text:
Why are there both stop and start codons?
Based on my understanding from wikipedia, there is the (RNA) start codon AUG and the stop codons UAA, UGA, UAG.  AUG can also encode Methionine, I'm assuming if it appears in the middle of a mRNA sequence.
But is there a chemical reason there are both start and stop codons?  Eg, if I only had a stop codon, would that also imply the next codon was start? Are there cases where there is a stop codon and the next codon isn't start?

Start and stop codons are instructions for the ribosome to start and stop protein synthesis, respectively.
The region between the start and stop codon (inclusive of them) is called ORF (open reading frame) or sometimes CDS (Coding sequence).
Why does ribosome need explicit instructions for start and stop?
Ribosome recognizes an RNA as a mRNA if it has certain features. In bacteria and other prokaryotes there is a region on the mRNA called the Ribosome Binding Site (RBS) that helps in initial recruitment of the ribosome. In eukaryotes there are Kozak consensus sequences that help in identification of a start site. When the ribosome encounters an AUG codon then the initiation reactions take place (there are some proteins called initiation factors that help in this process). The ribosome just keeps moving along the mRNA and producing a polypeptide unless it encounters a stop codon. When it does other proteins called release factors come into play and they dislodge the ribosome from the mRNA.
What about a second AUG codon?
If the ribosome encounters another AUG codon after the start then it would consider it as a codon for methionine. However there are situations when the second AUG can act as an alternative start site. You can see this paper for details.
Why is stop codon essential?
You can imagine a situation where ribosome just goes till the end of mRNA — why stop it? The reason for this is that the mRNA 3' terminus usually has regulatory regions and most importantly poly-A tails (in eukaryotes) that should not be translated. Moreover stop codon also signals the ribosome to dislodge from the mRNA. If such processes didn't exist then ribosome will remain attached to the RNA.
If I only had a stop codon, would that also imply the next codon was start?
No. Because stop codon works only when translation has already started. However it is not essential that the stop codon should be followed by the 3'UTR. Usually in bacteria a single mRNA codes for multiple proteins. There are many ORFs that are lined one after the other; such mRNAs are called polycistronic mRNAs. In these cases there is another start codon a few distance ahead of a previous stop codon.

Not all the RNA is to be translated into proteins. Actually most of it is for regulation and sometimes unknown use. There are non coding regions before the start codon and after the stop codon. Hence the need for both.

It is important to have start and stop codons so that the molecular machinery of the cell (ribosome etc.) "know" where the actual transcript starts and ends. This is especially important, since mature mRNA contains untranslated regions which are of regulatory importance. These regions occur on both sides of the coding sequence called 5' and 3'UTR (untranslated region), then you also have the CAP-region and the poly-A tail, see the illustration below (from here):

You only want the coding sequence between the start and stop translated into a protein and to recognize these borders you need a specific marker. Behind the stop codon is untranslated sequence, not directly the next gene.
Additionally there is a large number of non-coding RNA species, like miRNA, siRNA, lnRNA and so on which fulfill regulatory purposes, play a role in splicing, replication etc. These shall not be translated into a protein (this would probably block the ribosomes and would also cost immense amounts of energy) as they wouldn't give useful proteins.

Next to helping to define the region for translation on the mRNA, the stop codon also prevents transcripts that have been frame-shifted by a mutation from translating into big proteins, and also helps flagging the mRNA for destruction (nonsense-mediated RNA decay). This is because in random sequence, a codon has 3/64 chance of being a stop codon, so in a frame-shifted gene sequence there suddenly are many. The premature stop codon will prematurely end the first round of translation, but if any machinery for the splicing of the mRNA is still present (it is not at the normal stop codon), the mRNA will be destroyed so it can not generate additional mutated proteins.


text:
Why sigmoid curves appear in quantitative analysis of many biological phenomena?
I know two examples:
1-The binding of hemoglobin to oxygen (binding of oxygen to one site of hemoglobin induces conformational changes which increase the affinity of the other sites for oxygen - the curve could be interpreted as transition from a low affinity T sate to a high affinity R state). The plot can be seen here
2-The denaturation of DNA by temperature (when one segment of the double helix opens, base stacking is disrupted, making the denaturation of the rest of the molecule easier); Another plot
The two examples I gave were actually of positive cooperative phenomena, that is, the occurence of a first event favours the next events. There is also the titration curve, which is a sigmoid, but I don't think it's correlated.
I'm asking that because I found it amazing that the same sort of curve appeared in the study of such different subjects.
Are these examples somehow correlated, that is, for which sort of phenomena sigmoid curves are expected?

Logistic functions have a sigmoidal curve. Logistic functions are used extensively in ecological models. This question as it stands appears too broad. You can come up with lot of examples. You should narrow it down to a specific issue.

Agreed. These curves are widespread in population genetics as well.

Tons of examples in psychophysics and neuroscience...

Agreed - psychometric curves in a host of tests follow sigmoids.

can you rephrase question so that it is not encyclopedic but rather about biological principles? so far seems you can answer it extensively searching pubmed on sigmoidal curve

Dinosaur Growth Rates, neuron sensitivity to angle (auditory system) etc...

voted down for too broad scope

@aandreev I have reformulated.

seems more interesting now. can we remove hold?

I've already edited the question. Could you reconsider if it's still too broad or at least suggest other editions?

why is this question closed? i also want to know the answer/opinion. glad that there's still one person answered this.

I would suggest following: take any one-dimensional process that is described by gaussian function. If you integrate such process along variable, you will get a sigmoidal curve. For details see normal and cumulative distribution.
Now, the question is: how many biological processes are described/modeled by Gaussian distribution and dependencies? A lot!
Let's take a look at dinosaur growth from Revisiting the Estimation of Dinosaur Growth Rates

This figure describes how size of dinosaur changes with some time (model, I assume). Remember link between gaussian and sigmoidal functions? If you differentiate, that is find how fast aforementioned sigmoidal function changes, you will get gaussian bell-curve! Which tells you: dinosaur grows faster during middle age, and slower before and after that.
DNA denaturation curve is sigmoidal because efficiency of denaturation is again gaussian. At low temperatures very limited amount of molecules will denature, but at high temperature there are no more molecules to denaturate left, so the bell-curve. Anothe explanation goes like that: at low temperature additional heat doesn't change much because it is still too "cold", at higher temperature same amount of heat is just a drop in a bucket, barely noticeable.

How do you say that relationship of temperature and denaturation should be gaussian? Gaussian CDF looks sigmoidal; that doesn't mean that all sigmoidal curves have a gaussian explanation.

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text:
Are the proteolytic enzymes in syconiums and nettles identical to those in rennet?
I would like to compare rennet capability under various conditions. The issue is, I don't want to use calf rennet, but I can't figure out if nettle and syconium, which also coagulate milk, contain regular rennet or other enzyme? If so, what is its name? It's quite important.
Thank you.

Rennet is not an enzyme, but rennin is.
Any protease enzyme should be capable of causing milk to coagulate, or prevent gelatin from setting. Examples such as papain and bromelain are all cysteine proteases, and all of them will cause milk to coagulate.
The example of fig protease that you mentioned is a cysteine protease (no specific name found, referred to in scientific literature as fig protease). Nettles are a highly polyphyletic group, and the specific enzyme cannot be named without a more specific phylogenetic group being identified.

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text:
Do cell membranes have more phospholipids in one layer than in the other?
Assuming the cell membrane to have a spherical shape, geometry tells us that the area of the inner leaflet is smaller than the area of the outer due to the difference in radius between them. Does this mean that the inner layer has fewer phosholipids? And, if so, how does it affect the fluidity relation between the layers?

The protein content and lipid type in each layer is likely to have a bigger impact on the number of phospholipids than anything.

Yes there is a difference in the number of phospholipid molecules because of the curvature. This is very evident when there is a lot of bending as in case of exocytosis (see here) but otherwise I do not think there would be an enormous difference in the number of phospholipids between inner and outer surface of the bilayer.
Assumptions:

Cell is spherical
Cell diameter = 1µm (overall)
Thickness of bilayer = 6nm
Width of a phospholipid molecule = 1nm

Difference in circumference of outer and inner layers = 2π(6nm) ≅ 37.7nm
So approximately 37 more phospholipid molecules in the outer layer in this cross section of the cell. This is just 0.6% of total number of phospholipids in the outer membrane.
I don't think fluidity will be compromised because of this - only if a layer is overpacked will the fluidity be affected.

Don't you have to look at the total area instead of the radius?

@MarchHo yeah.. I have to calcuate total area instead of circumference.. just a simplification. I should mention cross section.

These assumptions are sensible for vesicles, but I'm not sure if they translate well to cells. Have you any evidence that this is true for cells rather than vesicles?

@GoodGravy I guess cell is nothing but a huge vesicle. But I did say that this will matter the most in case of vesicles. Yes I agree that there are membrane proteins and cellular shape is not uniform. I can only extrapolate based on these assumptions. I don't think there are any studies for whole cell.


text:
Why AZT is selective towards HIV and doesn't impair human DNA replication?
I've found this article, which is a very old one (from the time when nucleoside analogs where researched as a possible way to prevent replication of virus genetic material, before the HIV epidemics).
In the last page, the authors suggest that cellular repair enzymes could remove azidothymidine (AZT, zidovudine) from cellular DNA if it's incorporated, but viruses' polymerases lack this ability.
As it's an old article, I would like to know if this hypothesis was confirmed. As both azidothymidine and thymidine can form normal base pairings, how could human enzymes detect an azidothymidine was incorporated?
If someone is not familiar with AZT mechanism: basically, it's an analog of thymidine which has an azide group instead of 3'-OH

It can be phosphorylated by cell kinases and incorporated to the growing DNA chain; however, this will stop the polymerization because it depends on free 3'-OH. The natural question which follows is: why wouldn't AZT also block the replication of human cells' DNA?

it does and that is why the side effects

http://www.tandfonline.com/doi/abs/10.1080/15257771003741018 It has been shown to poison mitochondrial thymidine kinase, amongst other side effects.

Stalled replication forks can be repaired. See this paper, for example: http://cshperspectives.cshlp.org/content/5/5/a012815

@WYSIWYG it has side effects, but they're not compared to nucleotide analogs that target cancer cells, for example cytosine arabinoside.

Now that I'm getting a closer look at that structure, the AZT looks wrong, shouldn't that 3' amine be an azide?

@User137 indeed, it's $N_{3}$

Retroviruses depend on being able to convert their RNA genome into a DNA copy, and have a reverse transcriptase enzyme to do that. This unique activity is not found in human cells, allowing for potential antiviral therapy if a drug can be used to inhibit the reverse transcriptase while not affecting the human enzymes.
AZT is one such drug, by mimicking the nucleotide thymidine, it can it can act as a substrate for nucleotide kinases and become 5' phosphorylated. AZT is phosphorylated by host cell enzymes, specifically thymidine kinase, this means that the levels of AZT phosphates are similar between HIV infected and non-infected cells. Once the 5' triphosphate is formed, the drug is a substrate for the viral reverse transcriptase. If an AZT is incorporated into the DNA backbone, it terminates the DNA because the 3' OH is not available for further polymerization.
However, at high enough doses AZT can be toxic to healthy cells. One mechanism for toxicity is the depletion of thymidine, because AZT competes with thymidine for the kinase enzymes, but is phosphorylated at a slower rate. At high doses, >1mM, AZT can act as a substrate for human DNA polymerases. Thankfully, AZT is about 100 fold more selective for HIV reverse transcriptase than human DNA polymerase.
The mitochondrial DNA polymerase seems to be a little more sensitive to AZT than other human DNA polymerases. This can lead to toxicity in the heart, skeletal muscles, hepatocytes, or other cells that use a lot of mitochondria. This toxicity is generally reversible if doses are reduced.
For more information, read about other nucleotide analogs, such as acyclovir, ganciclovir, and others which work through similar mechanisms.

All you wrote is relevant, and thanks about the suggestion of the other nucleotide analogs. However, I still don't know the molecular mechanism that would explain that "AZT is about 100 fold more selective for HIV reverse transcriptase than human DNA polymerase". There are other nucleotide analogs (such as cytosine arabinoside) that actually impair human DNA replication, so they're used to target cancer cells.

Maybe (just a hypothesis) the higher rate in which the virus proliferate could make it more susceptible (by a similar mechanism for which the traditional chemoterapeutic drugs target cancer cells). However, just that doesn't appear to be sufficient, since AZT or acyclovir have fewer side effects than chemoterapeutic drugs...

@ElCid Even though the nucleotide analogs have the same general mechanism, they have different structures. This could explain why some bind to human enzymes more efficiently than others and account for the side effects. I'm not aware of any binding studies or crystalography to support this, but it probably exists.

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text:
How do we share pain?
When somebody else tells me about his or her itching or pain in some specific body part, I sometimes begin to feel similar feelings.
I can think of about three explanations:

I feel pain all over my body all the time for many different reasons but my entrance neural pathways stop it as unimportant of these signals but when I focus on a single signal, it begins to be important for me.
Mirror neurons are doing their job.
For an unknown reason, I psychosomatically induce my friend's feelings.

Which of these theories is at least partially engaged in said phenomenon?

can't say unless we do an fMRI of you :P

@Probably - this isn't a universal phenomenon, therefore it's unique to the person experiencing it. I would guess that it's a manifestation of suggestive hypervigilance or valetudinarianism.

what about situation when male watch other male kicked in crotch? Is there universal reaction across male or general population to such video?

There are research articles in the area: http://www.ncbi.nlm.nih.gov/pubmed/19857517

@aandreev - there is a difference between empathy and sensation. If you see someone get kicked in the crotch, and you double over and tearfully cry out, that's not normal.

There has been a study by Jackson, Meltzoff & Decety (2005) who investigated the neurocorrelates involved in the perception of pain.
In order to assess this, they carried out an fMRI study in which their subjects were shown photographs of of feet and hands in situations that are likely to evoke pain and also a control set of photos that were free of any pain evoking stimuli.

Their results display that with the experimental photographs, there is a strong increase in bilateral changes in several regions that we know are involved in the perception of pain, namely:

the anterior cingulate, the anterior insula, the cerebellum, and to a lesser extent the thalamus

Notably, the activity of the anterior cingulate was most strongly correlated with the participants rating of the other persons pain, which suggests that the anterior cingulate is especially modulated according to the subjects reactivity to pain of others.
Source:

Jackson, P. L., Meltzoff, A. N., & Decety, J. (2005). How do we
perceive the pain of others? A window into the neural processes
involved in empathy. NeuroImage, 24, 771-779.
doi:10.1016/j.neuroimage.2004.09.006

Welcome back @jordizambrino (did I spell it right?) Haven't seen you answer for a while :)

@another'Homosapien' well thank you very much! It's good to be back :) (and yes you did)

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text:
How would i describe a Cladogram as paragraph?
I have this paragraph that i have halfway finished, but i do not know what to put in the spaces.

A Cladogram is a branching diagram that represents the proposed phylogeny or evolution of a species or a group. The groups used in Cladograms are called clades.. To construct a cladogram, two characters are defined. Then the outgroup of various species are identified based on the sequencing or closeness of the derived characters in the clades. In making a cladogram, ______ assume that groups that _____ more derived characters have a more close common ancestor.

The letters that are italicized are words that i think are correct. This paragraph is needed for part of a recite that i have to do in front of my class. The prof. gave me a page like this. And  I don't know what those spaces are. Can someone help me.. please?

Maybe: construct=infer, two=homologous, outgroup=ancestors, sequencing=presence, closeness=absence, clades=clades, _____(1)=always, ______(2)=share, close=recent. The last sentence assumes you are only considering maximum parsimony.

ok, this is to all the people that put this on hold HAVE shown an attempt to answer.my answers are the ones in ITALIC. So, can you please explain to me why you put it on hold? Because clearly, you can see the italic words.

@mcg256 thanks. and thank you for the explanation, you are very kind.

I provided some edits in my comment -- hope the following clarifies things for you a little bit.

To construct a cladogram, two characters are defined.

You may be confusing character and character state. It's valid to have a cladogram with a single character (e.g. the single character, "warm-blooded"), but you will need at least two character states to infer a non-trivial cladogram. The states for the character warm-blooded would be Yes or No.
A molecular example would be a cladogram inferred from a column of a sequence alignment. That column is the character, and for, say, DNA, the character states are the set {A,C,G,T}.

Then the outgroup of various species are identified based on the sequencing or closeness of the derived characters in the clades.

The outgroup is specified by you, the investigator. It's typically a hypothesis (viz. model parameter), which is either a guess or is based on some external evidence.
In short, the analysis starts from character-state data for some number of taxa ("species" in your paragraph). From this data you are selecting (constructing) a tree-topology that best fits this data.
E.g. for four taxa, labeled A,B,C,D, with D the outgroup, the process is like:
 start  --> cladogram
 ABC(D)     A  B C (D)
             \/ / /
              \/ /
               \/

There are many different methods to construct the cladogram. One popular method is  maximum parsimony, but the assumptions of that model are severe. However, any method is effectively selecting a tree topology out of all the finitely-many possible tree topologies over N leaves, where N is the number of taxa (species) in your investigation.

In making a cladogram, ______ assume that groups that _____ more derived characters have a more close common ancestor.

In this sentence, you seem to be expressing a relationship between the number of shared derived characters (synapomorphies) for a given clade, and the common ancestor of that clade.
This can be very confusing, maybe an example will help. Let me annotate the above tree with a binary character, having states + and -.
            +   +  -   -
            A   B  C  (D)
             \ /  /   /
              +  /   /
               \/   /
                -  /
                 \/
                  -

The idea is that the ancestral state for the entire group is -, as was the state for the ancestor of {A,B,C}. However, the + state was derived after the ancestor of {A,B,C} but before (or "in") the ancestor of {A,B}. Then it was passed to the terminal units, A and B. (Note: typically you don't have this ancestral-state information, only the information at the tips of the tree. You're actually inferring the ancestral states and topology from the data at the tips.)
I would claim that, in general, taxa that share more derived character (states) have a more recent common ancestor than taxa that do not. Although, this can be confounded by homoplasy.

thanks for the in-depth explanation. you deserve more than one upvote! Not enough thanks to be given.


text:
What is the basic structure of the nuclear lamina

What gives the nucleus
  its shape is a mesh of intermediate filaments called the nuclear
  lamina. It forms an interface between the chromosomes and the inside
  of the nuclear envelope. If these large protein fibres were to be
  temporarily separated into their component nuclear lamina, the nuclear
  envelope would pull away from the chromosomes and withdraw into the
  endoplasmic reticulum. Problem solved.

I am confused by the last sentence starting with "If these large proteins..." Could someone explain this in another way? I would appreciate any response. Thanks!

Can you articulate what exactly confuses you about the sentence?

Watch this animation and you'll understand the general process of mitosis:
http://www.sumanasinc.com/webcontent/animations/content/mitosis.html

This doesn't answer the question

This is a fair question, his text or source words it funny.
To keep it simple, the nuclear lamina is a network of filaments inside the nucleus and it includes the proteins associated with the nuclear membrane.
It's connected to the inner face of the nuclear lipid bilayer that makes up the nuclear envelope whereas the outer face is continuous with the endoplasmic reticulum.
Look at most any cartoon of a cell, it shows the nuc envelope attached to the ER, which it is. Makes up a big part of the cells endomembrane system.

I think in other words the author is trying to say if the lamina came apart, the envelope would essentially just be a continuation of the ER, as it's the lamina that essentially folds up that "portion of the ER membrane" up to create the nuc envelope.

This doesn't answer the question.

How is that? @OminousOwl

Okay, so your nuclear lamina is composed like so,

Source: Wikipedia
When cdc25 is upregulated between G2 and M, we see dephosphorylation of Cdk1 and it's subsequent association with cyclinB. Cdk1-Cyclin B activates the MPF, and the MPF initiates phosphorylation of the proteins called lamins. As the nuclear lamina depolymerizes, it's resorbed into the ER,

Source: http://www.jbiomedsci.com/content/16/1/96
What we find is that lamins actually help anchor heterochromatin (tightly packed) to the nuclear lamina, so when we phosphorylate the lamins, the heterochromatin is shown to move from the periphery to the more central areas of the nucleus. So we couple this uprooting of the chromatin from the lamins, and the resorption of the lamina to the ER through phosphorylation of the lamins during mitosis to broadly answer the question.

This answer has more details than mine, good answer.


text:
Nutritious protein substance for vitamin enhanced crop?
I am not a bio or science major, but we have a subject, like an elective on biotechnology and we were tasked to think of a product that hasn't been invented yet. My groupmates and I thought of a vitamin enhanced crop to help fight against malnutrition. As for the crop we thought of using sweet potatoes and altering its DNA to produce a more nutritious one.
Our plan is to use agrobacterium tumefaciens, cut its plasmid and insert a foreign DNA to it. Now we are stuck with what foreign DNA can we add to it so that we will produce a more nutritious sweet potato.
Our teacher gave us a hint that whatever we will add to the organism should be a protein because the DNA only codes for protein. So if we plan to add vitamins to the sweet potato then it should be protein-based.
Sorry but I am very confused with biotech terms because I am not a bio major. But any help would be very much appreciated! thank you in advance!

Proteins are not vitamins. It's plausible that you could add proteins to synthesize a vitamin. That  said, I think plants already make all the vitamins they need. I think you need to reevaluate your objectives.

Thank you for your reply! can you give example of proteins that could synthesize a vitamin?

This question is broad. There are many vitamins and each of them has a different biosynthetic pathway. You should also make an attempt to answer before asking others. If you have done so then please add it in the question.

You might want to look into http://en.wikipedia.org/wiki/Golden_rice

I'd start by looking at the nutritional facts for a sweet potato. What does it lack in? Now, look at biosynthesis pathways for your compound, and get a handle on what the precursors are, and what proteins are necessary. It could be just as easy as a Google search like "Vitamin C biosynthesis." There's also the Monsanto route ala Bt corn, but it'll take some digging through literature either way.


text:
Primer design for HLA locus
i have designed primers for HLA locus DPA1(exon 2 region) based on Real-Time PCR (qPCR) Primer Design guidelines. primer will start from intron regions to cover full exonic region.
F-CAGCAACAGAGAATGTCAGC
R-CCCTGAAGCAGCAATTGATG
to check for amplification of only a single region  i have used in silico PCR UCSC but it shows multiple region from chr6.
pls kindly help me with solving this.
thanks

Well the obvious solution is to redesign new primers that anneal elsewhere in the introns. Is it other HLA genes that are being amplified? Presumably you've hit a conserved region.

When designing rtPCR primers always check the extensive and well validated  taqman library for the ABI system, the primers for the region you want are already well characterized:
http://www.lifetechnologies.com/order/genome-database/details/gene-expression/Hs01072897_m1#more-information-section


text:
How do I identify the protein with the highest Disulfide bond density? i.e protein with highest ratio of Disulphide bonds per Peptide bond?
I want to list all proteins in the protein database and list them by the ratio of number of disulphide bonds per peptide bond.
I am not particular about the reliability of identification of disulphide bond.
--EDIT 1
I've been doing some research on this topic, and heres what i've found.

The PDB structure file lists all the Disulphide bonds in each structure.(SSBOND)
The PBD structure file does not list the number of peptide bonds, however it does
mention the number of amino acids. And number of peptide bonds = [no. of amino acids - 1].
We can generate a list of all PDB structure IDs with atleast 1 disulphide bond, using PDB.org's advanced search feature. This gives a list of 22543 structures.
Downloading all the 22543 structures and then parsing them using any programming language would be easy, except for the difficulty of downloading all the 22543 sturctures.

So the question now is:
 How do I parse all the 22543 structures to output only the number of disulphide bonds and the number of amino acids in each chain, without downloading the PDB structure files?

Count the number of cysteines and divide by total number of amino acids- that would be a not so reliable method.

That is the obvious answer for a single protein. I am looking for a way to do it across all the proteins in the PDB.
Essentially I want a way to query the number of Disulphide bonds from all proteins and the number of amino acids from all the proteins, and print a list.

You can download all sequences from the PDB in one file: (gzipped fasta format)

Thanks Mad Scientist, I did not realize that it would be such a small file. I guess i'll have to do a little bit of coding to get the rest of the answer.

@user8338 for PDB files you can actually find real disulphide bonds instead of counting cysteines. They would be annotated. If you are looking at all possible disulphide bonds, you can download the Refseq protein fasta file and count cysteines

@user8338 Parsing is a programming question and is off-topic; suitable for stackoverflow. However you should make an attempt at it before asking in SO.

I'm voting to close this question as off-topic because it is about text-parsing.

@WYSIWYG I agree the text-parsing part is off topic. My problem is about if it can be done on any server without me downloading the text files.

@user8338 I don't think so. The files are not that huge; you can download them without any problem.

@WYSIWYG the complete list of 22543 PDB files is in an excess of 2GB, compressed as gzip. I've been trying since last night to get them as a compressed file, and failed. Now I'm trying to download them uncompressed.

@user8338 Try doing with wget if you have a linux system. It is also available for windows with the GNUwin32 package.


text:
Why do haemophillic females $X^hX^h$ die before birth?
I just came across a statement in my book , while reading genetics, that haemophiliac females do not survive till birth (the reason not mentioned here why) . Before posting this question here I conducted quite a bit searching on the net but couldnt find any document on this. Can anyone tell me the reason why don't haemophiliac foetus make till birth ? I mean where is the problem, when a haemophiliac male having XhY can survive why not an XhXh  female ?

What book are you referring to and can you include a quote?

Dinesh Objective Biology Vol III, ISBN 978-81-7608-229-7 Page no 261 , first paragraph 4th line

I have editedy question and attached the screenshot from the text

Please refer to a standard book on genetics. From CDC website: Females can also have hemophilia, but this is much rarer. In such cases both X chromosomes are affected or one is affected and the other is missing or inactive.  In these females, bleeding symptoms may be similar to males with hemophilia.

This book is also trying to be too modest. Marriage between a carrier female and haemophiliac male it seems. Mating produces children, not marriage :P
@DhrubaBanerjee I am from the same country and I never heard of this book. Always refer to standard books. And now since you have internet you can refer from authentic websites too.

Well, Dinesh Objective Biology is a revolutionary book amongst the community of PMT aspirants. Amyway, I didnt find anywhere in the website you quoted which mentions that "Haemophillic females survive. Its only talking about carrier females. Can you highlight for me please.

@DhrubaBanerjee Entrance exams have destroyed real education. Anyways this is not the right place to discuss such things. You can come to chat if you want. And I quoted the line verbatim from that website. Look carefully

How to join chat here ? I am new to this forum. I am more active in the chemistry forum.

Let us continue this discussion in chat.

I'm voting to close this question as off-topic because it is based on an incorrect information.

Correcting misconceptions does not fall within the scope of this site? @WYSIWYG

@CRags Yeah I thought about it. And that's why answered the question.

I also think this question should remain open. It doesn't match any of the close reasons, is narrowly scoped and perfectly answerable. We address incorrect information all the time, that's one of the reasons this site is here.

Haemophiliac females are rare but they can survive just like affected males do. However, the case is slightly more complicated in women because of menstruation.
I could not find an article from any medical journal but this site seems authentic enough for a reference.

Maybe there is some clinical cause which leads to bleeding like breaking if placenta.


text:
What is the probe that absorbs at 450nm in the presence of NADH in this assay?
The colorimetric assays by Biovision and Sigma Aldrich seem to utilise a probe that binds to or reacts with NADH in order to cause absorbance at 450nm which can then be quantified by a spectrophotometer.
What is the chemical basis of this reaction?

I don't think they would reveal it but perhaps the substrate is this molecule.

@WYSIWYG Thanks! You should convert that to an answer.

I am not sure if that is the same compound.

They will most likely not reveal which substance they are using. Most likely it is something which is oxidized by NADH and then gives a blue color.

@Chris it absorbs 450nm it may emit a longer wavelength.

@MarchHo the substrate can also be Dansyl aminoacetaldehyde (See here). But Sigma does not mention a fluorimetric assay and DAAA absorbs at a lower wavelength; so can't really comment on what that substrate can be.

This is not an answer, but you don't need the mysterious probe to measure NADH production. NADH absorbs at 340nm (while NAD+ is flat at 340nm) and A340 is measured in many well-documented colorimetric (coupled) kinase assays before any kinase assay kit was in the market.

@SYK Thanks for the note, but I am aware of it (and am actually using it in some of my experiments). I was just curious on the chemical nature of this assay.


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How to tell if a beverage will hydrate or dehydrate?
Beverages of any type generally contain some measure of water. However, in the case of some liquids, the non-water components take more water from the human body to filter out than the water contained in the beverage.
The most-known example of this is salt-water from the ocean - there is too much salt so the body tries to use water from the body to "water down" the salt water.

Given a beverage with unknown additives, how would one determine if the beverage would actually hydrate or dehydrate a person?
If you knew the ingredients (and the amounts), could you tell that way?
Edit:comments seem to indicate that it depends on the solutes and tonicity of the solution: are there any other factors to be aware of?
What (common) solutes will have the largest affect on whether the human body will be hydrated and why?
if you need "common" to be defined, consider it defined as: contained in many[more than 3] store-bought beverages

It will depend on the tonicity of the fluid, I guess. Sea water is hypertonic while distilled water is hypotonic. Hypotonic fluids would move into the body faster due to osmosis. By the same reasoning hypertonic fluids would pull water from the body into digestive tract till sufficient electrolytes have been absorbed.

@CRags Thanks for the info! I guess what I'm looking for is how to measure the tonicity of a fluid. A quick google search didn't come up with much, but I didn't have much time to look. I'll have to check it out later.

It depends on the solutes. Glucose can be metabolized. Some things inhibit vasopressin (anti-diuretic hormone) excretion, others stimulate it, influencing the outcome. This question might be too broad.

Yes it depends on the solutes; it is not just tonicity. Note that marine fishes do drink seawater; the salt is actively filtered out. @anongoodnurse You can expand on your comment and post it as an answer. So the question "Is it possible to know if some beverage is hydrating or not" can be at least answered by "no".

I think at the least a list of things that will determine if a drink will cause hydration or dehydration can be provided for this question. It is an interesting one after all!

I'd say the diuretic effect of the drink is more important than the plasma osmolality it might alter. Alcohol is far more "common" than sea salt as solutes in beverages, and it has strong diuretic effect. Also, thirst-triggering is not necessarily equal to dehydration, but water in the bladder is probably not available for the rest of your body.

Osmolarity does not depend on type of solute (as long as the solute is not a huge molecule that actually forms a colloid). Osmolarity depends on the van't Hoff factor of the solute molecule.


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Can virus resistance be acquired through generational exposure?
If I have a squash plant that has a mosaic virus of some kind, and I breed its descendants (via seed) for generations, each with exposure to the same virus, will future generations be likely to eventually obtain resistance to the virus, and if so, how long would this typically take?
It seems to me that this might be how the resistant plants would have first developed resistance, but I could be wrong.

Perhaps the answer is in natural selection. Over many generations, if these plants are constantly exposed to the same virus, one of them may obtain a mutation or something similar that allows it to be resistant, thus that plant will have higher survival and growth rate and thus more seeds.
The current plant itself may also adapt to the presence of this virus (perhaps in growth patterns, etc.) over a long period of time.
As for the time for the genetic resistance to take place, it is almost impossible to say as it is almost completely random (and would also depend on what other plants you may pollinate it with as an already resistant plant would, of course, cancel the need for a mutation).
I hope this helps.


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Are all dinosaur bones radioactive?
I watching some TV program some time ago and a guy in it mentioned that when-ever museums display real dinosaur bones (as opposed to a replica) the bones are painted over with a lead paint, because they are radioactive.
The sentence was not qualified (so he did not e.g. say that just some bones found somewhere are radioactive).
So is this true of most or all dinosaur bones, or just some of them? If I ever find a huge dino fossil somewhere, should I be concerned?

I think I've seen that show, were they claiming that the dinosaurs were killed off by ancient aliens using nuclear weapons?

Partially definitely yes - that's the principle of radiocarbon dating ;-)

@Probably: Not in fossils that are millions of years old. C14 (the isotope used for radio carbon dating) has a half life of roughly 5700 years. The isotopes which are interesting here are potassium 40, various uranium isotopes and probably thorium and radium.

Here's one theory: http://truthisscary.com/2012/05/most-dinosaur-bones-discovered-are-highly-radioactive/

@Chris Radium has a very short half life.

@WYSIWYG That'S correct. But since it is part of the Uranium-Radium-decay-chain, it is generated new from decaying uranium. Otherwise it wouldn't be possible to isolate it from natural sources as the Curies did it.

The paragraph "Elemental uranium does not occur in nature. This isotope forms through combination with oxygen and several uranium oxidized minerals and compounds." form http://truthisscary.com/2012/05/most-dinosaur-bones-discovered-are-highly-radioactive/ is pure nonsense.

While it is true that some fossils can be radioactive, not all of them are. According to the ressources I have found, it depends on the place where these minerals are found and also the other minerals present at this place.
When there are uranium and or potassium rich ores available, the fossils seem to enrich these radioactive isotopes in the calcium matrix of the bone during fossilation. See the reference for some more details on this.
The isotopes which are occurring there are Uranium (U235 and U238), Potassium (K40)) and Rubidium (Rb87), all of them with half lives in the billion years. Carbon does not play a role in these very old fossils (millions of years old), as the half life of the relevant carbon isotope is to short. These elements are also used for radiodating these fossils, see the table below (from here):

Regarding the radioactive safety I think there are some fossils where you should be cautious and carry them around all day long in your pocket. Most of these isotopes release $\alpha$ and $\beta$ radiation, some $\gamma$. While the $\alpha$ radiation is relatively easy to shield, lead can have detrimental effects due to the occurance of retardation radiation of the slowed down particles. In the lab we use thick acrylic glass shields to protect us from $\beta$ radiation.
Additionally I have found some secondary sources for painting the dinosaur bones with lead paint, but no real first hand source from a museum or so. Additionally the rules for radiation safety are pretty strict. If the bones would be so radioactive that a short visit would endanger you (how long are you looking at such pieces, a few minutes at maximum I would say) than they couldn't be shown anyway. Let alone the dangers for the scientists which analyze them. So I would think this is an urban legend.
Reference:

Radioactivity in fossils at the Hagerman Fossil Beds National
Monument

The Uranium or other radioisotopes are not present in such levels as to cause problems. This much of radioisotopes even living organisms accumulate. The possible radioactivity could be only because of proximity to radioactive minerals. This should not be because of bioaccumulation.

@WYSIWYG This process happen not via bioaccumulation but after the death of the animals. If the rock in which it is embedded contain radioactive isotopes the enrich in the bones.

All fossils are radioactive, because to some degree everything is radioactive, including the human body.  It's simply a question of how radioactive.  Dinosaur bones are probably just as radioactive as any other sedimentary rock.  See e.g. http://hps.org/publicinformation/ate/faqs/faqradbods.html and http://www.sciencedirect.com/science/article/pii/S1001804206600249

Some rare fossils are radioactive enough to be dangerous (don't keep them in your pocket dangerous) others are less radioactive than the person looking at them. lead paint sounds like a total urban legend likely caused by some confusion, no one paints real bone, However repaired sections or missing pieces (replaced by sculptures or casts for mother individuals)  are usually painted however and some older ones will of course be painted with lead paint which was really common at one time. likely some one head about some museum cleaning lead paint off older mounts and jumped to a conclusion.


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Are there multiple meanings to "clone" as in "clone a gene"?
I originally thought that cloning a gene meant to put it into bacteria and have them express it. But sometimes I see it used and it seems like it's just a synonym for "identify the sequence and/or location of". So what does "clone a gene" really mean"

Possible duplicate of What does it mean to clone a gene?

"Cloning a gene" also just means making tons of copies of it, like in PCR, so you can sequence it

isn't making 'tons of copies' not regarded as 'amplification'?

I think it can be referred to as either amplification or cloning


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How can E. coli proliferate so rapidly?
The E. coli has a genome with approximately 5×106 bp. The main DNA polymerase involved in its chromosome duplication (DNA pol III , the one with highest processivity) can polymerize ~103 nucleotides per second.
By a simple calculation, we would conclude that the whole chromosome duplication would take ~ 5000 seconds ( about 80 minutes, so more than an hour). The whole cell duplication would probably take much more than that, considering not only DNA Pol III is involved.
However, in optimal conditions, E. coli can actually duplicate in ~30 minutes.
How could that be possible?
OBS.: all the numbers used here are aproximate, but sufficient to account for the correct orders of magnitude.

In bacteria there's only one (oriC), right?

The replication is going on at several spots at the same time.

I retract my previous incorrect comment. http://www.annualreviews.org/doi/abs/10.1146/annurev.ge.26.120192.002311 seems to suggest that there is only one origin of replication in E. coli.

Keep in mind that replication proceeds in both directions from oriC so, based on your calculations, DNA replication takes 40 minutes (which is still too long). The solution is to start replication again before the previous round has completed. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063475/

This is an excellent response canadianer! Why is such a great answer sitting in the comments section? ; )

@CDB Thanks. I'm a touch busy but I'll post an answer later if I can.

Adding to @canadianer comment: at any point the E.coli genome is not exactly haploid. The copy number is greater than one. The chromosome looks somewhat like a wedding ring. Canadianer, you should convert that comment to an answer.

Larry Moran has a nice description of the process, complete with diagrams, on his blog: http://sandwalk.blogspot.com/2008/05/dna-replication-in-e-coli-solution.html

Simple organism. Look at what craig ventures team has been able to do with the E. coli genome

Though Escherichia coli has only one origin of replication (oriC), replication proceeds in both directions from it. Thus, based on your calculations, DNA replication takes 40 minutes (which is still too long if the doubling time is 30 minutes). The solution is to start replication again before the previous round has completed, and here's some research which shows just that:

Yoshikawa H, O'Sulliven A, Sueoka N. 1964. Sequential replication of the Bacillus subtilis chromosome. Prod Nat Acad Sci 52:973-980

Obviously, dichotomous replication is advantageous for bacterial growth because the bacteria can replicate chromosomes faster than by having one replication point. With one replication point, the replication time, and consequently the cell generation time, would be limited by the maximal rate of DNA polymerase.

Cooper S, Helmstetter CE. 1968. Chromosome replication and the division cycle of Escherichia coli B/r. J Mol Bio 31(3):519-540

…cells growing faster than 40 minutes per doubling must initiate new replication points prior to the completion of DNA synthesis at the previous points; in other words, there should be multiple forks.

Skarstad K, Boye E, Steen HB. 1986. Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J 5(7):1711-1717

In rapidly growing cultures, with parallel replication of several chromosomes, cells will end up with 2n (n = 1, 2, 3) chromosomes if initiation occurs simultaneously at all origins. A culture with asynchronous initiation may in addition contain cells with irregular numbers (not equal to 2n) of chromosomes. The frequency of cells with irregular numbers of chromosomes is a measure of the degree of asynchrony of initiation.

Fossum S, Crooke E, Skarstad K. 2007. Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli. EMBO J 26(21):4514-4522

…initiation occurs at two origins in the ‘mother' cell. It can even occur in the ‘grandmother' cell at four origins if the time it takes to replicate and segregate the chromosome exceeds two generations.

This last image is interesting because you actually see the multiple replication origins in single cells by fluorescence microscopy.

Cell division rates may exceed DNA replication rates, because DNA replication can occur in parallel, while cell division is always serial. In a circular chromosome like E. coli, replication starts at the origin of replication. Once the origin is replicated, another chromosome replication can be initiated there, while the former isn't even finished. This parallel replication hence allows for cell division rates exceeding chromosome duplication speeds.

Forked replication in E. coli. Source: Fossum et al. (2007)
 Reference
- Fossum et al., EMBO journal (2007); 26: 4514–22


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The Ancient Kingdom of Monera
Why exactly were bacteria and archaea kingdoms separated from the now unused kingdom of Monera? Aren't they the same? They are both prokaryotes, so what is the difference?

I'm surprised this term shows up much anymore. Though it's a part of history now, the following paper by Woese demonstrated the three domain system long ago.
This, however, is the net result of the sequenced genomes of eukaryotes, archaea and bacteria:

Source: Toward automatic reconstruction of a highly resolved tree of life.
The phylogenetic differences between these organisms shed light that bacteria and archaebacteria were not as closely related as was initially though, hence the abolishment of Monera.

As you note, "Monera" includes both Bacteria and Archaea -- but genetic analysis and molecular comparisons reveal without a shadow of a doubt that Archaea share a more recent common ancestor with Eukaryota than they do with Bacteria. Consequently, "Monera" is a paraphyletic group, not a proper taxonomic category.  Thus the term has been abandoned in favor of the three domain model.
Edit You'll find quite a nice explanation of this at the Wikipedia page for Monera.
While modern evolutionary biology textbooks tend not to discuss the now outdated term "Monera", each of the following textbooks lays out the relation among the three domains and discusses the reasons that we avoid paraphyletic groups: Futuyma Evolution 2nd Edition, Herron and Freeman Evolutionary Analysis 5th edition, Bergstrom and Dugatkin Evolution 1st Edition, Zimmer and Emlen Evolution 1st edition, Barton et al Evolution 1st Edition. (Presumably other texts and other editions would cover the same ground).

Can you substantiate with some references ?

Any basic biology textbook will explain the relationship among Bacteria, Archaea, and Eukaryota. Any evolutionary biology textbook will describe the problems with paraphyletic groups. But you don't have to go that far afield. The second paragraph of the wikipedia entry on Monera lays out pretty much what I've written above: with links to explain the three kingdom system and the problem with paraphyletic groups: http://en.wikipedia.org/wiki/Monera

If you know this much then please edit your answer and put appropriate references to it. Answers with out proper references are not welcomed even if you are 100% sure.

A question: is the wikipedia an appropriate reference? The advantage is that it is so easy to access directly from here: no books to request, etc., etc.

Wikipedia is an easily accessible free encyclopedia..OK.. you can use it as a reference or you can name the book you have referenced with the author's name. Am I clear ?

Could the down-voter explain what is wrong with my answer?


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Electroporation of one-cell embryo?
Would electroporation be successful on a one/two-celled mouse embryo? If it would, what buffer could be used and what percentage of cells would be viable?
Thank you.

The buffers are usually supplied with the electroporation instrument; at least Lonza provides buffers for different types of cells. Single cell electroporation techniques exist, but they have been mostly done on neurons.[1,2]
You can also try microinjection but it requires some practice. This study reports a transfection agent called VisuFect which can be used for zygotes as well.
I am not very sure about the success rate (AFAIK it is not that good) but I think it is anyway risky with organisms which do not produce a lot of embryos.


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(Why) are polar bears more common in Labrador than in southern Greenland?
The Labrador Sea is between Greenland, Labrador, and Qikiqtaaluk:

Map source.
A Greenlandic source on polar bears states:

In Greenland the polar bear lives and breeds in the northernmost parts of West Greenland and in Northeast Greenland, but is also occasionally seen elsewhere in Greenland, as it moves with the drifting ice.
However, it is extremely rare for either local inhabitants or tourists to see a living polar bear. The chances of seeing a polar bear are greatest when sailing by ship along the coast.

On the other hand, Parks Canada for Torngat Mountains National Park (northern Labrador) states:

Polar bears are true carnivores and can be a significant risk to human beings. Visitors travelling and camping in the park are in polar bear country and are at high risk of encounters. Polar bears are almost always present along the north Labrador coast.

The observation that polar bears are more common in Labrador than in southern Greenland is supported by Derocher (2010), Nature:

Derocher (2010), Nature
Polar bears like the sea ice edge, but this is very far from either Labrador or Greenland when at its fall minimum.  When sea ice is at its spring maximum, both Labrador and almost all of Greenland are packed deeply in ice (see maps below).
Then why are polar bears so much more common in Labrador than they are in southern Greenland?  Arey they really?  And how do they survive all summer long, when the sea ice is very, very far away?  The occasional tourist might not be enough, I guess.

Arctic minimum sea ice from NSIDC

Arctic maximum sea ice from NSIDC

(I was hesitating between Biology and Earth Science for this question)

I'm not a polar bear biologist, but Labrador has trees and caribou and things, while Greenland has a lot less of those things. Labrador has 150 forest fires a year, but searching for 'greenland forest fires' mostly turns up ash from other places landing on Greenland. Labrador has a higher carrying capacity for large predators, I guess. On the other hand polar bears eat seals? I've heard that. So. I guess 'food' but I'm not sure.

@Resonating It is true that Greenland is almost completely treeless, whereas Labrador has forest — but the forest is mostly inland.  Inland forest is not a natural habitat for polar bears.  Also, as far as I know, Labrador polar bears are mainly in the north; see for example the Torngat Mountains links.  The Torngat Mountains don't have a lot of trees.

Then I officially have no idea. Excellent question!

I think the lack of sea ice coverage would point you somewhere- even with the maximum sea ice coverage picture, the SW corner of Greenland has next to none, which may impact the carrying capacity for both bears and prey animals on that narrow strip of land between the ice cap and the sea- less space and less things to hunt, less ways to get around, etc. And then there's not much continental shelf over there, either.
Labrador is surrounded by more continental shelf, which might contribute to higher levels of sea ice at high levels and greater seasonality. Might lead to more prey?
This article might get you somewhere:Polar Bears in a Warming Climate

Hmm.  But during maximum sea ice coverage, polar bears are hibernating, aren't they?

Polar bears don't generally hibernate- they need the sea ice to hunt seals (ambushing them at their breathing holes, for example).
See: "However, polar bears, with the exception of
pregnant females, do not hibernate like other bear species, they rather roam the ice in search of seals in winter (DeMaster and Stirling, 1981)." From Lennox and Goodship, 2007

The pregnant females tricked me!


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Degree of dosage compensation in Drosophila melanogaster
In this paper the authors state that the dosage compensation seen in Drosophila is approximately twofold, but they do not provide any source or numbers (as far as I can see) for this. What is the mean degree of dosage compensation in Drosophila (melanogaster)? For example, if X linked genes are, on average, perfectly upregulated the X:AA ratio in males would be 1, while if they are nearly perfectly (but slightly under) upregulated it will be ~0.9.
Here is a similar (but different) question RE perfection in DC in general (here I am specific to Drosophila melanogaster).

please explain downvote

I checked for RNAseq experiments in male and female drosophila but couldn't find any. If you can find one study then I can tell what is the mean degree of DC.

There are studies here and here which explore compensation via the MSL complex (I think Straub et al. has the correct info but they reference the Hamada paper as well). I apologize, I haven't time to read them thoroughly myself, if anyone could give them a look over.


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Find the probability of Filium (child) that are dark (and) heterozygote
Two mice are crossed and both are dark and heterozygote. Find the probability of their filium(children) dark (and) heterozygote in F1.
Here's what our teacher explained:

I don't understand. I thought it would be 1/2.

You are correct, the teacher must have made a typo

Well, she insisted in her answer and said that this is quite a difficult exercise, but if we do it in my way it is so easy.

What is the entire question? Is there more to it than what you posted?

No, it's not. I've posted the whole question.

Is hair color inherited in a Mendelian way?


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Does malaria have a reservoir host?
Can warm blooded vertebrates other than humans act as reservoir hosts for malaria parasites? I'm mainly interested in Plasmodium vivax and possible reservoir hosts in the wider area of Europe/ Eurasia.

There are a few species of monkeys which can be infected the question here is if there are reservoirs or not. As far as I know humans are the main host for these microoragnisms.

Thanks for your response @Chris, I wasn't entirely sure. I shall drop that line of inquiry!

There are 5 species of Malaria the can infect humans, and Chimpanzees and gorillas have also been found with 5 species, including vivax and falciparum.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089193/
The parasite can go dormant in the liver for days to years, causing no symptoms and remaining undetectable in blood tests. They form what are called hypnozoites (the name derives from "sleeping organisms"), a small form that nestles inside an individual liver cell. The hypnozoites allow the parasite to survive in more temperate zones, where mosquitoes bite only part of the year.
Cows are known to carry falciparum protozoa, which has at least four reservoir species. (cows, chimps, gorillas, humans) Human with sickle cells also act as a reservoir in a different way, perhaps more or less invisible or innocuous, i haven't studied recent research, and sickle cell may also have some effect in cows and chimps and gorillas.

From Wikipedia Plasmodium spp. have a huge range of hosts, including: human, primates, mammals, reptiles and birds.
Four important points to note:

The Plasmodium genus contains about 200 species.
Further important to note is that P. falciparum, P. vivax, P. ovale, and P. malariae are responsible for almost all of human malaria infections, and the distribution of Plasmodium species varies between different animals.
Humans are not in fact the definitive host of Plasmodium species. Vertebrate hosts simply serve as a site for the parasite to replicate asexually, and the sexual replication occurs in the mosquitoes.
To act as a reservoir, the host needs to suffer a long term infection. P. vivax is one species noted for its ability to form a dormant stage in the liver, and cause relapses.

So I think it would certainly be possible for there to be other vertebrate hosts (warm blooded or not) aiding in the spread of malaria to humans, but I think it's unlikely to be occurring at an epidemiologically significant rate. I think if that did happen, we would already know about it, given the considerable study that has been done on malaria.


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Do our ears or brains gradually adapt to noise pollution?
Having lived in various places all over the world for the past 9 years of my life, one thing stood out to me throughout this time, and now in particular. From a quiet place on the countryside in Sweden, I moved to Manchester for my studies. When I first arrived there, I felt the city was very noisy, a feeling which gradually reduced as I presumably got used to the noise levels there. From Manchester I moved over to Saitama in Japan, an enormous city right next to Tokyo with a considerable amount of noise during the day, and buildings that have little to no sound insulation. With the exception of particularly loud noises, I again adapted to the sound levels in the country, which at the time, I felt was no more than a natural response in terms of how much attention we pay to the noise. If I'm distracted by work or other activities, I have little reason to dwell on the sounds of driving cars and talking people.
The thing I couldn't explain purely by the 'paying attention' argument however was when I moved back to the Netherlands, to an apartment with excellent sound insulation. My apartment is located in front of a somewhat larger road, and cars pass by almost consistently. However, when I moved in I could barely hear these cars driving past, something that stood out to me as fairly pleasant. I thought a little bit of ambient music would kill the sound of these vehicles driving past altogether.
Now skip ahead one month, and I can hear the cars almost as if I'm standing next to them, an exaggeration of course, but the sound is much clearer than it was when I moved in. I know that nothing has changed in terms of insulation and I know that no windows are open. Strangely the only thing that appears to have changed is the clarity in which I perceive this noise, as none of the other people whom I've asked seem to share the same opinion (that is, that the noise has grown louder). This made me wonder - does our hearing adapt to noise pollution, and if so, how does it work?

This is a fascinating case of sensory adaptation and neural adaptation. Another example of this would be when you stop smelling something after being exposed to it for long periods of time (as you probably know, this "long period of time" happens to only be a few minutes). A great representation of this happening with the nerves in the skin was done by Georg Meissner:

This image is from https://www.boundless.com/psychology/textbooks/boundless-psychology-textbook/sensation-and-perception-5/sensation-37/sensory-adaptation-160-12695/
When stimulus is applied, these nerves begin rapidly sending messages to the brain in the alarm period. The rate of these signals slowly start to decrease over time in the resistance period until they finally reach exhaustion and stop completely in, of course, the exhaustion period. Keep in mind that the time it takes for all this to happen varies greatly upon what type of cell it is (obviously olfactory cells have a much shorter exhaustion time than, say, hair cells (hearing cells)). After these cells have had a chance to recover (more like recalibrate actually), we can begin to hear/smell/feel/taste again.
I hope this helps.

Are the signals from the nerves themselves no longer being sent, or is the brain just choosing not to pay much attention to them?

In most cases it is the original nerve that sent the message that becomes exhausted (sensory adaptation) and no longer sends the message (or at least the message becomes so weak that the brain hardly notices it).

Very quickly and totally from the top of my head: Traffic noise is in many cases dominated by low frequencies, with the whole spectrum somewhat similar to a distorted 1/f function, with a few tonal peaks for exhaust noise and tyre/tread sounds. Now add the structure you are living in: "excellent sound insulation" in the EU is (still) dB(A)-focused, meaning architects and planners are aiming for a "wow" effect in noise reduction by eliminating that what's easy to eliminate - high and mid frequencies, ignoring mostly the low (and energy-rich) frequencies, which are incidentally the ones the A-weighing of noise is (historically) ignoring as well. As a result, you are basically living in what's known as a low-pass filter, one that is also "drawing" tonal peaks (resonances, room nodes) out of that low-frequency noise mixture. At first, your cochlea's short-term adaption mechanisms will do their job well and tone down signals that are not meaningful (MOC reflex).
Over time however, the presence of low-level tonal, continuous sounds can damage ("wear out") a specific sensor type necessary for this reflex to work. As a result, even inaudible LFN noise can, over time, lead to a distal sensitization effect. In many cases the culprit is actually not the traffic noise itself, but HVAC installations like heat pumps, A/Cs and gas turbines. The effect of "I can hear too much" (being aware of noises) as a result of sub-threshold LFN-exposure is known in the medical literature as a symptom of VAD stage I / II and in fact quite common in the urban population. Certain medications (Gentamycine, cis-platines) as well as organic solvents (acetone) and some disinfectants can speed up this process, which is non-reversible and poses a risk factor for suffering atypical (early onset) hearing loss later on... The "I hear too much" effect has been quite a solid indicator of long-term, low-level IS/LFN noise pollution.
To be on the safe side and to rule out a sub-threshold LFN-problem, you should an seek medical advice.
Sources:
Bakay, W.M.H., Anderson, L.A., Garcia-Lazaro, J.A., McAlpine, D. and Schaette, R., 2018. Hidden hearing loss selectively impairs neural adaptation to loud sound environments. Nature communications, 9(1), p.4298.
Branco, N., 2005. Clinical stages of vibroacoustic disease (VAD) for health professional continuous research. Mat. 12th int. sym. Lisbon, p.145.
Burt, T., 1996. Sick building syndrome: acoustic aspects. Indoor and Built Environment, 5(1), pp.44-59.
Ebner, F., Eulitz, C. and Möhler, U., Approaches for a comprehensive determination and assessment of infrasound effects in Germany. DAGA 2013 Conference Paper.
Findeis, H. and Peters, E., 2004. Disturbing effects of low frequency sound immissions and vibrations in residential buildings. Noise and Health, 6(23), p.29.
Kugler, K., Wiegrebe, L., Grothe, B., Kössl, M., Gürkov, R., Krause, E. and Drexl, M., 2014. Low-frequency sound affects active micromechanics in the human inner ear. Royal Society Open Science, 1(2), p.140166.
Paulin J, Andersson L, Nordin S. Characteristics of hyperacusis in the general population. Noise Health 2016;18:178-84
Waye, K.P., Clow, A., Edwards, S., Hucklebridge, F. and Rylander, R., 2003. Effects of nighttime low frequency noise on the cortisol response to awakening and subjective sleep quality. Life sciences, 72(8), pp.863-875.

I removed the medical advice and inserted a referral to an expert.

Maybe keep the referral to a certified acoustician as they will have the means to validate/rule out sub-threshold IS/LFN-immissions, whereas a ENT doctor will only see the effects (symptoms) which could also be the result of extended exposure to ototoxic substances like you would find them in nail polish remover...


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How Do White Blood Cells Learn? Or Do They?
So I get the concept that a vaccine is a weakened form of a virus so that the body can "learn" to fight it and make a person immune to that disease, but how exactly does this learning take place? What learns? The white blood cells? Do they have their own database or something and do they go from cell to cell informing them of what they learned? I read that they only last around 5 to 7 days so that means there's constantly new white blood cells that also need this information for all diseases ever encountered. How does this work? Thanks!

See: quorum sensing and controversial study about Electromagnetic Signals from Bacterial DNA where it indicates a "wireless" version of intercellular communication which was found in bacterial communities, so it could be similar for white blood cells.

So while some kind of a biological database might have been an evolutionary option, the way we evolved is different from this. Rather than 'planning' what diseases could be recognized in the environment and recording this, our bone marrow constantly pumps out naive B and T cells that have a randomized receptor on them. The effect of this is that every new B and T cell that your bone marrow makes will recognize a unique, random protein sequence, and you will have billions of these cells floating around in your blood circulation at any given time. These cells however will only float around in circulation for a short period of time before dying and being replaced by other cells with new random sequence receptors.
When you get a vaccination, you are injecting in specific protein sequences from a specific pathogen. As these injected protein sequences circulate through your blood they will eventually bump into a B or T cell that has a receptor that recognizes them. When this happens, the B or T cell will now start to divide and give rise to long lasting memory cells that express the exact same receptor and will therefore recognize the exact same protein sequence again in the future. These cells will float around in your blood for most of your life and make you 'immune' to the recognized pathogen. When you get reinfected with the same pathogen or the pathogen to which you were vaccinated these memory cells will rapidly divide upon recognition of the pathogen and give rise to a large number of effector cells that eliminate the pathogen before it can 'make you sick'.
What is really cool about this is that because each T or B cell carries on it a receptor that recognizes a random protein sequence, you currently have in you B and T cells that would recognize a protein that does not even exist on Earth, but might exist on Mars or somewhere else in the Universe. This makes our immune system quite valuable because any protein that nature creates for all of time anywhere in the universe will still be recognizable by our immune systems.

Thanks for the answer! Can you clarify how the memory remains if the B and T cells only last for a short while and would then be replaced by randomized ones from the bone marrow? I presume they must reproduce as well, but if they're reproducing while the marrow is making random ones, wouldn't the population be hard to manage?

So the recognition remains because of specific cells called memory B and T cells. These are almost identical to all of the naive short lived B and T cells but they last for most of your lifetime if not all of your lifetime. So they do not need to reproduce until you get reinfected with the pathogen. So typically these memory cells will be present in low numbers and just wait in the blood for 80 years, and then every time you get exposed to the pathogen they recognize they rapidly produce millions of new cells with the identical receptor to eliminate the pathogen. Make sense?

Ahh, so the "naive" B and T cells are short-lived, but if they come into contact with a protein befitting them they will create a "memory" B or T cell and those permanently remain?

Correct. The idea is that if a naive cell doesn't come into contact with and recognize a protein within a short while then it might not recognize a pathogen in your environment (or a protein sequence that even exists for that matter) and is eliminated so your blood doesn't just become a sludge full of too many cells. But when a naive cell does come into contact with and recognizes a protein it will produce a small population of memory cells that are very long lived so that they will be able to rapidly respond the next time you come into contact with the pathogen.

The B/T cell receptor is not only recognizing proteins, it is recognizing antigens in general. Most of these are proteins, but they don't have necessarily to be proteins.

There is also a subsystem to eliminate B cells that recognize "self" (which includes food).  Obviously it's not good for the immune system to go after "self" molecules.  And that's exactly what does happen in auto-immune diseases: the "identify self" subsystem glitches.

Right, I think a really good answer should cover clonal deletion and affinity maturation. The first explains why you aren't immune to "self" and the second is an important part element in making the polymorphic immune system even better.

Basically the adaptive immunity responds to shapes of the antigen, rather than sequence.

This is all also very relevant information. It's true that antigen recognition is far more complex that just the amino acid sequence of a protein. And yes many other compounds can show positive binding to the TCR/BCR especially some carbohydrates and lipids, though in those of these cases recognition is not straight forward, and other proteins must be available for this to occur.

As for the shape of the antigen determining binding to the TCR/BCR. In a sense this is correct in that the 'shape' of the receptor fits the 'shape' of the antigen, but to those without an in-depth biochemistry background this may be a bit misleading, because you could make an identically shaped molecule with vastly different charge distribution that would have no reactivity to the receptor. So because of this I find it easier to just explain it as the amino acid sequence determining binding. But all good points.

Recognition by peptide sequence applies much more to TCRs than antibodies.

If this is the case, how do some vaccines last longer than others?

@canadianer TCRs are structurally similar to immunoglobulin. AFAIK TCR recognize the shape of the peptide presented by the Antigen Presenting Cells. Am I wrong? The point about charge never occurred to me, although now thinking retrospectively it is obvious!

@Eric that would be an excellent question to ask separately

@CRags All receptors recognize shape insofar as it is defined by the spatial arrangement of atoms and electron distribution in a molecule. TCRs recognize short peptides that are proteolytically generated from larger proteins and presented on MHC. Although some local folding is expected, the peptides are pretty linear and are not in the native configuration found in the original protein. That is what I meant by recognizing peptide sequences. A BCR recognizes amino acids by their arrangement in the tertiary structure without any requirement for them being close in the primary sequence.

@Eric, some vaccines last longer due to mutations of the disease. The flu, for example, is different every year so the previous vaccination does very little for the new strain. I can only guess Tetanus must also mutate then but at a much slower rate or something. I'm not the biologist though so as CRags indicated, it's a good question to ask separately :-)

Afaik. TCR binds only to MHC1, so it won't recognize what you inject in a vaccine. Most of the vaccines are B cell vaccines. Creating T cell vaccines is much harder and it is bleeding edge science.


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What are the total number of action potentials in the human brain?
Is there an approximate figure of the total number of action potentials in the human brain? It's my understanding that there are ~ 60 billion neurons in the brain with ~ 100 trillion connections between them. Plus there are graded responses between those connections. Is there an estimated figure for what the total might be?

If firing rate is from 1 Hz to 200 Hz, 100 trillion to 20 quadrillion synaptic firings. Neuronal (say, measured from soma) firings  will add up to 86 billion to 17.2 trillion action potentials per second.
It important to remember, that synaptic firings "sum up" in soma or interfere between each other, so the are more of those.
Read more: http://neuroblog.stanford.edu/?p=4541

Awesome, thank you! I will check out the link.


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Fixation rate at neutral loci
It is a classical result that the expected time for a neutral mutation to occur and to get fixed is $2 N \mu \frac{1}{2N} = \mu$, where $N$ is the population size and $\mu$ is the neutral mutation rate (wiki).
I am not sure I understand what this actually mean. What is the probability of (at least) one fixation event to occur in $\frac{1}{\mu}$ generations? Is it 0.5? Could we calculate the probability that (at least) one fixation event occurs in $n$ generations? For example after $n=\frac{\mu}{10}$ generations, is the probability of observing (at least) one fixation event equal to $0.1$ or is it more complicated?
UPDATE
Following @DanielWeissman comments:
Let's consider we are starting with an initially monomorphic population (population of clones). In addition to that, let's consider that the population is relatively small $N\mu < 1$

You should probably specify whether you're considering an initially monomorphic population, or a steady-state population (with infinite alleles), or something else.

I didn't realize that would matter. Let's consider an initially monomorphic population. (see update)

First of all, the $\mu$ is not expected time for a mutation to occur and get fixed; it is the rate at which mutations are fixed in the population. The basic result states that if neutral mutations arise at a locus at rate $\mu$ within individuals, mutations at this locus will be fixed in the population at rate $\mu$ as well.
The expected time for a given neutral mutation to fix after arising, given that it is not lost from the population, is approximately $4N_e$, where $N_e$ is the effective population size. Kimura and Ohta (1969) derive this result using a diffusion approximation; Kingman (1982) develops coalescent theory and in the process obtains what in my opinion is a more elegant derivation of the same approximation.
Now what is the probability that some mutation goes to fixation in the population as a function of time? Even though the fixation rate in the population is $\mu$, this does not mean that with probability 0.5 some mutation fixes within $1/\mu$ time units. That probability will depend on the distribution of fixation events in the population. Here's a good way to think about it. If fixation events were evenly spaced and occurred at rate $\mu$, then with probability 1 you would have a mutation within an interval of length $1/\mu$. If fixation events were highly clumped, then you would have a very low probability of having a fixation event within an interval of length $1/\mu$ -- but if you did have one event, you would probably have many. If fixation events are distributed as a Poisson process--which I suspect they would be in a purely neutral model--the probability of having a fixation event within a time interval $1/\mu$ would be given by a (negative) exponential distribution and thus the probability of having at least one fixation event in a time interval of length $1/\mu$ would be $1-\frac{1}{e}$.

This final answer isn't quite correct -- it neglects the drift time mentioned in the second paragraph. If $N\mu \ll 1$ it's a good approximation though. (If $N\mu \gg 1$, the process of fixation is almost deterministic.)

@DanielWeissman Thank you for the informative correction.


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Can life forms exist from simple structures not made of the four bases?
I understand that all life forms on the planet are made from adenine, gauatine, cytosine and thymine, which chemically joined together to form RNA or DNA (correct me if I'm wrong). This goes on to form all complex life as we know it.
I was wondering if it was possible- even studied theoretically- that other life forms could exist made of different elements and compounds, perhaps let's say iron, cobalt or tungsten? Or are the 4 bases the only possible way of life as we currently know it?

If we think of a cell as the unit of life, these constructs are made up of lipids, carbohydrates, proteins and nucleic acids. Of course, viruses are considered non-living, and are composed typically of just nucleic acid and protein. At that, we have to make a cutoff between what is living, what's non-living, and what constitutes one or the other. For reference, nucleic acid is DNA/RNA. The take-home point though, is that you need more than nucleic acid to get a living organism as far as knowledge contends; ergo we'd need more than an element/polymer.

You seem to have a severe misunderstanding of biochemistry. The 4 nucleotides you mention A, G, T, and C are used to make DNA, but in RNA, the T is replaced with uridine, U. Additionally, RNA can contain many modified nucleotides. Of course, there are many many more compounds in living organisms than just the nucleotides. I recommend reading some wikipedia articles to get a better understanding, such as on DNA, RNA, how they're related.

possible duplicate of http://biology.stackexchange.com/questions/90/life-without-dna ?

Nobody knows for sure, but search Google News for "Life on Titan".

@user137 I was aware of the U base. When I said all life forms are made of the four bases, I just meant a large amount

So this question is difficult to answer because it has some errors in it, in that lifeforms being dependent on rarely used elements is a different question than lifeforms using different DNA bases, but I will answer both.
So for the question about whether or not organisms could exist that use DNA bases not found in organisms on earth, the answer is certainly yes.[1,2]
The above reference shows a very elegant example of completely synthetic DNA bases being incorporated into E Coli and propagated in culture without providing any noticeable negative effects. This provides strong support that life on Earth developed around the same 5 bases (CTGAU) by chance.
As for whether or not organisms could rely heavily on elements other than H,C,N,O, and P, this is certainly possible and evident already here on Earth. Extremophiles are a general class of organisms that have some pretty interesting properties to them. Some metabolize sulfur or metals, others live in really extreme temperatures or in areas of high radiation.
So really yes in both cases, life can really take numerous shapes and forms even when it seems completely impossible for them to do so.


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What mechanisms exist for the excision of specific sequences from DNA?
I already know about recombinases (specifically excisionases), but was wondering if there were other mechanisms present.

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The absolute standard way has to be PCR. http://en.wikipedia.org/wiki/Polymerase_chain_reaction
Design primers for each end of a known sequence, provide DNA containing that sequence, and (hey presto!) amplify the length between the primers.

If you're asking about how sequences are excised in nature, an interesting case is the CRISPR-Cas viral defence system of bacteria, where sequences adjacent to a particular "handle" or "signal" in the viral genome are excised and added to an array in the bacterial genome which acts as a memory for immunity. I don't know how the mechanism works!

What about endonucleases?

I know about the Cas9 mechanism as well.  I guess my question was more oriented towards the "cutting out" of a sequence of DNA and then a religation of the two flanking ends.  Cas9 does the first part, but not the second part, while recombinases do both.

Genome editing techniques like CRISPR-Cas and TALEN use non-specific recombinases coupled to a DNA-recognizing part that can be designed to be specific for any stretch of sequence, as it is constructed out of single zinc-finger 'modules' that each specifically bind a couple of nucleotides (one nucleotide each in the case of TALEN).


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If a gene is located on the X chromosome, does that mean males are never heterozygous for these genes?
As said in the title I am a little confused on the idea of traits located on the sex chromosomes. The example we worked on in class was haemophilia, a recessive trait located on the X chromosome. Does this mean males only have one allele to choose from while females have two? Does this mean that only females have the ability to be heterozygous in sex linked traits?

I guess the terms heterozygous or homozygous are not applicable because there is no homologous chromosome. I think this condition is called hemizygous if I am not wrong.

http://onlinelibrary.wiley.com/doi/10.1111/evo.12224/epdf

There is a specific term for this called hemizygous / hemizygote - meaning that only one allele of the gene is present. Therefore males cannot be heterozygous for genes on the X or Y chromosome (not counting for gene duplication or other chromosome disorders) since they naturally carry only one copy of these chromosomes.

Thanks! I knew there was a term for it when I posted my answer and I couldn't bring it to mind.

Do you mind adding a source that will make the answer complete and will be a good source for users who stumble upon your answer having the same question?

@SanjuktaGhosh Thx, good point well I could link wikipedia for quick fix :) I'll look for better source when I have time (may take a week, i'm quite busy atm).

In XY sex determination systems the females carry two copies of the X chromosomes, thus can be homo- and heterozygous. Males however, carry one X chromosome, meaning that all loci are hemizygous (excluding those with homologs on the X). Under conditions of complete dosage compensation, often through up-regulation of X linked loci, they are effectively homozygous, as demonstrated here where expression levels of X-linked genes are at a ratio of near 1:1 with autosomally linked genes.
An interesting potential consequence is that males will exhibit more additive genetic variance in X-linked loci.

I down voted because you say that all loci are hemizygous, which is misleading (see my answer). If you change it to "most loci", or something to that effect, I'll gladly turn that arrow upside down.

@canadianer Good point, edited

All of the other answers are basically correct, I just wanted to add that there are some genes which are present in both the X and Y chromosomes, in the pseudoautosomal regions. These genes are inherited in an autosomal manner (hence the name). A male has two copies of each, just as a female would, and can thus be homo- or heterozygous.

Because males only have one X chromosome, they can only have one copy of any gene found on the X chromosome, and therefore only have one allele. This means that in the case of a recessive disorder like hemophilia, should they happen to inherit a recessive allele from their mothers, they will have the recessive (disordered) phenotype because there is no other allele present to give them the dominant phenotype.
"Homozygous recessive" and "homozygous dominant" are perhaps a little misleading here because male individuals aren't homozygous at all, having only one copy of genes present only on the X-chromosome.
But yes, this means only women can be heterozygous for sex-linked traits. Men will have either the dominant or the recessive phenotype, and cannot be carriers.

It sounds like you pretty much have it. Hemophilia is recessive, meaning that a single function copy of the necessary clotting genes will be sufficient to function. So a female can inherit defective genes on one X chromosome and functional genes on the other and be perfectly fine. However, if a male inherits defective genes on one X chromosome he will have the disorder because he does not have another X chromosome to provide the functional genes to compensate.
I realize that you also said you are confused about traits located on sex chromosomes. They are essentially just like any other chromosome and carry genes just like other chromosomes. It just so happens that they also carry genes that are important in sex determination.


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Why do Lapidaria margaretae look like stones?
Previous Research
I stumbled across a trending reddit post "Lapidaria margaretae looks like stones" (as of 3rd Februrary 2015); but I could not find discussions as to reasons behind why.
Question/s

Why do Lapidaria margaretae look like stones? I am interested in both the morphological/physiological reasons, as well as possible evolutionary mechanisms.
Or perhaps I am asking the wrong question, then what should it be?

I've never seen a stone that looks like that…

"Teleology is like a mistress to a biologist: he cannot live without her but he's unwilling to be seen with her in public." - J.B.S. Haldane (1892 - 1964)
I can't tell you why Lapidaria margaretae looks like 'stones'. But I can deduce something from the way this plant looks.
First and foremost, I can say this plant probably evolved in an arid region, possibly a desert (less than 10 inches of water per year), because it is a succulent, with a shape that comes pretty close to minimizing it's surface to volume area (decreased evaporation, decreased transpiration). Seeing as it's a dwarf and shaped as it is, I might hazard that it's windy and sandy where this plant evolved, also because of it's shape - low to the ground, sturdy, low surface area, able to resist the wind. Finally, the light color of the plant suggests a lot of bright sun (reflects sunlight more than some darker colors).
None of that is foolproof, but in this case, it turns out to be right; the plant comes from southern Namibia, and is commonly called the "Karoo rose".
This is one image of the Karoo region:

Stones come in all kinds of shapes and sizes, also influenced by water, wind and other environmental influences. That this plant looks like stones is mostly coincidental.

I'm struggling to understand the significance of the quote :/

ah.. well in your defence @anongoodnurse hmm step (2) of the  scientific method (at least the Pirsigian six step flavour) requires us to dream up hypotheses!