purified out from the sample using polyT columns (since mRNAs have a polyA tail, this will attach to a polyT DNA chunk that is attached to some solid surface). This step is necessary because ribosomal RNAs are much more abundant than mRNAs, and for sequencing you only want to use mRNAs. Then the purified mRNA is transcribed to DNA using reverse-transcriptase and finally the cDNA is sequenced.
As for microarray a set of single stranded oligonucleotids (short DNA sequences) (aka. probes) are attached to a solid (usually glass) surface as small dots. This the so called DNA/RNA-chip. Then the chip is washed with the fluorescently labelled singlestranded sample, and the complementary strands attach to each other, the rest is washed away - this is a so called hybridization technique. The signal is then detected by reading the fluorescence signals at each spot.
The microarray technique is quite old and is less sensible and the number of probes are limited / array, while with RNA sequencing you can sequence the total mRNA population of each organism and examine anything you want. Also since most sequencing techniques include a PCR step less starting material is sufficient, and has higher sensitivity and specificity.
These wiki pages on RNA-seq and microarray technique provide detailed info on both.

To complete this answer, here a link to a study that compares microarray and RNA-seq. RNA-seq is definitely considered better and microarrays are less and less used.


text:
Is it known how the first viruses formed?
The oldest known virus is known to have infected prehistoric insects 300 million years ago. A virus is basically a parasitic strand if DNA or RNA encapsulated in a protein coat. It enters cells by "wearing" a protein coat made out of proteins needed by a certain cell (e.g. Lung cells and flu virus).
Now, my question:

Do we know how viruses naturally formed? To simplify the question, if we went back to the first virus, how would it form?

Note that I am looking for a scientific answer, and not wild-ass speculation. While I can accept some degree of speculation the accepted answer will NOT be based entirely on speculation if it is avoidable.

And most likely the first viruses would be much older than the 300 million year old you mention, and probably infected bacteria or whatever was floating around back then. I suppose even an RNA world could have virus like parasites that manage to hijack some replication machinery, but now I'm getting into the speculation you didn't want.

After further research I came upon this question which seems closely related.....do you think mine is a duplicate?

I'm not sure any of the answers will be proven. You're talking about an age we simply do not know much about. 300 million years ago is a very long time to be sure about such things.

One of the main points of contention in the study of virus evolution is whether or not they appear before the last universal cellular ancestor (LUCA) or afterwards (commonly accepted: genes that "escaped" from host organisms aka the escape hypothesis or vagrancy hypothesis).  Basically though, the LUCA is the most recent ancestor that all organisms living on Earth are derived from.
Increasing evidence support that ancestry of viruses may predate the LUCA, for example an idea is that there "was an 'ancient virus world' of primordial replicators that existed before any cellular organisms and that both RNA (first) and DNA (later) viruses originated at this time, donating some features to the first cellular organisms.  However, "a competing theory is that RNA cells existed before the LUCA and that RNA viruses were parasites on these RNA cells that later evolved DNA as a way of escaping host cell responses."
So basically, some theories support the pre-LUCA ancient virus origin and some support post-LUCA.  Because it's impossible to replicate conditions from billions of years ago, several approaches using evolutionary genetics and probability models are recommended by the author of the paper, referenced below.  He also discusses the specific supporting criteria for the theories that you can read in greater detail.
Holmes, E. C. (2011). "What does virus evolution tell us about virus origins?" J Virol 85(11): 5247-5251.

Also good to keep in mind that viruses are not a monophyletic group but have multiple origins. Some viral clades like Caudovirales probably predate the divergence of the cellular domains whereas e.g mimiviridae have much later (but still quite ancient origins). Also, neither of these groups is in any way related to e.g. ssDNA viruses

Great question. There are several hypotheses, but in reality no one really "knows" because this is incredibly difficult to prove. We may never know for certain.
Anyway, on to the three main hypotheses, I got this from http://en.wikipedia.org/wiki/Viral_evolution, I think you'll find it to be helpful.
"There are three classical hypotheses on the origins of viruses: Viruses may have once been small cells that parasitized larger cells (the degeneracy hypothesis or reduction hypothesis); some viruses may have evolved from bits of DNA or RNA that "escaped" from the genes of a larger organism (the vagrancy hypothesis or escape hypothesis); or viruses could have evolved from complex molecules of protein and nucleic acid at the same time as cells first appeared on earth (the virus-first hypothesis)."
However, as you may have guessed, there are plenty of questions that these theories do not answer. The next paragraph:
"None of these hypotheses was fully accepted: the regressive hypothesis did not explain why even the smallest of cellular parasites do not resemble viruses in any way. The escape hypothesis did not explain the complex capsids and other structures on virus particles. The virus-first hypothesis was quickly dismissed because it contravened the definition of viruses, in that they require host cells. Virologists are, however, beginning to reconsider and re-evaluate all three hypotheses."
There is a little more information on the Wikipedia page, I would recommend that you read that and do a little research on the different theories if you would like to know more.
I hope this helps,
CDB


text:
How to get only perfect matches with blastn?
I have installed Blast locally and I've configured the nucleotide database to use. I want to search some sequences (from a .fastafile) in this genome. So I used blastn:
blastn -db NewDb -query input.fasta -out blast.txt

Then I added some options to require a 100% identity and no gaps:
blastn -db NewDb -query input.fasta -perc_identity 100 -ungapped -out blast.txt

But I still have some results where only a subpart of the string is matching the genome:
BLASTN 2.2.29+

[…]

Database: […].fasta
           20 sequences; N total letters

Query= Mutant M :

Length=226
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  chrom19                                                               435   3e-122
  chrom2                                                                429   1e-120

> chrom19
Length=W

 Score =   435 bits (226),  Expect = 3e-122
 Identities = 226/226 (100%), Gaps = 0/226 (0%)
 Strand=Plus/Plus

[…]

> chrom2
Length=Y

 Score =   429 bits (223),  Expect = 1e-120
 Identities = 223/223 (100%), Gaps = 0/223 (0%)
 Strand=Plus/Plus

[…]

Both results have an identity score of 100%, but the second result only use 223 of the 226 bases from the input sequence.
What parameters can I use with blastn to get only perfect matches, with 100% identity and all the nucleotide bases from the input sequence used?

From my experience, I don't think this is possible. BLAST was designed to find many distant hits, so it wasn't made for this very strong requirement of identical sequences. But you can probably filter it afterwards, no?

If you want perfect identity, won't a simple string comparison program (in any language) do the job?

Yeah I concur with @MarchHo. Just do a string search. You can use grep

this might be of help: http://seqanswers.com/forums/showthread.php?t=27735

@MarchHo in fact it was my first test, I used BioPython in order to read the genome and sequences. Nothing matched but now I realize it was due to the fact that the sequences can be backwards or complementary of the genome.

Agree with @MarchHo. Would rather use Perl =~ operator for matching (used as $template =~ /query/) than grep. And yes Blastn was not designed for that and will match smaller sequences that are 100% similar.

This is a grep question rather than a blast issue, and nothing much to do with biology. I'm voting to close it as off topic.


text:
How pain can stimulate the vagus nerve
I'm trying to find out why a prompt, severe, short pain is causing a stimulation of the vagus nerve. What could the physiological explanation be?
Is that because the pain is triggering the sympathetic system (Huge stress because of the pain), and directly after that the parasympathetic system is trying to balance it, but it's overreacting? and then the sympathetic system is going back to normal when parasympathetic stays high ?
Is there a physiologic explanation ?
Thanks

Could you elaborate on where the pain is and what symptom accompanies the vagus nerve stimulation?

Hello, it's quite a theoretical questions. If I'm not wrong. Syncope can be triggered by strong and sudden pain, sudden Heat, see of blood. I think that in those 3 example, the reason of the syncope will be stimuli of the vagus nerve. But how those 3 things Are doing this stimuli, physiologically talking? A 4th example is by applying directly pression on the vagus nerve pulse will go down, vasodilation, and syncope. In this last case, it's quite clear how the vagus nerve has been stimulated, but not the previous ones. Hope it's more clear now. And thanks

Short answer
Given your comments you are referring to the cause of fainting after being triggered by certain stressors. The reason is a sudden drop in blood pressure due to parasympathetic nervous system activation (vagus nerve activity). This leads to reduced blood flow to your brain, which results in a brief loss of consciousness (Mayo Clinic).
Background
There are various types of fainting (syncope) with various causes. The type you are referring to is neurally mediated syncope (Arthur & kaye, 2000). It is evoked by emotional activation due to stressors (pain, fear etc.) Stress responses are accompanied by the release of stress hormonses, most notably Adrenaline (epinephrine). Epinephrine release results in sympathetic nervous system arousal, resulting in increased blood pressure, increased pulse and sweating. It also increases amounts of blood being funneled to peripheral organs. These mechanisms aids in the fight,fright and flight response, as more blood in the periphery allows more glucose to be transported to the muscles (Agarwal, 2007). The funneling of blood in the periphery (venous pooling), however, can reach a point in which venous return of blood to the heart falls too sharply. This in turn can lead to a substantial increase in the muscle activity in the ventricles, as they are likely struggling to pump the small available amounts of venous blood into the heart chambers. The increased muscular activity in the ventricles is believed to activate mechanoreceptors that would normally fire only during stretch.
Stretch of heart muscle is normally associated with a high blood pressure. The warning message of a high blood pressure by the mechanoreceptors is sent to the medulla in the brainstem, which in turn leads to parasympathetic nervous arousal. As a part of the parasympathetic response, the vagus nerve is stimulated which reduces heart activity to reduce blood pressure.
However, when the mechanoreceptors are stimulated due to the overt contractility of the ventricles due to a low blood volume, they sent the same neural input to the medulla which normally signals hypertension, thus causing vagus nerve stimulation and hence a paradoxic parasympathetic arousal that results in low blood pressure (hypotension), low heart rate (bradycardia), and ultimately fainting (syncope) (Grubb, 2005).
References
Agarwal et al., Postgrad Med J 2007;83:478–80
Arthus & Kaye, Postgrad Med J 2000;76:750-75
Grubb, Circulation 2005;111:2997-3006

Why the downvote? Downvotes are great, but they should help to improve an answer. Isolated downvotes without comments  don't help.

I elaborated my answer to try to make it more clear.


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

I don't understand your question.

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

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

@FloriOn - It is your sole decision :)

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

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


text:
How to increase the shelf life of yogurt without refrigeration?
When we make yogurt at home and do not refrigerate it, it will become sour because of conversion of lactose into lactic acid by Lactobacillus bacteria, but this does not happen in case of Nestle's yogurt or any other brand until it remains air tight.
I wonder though bacteria is still present in it and continue to convert lactose into lactic acid then why does not packed yogurt becomes sour? How these companies increase the shelf life of yogurt..?

most likely they kill these bacteria after the product is made and / or use preservatives.

high-energy X-rays might help kill a lot of bacteria. But you need to control dose not to overheat sample

@poka.nandor In that case, what about those yoghurts advertised as being "live culture"? It seems incongruous to use preservatives (which are essentially poisonous to the bacteria)

well in those case I think they use bacterial spores that are not active bacteria but under the right conditions can revive them selves. For example: http://en.wikipedia.org/wiki/Bacillus_coagulans

you can get a lot of info from microbewiki. the basic answer is the presense of oxygen results in a diffrent metabolic pathway in the bacteria and thus a diffrent poduct. However the simpliest answer might be that most comercial yogurts add extra sugar after fermentation. https://microbewiki.kenyon.edu/index.php/Yogurt

lactobacilllus (culture) survive at certain temperature, therefore to stop further fermentation after normal fermentation, the fermented youhurt have to be subjected to higher temmperature to kill the bacteria

This article gives an excellent review on yogurt manufacturing, but to summarize:
-Raw milk goes through centrifugation to remove somatic cells and other solid impurities.
-Thermalization is conducted at "60–69 °C for 20–30 s, aiming at the killing of many vegetative microorganisms and the partial inactivation of some enzymes."
After this point, the milk may be inoculated with lactic acid bacteria or other microfloras.
-Then, standardization occurs which for milk refers to the standardization of fat and solid-non-fat content (SNF).  This in short affects the fermentation process ("an increase of SNF increases the duration of the fermentation process").
-The next step is homogenization, which prevents milk fat from rising to the top of the liquid.  This has an effect on the stability of the emulsion.
-I think this step is where "sterility" comes into play, "heat treatment of milk reduces the number of pathogenic microorganisms to safe limits for the consumer’s health. Various heat treatments can be applied, which are classified based on the duration and the temperature. The most common are known as thermalization, low and high pasteurization, sterilization and UHT (Ultra Heat Treatment)."  The review goes into more detail about each type and what they eliminate or don't eliminate (spores, vegetative bacteria, etc.).
-The fermentation process is the most important one for developing flavor and texture.  The two live bacterial strains of Streptococcus salivarius subsp. thermophilus (ST) and Lactobacillus delbrueckii subsp. bulgaricus (LB) are the two most basic strains used in yogurt.  LB is what metabolizes lactose into lactic acid and LB and ST acting in synergy is what causes a decrease in milk pH.  "When the pH of the yogurt approaches 5.0, activity of ST subsides and LB gradually dominates the overall fermentation process until the target value of pH is reached and the fermentation process ceases. Normally, the fermentation period is terminated by lowering the temperature to 4 °C. At this temperature, the culture is still alive, but its activity is drastically limited to allow controlled flavor during storage and distribution."  I think to answer your question, yogurt manufacturers probably have a very sensitive gauge for pH and can control temperature fluctuations finely to maintain yogurt pH and flavor (not too sour).  "After the pH of yogurt reaches the value of 4.7–4.3, the yogurt is cooled to around 5 °C. This inhibits the growth and metabolic reaction of the starter culture and prevents the rise in acidity. Cooling of yogurt can be in one or two phases. One-phase cooling involves the rapid decrease of the coagulum temperature to less than 10 °C, where the fermentation process is inhibited leading to yogurt with low viscosity. Two-phase cooling is initiated by rapidly decreasing the temperature to less than 20 °C and then gradually reaching the storage temperature of 5 °C leading to yogurt with an increased viscosity and limited syneresis. This is quite common in the yogurt manufacture process, especially when fruits are to be added."
You can read about the other innovative methods involved in yogurt making such as: Ultra High Pressure (UHP) which inactivates pathogens and microorganisms that cause milk to spoil, High Intensity Ultrasonication and Pulsed Electric Field (PEF) which all can reduce microbial content.
Edit: Forgot to mention that some DIY yogurt instructions mention that if you ferment longer and/or in warm temperatre the more sour it will be so to reduce how sour it is, either ferment it less and/or start fermentation at a lower temperature (source).
Sfakianakis P, Tzia C. Conventional and Innovative Processing of Milk for Yogurt Manufacture; Development of Texture and Flavor: A Review. Foods. 2014; 3(1):176-193.

Commercial yoghurt usually contains alive Lactobacillus, as exemplified by the fact that you can use them to "seed" your yoghurt at home. I actually don't think they add anything. In France at least it is just pasteurized milk and lactobacillus (ex from Auchan yogurt list of ingredients: Semi-skimmed milk, lactose and milk protein, lactic ferments). Some preparations that are not yoghurt stricto-sensu might have added sugar, starch, pectin or gelatin.
I think they just do yoghurt in an aseptic environment (ex) preventing bacteria other than Lactobacillus to chime in and further mess up the mix. That would go well with your own observation that opening the "brand" yoghurt make them "spoil" faster.

It would be better if you can provide a source to back up your claim.


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

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

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

What got me thinking was the Hyra's budding

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

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

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

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

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

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


text:
Contact Inhibition of Cell Division: Signaling Pathway
The following article refers to contact inhibition of cell division in epithelial cells, specifically MDCK cells: Collective and single cell behavior in epithelial contact inhibition.
In their review of the literature, there are a number of possible signalling pathways implicated in contact inhibition of cell division. These pathways are outlined in the following quotes:

It is widely accepted that contact inhibition requires establishment of E-cadherin-mediated cell-cell contacts and subsequent maturation of the adherens junctions (AJs) that link E-cadherin and F-actin in a synapse-like complex involving numerous other proteins
One possible pathway involves β-catenin, a mediator of Wnt signalling, that, in addition to its function as a transcriptional cofactor, is associated with the AJs at the cell surface
A contact inhibition role has been reported for NF2/Merlin, a tumor suppressor gene that encodes a membrane-cytoskeletal scaffolding protein, which most likely acts via the Hippo kinase pathway, controlling nuclear localization of the transcriptional activator YAP—itself a known regulator of cell proliferation.
Contact inhibition is known to involve the MAPK pathway, which, in turn, promotes cell cycle entry by regulating the expression of cyclinD1. Also implicated are Nectins—a family of cell adhesion molecules that are involved, together with integrins and other proteins, in the regulation of cell motility and proliferation. Yet, this accumulated knowledge falls far short of a comprehensive picture of contact inhibition.

In the article, the findings were as follows:

Our findings show that contact between cells is not sufficient for inhibition of mitosis in MDCK cells. Instead, inhibition of cell proliferation is a consequence of mechanical constraint that causes successive cell divisions to reduce cell area.

Where, in the discussion, they note the following:

Our measurements also suggest that inhibition of cell division is a distinct single cell state rather than a global state induced by cell-cell signalling across the layer, as illustrated in Fig. 4E. In fact, confluent MDCK cell cultures with an average cell density corresponding to the morphological transition are often sufficiently heterogeneous in local cell density that highly motile cells and completely arrested cells coexist in the same colony. Thus contact inhibition is a local phenomenon...

Published later, the article Spatial constraints control cell proliferation in tissues showed that reducing the amount of space in a tissue prevented entry into S-phase. Actually stretching the tissue quickly reactivated the cell cycle, and compression leads quickly to arrest. More so, they found that cells had no memory of past constraint, and were able to suggest a model of growth in relation to the spatial constraint.
I'm editing my question because the way I posted it initially, to me, was unanswerable. Being said, I suspect that at this point cell volume and extracellular contacts are synergistic. This is probably going to need two separate questions, but:
1) How does the mitotic entry machinery roughly respond to cell volume? I'm currently reading into Cdc25/Wee1 regulation in addition to some stuff about internal fluidics that are influenced by water, ion channels, etc. but I still don't fully understand.
2) What's a relatively straightforward downstream pathway (core elements), starting at the adherens junctions, that illustrates how cell-cell signalling gets the STOP signal to the mitotic entry machinery (based on what we know)? This might require some much more in-depth knowledge about the field, however, but articles with some good figures are appreciated, too.

As far as I know our knowledge is incomplete. We understand some pathways involved (notably MAPK) but don't really understand the interactions between pathways. As an example the AMPK and MAPK/ERK pathways share common downstream molecules and have some positive/negative feedback loops which are hard to model (I know I tried to model the ERK one) as we don't know all the involved players and the interactions between them. As an example in the MAPK/ERK pathway MEK can self-dimerize which was discovered late last year and actually this provokes a buffering effect on the response.

Agree that we don't really know. I think that you might gain some perspective by looking at related pathways, e.g. effect of mechanical forces on mitotic spindle orientation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169662/. I believe there is a lot of work in Drosophila on this subject, cursory googling suggests that preferential elongation along a particular tissue axis is mediated by mechanical forces: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086725, using the wing as a model.

How does the mitotic entry machinery roughly respond to cell volume?

This is a broad question but luckily there is one article that addresses this precise question in detail. However, it is very likely that more discoveries are made on this topic in future.
Neurohr et al. (2019) have extensively studied the effect of cell volume on mitotic re-entry and cell cycle progression. They used Saccharamyces cerevesiae with temperature sensitive alleles of CDC28 to arrest the cells in G1 phase. At this stage high glucose concentration (2%) led to increase in cell volume compared to that of starved (0.1% glucose) or protein synthesis inhibited (2% glucose + cycloheximide) cells. Using this model they find that cytoplasmic dilution causes impairment of transcriptional regulation during cell cycle progression. This is because the transcription factors do not scale with cell size.
Read the paper for more details.

What's a relatively straightforward downstream pathway (core
  elements), starting at the adherens junctions, that illustrates how
  cell-cell signalling gets the STOP signal to the mitotic entry
  machinery?

This is again a broad question if you expect all details. However, google scholar search on "contact inhibition pathway" suggests that the main downstream pathway is the Hippo signalling pathway.
Top hits on this topic:

Zeng, Qi, and Wanjin Hong. "The emerging role of the hippo pathway in cell contact inhibition, organ size control, and cancer development in mammals." Cancer cell 13.3 (2008): 188-192.
Kim, Nam-Gyun, et al. "E-cadherin mediates contact inhibition of proliferation through Hippo signaling-pathway components." PNAS 108.29 (2011): 11930-11935.
Gumbiner, Barry M., and Nam-Gyun Kim. "The Hippo-YAP signaling pathway and contact inhibition of growth." J Cell Sci 127.4 (2014): 709-717.

Huuuuh I'll admit this question was really broad at the time but that first article, well one I've become so busy it dropped off my radar, but I also didn't expect those conclusions either. I will need to research the latter half better, but thanks for a point in the right direction!

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


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Examples of Vestigial Genes
I consider the existence of a broken GULO gene in humans to be the clearest evidence for human evolution - just what else is it doing there otherwise?
Are there any other examples of vestigial genes in the Human genome? Or perhaps vestigial proteins?

I think you are simply looking for examples of pseudogenes, right?

Yes, I guess I am :)

@Corvus pseudogenes do not express. I would assume that a vestigial gene is something that is expressed but is dispensable.

@WYSIWYG pseudogenes are often expressed. As described here and here. They just don't produce a protein. I guess they can't be strictly called vestigial genes, they might still have some effects.

@cagliari2005 By expressed I meant formation of the original intended product which could be ncRNA or protein.

@WYSIWYG great. just wanted to make sure :).

BTW, some examples of these would still be appreciated :D The wiki page above only gives one other 'disabled' gene comparable to GULO. Thanks

So, do we feel like we know what the OP means by vestigial genes? Are examples easy to find? @Tom, was the other vestigial gene you found on wikipedia the caspase 12 gene?

@Remi.b Yes, that's the one. I find these really interesting. On a more personal note, I have a number of intelligent friends influenced by the ID movement, so I always like to have as much evidence as possible :)  According to some, the 'difficulties' posed by the GULO gene/chromosome 2 merging has already been explained away.

Genes that were once functional but no longer are are called pseudogenes (as Corvus pointed out in the comments).
Many genes that are similar today (homologs) are hypothesized to have come from duplication events in the past.  In most cases, these duplicates diverge.  The divergence can happen in several ways:
1) one retains the original function while the other obtains a novel function
2) a dosage response occurs where both (keeping the original function) become necessary for that function
3) one retains its function while the other loses all functionality.
This third group are the pseudogenes.  This isn't the only way pseudogenes come to be, but it is probably the most well-characterized.
There are several resources for lists of these.  I'll just point you in that direction.  I assume you are interested in a particular group (i.e. genes important in development or patterning), so that you can dig more deeply into:

http://seqanswers.com/forums/showthread.php?t=32054
http://www.genomebiology.com/2012/13/9/r51


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Can silverfish climb and produce silk?
I am equally disgusted and fascinated by the "Silverfish" (Lepisma saccharina) that we regularly find in our UK home. I tried searching for information on the internet but they seem poorly understood.
We only ever find them on the work surface in the kitchen when we switch on a light at night. They are presumably feeding off food residues - but they never seem to be found in the most obvious place, among the crumbs under the toaster.
When caught by the lights, they run for cover but never, ever climb. You would think them unable to climb at all but then how have they reached the work surface?
The other day there appeared a new twist; 2 "husks" hanging from silk threads between 2 containers, maybe 8cm from the surface. If they were caught and eaten by a spider, why did it take them to a rudimentary web when it (presumably) caught them on the surface? There was no sign of a spider around. The only other possibility I can see is that they somehow suspended THEMSELVES from the silk and this was a moulting behaviour. Thus they now CAN climb - and very well - and also produce silk!
Can anyone explain the mystery?

Hi. Is your question: "What is the function of silk in Silverfish?" (I didn't know they could produce silk).

@Remi.b -  I think POs title question should be "Can silverfish climb and produce silk?"

Modified question title, feel free to rollback if it doesn't match what you are trying to ask. Also, a photo of the aforementioned "husks" would be helpful.

You read my mind @MarchHo

According to a paper by Walker et al. (2013) (found by googling "silverfish + silk", so not very hard to come by), silverfish can indeed produce silk. The paper also mentions that silverfish (Thysanura) and bristletails (Archaeognatha) use silk to transfer their sperm, and they also use it for "...tactile cue during courtship (Sturm, 1956)". This webpage (from NY State University) explains that male silverfish will deposit a spermatophore on a silk thread that is vertically suspended, and the spermatophore is later picked up by a female.

Abstract:
  Silks are semi-crystalline solids in which protein chains are associated by intermolecular hydrogen bonding within ordered crystallites, and by entanglement within unordered regions. By varying the type of protein secondary structure within crystallites and the overall degree of molecular order within fibers, arthropods produce fibers with a variety of physical properties suited to many purposes. We characterized silk produced as a tactile stimulus during mating by the grey silverfish (Ctenolepisma longicaudata) using Fourier transform infrared spectroscopy, polarized Raman spectroscopy, gel electrophoresis and amino acid analysis. Fibers were proteinaceous-the main component being a 220 kDa protein-and were rich in Gln/Glu, Leu, and Lys. The protein structure present was predominantly random coil, with a lesser amount of beta-structure. Silk fibers could readily be solubilized in aqueous solutions of a mild chaotrope, sodium dodecyl sulfate, indicating protein chains were not cross-linked by disulfide or other covalent bonds. We conclude that entanglement is the major mechanism by which these silk proteins cohere into a solid material. We propose silks used as short-term tactile cues are subject to less stringent requirements for molecular order relative to other silks, allowing the random coil structure to be favored as an adaptation promoting maximal entanglement and adhesion.

The linked paper contains several references that should be useful if you want to look deeper into how silverfish use silk.
From what I've seen, they don't use silk for climbing. Silverfish can usually climb rough surfaces, but not smooth surfaces, which is why they are often found trapped in sinks, bathtubs etc.

This species seems to be different to the one we have in the UK and is more an American variant according to Wikipedia. However, it seems strange that a species would develop silk glands simply for such an undefined function - even one related to reproduction.

@Lefty Since the paper seems to claim that the ability of produce silk covers the entire order of Thysanura (along with bristletails, spiders etc), it is unlikley to be specific to their particular study species. To use silk for courtship and sperm transfer is hardly "undefined", since reproduction is essential in the life history of a species.

No, these papers are more interested in the structure of the silk, not the lifestyle of the Silverfish. The only thing it does is to confirm that they do indeed produce silk for the purpose of reproduction - although to transfer sperm packets, not as a "tactile stimulus" in your extract. I'm interested in their reluctance to climb and whether the silk is used in the moulting process.

@Lefty in that case, please edit your question so the actual question being asked is clearer.

It seems pretty clear to me, just read the question text rather than the title.

@Lefty Yes, for tactile cues. Read the entire paper, if you are honestly interested in an answer:   "Approaching the end
of the courtship ritual, which consists of antenna-tapping and
repeated responsive movements between male and female (Sturm,
1956,1987), male L. saccharina cover an area of the substratewith Y-
shaped networks of fibers and deposit a spermatophore nearby.
Detection of the Y-shaped tactile cues by the female induces a
sequence of behaviors that culminates in her uptake of the sper-
matophore (Sturm, 1956)."

@fileunderwater I've never used pubmed and from what I can see, I can't just view this paper without signing-up in some way. If I'm wrong please correct me. Either way, my original question without all the chatter can be condensed into 4 parts: 1) What are they eating if breadcrumbs are not on the menu? 2) Can they climb? 3) Can they produce silk? 4) Do they suspend themselves from silk and moult? From what you've said so far, this paper appears to answer point 3) with "Yes".

@Lefty Sorry, forgot to mention that the paper is available for free here (view/download to the right). 1) dead insects, starch (wallpaper glue), paper, fabric etc. 2) Yes, but not on smooth surfaces, and not using silk from what I know. 3) Yes (see above), 4) I don't know about their molting behaviour, except they molt many times during their lifetime, and the paper linked above doesn't mention molting in relation to their silk.

Thanks @fileunderwater I'll have a read of it then. 1) The Wiki article mentions the same foodstuffs you've listed - none of which would appear to be present on my (tiled) work surface. Nonetheless they would appear to be able to thrive there somehow. 2) Bizarrely, most of the vertical surfaces are actually rough (wood) yet they never appear to climb them but 4) the objects they were hanging from were smooth porcelain containers.


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Is the Klein's bottle a good analogy to the relation between T-tubule and sarcolemma?
I am not quite seeing how the T-tubule and sarcolemma is connected. It says that the T-tubule is an "invagination" of the sarcolemma, which is sarcolemma folded from the inside to form a T-tubule
Can someone verify whether the following picture is a good presentation of this relationship?

Klien bottle has zero volume. It is not distantly related to the t-tubules or other such structures.

Can you provide a citation stating the relationship between the two structures?

So he's just trying to find an analogy for how the sarcolemma folds into the t-tubule, and if this is anything like how a klein bottle works.

If we're looking at diagrams for the t-tubule with respect to the sarcolemma, we see the two are actually fused:

The function therein is to allow depolarization to penetrate the interior of the cell quickly. The surface isn't transected anywhere, it simply folds inward. You can visualize this by sort of pushing a hole through some putty with a finger, and making a hole to the other side. Really no need to upvote me here, just easier to paste images in answers.


text:
What percentage of a cell's volume is occupied by protein?
I was looking at one of David Goodsell's illustrations of a cell:

And it seems to suggest a very crowded picture of the intracellular environment. Just how crowded are cytoplasms? What percentage of the volume is typically taken up by protein, water, and other major species?

According to this, that picture is probably pretty close.

What kind of cell? It would be best if you can specify a certain kind of cell, since protein content clearly varies between cells (eg a WT E. coli, vs one that is overexpressing a protein from a plasmid)

@MarchHo Pick whichever one you want.

I'm sure you're aware of this, but that picture is in no way an accurate representation of a real cell.

The tricky part is to define what is the volume of a biomolecule as it is a folded chain full of bumps and holes. Water is all around and in the folded structure and is actually important to keep the conformation of at least some of the proteins/RNA/DNA.
At the same time we know that 60% of your body in mass is water. Let's visualize that. Bio molecules have roughly the same weight per volume than water. Now add into the equation that a good third of the filled actually is water due to the structure holes, adsorption etc. You now have roughly:

% empty space = 60%-(40%/3)= 47%

To help think about it imagine a grid with roughly one cell out of two being filled. That looks pretty crowded to me. Then you of course have variations with blood and secretions on one side and bones on the other but you have the big picture.
For an example look at an electron microscopy picture of a striated muscle cell: http://histology.med.umich.edu/sites/default/files/muscleQ4.jpg. It looks pretty much like the half filled grid isn't it? Of course seeing individual molecules is hard but the white space correspond to mostly empty space with a couple of actine fibers. The dark corresponds to actine+myosine fibers: an extremely tight space. And we have roughly half of each :-)

According to the Molecular Biology of the Cell, (4th Ed), the cell is ~70% water, the remaining 30% of which is composed of macromolecules (proteins, nucleic acids, and carbohydrates). While this is just a single citation, there are lots of other sources in the literature that cite similar values.

I'm afraid this is a description of the mass percentage while the question was about the volume.


text:
How to make µg/ml concentrations of proteinase-K?
How does one prepare concentrations in the mass/volume (weight/volume) form, for substances like nucleic acids or in this case, proteinase? A detailed example would be helpful.
I need to prepare squishing buffer for a DNA extraction /PCR exercise to help me learn the materials better for a in class "internship".
The squishing buffer recipe I found from a laboratory class manual describes it as: 10 mM of Tris-Cl, pH 8.2, 1 mM of EDTA, 25 mM of NaCl , and 200 µg/ml of proteinse K (freshly diulted).
I understand molarity concentrations well enough. One only has to determine the total molar mass of a substance, in this case NaCl, and with that molar mass (g/mol) then use the given desired molarity (in this case 25 mM of NaCl, which equals 0.025 mol /one liters) to get the number of grams of the substance needed. In this case, since we need 0.025 moles / 1 Liter, we would need to multiply that by the molar mass to get: (g/mol) X (mol/l) = g/l of NaCl.
I understand percent solutions (to a degree) as well. If I  needed 1% agrose gel, I would take 1 gram of agarose solid powder and bring that to 100 ml total to obtain a 1%, either using water or buffer?
I am having trouble understanding the concepts of concentration, in reference to mg/ml.
From what I understand, µg/ml is a weight (mass)/volume type of concentration. Therefore, should it be the case that if I wanted to prepare
200 µg/ml of proteinase (freshly diluted), how would I go about it? Would I add 5 ml of deionized water to get a working volume of 1000 µg of proteinase per 5 ml of water, which would be equivalent to 1 mg of proteinase per 5 ml of water. From that 1mg of proteinase to 5ml of water, should I then draw 0.2 µl (or 200 ml) of solution to then have the 200 µg/ml? Or am I totally wrong? I tried googling for more information, but I became more and more confused.

What is a "squishing buffer"? The composition seems to indicate some kind of protease lysis buffer, but I have never heard of anything by that name.

@MarchHo              Yes it is a buffer used to break down the flies protiens via the protienase. Since I will be doing PCR on flies.

@canadianer      So lets say I  have some of that lyophilized powder. Could you give an example of doing so? I just cant seem to picture doing the process for some reason.

Using your agar example, your agarose is 10g/L = 10mg/mL.

What is NaCl₂ ??

It depends on what form your proteinase K is in.

You may have a stock solution of some concentration, in which case you just add a specific volume according to $C_1V_1=C_2V_2$.
Example: Let's say you want to prepare 5 mL ($V_2$) of 200 µg/mL ($C_2$) proteinase K from a stock of 1000 µg/mL ($C_1$). You're looking for the volume of stock solution to add ($V_1$).
$$V_1=\frac{5\ mL\ \cdot \ 200\ \mu g/mL}{1000\ \mu g/mL}=1\ mL$$
So you take 1 mL of the stock and bring it up to 5 mL.

Or you may have a lyophilized powder. In this case, you have two options:
1) You can make a stock solution from the powder and, again, use $C_1V_1=C_2V_2$. This has the advantage of not having to weigh the powder every time you need to use it. This may not be a viable option, however, as I'm not sure of the stability of proteinase K in solution.
2) You can just weigh out the amount that will give you the desired concentration (which depends on the volume of buffer you're making).
Example: Again, you want to prepare 5 mL of 200 µg/mL proteinase K. The total mass you need is:
$$200\ \mu g / mL\ \cdot \ 5\ mL=1000\ \mu g$$
So weigh out a milligram and bring it up to 5 mL.

There's nothing special about mass concentration; you can convert it to molarity given the molecular weight of proteinase K. According to Wikipedia, proteinase K is 28.9 kDa or 28900 g/mol. If you are making this conversion, however, make sure you find the actual molecular weight of the protein you're using. 200 µg/mL is equal to:
$$\frac{0.2\ g/L}{28900\ g/mol}=6.92\ \mu M$$


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Sequence compression method / format
As someone working with sequencing data and sequence files I was wondering whether is there a compression method / format for sequence / read files? Of course one can use general compressors like rar or zip to compress a fasta file, which is suitable for transferring data, but reading the sequence out of it is infeasible. Also I'm aware of BAM file format which is a block copressed gzip file of a SAM file, but as far as I know it is mainly used in alignments. But is there a compression for plain fastq(-like) files for storing millions of reads or a collection of sequences while being able to get sequence and quality info directly from the file?

Normally one gzips such things. Do you actually need random access and, if so, how many reads/sequences are we talking about? BTW, BAM isn't a bunch of block gzipped SAM files, it's its own binary format that's block gzipped.

Yes, I know I just didn't express myself well I'll edit my question, thx for pointing that out

Ohh I forgot to answer your question in my previous comment. I'm talking about millions of reads or tens of gigabytes of data.

Sequence files can be compressed after Burrows-Wheeler transformation; but you cannot read them directly. See here. Bowtie indices are burrows wheeler compressed; you can use bowtie-build to transform your fasta file.

Note that block compression can be applied to any type of file, including fastq or fasta, using the bgzip utility that comes with samtools. That said, I don't know to what point this makes the file more easy to deal with than just using plain gzip. Biopython has some degree of support for bgzip.

I can conceive of two scenarios when block compression of fastq files would be useful. Firstly, if for some reason one wanted to search for a specific read, then sorting the file by xy read position would make the search quick. Secondly, in theory a super super fast aligner could have multiple decompression threads. In the first case, I really doubt anyone would want to do that. In the second case, I hope the files are in memory or on a solid state drive (and I would LOVE to use an aligner fast enough to care about this scenario!).

BAM is the current standard for sequence alignments, and can be used to store unaligned reads/sequences, but when used for unaligned sequences also contains unused alignment data that would bloat the file.
An alternative way to compress a DNA sequence file is via 2-bit (or 4-bit encoding) which can compress the sequence content by 75% (in 2-bit encoding, each nucleotide can be represented by 2-bits in the file eg A: 00, G: 01, C: 10, T: 11). I do not know of a generalizable tool that will compress/decompress aside from rolling your own. Further, the data must be de-compressed prior to streaming it into any alignment/sequence software. For general purpose compression algorithms, bzip2 can outperform (at least in compression) other algorithms (eg zip, gzip)

Hi, thx for the answer. I was thinking about the 2 bit compression myself but as you pointed out it needs to be decompressed for currents softwares. My 'problem" with BAM file is the as you said it contains many extra data that is useful for alignment but not otherwise.

With a 2-bit encoding you cannot have Ns, right?

You can, the format isn't exactly 2 bits per base. Instead it's actually 4, with the additional 2 bits being a mask that can convey information like, "it's an N", or "it's soft-masked". What this can't do is store quality information (or IUPAC ambiguity codes, as sometimes appear in fasta files). In fact, the space savings of a 2-bit variant format over straight fastq are 0.5 bytes per base in the sequence plus 3 bytes per read. Standard compression has better compression than that (you can, of course, compress 2-bit data).

BFQ = binary fastq
Described here:
http://ngsutils.org/modules/fastqutils/
I have not used it myself, but I gather that the maq aligner package can use (or generate) these files.
Even though the bam format already incorporates the block compression (described by yourself and others), we routinely deal with gripped bam files and my sense is that there is some additional compression that takes place (I haven't calculated a percentage)

It should be noted that bfq can't store quality scores above 61 (it says it can go up to 62, but a T with a phred score of 62 is an N...). Anyway, a compressed bfq file is about 90% the size of a gzipped fastq file, so space savings are marginal (particularly given the added overhead of processing bfq). An uncompressed bfq file is about half the size of an uncompressed fastq file.


text:
Is this a legitimate teratoma for a human pluripotent stem cell assay?
I can't quite make out this teratoma:
                                    [Source: FIG 3B]
I can kind of guess at ectoderm, mesoderm and endoderm structures based on generalized textbook developmental biology references but it looks like the stain was messed up. Shouldn't a hematoxylin-eosin stain be blue and red? Is this a legitimate confirmation of germ cell development from human pluripotent stem cells?


text:
Using an analytical balance (0.0000 precision) to measure µg (micrograms)?
If i needed to prepare 200µg/ml of proteinase K, and the proteinase K  was in a solid powder form, would I  have to weight out 200 µg using an analytical balance, and if so, is it possible with a balance that only goes up to four decimal places? (i.e. 0.0000) I assumed 1 microgram is 1×10-6 gram and therefore 0.000001 gram.

How is this a biology question? If you are interested in the finer points of using a balance, you might enjoy reading this: A question of balance

As others have said, that mass is too small to measure with a standard analytical scale. There are two options you could use:

Make a larger volume of your 200 ug/mL solution.
Make a concentrated stock such as 20 mg/mL. This a 100X stock; you can make 1 mL of 200 ug/mL proteinase K with 10 uL of stock and 990 uL of buffer. Small volumes are easier to measure than small masses (with a micropipette).

I guess i still am having issues with the concepts of concentrations. It is just such a hard concept to wrap my head around, i wish i could have practice with it.  For your first option, making a larger volume, what would that entail? The recipe requires 200ug/ml , so i wouldnt know how to deal with anything else. For the second option, how would i go about making the 20mg/ml stock? Would I measure out 20miligrams of the powder = 0.020grams on the scale? And then mix that with 1 ml of water? But even with that more concentrated stock, i dont understand how i go from the 20mg/ml to the 200ug/ul

@RoSiv You should practice. I imagine your teacher could help you and there are many resources on the internet.

In this case make a large quantity and store it as stock - this is a general lab practice. Preparing 10 ml of your protK solurion would you need 2000ug (=2mg) of protK powder.