text:
Are memory updates local in mammals?
What I mean is, during long term potentiation (LTP) or long term depression (LTD) for a particular memory, do the strengthening and/or weakening of neuronal connections only occur in a small patch of neurons or regions spread out in the cortex?

LTD and LTP happen at individual synapses (not even whole of neurons). However LTP/LTD at one synapse can affect others in the vicinity.

OK I meant something like when a single episodic memory episode is stored, is the memory stored in diffuse locations or rather localized?

LTP and LTD are processes that operate on single synapses. We don't know how "memories" (there are several types of "memory") are encoded in the human nervous system. As a consequence, we don't yet understand the explicit link between some group of synaptically connected neurons, and a given memory.
So the short answer is "we don't know". Take a look at some of the other questions about memories in human brains: 1, 2


text:
What is the number of DNA strands per cell?
I wonder if each cell possess only one strand of DNA which according to my book is more than "7 feet" long(if uncoiled), then why does human has 46 chromosomes which are actually coiled chromatin (DNA wrapped around histone proteins)? Does DNA break into parts and form 46 chromosomes during cell division (I am just guessing I am not sure about it)?

I think you are misusing the term "strand". "filament" instead? Or perhaps, you have the "chromatin string" in mind? Can you clarify it in your question, please?

I am referring to DNA molecule (entire chain of polypnucleotide) or you can say how many chains of deoxy ribonucleic acid are found in each cell?

Referring to this picture https://en.wikipedia.org/wiki/DNA#/media/File:Lambda_repressor_1LMB.png the DNA molecule is composed of the red strand and the blue strand.  A chromosome is composed of one DNA molecule or two DNA strands.

So that means if one chromosome is composed of one DNA molecule and there are 46 chromosomes therefore 46 DNA molecules are present in each DNA. Right?

Yes, in each diploid human cell there are 46 molecules of DNA

I agree with this formula , because each Chromtid contain only one DNA then 1 chromosome contains 2 DNA it means that 46 chromosome contains 92 DNA..... Then what about MMitochondria which has its own DNA

Put it this way according to my understanding. Every human cell has 23 pairs of chromosomes and every pair contains 2 seperate DNA molecules. That means every human cell contains 2 X 23 = 46 separate molecules. So human genome means actually decoding 46 DNA molecules. That's all

Human cells contain 23 pairs of chromosomes (46 chromosomes in total).
Each chromosome is formed by 2 strands of DNA tied by hydrogen bonds to each other making the classic  DNA double helix (double-stranded DNA). So, in total there are 46*2=92 strands of DNA in each diploid human cell! Gametes contain half of the chromosomes, so half of the strands as well.

Ah yeah, if you consider each plus and minus as a strand then the number doubles, good point!

@JoeHealey — although the OP probably was misusing strand, and his major concern was how many copies of each dsDNA chromosome there were.

Each chromosome is present twice in every cell (excluding sperm and eggs, where only one of each is acquired in meiosis). So yes, that is 46 'strands' of DNA wrapped around histones as you said.
During mitosis each chromatid is replicated, and then in anaphase the sister chromatids are separated in to each daughter cell.
Any basic high school/university text book will have a good diagram of this.

So you mean human cell have 46 DNA strands which are coiled to form chromosomes?

Yes exactly (with the exception of the gametes as I mentioned, which are haploid rather than diploid).

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text:
Do trees grow from the bottom or the top, or is that oversimplifying?
I was wondering how trees grow. I wonder if it was similar to hair growth which occurs from the follicle. but clearly branches grow from the trunk so there is definitely a difference with hair growth.
I looked here and couldn't find a verifiable source, there are contradicting answers.
Here it says trees grow from places in places called meristenes, and it denies trees grow from the bottom, but more like from the branch tips and root tips.
If I carve and inscription in a young tree, will it get up with time?

Wikipedia / meristem

It appears you are mostly interested in the vertical growth of trees. As @Joe Healy points out, this is done only by cells in the apical meristem. This region always remains at the top tip of the tree, that is where the upward growth occurs. The apical meristem, as it continues upward with growth, will leave portions of itself behind that may result in branches (axillary merristems). So yes, unless you carve at the very tip of the tree, your initials will remain at the same height you carved them.
A very simple experiment that I've done many times with students demonstrates this. Germinate some corn seeds until the shoot and the root are about 2 cm long. With a fine Sharpie, mark each with lines every 4 mm or so. Continue the germination. After a few more days you'll note that the line spacings nearest the kernal are the same as when you drew them. But on the very outboard end, near the tips of shoot and root, the spacing will appear stretched out.
Another type of meristem, the vascular cambium, is responsible for the increase in diameter of a tree. It is a sheath that lies between the bark and wood producing new wood to the inside and new bark to the outside.

Yes in general a tree's primary direction of growth will be from the tip of a new shoot, though not exclusively (for instance the additon of new tree rings occurs from the inside out.
Most growth occurs at the apical meristem of a new shoot as cells continually push outward.

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Does light from the left visual field reach the temporal left retina?
A diagram of the visual pathway is shown here. Light from the left visual field reaches the left nasal retina and the right temporal retina. On the other hand light from the right visual field reaches the right nasal and the left temporal retina.

The optic fibers from the nasal parts of the retina cross, whereas the fibers from the temporal hemispheres don't. This configuration leads to the projection of the left visual field to the right occipital cortex and vice versa.
My question is, why can't light from the left visual field reach the temporal left retina and vice versa? I have illustrated this in the picture below with blue arrows.

Obviously, if it would, it would interfere with the normal pattern of projection. Now my question is what prevents light from the left field of view reach the left temporal retina? Or is there some overlap between the visual fields?

Very interesting and well researched question +1d. I hope you get a few more upvotes.

@Christiaan Just wanted the answer! Not the upvotes. Thanks :)

There is overlap between the left and right visual fields, as shown in Fig. 1. This overlapping part is referred to as the binocular field of view. The monocular field of view (FOV) is 160o (w) x 175o (h), and the binocular FOV is 200o (w) x 135o (h). The region of binocular overlap is 120o (w) x 135o (h) (Kolb, 2016). The visual disparity in the binocular FOV of the both retinal projections forms one of the most important depth cues that allows us to estimate the distance of objects.

Fig. 1. The left and right visual fields have an overlapping area, the binocular visual field. source: Harvey Mudd College
Fig. 2 below shows why only a certain part of the visual fields overlap. Firstly, the retina has a finite size and secondly, the anatomical location of the pupils restricts the angles of the visual field. The most eccentric parts of the left visual field simply cannot reach the temporal left retina (and vice versa), because the angle of the pupil with respect to the retina simply doesn't allow for it. The same holds for the most central part of the left FOV, which cannot reach the nasal part of the right retina; it can only project to the the temporal right retina because of the restrictions due to the localization of the pupil, the retinal size limitations, as well as the nose blocking a certain part of the FOV.

Fig. 2. The left and right visual fields have an overlapping area, the binocular visual field. source: Ohio State University
Reference
- Kolb, Facts and Figures concerning the human retina. In: Kolb et al (eds). Webvision, The Organization of the Retina and Visual System. Utah University (2016)

But one doubt remains. If the fields of view are overlapping, a lesion in the visual pathway like, lesion 2 (bitemporal hemianopia) in the picture in the question - shouldn't be so well defined/ straight line. Is the picture wrong in showing the visual defect to be etched out so clearly?

@Polisetty - the picture is valid and the symptoms are indeed pretty much as depicted, as the retinal hemispheres are divided in half.


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Which server to use for volume and accessible surface area calculation of proteins
I want to find the accessible surface area and the volume of a protein, giving PDB file as the input for the protein. I used two servers, 3vee and Vadar. For the PDB id, 1LTM, the websites are giving me different volume and surface area measures as follows:
3vee (vol: 50951 A^3; Surface area: 10837 A^2)
Vadar(vol: 40937.8 A^3; Surface area: 14680.6 A^2)
Can anyone tell me which server to use, which server is more accurate? If you know of any other server giving accurate result, please let me know that too.

Note: Both the publications are from Nucleic Acids Research, I guess I do not need to validate them. 3vee has been published in 2010 with citation of 164 and Vadar was published in 2003 with citations of 416. Is it okay if I take 3vee since it is the latest tool?

How big is the protein/complex? Can you download something like UCSF Chimera or Pymol and calculate it yourself to see if it agrees with either of those numbers? You may also want to check that the surface calculation parameters in both programs are using a similar probe radius. I'd guess from the fact that Vadar has a smaller volume but greater surface area, that it's probe diameter is smaller.

how does pymol calculate a volume ? cannot find any reference , I can generate volume objects but no way to get their value

You can use PDBSum and PDBe-PISA servers for calculating accessible surface area and buried surface area and Castp server for finding pockets within your protein molecule. If your protein is globular, you can measure the diameter in pymol and calculate its volume. Hope it helps.

can you add some references and/or links so that others who are less familiar with your answer and the question can follow along? it would definitely strengthen your answer

The results depend on the atomic radii and on the probe radii.
Without them, it is impossible to have an opinion about the volumes and surfaces values.
Using C=1.75, N=1.55, O=1.4, S=1.8, and adding 1.4 for the probe, running the Monte-Carlo method interactively available in ASV outputs for 10000000 random points (only ATOM records were input):
V = 57335.548996 +/- 1.96*34.439 ;
S = 14887.818374 +/- 1.96*20.345
You can download ASV from:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html ;
No installation procedure is required, just flag the binary as executable with the chmod command.
Monte-Carlo f77 source routines are supplied too.
References:
M. Petitjean, J. Comput. Chem. 1994, 15[5], 507-523;
M. Petitjean, Spheres Unions and Intersections and Some of their Applications in Molecular Modeling. In: Distance Geometry: Theory, Methods, and Applications, chap.4, pp.61-83, Springer, 2013.


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Do HIV particles die without host cells?
When a person is on antiretroviral therapy (ART) which blocks HIV particles from infecting cells, where do those particles go? Do they die out while floating in the bloodstream? I particularly want to understand if this is the reason viral loads go down once a person starts ART.

What do you qualify as dying? It's questionable whether to call viruses "alive".

I mean infectious by alive. Sorry for the terminology

I've learnt that our circulatory system can clear foreign matters from blood stream. Phagocytes can engulf and breakdown virions. Our liver and spleen is the blood filter system, which sequesters foreign matters all the time. So free floating HIV virions can't stay indefinitely in our blood stream.
However, without an effective adaptive immune response, these mechanisms are still unable to suppress viral replication. That's why HIV patients still have high viral load if untreated.


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Why is a membrane polar on the outside and non-polar in the inside?
Why would the phospholipid bilayer want to be polar on the outside and non-polar in the inside? why would it not want to be the opposite?

why do you think it would be the opposite?

Well, i'm not exactly positive. Both the interior and exterior are aqueous solutions if i'm not mistaken. So why would one be different from the other. Why wouldn't you want the fatty acid chain to be on top?

check out this link and see if that helps...look at the picture of the lipid bilayer and think about what its structure is chemically... https://www.boundless.com/biology/textbooks/boundless-biology-textbook/biological-macromolecules-3/lipids-55/phospholipids-300-11433/

Possible duplicate of http://biology.stackexchange.com/q/9261/3340

Phospholipids in aqueous solution under the proper conditions organize themselves into micelles and other structures - the minimum energy state.  This allows the polar head groups to interact with water in the bulk solution, while the non-polar carbon chains are 'protected' from the polar environment.  Water is attracted to water, and the polar head groups are attracted to water, the non-polar carbon chains are excluded.
You can get inverse micelles in non-polar solvents.

There is a misunderstanding here.  The questioner mentioned "Both the interior and exterior are aqueous solutions", which is absolutely correct.  However it makes evident he was thinking the non-polar part of the membrane molecules are in contact with the interior of the cell, which is wrong.  The non-polar ends of the membrane molecules are entirely inside the membrane, in contact with other non-polar ends of the other layer of the lipid bilayer which forms the membrane.  Both the interior and the exterior are in contact with the polar ends of the molecules.

so the interior and exterior ends are both polar?

Yes, the ends facing the interior and exterior are both polar.  But membranes have two layers, so there are molecular ends in the middle of the membrane, and the ends in there are non-polar (and thus forced away from the aqueous environments of the interior and exterior).


text:
Mitochondrial donation - why is the second woman needed?
Mitochondrial donation or the latest case procedure describes that an egg of the second woman is used as a host with healthy mtDNA.
Being a complete layman I'm interested in whether it is a restriction of the method or some fundamental requirement. Is it in principle possible to replace broken mtDNAs of a mother with mtDNAs of a father, which are mtDNAs of his mother?

It looks like the current techniques might better be described as "nuclear donation".  You take an ovum with healthy mitochondria, remove the nucleus, and insert the desired nucleus from the woman with bad mitochrondria.  So yes, currently, the mitochonrdria have to come from an ovum, and therefore a woman.

+1, a better term would be "cytoplasm donation"


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Why isn't acetyl-coA an entry point for gluconeogenesis?
The process of gluconeogenesis starts from various possible precursors - plausible entry points like, Pyruvate, OAA, Fumarate, Propionate (as succinate) and alpha-KG. It is important to note that, acetyl-coA is not an entry point for Gluconeogenesis.
Entry points shown as blue circles.

The most common reason cited for this is the irreversibility of the enzyme, pyruvate dehydrogenase. Since it is irreversible, Acetyl coA can't get back to pyruvate to go on forming glucose.
But, Acetyl CoA naturally enters the Krebs cycle, so why can't it go ahead and form glucose via gluconeogenesis using one of the Krebs intermediates?
I have had this doubt for very long and tried to come up with an explanation to satisfy myself but I still don't know if it is valid.
So here it goes. All the entry points to gluconeogenesis (mentioned before) are an addition to the Krebs cycle. They get on the boat, sail along, get off at oxaloacetate and leave. They don't bother the boat in any other way. Even Pyruvate, forms oxaloacetate via pyruvate carboxylase and then gets on the boat for gluconeogenesis.
On the other hand, Acetyl coA would be a part of the Krebs cycle itself. It is not adding anything to it (2 carbons that are added are lost as CO2). So an Acetyl CoA added, can't leave as OAA. It would be analogous not sailing on the boat but eating it down itself. Slowly, it would lead to a decay and loss of the intermediates Krebs cycle and it would come to a standstill (?)
Is this explanation right? Are there any other ways to explain why irreversibility of PDH results in this?
Although acetyl-coA can enter gluconeogenesis via pathways like glyoxylate cycle (not in humans) and pathways to make pyruvate from acetone (not economical) to form glucose, the question is why it can not do so directly via the Krebs cycle.
Image: Harper's Biochemistry, 29th Edition.

There is also this paper that shows alternative pathways in silico that could be used to convert FAs to glucose, but at a high energetic cost to the human host. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002116

Does this answer your question? Can the human body create glucose out of fat?

The problem is that acetyl-CoA enters the TCA cycle by condensing with oxaloacetate in the citrate synthase reaction. Therefore, you need 1 oxaloacetate for each acetyl-CoA added. Now, if the citrate formed goes on to oxaloacetate which is then removed for gluconeogenesis, there is no oxalocatete left for the next citrate synthase reaction. The reactions do not balance. Therefore, an anaplerotic substrate like glutamine or asparate is needed to replenish the lost oxaloacetate.

Maybe it's also useful to note that organisms that have the glyoxylate shunt can bypass the decarboxylation steps in the TCA cycle, and in fact can use 2-carbon substrates like acetate (that enter through acetyl-CoA) for gluconegenesis and growth. (https://en.wikipedia.org/wiki/Glyoxylate_cycle)

Yes, but I think the OP is already aware of this; see the last paragraph of the question.

The main point is specified above - that Krebs is a cycle. It starts with a 4-carbon molecule (oxaloacetate), adds 2 carbons (acetyl from acetyl Co-A) to make a 6-carbon  (citrate) and burns off 2 carbos as CO2 in a set of steps until it gets back to the 4-carbon starting point (oxaloacetate) to add another Acetyl.
If you siphon off any of the components of that cycle there's no feed to the next step and the cycle stops.
the second point is that Krebs cycle enzymes are inside mitochondria, and gluconeogenesis enzymes are outside in the cytosol. It is within Mitochondria that Acetyl is snipped off fatty acid chains (i.e. 2 carbons at a time) and linked to CoA and enters Krebs.
As a general point, most molecules cannot exit (or enter) mitochondria without a specific protein that will carry that specific molecule across the membrane, so there has to be a specific gene for that function.
So any specific molecules in Krebs have to have a gene to exit the (two) mitochondrial membranes. Humans don't have genes for that.
(NB - you can generate a small amount of glucose from fat from (a) the 3-carbon Glycerol that joins 3 fatty acids together and (b) the few odd-number fatty acid chains that will leave a 3-carbon molecule after a load of 2-carbons are snipped off)

Welcome to Biology.SE! This looks like a good answer, but answers are much more likely to receive a favorable response if you cite supporting references (primary literature is best). This allows non-experts to verify your answer and provides a starting point for further learning. A good example of how to format references. (NB: Standards have increased from when the accepted answer was posted.) ——— You may also want to take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site. Thank you!

(+1) As I understand things, the basic problem is that for each acetyl-CoA (a two-carbon compound) entering the TCA cycle, two carbons are lost as CO2 for each round of the cycle. Thus there can be no net synthesis of any carbon compound from acetyl-CoA via the TCA cycle. This is not true of the glyoxylate bypass where the CO2-losing steps are effectively bypassed, and this pathway is often a prerequisite for growth on acetate as sole carbon source (This is what so impressed Hans Kornberg).

See Tricarboxylic Acid Cycle and Glyoxylate Bypass, for example.  Plants (and bacteria) can make glucose from acetyl-CoA if they have the enzymes of the glyoxylate pathway. More can be found in Kornberg's papers (Hans Kornberg, that is) on the glyoxylate cycle.

Please do not refer to the Krebs Tricarboxylic Acid Cycle as "Krebs". This is not standard practice (I have never heard it before) and appears disrespectful to the memory of Hans Krebs (although I imagine that was unintended). "The Krebs Cycle" is acceptable, although people use the name "Tricarboxylic Acid Cycle" or "Citric Acid Cycle" because Krebs was also responsible for elucidating another metabolic cycle — "The Urea Cycle".

Your emphasis on loss of C2 via carbon dioxide is a useful clarification/extension of the accepted answer. However, your remarks about mitochondria are incorrect. Oxaloacetate (OAA) is a constituent of the TCA cycle and is normally produced from fumarate in the mitochondrion. In "normal" oxidative metabolism it condenses with Acetyl CoA to complete the cycle. However if there is direct or indirect input of OAA from amino acids it can act as a gluconeogenic precursor through conversion to PEP by PEP carboxykinase. To do this it is exported to the cytoplasm as malate via a malate transporter.

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text:
Measuring Bioluminescent Algae Intensity
For a science project, I am required to measure the intensity of the light given off by the Algae, Pyrocystis lunula. Can a photometer with a range of 1-50000 lux be able to pick it up? If not, what are some tools to measure the intensity(without costing to much money.)?

As stated here:

The lunate cysts of Pyrocystis lunula have a bioluminescent emission spectrum with a peak intensity of 477.5 ± 1 nm.

So, almost any spectrophotometer should be able to detect it, it's just bluish visible light.

So even the cheap ones?

Even a phone camera


text:
Does tardigrade eat mould?
There is a problem of devastating mold in ventilation of old buildings in Europe. I guess tardigrades might be better solution because chemicals is not a good idea for ventilation because people are breathing with this air.

can you add some links to the terms - especially "tardigrade" - in your question? it's kind of hard to follow - it would definitely benefit from some more background information.

'mold' is an informal term for various cotton-like-looking fungus of separate taxonomic group. From description I think, that ventilation might build-up of mostly dust and soot ((as seen in cities, characteristically on ceiling fans)), not solely moulds. Is that?

The wikipedia page (https://en.wikipedia.org/wiki/Tardigrade) shows tardigrades are aquatic. So why they will stay alive in your ventilators to eat the moulds? Why you thought that... are you telling about any particular sort of tardigrades that is terrestrial and can eat moulds? Do you have any sort of source?

Majority of more then nine hundred of known species of tardigrades are populates mossy and lichen pillows on the earth, the trees, the cliffs and the rock walls. I seen huge black tardigrades about 1.5mm at wall with mold.

Mould in buildings can be serious.  It is treated by removing and destroying (fire is good) the things the mould is growing on, and lots of cleaning.
The mould grows on wet cellulosic material like fiber board, gypsum board, paper, or wood.  It can be prevented by fixing the leaks so stuff doesn't get wet, and more cleaning.
You could pour bleach on the contaminated material, kill some of the mould, and what survived would grow back.  Neither chemicals, nor tartigrades are any help here.  Just more cleaning.
Details:  http://www.cdc.gov/mold/stachy.htm


text:
How to get sulfate reducing bacteria?
How can I find and get sulfate-reducing bacteria? Where and how can I store them for a long time?

What are your plans?

The plan is to put it into an apple size capsule that would be sent to Mars. So basically the bacteria should stay alive during the travel period and after impact to the planet.

Another point is to make them to be the only of microorganism species in the substance. Because I do not want something oxygen consuming to get there before some source.

The oxygen might be needed for algae.

Sulfate-reducing bacteria are everywhere, one spoon of soil contains several different species of them. The problem is how to isolate them from the other bacteria.
This old paper explains how to do it, I am sure there are newer techniques to do the same, it's up to you to dig into the literature to find the one you prefer if you want to isolate them by yourself.
Otherwise, just buy it from a collection.

Old paper page is not available. Do you have it in webarchive?

Wired, the link was active few hours ago.. I have uploaded the file here http://www.filedropper.com/mic-3-1-46

I have updated the link of "This old paper" now it should work.


text:
Why is there complementary base pairing for DNA?
Why is there complementary base pairing for DNA? Why can't A pair with C given that they can all form hydrogen bond?

When you say that "A pair with C" can you please provide a diagram to show what you mean and how you envision they would fit together?

It's to do with the physical space the base molecules occupy. There are 2 classes of molecules in DNA bases, purines and pyramidines.  One of each always pair together as there will be a total of 3 ring moieties present.
E.g., Adenine (a purine) pairs with Thymine (a pyrimidine).

If you were to pair 2 pyrimidenes together, you would induce a kink in the DNA backbone and destabilise it.
That said, there is no chemical reason 2 purines or 2 pyrimidines can't hydrogen bond, and they do. This causes mismatches and DNA mismatch repair enzymes recognise the torsion it induces in the DNA backbone and they replace the mismatched base in the proofreading process. If the enzymes miss one mispairing, which can happen as it occurrs often (but the enzymes are very effective), then you end up with a mutation.

When you say that two purines can hydrogen bond to form an anti parallel double helix, or alternatively two pyrimidines can hydrogen bond to form an anti parallel double helix, can you draw or describe how you envision the H-bond donors and a H-bond acceptors would align with each other?

I don't have/can't find a good diagram of this from a quick look. Maybe someone else will find one. It is structurally less stable, so the bonds are likely semi-transient, switching between single, double, and triple bonds depending on molecular vibrations and so on. They all contain O, N and H groups with varying electronegativity though so the most proximal of those are likely to interact. I'm afraid I don't have a very good answer for you though.


text:
What kind of spider is this?
I spotted this spider in my garden (Northern UK). The body is about 20mm long, and it's made a sizeable (50cm) web on a wall.

There's another semi-identical one on a nearby hedge.

What kind is it?

Do you have any larger or clearer pictures of it?

@MattDMo - Larger, yes. Clearer, not especially. Hang fire while I go and get some more.

Thanks for the pictures! That's the European Garden Spider (Araneus diadematus)
They are most commonly seen from June to October, but they reach a peak around right now.  This species is all over UK, and is widespread in gardens, woodland, and meadows.  Here is another picture for reference:

Fun Fact: After laying their eggs in late autumn, the females die and only the eggs make it through winter.  Upon hatching, they look quite different from the adults:

Why have I never seen these little beasties before?

@Valorum - I'm truly shocked that you haven't, actually.  They seem to be one of the most common spiders around my parts (West Midlands) at the very least.  Although they do seem to have less of a tendency to end up indoors than most others.

@Jules - Never seen them. We get loads of house spiders, crane flies, daddy long-legs, wasps, ladybirds and the occasional bumble-bee but never one of these.


text:
Does the SMUG1 enzyme break single-stranded DNA?
The SMUG1 gene codes for the enzyme single-strand selective monofunctional uracil DNA glycosylase.  This enzyme can remove uracil from single-strand (unpaired) DNA.  (Uracil can occur in DNA due to deamination of cytosine.)
What happens when this enzyme removes uracil?  It seems what would be best is that a cytosine would replace the uracil in the DNA strand to restore the original DNA sequence, but I haven't found mention of this.  The alternatives would seem to be that the enzyme simply splits the strand into two strands by removing the uracil (which are then unconnected since this is single-strand DNA), or it joins the two adjacent bases together, deleting the uracil but keeping the strand intact.

I think you needed to click just one more link: https://en.wikipedia.org/wiki/Base_excision_repair
It just cuts out the base so there's an empty spot on the ribose. I was looking for a picture and the top hit was actually this site (at A):
What is the mechanism of monofunctional glycosylases?

Yes, I now see SMUG1 just removes the base, leaving the sugar and phosphate. It seems then that the information that U had been present (and thus cytosine is appropriate) is lost.  The fate of the baseless sugar-phosphate is unclear to me from the Wikipedia articles; most of the discussion seems to suggest that breaking of the phosphate backbone is usual (which would leave two unconnected DNA molecules).


text:
How do you determine the length of an annelid?
I'm currently studying a horse-leech, and would like to know if it is fully grown or not. When I read about different annelid species a maximum length is often given, so I wonder if there is some standard way of measuring these elastic animals?
For example, my leech varies from 2 to 10 cm, but often seems to prefer to stretch out to about 6 cm when not moving.
(Possibly I should modify this question to be just about leeches, but I also wonder about earthworms, and probably other soft and difficult worms as well...)

Leeches:
According to Taube (1966)$^1$:

The adults of American leeches range from about 1/4 inch to 12 inches in contracted length.

Because leeches can bloat to more than 10x their "normal" size after a meal (and can undergo up to a 300% change in length), it seems that measuring a leech at anything but their contracted state would lead to wildly too variable of measurements. Therefore, it seems likely that only contracted size would prove to be truly useful.

However, see Klemm (1982)$^2$ (or Klemm,1995 $^3$) for comments about preferred preservation for identification purposes:

[Leeches] have a soft, highly contractile body. Therefore, if leeches are dropped alive into preservatives such as 70% alcohol (ethanol)...they contract strongly and sometimes such features as the eyes, general body shape, and the genital pores become distorted and difficult for the non-specialist and occasionally even for the expert to discern. When leeches are properly anesthetized prior to fixation, there is usually less muscular contraction. the body shape remains more uniform, and there is less variability of the anatomical structures. ... The preserved leech should be straight, moderately extended and undistorted.

However, Klemm does not use body length as an identification feature in his key, and therefore his directions seem to be more concerned with preserving other anatomical features (not to ensure accurate length measurements). He does provide "average size" for species in his key but notes that "contraction during processing" can lead to variation in measured length.

Other Annelids:
Interestingly, naturewatch.ca provides the followign instructions for measuring earth worms:

1.Allow the worm to freely extend itself as if it was crawling.
2.Measure the maximum distance the earthworm covers when completely stretched out.

Similarly, a Ph.D. dissertation by Cynthia M. Hale (2004)$^4$ measured earthworms by preserving them and then

measur[ing] on the longest axis of the straightened individual.

Takeaway:
It seems as though ranges of body length are almost always provided for each species. Although this is not uncommon for any taxa, many sources (including those cited) mention that variability in preservation methods/ body orientation  can lead to variation in lengths recorded (as can age, vitality, gut content, moisture content, etc.). Klemm, in particular, suggests using numerous museum specimens to make conclusions about species because of these variability issues.
As a result of these discrepancies/inconsistencies, I would guess that you're best off citing a methodology source (e.g., Taube 1966) and explicitly indicating your measurement methods.

Lit Sources:
[1] Taube, Clarence M. 1966. Leeches. Institute for Fisheries Research Report No. 1713. http://quod.lib.umich.edu/f/fishery/AAG2862.1713.001?rgn=main;view=toc.
[2] Klemm, Donald J. 1982. Leeches (Annelida: Hirudinea) of North America. EPA-600/3-82-025. Cincinnati, OH.
[3] Klemm, Donald J. 1995. Identification guide to the freshwater leeches (Annelida: Hirudinea) of Florida and other southern states. Florida Department of Environmental Protection. Tallahassee, FL. http://publicfiles.dep.state.fl.us/dear/labs/biology/biokeys/leeches.pdf
[4] Hale, Cynthia M. 2004 Ecological consequences of exotic invaders: interactions involving European earthworms and native plant communities in hardwood forests. PhD dissertation. University of Minnesota.

Wow, after so long with absolutely no activity I had almost given up on this one! Thank you for the thorough answer (and for correcting my sloppy spelling).


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How does dsDNA become ssDNA when binding to a nitrocellulose membrane?
I would like to know how double stranded DNA becomes single stranded when binding to nitrocellulose membrane in southern blots. Does it require a special reagent? Is denaturing a special property of the membrane itself?

The DNA is denatured in-gel prior to transfer using alkali conditions, most commonly a solution containing 0.5 M NaOH (buffered with 1.5 M NaCl). Following that the pH of the gel is neutralised in 0.5 M Tris-HCl, pH 7.5; 1.5 M NaCl.
I have found the Roche DIG application manual to be a well-written and reliable resource for performing Southern and Northern blots. The section on Southern blots starts at page 94 and you can modify the protocol to suit other detection systems.

No, there is no such property present in membrane. After transferring to membrane they treat with alkaline solution to denture dsDNA to ssDNA for binding of probe.

Don't most transfer methods only allow ssDNA to transfer from the gel to the membrane?


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Can an attenuated virus cause infection in some rare cases?
I just read in some comments, that some children got measles one week after getting the MMR shot. Afaik. MMR contains attenuated live virus, and the incubation period of measles is 10 days (+/- ? days). Can we be certain, that they didn't get infected by the vaccine?

There are two possibilities for getting the measles directly after a vaccination:

The kids where infected shortly before the immunization. Since it takes about two weeks to develop humoral immunity, it is possible that these two events overlap. The measles have an incubation period of 7 - 21 days (see reference 1), with a rash occuring around day 14. So if the kid was around day 7 of his infection, this would fit.
Since the measles vaccination is a live attenuated virus, it is possible to get a rash from it. However, these are relatively rare cases (depending on the source between 2 and 5%) and the infection is mild and not contagious. See also reference 2.

References:

Measles (from the CDC)
Measles: Questions and Answers

"About 5% of people develop a mild rash." - This is in your second reference. Is it 5% or 1/10000%?

@inf3rno I put in a wrong number, don't ask me why. Thanks for the notification.


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Standard graph - Determining sizes of restriction fragments

I have marked out Lane M and gotten a roughly straight line, it then says that I am supposed to estimate the length of lane H and R. I am not sure what they are asking. I am still supposed to measure the distance migrated and then just plot it next to lane M on the graph or am I using lane M in order to actually plot the rest of the lanes, is it that by having both the length and fragment size of lane M, that I should be able to look at the fragment size and by using lane M be able to tell how far the DNA has migrated?

could you rotate the picture 90 degrees counterclockwise?

PLEASE DO NOT POST TEXT AS IMAGES. Copy and paste the text into your question. Images are not searchable, and can not be interpreted by screen readers for those with visual impairments. Use the [edit] link to modify your question. See this for more information.

The lane marked 'M' contains molecular weight markers of known sizes (in this case we are not using the actual MW of each double-stranded DNA fragment, instead we are using the length of each dsDNA fragment, measured in either base pairs (bp) of kilobases (kb)).

Plot the size of the MW standards on the log axis of the semi-log paper, and plot the distance that each fragment migrated through the gel on the other axis (the linear axis). Depending on the electrophoresis conditions you should be able to connect these points in a smooth line with a negative slope. At higher MW the line's slope will curve and get steeper.
Measure the distance that each band in lane 'H' migrated through the gel. Take those distances, and see where the fall on your standard curve that you plotted at Step. 1. You should be able to place the distance on the x-axis and read off the corresponding dsDNA fragment size on the Y-axis.
Repeat Step 2 using the distances that you measured for the fragments in lane R to find out the approximate sizes of those dsDNA fragments as well.


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Are enhancers and silencers considered as epigenetic modifications?
Are enhancers and silencers considered as epigenetic modifications? I am confused as it seems like enhancers and silencers are sequences on the DNA and how they work is through binding with proteins, while epigenetic changes seem to be changes made to the bases for instance adding a methyl group.

No.
Epigenetic information is (by definition) NOT included in the nucleotide sequence, but affects genetic expression.
Enhancers/silencers are themselves nucleotide sequences, and therefore not epigenetic information.
Methylation is an example of epigenetic information, but a DNA sequence itself is genetic information, even if it affects a gene.
CgATgCCAg= Genetic
Acetylation of a histone/DNA methylation= epigenetic
Hope that helps!
Further reading: http://www.whatisepigenetics.com/fundamentals/

Welcome to Biology.SE! Thanks for the clear answer.

@James Thanks, looking forward to contributing to and learning from the community!

The biosphere chatroom is sometimes quite active if you fancy saying hi!

Even with basic answers it is good practice to add sources to allow users to background read on the topic

Strictly speaking, enhancers and silencers are not themselves epigenetic modifications. Rather, they are genetic elements that directly regulate gene expression through their interactions with various proteins.
An epigenetic modification is a chemical change to DNA bases, generally through either methylation or acetylation.
Enhancer and silencer sequences can be, and often are, epigenetically altered by the addition or removal of these chemical groups. This is not uncommon along the course of development for many genes, whose expression must be regulated differently at various stages of development. Enhancers and silencers are also epigenetically regulated in different cell types, which enables cells to use the same genes found in every cell to maintain different cell type identities.
So in short, enhancers and silencers are genetic regulatory elements, but they are very often epigenetically modified. Hope that helps.

So there are certain combinations of marks we've found that tend to mark regions of DNA that will enhancer/silence expression of reporter genes when we stick them into plasmids and do reporter gene experiments. People often define regions and call them 'enhancers' using these biochemical marks alone, but it's an approximation. There's no guarantee all such regions will be enhancers/silencers, and there's certainly no guarantee that all enhancers/silencers will have the marks.

Epigenetics is defined as heritable changes in gene activity and expression that occur without alteration in DNA sequence (not encoded in the sequence), and it is influenced by chemical modification of the DNA like in the case of methylation. Enhancers and silencers are sequences of DNA, like genes, but they do not encode for proteins, rather they have gene-regulatory effects. An enhancer/silencer can be methylated and thus be epigenetically controlled.


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Interpretation of agarose gel electrophoresis of a plasmid
I am performing agarose gel electrophoresis of plasmid which is 2.5-3 kb in size. I am getting more than 3 bands, after restriction I got single band at 3.5kb in size.
Electrophoresis conditions- 0.5X TBE, constant voltage 150V.
why am I getting more than 3 bands after agarose gel electrophoresis of plasmid?

Please convey the question in the title

It is probably due to the presence of supercoiled plasmid. You can try to heat up your plasmid in a thermocycler , 90 C for 20 min, this will denature the proteins responsible for the supercoiled structure and you will eventually see only one band representing the circular plasmid. The fact that you see only one band after digestion it's a good sign that you indeed have only one plasmid in your prep.

Thank you for reply. I am using sure spin column for extraction of plasmid. how does protein present in sample?

@alec_djinn Is it known which bacterial proteins are responsible for maintaining the supercoils in purified plasmid DNA?

@RosieF specific DNA gyrases are responsible for inducing the coiling, then histone-like bacterial proteins keep the structure in place. Have a look here https://en.wikipedia.org/wiki/Bacterial_DNA_binding_protein and here https://www.ncbi.nlm.nih.gov/pubmed/26928284

@SonamPatil the silica columns used for minipreps retain the DNA and the  histone-like proteins attached to it. Sometimes more, sometimes less, you always have some protein (and RNA) contamination, you can check it by spectrophotometric analysis (260:280 / 260:230 Ratios), it's not uncommon to co-purify some proteins together with your plasmid.

The closed plasmid comes in three different forms: nicked-relaxed, supercoiled and circular single-stranded. All three forms have a different tertiary structure and thus they run differently on the gel. This should look like this (image from here, there you also find a more detailed explanation):

When you digest the vector you linearize all the forms and they all have the same tertiary form.


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What does the 4DTv (four-fold synonymous) mean?
I saw this sentence "4DTv is the transversion rate at fourfold synonymous codon positions, and ranged from zero (for recently duplicated paralogs) to ~0.5 (for paralogs derived from an ancient evolutionary past)." at this paper and another paper.
I have searched 4DTv or four-fold synonymous on google, but I did not find the answers showed at the following lines.
And my questions:
(1) Does the value of 4DTv range from 0 to 0.5?
(2) Why 4DTv closed to 0.5 indicate that an ancient evolutionary was happended?

I was about to ask the same question: did you answer yourself? Can you post your answer in that case?

After one month of research, I have some insights about it.
First of all, more than "fourfold-synonymous", the correct research is fourfold degeneracy. The genetic code is degenerate, in the sense that there is usually more than 1 codon encoding a certain amino-acid. The degeneracy usually takes place in the third position of the codon, that can be 2-, 3- or 4-fold degenerate. A 4-fold degenerate site would be the third position of a codon, where regardless of which nucleotide you have, the outcome doesn't change. Example: GGT, GGC, GGA, GGG all code for Glycine. As there are four variants at the third site of the codon, the third site is said to be fourfold-degenerate (4D). As the encoded amino-acid does not change, there is virtually no selective pressure on these variants, therefore they can be used as a "clock" to estimate times, given that you know the mutation rates per position.
Now for your other questions:
Yes, the value ranges from 0 to ~0.5, and this can be explained in a simple way. Transversions (Tv) are considered to be more rare than transitions (Ti). Therefore, if you calculate the ratio of Tv among all the variants, you expect this value to be < 0.5 (i.e. to have less Tv than Ti, otherwise it would be >= 0.5). Now, in order to accumulate Tv at 4D sites you need time to pass, so the more of them you have, the more time has passed, and that's why 4DTv ratios define time.


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regenerative capacity of human body
Is liver the only internal organ in human body with regenerative capacity? How about endometrium?and what is the difference between regeneration and renewing?

No, many tissues regenerate, otherwise we'd never grow or heal from wounds. Skin, muscle, lining of the intestines, bone, to name just a few.

blood is an example too, so that after participating a blood donation we regain the blood-volume ( with same number-density of blood corpuscles as initial) in few months

I'd say renewing refers to a constant process wheras regeneration applies to wholesale rebuilding due to trauma.
For example, your skin is constantly "renewed" by the undermost cells, adjacent to the basement membrane, dividing to produce new cells that migrate outward. These cells are modified to protect and eventually slough off to feed the mites in your bed. Ditto to cells lining the stomach which are replaced/renewed about ever three days due to abuse of stomach acid and salsa.
Humans can regenerate much of the last joint of a finger, bone and all. I'm not sure if this is age dependent nor how much of the knuckle needs to remain. Search "regeneration of fingers in humans" to find many references to this.

Some of the information contained in this post requires additional references. Please [edit] to add citations to reliable sources that support the assertions made here. Unsourced material may be disputed or deleted. Specifically, please provide a reliable scientific reference for the claim made in your last paragraph. "I just saw a show" is not a reliable reference.

Yep, a search turns up a third of a million references to 'regeneration of fingers in humans'. Maybe it was my colloquial parlance that triggered your comment. As an educator, I try to taylor the response to the student, but maybe it was too homely for this forum. I've removed it. Uncommon theories and arkane assertations should be referenced. Referencing each and every fact detracts from the clarity of the discussion. Imagine your comment to the OP, replete with references.

No, referencing facts does not detract from the clarity of the discussion, it enhances it. References provide suggested additional reading, allowing those who are interested to learn more about the topic. And since we're on that new-tangled "internet" thing, you can make inline links and continue with the flow of your prose without those annoying superscripts. We've discussed this on Meta, and the consensus is to link all but the most basic facts. Wikipedia is frequently used. Your thumb claim should be linked, as it is not common knowledge. I'd also link "basement membrane".

However, your refusal to put even a basic link into your text is just petty. It tells people "oh, you should know this, but if you're too dumb to, I'll tell you to google it because you probably wouldn't think to do that on your own." I've found that some of the best answers on here have tons of supporting links, but they're there for reference, and usually not quoted from directly. Instead, the authors synthesize what's contained in them, but leave the link if you want to know more, or want to check their claims. Your answer does none of that.

It wasn't a refusal, nothing petty on this end. I honestly thought my edits would satisfy your complaint, my mistake. I also though it was good pedigogy to provide general direction as opposed to choosing one of 300,000 plus hits. I feel your damning comments ill deserved.


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Can you do better than "Sock-Wasp"?
I met this beautiful fellow when I was choosing my socks this morning. It seems I had found her cozy place. A stowaway, supposedly sneaked into my bag while camping, and me taking her all the way home. She just sat there for about a minute (probably just as tired as me, thinking "Duuuuuude, why did you wake me?"), then stretched her neck and and set off, searching for a calm spot to get her 5 more minutes.

Ca. 3 cm long. At home in Austria/Southern Germany.
I searched the internet a bit, and I think it's a female wasp, possibly Dolichovespula because of the pointy snout(?). I don't think it's a commom wasp, due to its size. Also no median wasp queen, because there's no red.
Maybe a tree wasp?
TL;DR: Can you help me identify this buzzer?

End of story:
After a lot of buzzing on her side, me chasing her with glass and cardboard in hand, and she dozing off two times in very uncomfy places (I was a bit embarassed about how un-hospitably dusty everything was), she settled for a box of clothing and snuggled her way into my shirts. I praised her sense of Cozyness, but then carefully emptied the box piece by piece outside and found her inbetween a flowery garment. She slowly stuck her head out from the folds ("DUUUUUUDE, again?!") and flew around the terrace for a while. I hope she's found a snug place out there.

It really is beautiful.

I presume it is a female Dolichovespula adulterina living in the Palearctic (Austria and Germany) and Nearctic regions.


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How are the very first telomeres added?
Here is an image of telomerase adding telomerase.

As we can see, the telomerase sort of binds to a bit of the existing "3' flanking end of [the] telomere" - it's almost half and half.
My question is, where did that existing telomere come from? And the telomere before that?
Essentially, the telomeres must have begun from some point on the chromosome/DNA, but how were those telomeres added if the telomerase has a preset RNA sequence that it uses to bind to specific nucleotide bases? Does our human DNA coincidentally end with TTAGGG as well or something?

See telomerase and TERT.

So I understand that it has to use reverse transcription to do it, but I cannot find anything specific to telomerase adding the first telomeres. Any help?

I won't be able to help you, as I know little about molecular genetics. But given the number of upvotes, you will probably get the attention of someone who will be able to answer such as Chris or WYSIWYG.

Telomere might have evolved from a retrotransposos. http://www.nature.com/scitable/content/t-loops-and-the-origin-of-telomeres-26791

Telomeres are maintained by telomerase (in certain cell types, not all of them) at every replication. So, the answer to your questions "where did that existing telomere come from? And the telomere before that?" is: "because there was already a telomere to extend at the end of this chromosome".
Your questions boil down to "how did telomeres appear in the first place?" (because once telomeres and a maintenance mechanism have been established, they will simply remain unless some major genomic catastrophe happens), and this is a difficult question. As Whitney pointed out in the comments of your question, some hypotheses about the origin of telomeres are discussed in this article.
Interestingly, Drosophila doesn't have telomerase, and maintains telomeres by a transposition mechanism. Somehow this is a clue about how telomeres appeared: Drosophila telomeres could be an intermediate between circular chromosomes and telomerase-based maintenance of linear chromosomes.
This is a complicated topic, but the scientific literature about the appearance of telomeres is fascinating. Some bacteria (Borrelia and Streptomyces taxa) have linear chromosomes, but maintenance mechanisms that have nothing to do with transposition nor telomerase.
Here are some references:

Drosophila: https://doi.org/10.3389/fonc.2013.00112
Borrelia: https://doi.org/10.1146/annurev.micro.112408.134037
Streptomyces: http://link.springer.com/chapter/10.1007/7171_2007_090

If you can read French, you will find more info in the introduction of my PhD thesis.


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What does differentiation of B-cell mean?
Does differentiation of B lymphocytes mean the formation of plasma cells and memory cells by matured B lymphocytes?

Immature B lymphocytes mature into either plasma cells or memory cells. If a B cell is mature, that means it's already a memory or plasma cell.

Could you cite some references?


text:
Do all plant hormones of one group show the same qualitative effect with respect to their target pathway(s) and the biological response?
I wonder, terms like "Auxin", "Cytokinin", "Gibberellin" etc means NOT a single compound; but a class of compound.
For example "Auxin" does-not mean a single compound, but several compounds such as : natural auxin (IAA in all plants*, 4-Cl-IAA in pea*, IBA in mustards*) and their synthetic analogs like NAA, 2,4-D, 2,4,5-T, dicamba ( * ), etc.
Similarly there are more-than one natural compounds under the group "Gibberellin" (such as GA1, GA3, GA4, GA7 etc),
and similarly more-than one compounds under cytokinins: natural: cis-Zeatin, 9RiP ( * ) etc. and their artificial analogs such as kinetin ( * ), 6-BAP , etc
Now, my question is, would all the auxins work in exactly the same way? or would there be slightest difference (qualitatively) between their actions? and similarly, Would all the cytokinins work the same way? and would all the gibberellins work in the same way?
(So far I heard that they have difference in their 'strength' i.e. in which concentrations they are undetectable/optimal/toxic to a cell. (i.e. quantitative difference), but don't have any references for this.)
But beside that;  my question is, would there be ay qualitative difference?
So far I haven't found anything clear-cut about this in any book or on the web.
Any help welcome

(  *  )  (ref.  Plant Physiology/ Taiz and Zeiger, ed3; chapter 19, fig. 19.3, fig. 19.4)

Update:
In one source, Plant Tissue Culture: Theory and Practice/ Bhojwani and Razdan, (edition= ? ) 3.2.3. Growth hormones; , it is told that "IBA and IAA are widely used for rooting, and with a interaction with a cytokinin, for shoot proliferation.  2,4-D and 2,4,5-T are very effective for the induction and growth  2,4-D and 2,4,5-T are very effective for the induction and growth of callus. 2,4-D is also an important factor for the induction of somatic embryogenesis."
However there I could not found,  is this difference is really due to a difference in biological (signaling-path) process, or due to some-other superficial difference (solubility, binding with same receptors, etc) of these applied molecules.

maybe this atricle will help you (ps I'm not sure if you can acces it for free): https://www.ncbi.nlm.nih.gov/pubmed/22554243 if not maybe you can read this (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151247/) however this one is more focused on Arabidopsis

I have edited your English and the layout to try to improve readability and hence your chance of getting an answer. However I would suggest your question is too general. This is not my field, but I can see no reason why what might be true for a family of auxins need also be true for gibberellins or thyroid hormones. Obviously someone might answer for one particular case, but if you assume there is a general principle to which the answer is yes of no, I am sure you are mistaken. Biology isn't like that.

@David Thanks for your edit. I'm not fluent in English so please feel free to do/suggest edit. However I'm not generalizing among auxins, gibberellins etc. What surprised me, 'auxins' is a group or class of signaling-compound (IAA, IBA, NAA etc), not a single compound. (similarly 'gibberellin' is a group or class). Undoubtedly IAA, IBA etc have very 'similar' action so they are considered in a single group, 'auxin'. But no-one source I've yet found that claims 'their action is the exact same'

@David Should I specify this question only for plants?

I think that would probably be better.

I am happy that you have received a comprehensive answer, but less so that the modified question reverts to the original poor style. It deserves better. Please note 1. Conjugation of verb do — does a hormone, do two hormones. 2. It is bad style to use low numerals such as 1 instead of spelling them out. 3. Your original hyphenation is incorrect. "Plant hormone" stands on its own. You would only hyphenate if you used this as a compound adjective e.g. "Plant-hormone action". 4. Something that is qualitatively similar cannot be exactly the same.

Preface: As @David says, the question is very broad. So, here, I'll take up the most common plant growth factors i.e. auxins to give you an idea.
Short Answer: We don't definitely know yet whether the pathways of two auxins (I take indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) here) are exactly same or not.
Background: We know that auxins have very similar functions1:

Auxins are a class of plant hormones (or plant growth substances) with some morphogen-like characteristics. Auxins have a cardinal role in coordination of many growth and behavioral processes in the plant's life cycle and are essential for plant body development.

So much similar that2:

genetic evidence has been found that suggests that IBA may be converted into IAA through a similar process to $\beta$-oxidation of fatty acids.

Now, when it comes to whether the exact mechanisms of how IAA and IBA work are similar or not then, as I said, we don't know yet.
When we talk about IAA, there is a theory known as Acid Growth Theory3 (though there are evidences against it):

Plant cells elongate irreversibly only when load-bearing bonds in the walls are cleaved. Auxin causes the elongation of stem and coleoptile cells by promoting wall loosening via cleavage of these bonds. This process may be coupled with the intercalation of new cell wall polymers. Because the primary site of auxin action appears to be the plasma membrane or some intracellular site, and wall loosening is extracellular, there must be communication between the protoplast and the wall. Some "wall-loosening factor" must be exported from auxin-impacted cells, which sets into motion the wall loosening events. About 20 years ago, it was suggested that the wall-loosening factor is hydrogen ions. This idea and subsequent supporting data gave rise to the Acid Growth Theory, which states that when exposed to auxin, susceptible cells excrete protons into the wall (apoplast) at an enhanced rate, resulting in a decrease in apoplastic pH. The lowered wall pH then activates wall-loosening processes, the precise nature of which is unknown. Because exogenous acid causes a transient (1-4 h) increase in growth rate, auxin must also mediate events in addition to wall acidification for growth to continue for an extended period of time. These events may include osmoregulation, cell wall synthesis, and maintenance of the capacity of walls to undergo acid-induced wall loosening. At present, we do not know if these phenomena are tightly coupled to wall acidification or if they are the products of multiple independent signal transduction pathways.

However, there are evidences supporting this hypothesis, like this one4:

When auxin stimulates rapid cell elongation growth of cereal coleoptiles, it causes a degradation of 1,3:1,4-$\beta$-glucan in hemicellulosic polysaccharides. We examined gene expressions of endo-1,3:1,4-$\beta$-glucanase (EI) and exo-$\beta$-glucanase (ExoII), of which optimum pH are about 5, and molecular distribution of hemicellulosic polysaccharides in barley (Hordeum vulgare L.) coleoptile segments treated with or without IAA. IAA (10–5 M) stimulated the gene expression of EI, while it did not affect that of ExoII. IAA induced gene expression of EI after 4 h and increased wall-bound glucanase activity after 8 h. The molecular weight distribution of hemicellulosic polysaccharides from coleoptile cell walls was shifted to lower molecular weight region by 2 h of IAA treatment. Fusicoccin (10–6 M) mimicked IAA-induced elongation growth and the decrease in molecular weight of hemicellulosic 1,3:1,4-$\beta$-glucan of coleoptiles in the first 4 h, but it did not promote elongation growth thereafter. These facts suggest that acidification of barley cell walls by IAA action enhances pre-existing cell wall-bound glucanase activity in the early first phase of IAA-induced growth and the late second phase involves the gene expression of EI by IAA.

But when it comes to IBA, all we have is this2:

Although the exact method of how IBA works is still largely unknown, genetic evidence has been found that suggests that IBA may be converted into IAA through a similar process to $\beta$-oxidation of fatty acids. The conversion of IBA to IAA then suggests that IBA works as a storage sink for IAA in plants. There is other evidence that suggests that IBA is not converted to IAA but acts as an auxin on its own.

So, if IBA is converted to IAA before use then, obviously, it works the same way. But the article below suggests that either the mechanism or effectiveness of IAA and IBA is different5:

We have examined in vitro rooting of apple ‘Jork 9‘ shoots exposed for three weeks to each of the three auxins commonly used for ex vitro rooting: indole-3-acetic acid (IAA), indole-3-butyric acid (IBA) and $\alpha$-naphthaleneacetic acid (NAA). During the initial five days of the rooting treatment, the cultures were incubated in darkness. In this period, the root initials are formed. Then, the cultures were moved to the light. NAA resulted in a low (ca. 8 roots), and IAA or IBA in a high (ca. 15 roots) maximal root number. The maximal root number was reached at a wide range of IAA concentrations (10-100 $\mu$M) but at only one concentration of IBA (10 $\mu$M) or NAA (3 $\mu$M). With NAA and IBA, growth of roots and shoots was much more inhibited than with IAA. For these reasons, IAA is the preferable auxin for in vitro rooting of apple ‘Jork 9’ shoots.

This suggests that IAA and IBA use different mechanisms or that IBA can't use the same mechanism as effectively as IAA.
References:

Auxin - Wikipedia
Indole-3-Butyric Acid - Wikipedia
The Acid Growth Theory of auxin-induced cell elongation is alive and well
Auxin-Induced Elongation Growth and Expressions of Cell Wall-Bound Exo- and Endo-$\beta$-Glucanases in Barley Coleoptiles
Effectiveness of indoleacetic acid, indolebutyric acid and naphthaleneacetic acid during adventitious root formation in vitro in Malus ‘Jork 9’

Thanks for your clear-cut mention.. "We don't definitely know yet whether the pathways of two auxins (I take indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) here) are exactly same or not".

Yes I could not imagine this question is going to be very broad because practically it requires experimental record for each compound... such as maybe auxin-1 (for say), auxin-2, 3, 4 work exactly the same but someone found auxin-10 is working differently. and this way broad variation could exist within other-classes such as gibberellin, cytokinin etc. However it is a very new information to me, that working of all plant-hormones of 1 class could or could-Not be the exact-same. It is the answer which I'm looking for.

I was selected that +50 without any sort of hesitation, but it is telling me to wait for more 3 hours.


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When is a DNA sequence a gene?
I am a newbie is DNA sequencing and BioInformatics. I am writing a school project that determines whether a DNA sequence is a gene or not using a Machine Learning Algorithm, Hidden Markov Model. After understanding the the algorithm, I now want to know when we can say this particular DNA sequence is a gene. Any help or pointers would be appreciated. Thanks

This question is too broad. From the [help/dont-ask]: Your questions should be reasonably scoped. If you can imagine an entire book that answers your question, you’re asking too much. Entire books have been written on HMMs and other algorithms for finding genes, depending on the exact situation. Please [edit] your question and narrow it down to one particular circumstance.

We can devide algorithms for protein-coding genes in eukaryotes in two main categories:

Extrinsic, these algorithms rely on the comparison with external data sources,  such as comparing genomes
Intrinsic, I suggest you are more interested in this one when you acctualy want to predict gene coding regions on your own (If I'm wrong I will further explain extrinsic methods). The intristic methods are based on ab into predictions.

I will continue on Intrinsic methods, so what can we use to identify coding genes in the sequence. Ofcourse we need to know the charasticts of those coding regions:
Most of the time we see CpG Islands(regions of a higher than expected occurrence of CpG dinucleotides over a patricular region).

About 70% of human promoters have a high CpG content (Wiki)

Those CpG islands are important for the regulation of gene expresion.

the basics of a coding sequence are the promotor, introns and exons.
you are probably familiar with the fact that a mRNA has to be spliced in order to cut the introns (non coding regions) out, this is done by the splicesome wich recognizes special sites where it can cut, So you can search for these sites in your DNA sequence.  I will summarize some points about the coding regions here:

CpG Island near the promotor
splice sites for splicesomes
Start and stop codons (I hope you are familiar with these)

There are more things to consider but I would to suggest to look at the algorithms of these programs: GENSCAN, FgeneSH, GeneMark, Xpound and to read this atricle which is about identifying the protein-coding regions

This is in general not a totally solved problem. How difficult it is will depend a lot on the exact nature of your problem. For instance:
1) Are you working in a eukaryotic organism, or in a prokaryote? Most bacteria lack introns - this makes finding genes much easier, you can just look for start codons followed by regions with no stop codons - open reading frames or ORFs
2) Are you using other data sources as well? RNA data, e.g. mRNA sequences, make it much easier to find genes. Comparing to other organisms also helps a lot.
3)Do you only want coding genes, or are you interested in noncoding RNAs as well? Finding these is much more difficult. Finding very small coding genes is also very hard.

You are right his question is quite unclear

Sorry if my question is not clear. I really have no idea about how wide the subject in question is. I am a student just trying to implement the HMM algorithm to find whether a DNA sequence is a gene or not. I have successfully been able to determine if its from a CpG island or not. So was confused whether if a DNA sequence is from CpG Island then its a gene.


text:
Mass Spectrometry (proteomics): How isotopes can be used to to determine charge of the peaks?
I'm trying to understand how isotopes can tell me something about the charge of the different peaks. This pdf file mentioned the following about isotopes in correlation with the charge of the peaks:

Isotopes
  If the mass spectrometer you are working with has sufficient resolution look at the isotopes, a singly charged ion will show isotopic peaks that differ by 1 mass unit, a doubly charged ion will show peaks that differ by 0.5 mass units and so on. This is another way to deduce the charge state of a peak and thus the mass.

So let's suppose the spectrometer has a sufficient resolution to look at the different isotopes. It's not really clear for me at which peak I have to start. So to summarize my questions realted to this topic:

Which peak do I have to look at when determining the charge based on the isotope distribution?
Why would the peaks differ 0.5 mass units (see above)?

update

source: http://mascot.proteomix.org/help/mass_accuracy_help.html

When looking at the above graph, there is a difference of 1 amu between the different peaks.

What do the isotopes have to do with the charge?
What does this charge (and isotope distribution) tells us about the peak on which we zoomed in to create the above graph?

It's not clear whether your second quote is talking about mass, charge, time of flight (which is not measured in all MS systems, only TOF ones), or a ratio of two of those parameters. Also, is this single or tandem MS?

The source says it's about ESI @MattDMo, I'm not really into this subject so I can't clearify it that much...

I happen to work with a bunch of people using nanospray LC-MS/MS for protein sequencing and analysis of post-translational modifications, so I'll forward this question on to them and see what they think.

Would be great! @MattDMo

@RickBeeloo; the first article is referring directly to TOF analysers in your quote. It is irrelevant to your question and should be removed.

If you have an ion of mass 100 and charge 2, the m/z ratio (let's exclude the root) will be 100/2=50. If you have isotopes, then you expect to find several peaks for a given fragment. For example, the masses of different isotopes of the same molecule could be like: 100, 102, 105 and 107. In this case the spectrometer will detect four peaks, instead of one, for the same molecule (will look something like this): 100/2, 102/2, 105/2 and 107/2. The charge of all that peaks is the same.. it's only the mass that differs.
The page you linked simply makes an example, "singly charged ion will show isotopic peaks that differ by 1" example m=10 z=1 m/z =10, for the isotope m=11 z=1 m/z=11 (difference of 1). If you have a doubly charged ion m=10 z=2 m/z=5 and for the isotope will be 11/2=5.5 (difference of 0.5).
So, if you take the spectra of a compound and you see the isotopic peaks having a distance of 0.5 among each other, you are looking at a doubly charged ion, if the distance is 1, it's a singly charged ion.
What do the isotopes have to do with the charge?
Given that the isotopes peaks are around 1 units far from each other, you can conclude that the ion you are looking at has 1 charge.
The last question is not clear to me.

That's exactly what I thought until I read the givin citation that isotopes can be used to determine the charge of ions in the spectrum @alec_djinn

Do you have a spectrum example of this to clarify what you are suggesting? alec_djinn

Here you see the spectra of a molecule having 2 positive charges, the zoom-in picture on the right shows how the peaks of that specific compound are 0.5 units distant from each other.

If the ion has only one charge, m/z=m , since there are no "half masses", the isotopes can differ only by full units of mass (+1, +2, +3 ...). To explain a difference of 0.5 units in an m/z chart, z must be 2! It's not the mass that is 0.5.

Thankyou for your effort! Can you please answer the questions beneath my update. If I get those two questions clear I think I'm done and can mark your answer. (answer them in your answer please) @alec_djinn

I've changed the order of your questions so that the answers follow from one another.

What do the isotopes have to do with the charge?

The presence of isotopes has no effect on the charge of the molecule. The physiochemical properties of the molecule and how the MS has been setup dictate how molecules acquire charges.
This is important as methods which utilise isotopic labelling rely on the presence of isotopes in molecules having no effect on their physiochemical properties. Secondarily, life would become untenable if the incorporation of isotopes altered the properties of proteins (see below).

Which peak do I have to look at when determining the charge based on the isotope distribution?

The m/z of the isotope peaks provides information about charge so you use the spacing between isotope peaks. It is important to use the most accurate measurements, which will be the strongest peaks, to calculate the mass difference. There is no need to use the monoisotopic (M) peak which in some cases will not be present.
~ 1.1% of the carbon on the planet is C13 so on average in biological molecules 1.1 out of every 100 carbons will be the C13 isotope. Therefore, as biological molecules get larger C13 will be incorporated more frequently and the chances of measuring the monoisotopic peak reduces.

What does this charge (and isotope distribution) tells us about the peak on which we zoomed in to create the above graph?

Lets assume the m/z difference between the monoisotopic peak (M) and the isotope peak with 1 isotope per molecule (M+1) is; 1086.55 - 1085.55 = 1
We know that the mass for the isotope is ~1 so z must equal 1 when the isotope peaks have a difference of 1 m/z.

Why would the peaks differ 0.5 mass units(see above)?

Let's assume we're working with the same molecule as above (M = 1084.543) but it is  doubly charged. In this instance it will have an m/z = 543.778 and the first isotope peak (M+1) will be measured at 544.278 m/z.
We know that m = 1 when a single isotope is present so the difference of 0.5 m/z => 1/0.5 = 2. The charge (z) is 2.
Note that every charge adds a proton at 1.007276 mass units to the monoisotopic mass of the charged molecule. However, when we talk about the monoisotopic mass of the molecule we don't want to include protons. That is why M = 1084.543 rather than the 1085.55 m/z (and mass) of the singly-charged molecule that was shown in the image above.

Thankyou great explanation! I still have a question, let's assume I need to anlyse a spectrum by hand. I first have to look at the charges of the ions (thus peaks) to determine the molecular mass right? but how can I determine the charge of a peak? I know I can look at the spec and see if there are peaks with half the mass so I know they are doubly charged, but are there other methods? @Michal_A

No worries. The question(s) about MS/MS should probably go in a new question. The details depend on how the fragments were produced and the detector that was used. Mascot provides good details about fragmentation.

Thankyou I appriciate your help! I posted a question which is related to spectra analysis http://biology.stackexchange.com/questions/52034/mass-spectrum-analysis maybe you are interested answering this one @Michael_A. Feel free to edit this question because as I said earlier I'm not really into this topic but really want to understand it.

OK, I've edited your question to exclude references to calculating "t" as it was based on a misunderstanding of the original paper. I think the question is clearer/better without it.


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Does Goryaev's chamber have the same grid layout as the conventional counting chamber used in the West?
I'm translating a Russian biotec text where some cell counting operations are mentioned. The piece of equipment the authors mention in this context is "Goryaev's chamber" (камера Горяева):

We discarded the supernatant, washed the cells with DPBS twice (suspended and centrifuged them for 10 min at 200 g), then diluted with 10 ml of ADCC assay medium and assessed the concentration and viability of the cells in a Goryaev's chamber.

Is a Goryaev's chamber any different in terms of its counting grid layout from the conventional hemocytometer chamber described in Wikipedia?
I would like to translate the phrase simply as "using a cell counting chamber" or "using a hemocytometer". The Multitran dictionary does offer these words as possible translations, but it occurred to me that Goryaev's chamber might differ somewhat.

From the description at http://cldtest.ru/hdbk/chamber
It appears to be functionally the same device, except the only the smallest square are marked (0.25 nL and 4 nL), and the total capacity is 90 nL instead of 100 nL. A hemocytometer could be used in place of a Goryaev's chamber (though not necessarily the reverse).

Welcome to the site, Eliane!


text:
Potentials between endolymph/cytoplasm and endolymph/perilymph
I am studying for an exam and there is something I can't seem to understand. My textbook says that the endolymph contains 150mM potassium, 2mM Na+ and 130mM Cl-. The perilymph contains 5mM potassium, 140mM Na+ and 110mM Cl-. "Thus" the electric potential between perilymph and endolymph is +80mV (endolymph being positive).
I can see that there are chemical gradients but why is the endolymph so much more positively charged than the perilymph?

I've already asked this question before and it was closed as a "homework question", which I would need to give suggestions on myself.
However, I seriously don't know what to suggest because I do not have the faintest idea how the endolymph can be +80mV as compared to perilymph, although the listed ions suggest that the surplus of positive charges is higher in the perilymph. I would love to make suggestions but I honestly don't have a clue.

Thank you in advance!


text:
Why are adults so suceptible to dizziness?
I have a child and she, like pretty much all the others it seems, loves spinny rides in the park. Adults often can't stand them.
In fact, I recall going from loving to hating dizziness over the space of about 3 years, at about the beginning of puberty.
Why do adults react more badly to dizziness than children?

Do you have any data to support your assertion "adults react more badly to dizziness than children" ? Because that could be just your own experience, not a general fact per se.

@alec_djinn Well, I know this isn't exactly what you were going for, but when you think about it, if you ask most adults, they'll tell you they don't really like being dizzy.

I found quite opposite: when I was kid, I was probably more sensitive to dizziness on rotation, and vomited easily. But in adult-age I'm much less sensitive to dizziness in rotation, and doesn't vomit in that so easily. but seemingly the direct amount of dizziness is probably as same as childhood.

Maybe than adults the childrens are less worried about dizzy feeling (and more enthusiastic to rounding rides)... so maybe they report it a less. Also; maybe kids habituated in it for daily basis got desensitized... like professional Katthak dancers (https://en.wikipedia.org/wiki/Kathak)


text:
What species is this bird?
This bird is a frequent "visitor" at a lake south west of Berlin, GERMANY.

For more pictures here's a link:
https://goo.gl/photos/ADVSZwbDQUpbomCBA

It's a BLACK KITE (Milvus migrans). I bet you took the pics this summer because the great majority of the population is in Africa at the moment.
It is a black kite because:

rather uniform dark brown color
squared tail (it form a shallow v during gliding)
uniform underwing color and lighter head is a shared with marsh harrier but the absence of darker patch around the eye, the dark shoulder and 6 digitated primaries assure us is a black kite.

Here is a picture for reference:


text:
Does food really give our bodies the energies that we have determined by burning them in the lab?
You are likely to have come across numbers like sugars 17kJ/g (4kcal/g) as the energy supposedly available to our bodies after eating. Yet these values have been determined using very artificial means, typically lighting up food with a red hot iron in a steel chamber at high oxygen pressure.
Many historic energy values have been proven wrong in the past. For example, salad leaves had zero calories in many historic energy tables before we realized that bacteria in our gut can break them down and we in turn can break down bacterial products, gaining back part of the chemical energy of the plant.
Are you aware of any research that has determined the energy value of different foods in more natural conditions, ideally in humans? I expect some calorie values to change from those determined by the bomb calorimeter, don't you?

The device you refer to is a bomb calorimeter. Inside one of these, a sample of material is completely combusted. Typically, the heat from the combustion warms a measured mass of water and the rise in temperature is used to calculate the Calories/Joules in the material.
Of course our cells don't ignite food and burn it to completion. Even if they did, some of the heat from the process would escape collection. Cells use the process of cellular respiration to harvest the energy. The basic version of cellular respiration describes the utilization of glucose to create ATP, by far the most used substance to power the energy needs of the cell. Here's just one source that takes you through the calculations of how efficient this process is: http://www.tiem.utk.edu/~gross/bioed/webmodules/ATPEfficiency.htm
So, at least for the very common sugar glucose, only about 40% of the total Joules, as measured in the calorimeter, end up as ATP. Most other food substances we use for energy share much of the same chemical pathway as glucose. I haven't seen calculations of their efficiency but suspect it would be roughly similar.
One of the most basic and important lays of physics is that no transfer of energy is 100% efficient. (Read more here: https://en.wikipedia.org/wiki/Energy_conversion_efficiency ). The remaining energy in the glucose that was not converted to energy in ATP is "lost" as heat. By lost, it is meant that it's not avaible to do any useful work other than heat us up. Of course, being homeothermic ("warm blooded") animals, that's useful too.

The U of Tennessee link you sent is great. They propose a very simple calculation that gives a good first approximation. Energy captured in ATP divided by theoretically available energy from glucose combustion ~ 50% after correcting for concentrations.

But that's does not yet take into account the energy required to metabolize glucose. Most of us get our glucose from polymers, so we need to make enzymes to break them down. Then we need to import and ship it to the cells that do the chopping; more energy required. Then in the cell that gets that molecule of glucose, the glycolytic enzymes don't come for free, right? What would be left of the 50% efficiency estimate when all these expenses are taken into account? 25%, 10%,..?

It's true there are a few steps in glycolysis that require energy but, in subsequent steps, this investment is returned. The calculations include this, they are a net value of the process.  As to parsing out the energy required to produce the enzymes involved, and to manufacture mitochondria to govern most of this energy harvesting, I've never heard of anyone attempting to calculate this. All of that is generally included under the category of "what we need the energy for".

I think there are two different things you are asking about.
The first is the standard enthalpy of combustion, which is indeed measured more or less as you describe. There's absolutely no problem with that, because the total energy released by the metabolism of glucose to CO2 is exactly the same as released by combustion. On the way down the energy slope you might even use some of it to make ATP and actually do some "work". There might be some small corrections needed (you run at 37C and not at 25C for example) but no matter which way you take, turning glucose and oxygen in carbon dioxide and water will release the same amount of energy. And remember, we need a lot of this energy just to keep warm, so the waste heat in metabolism is not really a waste.
The second part is a bit more complex, when you're talking about food. Here the bomb calorimeter part is a bit misplaced, because most foodstuffs will be analyzed using other techniques to determine the amount of carbohydrate, fat and protein. Then they'll do a calculation to get the number of calories in your food. This should get you quite close to the real number of calories, as stuff that's not digestable by humans is not counted. Regarding the salad bacteria: I'm not sure if they put it on the labels, but we know whether or not certain fibers will be metabolized, and you could take those into account as well if you wanted. It wouldn't make much of a difference though, almost all of the fiber we consume is coming out the other end.
If you want to know more, you're getting into a swamp of definitions and standards. For example you could skim this FAO report:
http://www.fao.org/docrep/006/y5022e/y5022e03.htm#TopOfPage (chapter 2 METHODS OF FOOD ANALYSIS)
http://www.fao.org/docrep/006/y5022e/y5022e04.htm#TopOfPage (chapter 3 CALCULATION OF THE ENERGY CONTENT OF FOODS - ENERGY CONVERSION FACTORS)
This shows that people are working hard on the problem you're posing, using a wide variety of approaches. It shows that every method has its problems, but also that all the values are quite close to eachother.

Hi VonBeche, sure the enthalpy of combustion of glucose is per definition constant, but it's of course more interesting to know what fraction of that potential can be captured by our bodies for its own purposes as in ATP, NADP, and the like. It also probably varies between individuals how efficient this capture is. And it probably even varies in the same person over time. I'd venture a guess that we recover more from food if we are fasting than if we have just had too far much to eat. I'll check out your links. Thanks.

That's the 40% of the other answer, and also that will be roughly constant (there are only so many pathways). You might just "burn up" the ATP in some cases (in brown fat for example), but the glucose isn't going anywhere without your body getting all the products from glycolysis (or whatever pathway is used).


text:
How do nasal and aural passages connect?
I have had a bad flu with a lot of congestion.  My husband suggests a way to clear my stuffed ears is to pinch my nose shut then blow air through.  Sometimes that helps, sometimes there's just too much congestion.
What is happening exactly when I do that?  I've looked at diagrams of nasal and aural passages, but it's not clear to me what's happening when you block the nasal passage and then blow air through.  I would like to know exactly what the passage of air/fluid is.
Also, is it a bad idea to do it?
Thank you.

The eustachian tube connects the nasopharynx to the middle ear, on each side. The (naso)pharynx is basically the back of the mouth, and the middle ear is a cavity behing the eardum.
https://en.wikipedia.org/wiki/Eustachian_tube
It is normally closed when there is no pressure difference between the middle ear and the nasopharynx, by extension between the middle ear and the air around one. Its function is to avoid a ruptured eardrum that could be caused by such difference in pressure. (This could be the case when ascending a mountain, or diving underwater, where the ambient pressure drops or increase, but not the pressure inside the middle ear)
What you are doing is closing all passages for the air to flow out (mouth and nose closed), yet trying to blow it out : this artificially increase the pressure and opens the tubes. While it is usually a passage for air, if there is a fluid buildup it could flow through it too.
Whether it is safe is a more of a medical question, which would be better suited for your physician.

Good answer, but please do not provide any sort of medical advice on this site. Instead, encourage them to ask their physician.

Thank you very much for your very helpful answer, much appreciated.

The Eustachian tube, also called the auditory tube (or canal) connects the middle ear to the nasopharynx (the back of the nasal cavity):

From Brigham and Women's Faulkner Hospital
Here is where it connects:

From Wikimedia

+1'd for good diagrams. The second diagram shows the "entrance to auditory tube" at a position which could not be seen through the mouth unaided. Is that?

@AlwaysConfused that is correct. The nasopharynx is in the back of the nasal cavity, and the opening of the auditory tube is some distance above the soft palate, so there is no way of seeing it through the mouth. The back of the mouth is called the oropharynx (oro- being derived from oral). Pharynx is a general term for the tissue at the back of the throat, stretching from the nasal cavity (nasopharynx) to the mouth to the larynx (laryngopharynx) just above the split between the esophagus to the stomach and the trachea to the lungs (which actually contains the larynx).

Thank you very much for these wonderful diagrams, very helpful in allowing me to visualize it.  Thank you.

@user26702 if you are satisfied in an answer, you could accept that by click on tick mark


text:
Will omega 7 make it harder to produce high quality meat?
I heard from a medical show that Omega 7 makes it harder to gain weight, and was wondering if I would be be able to put on muscle better if I have sheep and pigs getting omega 7 through sea berry branches.

can you add some references/information sources? which medical show? is it published anywhere? etc etc

https://vimeo.com/107166478

No. The only sure thing about omega-7 is that the suppliers are making money.
There's no evidence that it's doing anything more than just being an unsaturated fat in humans. This make it extremely unlikely that it would do anything after you put it through a pig.

So if your trees are producing it, you will be making more money?


text:
Restriction enzyme digestion
A circular plasmid of 10,000 base pairs (bp) is digested with two restriction enzymes, A and B.  This produces a 3000 bp and a 2000 bp bands when visualized on an agarose gel. When digested with one enzyme at a time, only one band is visible at 5000 bp.
If the first site for enzyme A (A1) is present at the 100th base, the order in which the remaining sites (A2, B1 and B2) are present is -
(A) 3100, 5100, 8100
(B) 8100, 3100, 5100
(C) 5100, 3100, 8100
(D) 8100, 5100,. 3100
NOTE: This is a Kishore Vaigyanik Protsahan Yojana 2014 exam (stream SX) Question. I really couldn't understand the diagram shown in the solution, and my teachers were of no help either. The diagram in the solution is:

Examine the effects of Enzyme A on its own.
Enzyme A performs two cuts that result in 2 fragments that are 5000bp long.
We know that the first cut is made at the 100th bp.  Therefore the second cut is made at the 5100th bp (A2).
You can stop there and determine that the answer is C.  C is the only answer that states A2 = 5100.


text:
What is the mechanisms responsible for downregulation or loss of MHC-1 expression on the surface of cancer cells？
Downregulation or loss of MHC-1 expression on the surface of cancer cells generally have been thought to be involved in the mechanism of immune escape.
It seems to be very attractive but I don't know the mechanisms of downregulation or loss of MHC-1 at cancer cells. Would you tell me the molecular mechanism,

There is no single mechanism (as you'd expect, since there is no evolutionary relationship between different individuals' cancers).  The most common mechanisms are various forms of mutations, ranging from point mutations in single MHC molecules to large deletions of the MHC locus. Mutations in genes involved in antigen processing, that are not themselves part of the the MHC locus (e.g. TAP, b2-microglobulin), are also fairly common.  Epigenetic changes are also not uncommon.  There are several reasonably recent reviews, including

MHC Class I Antigen Processing and Presenting Machinery: Organization, Function, and Defects in Tumor Cells
Different regulation of MHC Class I antigen processing components in human tumors
The escape of cancer from T lymphocytes: immunoselection of MHC class I loss variants harboring structural-irreversible “hard” lesions

thanks for some reviews concerned with the topic.I will read them.


text:
Does the anterior primary ramus of T6 innvervate the Rectus abdominis?
Anatomy and Human Movement Structure and Function writes in the section about Rectus abdominis:

Nerve supply
  By the anterior primary rami of the lower six or seven thoracic
  nerves (T6/7 to T12).

What does "or" mean? Does it means that in some humans this happens and in some it doesn't?

Because muscle (mesoderm) and peripheral nerves (ectoderm) develop from different embryonic germ layers, the pattern of innervation is somewhat variable. The muscles are condensing from mesenchymal tissues more or less in place, and nerves are growing out into the muscle masses to innervate them. Because of this, the specific spinal segments that innervate muscles can vary somewhat. This is particularly true in the brachial and lumbosacral plexuses. In the brachial plexus for example:

Grayed out text for C5 in the median nerve and C7 in the ulnar nerve suggest variable contributions from those segments.
In this case, rectus abdominis is "always" innervated by at least T7 to T12. But sometimes T6 as well in some, but not all, people.

Does sometimes mean "in some people"?


text:
What winged insect is in this photo? Is it Axymyia furcata?
Posting on behalf of a neighbor who asked:

Can anyone identify this insect? It's about 3/8" long. There are, it seems, hundreds flitting low over our lawn. There were none 2 days ago.

This is the Northern California Bay Area Peninsula.

$\frac{3}{8}$'' is a weridly accurate measure so just to confirm, it was $\frac{3}{8}$ of an inch, that is 0.95 cm, is that right?

Yes, " indicates inches. So about 1 cm.

One concern is that they are swarming termites.

My neighbor submitted the photo to http://bugguide.net and it was identified as a sugar cane soldier fly,
"Inopus rubriceps"- Female
http://bugguide.net/node/view/1299782
They are from Australia and were accidentally introduced to San Francisco 50 years ago.  It feeds on grasses.

Great pictures.  First, fly or wasp?
In the second picture, under the head you don't see jaws of a wasp, but do see a bit of a tongue-like organ, like a fly.  Further down, you can see that there are only 2 wings.  Just below where the left wing meets the thorax, you can see what looks like a tiny wing or paddle.  That's a haltere, a reduced wing that vibrates to provide stability, like a gyroscope.  Flys have halteres.  Finally, in the first picture at the very end of the abdomen are 2 points.  That ain't a stinger, it's an ovipositor.  It's a fly, female, and from the size of the abdomen, gravid.
The closest I've gotten to identifying this one is Axymyia furcata http://bugguide.net/node/view/1216479.  Everything matches, as well as we can see from a photo, except the coloration.  Also, A furcata is associated with streams and is found in the north-east and north-central US, while, your bug was found on a lawn in CA.  For more information about A. furcata than you need, there is a master's thesis available:  http://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1882&context=etd.
I've looked at hundreds of fly pics to find the one I linked to above.  That's the only fly I found that matches the shape of yours.  Maybe it's a different fly within that genus, maybe it's just a color variation.
Their maggots live in rotten wood and decaying plant material, and the adults are mostly interested in more maggots, so this isn't a pest, just a neighbor.
Edit: furicata --> furcata, oops.

Can you fix furicata to furcata?  (I can't -- the edit isn't large enough.)