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Difference between Condensin and Cohesin proteins?
The chromosomal DNA is stacked with help of cohesin and condensin protein in which particular manner? Can cohesin be said to form kinetochore? How would they vary exactly?
The terms are so narrowly windowed that they squeeze my brain through...!!! thank you for your kind help ^_^

Hi and welcome to bio.SE! When asking your questions, try to be as clear and provide as much information as is possible/relevant to help you get the best answer. Here, I think you need to separate your questions out a bit - you're asking about the difference in functions of the 2 proteins (cohesin and condesin), and you're also asking about cohesin's role in forming the kinetochore (related, but slightly separate). And what are you referring to when you ask 'how do they vary'? The 2 proteins? Don't be afraid to write a couple of paragraphs so that it is clear what you're asking. Thanks.

Hello sir...thank you so much for you guidance. When i said how do they vary am asking for the difference in their functioning sir as you rightly guessed. Once again thank you for your feedback and guidance.

You can edit your original question (by clicking 'edit', next to the vote buttons) to make it clearer, and tidy it up. I can do this if you would rather. Also my name is Luke, feel free to use it! :)

Condensin
Condensin I: present in cytoplasm during interphase, has access to chromosomes after prophase. Contributes to condensed chromosome assembly during prometaphase and metaphase [1].
Condensin II: present in nucleus during interphase, involved in chromosome condensation. Contributes to condensed chromosome assembly during prometaphase and metaphase [1].
Cohesin
It keeps sister chromatids connected with each other during metaphase and ensures that each sister chromatid segregates to opposite poles. "It facilitates spindle attachment onto chromosomes. It facilitates DNA repair by recombination." [2]

References:

Wikipedia contributors, "Condensin," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Condensin&oldid=606814199 (accessed July 29, 2014).
Wikipedia contributors, "Cohesin," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Cohesin&oldid=617481362 (accessed July 29, 2014).


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Why does non-continuous sleep makes you feel tired?
Let's say, hypothetically, that you fell asleep at 10PM, and you were woken up by a noise at 1AM. If you went back to sleep immediately and woke up at 6AM, you will feel tired even though you had slept for 8 hours. However, if you sleep for 8 hours straight , your body will feel rejuvenated. Is it because of REM sleep being cut off and restarting again?

Yes, but I'm guessing. OTOH, you can be well rested after 1 hour, if you know beforehand (=expect) that it will be short. So, it's more a question of psychology, not biology IMHO.

Sleep is not homogenous - there are different phases of sleep - REM, NREM-1 to NREM-4. And these different stages may play different roles in 'rejuvenating' the body (as you put it).
When you first fall asleep, you go into NREM-1 phase, which is the lightest sleep, and progresses into NREM-4, and for the first half of your sleep cycle, this cycles so you go from NREM-1 > NREM-2 > NREM-3 > NREM-4 > NREM-3 > NREM-2 > ....
On the first half of your sleep cycle, the NREM3 and NREM4 phases dominates, only on latter half of your sleep cycle are REM phase observed and progressively dominate.
Depending on how much you are waken up by, once you escape your sleep cycle, you may re-enter back at a different stage, which may mean you are no longer able to have much REM sleep. Subsequently, you will not have the rejuvenation that is associated with REM sleep and you feel tired.
Interesting note: There are people who have tried a method called polyphasic sleep, where they nap/sleep periodically and regularly, instead of sleeping once a day for 8 hours, say. People who promote this says that people do not feel tired because as soon as they nap, they go in REM sleep, and so the amount of REM sleep you get per day will still be the same. I'll let you make your own mind up about this one.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


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Do goldfish really have a 5 second memory span?
I heard that when people place goldfish in another tank, they just forget where they where previously? True or False ?

There's already a question about this on Skeptics: http://skeptics.stackexchange.com/questions/6474/do-goldfishes-have-a-two-or-three-seconds-memory

@MadScientist, nice link! Why don't you write it up as an answer?

My answer might sound unscientific, since I haven't had tanks filled with goldfish. However, I have had fish and other pets over the years, including cats, turtles and a very sick lizard. I have a scientific background, and on this strength, I will report based on personal observation, albeit with a small sample size.
My fish always "knew" me. When I approached the tank, they knew it was their "feeding person", and even when they were not getting fed, left what they were doing aside and came to the surface to "greet" me, or more likely, impending food. I even experimented by asking others to walk up to the tank and saw that most of them did not respond in a similar fashion, although sometimes they did. With me, I enticed the same reaction every time, even  after a new tank was populated or new additions were made.
This makes me conclude fish, and goldfish, which I did keep, have "better than expected" memory.
When they are put in a new tank - well, I suggest you move to a well crowded city that is new to you, and see how long it takes for you to get your orientation right.
Hope it helps.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Can visual acuity be improved?
Is it possible to completely cure myopia using natural methods (i.e. not with Lasik etc.)?.
I have seen websites claiming that exercising the eyes will help improve eyesight.
Is this true?

What is perfect vision?

@Kevin: 20/20 vision I guess (see http://en.wikipedia.org/wiki/Snellen_chart )

While there is no such thing as perfect vision, growing evidence from Asia shows that looking often at distant objects (which one does naturally when being outside) can stop myopia progression. Vice versa, progression appears to increase when myopic children mainly live indoors.
D. J. Park, N. G. Congdon: Evidence for an "epidemic" of myopia. In: Annals of the Academy of Medicine, Singapore. 33, 1, Jan 2004, 21–26. PMID 15008557. (Review).
K. A. Rose, I. G. Morgan et al: Outdoor activity reduces the prevalence of myopia in children. In: Ophthalmology. 115, 8, Aug 2008, 1279–1285. DOI:10.1016/j.ophtha.2007.12.019. PMID 18294691.


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Is it possible to still grow taller after growth plates have been closed?
In addition, when do we know we stop growing taller? Or we keep growing taller?
To the first question:
Recently, I went to a doctor to have a check up, he said that my growth plates are closed and cannot grow taller anymore. True or false? Is it possible to have a second growth spurt. I am about 16.

No, because growth only occurs at the epiphyseal plate or growth plate. In the picture here, the epiphyseal plates are the two horizontal lines in the tibia and fibula, and bone growth occurs in the upward direction, or toward the middle (shaft) of the bone. Once the epiphyseal plates close, the bones can no longer elongate.
It's possible to have a second "growth spurt," but it's only because the epiphyseal plates haven't closed. David Robinson, the basketball player, was 6'7" as a senior in high school, but ended up being 7'1". The "growth spurt" is caused by the sex hormones, which is why a significant amount of growth occurs during puberty.


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Organize sequence database
I recently took up the task of organizing the sequencing database for a research project. I am still quite unsure of which database type I should use for this. Some advices/recommendations would be wonderful.
This research project is more like a class where students are taught how to sequence a piece of plasmid via Sanger sequencing method, with paired end primers. For each plasmid there will be two entries (~1kbp each). Then the students would BLAST the sequence, mostly to see if there is any close match with certain related organisms.
The main purpose of this database I'm creating is to monitor the sequencing progress, as well as to single out the samples that need to be redone. So far, the record-keeping is not exactly accessible, hence the need for re-organization. Additionally, the students would need to be able to view their own results and enter the BLAST results themselves. The last condition seems to necessitate a web-server type of thing that the student can connect to enter their information.
The total number of bacteria clones containing plasmids are ~18k, which means there will be ~36k entries in this database. It would be great if there is anyway to manage the trace files of the entries, or if not, I think I can add a column for the file path.
Is there a database management program that is appropriate for organizing sequence and trace file, with easy access for data entry by multiple users? It would also help if the program don't have a high maintenance need.
Disclaimer: I have very limited knowledge with database structure, having only taken an online intro to database class. About programming language, I am still learning Python. This project is a way to force myself to learn more.

I think this has more to do with the informatics end of it rather than the biological one.

I am afraid this is off topic here. That said, there is nothing special about managing sequence and trace files. They are simply text files like any other. Have a look at phpMyadmin, it should do exactly what you need.

Like it says below, text files should be good enough, but make them in fast format. If you haven't already, look at BioPython - it will provide a way to feed your text files into BLAST searches at NCBI.

Thanks for your suggestion, I will try that out. On the other hand, I was unsure which site to post.

Normally we ask that bio-informatics questions have a strong biological component to the question, this doesn't seem overly apparent here.


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What is the oldest example of DNA identified?
What is the oldest sample of genetic material (presumably DNA) identified? What are the prospects of pushing back much further into the geologic record?

419 million year old DNA from halophilic bacteria.
http://news.discovery.com/earth/oldest-dna-bacteria-discovered.html

My understanding was that DNA in non-living matter had lifetimes of thousands of years, not millions. How did such ancient DNA manage to be preserved? Does this result hold up?

Before DNA there was RNA. But ever heard of the polymerase chain reaction? See DNA and RNA don't actually need enzymes to replicate or a live cell. If you heat up and cool down DNA or RNA at certain temperatures and add in bases/nucleotides it will go ahead and do it by itself to make more DNA or RNA. Evolutionarily it's likely RNA came first, whilst the molecule itself was preserved (because it could self replicate) it wasn't conserved (the order of bases didn't matter so they swapped a lot). DNA is more stable, put RNA on a bench and it quickly degrades, so that's why DNA was required.

I rather think that if the proper chemical conditions can preserve the molecules within tissue, you can find very old DNA.  In this case the bacteria were preserved in crystalized salt and this seems to have kept the DNA intact.  Other examples are from insects preserved in amber and tissues from animals who were buried in permafrost.


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Why can't a human regenerate limbs like some other species?
When a person's arm is amputated, the arm will no longer be able to grow back. However, in salamanders, the arm actually grows back.
In comparison to a human, what is really happening to the cells in the wounded area in salamander ?

Certain parts of the human will regenerate, though (liver for instance)

well it is not as fast as the salamander .. lets say an arm why wouldn't it regenerate ?

Our limbs do regenerate - but only up to a certain point. If you cut off up to about 0.5cm from the tip of your finger, it will completely regenerate. (No, DO NOT try this just because I said so.)

After salamanders (or certain other amphibians) lose a limb, the epidermis migrates to cover the wound, forming a structure known as the apical epidermal cap. The underlying "stump" then generates a de-differentiated mass of cells from normal tissue. In most cases, these cells will express genes that are vital to the proper formation of limbs, such as HOX genes. This "lump" of cells at the stump of the wound are typically referred to as a blastema. Basically, the blastema continues to grow and regenerate the limb in a way similar to fetal growth. Though mammals (including humans) also have some regenerative capabilities, they are much more limited. In addition, many regenerated limbs will also be mildly deformed (square fingernails). In axolotl salamanders, it was found that certain retrotransposons, such as the LINE-1 element, were prevented from "jumping" around in the developing blastema during limb regeneration. The two active proteins PL1 and PL2 were responsible for inhibiting the activity of LINE-1 and other such retrotransposons. Active retrotransposons can potentially rearrange the genes in germ cells can be detrimental to the mechanisms that allow the blastema to replicate and differentiate, so the PL2 and PL1 proteins play a vital role in their regenerative capabilities. When the PL2 and PL1 proteins were "switched off" in certain axolotl salamanders, their regeneration was much less efficient. Since mammals lack the PL1 and PL2 proteins and have a different LINE-1 retrotransposon, they have reduced regenerative capabilities.
Sources:
Wei Zhu, Dwight Kuo, Jason Nathanson, Akira Satoh, Gerald M. Pao, Gene W. Yeo, Susan V. Bryant, S. Randal Voss, David M. Gardiner, Tony Hunter. Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration. Development, Growth & Differentiation, 2012; 54 (7)
Wei Zhu, Gerald M. Pao, Akira Satoh, Gillian Cummings, James R. Monaghan, Timothy T. Harkins, Susan V. Bryant, S. Randal Voss, David M. Gardiner, Tony Hunter. Activation of germline-specific genes is required for limb regeneration in the Mexican axolotl. Developmental Biology, 2012; 370 (1)
Odelberg SJ (August 2004). "Unraveling the Molecular Basis for Regenerative Cellular Plasticity". PLoS Biology 2 (8)

For salamanders, when they lose a limb, they have cells called fibroblasts that migrate to the wounded area. These cells are not differentiated and are able to be differentiated to whatever is necessary for regeneration. That sort of cellular differentiation for repair doesn't happen for us humans, yet. Give synthetic biology about 20 more years. :D

Sorry, but this answers only begs for the question: how are salamander fibroblasts different from human fibroblasts? By the way fibroblasts are differentiated cells.


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What protocol does the nervous system use?
I just read How does an inhibitory synapse communicate to the cell body of a neuron? and found myself asking this question ... hopefully I'm not asking the same thing
Any body possessed of a nervous system probably has hundreds of neurons. At one end of the neuron is the nervous system, at the other - the organ.
A neuron is connected to several others in the vicinity through it's dendrites.
When a 'signal' (for want of better word) is put on the system bus - how does a neuron know whether it has to act ( contract/relax it's associated muscle/organ ) on the signal, or pass it on ( forward ) after amplification of the signal, if necessary?
Is there something like a chemical protocol to identify the target neuron/group-of-neurons that form the destination?

Sensory neurone is the protocol I guess.

An analogy to a computer bus can easily mislead you. Neurons do not communicated via a multiplexed "bus" with different targets; rather the complex connectivity of the neurons itself works as a computing device as a whole. The area study for understanding the communication among neurons is called "neural coding".
If you are talking about just the motor and sensory peripheral nerves, they innervate specific targets.

I'm confused; does this mean that a neuron can identify what is meant for it's action without the signal itself carrying some kind of identification?

@Everyone, no it means that most neurons are hard wired for a specific task. Activating them results in a task-specific signal. That said, information "can" be encoded in the signal. Different chemical pathways in the neuron can be activated depending on the incoming signal, the same neuron can react in different ways to different neurotransmitters for example.


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Why do the feet of the Gecko Lizard not stick to Teflon surfaces?
I have noticed that lizards feet can stick to walls but not to Teflon surfaces?
Why is that?

Gecko feet have been the focus of a lot of research over the past 10 years.
Their ability to walk up vertical or even hanging from ceilings is attributed to tiny branching hairs growing from the pads of their feet.  The hairs branch down to the size of 100s of nanometers and its believed that this gives them large surfaces at the molecular scale, giving them a strong van der Waals adhesion force.

Teflon, being hydrocarbon chains covered with 'hard' electronegative flourine atoms doesn't provide the same attraction to the hairs, as van der Waals forces rely on mutual polarizability of atoms in close contact. That is to say, electronically fluffy atoms can stick together more readily.

Nice simple straightforward explanation. +1 for "electronically fluffy atoms"! :)


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Do male mammals other than humans have nipples?
When I grew rabbits, I had a pair, one male and one female. And while the female's nipples were quite prominent, especially after giving birth, I don't remember the male having any nipples at all.
Do males of other mammal species, have nipples like human males, or is it a trait that's unique to Humans?

You never heard the old saying "worthless as teats on a boar hog?"

At the very least, I know that male primates also have nipples like female, though they are very close relatives to human. On the other hand, in some of my dissection labs, I noticed that male pigs also have nipples just like the female ones. It seems to be the case that most male mammals have nipples, which probably has to do with mammals being breast-feeder and their developmental pattern.
There is a page on Wikipedia that I found about this topic:
http://en.wikipedia.org/wiki/Nipple#In_male_mammals

I can also testify as to the presence of nipples on male dogs and cats (or, at any rate, my male dogs and cats).

u dissect pigs in ur lab?

Most mammalian males have nipples. The duck-billed platypus does not have nipples but you begin to see development of nipples in marsupials (Park and Lindberg 2004) like the opossum and kangaroo.  Development of a complete nipple begins in the eutherian (placental) mammals.
The mammary glands develop early in the embryo along a pair of ridges called the mammary ridge, mammary lines, or milk line (shown in an adult human in the figure below, taken from Wikipedia). The nipples form along this line. In humans, this happens during the fifth week of development. Within a few days, nipples begin to form. The number of nipples pairs that form is characteristic of the species (e.g., 1 pair in humans to 9 pairs in pigs). The development of nipples occurs before sexual differentiation begins which, in humans, is during the sixth week of development. That's why both males and females have nipples. This same order of develop occurs in other mammals, revealing our common ancestry.

However, because the process is under genetic control, mistakes can happen. Occasionally, humans (and other mammals) can develop extra nipples, the so-called supernumerary nipple(s). The most common places that humans develop one or more supernumerary nipples are identified by the circles in the figure above. The actor Mark Wahlberg is not shy about showing his.

For a general overview of mammary gland development, Dr. Jacqueline Veltmaat has a nice web page that highlights her research in this area. For those interested in the more technical genetic aspects of mammary gland development, a paper by Watson and Khaled (2007) reviews the genetic processes that regulate development of the mammary gland in mammals, based on the mouse model system. The article covers all stages of mammary gland development, from the embryo through puberty to pregnancy. Their Figure 1 shows one row of embryonic mammary buds (labeled MB1 - MB5) in the embryonic mouse. In the case of the mouse, all of the mammary buds will develop into fully functioning mammary glands.  Another paper by Robinson (2007) discusses the signalling pathways during development of the mammary glands.
Literature Cited
Park, C.S. and G.L. Lindberg. 2004. The mammary gland and lactation. pp. 720-741 in Dukes' Physiology of Domestic Animals, W.O. Reece, ed.  (Publisher not identified.)
Robinson, G.W. 2007. Cooperation of signalling pathways in embryonic mammary gland development.  Nature Reviews Genetics 8: 963-972.
Watson, C.J. and W.T. Khaled. 2008. Mammary development in the embryo and adult: a journey of morphogenesis and commitment. Development 135: 995-1003.

Yes, almost all male placental mammals have nipples, typically the same number of nipples as the females.  Notable exceptions: male horses and males of most mice species do not have nipples.


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What type of biome is this?
There is a region that gets about 812mm of precipitation and is mildly hot all year long.
I believe this region is a tropical savanna, but I'm not 100% sure.  Is this correct?

I'm not familiar with the definitions of a tropical savanna I'm afraid. Is this a homework question?

Well, first of all 812mm is a pretty precise value to be preceded by the word "about". "Mildly hot", on the other hand, is too vague a term for your question to be answerable. If you update your question with better parameters, you may get more helpful answers.
In any case, according to this page, a tropical savanna has mean monthly temperatures at or above 64°F (~18°C), which may or may not qualify as "mildly hot" by your standards, and annual precipitation averages between 30 and 50 inches which means between 762mm and 1270mm.
So, I what you are describing could be a tropical savanna, but as I said before, I can't tell unless you update your question with more information. Have a look at this site, it may be of help.

i made a typo.  i updated my question

Well, in that case @user832680, it may well be a tropical savanna :).


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Where are -HCl supplements absorbed in the human digestive system?
I see that quite a lot of drugs and dietary supplements sold in the USA have -HCl(hydrochloride) added to their name. For example pyridoxine hydrochloride for Vitamin B6.  I'm interested in knowing where in the digestive system -HCl compounds are absorbed? Is it in the stomach?
It would also help if I get a rough idea of how long it takes for -HCl supplements to be absorbed. Is it an hour or more?
Thank you for your input!

The hydrochloride ions are not what facilitate their absorption into the body. The HCl notation is from organic chemical reactions of a weak base (usually amines are involved here) with HCl to form a salt. The salt is what gets purified as a powder (otherwise the chemical remains in solution and can't be made into a pill/supplement). The bottle may say: "compound-HCl" or "compound HCl" implying that the two are chemically bonded together, but that is incorrect. What actually happens is that the compound is an ionic salt, in the form [compound]H+ Cl-. As far as absorption, that is entirely dependent on the compound(s) being absorbed. Once you swallow them, they dissociate back into the weak acid form and H+,Cl- ions.


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If proteins have an overall charge, how do membrane proteins traverse through the hydrophobic region of the plasma membrane?
These two concepts seem almost contradictory, proteins have a net negative charge due to the amino acids in them each having a small negative charge, yet membrane proteins are able to exist traversing the plasma membrane, which is impermeable to charged molecules (hence the need for membrane proteins).
How do these two statements remain true simultaneously?

which small charges are you referring to? The trans-membrane parts are usually made out of hydrophobic amino acids that don't have a significant charge.

So does the overall charge on the macromolecule not have any effect if part of it is uncharged?

And, building on that, how does the charged element of the protein pass through the membrane after synthesis to create a protein which protrudes through both sides of the membrane?

Just a minor comment on the background part of the question: the net charge on a protein will depend on the pH, and is certainly not always negative. Similarly the charges on individual amino acids will vary, but again are not always negative. So for example lysine and arginine side chains are positively charged unless the pH is very high. This is why histones (rich in these residues) are positively charged at physiological pH, thus interacting with negatively charged DNA.

Transmembrane proteins are inserted into the membrane in the ER in a rather complicated system, there is a whole chapter about translocation of proteins in "Molecular Biology of the Cell".
The proteins are moved through an aqueous pore in the Sec61 complex, which explains how charged parts of a protein are moved across the membrane.
The parts of a transmembrane protein that remain in the membrane are usually composed of hydrophobic amino acids that aren't charged.
I strongly recommend you to read up on the whole translocation stuff in a cell biology book like the Alberts I linked. There's a lot more to it than what I wrote here.

Also, lipoproteins use covalently bound lipids to anchor to the membrane.


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Bone conduction . Different from the normal hearing phenomena in humans?
Bone conduction, is it something different from the normal phenomena of listening through the ears. I checked on some literature . Is it so that Bone conduction has very less to do with the ears and more to do with vibrations of the bones in the skull. Maybe I am mistaken . Please anyone can present a simple picture here and maybe some text to refer .
Thanks !

It's interesting to note that bone and air conduction are used as standard medical tests for hearing. These are called the Rinne and Weber tests, and can give a rough estimate as to whether a patient has conductive hearing loss (i.e., due to the middle ear) or sensorineural hearing loss (i.e., due to the inner ear and cochlear nerve). In short, a tuning fork is used, and the results of bone conduction and air conduction are compared to determine the cause of the hearing loss.

Prologue: Bone conducted signals are considered to be evoked by the perilymph fluid moving back and forth out of the cerebrospinal cavity, via the cochlear aqueduct, towards the scala tympani. And not by mechanical deformation of the cochlea. “the fact that the bone conduction phenomenon is actually the result of the push-pull movement of the perilymph fluid instead of the presumed deformation of the bony structures.” some text to refer:
Applying physics makes auditory sense.
I am affiliated with this book. I am the co-author of the Appendices.
Year Article Author(s) Source
2010 1 Applying physics makes auditory sense : a new paradigm in hearing
Abstract  |  Full-text Heerens, W.C., Ru, J.A. de Medicine (2010), pp: 1-74
pp: 13:
Objections against the existing bone conduction signal transfer hypothesis: The common model for the transfer of a bone conducted signal is based on the vibration of the temporal bone. However, both the material and the construction of this bony envelope are extremely rigid, while the cochlear shape of the cavity excludes the possibility that parts of this cavity can function as the hypothesized resonators. Therefore, sound stimuli cannot be transferred in such a manner. Certainly not the weak vibration signals with pressure variations of approximately 20 mPa, equal to a pressure variation of
0.2 x 10^-6 atmosphere that are generated by a normal sound stimulus of 60 dB SPL. Hence ‘bone conduction’ must have a cause other than the deformation of the rigid petrous bone that forms the cochlear bony envelope.
The physiological structure data:
• The walls of the cochlear envelope are extremely rigid. Hardly compliant to not compliant at all. So bone conduction based on deformation of that envelope is not possible.
I assume that it is clear, without further explanation that the petrous bone can be regarded as a non-deformable body when confronted with the extremely weak impact of acoustic signals.  We see that for a completely normal 60 dB SPL sound pressure signal, clearly showing that the vibrations of bone in the cochlea offer only extremely small, and therefore completely negligible contributions.  It means that we are talking about deformations which is therefore completely negligible as a possible mechanism for signal transfer. I dare say, no waving arm statements.  Contributions that all result in deformations comparable to an incredibly small fraction, are all leading to naught, one cannot escape the conclusion that there must be another cause for the phenomenon of bone conduction.
Bone conducted signals are considered to be evoked by the perilymph fluid moving back and forth out of the cerebrospinal cavity, via the cochlear aqueduct, towards the scala tympani. And not by mechanical deformation of the cochlea.
pp: 47: It has been established that the rigid cochlear envelope is hardly deformable. This leads to the realistic hypothesis that the ‘bone conducted’ sound signals evoke stimuli by means of a similar process to those of the airborne sound stimuli, namely by means of a push-pull movement of the perilymph, in this case, out of the cerebrospinal cavity via the cochlear aqueduct.
pp: 19-21: Bone conduction: As the petrous bone is the toughest bone in the human body, it is practically impossible for deformation to occur through the vibrating movements that are caused by acoustic pressure changes. Therefore, there must be another means for this signal transfer. A bone conduction audiogram – apart from a reduced transfer of especially the higher frequencies – is not fundamentally different from a pure airborne tone threshold audiogram. It follows that the perilymph movement within the cochlea must somehow also generate the bone conducted signal transfer. And indeed there is such a possibility. The scala tympani is directly connected with the cerebrospinal cavity by means of the cochlear aqueduct, which has its opening in the vicinity of the round window. The cochlear aqueduct enables the perilymph to move backwards and forwards between the cranial cavity and the cochlear channels (scala tympani and scala vestibuli). The perilymph in this cranial cavity is exposed to the alternating pressures caused by the sound induced vibrations of the shell shaped cranial bones that are located in the front and the back of the skull. As a consequence of Newton’s fundamental law of motion we know that when a larger amount of fluid inside the skull must be brought into motion, the effect of these stimuli will be smaller for the higher frequency contributions than for those of the airborne stimuli for similar frequencies. Furthermore, the stapes introduces the airborne signal that results in a backwards and forwards motion of perilymph, in opposite phase to the back and forth motion of perilymph along the
basilar membrane, which is evoked by bone conduction. This results in a slight reduction of the airborne signal, which actually is the stronger of the two stimuli.
pp: 19-21: The alternating movement of perilymph between the cerebrospinal cavity and the scala tympani via the cochlear aqueduct will also be partially directed towards the round window. This splitting up into two directions of the perilymph movement creates a reduced perilymph velocity in front of the basilar membrane, and finally results in a reduction of the bone conduction signal. The rate of reduction depends on the mobility ratio between the oval window and the round window. A further decrease in round window mobility, related to the mobility of the oval window, results in a higher perilymph
movement in front of the basilar membrane, which evokes a higher bone conduction signal, while an increase would result in a lower one.
pp: 19-21: This hypothesis that bone conduction consists entirely of the push-pull movement of perilymph from the cerebrospinal cavity via the cochlear aqueduct, and is evoked by the vibration of the shell shaped bones of the skull, while the rigid temporal bone does not deform at all, is just one logical step further than the functional possibilities indicated by others.

This answer is copied in large part from this document, which I realise you are the co-author of the appendices for.  In future it might be a good idea to highlight this in your answers to avoid being accused of plagiarism.  Also, it's always a good idea (and indeed is required in our faq) to disclose your affiliation with any products for sale.

Sound travels faster through solid material than air.  It also travels more efficiently, the sound does not diminish as quickly over long distances as the molecules in the air do not collide as often and can cause the sound waves to decompose over time and distance.
This is accentuated when the solid through which the sound is travelling is long in one dimension.  This is why old westerns have scouts listening to at railroad tracks to see if a train is coming.  Sound travels along the rails much further than we can hear through the air.
Bone conduction uses this principle - you can touch a walking stick to your jaw bone and put the stick onto a wall and hear sound from the otherside of the wall more efficiently.  This cool hearing aid uses the jawbone and skull as a microphone to pick up sound waves.  I'm not advocating the product, but it demonstrates the idea - as microphones get smaller and smaller with shrinking hearing aids, it might make sense to use a different pick up for the sound.
Note that the bones of the middle ear use bone conduction to get the sound into the cochlea where the nerves actually pick up sound.  This serves to isolate the delicate inner workings of the ear from the outside.


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Do diurnal birds of prey recognize each other by their appearance?
Just what the title states.
I recognize people around me by their facial appearance to begin with, then by their little idiosyncracies; this applies perhaps to most other humans too. We rely pretty heavily on vision - perhaps because we are a primarily diurnal species gifted with the ability to distinguish colour. But then, so are birds of prey e.g. eagle, kite ...
Do diurnal birds of prey identify each other by their appearance?

Having seen some nature documentaries about Penguins identifying their offspring using sound alone (even in flocks of hundreds of thousands of other birds), my immediate impression was that sound is likely to be more important with regard to recognizing individuals of the same species.
This is corroborated by Melissa Mayntz, a bird enthusiast, who has written a great account on birds use of their 5 senses (Understanding Bird Senses).
To summarize, she explains that whilst sight is a birds most important sense in terms of hunting and avoiding being hunted, their hearing is is their second most important sense and they use this to identify individuals;

Birds hear a smaller frequency range than humans, but they have much more acute sound recognition skills. Birds are especially sensitive to pitch, tone and rhythm changes and use those variations to recognize other individual birds, even in a noisy flock.

Just going to the link (+: Thank you! ... but in the interim I would point out that flocking birds such as the penguin may identify each other differently than loners as birds of prey usually are

@Everyone that is true of course - but I imagine that a bird of prey would call to identify themselves to another bird, as you would have to be much closer to identify by sight. We use sound to identify people easily too - over the phone for example we can easily recognize a voice we know, without having any prior knowledge as to who it may be. I'm speculating of course, but it seems to me that sound would be much more useful to a bird in flight, or in a tree, because you may not be able to see one another!

Recent research has indicated that wild American crows (Corvus brachyrhynchos) can recognize individual human faces (Mazluff et al. 2010).  If crows can recognize individual people, then it might not be too farfetched that other bird groups can recognize each other by appearance.


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Ammonium sulphate precipitation assay pH dependence
In general does the pH effect the precipitation, e.g. would a pH of 6 cause less precipitation than pH 7.5. Or are they unrelated?

I think it would affect some proteins, but ammonium sulfate precipitation usually requires such large amounts of salt, that you would have to add a lot of base to adjust the pH.
When I have done ammonium sulfate precipitation, its to take a rough cut of proteins out of a whole cell/whole organ lysate - its more like a hammer than a pair of tweezers as far as protein purification is concerned.  I would rather use a charged plastic resin or a sizing column if I were to care about the isoelectric purification.

Thanks. I'm actually trying to stop precipitation when incubating a protein in ammonium acetate, and I wondered if an acidic pH would reduce this. Do you have any suggestions

Do you know the pI of your protein? Proteins are least soluble at pH=pI.

also consider detergent - might the protein be a bit hydrophilic?

@Anake, I would look up http://en.wikipedia.org/wiki/Hofmeister_series

the protein isn't hydrophobic, it is the ammonium's precipitating tendency as in the Hoffmeister series. I HAVE to use an ammonium salt, so the hoffmeister series cannot help me in that respect

So how did the pH change work?  Some proteins are just plain insoluable... is the solution quite dilute?  There are many possible things to try - its hard for us to guess.  maybe you can add a more complete description of your situation in the question...?


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Sparking during electroporation of plasmid DNA into bacterial cells
During electroporation of bacterial cells (I work with Mycobacterium tuberculosis, but I think this applies to E. coli as well), sometimes I get sparking. I've read this is due to salts present, either in the DNA sample or the bacteria.
I use the Qiagen plasmid prep kit, which includes EB (Elution Buffer). This contains Tris-Cl. Could this be contributing to the sparking? Can you explain how this works? Does eluting with water instead of EB reduce chances of sparking?

What media are the bacteria in during electroporation?

Hi notalily, what parameters were you using for MTb electroporation?

In my experience the elution buffer does not matter (both for E.coli and Mycobacteria). I have heard this before from co-workers, but it usually is based on superstition or anecdotal evidence. I have compared water/EB elution and never saw a difference in sparking (in fact, I usually get slightly more colonies with EB).
When I get arcing (sparks), it's usually because I did not wash enough, have bubbles or have to many bacteria. Arcing is a collapse of resistance.

Sparking occurs from having too many salts or possible not enough solution. After fine tuning my electroporation for very high amounts of DNA (16+ ug), what I've found to help are:

Make sure you are using the proper amount of liquid solution to transform. Too little will end up sparking
Clean up your DNA. I wash with twice the recommend amount of buffer PE, but I don't great evidence of how much the 2nd PE wash helps
Elute your DNA clean up with water
Drop dialyze your DNA. This is probably the most important step to prevent arcing


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Why does milk contained in cartons of milk expand?
In the morning, I went to the fridge to drink some chocolate milk. At night, when I took out the same carton of milk, the packaging seems expanded, like some kind of air is inside. Explain please !

There are probably several reasons. One that I can think of is that spoilage bacteria may have introduced gases that increased the pressure inside the carton. Probably that's why you notice the bulging.

Fermentation takes weeks to happen, and you would know it happened if your milk was spoiled. A lot of times what happens is just that the cold air inside the jug warms up and expands enough to bulge out the sides of the carton.

@user16893 say you have 1L of air at +4C temp (T=277K) and move it at constant pressure to room temp of +24C (T=297K). You should be able to calculate change in volume as PV=nRT, where P=const

Perhaps the culprit here is the packaging, not the contents.  Since you say 'carton', I'm assuming the ones with a square cross section, no?  So they're shipped, and on the shelves, packed tightly together and so hold their square shape.  Put a single carton in the refrigerator, and the sides slump a bit under the weight of the contents, since for economic reasons they're made no stronger than necessary.

The likeliest culprit here is fermentation carried out by bacteria present in the milk. Fermentation of a sugar, for example glucose, releases carbon dioxide (a gas) :
$$C_{6}H_{12}O_{6} \rightarrow 2 C_{2}H_{5}OH + 2 CO_{2}$$
Since this reaction produces a gas, the gas builds up in the milk carton causing it to bulge. This is not, generally, a good sign, make sure to smell the milk before drinking it!

Do the bacteria in milk undergo ethanol fermentation? It's always been my understanding that homolactic fermentation predominates, though that isn't actually based on anything.

@canadianer no idea, to be honest. I'd be interested in the answer if you look into it though!


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DNA as an acid?

Possible Duplicate:
Does DNA react in all of the ways most other acids do?

Even if DNA is made up of nucleotide bases, it is said to be an acid. Why is this?

voted to close.

First of all, DNA is not made up of "nucleotide bases" but of nucleotides. These consist of a sugar bound to one of the 4 nucleobases Adenine, Cytosine, Guanine or Thymine (Uracil in the case of RNA) and a phosphate group.
When these bases are bound to a sugar (2-deoxyribose for DNA), they form the nucleosides Adenosine, Cytidine, Guanosine or Thymidine respectively:

When the nucleosides are bound to one or more phosphate groups, they become nucleotides. The general structure of a nucleotide is (source):

Finally, nucleotides are joined together through their phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. This polymer is what we know of as DNA:

So, after this long introduction, the acidity of DNA is caused by the presence of the phosphate groups which are themselves acidic. You can see this by comparing the structure of DNA to that of Phosphoric acid:

As explained very well here:

If you compare the structures of phosphoric acid (Figure 1) and a
  short strand of DNA (Figure 2), you’ll see that in the latter, two
  protons of phosphoric acid are replaced by carbon atoms either in, or
  attached to, the five-membered ring. In chemical terms, such a group
  is called a phosphate diester. The remaining proton is now quite
  acidic, and is relatively easily lost, thereby giving DNA its acidic
  character. Indeed, under neutral conditions, DNA is deprotonated at
  this site, and the oxygen atom bears a negative charge. Despite the
  fact that DNA does contain many basic groups, their basic properties
  are masked somewhat because of the fact that they hydrogen bond with
  each other to form base pairs. Hence it’s the acidic part of the
  molecule that dominates, and that is why we know DNA as an acid.

Could we say that the weakening of O-H bond is due to -I effect of the sugar groups?

DNA is made of three types of molecules in equal proportions - basic nucleotides, sugar deoxyribose and acidic phosphate groups. The bases are on the inside of the helix and partly hidden from the outside. Deoxyrybose and phopshates are on the outside, forming a backbone.
Though the proportions are equal, the nucleotides are weak bases, so the overall pH is acidic.


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Which shades/hues of color are easiest to distinguish for humans?
I'm trying to represent data graphically and am using a variation of hue/lightness to distinguish one data point from the next. I would like to use a color that would allow me to convey most information visually.
What I'm interested in is which color I should use. I've read somewhere that humans are most capable of distinguishing shades of green, that is a human can differentiate more shades of green than any other color. Is it true?
Has there been any studies to distinguish the number of shades that a typical westerner can distinguish? I'm looking for information like : ### shades of green, ### shades of red, ### shades of cyan, etc.
Thank you for your input!

don't forget the XKCD Color survey - see the color cube map http://blog.xkcd.com/2010/05/03/color-survey-results/

Culture is more a factor than eye ability. You should ask on cogsci also

I've read somewhere that humans are most capable of distinguishing shades of green, that is a human can differentiate more shades of green than any other color. Is it true?

I'd say it's plausible, depending on your definition of "Green." While your eyes do, indeed, have RGB receptors (cones) and Rods for grayscale - they don't perceive the Visible Spectrum equally. Here are a few graphs I found from Photo.net regarding the human eye and the sensitivity of the Cones (first and second) and Rods (third):

What you should be noticing above is not necessarily the Y axis, but the X axis - which represents the Wavelength, and amount of Wavelength our eyes are sensitive to each color. While our eyes perceives the most Red wavelengths and the least Blue wavelengths, Green comes in just under Red's range for Wavelength coverage. However...

When combined with our Rod sensitivity, though, Green wavelengths produce nearly double the sensitivity the Red Wavelengths - and nearly quadruple the Blue wavelengths. What that means is that in low-light situations when the Cones are unable to produce a precise color image, your Rods will be able to pick out Green things (with a slightly loose definition of 'Green') more than other colors - which is perhaps the reason why night-vision goggles often use Green since they increase the Intensity of the light, which presumably stimulates the Rods more (although not knowing precisely how the image is produced - if the green coloring is enhancing that particular bit of the spectrum of falsely colored - take this with a grain of salt).
Does that explicitly prove you can see more Green shades than others? No. Your brain does a lot of processing - the entire color Yellow is a construction of your brain, and Tetrachromats (people with 4 types of Cones) are real.
However, like I said above, I'd say it's plausible.

Thank you for a very in-depth answer! I'll stick with green then.

Light is either monochromatic, or a combination of different wavelength in different proportions.
In the eye, there're 4 types of sensor cells: one is greyscale-only, another 3 is for color vision. See the graph here with the spectral sensitivity of the 3 color vision cells.
So, for any giver hue, you have very wide possibility of the light spectrum that makes you see that hue.
When you see the yellow color from the sodium-vapor lamp you see almost monochromatic yellow light. When you see the photo of the lamp on your PC display, there’s no yellow light at all. Instead, you see some combination of red and green light produced by PC display which doesn’t have yellow subpixels, only red green and blue.
That's why there's no simple answer to your question. The answer depends not just on hue (which only exists inside our brain), but also on the spectrum of the light you see (which also exists in the real world).
P.S. Even if you'll specify "color on a PC display", the question is still vague: there're different types of displays with different spectral characteristics.

Thank you for a clarification. I should say that I'm working with a backlight-based LCD display of an iPhone.

LCD display of an iPhone
For portable devices there's another important factor - ambient lightning. For example, under direct sunlight human eye can barely distinguish black from white (unlike AMOLED displays for example)


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Do all mushrooms have the same multicellular ancestor?
Do all mushrooms have the same multicellular ancestor? Did that ancestor feature common mushroom elements such as cap, stem, sporofore, vulva, bulb, etc.

All fungal species within the kingdom have the same common ancestor, which is unicellular (thought to be protistan). This common ancestor is the point at which it is thought that animals diverged, as suggested by this article.
In their words:

It is now well established that animals share a common single-celled ancestor with fungi, and that in the two sister lineages multicellularity arose independently

A fungal phylogenetic tree is shown below, which originated from this paper.
Note: all colored areas represent different phyla of fungi.

EDIT:
I will respond to a few questions addressed in the comments.

Is there a unique multicellular ancestor to all mushrooms?

I am rather sure (but can't explicitly confirm with a reference) that multicellularity in fungi only evolved once. If this were true, I would also hypothesize that mushroom-like characteristics also evolved only once, thus indicating that there is a multicellular ancestor to all mushrooms.

Are there multicellular fungi outside dikarya?

No. One branch of dikarya seems to consist of only unicellular organisms, suggesting that multicellularity evolved at some point within organism under only one dikaryan branch.

Was the common ancestor of Dykarya multicellular?

No. See previous answer.

Are those unicellular dykaria secondary unicellular or not? Given that the both branches of dykaria show similarities in fruiting bodies, it seems to be plausible that the common ancestors of dykaria had a similar structure.

I am not exactly aware of the similarities in fruiting bodies in both branches, but if the physiology behind fruiting bodies are similar, it is very likely because the dikaryan common ancestor had a similar mechanism.

Is there a unique multicellular ancestor to all mushrooms? Are there milticellular fungi outside dikarya? Was the common ancestor of Dykarya multicellular?

By mushroom, do you mean fungi in general, or specifically those having a stem, bulb, etc? PS. Not all Dikarya are multicellular: some are unicellular. http://en.wikipedia.org/wiki/Dikarya.

And as far as I know, there are no multicellular fungi outside of Dikarya, but I cannot confirm that statement.

Are those unicellular dykaria secondary unicellular or not? Given that the both branches of dykaria show similarities in fruiting bodies, it seems to be plausible that the common ancestors of dykaria had a similar structure.

Please see the edited question which adresses most of your questions.

Your new version is contradictory: you say that the common ancestor of Dykaria was unicellular yet you believe that multicellularity evolved only once. An image of fruiting body of a fungus belonging to ascomycota (sac fungi): http://upload.wikimedia.org/wikipedia/commons/8/82/Morchella_conica_1_beentree.jpg A fruiting body of a mushroom belonging to basidiomycota http://salavat.spb.users.photofile.ru/photo/salavat.spb/200388730/xlarge/208364390.jpg You still believe that the last common ancestor of these mashrooms was unicellular?


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At what substrate concentration will an enzyme work at 40% of its maximum rate if its Km = 0.095M?
The question involves the Michaelis-Menten kinetics equation.
Here is what I did: I took the Michaelis-Menten equation, replaced v with 0.4Vmax, canceled the Vmaxes (one on each side), and solved for [S].
I got -0.056 which is obviously wrong, because [S] cannot be negative.

To be honest I know very few about enzymes and absolutely nothing about Michaelis–Menten.
However, when I "took the Michaelis-Menten equation, replaced v with 0.4Vmax, canceled the Vmaxes (one on each side), and solved for [S]", my result is positive:
0.4 * Vmax = S * Vmax / ( Km + S )
0.4 = S / ( Km + S )
S = 0.4 * Km + 0.4 * S
0.6 * S = 0.4 * Km
S = Km * 2 / 3.


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Which cells will pass cancer to offspring?
Each of these types below contains a DNA mutation. Which type(s) will affect the children of the individual whose cell it is.

Red blood cell
T cell
Skin (epithelial) cell
Neuron from the brain
Sperm cell
Cell from lining of the uterus
Placenta cell
Stem cell

My attempt: I think it's only a sperm cell, because that is the only cell to get passed on.  Is this right?

(This should be a comment, but my reputation precludes me from doing that)
I just wanted to chime in and say that it looks to me that the last three are just Red Herrings that are supposed to make you think a bit.

Red blood cell
Will probably not. You inherit blood type, but not actual erythrocytes (though the mother's erythrocytes do interact with a fetus).
T cell
Will probably not. However, while in the uterus and for the first few weeks outside the uterus the Mother's immune system is effectively the newborn's immune system. While the mother doesn't pass on any myeloid progenitor cells, a disease affecting a leukocyte might also be passed on to the child (HIV).
Skin (epithelial) cell
Will not. You inherit many traits to do with skin (melanocyte activity resulting in melanin concentrations, for instance), but no skin cells are involved in the creation of the fetus.
Neuron from the brain
Will not.  Neurons are the last time of cell I'd expect to vertically pass on a mutation, not only because their environment is usually tightly controlled (Schwann Cells, Blood-Brain Barrier, etc.), but also because the fetus will develop the beginnings of its nervous system very early on and I'm not aware of the mother's CNS or PNS interacting with the fetus in any significant way.
Sperm cell
Can certainly pass on a mutation as long as the mutation is part of the sperm's DNA. Though the particular gene the mutation exists on may be inactivated, it would still be passed on to the offspring and potential future generations.
Cell from lining of the uterus
I'm not positive on this one. The fertilized egg cell must implant itself in the lining of the uterus, and the landing location eventually becomes the umbilical cord. I suppose it's possible, particularly if the mutation occurs closer to the child's end - like the obliterated artery.
Placenta cell
Probably not, though like Cell from lining of the uterus I'm not super positive on this one. Given that the placenta is detached from both the mother and child soon after birth, a mutation in a placental cell that hasn't metasticized won't affect either. However, there may be interactions I'm not aware of.
Stem cell
"Stem cell" is a little vague. The body has many specific types of stem cells, and the fertilized egg itself basically turns into all of the stem cells the developing fetus will ever have. If it's referring to the daughter cells of a fertilized egg, then only the child will have the cancer, as the genetic inheritance is unidirectional (the mother's genome is not modified to resemble the child's in any way).
If someone has better knowledge on the interaction between the fetus and the uterus/mother or can come up with some references, listen to them. It's been a while since I've studied development.


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Ultrasound during pregnancy
In a hospital I can see a long queue of pregnant women waiting for their turn for ultrasound.  Is it safe to go through the ultrasound during pregnancy, especially during last few weeks?
Is ultrasound really required?  What if it is not done? How does ultrasound affect baby?

As Luke points out, the ultrasound is very safe. However, in many cases it is not required. Typically by 20 weeks into the pregnancy, and sometimes earlier, a baby's sex can be determined by examining the genitals via ultrasound. My experience is that this is the most common reason for an ultrasound during pregnancy.
Of course if there are complications during the pregnancy, an ultrasound might be helpful to visualize the fetus and diagnose any problems. However there is no definite need for an ultrasound during the course of a normal pregnancy.

Nice. forgot there was a follow-up "why is it used" question when posting my answer!

The U.S. Food and Drug Administration (FDA) has the following information regarding the risks of ultrasound imaging;

Ultrasound imaging has been used for over 20 years and has an excellent safety record. It is non-ionizing radiation, so it does not have the same risks as x-rays or other types of ionizing radiation.
Even though there are no known risks of ultrasound imaging, it can produce effects on the body. When ultrasound enters the body, it heats the tissues slightly. In some cases, it can also produce small pockets of gas in body fluids or tissues (cavitation). The long-term effects of tissue heating and cavitation are not known.
Because of the particular concern for fetal exposures, national and international organizations have advocated prudent use of ultrasound imaging. Furthermore, the use of diagnostic ultrasound for non-medical purposes such as fetal keepsake videos has been discouraged.

FDA > Radiation Emitting Products > Medical Imaging > Ultrasound Imaging
Further information

I had a bit of a look through PubMed and Scopus for any papers relating to ultrasound risk, but didn't find any.

Radiation?! Ultrasound is sound is a pressure wave, while radiation means actual particles (including, but not limited to, light consisting of photons. I know you didn't write that yourself, but still this requires emphasis - ultrasound is not radiation

@TobiasKienzler that really didn't twig when I first read it, but you are correct. The FDA just lumps it in with other medical imaging (under Radiation Emitting Products). Presumably the blurb was written by a web-developer rather than someone involved with ultrasound...

I sure hope so - I wouldn't go as far as distrusting an actual doctor who claimed this, since it's a Physics detail that shouldn't taint the diagnosis, but still I'd be very careful with someone who claims false facts instead of simply admitting to not knowing for sure...

Ultrasound is just another techniques for medical imaging and it is very common to use radiation for imaging. Therefore the notice that this is not ionizing radiation might be important in this context. Besides, radiation is not limited  to particles emission only and can also be emission of waves, that ultrasound actually is.


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Have proteins been observed to come into existence through mutations and natural selection?
A protein that catalyzes one reaction can theoretically be modified by mutations and natural selection and eventually catalyze another reaction completely unrelated to the original. Has this been observed, documented, or at least postulated to be where a certain protein(s) came from?

What do you mean with "in real time"? Sequencing an organisms, adding an evolutionary pressure, sequencing again and suddenly finding a new protein?

The “real time” requirement is an incompatible criterion with the rest. It’s designed to make this question essentially unanswerable.

Mutation of a (duplicated) existing protein is the usual way a new protein evolves.

This sounds dangerously close to the fundamental biblical literalist Ken Ham's distinction between "Historical" versus "Observable" knowledge, which is utter tripe (refer to crime scene analogy). Especially with the odd parameter that "homologs don't count".  As @KonradRudolph eluded to, this question is designed to be unanswerable, but fortunately, the more patient users on this site have provided awesome answers.

@James I apologize for the poor quality of the original question. I was fresh off a heated debate when I asked this question. I have modified it to better reflect my ignorance seeking understanding.

How about EWS-FLI1 and other oncofusion proteins?
One could argue that cancer progression is as close to viewing "evolution in real time" (as you say) as possible.

how was this a new protein from scratch? thnx

Oncofusion is very similar to homologues, especially when there is not modification of function.  Your link on "EWS-FLI1" explains that a virus causes a cancer by modifying gene regulation, which is a change in DNA sequence not Protein amino acid sequence. I don't see how your answer addresses a change in reaction catalyzed.

From the following free review:

Here we review some of the successful strategies in creating protein
diversity and the more recent progress in directed protein evolution
in a wide range of scientific disciplines and its impacts in chemical,
pharmaceutical, and agricultural sciences.

Quoting three examples, but the article has much more:

Directed evolution has been successfully applied to DNA polymerase for
enhanced activity (233) and conversion to an efficient RNA polymerase
(232, 333).
Naumann and Reznikoff (216) used directed evolution to generate a
mutated Tn5 bacterial transposase that could function on transposons
with mutated end binding sequences.
Organophosphate-degrading enzymes have been evolved and selected for
broadened substrate specificity (53, 335). Broadened substrate
specificity of a biphenyl dioxygenase has also been achieved (33, 87,
164, 291). Efforts in cleaning underground water contamination
prompted the evolution of an enzyme for chlorinated ethene degradation
(41).

L. Yuan, I. Kurek et al: Laboratory-directed protein evolution. In: Microbiology and molecular biology reviews : MMBR. 69, 3, September 2005, 373–392. doi:10.1128/MMBR.69.3.373-392.2005. PMID 16148303. PMC 1197809.

Assuming that the OP was really interested in "natural selection" I guess these don't provide an answer. Of course, in the broader sense, human activity could be deemed to be an agent of natural selection.

These are fascinating modifications of proteins. I was hoping for something more drastic than modified binding specificity and catalytic efficiency. Has there been a change in function from one reaction to a completely unrelated one?


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Which poison makes seastars inedible to possible predators?
In the new citizen science project (see: Sea Floor Explorer), numbers of seastars, scallops, crustaceans and other animals are counted. Already one can see a heavy bias in favor of seastars, both the fat and brittle kind.
I would be interested in why this creature is so succesful, especially if it is poisonous to e.g., crustaceans, and what poisons exactly are responsible.

it may not be that they are poisonous. seastars have extraordinary reproductive capabilities

That is the other factor of success. But they are really poisonous, see the answer.

Asterosaponins are the class of compounds - they have a cholesterol like organic core.
Apparently, these saponins make pore-forming complexes with Δ5-sterols of cell membranes, and so are deadly to all usual kind of life, including bacteria and fungi. Quote:

Starfish and sea cucumber cell membranes are resistant to their own
  saponines due to the presence of Δ7- and
  Δ9,11-sterols, sulfated Δ5-sterols, and
  β-xylosides of sterols instead of the free Δ5-sterols.


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Methods of nuclear transfection - nuclear transport
I am reading through the ENCODE papers, which is taking me well out of my comfort zone in terms of modern laboratory techniques. At the risk of asking a question which may well be thoroughly answered somewhere else on the internet, I was hoping for a brief explanation of nuclear transfection.
In Whiteld et all, they describe the direct assay of transcription factor binding site efficacy in human cells.  To do this, they transfect a luciferase plasmid, presumably into the nucleus of the cell (because they subsequently observe that the luciferase plasmid is transcribed).
Reading through Materials and Methods and getting to the supplementary file, they disclosed their transfection protocol. The relevant reagants appear to be:
FuGene 6

a nonliposomal formulation designed to transfect plasmid DNA into a wide variety of cell lines with high efficiency and low toxicity.

(From Promega's website.)
Lipofectamine LTX

efficient reagent for plasmid delivery and protein expression

(From Invitrogen's website.)
PLUS reagent

PLUS™ Reagent is used in conjunction with transfection reagents, such as Lipofectamine™, to enhance transfection in adherent cell lines.

(From Invitrogen's website.)
Apparently, the protocol is to combine the DNA plasmid with transfection reagent, wait a few minutes, and then add in the cells, and incubate at 37ºC for 24 hours. That's all that is required to get the plasmid into the nucleus.
I have consulted Wikipedia and Strachan and Read's Human Molecular Genetics 4th edition, but been unable to answer my question about this technique.
I think I have a pretty clear understanding of how these reagents are able to get through the cell's lipid membrane, but I don't have a similar understanding of how the DNA then passes to the nucleus.
In Human Molecular Genetics 4th edition, I can find only one paragraph about plasmid transfer across a nuclear membrane, page 704: "Transport of plasmid DNA to the nucleus of non-dividing cells is very inefficient because the plasmid DNA often cannot enter nuclear membrane pores. Various methods can be used to faciliate nuclear entry such as conjugating specific DNA sequences or protein sequences (nuclear localization seuqences) that are known to facilitate nuclear entry, or compacting the DNA to a small enough size to pass through the nuclear pores."
But nothing in the materials and methods section of Whiteld et. all mentions any of these techniques. I'm sure they would have mentioned if their plasmid included a DNA conjugation sequence, so that can't be it. Perhaps these reagents implicitly include some sort of DNA compaction polycation, such as PEG-CK30?
Isn't the cytoplasm an extremely hostile place for DNA plasmids? Shouldn't they just flail around in the cytoplasm until they are digested?
Or perhaps these vectors sneak into the nucleus during mitosis? (This is a theory that just occurred to me when contemplating the "non-dividing" qualification in the Strachan quote.)
Since the question isn't addressed in the paper, I can only assume the answer is elementary and something that a professional cell biologist would be expected to know. I've run out of obvious next steps for finding the answer, so I beg pardon in advance for asking it.

My attempt to find an answer has suggested that no-one knows how the DNA gets into the nucleus.
This fairly recent paper reports attempts to track the pathway of DNA entry and transfer to the nucleus.

Le Bihan et al. (2010) Probing the in vitro mechanism of action of cationic lipid/DNA lipoplexes at a nanometric scale. Nucl. Acids Res. 39:1595-1609

The technique used was transmission electron microscopy. Complexes of plasmid DNA + cationic lipids (lipoplexes) were labelled with silica-based nanoparticles to allow visualization.
The authors describe a transfection pathway with five steps:

(i) binding of the lipoplexes to the cell surface;
  (ii) entry of the lipoplexes into the cells mainly via endocytosis (a direct fusion with cell membrane cannot be excluded);
  (iii) DNA release into the cytosol;
  (iv) transport through the cytosol; and
  (v) entry of DNA into the nucleus and nuclear transcription.

The authors were able to follow each of the first four steps but:

our data show nanoparticles close to, but not within, the nucleus.

They speculate about what this might mean, but they do not refer to any previously published data. My conclusion is that the answer to your question is, as I said at the beginning of my answer: no-one knows how the transfected DNA enters the nucleus.

Thanks Alan! I'm upvoting this for the nice article summary, but leaving the question unanswered in case someone else can comment specifically on Whiteld or shed some more light.

The paper describes silicon nanoparticles in the 10 - 15 nm range, so it's not surprising they don't enter the nucleus, the nuclear pore complex won't let particles larger than about 5 nm through by passive diffusion and active transport requires a nuclear localizing peptide. Once the nanoparticles are attached to DNA liposomes, the sizes are even larger, maybe larger than the 39 nm maximum limit for nuclear pore complexes.

Zabner et al (J. Biol. Chem., 1995, 270, 18997-19007) monitored the lipid-DNA complex formation and uptake which was found to be predominantly by endocytosis. Dot blot experiment shows that cells (50% population) took up 60% of the DNA. The DNA-protein complex was observed to be deposited in the perinuclear cytoplasm and formed a series of regularly packed tubules. They also verified that the endosomes carrying the complex did not fuse with lysosome.
Some of the DNA escapes the endosome (which is a known mechanism of increasing the efficiency of endocytosis based transfections) and might be taken up by the nucleus. When they compared expression of a reporter gene upon direct injection into the nucleus and upon direct injection into the cytoplasm, no expression was observed in the latter (acc. to Capecchi (Cell, 1980) the ratio of expression is around 1000:1. PDF available on Utah Uni Website). This means that the DNA uptake by the nucleus from cytoplasm is very inefficient.
Lower amount of lipids in protein-DNA complex increases the efficiency.
Your question has been partly answered. How does all that DNA cell takes up gets inside the nucleus? It mostly doesn't. It accumulates around the nucleus. But some of the free DNA does get taken up by the nucleus. This, probably, was the starting point for Dean's group.
Vaughan & Dean (Mol.Ther., 2006, 13(2) 422-428) have proposed that the plasmids get transported into the nucleus with the help of microtubule associated motor protein Dynein. They observed that disrupting the microtubule network functionality inhibited expression. When the plasmids were injected directly into the nuclei of cells, this did not have an effect. Now, microtubules transport stuff with the help of motor proteins out of which Dynein transports stuff towards the nucleus. It was observed that inhibiting Dynein action reduced the expression. The mechanism of how dynein binds to plasmid is unknown. (I've worked with dynein; it's complicated when it comes to binding mechanisms. The whole negatively charged N-terminal is disordered.)

If you read the discussion of the paper, It'd become apparent that the process is chaotic. The more the dispersion of DNA in cytoplasm around the nucleus, the more is it's uptake by the nucleus.
There is no Nuclear localization signal involved here. Mesika et al (Human Gene Ther., 2005) have increased the efficiency of plasmid expression by binding the plasmids to a protein with NLS. This is not the natural process. Vaughan and Dean have speculated that the DNA targeting sequence (e.g. SV40, CMV etc.) binds to proteins that have NLS or have adapters to bind dynein(like, Transcription factors) which might help the plasmid uptake by the nucleus. This can also explain the sequence based differential uptake of plasmids. None of these mechanisms have been experimentally verified.
[I have also been wondering about this. I bugged a lot of seniors and scoured the net for the answers. And then I found this question. Thank you for asking]

Welcome to biology SE - you should summarise the paper a little more than you have so that the answer can stand-alone (e.g. what if the link goes dead), otherwise, it should just be a comment

This is one of David Dean's papers, they're not bad, but have been hard to replicate. He basically proposes that transcription factor binding sites on plasmid DNA binds to some transcription factor in the cytoplasm, then the NLS peptide on the transcription factor binds the whole protein-DNA complex to importin and drags it to the nucleus.

Dean likes to use the SV40 promoter region, which is 72 bases long and contains several transcription factor binding sites. I'm not sure if anyone's tried it, but it should be possible to just make a 100 base oligo that contains the SV40 sequence and fluorescently label it. See if that goes to the nucleus.

This is a question that keeps coming up now and then when PhDs or post-docs discuss transfection. A probable answer for which I do not have supporting literature is this: If you have the transfection complex in the medium while the cells are dividing, it is possible that they can enter the nucleus following mitosis when the nuclear membrane is still forming, thus giving it access to the transciption mechanism in the nucleus.

Hello and welcome to the site. Is there no supporting literature, or do you just not have it at hand? If the latter, then you are encouraged to add citations.

I don't want to add the citations myself, but this is most likely the case for rapidly dividing cells in culture. You really should find some supporting literature to improve this answer.

This could be one of the mechanisms, but does not explain the fact that the reagents above are useful for post-mitotic cells such as neurons.

@243 They may not be as useful as you think. What kind of transfection efficiencies are you seeing, and how do they compare with rapidly dividing cells using lipofectamine or PEI?

FuGene 6 and  Lipofectamine LTX are used to transfect plasmids into post mitotic neurons primary cultured. I would not say efficiency is high, but acceptable for some experiments. For example: http://www.ncbi.nlm.nih.gov/pubmed/11716945


text:
How does sex differentiation work in Paracerceis sculpta, the sexually tetramorphic isopod?
Paracerceis sculpta is a marine isopod species known for its unusual reproductive strategy:

female: medium-sized; lives in harems run by an α male
α male: large; keeps a harem of females
β male: medium; mimics a female in order to enter a harem and mate
γ male: small; mimics a juvenile in order to slip into a harem and mate

.
How does this 4-way sex differentiation occur? That is, what determines which of the morphs an individual develops into?

There's also the throat colors of the side-blotched lizard.

Shuster, SM & C Sassaman (1997)
  Genetic interaction between male mating strategy and sex ratio in a marine isopod. Nature 388: 373-377

As described in this paper, the chromosomal system of sex determination in Paracerceis sculpta is ZW=females, ZZ=males. Genetic evidence indicates that the morph of a ZZ male is determined by a second locus, Ams (alternative mating strategy) which exists in three allelic forms whose dominance relationship is Amsβ > Amsγ > Amsα. So for example, to be an α type male, an individual must be ZZ Amsα / Amsα.
That's the end of the answer, what follows is supplementary information.
The paper also describes an additional layer of complexity in the sex-determining system of P. sculpta involving sex changes in both directions. This is explained by a model in terms of two other factors: an autosomal locus Tfr (transformer) and a cytoplasmic factor ECF (extra-chromosomal factor) which interact as shown in the Table below (taken from the paper). However, this doesn't really add anything to the Ams story as far as male morphs are concerned, except that some of them start as females.


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What is this crow eating, and is it a common part of the corvid diet?
Here's a picture (by Rob Curtis) of a crow carrying and eating the corpse of what looks a bit like a small hawk or falcon:

Other pictures clearly show the crow is eating the dead bird. This image shows the underside of the head and beak; this one shows its legs, which are grayish.

What bird is being eaten?
Is this bird a usual part of the corvid diet? Or did the crow just opportunistically scavenge a dead bird?

Crows are omnivorous, and will eat almost anything they find or can kill.
In this case the prey looks like a Yellow-Shafted Flicker.

I would add that most corvid are scavengers, and there are also some that are "specialized" at that, such as the Carrion Crow (Corvus corone).

Also, do you think the crow killed the woodpecker (rather than scavenging it)?

@Mechanical snail - I don't think that there is any way that anyone could know the answer to this question unless they were a witness to what happened.

I agree with @AlanBoyd that we cannot know for sure but I would say it is unlikely that a crow could catch and kill a healthy flicker.  So just based on that, it seems more likely it scavenged it.

The crow looks like it is just admiring the dead flickers' colors. I think it picked it up in the way it would pick up any colorful thing. The flicker probable died by flying into a window.

It's eating a flicker woodpecker. And yes, it did kill it and is eating it. Crows and ravens are omnivorous but also predators. They will opportunistically kill any small prey they can catch. Most birds are too quick for a crow, but flickers and all woodpeckers are notoriously slow flyers. It's about the only type of bird that is both small enough and slow enough for a crow to catch. Attached are some images of crows as predators.

Welcome to Biology.SE! This looks like a good answer, but answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, it is hard to know whether this is normal behavior. This is a good example of how to format references. ——— You may also want to take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site. Thank you!

In addition, please provide a citation/source for the images you are using — images must be credited to their creators just like quotes are to their authors. This is generally considered good practice in scientific communication and will help other users understand by providing context.

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


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Influence of alcohol on brain cells
As I am not related to biology, I would appreciate if you can keep your answers as simple as possible.
My question is about the influence of alcohol on the brain. As far as I know, drinking alcohol is killing cells in the brain. But is it linear? E.g. if I have 1.0 per mil and it kills 1000 cells will 2.0 per mil kill 2000 cells?
(An equation would be nice)
Thanks

It's definitely not linear (100% ethanol will kill all your brain cells, but 0.01% will kill far fewer than 1/10000 of neurons). Also, it will heavily vary according to your metabolism (broken down faster by alcohol dehydrogenase, etc.)

See also https://en.wikipedia.org/wiki/Neurotoxin#Ethanol

@Mechanical snail: "100% ethanol will kill all your brain cells" does not mean anything, it depends how much you ingest, how you ingest it, for how long and oh so many other variables.

I corrected the units in your question to per mil (I assume promil is the German spelling). I apologize if you meant another thing, in which case feel free to revert the edit!

@nico: 100% blood alcohol content.

@Mechanical snail: well, that is a complete different thing. 100% ethanol, means pure ethanol (i.e. not diluted with water)! Anyway, I got your point.

The situation is definitely an extremely complex one, and you should probably forget about having an exact equation to define it.
When talking about the effects of a substance on the organism there are several factors to take into account. These are generally put together under the term pharmacodynamics.
Some of the factor to take into account are:

The dose of the substance
The route of administration
The metabolism of the substance
The target organ

The problem is, not all ethanol you drink will go to the brain, and it will not necessarily go there immediately, or all at the same time. All of this will change the effects on the brain. Also, there are several confounding factors, some of which I have tried to list.
I have summarized here a few information about ethanol metabolism, taken mostly from Principles of Forensic Toxicology - Chapter 10 by Barry Levine and Yale H. Caplan
Ethanol is normally taken through drinking, which means that it will have to pass through the gastrointestinal (GI) tract (i.e. stomach and intestine) before getting into the bloodstream. This route permits practically 100% of absorption of ethanol in the body, with the major site of absorption being the small intestine, absorbing ~75% of a dose of ethanol. The rest will be absorbed in the stomach and in the other parts of the intestine.
The absorption in the GI tract is dependent on the type of beverage: for instance carbonated alcoholic beverages are absorbed faster than "plain" ones.
The alcohol content also is important: a very diluted drink is absorbed slower than one with 10-30% of ethanol, as the latter will generate a bigger concentration gradient between the GI tract and the circulation, so it will diffuse faster. However, >30% ethanol will enhance mucus formation, which will slow down absorption. Furthermore, absorption depends on the status of the GI tract: preexisting conditions (e.g. inflammation) can modify the rate at which the alcohol enters the bloodstream.
But, we are still far away from the brain! After being absorbed, ethanol goes into the vena cava, and passes through the liver, where it can be metabolized (destroyed) by an enzyme called alcohol dehydrogenase (ADH), which converts ethanol into acetaldheyde, effectively reducing the ethanol concentration in the blood.
This is a well-known phenomenon for many drugs, and it is called first pass effect
Importantly, the human stomach also expresses ADH, so this first pass effect can start even before reaching the liver! The effects of ADH in the stomach obviously depends on how long the ethanol stays in there. So, it will be lower for an empty stomach then after a big meal.
Food, in fact, is also a well known factor that reduces the amount of ethanol in the blood.
For instance, these graphs show blood ethanol content in four healthy subjects after a 10 hour fast (filled circles) or after breakfast (empty circles), after drinking the same dose of 0.80 g ethanol/kg body weight, in 30 minutes.

From: Food-Induced Lowering of Blood-Ethanol Profiles and Increased Rate of Elimination Immediately After a Meal - Jones AW and Jönsson KA - J Forensic Sci., 1994.
As you can see, eating strongly decrease the ethanol blood content. Also see how there is quite a bit of variation between the different subjects (if you open the paper you will also see the graphs from other 6 subjects).
Also, you can look for instance at this paper (just got a random study, there seems to be a ton of them around):
First pass metabolism of ethanol. - Lieber CS et al. - Alcohol Alcohol Suppl., 1994
Coming out of the liver, ethanol goes into the right side of the hearth, and from there to the lungs. This poses no particular issue for most drugs, but ethanol is volatile! So, part of the ethanol is released through respiration (in fact the "classic" way of saying if someone has drunk alcohol is to smell his breath). However, this only accounts for a minor decrease in blood ethanol levels.
Finally, ethanol can start going around the body. Being a water-soluble molecule it will tend to diffuse into water-containing parts of our body (i.e. you will not find much ethanol in fat), which include the brain.
In the meantime, however, the process of elimination has started: ethanol can be excreted in urine, sweat and breath, although the major route of elimination is epathic metabolism by ADH, accounting for >90% of ethanol elimination.
There is a neat formula to express all of this, called the Widmark equation:
$A=\frac{Wr(C_t+\beta*t)}{0.8z}$
where
$A$ = number of drinks consumed
$W$ = body weight (important because of the content of water in the body)
$r$ = Widmark constant (depends on sex, age, etc.)
$C_t$ = blood ethanol concentration at time t
$\beta$ = acohol elimination rate
$t$ = time since the first drink
$z$ = volume of alcohol per drink
You can find examples of this formula in this PDF about Widmark equations
And now to the brain: ethanol does indeed have various effects on neurons. Short term effect essentially involve depression of neuronal activity, ethanol being able to modulate GABA signalling in the brain. Long term effect range from reduced neurogenesis (i.e. birth of new neurons) to reduced volume of certain brain areas, probably due to loss of neurons, to inflammation in the brain.
Again, the situation is very complex and it depends on the frequency of drinking, the amount of each drink and many other factors. A single dose of ethanol will probably have irrelevant effects on your neurons... as the amount needed (in one shot) for serious neurotoxicity will probably send you into ethilic coma. The exact mechanisms for these effects are only partially known and very likely to be derived by the interaction of numerous diverse effects.
This article explains some of the mechanisms for loss of neurons in the cerebellum.
Mechanisms of ethanol-induced degeneration in the developing, mature, and aging cerebellum. - Jaatinen and Rintala - Cerebellum, 2008

These mechanisms include: (i) excitotoxicity; (ii) dietary factors, especially thiamine depletion; (iii) glial abnormalities; (iv) changes in growth factors; (v) apoptotic mechanisms; (vi) oxidative stress; and (vii) compromised energy production.

I will not go into the details of all of this, but it should be clear by now that all the things I mentioned so far (and many other factors I did not talk about) make it extremely difficult to give an exact quantification of the number of cells killed by ethanol. Surely the relationship is not linear, in fact, for instance, positive effects of small doses of alcohol have been reported numerous times.
A few more references on effects of alcohol on the brain:
Reduced neurogenesis
Long-lasting reduction in hippocampal neurogenesis by alcohol consumption in adolescent nonhuman primates. - Taffe et al. - PNAS, 2010
Adolescent binge alcohol exposure alters hippocampal progenitor cell proliferation in rats: effects on cell cycle kinetics. - McClain et al. - J Comp Neurol., 2011
Brain volume decrease
Decreased volume of the brain reward system in alcoholism. - Makris et al. - Biol Psychiatry, 2008
Amygdala volume associated with alcohol abuse relapse and craving. - Wrase et al. - Am J Psychiatry., 2008
Hyperhomocysteinemia as a new risk factor for brain shrinkage in patients with alcoholism. - Bleich et al. - Neurosci Lett., 2003


text:
How well does it actually work to surgically reroute the optical nerve?
Two publications, Roe et al, 1992[1] and Metin & Frost, 1989[2], describe results pertaining to the ability of a region of cortex to process information from a different sensory mode than the one that it normally does.
Specifically, they describe studies in which:

input from the retinas of newborn rodents was rerouted, by
surgical methods, to parts of the cortex other than the visual;
the rodents were allowed to mature;
the responses of cortical cells in the new target region to visual stimuli were assess.

Now it's 20 years later, so I'm sure there have been many others.
Something of which these publications seem to make no mention is the behavior that developed in the test subjects. For example, did they appear to be completely blind from a behavioral standpoint?
Is anyone aware of any publication, relating to these studies or other, similar experiments, which addresses this question?

Roe AW, Pallas SL, Kwon YH, Sur M. 1992. Visual projections routed to the auditory pathway in ferrets: receptive fields of visual neurons in primary auditory cortex. Journal of Neuroscience, 12(9): 3651-64.
Métin C, Frost DO. 1989. Visual responses of neurons in somatosensory cortex of hamsters with experimentally induced retinal projections to somatosensory thalamus. Proceedings of the National Academy of Sciences USA, 86(1): 357-361.

Have you looked at the forward citations of the articles: RPKS92 and MF89?

I had read through most of the first, but only glanced at the second, one of which turns out to be what I was looking for.

@mac01021 - Thanks for accepting my answer, despite the fact you more or less answered your own question earlier. I did find an additional publication though :) Very nice question. I +1'd it earlier.

This seems more of an engineering-limitation than a biological-plasticity limitation: to sever a nerve and reconnect it with reasonable fidelity sounds VERY hard.

At least two follow-up studies have investigated the behavioral consequences of the re-routing of the optic nerve to the auditory cortex. In these animals the visual cortices were ablated, and the optic nerve re-routed by combined lesions of the superior colliculus and ascending auditory pathways to the thalamus. These lesions induce retinal axons to form permanent ectopic (i.e., re-routed) projections to the auditory thalamus and cortex. These ectopic visual projections result in the formation of retinotopic maps in the auditory cortex and in visually responsive neurons with receptive field properties reminiscent of cells in the visual cortex.
These re-wired ferrets and hamsters were shown to have functional vision, as shown by their ability to tell light from dark and to recognize simple visual patterns. Visual pattern recognition was absent in control animals that were blinded, but not re-wired. Visual function, as measured by grating visual acuity in re-wired hamsters and rats, was however not as good as in control animals with normal vision (Frost et al., 2000; Melchner et al., 2000).
References
- Frost et al., PNAS (2000); 97(20): 11068–73
- Melchner et al., Nature (2000); 404: 971-6


text:
When giving blood, what is the specific Iron measurement they take?
I went to give blood the other day, and they take an "iron" measurement prior to actually drawing the blood. My level was 16.4 -- but what specific type of iron were they measuring?
I've heard of ferritin, transferrin, iron binding cap, total, etc., but when I asked what the upper limit was, she said 19, which didn't really fit within the healthy ranges I can find for the above types.
Thoughts?

Most likely they were measuring the hemoglobin concentration, in units of g/dL (i.e. 101 kg/m3). Assuming by your username you are male, the reference range for [Hb] is approximately 13.8 to 18.0 g/dL (sources vary somewhat), which roughly matches the "19" you were told was the upper bound.
Wikipedia also notes that [Hb] "is typically tested before or after blood donation", making it likely that that was what they measured.
Calling it "iron" isn't strictly correct. The human Hb tetramer's molecular weight is about 65 kDa, yet it contains only 4 iron atoms, so the actual concentration of iron in your blood is actually much less.
Useful resource: Wikipedia's list of reference ranges for blood tests has a very detailed chart of commonly cited reference ranges for many substances, with citations.