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What is positive and negative supercoiling?
Is the following correct?
Positive supercoiling  = the coiling of DNA helix (B-DNA) on itself during intesified coiling of the two DNA stands in right handed direction
negative supercoiling  = the coiling of DNA helix(B-DNA) upon itself during uncoiling of the two DNA strands performed in left handed direction?
I'm a little confused.

Think of positive supercoiling as twisting the loop clockwise from the top, while think of negative supercoiling as twisting the loop counterclockwise from the top.

Positive means left handed or clockwise supercoiling. It results due to overwinding of dsDNA and thus relieve the torsional stress. Whereas the negative supercoil is just the opposite of the earlier.

The image from the web book seems to be contradictory with the text and the video.
(a) is a left handed helix, so is negative supercoil, (b) is a right handed helix, so is positive supercoil.
Cheers

According to this powerpoint from the SIU School of Medicine:

Right handed supercoiling = negative supercoiling (underwinding)
Left handed supercoiling = positive supercoiling

And from this Boston University webpage:

If DNA is in the form of a circular molecule, or if the ends are rigidly held so that it forms a loop, then overtwisting or undertwisting leads to the supercoiled state. Supercoiling occurs when the molecule relieves the helical stress by twisting around itself. Overtwisting leads to postive supercoiling, while undertwisting leads to negative supercoiling.

And finally from wikibooks:

Positive and Negative Supercoilings

Positive supercoiling is the right-handed, double helical form of DNA. It is twisted tightly in a right handed direction until the helix creates knot.

Negative supercoiling is the left-handed, double helical form of DNA.

Although the helix is underwound and has low twisting stress, negative supercoil's knot has high twisting stress. Prokaryotes and Eukaryotes usually have negative supercoiled DNA. Negative supercoiling is naturally prevalent because negative supercoiling prepares the molecule for processes that require separation of the DNA strands. For example, negative supercoiling would be advantageous in replication because it is easier to unwind whereas positive supercoiling is more condensed and would make separation difficult.
Topoisomerases unwind helix to do DNA transcription and DNA replication. After the proteins have been made,the DNA template supercoils by the force to make chromatin. RNA polymerase also influence DNA strand to have two different supercoiled directions. The region RNA polymerase has passed forms negative supercoil while the region RNA polymerase that have not passed forms positive supercoil. By these processes, supercoils are generated.

In the following image from web-books:

 (a) Positive supercoils (the front segment of a DNA molecule cross over the back segment from left to right). (b) Negative supercoils.
This video, titled "super coil (positive and negative) formation of DNA" should help you visualize this.

@SanjuktaGhosh Does this help clarify it for you at all?

I read this topic from a book which cleared my doubts and your answer reassured it.Thank you.


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What are sex linked traits?
Which of the two definitions of sex-linked trait is correct?

Traits controlled by genes present on the non-homologous region of sex chromosomes are called sex-linked traits.
Bodily traits controlled by genes present on the non-homologous regions of sex chromosomes are called sex-linked traits. Here by bodily traits I mean traits that are not involved with sex of an organism.

I read the first definition in the book Competition Science Visionand also from Instant notes genetics (page 163).
The following is an excerpt from the latter

Sex linkage is not displayed by genes which map to a small segment of X chromosome, the pseudoautosomal region, the part of X chromosome that pairs with Y chromosome in meiosis.

The second definition is made up but sounds potentially intuitive to me.

What do you mean by "traits that are not involved with sex"? Do you mean traits that are unrelated to (primary or secondary) sexual organs?

Yes that is what I meant

I edited your post. Feel free to roll-back. If you agree that the format is much more pleasant to read than before then you can inspire yourself for future posts and try to always use a pleasant format for the readers.

The first definition is correct.
A sex-linked trait is a trait affected by a locus on a sex chromosome.
If you google sex-linked trait, you will find this same definition (not the exact same words) over and over again.
The definition of sex-linked trait is NOT restricted to traits that are not unrelated to primary or secondary sexual organs. Any phenotypic trait can be sex-linked as long as the causal locus is on a sexual chromosome.

"a locus that is present in individuals of only one sex..."  isn't that wrong? Genes on the X are sex linked and therefore present in both sexes

Yes, you are right that was wrong! I edited it. Thanks.

@Remi.b What are X-Y linked traits then? Are they what the book says, traits controlled by genes present on homologous regions of sex chromosomes?

yes, traits causes by genes present on NON-homologous (you said the opposite in your comment) sequence on the X or Y chromosome. In case you did not know the non-homologuous sequence of X or Y chromosome.

Sex linked traits are those controlled by genes on the sex chromosomes, regardless of whether or not they are related to reproduction. This can be the major (e.g. X or Z) or minor (e.g. Y or W) sex chromosomes.

"Sex linkage applies to genes that are located on the sex chromosomes. These genes are considered sex-linked because their expression and inheritance patterns differ between males and females." - link

Note. Most traits are polygenic thus some of the causal genes may be sex linked, and others on the autosomes. Phenotypic traits can therefore have varying degrees of sex linkage.

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Why did multicellular organisms evolve when a single cell can survive on its own?
Since unicellular organisms can survive, why would there be evolution of multicellular organisms?

Potential duplicate of Why would a single celled organism evolve to be multi-celled?

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Stability of DNA double helix conferred by base stacking
Our school textbook states that base pairs confer stability to the B-DNA double helix in two ways:
1) Hydrogen bonding between purines and pyrimidines of opposite strands.
2) "Stacking of one base-pair plane over the other"
It's the second point that I'm not able to understand. I did try looking it up on the internet, but I'm not able to find anything relevant in that regard.
So could someone please try explaining that second point to me?

When you carefully look at the structure of DNA helix, you will notice that consecutive bases are partially layered i.e. one base is "on-top" of the other base. Stacking is a chemical phenomenon in which the cloud of the pi-electrons in an aromatic molecule interact with that of the other. This interaction is non-covalent. Since the DNA nucleobases are aromatic molecules, they also exhibit stacking which stabilizes the structure of the DNA. A study by Yakovchuk et al. (2006) suggests that base stacking has higher contribution to DNA stability than base pairing. Sponer at al. (1997) found that there is no great difference between the stacking energies of B- and Z- forms of DNA helix.

In short, because of the pi bonds in aromatic rings, they're attracted to each other when stacked (or in several other conformations). Explaining is maybe better done by the Wikipedia page, but this is what you're looking for:
https://en.wikipedia.org/wiki/Stacking_%28chemistry%29
For a more in-depth look you could take a look at this article for example:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1360284/


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What kind of kale is this?
I'm from Pennsylvania and I used to get this kale all the time at the grocery store, but I moved to the West Coast recently and can't find it anywhere! It looks exactly like this photo:

Image source: http://www.specialtyproduce.com/produce/Kale_Purple_764.php.
I've seen this referred to as purple kale, salad savoy, and flowering kale, but I don't think any of those are 100% accurate. The purple kale I've found here is tougher and more bitter, with spikier leaves and a more reddish color, and it doesn't come as a bunch like this but as individual stems. Does anyone know exactly what this variety is called?

It's just a variant of kale, part of the genus Brassica. I think you'd call this particular variant redbor or purple, bluntly, but you could go further because kale is often classified by the type of leaf. So in your picture, curly 'redbor' or 'purple' kale.
This is your specific name: Brassica oleracea Acephala Group.
(just sort of look at wikipedia)


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Why does migration distance depend on log of molecular weight in SDS-PAGE?
I really want to know why in the result of SDS PAGE, log of molecular weight(MW) and migration distance (distance from the loading well) have a linear relationship. Why is it log(MW) instead of MW? Thank you!

A newer, related question: How does SDS-PAGE separate based on mass?

An SDS-PAGE standard curve of Rf vs LogMW is linear because the standard you're given is engineered to behave that way. An expanded SDS-PAGE curve would show that the actual graph is sigmoidal: Structues that are too large can't enter the matrix, and too small they pass right through. Your standard has taken into account the % composing the gel, and the size of the proteins which the standard consists of that ensure you get the linear data points on the semilog graph.
If we look at the raw data though plotted linearly, the graph isn't entirely linear. The data is much prettier, and trivial to convert back to MW if we log transform the MW. It's the same data, just mathematically transformed. Some more reading on it here.

Perhaps there is a mathematical derivation for this. I can't find it myself and when I am trying to derive I am getting something else.

@WYSIWYG  I don't think the migration distance is actually logarithmic in mass. The log function is just a simple curved function that fits the data reasonably well in practice, over the relevant range of values. I would expect distance to be proportional to some power of the MW. It's basically a kind of chromatography, so perhaps there is a derivation in analytical chemistry literature.

I think this is just an empirical formula that (approximately) fulfills the non-linear response of the relative migration distance (Mr) with the molecular weight (MW) - an observational rather than mechanistic explanation. The formula Mr ~ 1/(log(MW)) is equivalent to say MW ~ 10^(1/Mr), which is a simple exponential. The exponential function is the simplest solution to this non-linear problem, having the advantage of being asymptotic, that means that it can explain the fact that relative mobility values Mr are constrained between two fixed values, i.e. 0 and 1, for ANY molecule, no matter how large or small it is. If Mr = 0, 10^(1/Mr) predicts a MW -> infinity. If Mr = 1 (dye front), 10^(1/Mr) predicts a MW -> 1 (or actually -> 0 if we consider a parameter a in equation MW = a*10^(1/Mr)).
A linear model would fail to generalize to any MW, since predicted Mr values would not be limited within the given [0,1] range, plus the fact that behavior is really non-linear. (The intuition tells that the bulkier the molecule is, its chances of passing through the gel pores reduce exponentially, as the chance of finding pores 4x the size of the average one would not be half of those of finding pores 2x the size of the average, even though this is perhaps more metaphoric than real).

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Common mistakes when sequencing?
I've sequenced two genes of 15 dogs for SNP analysis. the chromatograms of one gene looked perfect but the ones of the second gene didn't look as good. To be precise, the chromatograms of one exon looked relatively good with only a few spots where the bases seemed unreadable. But the chromatograms of the second exon were full of that. So there must have been an error somewhere and my question is where this could have happened.
My hypothesis is that I simply made a mistake during the mixing of the chemicals at some point.
Further useful information: The error must have happened befor the first pcr since i checked the pcr product with a fragment analyzer and the bands were only barely or not visible. Additionally, I noticed that many imprecisions seen in the chromatograms were only found at either the forward or backward strand.
Here is an image of several of the chromatograms of the exon that didn't work:

Looks like a dye blob.  A better job of clean up might help.
https://www.nucleics.com/DNA_sequencing_support/DNA-sequencing-dye-blobs.html

You almost give the answer yourself: the PCR doesn't look good. This might lead to insufficient PCR product to base your sequencing on. If you might have done something wrong: repeat. Otherwise try a few different conditions to get a decent amount of DNA.
Certain pieces of DNA will just sequence better than others for the same reasons PCRs sometimes work better or worse, that's why the reverse sequences might look better.
I don't know what caused the strange effect in the middle of your chromatogram. It might be a starting artifact, but also the rest of the chromatogram looks quite bad indeed.

Since i only had very limited time, I couldn't retry. I was just interested in whether one could pinpoint the problem exactly but it doesn't seem so.

Just for fun you could look at the absolute signal strength (or the scale) of your sequencing results. Probably your sequencing results are a lot closer to the noise than for a correct sequencing run.


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Solunar theory of animal activity
Solunar theory, which states that animal activity in wild (fishes, deer) depends on position of sun and moon in sky.
Based on the solunar calender, hunters seek for optimal time for hunting fishes.
I am wondering that how solunar calender is developed from the sun's and moon's rise/set timing or from their positions in sky? For instance if I know the position of sun and moon in sky how would one forecast the animal activity timings of that day? OR the solunar calender is based on some statistical forecasting?
Thanking you.

by observation!! all organisms have circadian rythm but their behaviors are different. some are diurnal while some are nocturnal

Right ! But my question is more mathematical. I am interested in how we derive the animal activity forecast from the sun/moon data ?

If there is a pattern based activity, you can mathematically model it and make extrapolations so as correctly mentioned above, you make observations, gather data and model it. What mathematical formulations people use I do not know but would be interesting if someone could point to a source. there is a similar version of your question here (http://answers.google.com/answers/threadview?id=295970)

are you looking for the kind of charts that are provided on this website. http://www.solunarforecast.com/

No. The way they find the best day of the month.


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What is the difference between organelle membranes?
Cells and organelles are contained in lipid bilayers. I'm particularly interested in eukaryotic organelle bilayers and the biophysicochemical differences between them.
Many papers assume a difference in membrane characteristics and some like Anderson et al., 2007 have categorised the relationship between these characteristics and protein function in depth.
Do any reviews or comprehensive studies exist in the field that compare the thickness of the membrane, the rigidity of the surface, any differences in lipid entropy, or the overall charge inside and outside across different types of organelle membranes?

Are you interested in all types of membrane bound organelles? I am sure there are studies on membrane composition individually for different organelles. I guess you have to do the comparison yourself. I remember that there was an article that compared chloroplasts of different origin and one of them still retains the peptidoglycan cell wall; I'll find that and let you know

I am interested in the biophysicochemical differences between membranes themselves of membrane bound organelles. Generally I am more interested in the net biophysical differences, but any references are more than welcome.

Great question. Turns out, there is some information about it.
For example, consider following resource: Membrane Protein Lipid Composition Atlas. Published by University of Michigan, it provides information on, primarily, protein content of different membranes from different species, but also has a list of lipid content.
Just as an example, consider following difference between membranes of mitochondria in yeast:

Now, concerning your interest in biophysics. To my taste, starting with just bulk lipid composition is a good first approximation. Although you also want to know about lipid raft formation and density/distribution of proteins. Next step, probably, will be symmetry considerations, that is, difference between sides of same membrane. You can imagine membranes with same bulk composition, but because of different lipid position (in/out) properties will be different.
It seems you can assess raft composition based on membrane lipid composition. Membrane capacity also is a property of membrane content.
Following quick walk through this Google Scholar search provides even more links between biophysical properties and lipid bilayer composition. However, it might be challenging to find exactly what you are looking for.


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Can bacteria release free DNA into their environment?
Natural transformation AKA natural competence involves the uptake of DNA into a competent bacterium (for horizontal gene transfer or as a food source). My question is about where this extracellular DNA can come from. Typically this "free" DNA originates from lysed bacterial cells. Are there instances where DNA is released without lysis that other bacteria can uptake via natural transformation?
Note: I am not interested in bacterial conjugation because I'm specifically interested in extracellular DNA that can be internalised by competent bacteria.

Natural Transformation
The process of Natural Transformation (Lorenz and Wackernagel 1994) has a very huge importance in evolution of prokaryotes. Definition quoting from (Stewart and Carlson 1986)

Natural transformation is part of the normal physiology of the cell.
It is the only form of bacterial genetic exchange whose functions are
encoded on the chromosome, and competence is a heritable trait,
subject to selective pressure.

This is almost similar to our daily use artificial transformation. You need some chemical like $CaCl_2$ to cell permiabalized, some chelating agents like EDTA and DNA material. You can imagine naturally occurring cell encountering such conditions, like decrease in temperature in presence of certain chemicals and proteins.
This concept of one cell externalising, and another internalising DNA got stronger when researchers observed free DNA in culture media (Catlin 1959, Sinha and Iyer 1971).
The Creation of eDNA
The release of eDNA (extracellular  DNA) can occur via spontaneous excretion or autolytic action.
There are known mechanisms for the release eDNA like formation of blebs (Dorward and Garon 1990). This extracellular DNA production is affected by many physiochemical factors than biotic (Paul and David 1989). There are many in detailed reports which shows such DNA can be passed through cell wall without any cell damage (Hara and Ueda 1981). Half life of such eDNA in various environment is reported in following table from (Lorenz and Wackernagel 1994)

Now there are even more novel ways of production of extracellular DNA like in Neisseria gonorrhoeae secretion of chromosomal DNA occure via new type IV secretion system (Hamilton et al 2005). Not just experiments, mathematical models also shows novel role of such process in gene-level selection (Draghi and Turner 2006). I haven't touched upon uptake of these DNA, which itself has lot of literature and unique mechanisms like this.

This is exactly what I was looking for. Could I also add that in the 2004 Chen & Dubnau review, they discuss H.pylori having a mechanism related to the type IV secretion system for exporting macromolecules such as DNA.

Indeed. That (Lorenz and Wackernagel 1994) paper is very nice. You will get all sorts of references from that. Surprisingly, I hardly found any recent papers on this (after 2000). Is terminology changed or something ?

When I first "read" the Lorenz & Wackernagel paper (it's a chunky paper!) I thought it was mostly discussing the uptake machinery which is what I was interested in at the time. On a re-read it has an entire section on excretion! As for recent papers, there is the 2010 Burton & Dubnau review that rounds up a lot of the more recent studies. Particularly I noticed the FtsK/SpoIIIE proteins. These are pretty different systems to anything I'm studying though.

Good question, the only thing I can add is that in biofilms, although the DNA is released via lysis, the lysis is controlled using quorum sensing and effects specific subpopulations (Okshevsky & Meyer, 2013).

That is bizarre! Very interesting, but unfortunately doesn't help answer my question. There may be some information in the paper but unfortunately it's behind a paywall!

@GoodGravy You can find a copy of the paper here.


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Can Nanodiscs be used to study membrane energetics?
Nanodiscs have changed they way we can study the structures, insertion, and functions of transmembrane proteins. Below is an image of a nanodisc bilayer.

The key difference, as far as I can tell, over traditional liposome studies are that one can alter the lipid composition more easily.
Have any studies been achieved on quantifying energetics in these nanodiscs ie energy transfer upon insertion, or stability of the protein in the nanodisc etc?

Do you have any references for these? What peptides are they using to wrap around that disc?

The peptides are "an ideal α-helix" whatever that means... I came across this bibliography in my hunt that also seems to have a few papers on biophysics of proteins in this system. Perhaps one of them explains more about the anatomy of a Nanodisc.

Nanodiscs are very powerful technology for membrane protein invented in Stephen Sligar's lab at the University of Illinois.
A nanodisc is composed of a membrane protein, lipids and two monomers of a "scaffold protein". The most used scaffold protein is an N-terminal truncation of apolipoprotein A-1 (apoA-1), which is the primary protein component of high-density lipoprotein (HDL) particles. But because the size of the scaffold protein defines the size of the nanodisc, membrane proteins with different size could require different type of scaffold protein.
The reconstitution of a membrane protein into a lipid disc is a self assembled process. The reaction consists in mixing the membrane protein solubilised in detergent with lipids (that can be chosen according to the protein) and the scaffold protein. Removal of the detergent (using for example Bio-Beads™ SM-2 Resin) starts the self assembled process and the nanodiscs are created.
Nanodiscs provide an environment where membrane proteins are stable and compatible with aqueous environments in a native-like phospholipid bilayer. The aquesous environment makes membrane proteins compatible with analytical methods that have primarily been limited to investigating soluble proteins. The lipidic environment, that can be chosen and optimised, keeps the membrane protein stable, monodisperse and active. The stoichiometry of the protein can also be controlled.
Compared to nanodiscs, liposome are large, unstable and difficult to prepare with precisely controlled size and stoichiometry.
Several membrane proteins have now been reconstitued into nanodiscs and used for different type of studies, for example for studying ligand affinities  and kinetics, for NMR, for studying protein association state, signalling properties, and ion channels (http://molsense.com/applications/trubind-at-work/ion-channel-inhibitors/).
http://www.sciencedirect.com/science/article/pii/S0014579309007960

A very thorough background to nanodiscs. Perhaps you could expand or provide a reference to the kinetics experiments. I am unclear if you are talking about ligand kinetics, or protein-bilayer kinetics.

Here are some examples: studying the kinetics of ligand binding to membrane protein (http://www.ncbi.nlm.nih.gov/pubmed/25935416, http://www.ncbi.nlm.nih.gov/pubmed/18616345), studying protein-protein interactions (http://www.ncbi.nlm.nih.gov/pubmed/20804721) and studying protein-lipid interactions (http://medx.mech.northwestern.edu/publications/papers/197.pdf). I think nanodiscs are a really powerful technique and as prove there are many really interesting publications around!


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How does ethanol interact with insulin?
I know that ethanol increases insulin secretion--could someone explain why?
All I have found till now is experimental data analyses.  I am interested in mechanism of alcohol consumption.

Consumption of ethanol? Injection of ethanol? ethanol secreted by the body? Could elaborate a bit and possibly give us some links to your claim of "ethanol increases insulin secretion"?

@Manishearth Thank you for your answer! Here is my source of information: http://www.medicinenet.com/alcohol_and_nutrition/page4.htm , and I am interested in mechanism of peroral alcohol consumption.

@permeakra Thank you for participation! I won't be against, if my question will be moved to biology SE, if it will more likely receive answers there. As you see, that is my first question here, so I am not sure about local foundations.


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What percentage of protein isoforms have different functions?
I am looking for studies on how many protein isoforms have different functions, preferably in human. We know that a great many, if not most, of human genes are alternatively spliced and that many produce different protein isoforms. Has anyone looked at how many of these isoforms have different cellular functions? If someone could point me to a published paper, that would be great.
If no such study has been made, can anyone recommend a database from which this information could be extracted? GeneOntology is gene based so the information cannot be found there. Genes will be annotated to specific terms, not their protein isoforms. Also, I would need to be able to do this in a high throughput manner, I am not interested in specific proteins but in what percentage of all isoforms have different functions.
Ideally, I would like to be able to extract, for every human gene, the list of the different protein isoforms it encodes and whether their functions differ, or at least what those functions are.

I don't think isoform specific information is in a database yet. Testing isoform specific functions is tricky since not all isoforms are expressed in all cell types. Recently have researchers been looking at splicing genome wide and figuring out which splice forms are in certain cells (differential exon usage in RNA-seq to infer different isoforms). As you have encountered, functional info is typically summarized by gene. Swiss-Prot mentioned by @MattDMo is one of the few db where info is hand-curated. If isoform specific function was annotated, it would probably appear there first

It seems that most functional annotation these days is inferred from sequence similarity to previously annotated genes/proteins: this is certainly true of high-throughput functional annotation. It's hard to know how many layers of inference there are between your query sequence and an actual experiment verifying the (possibly tissue- or condition-specific) function of a gene/protein. But alas, I digress...
One confounding factor for is that alternatively spliced isoforms share a lot sequence in common, which means that they might share best hits when searching against a database of annotated transcripts and end up getting assigned the same GO terms.
But as others have mentioned, I think the biggest limiting factor you will encounter is the low-throughput step: in many cases the experimental work required to characterize the functions of alternative isoforms simply has not yet been done.

Yes, that is the problem in a nutshell. Most (all AFAIK) high throughput experiments tag genes, not proteins and assign function to the gene as opposed to a specific isoform.

I'd tend to agree there's very little data on this, esp given how many isoforms there are.  I believe that even some cases of pseudogenes may have function as a protein.  I'd bet that most of them have some unique functional aspects.
I think we'd all agree we can't prove that they do in all cases, but let me sketch out how these different functions might arise or are known.
Protein Isoforms usually come from two causes.  The first being that there are two very similar copies of the same gene, from a gene duplication event.  The second coming from alternative splicing.
Alternative splice isoforms are often missing or adding a few amino acids - the sequence is different.  This can be from truncation of a large portion of the protein such as the leptin receptor. Leptin receptor has two full length variants that have different expression patterns at different temperatures and import leptin into the cell at different efficiencies.  Leptin also has several short isoforms, where only a short portion that faces the cell interior is produced.  These variants compete with the full receptor to modulate the cells sensitivity to leptin.
As you can imagine, mapping all this out in just one case took years of work. Complete characterization of all human isoforms would take a long time.
Isoforms from gene duplication have many of the same properties as splice variant isoforms; they can have completely different regulatory machinery - popping up in different biological states than the main gene and they can vary in sequence a little bit or a lot.  It has been implied that these gene duplicates persist in the genome because they quickly find a new niche role.  This paper shows that 30% of 195 new genes that have shown up since two strains of fly have diverged are necessary for viability.
Evolution doesn't let genes sit around because they are completely identical; they can be removed as easily as they show up, only differential function will keep an isoform in the mRNA repertoire for a prolonged time.

Thanks shigeta but I would not call proteins coded for by different genes isoforms (and neither does the wikipedia page you linked to, it talks about alleles of the same gene). They are paralogs or orthologs depending on their evolutionary history. I would only use isoforms to describe products of the same gene. I am also assuming that most isoforms have different functions, hence my question. I am looking for data to back that assumption up.

I would take a look at UniProt to begin with. It's my go-to whenever I need to look for isoforms or functional data, so it should help you as well. You could start by comparing the information in Swiss-Prot to TrEMBL, which are manually and automatically annotated, respectively. One issue that I've come across in my research on isoforms is that there often isn't a great deal known about them, as studies may have focused on just one or a few out of many possible. One way to get around this could be to use structure/function predictions based on sequence, then try to predict variations by looking at what's added or missing in the various isoforms.
I hope this helps...

Thanks, but I'm interested in whole proteome data. Uniprot has no parseable information on isoforms apart from how many a given protein has and their sequence. Sometimes the function field has some information, sometimes it doesn't.


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What is this hummingbird-like insect?
I just saw this insect collecting polen from bougainvillea blossoms on the Greek island of Skyros, in the Aegean sea. For future reference, this is in the middle of August and the sighting was at around 17:00.

I posted all 4 photos I took since the rude little thing didn't have the decency to sit still to let me get a clear shot. I'd say it was about 2cm long, certainly no more than 3.

Had you asked this earlier, you would have gotten 40 points: http://biology.stackexchange.com/q/50432/3340

@WYSIWYG aww, dang! :P May as well close as a dupe then.

Hummingbird hawk-moth (Macroglossum stellatarum). For what it's worth, there are also a variety of sphinx moths around the world.
Here's a photo from the linked Wikipedia page. As you can see, it looks very much like the one in yours:


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Does zygosity have meaning for mitochondrial variants?
I am working on a system that annotates variants in human DNA sequences. One of the pieces of information reported is the zygosity of the variant. I noticed that mitochondrial variants are also shown to be either homo- or heterozygous.
How does that make sense? Does it make sense? As far as I know, the mitochondrial DNA is just a single, circular DNA molecule. So I can understand considering all mitochondrial variants heterozygous, by definition. I could also accept that one could think of them as homozygous by definition. I just don't see how some variants can be homo- and others heterozygous. Am I missing something or is the annotation system I'm using not making sense?

Since all the mitochondria in a cell (I'm thinking mammalian, through it may apply to others) are derived from the mother, mtDNA should all be homozygous - in fact, I don't really understand how zygosity even makes sense when talking about mitochondria. I suppose it's possible that some mtDNA in a cell is damaged or mutated, likely through the action of ROS, so there theoretically could be two (or more) "alleles" in a cell if there is a mixed population of mitochondria. I don't know quite enough about mitochondrial genetics to make this an answer, though. Just my 2 cents.

@MattDMo ah, I hadn't considered mized populations, that makes sense. I guess it's theoretically possible to have ~50% of mitochondria having a given variant but I would expect that to be vanishingly unlikely. If there is a variant specific to a given mitochondrion, I don't really think there would be enough sequence data to be able to call it. I guess my main question is whether mtDNA is somehow doubled in a way that makes zygosity even remotely relevant.

as far as I know, the only doubling is mtDNA replication just before a mitochondria undergoes fission. You probably want to verify that, though.

You abosolutely can have mixed populations of mitochondria in a cell (it is in fact very common). Therefore when you sequence the mtDNA you will get a completely variable percentace of reads containing a variant from close to 0% to 100% (there is a lower limit based on the quality and read depth of the sequencing data).
You can't consider the variants to be heterozygous or homozygous as conventional zygosity doesnt apply. Heteroplasmic and homoplasmic are the terms which are used.

So how would I, or a variant caller, call one or the other? Some arbitrary threshold like ">70% reads carry the variant so it's homoplastic" and "~50% carry the variant so it's heteroplastic"? Is there some literature you could point me to? Your whole answer could really benefit from some references to back your claims (I know your claim is true, but you're not supporting  it in you answer). Still, it sounds like it would make more sense to just look at allelic balance values and forget zygosity for mt vars.

Welcome to Biology.SE! Your answer would be even better if you included supporting references (primary literature is best). ——— You might also want to go through the [tour] and then consult the help pages for additional advice on [Answer effectively] on this site. Thanks!


text:
Does blood clot reduce blood flow?
I read that blood clot reduces blood flow from few website and from doing an A level biology question; and if this blood clot is formed in pulmonary thrombosis, this can reduce gas exchange in lung.
However, how are we so certain this is true? If there is a blood clot, then blood pressure around that region increases I believe thus implying the blood will travel faster in that region? If so, then we can't firmly conclude blood clot will reduce blood flow as although blood clot will reduce the lumen of the vessel, the blood will also be travelling faster.

A blood clot can nearly completely or completely block an artery, in which case the blood flow will be reduced or stopped.
How do we know this?
Pulmonary Embolism (Merck Manuals):

Pulmonary infarction is when some of the lung tissue does not receive
  enough blood flow and oxygen and appears on imaging studies to die due
  to blockage of a lung blood vessel by a pulmonary embolus.

An embolus is a blood clot that usually develops in the leg veins in individuals with deep venous thrombosis, detaches and travels to a certain pulmonary artery and blocks it.
Similarly, atheroma (atherosclerotic plaque) that builds up within the artery and only partially blocks it, can reduce the blood flow to the target organ. For example, a partial blockage of a coronary artery can result in decreased blood supply to the heart and consequently in angina pectoris or myocardial infarction. It is then the investigation called coronary angiography that can show that a certain coronary artery is partially blocked.
When a clot interferes with blood flow (Harvard.edu):

In venous thromboembolism, a blood clot slows or stops the flow of
  blood through the veins...

Thank you for the answer, but I'm not sure if your last paragraph answers the question as I understand that decrease in cross sectional area can potentially decrease the flow rate (as there is a smaller cross section for blood to travel through) but this decrease can be compensated by an increase in fluid velocity thus the end result is that flow rate is not changed - this is the idea behind the continuity equation in physics. But I get your argument in the first few paragraph.

I deleted the last paragraph and added one new source. Also, look at the first image in this coronary angiography article and you'll see that a part of the coronary artery is narrowed, not completely blocked, so the flow of the contrast substance is not discontinued. But that narrowing results in decreased blood flow and hence in angina pectoris or myocardial infarction. So, it is a result from which you can conclude that the blood flow is decreased.

@BøbbyLeung This answer is correct. It looks like, though, you're looking for a physicsy physiology answer, though. I've supplemented this answer with some of the physiology in mine.

Given the context of your comment on @Jan's answer above, it looks like you're asking if the continuity equation, $\rho_1A_1v_1 = \rho_2A_2v_2$, applies to blood flow through a local vessel. The answer is that it doesn't, because the local vessel is not a closed system.
The continuity equation is derived from the principle of conservation of mass (see the earlier link) and requires that everything coming in at position 1 exit at position 2. Here, a blood clot, or specifically in your example, a pulmonary embolism, increases the resistance in one of a number of vessels in parallel. Blood flow is diverted to the parallel vessels with lower resistance, the ones without the clot. This is useful in a helpful clot at the site of injury as well as an unhelpful clot like a pulmonary embolism. Thankfully, a clot in an injured vessel has the ability to slow and finally stop the loss of blood. Again, this is allowed despite the continuity equation because there is an alternative path. Blood can either flow out of the vessel at the site of damage, or flow through the vessel.
The fact that changes in vascular resistance are met with changes in flow is a principle used to beneficial effect in normal physiology, not just the response to a clot. Arterioles, for example, regulate flow through vascular beds as needed, by increasing or decreasing resistance.
There is a case, a saddle embolus, where there is no parallel path. Here, though, flow still decreases because the pump fails (and pressure is lost). The rapid increase in resistance cannot be compensated for by the heart, and sudden death results.
Generally, when applying fluid dynamic principles to blood flow and the circulatory system, you have to consider whether the assumptions hold. Generally, you can apply the continuity equation to portions of the circulatory system in series (e.g., the cardiac output of the right heart has to equal the cardiac output of the left heart), but there are still caveats (vessel walls are not rigid -- they have a capacitance).
These principles are discussed in Costanzo Physiology Ch. 4.

Thank you very much for the detailed answer. If you have time, could you please elaborate on why is the local vessel not a closed system? A sketch of it would be helpful.

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


text:
Why does atheroma contain thromplastin/tissue factor?
From my understanding, when the endothelial lining of arteries is damaged, atheroma is formed at the site of the damaged area. If the atheromas is ruptured, thromboplastin contained in atheroma is released into blood stream thus thrombus is formed after atheroma gets ruptured - this phenomenon is known as atherothrombosis. As a result, atheroma is characterised by its thrombogenic activity.
My question is, how come atheroma contains thromboplastin thus when it is damaged, thrombosis occurs? What was the source of this thromboplastin? Was it in the bloodstream? If thromboplastin was always present in the blood in which it entered into the atheroma during the formation of atheroma, why don't thrombosis occurs at the start when endothelial lining of the artery is damaged (without the need for an atheroma to rupture)?
I've read a couple papers and watched some videos on this topic. I've put one of my research below for reference to back up 'my understanding'.

Rupture of the fibrous cap will typically release all the semiliquid
  material from the central portion of the atheroma. Because this
  material contains thromboplastin, it will trigger blood clotting, and
  a thrombus will develop at the site of intimal ulceration.

Tissue factor is present in subendothelial tissue and leukocytes - in this case this would be within the atheroma since the atheroma consists of damaged endothelium.
Tissue factor's presence in the subendotheilum in general implies that whenever the endothelium is damaged, tissue factor is released which promotes clotting at that site. Clotting starts after an atheroma ruptures because up until that point all the tissue factor is encased within the atheroma, protected from direct contact with the bloodstream - there is still no superficial injury to the endothelium to expose the underlying tissue factor that would signal the clotting cascade to begin. Therefore, clotting only starts after the atheroma ruptures and all the tissue factor stored within the atheroma is released into the blood vessel.
It is worth noting here that in homeostasis without any injury, the coagulation cascade and fibrinolytic pathways (the clot-lysis or pathways) are both active, but they balance out each other's effects. Disruption of this balance due to pathology, injury, or other insult causes an imbalance between the two pathways which the body seeks to rectify. The imbalance is what leads to clot lysis (in the case of wound healing - after the wound has healed) and clot formation (in the case of a new injury).
Sources:

https://www.ahajournals.org/doi/full/10.1161/01.CIR.94.6.1226
https://www.ahajournals.org/doi/full/10.1161/01.CIR.96.2.396
https://ascpt.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1752-8062.2011.00351.x


text:
Can a hinge joint technically allow rotatory motion?
Let's use a hinge joint and pivot joint as examples.
When talking about the difference between them in terms of movements permitted, I see that on any websites and textbooks, the term 'rotation' is applied to pivot joint only rather than hinge joint.
For example, according to Moore Clinically Oriented Anatomy 10th edition.

Hinge joints permit flexion and extension only, movements that occur in one plane
(sagittal) around a single axis that runs transversely; thus, hinge
joints are uniaxial joints.
Pivot joints permit rotation around a central axis; thus, they are
uniaxial. In these joints, a rounded process of bone rotates within a
sleeve or ring.

I never see the word 'rotation' being used to describe hinge joints' motion, however, doesn't hinge joint technically allow rotation, just that the rotation for hinge and for pivot joints are over a different axis? For example, at the anatomical position, flexion in the elbow's hinge joint involves rotating the joint along the tranverse axis.
So my question is, can a hinge joint technically allow rotatory motion? If not, am I misunderstanding what is meant by 'rotation'/'rotatory motion'?

Do you understand the difference in between a hinge (elbow) and a pivot (hip)? Rotation just means move-round in an arc. It can be used as a general term in anatomy, to describe moving around a central point in an arc. The sense is slightly figurative if you compare it to a literal mathematical rotation, i.e. an arc of a compass. Anatomy also talkes about sinusoidal movements, and straight lines. even though they are just general descriptions. I don't understand the question though.

@aliential the hip is not a pivot joint, it is ball and socket.

You seem to understand how these joints move, so your question seems to be more about English usage in this context rather than anything fundamentally biological. If this is true then I don't think your question belongs on this site. If I'm misunderstanding your question would you please clarify?

@tyersome you're right, I think it's more about the English usage in this context. I thought it'd belong to this site as scientific terminologies and nomenclatures play a big part in biology.

It is about the movement of the bone along its major axis of movement. A hinge joint moves like a lever while a pivot joint involves rotation side to side like an axle.
It helps if you look at a example of a bone that has both types of joints. The radial head is part of both a pivot and hinge joint, with the ulna it rotates allowing the hand to pronate and is a pivot joint, while with the humerus it is a hinge allowing the arm to swing through an arc.
Keep in mind these are biological terms and not strict engineering descriptions, biology is more interested in how tissues move relative to each other. Biological terms are not interchangeable with geometry and engineering, nor are they designed to be perfectly rigorous, they are descriptive in nature. In biology rotation is a term reserved for more wheel and axle type motion where a bone is revolving around its own axis.

Find more help here.


text:
How do veins's valve pocket sinus tend to become hypoxic?
For context, this question relates to the formation of deep vein thrombosis as I read that hypoxemia in vein can trigger coagulation cascade and cause a thrombus to form in vein.
I read that vein's valve pocket sinus tend to become hypoxic due to vortical flow. The diagram I attached below has oxygen tension color coded with a gradient from red to blue; the darker the blue is, the greater the hypoxia.
However, how exactly does vortical flow have to do with hypoxemia in those regions? From my understanding, the lack of blood circulation in vein's valve pocket shouldn't affect the amount of O2 bound to the haemoglobin stucked in the vein's pocket? As veins are not permeable to O2 thus O2 can't escape into surrounding cells.
References:
Bovill EG, van der Vliet A. Venous valvular stasis-associated hypoxia and thrombosis: what is the link? Annu Rev Physiol. 2011;73:527–545. doi: 10.1146/annurev-physiol-012110-142305.
Mackman N. (2012). New insights into the mechanisms of venous thrombosis. The Journal of clinical investigation, 122(7), 2331–2336. doi:10.1172/JCI60229
https://www.jci.org/articles/view/60229

As veins are not permeable to O2 thus O2 can't escape into surrounding cells.

Veins are not like impermeable rubber tubes, they are 'living' structures requiring, like all cells, Oxygen and glucose to survive. Smaller veins get the O2 from diffusion, while the larger veins need help from vasa vasorum, small blood bessels that bring blood to the walls of the veins.
The innermost cells lining veins are epithelial cells. They also line valves.
In the picture you posted, blood is not circulating well behind valves. The cause of hypoxia is that epithelial cells are continually removing O2 from the blood.
When enough O2 is removed to cause hypoxia, the endothelial cells may become damaged by the lack of O2, causing inflammation and (possibly) potentiating clot formation.

Activation of endothelial cells by hypoxia or possibly inflammatory stimuli would lead to surface expression of adhesion receptors that facilitate the binding of circulating leukocytes and microvesicles. Subsequent activation of the leukocytes induces expression of the potent procoagulant protein tissue factor that triggers thrombosis.

Mackman N. (2012). New insights into the mechanisms of venous thrombosis. The Journal of clinical investigation, 122(7), 2331–2336. doi:10.1172/JCI60229


text:
When endothelial cells in blood vessels (arteries or veins) are damaged, does atheroma form first or blood clot?
I have learnt from Khan Academy's video on atheresclerosis that when the endothelial cells of an artery are damaged, atheroma forms at the site, and if the atheroma’s fibrous cap is ruptured, thrombogenic material is released from the atheroma, causing a blood clot. Having read other articles on this issue, this phenomenon is known as the atherothrombosis. And I believe that the fact that atheroma is formed before thrombosis is because thrombogenic material isn’t released when endothelial cells are damaged; thus cholesterol deposits in the area to form atheroma first.
However, in another video, when endothelial cells in blood vessels are damaged, platelet activation occurs due to the exposed collagen, and thrombosis occurs. Why is it that blood clotting occurs first instead of atheroma?
I have also learnt from my other question on Biology StackExchange that hypoxemia in the valve pocket of the large veins can cause endothelial damage that triggers the clotting cascade.
Therefore, I am confused as to which of atheroma or blood clot is formed first when endothelial cells are damaged; and if either one is formed first, why is that so? I’m certain that after a blood clot is formed, atheroma won’t be formed as I’ve not found any article that supports this sequence.
References:

https://www.khanacademy.org/science/health-and-medicine/circulatory-system-diseases/coronary-artery-disease/v/atherosclerosis
https://www.youtube.com/watch?v=R8JMfbYW2p4
https://academic.oup.com/eurheartj/article/25/14/1197/509341
How do veins's valve pocket sinus tend to become hypoxic?

It is unlikely that atheroma would develop as a complication of a thrombus.
Atherosclerosis and thrombosis are two independent disorders and not two stages of the same disorder. Atherosclerosis is a disorder of the arterial wall and atheroma develops in the arterial wall. Thrombosis is a disorder of the blood and thrombus is merely attached to the atheroma or arterial or vein wall.
In veins, only thrombosis, but not atherosclerosis can occur, as mentioned here.
In arteries, thrombosis usually occurs only as a complication of an atheroma or calcification (PubMed, 2017):

The majority of coronary thrombi are caused by plaque rupture
  (55–65%), followed by [plaque] erosions (30–35%), and least frequently
  from calcified nodules (2–7%).

It is very rare that thrombus develops in arteries that have previously not been damaged by atherosclerosis (PubMed, 2015).
Further evidence that thrombus formation is an unlikely initial event in the development of an atherosclerotic plaque:

Thrombosis is not mentioned as an initial stage or risk factor in development of atherosclerosis in various texts: Textbookofcardiology.org, Pathophys.org
Genetic coagulation disorders are not likely risk factors for atherosclerosis (Atherosclerosis, Table 2 (PubMed, 2010):


text:
Cannibalizing behaviour in ants
Today I saw an ant question biology and was reminded of a picture I had clicked 2 years ago.
Here, you can see these black guys cannibalizing this other black guy.
To reiterate, these guys had their nest inside a tree. I had cornered one of them.
If I remember correctly the ant was walking fine and the only fault might have been that I lead the guy astray a bit (not further than the farthest guy in the colony) and near the colony I turned it on its back which lead to a lot of difficulty for getting up again (as any ant knows). I mean I waited maybe a few minutes but it just kept waving it's legs in the air.
So later on as soon as these other ants got sight of their lost friend when it was able to hobble back near the nest, they came over and just pulled him apart.
In the picture you can see the first guy just got to him and the others started aggregating as soon as this guy came over. Within five minutes some 10 or 15 ants were all over the place.
Which ant species is this?
Why did they murder/cannibalize a member of their own colony?
Is this a common behaviour among ants?

Interesting observation! From what I understand it can be very difficult to get the species from a photo like this (but I'm no expert, someone else might know better). Also, you're using "guy" and "him" in your text, but most likely these are female ants since all workers are female.

I did not mean male or female. I'll change everything to it. Tried to keep the post jovial

Yeah, I understood what you meant, I'm just being pedantic and ruining all the jovialness...

Potentially a nice question but you might run into problems as you're asking more than one thing - as you can see below, you already have an answer to the species-id part which is probably correct as far as it goes but it would be a shame to ignore the interesting behavioural parts. Since this has been answered now, you could consider editing this into a species-id question and paste the rest into a new behavioural question? Maybe? (I don't know, I'm fairly new to this).

Where did you found them? Which country?

India! new delhi!

Scientific name: Camponotus compressus
Common name: Common Indian black ant

Camponotus compressus tending soft scale insects growing on a stem

Source:

Common Indian black ant
Wikipedia

Cannibalism is common in social insects. It is a way through which they control the population of the colony and conserve nutrients. Members of Hymenotpera (this ant being one) are very quick to consume injured eggs, larvae and pupae. It has been experimentally observed that when a colony of Zootermopsis angusticollis(a species of termite) was kept on a diet full of cellulose i.e. deprived of protein, they attacked their own kind. But cannibalism dropped to zero when casein was introduced in their diet. So it is safe to  assume that these ants too engage in cannibalism for the same reason, proteins.
Reference: This book.

you say tending soft scale insects..Is there some sort of symbiotic relationship between these insects?


text:
Which of these versions of allopatric speciation is correct?
I'm confused with the illustrations of allopatric speciation. Here are two diagrams-

Which one of them is correct and why?
According to wikipedia the second figure is correct but I'd like to know why is it so, or why can't be the first one be right?
All I know about allopatric speciation is that it is a process of formation of new species from existing species in the following way-

A large ancestral population is firstly spatially divided into two subpopulation
Evolutionary forces act on the subpopulations
Eventually with large span of time reproductive isolation develops between them and finally lead to new species

According to my concept fig 1 is correct but I find the other diagram all over the internet.

For the millionth time, when asking homework questions, you must show your attempt at an answer. "Because I read it on Wikipedia" is not an attempt at answering. With all of the low-quality questions you ask, you are at risk of being question-banned on this site. PLEASE improve your questions.

@MattDMo I've added some information. I didn't write this before because it was not related to my question directly.

Both are correct. From Wikipedia, the causes of genetic change within each now-separate population are: (a) they become subjected to different selective pressures, (b) they independently undergo genetic drift, and (c) different mutations arise in the gene pools of the populations.
It is possible that factors a, b, and c cause the emergence of 2 new species -- or just 1 (which is possible considering that the original species probably is well-suited to its current habitat).


text:
Does depolymerisation take place at the minus end of microtubule?
Wikipedia says that

Dynamic instability refers to the coexistence of assembly and disassembly at the 'ends' of a microtubule.

but Karp's Cell Biology, 7th edition says

Dynamic instability is an inherent property of microtubule itself, more specifically, of the plus end of the microtubule.

I was of the opinion that the GTP bound to the minus end does not hydrolyse and so no depolymerisation take place at the minus end.
But again from The Cell: A Molecular Approach. 2nd edition I found that

treadmilling is a dynamic behavior in which tubulin molecules bound to GDP are continually lost from the minus end and replaced by the addition of tubulin molecules bound to GTP to the plus end of the same microtubule.

The concept I have developed so far is completely shattered by this treadmilling thing. Can somebody explain,
i) Whether GTP remains attached to the minus end?
ii) Whether depolymerisation occurs at the minus end?
iii) If depolymerisation does not occur, then is treadmilling a special condition?

I think the reason why the literature contain these contradictions is that all these phenomena do happen, but in most conditions the dynamics is strongly dominated by the plus-end dynamics (growth and catastrophies), leading most research to disregard minus ends completely.

Treadmilling, AFAIK, happens in actin filaments not tubulin.

@WYSIWYG no, it happens in microtubules. See this.

@MattDMo Interesting. The textbook that I used to read never mentioned that even though the article you mention is quite old. I found a more recent article on this topic. Thanks for correcting me.

@WYSIWYG no problem. I found that article while researching an answer I've decided not to write - seems the idea of treadmilling has been around for a long time.

Often microtubule (MT) dynamics and actin dynamics are taught side by side, which can be quite confusing as MTs display unique characteristics relative to actin filaments. Indeed, treadmilling is an in vivo behavior primarily associated with actin, while dynamic instability characterizes MT growth. But why?
Both actin filaments and MTs are "sided" (polar), with actin having barbed- and pointed-ends and MTs having plus- and minus-ends. This polarity emerges from two properties: 1) the energetic state of the individual monomers that make up the filament and 2) the rate of growth.
For actin, the barbed-end is compromised mostly of ATP-actin (high energy), while the pointed-end is made up of ADP-actin (low energy). This composition preferentially adds new ATP-monomers to the ATP-rich barbed-end, yielding a faster rate of growth than at the pointed-end. Disassembly at the pointed-end occurs more readily as ATP-actin is converted to lower energy ADP-actin. Treadmilling occurs when the rate of assembly at the barbed-end is equal to the rate of disassembly at the pointed-end (Pollard and Borisy, 2003).
Similarly to actin filaments, MTs are polar, with their plus-ends made up of GTP-tubulin monomers and GDP-tubulin concentrated at their minus-ends (Desai and Mitchison, 1997). Unlike actin filaments, which can form sporadically almost anywhere in the cell (Pollard and Borisy, 2003), MTs are initiated at what we call a microtubule organizing center, or MTOC (Kollman, 2011).
The bulk of MTs within the cell are attached to the MTOC through their minus-ends, though there are unattached sub-populations. Both in vivo and in vitro data indicate that growth and shrinkage at the minus-ends does occur, but that the rates are slow relative to those occurring at the plus-ends (Hendershott, 2014). In these instances, MTs can undergo treadmilling in a manner similar to that as actin and this behavior is readily observed in vitro (Waterman-Storer, 1997). Recent studies have suggested that MT minus-ends are under tight regulation in vivo, likely limiting their dynamics (Akhmanova, 2015). Therefore, MT growth and shrinkage primarily occurs at thee plus-ends. Enter dynamic instability.
MT plus-ends undergo a cyclical process of growth and shrinkage known as dynamic instability (Mitchison and Kirschner, 1984). The key to this process is the difference in shape between GDP-tubulin and GTP-tubulin (Buey, 2006). One can imagine GTP-tubulin as a rectangle, with perfectly straight lines connecting its angles. On the other hand, GDP-tubulin has a small bend in the center of one of its long ends.
As a MT grows, GTP-tubulin is added to the plus-end forming a "GTP cap." The role of this cap is to counteract the inherent desire of GDP-tubulin to bend outward, thereby forming a straight filament and ensuring continued growth of the MT (Desai and Mitchison, 1997). However, the MT will lose its cap when the rate of GTP-tubulin addition drops below the rate of GTP to GDP conversion, thereby exposing GDP-tubulin. This event characterizes the "catastrophe" stage of dynamic instability (Mitchison and Kirschner, 1984). The shape of GDP-tubulin is no longer constrained in this stage, and instead, bends outward causing rapid disassembly of the MT. Because the cell is chock full of GTP-tubulin, recovery of the GTP cap rapidly occurs and the MT re-enters productive growth. This cycle of growth-catastrophe-recovery is the hallmark of MT dynamic instability.

Answer is mostly fine, but, as per the earlier comments on the original post, MTs can become detached from the MTOC, and then undergo treadmilling.


text:
What are the significances of chromosome mapping?
The few point that I have come across are:
The following are the significances of chromosome mapping:

Chromosome maps help identify the location of gene of interest on a chromosome for genetic studies.
It helps to locate the region of a chromosome surgery.
Maps of the animals chromosome provides methods to study evolution process.

Can somebody add some more points to this answer?

As I understand your question, you ask about genetic mapping which has been demonstrated in the HGP (human genome project).
The human genome project:

enabled humans to find the gene responsible for relatively rare, single-gene inherited disorders such as cystic fibrosis and Duchenne muscular dystrophy
is useful in guiding scientists to the many genes that are believed to play a role in the development of more common disorders such as asthma, heart disease, diabetes, cancer, and psychiatric conditions
allows the production of new drugs based on DNA base sequences of genes or the structure of proteins coded for by these genes
gives the chance to study migration patterns of humans and origins
improved knowledge of the evolutionary relationships between humans and other organisms, which will help to develop better, more accurate classification systems

Sources:

https://www.genome.gov/10000715/genetic-mapping-fact-sheet/
https://www.genome.gov/12011238/an-overview-of-the-human-genome-project/
https://www.genome.gov/10001772/all-about-the--human-genome-project-hgp/

nice answer, but I think that OP asked for chromosome mapping (general), not HGP.

Yes that is correct I asked for chromosome mapping in general, still thank you for your efforts.


text:
Questions regarding PCR
Background:
From Genomes:
The temperature of a PCR mixture is first set at 94 °C so that denaturation of DNA can happen. Then it is reduced to 50–60 °C, which results in some rejoining of the single strands of the target DNA, but also allows the primers to attach to their annealing positions. After this DNA synthesis begins as the temperature is raised to 72 °C, the optimum for Taq polymerase.

In this first stage of the PCR, a set of ‘long products’ is synthesized from each strand of the target DNA. These polynucleotides have identical 5′ ends but random 3′ ends, the latter representing positions where DNA synthesis terminates by chance.
  [Subsequent cycles give] rise to ‘short products’ whose 5′ and 3′ ends are both set by the primer annealing positions.

Now Wikipedia says:

[...] Final elongation: This single step is optional, but is performed at a temperature of 70–74 °C (158–165 °F) (the temperature range required for optimal activity of most polymerases used in PCR) for 5–15 minutes after the last PCR cycle to ensure that any remaining single-stranded DNA is fully elongated.

Questions:

I’m wondering that if the shortening of the length of new DNA is purely by chance. From Wikipedia it appears that the length of the DNA synthesised can be controlled by the temperature of the mixture?

To carry out a PCR experiment, the target DNA is mixed with Taq DNA polymerase, a pair of oligonucleotide primers, and [...]

A pair of primer cannot support the increasing number of PCR cycles, are primers added later/ throughout the process?

Besides it seems to me that the temperature of the mixture has to be changed according to the phases of the cycle. Is it changed? How is it determined that which phase of the cycle the DNAs are in?

P.S. I'm not sure if this post should be broken down into two posts or more. Suggest if you feel that's necessary.

Ideally amplification happens between the two primer pairs and results in one product. However, complicated secondary structures, the depletion of some of the reagents may cause pauses and fall off of the polymerase. This happens often later in the reaction and results in shorter products. This final amplification step is introduced to finish all these shorter products.
A pair means the combination of a forward and a backward primer (see the image below from here). Bothg primers are added in a concentration high enough that both are not depleted and enable long PCR runs. No primers (or other reagents) are added during a standard PCR reaction.

The temperature of the PCR reaction is changed through 1 reaction cycle: First you start with the denaturation of the DNA at 94°C, then cool down to anneal the primers (typically between 50 and 60°C, depending on the primers), followed by the amplification step at 72°C (it'S length depends on the length of the amplified DNA piece, Taq polymerase processes about 1kb/min) (see figure below from here). This is one cycle and you know where you are, because the PCR machine counts this cycles.


text:
What is linkage strength?
Background

If linkage strength between any two gene loci is 70%,
  what would be the amount of crossing over between
  these loci?
(a) 15% (b)30% (c) 70% (d) none of
  these.

My approach at understanding the concept
I didn't find much about linkage strength from any authentic source.
I can think of two things :

The strength of a linkage would be greater if the spatial separation between two genes is less and the lesser if the separation is more. This is semantic. But,
how can it be represented in percentage? What does this 100 mean in this 70%? The separation between two genes can be more than 100 map units.

Question:
What does linkage strength mean? How is it related to amount of crossing over (number of recombinants)?
N.B. I would appreciate answers citing some authentic sources.

https://www.nature.com/scitable/definition/linkage-51

With the above source answer is b) as the two gene loci are inherited together in 70% of the cases (which is the linkage strength). In cases were the distance is large the linkage strength depends on the ploidy level of the organism. Eg. 100% if haploid, 50% if diploid, 33% if triploid and 25% if tetraploid. In other words the linkage strength can only reduce to the lowest level possible, if the process is entirely random.


text:
How is receptor production (recycling) regulated?
My understanding of receptor downregulation is that when activated, a receptor then gets absorbed into its cell, as shown in this weird video. It then gets either recycled or degraded. Tolerance presents when more degradation than usual happens.

Receptor activated (ligand binds to receptor)
Receptor-ligand complex internalized to cell
Some complexes recycled, others degraded
Tolerance = more degradation than usual, resulting in lower
receptor density at cell surface (called downregulation)

So, what is causing the higher degradation than usual? Is it the lack of the materials required to produce the receptor? If so, can this be compensated for via diet or supplementation (i.e. eating more dopamine precursors if you're trying to avoid dopamine receptor downregulation, for example?)

So, what is causing the higher degradation than usual? Is it the lack of the materials required to produce the receptor?

Lack of materials is almost never the reason. Receptor turnover is actively controlled by different mechanisms. Ubiquitylation is one of the common mechanisms. Ubiquitylated receptors are internalized; these internalized receptors can later on be sent back to the membrane (recycled) or be degraded depending on the conditions.
Receptor downregulation can also happen by stopping their production either at the level of transcription or translation (For an example see this).


text:
Why do neurones use chemical signalling at synaptic junctions?
When a neurone fires, it sends an electrical signal that jumps down the axon via the nodes of Ranvier very rapidly. At a synaptic junction, chemical Brownian diffusion signalling with receptor surface proteins is relatively slow and is often exploited by venoms and susceptible to toxins (on the plus side it's the reason a lot of medical drugs work). It seems flawed for evolution to have selected for this rather than some alternative quicker and more direct electrical interface.
Question. Why are chemical synaptic interfaces used in higher organisms at the synaptic junction?

This is the coolest part. Those synapses are the reason the brain is so complex! Basically you've got the first part right, the neurones are quicker and they transmit messages from one end to the other. The other thing you have to do is analyse and calculate. Signals from multiple neurones feed into a single neurone using a chemical synapse. Similarly the converse is true, a single neurone can feed multiple synapses. So when we for example walk, receptors monitoring our balance can feed this to our conscious and unconscious mind, but I'm grossly simplifying this. What our brain does is take hundreds and thousands of ports of information, with where the chemical synapse is and the type of synapse and the receptors and a million other things just slightly changing the information until it's perfect and then send that information a million ways however it likes.
The most important thing is this allows inhibition. Most of the brain uses inhibitory GABA rather than activating signals. Furthermore, the system uses the delay created. Different transmitters act for different durations and send a different volume of signal. An impulse is all or nothing, it's of a fixed amplitude, however a chemical signal can be fine tuned. Neurones can not only interact to inhibit themselves or other neurones to increase the resolution of a signal etc. Conversely a system of just physical connections allows little regulation, in fact it'd be practically a seizure.
Does that make sense?

I think I understand the principle, but would it not be more efficient to have interlocking physical connections that could carry a voltage?

The most important thing is this allows inhibition. Most of the brain uses inhibitory GABA rather than activating signals. Furthermore, the system uses the delay created. Different transmitters act for different durations and send a different volume of signal. An impulse is all or nothing, it's of a fixed amplitude however a chemical signal can be fine tuned. Neurones can not only interact to inhibit themselves or other neurones to increase the resolution of a signal etc.
Conversely a system of just physical connections allows little regulation, in fact it'd be practically a seizure.

If it still doesn't make sense or there's anything else just ask :)

I hadn't thought about it in terms of an analogue signal. I think that's they key bit I was missing.

No problem :) updated the original answer to everything so far.

There are both chemical and electrical synapses in many organisms.  The electrical synapses are called gap junctions.
As you point out, the primary advantage of gap junctions is their speed, and they are commonly used in systems involving defensive reflexes.
However, as AndroidPenguin indicates, chemical synapses allow for greater computational abilities (changing the gain, integrating multiple inputs, etc).  Gap junctions are also disadvantageous because they often (but not always) transmit signals in both directions; chemical synapses tend to be more unidirectional (of course, there's always backpropagation).

There are indeed 'gap junctions' which pass current directly from one cell to the next. So what advantages do we get out of chemical synapses that gap junctions do not provide?

Asymmetry. Synapses do not operate in reverse, thus the postsynaptic cell cannot generate currents in the presynaptic terminal (although there are secondary forms of communication which may operate in the reverse direction).
Ion Selectivity. A synapse allows one set of ionic currents to be transformed into any other set. Thus sodium and calcium influx at the presynaptic terminal might translate to chloride influx to make the synapse inhibitory. Furthermore, the ability of the postsynaptic cell to control calcium levels is critical for plasticity mechanisms.
Insulation. Gap junctions increase the conductance of the cell membrane, which can reduce the fidelity of signals as they propagate along the dendrite. In contrast, an inactive synapse might have virtually no effect on the postsynaptic cell--it does not pass currents.
Kinetics. Because chemical synapses generate their own ionic currents, they are also free to modify the speed of those currents (how quickly they rise and fall). This is much more difficult to achieve with gap junctions.

There is a very long list of functionality provided only by synapses which I have not listed here, but I think most of those are things which could, in principle, also be achieved with gap junctions (for example: amplitude control, metabolic responses, short- and long-term plasticity).


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What factors govern the variable age of onset in Huntington's Disease?
"Huntington's disease (HD) is a neurodegenerative genetic disorder that affects muscle coordination and leads to cognitive decline and psychiatric problems." As we all know, this genetic disease exhibits a generally late age of onset. It has been shown that a increase in the number of CAG repeats in the hungtingtin gene is negatively correlated to the age of onset of the disease. However, patients having a  particular number of CAG repeats still have an extremely variable age of onset, which leads to believe that other factors are contributing to the Huntington phenotype.(reference)
 (reference)
What other genetic or environmental factors have been shown to vary the age of onset of Huntington's disease?

References
Andrew, S. E. et al. The relationship between trinucleotide (CAG) repeat length and clinical features of Huntington’s disease. Nature Genetics 4, 398–403 (1993).

There is quite a bit of data available from Venezuelan HD families, but they haven't identified the factors themselves. From the abstract of the paper, emphasis mine:

Analysis of the 83 kindreds that comprise the Venezuelan HD kindreds
  demonstrates that residual variability in age of onset has both
  genetic and environmental components. We created a residual age of
  onset phenotype from a regression analysis of the log of age of onset
  on repeat length. Familial correlations (correlation +/- SE) were
  estimated for sibling (0.40 +/- 0.09), parent-offspring (0.10 +/-
  0.11), avuncular (0.07 +/- 0.11), and cousin (0.15 +/- 0.10) pairs, suggesting a familial origin for the residual variance in onset*. By
  using a variance-components approach with all available familial
  relationships, the additive genetic heritability of this residual age
  of onset trait is 38%. A model, including shared sibling environmental
  effects, estimated the components of additive genetic (0.37), shared
  environment (0.22), and nonshared environment (0.41) variances,
  confirming that approximately 40% of the variance remaining in onset
  age is attributable to genes other than the HD gene and 60% is
  environmental.

*This paper also suggests the same, with a smaller (but different) samples.
A recent study of an Italian sample suggests that a polymorphism in Atg7 (autophagy-related gene) is a modifier of age-of-onset, but this result does not generalize to a European cohort.

What is apparently not linked to age of onset in HD? β-defensin copy number variation.
Also, CTCF doesn't appear to be linked to the CAG repeat instability (mutations in CTCF have previously implicated in triplet repeat instability).
Mutations in PGC-1α, mitochondrial regulator, were previously associated with age of onset, but a more recent study suggests that this might have been due to stratification of the sample.
Similarly, a polymorphism in HAP-1 was previously associated with age of onset, but a subsequent study found no evidence of association.

Altogether, these results suggest that population stratification needs to be taken into account when evaluating associations between age of onset and genetic polymorphisms.  It is also possible that there are population-specific genetic factors that affect age of onset.


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What does conditional analysis of a SNP in a GWA study entail?
I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any explanation. Is it some sort of mathematical manipulation in which the significance of a tag-SNP is reduced to zero, to see if other SNPs are directly associated to the phenotype in question?

In GWA studies you tend to analyze your "lead" SNPs in regions where genotypes are correlated (known as linkage disequilibrium).
If you find an association between another SNP with the outcome, and this SNP is correlated with the original variant, you can perform a conditional analysis where you adjust for the original SNP in the model. This is to test if the association between the 2nd SNP is independent of the first, or whether it is just because they are correlated (in LD).
So performing a conditional analysis is just seeing if the association observed is an independent signal.
At least, this is how I have interpreted it perviously!

E.g. SNP-A is found to be associated with increased risk of type-2 diabetes (T2D).
SNP-B is later found to be associated with risk of T2D as well.
SNP-A and SNP-B are correlated.
To see if the association between SNP-B and T2D is independent of the first association, you would adjust for SNP-B in the model (a conditional analysis).
First model: lm( T2D  ~  SNP-A + confounders)
Second model: lm( T2D  ~  SNP-A + confounders + SNP-B)

If the association between SNP-A (and/or SNP-B) and T2D is still significant then they have some independent effect on risk of T2D. If the association disappears then they are only both associated because they are correlated in the individuals.

What if SNP-B isn't significant in the second model.
Does that mean SNP-A is the causal (or lead variant) or SNP-B is?


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How do cells slowly degrade 5,5'-dibromo-4,4'-dichloro-indigo?
5,5'-dibromo-4,4'-dichloro-indigo is the product of X-gal cleavage, often used as a reporter with B-galactosidase. I've made the (unreferenced) observation that it seems as though the blue product slowly degrades over periods of time within the cell, allowing for cells to lose their blue coloration.
What mechanisms can explain the degradation of 5,5'-dibromo-4,4'-dichloro-indigo within cells?

Can be 3 reasons: 1. Dilution 2. Reductive conversion to colorless leuco-indigo 3. Metabolic decay: I suspect the metabolism would be similar to that of purines

^ that was purely speculation

Indigo compounds are so damn insoluble I don't know if you can get it into an enzyme easily. I've made indigo ( not the x-gal indigo in the question, but same core structure ) just for fun while my boss isn't watching, and I haven't found any solvent that will dissolve it. But maybe glutathione can slowly reduce it. When I reduce the indigo I make, I use sodium dithionate and boiling water. GSH wouldn't be as powerful, but you don't need it to work as quickly. More pure speculation.


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What are the distinctive structural features of single- or double-stranded xRNA, or where can I find them?
I am interested in the structural differences caused by benzopurines and benzopyrimidines at the oligonucleotide level between RNA and xRNA, both in single-stranded and double-stranded form.
I am aware of RNA's tendency to be found in the A-form, of which the details are found here. However, other than the obvious nucleobase expansion, I can't seem to find any details about xRNA's secondary structure.

The only paper I found that examined the question is "Structural, Dynamical, and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases". They state

The results confirm that the structural and flexibility properties of
  the canonical DNA are globally little affected by the presence of
  benzo-fused bases. The most relevant differences are found in the
  enhanced size of the grooves, and the reduction in the twist.

They also have a picture comparing the structures of conventional DNA and xDNA:

So while the basic structure seems similar, the difference in diameter and twist look rather large to me.
This is for xDNA, I would assume that xRNA behaves comparably if double-stranded. It would have to somehow fit the larger nucleobases into the helix like xDNA. And the structure of single-stranded RNA is variable, helical parts would probably look similar to xDNA, hard to say how the modified nucleobases would affect tertiary structure.


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What is the difference between abiogenesis and spontaneous generation?
As we all should know, abiogenesis and spontaneous generation are far from identical. For one, spontaneous generation was disproven with Pasteur, and abiogenesis seems to be a solid scientific theory. However, one can loosely summarize both as "the emergence of life from non-living materials" which, at the very least, is confusing for the layman.
My question is: What truly differentiates abiogenesis from spontaneous generation? For example, if abiogenesis were to happen again, how would we differentiate the two terms?
Is time the most contributing factor (abiogenesis happened over hundreds of millions of years)? Or the fact that abiogenesis generates "primitive organisms", while spontaneous generation assumes the generation of evolved, complex organisms?

I’m not sure why this question resurfaced after seven years, but is a good example of a bad question. It gets off to a bad start with “As we all should know”. This really antagonizes me. I don’t know, I feel there is no reason why I should know, and I resent being told I should by someone who doesn’t seem to know himself. If you talk about scientific terms on a science site you should define them, or if you don’t know the difference cite the definitions you have read that are causing you confusion. You are supposed to do some research yourself before posting here.

One important difference is that spontaneous generation is a form of "mechanism" by which a certain species is "born", so it is repeated many times. For such complex organisms this would be part of their "life cycle". It would also need to be a regulated, robust process.
Abiogenesis, on the other hand, would create an organism which from that point on does not rely on abiogenesis in any way, so it would be a unique event. Abiogenesis is highly probabilistic which is why it would result in very simple organisms.

What truly differentiates abiogenesis from spontaneous generation?

There are three differences.

Frequency

Abiogenesis occurs very infrequently. Perhaps only once in all of earth's 4.5 billion year history.
Spontaneous generation happens very frequently, in fact every new species could be a product of spontaneous generation. It occurs so frequently you just need to wait a week (given the Spontaneous generation example of fly generation from rotting meat)

Complexity.

Abiogenesis only make very primitive organism... there are even thoughts that the abiogenesis event on Earth produced something that was only half alive, the ability to multiple and maintain a separate internal environment with a very basic and simple metabolism.
Spontanous generation on the other hand can produce both simple and complex organism. Bacteria, worms, cows, flies, humans. Anything.

Reproducibility

Abiogenesis if it were done again... we might get very different biology. There are more than the 20 types of amino acid.  There are actually a few more bases than the 4 we have in our DNA. And the codon usage...  ie which 3bp of DNA encode for which amino acid could also be very different.
In spontanous generation events, you can get it to produce the same organism multiple times, right down to ability to mate with each other. Flies were the example.

The only reason abiogenesis is not disproved is because it can't be tested like evolution it is supposed to have happened in the past and won't happen again  (at least not in the same way) abiogenesis is a theory proposed only because the origin of life is unexplainable by normal natural means.
Spontaneous generation was an earlier attempt at answering the origin of life that could more easily be proven or disproven.

Please add some references :)


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Is Phenylalanine hydroxylase gene biallelic?

Since the PAH gene is biallelic, and there are many disease causing mutations, most PKU patients are compound heterozygotes.
  (paper)
Compound heterozygosity in medical genetics is the condition of having two heterogeneous recessive alleles at a particular locus that can cause genetic disease in a heterozygous state.
  (wikipedia)
More than 400 disease-causing mutations have been found in the PAH gene. (wikipedia)

Why is Phenylalanine hydroxylase gene considered biallelic when PKU is also caused by the presence of two different mutant reccesive alleles at a locus with more that 400 types of mutations occurring in nature?

I've edited the link.

In this context I would guess the "biallelic" was just meant to indicate that the gene is on a somatic chromosome (not X or Y), so that there is always two alleles of PAH in an individual.

@Roland Not only in this context but in many books(Principle of Genetics by Snustard for e.g) PKU is considered an autosomal recessive trait controlled by biallelic gene. Many times in other books too PKU has been mentioned in Pedigree analysis and Hardy Weinberg sums (taking only p and q the involved frequencies).


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Goodness of fit: How to decide which ratio to deal with?
While solving problems of Goodness of fit, I'm faced with an issue, how to decide which ratio to consider to find the test statistic from given set of observations.
E.g. 1

A supplied sample contains four types of seeds and the total number is 64. The types of seeds are large red 42, large white 8, small red 10 and small white 4. Calculate goodness of fit.

Problem: As df=3, Ratio= 9:3:3:1 / 1:1:1:1?
E.g.2

You are supplied with two different varieties of plant samples;tall-76 and short-24. Determine the observed number, apply Chi square test to state whether it is in agreement with expected ratio.

Problem:  As df=1, Ratio= 3:1 /1:1?
I was vaguely told by my propessor that which ever ratio seems to apply(by logical guess) we should choose that one to determine the expected values and thus the statistic.
I couldn't find any good read in this regard, except those that are full of mistakes. I've been reading Statistics blogs to understand the concepts but they don't cover these typical biological problems and those that did had the ratios mentioned.
I've another question in mind, from experimental result it is also likely that we won't get one of the four types of seeds (given that mating is random and the progenies appeared by dihybrid crosses) so determining the actual ratio behind becomes more difficult as df = 2  =/= 3!

Without more information, as in a specific hypothesis to test (which should come from your professor), you can't be expected to come up with the hypothesis yourself. If your professor won't be clearer with the questions, then I say you expect 42:8:10:4 for the first and 76:24 ratios for the second. Chi^2 = 0 and you are done.

I think she's supposed to decide which hypothesis to test, based on how genes are inherited

For Pearson-χ² test, you can use any one frequency (for instance the frequency of heterozygotes). However, both your example questions lack important information regarding what is the expected frequency. Why should you even expect 3:1? Any expected model has to have some basis. These examples do not indicate any. The first step of a statistical test is to define the null hypothesis.

@WYSIWYG 3:1 because there are two classes of the nominate variable (that's how we were expected to solve by our professor). So we can't actually proceed without information (as in this question) as which null to disprove? I also found some questions from a book. I can't get how they are deciding the H0? (should I post them as another question?)

@SanjuktaGhosh You don't have to find out what the H₀ is. The null hypothesis is your basic question. You will, of course, know that before performing the experiment. In your case of 3:1 you will have the assumptions such as: there is dominance, the cross is between two heterozygotes etc. This appears to be the case but I can invent arbitrary cases in which you may see 3:1 ratios. I can also argue that 76:24 is not 3:1 but actually different from it. Unless you have multiple samples, there is no way to prove it.

@SanjuktaGhosh, you don't always need to disprove the null hypothesis. In some cases it makes more sense to run a model to check to see if the null hypothesis is correct - particularly when you are not entirely certain about what the alternative hypothesis could be. This is what Chi-square analysis is for. You have determine whatever ratio would make the most sense, logically. Then you run the observed values against the null hypothesis's ratio - using the same number of samples. So, run a Chi-squared test with a ratio of 75:25 against the observed ratio of 76:24.

Example:   ∑ ( (Observation - Expected) ^2) / Expected = χ^2

( (24-25) ^2) / 25) + ( (76-75) ^2) / 75) = 0.0533.. Which is approximately equal to to an alpha value of 0.9. Therefore, the p-value = 0.45, and you can reject the alternative hypothesis in favour of the null hypothesis: there is no difference between the observed ratio, and the expected ratio

@WYSIWYG Thank you for your insight. It really cleared things up. But if I find a question like this I'll have to look for patterns as what the Ha they are expecting us to assume.

For any statistical test you need to know the null hypothesis. The alternative hypothesis does not matter. In fact all.the tests check if null hypothesis is valid or not. They don't really have any information about the alternate hypothesis. The alternatives can be infinite

Are there cases in which we have no established scientific theory  (that would have been be our Ho) to compare our data with? What do we assume our Ho then? @WYSIWYG

When the p-value exceeds 5% the result is called significant and when 1% it is called highly significant (given that the test is motivated by rejection of the null). But what about a p-value not exceeding the critical value (which is something certain when the Ho is true, well Type I error excluded), do we call the result significant then? What do we call the result in that case?@WYSIWYG

Statistical test cannot be performed if you do not have a prior hypothesis. Your hypothesis can be as simple as "both samples are the same". When you do a t-test you have one additional clause that both samples are normally distributed. P-value is the probability that the null hypothesis is correct. The smaller that value is the higher will be your confidence. In general, we define our confidence interval before performing the test. The choice of confidence interval is arbitrary; usual choice is 95% (p < 0.05 is considered significant) but you can be more stringent depending on the situation.

To solve this question you need to have a basic understanding of Mendelian genetics. Contrary to peoples' comments, this problem does provide enough information.
Genes are inherited from two parents. That is, the offspring will inherit one allele from each parent. Genes also interact with each other in a dominant/recessive nature. A dominant trait will be expressed, no matter what if this is carried by an organism. A recessive trait will only be expressed if the organism is carrying two copies of the same allele - the organism must receive the recessive gene from both parents.
In the first question, there are four genes. One gene encoding large seeds. One gene encoding small seeds. On gene encoding red seeds. One gene encoding white seeds.
The dominant genes are those that code for: large & red
The recessive genes are those that code for: small & white
For this question, you assume that both parents are carrying a single copy of each gene. This means, each parent has one copy of a gene coding for large seeds, one copy of a gene coding for small seeds, one copy of a gene coding for red seeds, and one copy of a gene coding for white seeds.
As a side note, this would mean that each parent came from a large red seed. There is also a chance for any of the four genes to be passed to the offspring.
Each parent could pass the genes for: Large red seeds, Large white seeds, small red seeds or small white seeds.
This means that the following gene-combinations are possible:
-large red, large red
-large red, large white
-large red, small red
-large red, small white
-large white, large red
-large white, large white
...etc...
And, I'm sorry, I've been trying for twenty minutes to upload a picture to show you what I mean. But, you can do this yourself also to see what I mean:
Draw a 4x4 grid, and in each box fill in each possible combination of genes that can be inherited by an offspring. They call this a Punnett square, and it is used to predict the phenotype of an offspring bred by two parents. If you search Punett square you will understand how this works.
But the thing to remember is this: If the offspring carries one copy of a dominate gene (large seed, red seed) then these phenotypes will be expressed. In order for a recessive trait to be expressed, the offspring must carry two copies of the genes (small seed, white seed), ie. it must have received the same recesssive allele from both parents.
Now, to solve the problem statistically, you will use the ratio 9:3:3:1. The null hypothesis is that there is no difference between the observation and this ratio. The alternative hypothesis is that there is a statistically significant difference observed from the sample in comparison to the test-ratio.
This means, a p-value < 0.05 indicates that the 9:3:3:1 ratio is false. And the gene-interaction must be explained by another means - not by Mendelian inheritance. Or, I suppose it could also indicate that the parents did not in fact carry one copy of each allele and some other combination, that maybe you need to find. Eg. One parent could have had two copies of each recessive trait, while the other parent could have had in had one copy of each trait. (Play with the Punnett square, and maybe you can figure out if this is true)

Oh yeah, and obviously they aren't a 1:1:1:1 ratio. So isn't this question basically "free marks"?

@Sanjukta Ghosh, my apologies - when I first answered your question I was under the assumption that you had an understanding of Mendelian genetics and inheritance. I have edited my answer, and provided you with some background information required to solve this question. I was also trying to upload pictures, but I had no luck with this. I'm sorry. I hope my new answer clears things up for you. If you have any more questions, please feel free to ask.

And this is a link to dihybrid crosses. It will explain why 9:3:3:1 ratios are expected. https://en.wikipedia.org/wiki/Dihybrid_cross

I'm aware of Mendelian genetics. Thanks for your efforts and this comment. I agree with them that the information(data) provided is not enough to establish a scientific hypothesis but questions like this are mentioned in books followed by my university.  I prefer your previous answer though. I would like to ask can you support your answer with some authoritative reference.

By your answer I meant the previous version where you talked about the technique.

Would you like me to change it back to the unedited version, or perhaps I could update my answer again if we are able to reach a conclusion on this problem? And, I have recently found this website from the University of Arizona explaining the purpose of dihybrid crosses. I think their links, numbered 10 & 11, will show example situations where a statistical model would successfully reject the null hypothesis.