text:
How fast is the blood flow in various vessels?
How fast is the blood flow in different blood vessels, such as the aorta and capillaries?

At rest, during sleep or in the midst of strenuous exercise? In human adults?

I didn't think the flow varied much between rest and high activity? A comparison would be nice. Yes, human adults.

You will have to account for mass balance using the Navier-Stokes equation which accounts for the cross-sectional area of the vessels.

@bobthejoe: Even with a good model of the arterial system, calculating these velocities through a model would probably not work. I'm looking for actual measurements, e.g. as those Larry posted for the MCA.

In the middle cerebral artery blood flow at rest is 73.7 cm/s. After a period of 3 minutes of hyperventilation, blood flow in the same artery decreases to 37.6 cm/s. This is published work.
Vena cava measures: Peak velocities during ventricular systole ranged from 30 to 45 cm/sec in the inferior, and from 10 to 35 cm/sec in the superior, vena cava, also published.


text:
Does arterial blood always flow away from the heart?
Is there a negative net flow of blood in human arteries at any point of the cardiac cycle? I realise that blood flow can be turbulent, e.g. in the aorta or around stenotic arteries, but then the average is still flowing away from the heart.
The question was provoked by this graph, which admittedly I haven't seen in its context:

A similar graph showed negative velocities in the aorta and innominate artery of humans.

oh no, which one should I accept?

Simple answer, yes.
It really is a matter of how technical you wish to be. By defintion, all arterial flow conveys blood away from the heart. The largest arteries exhibit the Windkessel effect which allows for the compression-based effects that bobthejoe inferred. Explicity, as blood is pumped out of the left ventricle, it stretches te aorta, and this tension in turn causes compression on the artery and pushes blood forward. On the flip side, venous vessels (except the pulmonary vein) return blood to the heart, but here you are likely to encounter local areas of reverse flow. This is counteracted to a degree by one-way valves present in the large veins to keep the net movement of blood in the body always toward the heart.

Despite my contradicting conclusion, I fully endorse this answer. The answer entirely depends on how you calculate velocity. Is one looking at streamlines or bulk effects? If bulk, then the average flow should be going away as explained by @leonardo.

Quick answer, no.
Imagine a balloon; as you compress the balloon, there will be a lot of air that leaves it. But as you let it relax, the balloon pulls in surrounding air even as you fill  it from another side. When the aortic and tricuspid valves are closed, there is blood flow forward but due to conservation of mass, the blood goes back to fill in the empty region.

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text:
What are the effects of caffeine on the mammalian circulatory system?
A friend of mine told me an anecdote about his mother, who drank too much caffeine, to the point she became hypotensive and would pass out. Because caffeine acts as a stimulant, I'm assuming the decreased blood pressure was some kind of tolerance effect.
How exactly would caffeine have disrupted her circulatory regulation and caused her normal pressure to decrease?

I can't speak to the causes of hypotension, but you are indeed correct, caffeine is a stimulant. As a stimulant, there is a well documented acute period of hypertension that lasts for up to 4 hours. Interestingly, there is no causal link established between caffiene consumption and chronic hypertension leading to cardiovascular disease (see here and here).
Having said that, caffeine is also a diuretic, which could cause someone who is already fairly dehydrated to exacerbate that state. It's possible to faint from a result of severe dehydration but I think it would have to be pretty severe.
It's possible someone is prone to fainting for non-medical, purely physiological reasons, such as standing for long periods, standing up too quickly, hypoglycemia, or some other predisposition.

Caffeine's mechanism of action,, Hindawi journal (https://www.hindawi.com/journals/ijvm/2010/834060/)
Direct effects of caffeine:
On vascular smooth muscle:
Caffeine inhibits phosphodiesterase enzyme , which is responsible for degradation of cAMP to 5'AMP , so concentration of cAMP increases which activates protein kinase A which phosphorylates myosin light chain kinase (MLCK) . MLCK, on activation by calcium- calmodulin complex, phosphorylates light chain of myosin which then binds to actin and causes smooth muscle contraction. But MLCK in phosphorylated state is insensitive to calcium and hence can't be activated which results in relaxation of smooth muscles . So caffeine increases MLCK concentration in phosphorylated state which is insensitive to calcium hence cause vasodilation
Indirect effects:
On endothelium:
Caffeine inhibits phosphodiesterase, required for degradation of cGMP to 5'GMP.
It increases nitric oxide (NO) production in endothelium by activating nitric oxide synthase via increased cGMP .  NO then diffuses to vascular smooth muscles where it causes relaxation which results in vasodilation.
Hence caffeine causes vasodilation by both direct and indirect effects.

Welcome. Can you add your sources to this answer?

I added my reference now ,, it's form a journal on Hindawi : caffeine vascular mechanism of action

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What type of CCD system is required to take photos of luciferase
I'm working with luciferase and I want to be able to take a photo of it. The trouble is, I can see the luciferase glowing in all of its glory in front of me but no matter how hard I try, I can't take a photo of the luciferase with my DSLR (Nikon D80).
I'm curious if I'm missing a certain lens or if I should be shooting using a different lighting setup. I'm already exposing for 30". Perhaps longer?

You might want to look at photography.se too

That I have done http://photo.stackexchange.com/q/20976/8852

Seem to have got some quite thorough answers there :)

You'll also want to make sure that you are imaging in complete darkness because you may have very low photon emission from your luciferase system and any amount of background light can overwhelm your signal with noise.

You are looking for a bioluminescence imaging device. These have very sensitive CCD camera and exposure times are around 5 minutes in complete darkness.

here's an example: http://www.berthold.com/ww/en/pub/bioanalytik/produkte/lb981.cfm


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What is the difference between HPLC and FPLC and why is FPLC preferable for protein purification?
I've used HPLC (high performance liquid chromatography) before (once, so I'm barely even qualified to know what it stands for) so I was surprised when my labmate told me she would be using an alternate technique to isolate a protein.
What exactly are differences in HPLC and FPLC (fast protein liquid chromatography) instruments, and why would FPLC be a better technique than HPLC to use with proteins? What situations make HPLC preferable?

The only difference between FPLC and HPLC is the amount of pressure the pumps apply to the column. FPLC columns have a maximum pressure of about of 3-4 MPa, whereas HPLC columns can withstand or require much higher pressures. As a general rule, HPLC columns won't work with old FPLC equipment; FPLC columns can go on HPLCs as long as the pressure can be regulated.
Manufacturers have been marketing separate equipment to handle these different classes of columns, but the trend seems to be heading towards machines that can handle both types of columns without issue. A GE rep told me a few years ago that they've improved the pumps on the AKTAs to the point that "they're technically HPLCs now." The term "FPLC" is probably on its way out.

I wouldn't say that's the only difference, but it's a large difference. Most of your HPLCs will expose the compounds to several metal components, which can denature some proteins, while FPLCs are designed to minimize metal exposure and preserve protein structure better. HPLCs usually have better detectors, often with monochromators for full wavelength selection, while basic FPLCs have simple detectors with 2 wavelengths, 254 and 280nm, which is usually fine for proteins. Reverse phase HPLC will often use organic solvents, while FPLC usually uses buffered aqueous solutions.


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Compare and contrast "Rubisco activity" and "assimilation rate" (is there a difference, and if so, what is it)?
I am confused about the variable "RuBisCO activity". How is it measured, and is it any different from the net assimilation rate?
Based on some background reading (e.g. Kling, 2008; Lambers et al 2011)  the only difference that I can find is the units. Both would have "carbon fixed per unit time", but RuBisCO activity is expressed per unit mass of the enzyme, while assimilation rate is per unit leaf area (or less commonly, leaf mass).

Both are measures of carbon fixation rate.
RuBisCO activity specifically refers to the rate at which the enzyme RuBisCO fixes carbon to RuBP, and is measured by isolating the enzyme from tissue samples and, usually, using radiolabelled CO2 to measure how much carbon is fixed in a set amount of time in controlled conditions and with controlled supply of substrate.
Carbon assimilation rate is generally a whole-plant or whole-leaf variable, measured on a larger scale. It is usually measured by measuring leaf sugar carbon before and after a set period, again using radiolabelling. Conditions may or may not be controlled, and it can be measured in the field (unlike RuBisCO activity).
RuBisCO activity might differ from net fixation in the short term in plants which have an intermediate carbon fixation step, such as in CAM or C4 plants, if the net fixation measurement includes the intermediates - the pool of intermediate carbon-containing molecules have technically been fixed but not by RuBisCO. However, over longer time periods this effect will disappear, as ultimately all CO2 is fixed or re-fixed through RuBisCO.

This is a useful answer, and it does answer my question. However, I was not familiar with measuring assimilation using 14C-CO2. Almost every leaf-level measurement I have found in the literature has been measured with a LI-6400, which measures exchange of [CO2] and [H2O] between the leaf and atmosphere. In what cases is 14C used?

Are you asking for specific cases, or a general reason why people would choose 14C?

more or less in general. It seems like a less direct measure (since the sugar pool presumably has losses to respiration as well as inputs from assimilation). It also seems more difficult in general, although perhaps less expensive.


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How do insects breathe?
Do ants even breathe? If they don't, how do they stay alive? On what resources do they depend upon to stay alive? How are they different form mammals?

Insects breathe by simple diffusion through the cell walls. They do not breathe in the same sense that we humans do. They intake oxygen through spiracles in the insect's cuticle. It goes through the insect's trachea by dissolving into the tracheal liquid. From there it diffuses throughout the insect in tracheal tubes. At the ends of the tubes, the oxygen is taken by body cells.

Some insects are able to pump their abdomens in order to move air through the tracheae more effectively.

And how are they different form mammals?

Mammals happen to have lungs.

That is, by the way, one of the constraints that limit the size of insects.

@nico any reference on that? It is really interesting and does seem logical :).

@Zenon as an example: http://www.pnas.org/content/104/32/13198.short and: http://rspb.royalsocietypublishing.org/content/277/1690/1937.abstract

Also I'm sure I've seen somewhere a calculation from physical principles showing that the tracheal size limit is true. If I find it I'll post it.

The main difference between tracheal gas exchange, and other forms of gas exchange (except simple diffusion) is that it is generally a passive process. Organisms with lungs, gills, or other modified respiratory organs can actively pump the oxygen-containing medium (usually air or water) across their respiratory surface, and some also pump their blood across in the opposite direction to cause a countercurrent exchange to enable maximum efficiency of oxygen/CO₂ transfer.
The tracheal system is a more efficient mode of gas exchange than diffusion since it does not only involve the oxygen passing over the organism's body surface (a semi-permeable membrane) which limits the rate of movement. Instead the epidermis is invaginated to form tracheae (tubes) through which air can travel passively. The tracheal system is highly branched and terminates at tracheoles (fluid-filled sacs) which closely line respiring tissues to provide oxygen and allow release of CO₂.
Tracheal respiration limits the size of insects since their oxygen demands will not be able to be met if the air has to diffuse very far. Some insects require more oxygen than others: many larger insects and more active insects have evolved to supplement the tracheal system with pumps, gas gills (permanent or temporary bubbles of air which aquatic insects carry), or mechanically ventilated air sacs (honeybees have these, see Gullan & Cranston, 2005; and Snodgrass, 1956).
Furthermore, tracheal systems can be 'open', 'closed', or the insect can engage in discontinuous gas exchange. Insects with open tracheal systems have spiracles (holes in their cuticle). Closed tracheal systems are more common in aquatic insects, they come in two major designs: highly branched systems over the internal surface, allowing cutaneous gas exchange; and filamentous or lamellate  arrangements, which are analogous to a primitive gill (see Wigglesworth, 1964 or Gullan & Cranston, 2005 chapter 10 for more on aquatic insect adaptations). Discontinuous gas exchange involves co-ordinated opening and closing of different spiracles which results in a uni-directional current allowing more effective ventilation.
References

Gullan, P.J. & Cranston, P.S. (2010) The Insects: An Outline of Entomology. John Wiley & Sons.
Snodgrass, R. (1956) Anatomy of the honey bee, Comstock Publ. Assoc. Ithaca, New York,.
Wigglesworth, S.V.B. (1968) The Life of Insects. New American Library.

Comprehensive and logical answer, +1


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What is the maximum potential sucrose concentration of plant sap? What keeps plants below this potential?
I am interested in identifying the maximum potential dissolved sucrose (%w/w) that plant sap could have, and which (biological, physical, chemical) factors constrain the observed sucrose concentrations.
For example, sugar maple has one of the highest sucrose contents at 6%, and the solution also contains fructose, glucose, organic acids, minerals (K, Ca, Mn, Zn, Na, Cl), amino acids, volatile organic compounds, phenols, enzymes  (according to Wikipedia), and most sap flow occurs when temperatures cross the freezing point each day.
Is there a way that I can calculate this theoretical maximum from "first principles" of organic- or bio-chemistry, or is this a question better suited for empirical study?
this is a biological application of my question at physics.SE

As the concentration of sugars in the sap increases, so does viscosity. At high viscosity, the sap will not flow at a sufficient rate to provide nourishment to the different plant tissues.
In addition, there are limitations to concentrating the solutes in the sap. As the sap becomes more concentrated, the plant would be working against a osmotic gradient to further increase that concentration. That energy cost may be too great.


text:
Serological assays not detecting native proteins
Is there anyone out there who has done much work with serological assays? We have antiserum for a manufactured viral protein but no luck so far getting it to detect native protein (unless today's attempt worked which we will find out tomorrow).
What are any common problems or possible considerations that we should bear in mind when testing?

It would probably help if you would add as much detail as possible about the specific assay you're performing. As it stands know you can only get very general advice, and the answerers have to guess the details.


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Why do animal teeth get darker if exposed?
I was wondering why the teeth of cats (And dogs, as far as I know, plus possibly some other animals or even humans) get darker if they are exposed to air / light?
Example:

(See the lower end of the tooth, which sticks out if the mouth is closed. No, the cat was not resisting, just slightly annoyed.)
So, my question is:

Why does this happen?
Would it happen to human teeth, if they would stick out of the mouth like the ones of cats do?

My guess is that it has something to do with the teeth reacting to air and corroding, but all my knowledge about biology comes from two years of biology in school, so I'm asking here.

Could you provide evidence that this is frequent or invariable? I can think of an explanation, but I'm unsure if this is common.

it probably wouldn't happen if they brushed their teeth more.  Its hard to imagine human teeth are that different... :)

Yeah. I think it has something to do with REDOX.

As far as I know, oxygen and other oxidizing agents make the teeth whiter by bleaching it (Potassium permanganate and hydrogen peroxide solutions are used to bleach teeth). Anyways, your question isnt  addressable as long as you dont support this with some more evidence. [More biological replicates!!!   :P ]

The incisal and occlusal edges of teeth are more translucent since there is only enamel in this area and the dentin core is deeper inside. The dentin is more opaque and reflect the light back and it looks lighter whereas the enamel is translucent and allow more light to pass through and less light is reflected back so it looks darker. Many human teeth the incisal edge is translucent or darker for the same reason.

According to me animals use these teeth to chew meat particles etc. So because they don't brush these food particles get exposed to bacterial agents which in turn causes corrosion of teeth. As we see the structure of the animal teeth the food particles are trapped in between resulting into high bacterial corrosive activity. But in humans, regular maintenance and high use of water it decreases the acidity caused by the food in our mouth this prevents excessive corrosion and bacterial activity and growth. On the other hand canines have an initial use of tearing so the usually are not much affected by the food particles and also because of their protruding shape.
The exposure of air and light increase the bacterial activity.

Do you have a reference other than yourself?

This has the right idea, but the baffling (if refreshingly honest) "reference" needs to be corrected.


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What is the mechanism that directs myosin walking?
Myosin, dynein and kinase all "walk" towards specific ends of the microtubule or actin filament they are on. I'm most familiar with the walking mechanism for myosin, where ATP fuels conformal changes in the binding region, but I don't understand how it chooses to go one direction over another. Actin fibers' positive and negative ends are fueled by the addition of G-actin via ATP and its subsequent reduction to ADP, so I suspect that this process is somehow involved in determining the direction of myosin's movement.
As just a secondary thought, are there differences in the mechanisms of the movement between the three walking molecules listed above?

Good question that got me waist-deep in PubMed. It appears that the directionality of myosin motors is due to the angle at which the actin-binding catalytic domain is attached to the neck region. This review by Vale and Milligan, 2000, sums up the "unzippering" of the neck region that contributes the force for the movement (a video from the review adapted for Alberts' textbook is also informative).
Most myosins move towards the plus end of actin, but myosin VI moves towards the minus end. The neck region of myosin VI attaches to the head region at a different angle than conventional myosins and this is the apparent reason for the change in direction preference (see Figure 1 in review by Rodriguez and Cheney, 2000; also Volkmann and Hanein, 2000; Masuda, 2008).
And for your entertainment, an awesome movie of myosin V walking by Kodera et al, 2010 on YouTube.


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Is there a standard format for plant community composition data?
FIA has a nice database of forest Inventory data, this would be great except that it does not seem capable of handling data from non-tree species (e.g., grasslands, wetlands).
Is there a standard database or flat-file format for collecting plant community data (e.g., biomass, cover, dbh as appropriate)?

There does not appear to be a current standard, but Veg-X is a standard that has been developed to facilitate exchange of plot-based vegetation data, and may provide the closest to what you are looking for.
Veg-X is described in Wiser et al 2011 and the project home page is http://wiki.tdwg.org/Vegetation/
From the abstract:

The exchange standard for plot-based vegetation data (Veg-X) allows
  for observations of vegetation at both individual plant and aggregated
  observation levels. It ensures that observations are ﬁxed to physical
  sample plots at speciﬁc points in space and time, and makes a
  distinction between the entity of interest (e.g. an individual tree)
  and the observational act (i.e. a measurement). The standard supports
  repeated measurements of both individual organisms and plots, allows
  observations of entities to be grouped following predeﬁned or
  user-deﬁned criteria, and ensures that the connection between the
  entity observed and taxonomic concept associated with that observation
  are maintained.

Wiser, S.K., N. Spencer, M. De Caceres, M. Kleikamp, B. Boyle, & R.K. Peet. 2011. Veg-X -- An international exchange standard for plot-based vegetation data. Journal of Vegetation Science 22:598-609.


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Can methylation from DNA get copied to RNA during transcription?
Methylation on gene-body and 3'UTRs if copied to mRNA can potentially regulate post-transcription modifications or expression regulation. But I'm not sure if they are maintained after transcription or if they get all de-novo methylation.

I don't believe anything should change in the majority of DNA->RNA transcription. DNA methylation typically occurs on the non-watson crick side of Cytosine so it shouldn't affect the base-pairing.
However, there are a few hypothetical situations that would result in alterations of the transcribed RNA. The sponatneous deamination of the 4' amine would convert the base into uracil. If there is an additional 5' methyl, the 5-methyluracil would be recognized as Thymine.
(edit) I've talked with several genomics folks about this topic and it turns out that M5Cytosine is very resistant to deamination due to the presence of the Methyl group. As a result, the instance that I have just described is actually very rare.

5mCytosine to Thymine deamination
The other situation would be to errors in DNA proofreading. Does the 5mCytosine affect the fidelity of RNA polymerase? I honestly don't know but it would be worth examining.

Is there any citation of altering cytosine on RNA to 5mC?

@Garima Kushwaha. Does this count? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836557/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307917/ This paper has the opposite view; that the rate of deamination is higher in the methyl version which accounts for its increased mutation rate.

There is an article in PNAS Conservation and divergence in eukaryotic DNA methylation who used:

next-generation sequencing to investigate the DNA methylation patterns
  in eight divergent species, including green algae, flowering plants,
  insects, and vertebrates. Their data allowed a comprehensive
  comparison of whole-genome methylation profiles across the plant and
  animal kingdoms, revealing both conserved and divergent features of
  DNA methylation in eukaryotes.

So there is some conservation.

That evolutionary conservation seems very interesting, but the question is whether it is maintained somehow into the transcribed RNA


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How to decide which is the correct scientific name for a particular species
To start with, I am not a person having sound knowledge in biology. When I started my search for phyto-chemicals in a particular family in the plant kingdom, I got confused. The scientific papers use a particular name, and when I searched in these 2 websites, (just to name it) I got the message that some of the names are  "not resolved"  or "synonyms".
My questions are

Biologists do they accept  the names mentioned in  website 1? If not where can I find authentic names?
Who controls / monitors the name of these plant species?

Out of curiosity, what name are you looking for?

I would go with results from the first site you mention (www.theplantlist.org)

iPlant provides an automated name resolver: http://tnrs.iplantcollaborative.org/TNRSapp.html

When it comes to plants and animals, common names clearly differ from region to region.
A first effort to univocally classify them was done in the 16th century by Carl Linnæus (see my answer to this question for some historical background).
The nomenclature of plants is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN), and for animals from the International Code of Zoological Nomenclature (ICZN).
The fact that there are rules, however, does not imply that names are conserved over time, nor that there is a rule for everything!
As time goes by rules change, certain species may be assimilated by others, or a certain subspecies will separate and become its own, and at times name changing proposals even raise havoc in the scientific community.
In summary, it is important to remember that taxonomy poses rules that are there to facilitate talking about science. Those are not absolute rules, sometimes they are arbitrary, and therefore for certain species there is no univocal name (and surely there is no correct name).

can you just share the "Official" website of ICN. I could not any hits when i googled it.

@Anil: The International Association for Plant Taxonomy hosts the full text of the Vienna code. I could not really find the latest version (Melbourne code), although the IBC2011 website may be of help.

For completeness' sake, the Melbourne code is now up at http://www.iapt-taxon.org/nomen/main.php

Nico provides a nice answer, but implies that the names are more fluid than they actually are.
It is possible to get an current standard nomenclature, and to update it each time the ICN releases a new edition.
The ICN requires that any changes be made by an international botanical congress, and changes are included when a new addition of the ICN is released. Also, note that the ICNCP is used for cultivated plants.

You misunderstood my point. What I am saying is that, well, names are names, and can change. That is why nowadays you would say Chroicocephalus ridibundus, rather than Larus ridibundus when talking about a Mediterranean Gull, although some years ago the opposite was true. That does not mean that anyone can change the names at his own will, but it is important to remember that there is no strict rule for nomenclature [continues...]

[continued...] The case of Drosophila Melanogaster vs Sophophora Melanogaster is a beautiful example of this flexibility: the name ought to be changed, sure, but everyone knows Drosophila by that name, so we will keep it like that, even if there are scientific reasons to opt for a change.

I was mostly pointing out that name changes are tractable through the ICN, and that the keeping up to date with the ICN is sufficient.

I realize this question is very old, but there is an important point missing from the current answers: That is the difference between the nomenclature and the taxonomy.
By "taxonomy" I mean the understanding of how organisms are related to each other. Key questions here would be whether taxa sharing some group name (the same genus, for example) form a clade (i.e., there exists an ancestor whose descendants include all and only members of that genus), and whether particular taxa or specimens are the same species or not.
By "nomenclature" I mean the names applied to each taxon and groups of taxa.
The key point is that nomenclature exists within some accepted taxonomy, and that when name changes occur, it's usually because of a conflicting or updated understanding of taxonomy. The rules of nomenclature are comprehensive and quite rigid, but for taxonomy there are no rules at all. Each researcher is free to adopt a taxonomy based on their own understanding of the evidence, however within the taxonomic framework they choose, they must follow the rules of nomenclature.
A "synonym" refers to a named species that the current author considers to be a part of another, earlier named species. For example, the white-veined wintergreen, Pyrola picta Sm., was described in 1819. Later, the cryptic wintergreen, Pyrola crypta Jolles, was described in 2014 when the authors determined that molecular evidence and subtle morphological features marked some P. picta as distinct.
Botanists can (and do) have good-faith disagreements about whether these represent two species. There is no over-arching authority that makes that determination. Botanists who think they are different will use both P. picta and P. crypta, respectively. Those who think they are best considered a single species must use the name P. picta for all of them, and list P. crypta as a synonym.
The example previously given of Drosophila melanogaster possibly being renamed stems from a different issue. Each genus name is pinned to one particular species (the "type species"). In the case of Drosophila it is D. funebris. This means that if the genus Drosophila is recognized as a genus, then it must contain the species D. funebris, but not necessarily any other species. What probably happened is that a new family tree (phylogeny) of Drosophila and related genera was constructed, and D. melanogaster came out as being more closely related to flies in a different genus, than to D. funebris.
Ideally, all the members of a genus would form a clade, because, for example, it can be confusing to have Drosophila melanogaster be more closely related to some other genus, than to other members of Drosophila. So to remedy this, some fly taxonomists suggested reshuffling these taxa to make more neat clades and less of a jumble (D. funebris though, would have stayed in Drosophila).
Normally this happens and nobody notices except for the few researchers who work on that group. Here, however, scientists from all over the world in a dizzying array of disciplines have studied and published results related to "Drosophila melanogaster". It would have lead to huge headaches and confusion to rename this iconic species. In this case, a formal proposal was made to create an exception to the normal rules by changing the type species of Drosophila from D. funebris to D. melanogaster. That way, as long as Drosophila is recognized, then D. melanogaster would also exist.
One final point is that @nico's statement "surely there is no correct name," is incorrect. In the world of nomenclature "correct" is a term of art. For a particular taxonomy there is exactly one correct name. It's just that the taxonomy is subject to the interpretation of the researcher or author.

Excellent answer. The only way it could be slightly improved would be to provide links to back up your answer - I realize that's pretty difficult for this topic, as I don't think the rules (other than nomenclature) are defined particularly well.


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Why do pandas have a high probability of giving birth to twins?
According to the BBC documentary "Wild About Pandas", about half of panda birth result in twins.  Why do they have such a high probability compared to other mammals?  What factor(s) control that fraction in general for mammals?
Additional question about the allometry formula:
I am a little surprised that it is not the ratio between the neonatal mass and the adult body mass that enters the formula, but just the neonatal mass.  Any ideas on that?

I don't know that they have a particularly high rate for multiple births up against other mammals when you consider cat litters of up to ten and beyond?

So you are saying it is rather normal for mammals to have high rate of multiple births, and panda is just an example?  If so, why human normally have single birth?

See Kevin's great answer :D

Charnov and Ernest (2006) present data on offspring number per year and neonatal mass for 532 species of mammals. The two are related by the linear regression equation:
ln(offspring/year) = 2.4 - ( 0.3 * ln(neonate mass) )
Giant panda neonates weigh 100-200 g and are weaned at 46 weeks.
So, according to the regression, pandas should have, on average, 2.8 to 2.2 offspring per year (for 100 and 200 g respectively). With a weaning time of 46 weeks, they could have 1.13 (52/46) litters per year. If every litter were exactly twins, that would be 1.13 * 2 = 2.26 offspring per year, which is within the predicted range.
Humans (neonatal mass of 3400 g) are predicted to have 0.96 offspring/year.
Charnov EL and SKM Ernest. 2006. The Offspring‐Size/Clutch‐Size Trade‐Off in Mammals. American Naturalist 167:578-582.

Thanks for the answer based on allometry.  What's a good survey book on animal allometry? I've read Niklas' Plant Allometry for plant allometry.

I wonder why the duration of pregnancy (95 - 160 days for panda) doesn't enter the computation?  Or is it included in the weaning time?

Could you check the correctness of my reasoning in the original post, including the use of duration of pregnancy?

Good point. You should probably include gestation in the calculation. There are a lot of other regressions in the paper mentioned above. I'm not sure if neonatal vs. adult mass is included though.

Basically a summary and details-filled version of the above.
Based on

ln(number of offspring/year) = 2.4 - ( 0.3 * ln(neonate mass) )
(c.f. Charnov EL and SKM Ernest. 2006. The Offspring‐Size/Clutch‐Size
Trade‐Off in Mammals. American Naturalist 167:578-582.)
litter/year = 1 / (pregnancy duration in years + weaning time in years)

it can be deduced that

number of offspring/litter = exp(2.4 - 0.3 ln(neonatal mass in grams)) / (pregnancy duration in years + weaning time in years)

For pandas, the parameters have values

neonatal mass in grams = 150 - 200
pregnancy duration in years = (95 - 160) (days/years) = 0.26 - 0.44
weaning time in years = 46 weeks/years = 0.88

Therefore, for pandas,
offspring/litter = exp(2.4 - 0.3 ln(200)) / (0.26+0.88) to exp(2.4 - 0.3 ln(200)) / (0.44+0.88) = 1.7 to 2
This means, pandas on average have slightly less than 2 offsprings per litter, which means a high probability of having twins, and sometimes single, but rarely higher multiples. Comparing to human which has about 0.7 offsprings per litter, panda has higher probability of having twins mainly because of much lighter neonatal mass.

I think this article provides some relevant information for your question. It specifies that the rate of twins is high (50%) in captive pandas, and low elsewhere. The article mentions that there is a genetic component to twin predisposition (which is true for humans as well, see here), but that the primary reason is the technology used for captive pandas to increase breeding success:
"To increase the chances of pregnancy, technicians will impregnate a female with at least two male panda semen after natural mating, which makes twins and triplets pretty common for captive pandas."
This doesn't relate to the allometry equations or allometric theory, but provides a practical reason for the phenomenon you are inquiring about.


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Why is methylcellulose used in pharmaceuticals?
Why is methyl cellulose used as a pharmaceutical excipient? Is it due to certain chemical properties? What are the reasons for relying on the chemical properties of methyl cellulose?

Methyl cellulose is a dry binder. It is used to make a pill with a small mass of active ingredient and as much binder as required to make the pill a manageable size.
The following properties make methyl cellulose a good dry binder:

inexpensive
non-allergic
vegetarian
soluble in cold water
non-digestable
nontoxic

Most of this information is from the Wikipedia article.

Like cellulose, it is not digestible, not toxic, and not an allergen. Bacteria cannot digest, methyl cellulose, so they cannot grow using MC as carbon source. It is artificially synthesized produced by heating cellulose with NaOH.

It is a filler/binding agent. Thus MC belongs in the context of a drug to the group of so called excipients. The study of the best suitable excipients (as a tradeoff of factors such as cost, and ease of approving the drug) is called
galenics.
Methyl cellulose is also present in your toothpaste and some of the foods your eat and in the construction industry. It can be considered to be metabolically inert for humans, but can serve as a matrix for enhancing bacterial adhesion and biofilm formation.
The gradual smudging and staining of your bathroom washbowl may be largely attributable to MC and bacteria.
MC is a polymer that is sold as dry powder of various mean chain lengths. It is hydrophilic and can retain large volumes of water.

I'd avoid using code formatting for emphasis, it looks a bit out of place and that is not what this option is meant for. There's also bold and italic available, though I wouldn't emphasize that many parts in a post, too much and it gets distracting again.

Unless it is explicitly prohibited, I will prefer that formatting. Thanks for understanding. I consider bold formatting to be more out of place. Different strokes for different folks...

@LoSauer it's considered extremely bad practice across the network, therefore it would be much better not to use the formatting in this way.

@RoryM You point towards an stackoverflow-thread, yet there is a meta-site for this biology community. I put this issue up for discussion on meta. Till then please regard the editing guidelines. thanks.


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Why is blood pressure higher the more distal an artery is?
Why is blood pressure generally higher in more distal arteries?

Because of reflected pressure waves and the stiffness of the blood vessel.  The forward pressure wave from the heart travels much faster than the blood itself and is reflected at areas of tapering and branching.  This backward wave slows the forward flow of blood, and at the same time, when it meets the next forward pressure wave, that forward pressure wave is augmented...so higher pressures distally...And now you know, and knowing is half the battle...

The cardiovascular system is affected by three types of pressure.  These are:

Heamodynamic - caused by the contraction of the heart, which would give the view of pressure being higher closer to the aorta as in Kevin's answer and my first thought too.
Kinetic  - caused by the action of skeletal muscles in movement in squeezing primarily veins to return blood to the heart.
Hydrostatic - the combination of fluid density and gravity that leads to pressure on the vessel endothelium.  The pressure at a given point is proportional to the volume of fluid above it.  This means that pressure is highest at the bottom of the vessel.

Arteries can of course be treated as one long tube due to their lack of valves, therefore the hydrostatic pressure could be significant in contributing to total blood pressure.  If hydrostatic pressure is more significant than heamodynamic pressure then this would explain why pressure would be higher the more distal the artery is - when standing there is simply more blood pushing down on it.

Critical Care Nurse. 2002;22: 60-79


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How does herpes (HSV) infection suppress HIV?
HIV compromises the human body to defend against infection. Yet people who are infected with herpes are at less risk of developing AIDS.
How does this work?
This question comes from this paper, which is hard for me to follow since I am uneducated on this field. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716975/

Can you please clarify to which Herpes virus you are referring? There are a dozen or so that infect humans, each of which target either mucosal/epithelial tissue, B cells, T cells, lymphocytes or other leukocytes.

I think HSV is sufficiently descriptive enough to characterize and generalize herpes.

@bobthejoe I don't think it is. For example, HSV-1 and HSV-2 are massively different infections, and both are extremely common in humans.

Also, can we have a citation on this claim? Most of what I've seen suggests that HSV-2 is a risk factor for the acquisition of HIV, and that is is the suppression of HSV using acyclovir that helps prevent HIV.

Thanks @EpiGrad. I'm happy someone with more knowledge of HSV could ask for some clarity.

Yes, sure. Give me a moment

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716975/ Here is one. Its hard for me to follow, no where near that educated on the matter.

Alright, having read the citation linked, and doing a little poking of my own, here's my approach at an answer:
Some human herpes virus infections may compete with HIV infection. Essentially, some strains (not the ones you normally think of) infect CD4 cells - the same cells targeted by HIV. These strains down regulate transcription in CD4 cells, which in turn interferes with the HIV infection process. This pertains, it appears most notably, to HHV-7.
However the actual impact on HIV disease isn't clear. Strain competition triggers some fascinating evolutionary pressures, but HIV is notoriously prone to mutation, and competition for CD4 cells might not impact HIV infection on a clinical - rather than microbiological - scale.
Additionally, the two most commonly thought of forms of herpesvirus infection, HSV-1 and HSV-2 are associated with increased acquisition of HIV infection. The clearest reasons for this are genital lesions and inflammation at the site of HIV infection. There's also some interesting dynamics in play for active coinfection, such as the impact of acyclovir treatment for HSV impacting HIV, or HAART treatment for HIV impacting HSV.

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


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In what ways, if any, does administration of rapamycin *not* mimic calorie restriction?
Numerous sources like this say that rapamycin increases lifespan. And mTOR antagonism appears to be a large part of this (mTOR antagonism also appears to be a large part of calorie restriction's mechanism too).
Is the effect of calorie restriction equal to that of rapamycin treatment or are there differences?

I included the actual question in the main text, as it was not immediately clear what was the point of the question (I had to go back and re-read the title and then I understood).

Rapamycin specifically inhibits the mTOR pathway (mTOR = mammalian target of rapamycin), which has numerous downstream functions including protein biogenesis, regulation of cell cycle, immune function and apoptosis. The upstream effectors of mTOR include growth factors and amino acid availability, so you can certainly see that the lifespan enhancing effects of caloric restriction will be (at least in part) mediated by the mTOR pathway.
But there are key differences. mTOR also receives signals relating to DNA damage and inflammatory changes (to name just 2) that are essential for healthy survival. So any direct inhibition of this pathway will affect all the functions - I can't find the reference now, but I have definitel read in one of the numerous rodent studies that rapamycin treated mice have reduced immune function (i.e. the lifespan increased effects can only be seen in a controlled lab environment - in the wild mTOR-inhibition to this degree would be a disadvantage).
I think therefore it is fair to say that the effects of caloric restriction on longevity are mediated by mTOR, but administration of rapamycin is not an equivalent treatment.

Update
Really great review came out last month (http://www.ncbi.nlm.nih.gov/pubmed/22500797) - I recommend you give that a skim if you want detail!

Please add some sources...

@inquilinekea - It is important to note that 'caloric restriction' is not actually a single process - there are different types (e.g. 'diluted' food, or alternatively eating every other day) that are mediated by distinct molecular mechanisms - some of which are mTOR, others may be IGF/insulin signaling (these effects are additive!) [Greer et al (2009) Different dietary restriction regimens extend lifespan by both independent and overlapping genetic pathways in C. elegans]


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What are the effects of combining rapamycin with dietary restriction?
Are the effects additive or subadditive? In many ways, rapamycin acts like a CR mimetic, but even CR can only go so far.

Please explain the question more clearly without reliance on jargon

To clarify; administration of rapamycin (a drug) to lab organisms (including mice [1]) extends lifespan. Similarly, restricting the intake of nutrients to the minimum without causing malnutrition also extends lifespan in lab animals (including primates [2]).
Rapamycin inhibits the mTOR pathway (mammalian Target Of Rapamycin) - specifically mTORC1 (Complex 1) - which influences protein synthesis, autophagy and inflammation (among others). Upstream factors of mTOR include nutrient availability and insulin signaling (see "Deconvoluting mTOR biology" for good review [3]).
It has been hypothesized that the lifespan-extending effects of caloric restriction (CR) are mediated by mTOR (one can see why - mTOR is affected by nutrient availability). In fact it may depend on the method of CR;
Greer et al [4] report that different methods of CR in C.elegans, for instance feeding them a diluted food source, or conversely feeding them on alternate days, do not necessarily require the same genetic pathways. Not only this but CR combined with a genetic mutant (eat-2) have additive lifespan-enhancing effects.
So whilst the evidence is not concrete, and I look forward to other studies in mammals similar to the one by Greer et al, it looks as though rapamycin and CR have similar but not exactly the same effects on lifespan; rapamycin specifically inhibits an individual pathway which is involved in many processes, and some of its effects are not necessarily desirable (e.g. rapamycin inhibits the immune system [5]). On the other hand, CR (most of the different types) seems to be mediated by mTOR - this difference is critical: mTOR is not necessarily inhibited by CR, it is just required for its effect.
Therefore combining rapamycin and CR is unlikely to have an additive effect as rapamycin may override any influence CR has on mTOR signaling, but I have not seen a study in which this has been tried. Combing different methods of CR (or developing drugs to do just that) may well have additive lifespan-enhancing effects.

Harrison DE, Strong R, Sharp ZD, et al. Rapamycin fed late in life extends lifespan in genetically heterogeneous mice. Nature. 2009;460(7253):392-5.
Colman RJ, Anderson RM, Johnson SC, et al. Caloric restriction delays disease onset and mortality in rhesus monkeys. Science (New York, N.Y.). 2009;325(5937):201-4.
Weber JD, Gutmann DH. Deconvoluting mTOR biology. Cell cycle (Georgetown, Tex.). 2012;11(2):236-48.
Greer EL, Brunet A. Different dietary restriction regimens extend lifespan by both independent and overlapping genetic pathways in C. elegans. Aging cell. 2009;8(2):113-27.
Thomson AW, Turnquist HR, Raimondi G. Immunoregulatory functions of mTOR inhibition. Nature reviews. Immunology. 2009;9(5):324-37.


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Do we know if RHEB is more sensitive to some amino acids than other amino acids?
RHEB (Ras homolog enriched in brain) senses amino acid levels in order to recruit mTOR.
See this review describing the process of how RHEB recruits mTOR. So does RHEB have differential selectivity towards different amino acids.
We also discussed this in Matt Kaeberlein's class yesterday and I posed this question but no one could answer it (that said, Matt Kaeberlein called it a good question).

Might be a good question in the context of your class, but that doesn't make it a good question for this forum since it does not provide any of the necessary context to readers.

RHEB does not sense amino acids. See the abstract of this paper.

Activation of this pathway requires inhibition of the tumor suppressor
  complex TSC1/2. TSC2 is a GTPase-activating protein for the small
  GTPase Ras homologue enriched in brain (Rheb), GTP loading of which
  activates mTOR by a yet unidentified mechanism. The level at which
  this pathway senses the availability of amino acids is unknown but is
  suggested to be at the level of TSC2. Here, we show that amino-acid
  depletion completely blocks insulin- and TPA-induced Rheb activation.
  This indicates that amino-acid sensing occurs upstream of Rheb.
  Despite this, amino-acid depletion can still inhibit mTOR/S6 kinase
  signaling in TSC2-/- fibroblasts. Since under these conditions
  Rheb-GTP levels remain high, a second level of amino-acid sensing
  exists, affecting mTOR activity in a Rheb-independent fashion.

RHEB also doesn't have any amino-acid binding (or any small molecule binding) domain.


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If inhibiting S6 kinase decreases protein translation, then could inhibiting S6 kinase could possibly slow down long-term potentiation in neurons?
From http://en.wikipedia.org/wiki/P70S6_kinase...

Phosphorylation of S6 induces protein synthesis at the ribosome.
P70S6 kinase is in a signaling pathway that includes mTOR (the
  mammalian target of rapamycin). mTOR can be activated in distinct
  ways, thereby activating p70S6K. For example, branched chain amino
  acids such as leucine are sufficient to activate mTOR, resulting in an
  increase in p70S6K phosphorylation (and thereby activating it). mTOR
  is also in a pathway downstream of the kinase Akt. Akt is typically
  activated upon stimulation of a cell with a growth factor (such as
  IGF-1). Akt then activates mTOR (by inhibiting the Tsc complex),
  leading to p70S6K activation.

We also found a paper showing that downregulation of S6 kinase also results in a decrease in protein translation in yeast (but I'm waiting for Matt Kaeberlein to email me the slides from yesterday).

Could you please summarize the potential link between S6kinase and neurons? Your question seems to rely entirely on an abstract and lacks context.

S6 kinase is involved in protein translation.
Long-term potentiation relies on protein creation. So fewer proteins are made with reduced S6 kinase levels, which could imply slower rates of memory formation through LTP

I can't rule it out, but it sounds a lot like trying to tune a piano with sledgehammer.
Neuronal LTP depends on protein translation, but so does absolutely everything else in the cell. Inhibiting protein synthesis at the ribosome will block the formation of all proteins, not just the ones responsible for LTP. Unless there's a link I don't know about between LTP and total levels of protein translation, you're really going to want to look into inhibiting the production of proteins specifically responsible for LTP and not protein synthesis in general.


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Single hormone opposite effects
Often, a smooth response to a hormone means that some processes must be sped up and others must be slowed down.
How can a single hormone have opposite effects like this?

An hormone is not different from most other molecules. To have an effect on a cell it binds to a (more or less specific) receptor, located either on the plasma membrane or inside the cell, and it initiates an intracellular cascade of events1.
There are several ways an hormone can have different effects:

there can be multiple receptors for the same hormone. For instance, prolactin can bind to two receptors, called prolactin receptor (PRL-R) short and long form. The short form of the receptor has been shown to lack the ability to promote milk protein genes transcription (See Lesueur et al., PNAS - 1991).
the same receptor can be coupled to different intracellular pathways in different cell types / physiological conditions, thus resulting in different effects.
each cell type/tissue expresses a set of protein that will interact in a different manner with the intracellular cascade promoted by the hormone.
an hormone can interact with receptors for other molecules. For instance allopregnanolone, a metabolite of progesterone, is a potent agonist of the GABA-A receptor, giving it anxiolitic properties.

An interesting example is that of estrogenic compound. Several receptors exist for estradiol (E2). The "classical" receptors are called ER-alpha and ER-beta, and they are located in the cytoplasm. The binding of E2 to the ER promotes their dimerization and entrance into the nucleus where they can promote the transcription of various genes. ERs can also bind to other transcription factors and modulate their activity. So, depending on which transcription factors are present different genes will be transcribed in response to E2. Moreover, ER-beta can have opposite effects then ER-alpha (see for instance Weihua et al., PNAS - 2000). In addition, receptors like ERs can be activated also in absence of the endogenous hormone: for instance, dietary amino acids activate ER-alpha in liver by a mTOR-dependent phosphorylation (Della Torre et al., Cell Metabolism 2011)
To make things more complicated, membrane receptor for estrogen have been described, such as GPR30 (Revankar et al., Science - 2005), membrane "versions" of the classical ERs, plus various splicing variants of the ERs (mostly expressed in tumoral tissue).
GPR30 in breasts has been shown to activate certain molecular pathways (notably Erk1/2) that contribute to cellular growth (Filardo et al., Mol Endocrinol. - 2000), possibly linking it to proliferation of ER-negative breast tumours. Other tissues that do not express GPR30 will lack this E2-induced proliferative stimulus.
So, tissue- or time- dependent modulation of the receptors and of the intracellular pathways associated with it can allow the body to respond to the same hormone (or, more in general, to the same molecule) in opposite ways.

1 This is a simplification, not every substance (and not every hormone) acts by binding to receptors, but let's keep things simple.

Also, I would add that often hormonal system have all kinds of negative feedback loops that allow for "smooth" responses, although these include at least two hormones.


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Free Radicals for aging
From my understanding free radicals play a slight role in ageing.
In what ways are they so damaging, and can a restricted diet reduce production of free radicals?

Free radicals are damaging because their unpaired electrons (or not fully filled valence shell) makes them highly reactive species. They are often considered together with highly oxidizing "reactive oxygen species" (ROS) such as peroxides. They are especially problematic for cell membranes and DNA. In the latter they can react with (oxidize) heterocyclic bases.
As suggested first by Gerschmann et al. (1954), since oxidative damage to cells and cell structures is seen to accumulate with age, the corollary of this could be that aging is a result of oxidative damage. The very fact that cells have antoxidant enzymes such as superoxide dismutase (SOD) suggests that suppression of these species is important in the cell.
Many (but not all) ROS originate from mitochondria during cell metabolism. Therefore, it has been suggested that by regulating metabolism (that is, reducing the metabolic rate) the "rate of living theory" (Harman 1981) the rate of oxidative damage can be reduced. One way to do this may be calorie restriction.
This idea seems to fallen out of favour though. Another possibility is that the rate of mitochondrial ROS has nothing to do with metabolic rate per se; rather it might simply be a longevity determinant.
However, having said all this there is evidence that ROS are actually crucial in a number cellular pathways. It may be that it is the deregulation of pathways managing ROS that can contribute to aging rather than simply damage accumulation with age.
Gerschman, R., Gilbert, D. L., Nye, S. W., Dwyer, P., and Fenn, W. O. (1954). "Oxygen poisoning and x-irradiation: a mechanism in common." Science 119(3097):623-626.
Harman, D. (1981). "The aging process." Proc Natl Acad Sci U S A 78(11):7124-7128.

Good answer! I'd like to add that for further reading, Nick Lane explains this theory in very entensive detail in his book "Power, sex, suicide: mitochondria and the meaning of life".

Nice answer by Poshpaws +1. Free radicals can damage membranes (especially important for mitochondrial and endoplasmic reticulum membrane function), DNA (genes, telomeres,  and mitochondrial DNA, eg), and microsomes. These are the things we consider with regard to ROS for our research on aging.
The role of diet is not clear. Smoking and alcohol may have greater effects on ROS levels than diet itself. However, people who smoke too much or drink too much generally have poorer diets (based on our (and others) epidemiological data). The role of homocysteine (Hcy) in ROS levels cannot be discounted and Hcy is influenced by genetics, diet, inflammation state in addition to other factors. In short, the evidence is not conclusive that a "restricted diet" (did you mean caloric restriction?) will certainly lower ROS levels.

ROS can inflict DNA damage in cells and if this damage is persistant and cannot be repaired, the cell can undergo cellular senescence.  Cellular senescence appears to play a major role in ageing (see here for example). When cells become senescent they can no longer divide and replace damaged tissue.  Also, they secrete pro-inflammatory factors which can damage the microenvironment leading to disease and ageing.  Senescent cells also have dysfunctional mitochondrial leading to increase ROS levels and possibly further damage.


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What's the name of this bird?
This morning I saw a bird that I have never seen before. Since it was quite big, I'm very interested in knowing its name.
The bird was quite big, at least 2-3 times of a common blackbird. The wings were completely black but the whole back strip was quite yellow. Also the tail was yellow. The tail widens towards the end.
The bird flew very strange... it trundled towards the ground and then flew back up some meters before trundling down again. I observed the bird in Zurich, Switzerland at the outer border of the city. A big forest is quite near and there are some huge trees very close to the bird.
Then one last thing to add: I'm not really sure about that, but it could be that the bird had a nest on top of a big tree.
Any ideas which bird that could be?

When you say "yellow" do you mean bright yellow or brownish/cream?

It's rather bright yellow.

It's behavior and size makes it sound like a bird of prey... but its colors are definitely not those of a bird of prey.

Could it be a red kite? it is quite common in your area and there is no proof of vulture or eagle seen that period of time around Zurich (I guess it would be reported if it was); the form of the tail could be useful, the kites are the only one with a forked tail if not forked, it is another bird of prey (if you can confirm this point as well)

There is no photograph.

Following your answer to my comment, I deduced the “yellow” color to be more brownish as there is not big bird with really bright yellow color (like the golden oriole).
 With these parameters I search as well in the ornitho.ch database (all observations given by ornithologist professionals and amateurs) : there was no observation of vulture or eagle in that area (could be possible sometime when they migrate).
Then the more possible answer was a red kite which is quite common summer time in this area (mainly on the north part of Switzerland).

Next time you see a bird of prey, try to take notice of the tail form (forked or flat or round) that can help more for determining the bird.

Hmmmm... the only one I can think of fitting at least in part your description would be the golden oriole (Oriolus oriolus).
I say partly because it definitely is not 2-3 times a blackbird, could be slightly bigger, but on average it is the same size. Also it sounds extremely unlikely that you have spotted it in early March in Zurich, as they should be in Southern Africa right now.
Image, from Wikipedia:

I could not find anything else fitting your description in my field guide (Mullarney & Svensson - Birds of Europe)

It was definitively way bigger. More like a eagle or vulture. And the black part is way bigger. The yellow part is only a small strip over the back and the tail.

hmmm... I cannot find anything like that. We'll have to wait for some ornitologist :) I'll leave the golden oriole photo as it is a very nice bird!

From what I understand of the flight description you give, and given the size and habitat, I would suggest to have a look at woodpeckers. Dryocopus martius is large and black.
Another idea (my favourite, actually): a bird of the genus Tetrao: they can be black and large, live in the forest, and the tail widens towards the end.
Other suggestions, but I really doubt it's relevant:
- cormoran (Phalacrocorax for the size, dark color, and I've seen some perched in trees, and ther's a lake in Zürich);
- Accipiter (for the flight and habitat):
- Milvus (for the size, the tail, and the dark colour):
- cuckoo (Cuculus canorus);
- magpie (Pica pica, black, makes nests on top of high trees, but I suppose you would have recognised it without hesitation).
The yellow stripe on the back matches none of the above suggestions.


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Which organism has the smallest genome length?
Which animal/plant/anything has smallest length genome?

Since you said plant/animal/anything, I offer the smallest genomes in various categories...
(Kb means Kilobases, Mb means Megabases. 1 Kb = 1000 base pairs, 1Mb = 1000Kb)

Smallest plant genome: Genlisea margaretae at 63Mb (Greilhuber et al., 2006)
Smallest animal genome: Pratylenchus coffeae (nematode worm) at 20Mb (Animal Genome Size DB)
Smallest vertebrate genome: Tetraodon nigroviridis (pufferfish) at 385Mb (Jailon et al., 2004)
Smallest eukaryote: Encephalitozoon cuniculi (microsporidian) at 2.9Mb (Vivarès & Méténier, 2004)
Smallest free-living bacterial genome: Nanoarchaeum eqitans at 491Kb (Waters et al., 2003)
Smallest bacterial genome: Carsonella ruddii (endosymbiont) at 160Kb (Nakabachi et al., 2006)
Smallest genome of anything: Circovirus at 1.8Kb (only 2 proteins!!) (Chen et al., 2003)

Refs...

Chen, C.-L., Chang, P.-C., Lee, M.-S., Shien, J.-H., Ou, S.-J. & Shieh, H.K. (2003) Nucleotide sequences of goose circovirus isolated in Taiwan. Avian Pathology: Journal of the W.V.P.A. 32 (2), 165–171.
Greilhuber, J., Borsch, T., Müller, K., Worberg, A., Porembski, S. & Barthlott, W. (2006) Smallest Angiosperm Genomes Found in Lentibulariaceae, with Chromosomes of Bacterial Size. Plant Biology. 8 (6), 770–777.
Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., Nicaud, S., Jaffe, D., Fisher, S., Lutfalla, G., et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 431 (7011), 946–957.
Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H.E., Moran, N.A. & Hattori, M. (2006) The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella. Science. 314 (5797), 267–267.
Vivarès, C.P. & Méténier, G. (2004) Opportunistic Infections: Toxoplasma, Sarcocystis, and Microsporidia. In: World Class Parasites. Springer US. pp. 215–242.
Waters, E., Hohn, M.J., Ahel, I., Graham, D.E., Adams, M.D., Barnstead, M., Beeson, K.Y., Bibbs, L., Bolanos, R., Keller, M., Kretz, K., Lin, X., Mathur, E., Ni, J., et al. (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proceedings of the National Academy of Sciences of the United States of America. 100 (22), 12984–12988.

Well done! How did you find these?

The plant and bacterial ones I had floating around in my memory having read about them previously, so a bit of googling confirmed the names. The animal ones I got from the Animal Genome Size DB, and from Wikipedia. I guessed that viral genomes would be the smallest, so I also searched for the smallest viral genome. Then I went back to the literature (by searching Google Scholar for organism name + "genome size") to check all my facts and provide reliable references.

Nice answer Richard.

Smallest free-living bacterial genome: Nanoarchaeum eqitans at 491Kb (Waters et al., 2003)
I downloaded this paper it says that this is archaea and its obligate symbiont not a free living bacteria. Please read carefully and then upload it.

"Smallest genome of anything" is wrong. There are virus-like elements like viroids with as little as ~200 bp 'genomes'. Some viroids have as little as one RNA enzyme, others have not even this.

I want to say Mycoplasma genitalium with a genome size of 582,970 bp. Turns out the answer is Nanoarchaeum eqitans with a genome of 490,885 bp.
http://en.wikipedia.org/wiki/Nanoarchaeum
http://www.ncbi.nlm.nih.gov/pubmed/14566062

That's the smallest genome of a free-living organism. And until 2003 you would have been right about Mycoplasma, which were previously the smallest known in that category.

Both Mycoplasma genitalium and Nanoarchaeum equitans are obligate parasites / endosymbionts. This means that they depend heavily on their host to support their vital functions and they have lost many of their own genes.
A really free-living organism with an extremely small genome (~1309 kbp, 1354 genes) is the heterotrophic marine alpha-proteobacterium Pelagibacter ubique [1].
See a larger analysis here: https://alamot.github.io/smallest_genome/
[1]: https://www.ncbi.nlm.nih.gov/pubmed/16109880 Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, et al. (2005). «Genome streamlining in a cosmopolitan oceanic bacterium». Science 309: 1242–1245.


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Genetic carrier Pedigree of Recessive Traits
A human male and female couple with normal colored ears discover that, in both of their families, their fathers (who have normal ears) each had siblings with red ears.  Red ears is a rare autosomal recessive disorder.  None of their grandparents had red ears.  Assume that the red ears in both families were caused by mutations in the same gene, that there were no new mutations within the pedigrees, and that the mothers of the couple were not carriers of the disease gene.
A) based on the information, what is the probability that the male in the couple is a carrier of the red ear disease gene?
B) if the couple had 1 child, what would be the probability that child would have red ears?
I was discussing this problem over with a friend and we got different answers.
A)I think the answer is 25%.  I multiplied 1/2 and 1/2.
B)6.25%.  I multiplied 1/4 and 1/4.

Is red turning to green a copy error or is it another distinct phenotype?

@RoryM i mixed up the colors.  the question is edited

What's the question? The probability that this male and female will have a child with red ears?

@leonardo updated question

Great! Now we can help. :)

Let's take Question A:
Both fathers have siblings with red ears, and red ears are an autosomal recessive trait. The grandparents did not have red ears, we know then that they were carriers of the recessive allele. Each grandparent was Nr (for Normal and red alleles respectively).
The fathers have normal ears, so they could be NN (probability 0.33) or Nr (probability 0.67).
The answer then is that each father independently has a 2/3 chance (0.67 probability) of carrying the red ears gene.
The male's mother, being RR, makes the male a carrier only if the male's father is himself a carrier. To put it mathematically, he has a 1/2 chance of being a carrier with 2/3 probability that he was a carrier to begin with. (2/3)*(1/2) = 1/3.
Therefore the male can be carrier with 1/3 chance.
Now Question B:
Short answer:
Since the male and female have symmetrical pedigrees, and we just solved the chance of the male being a carrier with 1/3 chance, then the chance of them having a child with red ears is (1/3)*(1/3) = 1/9.
Long answer:
The male's and female's fathers may each be heterozygous or homozygous normal, given the information, with both mothers being homozygous normal (NN).
If Father A is NN (crossed with Mother A, also NN), there is a 0 probability of passing on the red ears allele.
If Father A is Nr, then Person A has a 0.5 probability of carrying the red ear allele.
Person A can now be NN (with 0.25 probability) or Nr (with 0.5 probability).
Likewise with Person B.
Now lets consider all 4 combinations of genotypes that Person A and B can have when they have a child. I will write a table with one Person on each side of the table, with the probability of their genotype written in brackets beside. Each intersection will represent the frequency of carrying the red ears allele.
                Person B
             (1/3)     (2/3)
Person A      NN        Nr
(1/3) NN      0/4       2/4
(2/3) Nr      2/4       2/4

Carrying the red ear gene: (A more interesting example)
There are a total of 6 outcomes in which the child carries the red ears allele, but these must be weighted by the probability that each parent has the associated genotype.
Probability of carrying 'r' = [ (1/3)(1/3)(0/4) + (1/3)(2/3)(2/4) + (2/3)(1/3)(2/4) + (2/3)(2/3)(2/4) ] / [ (1/3)(1/3) + (1/3)(2/3) + (2/3)(1/3) + (2/3)(2/3) ]
 = 0.25
Having a child with red ears:
Probability of having red ears = [ (1/3)(1/3)(0/4) + (1/3)(2/3)(0/4) + (2/3)(1/3)(0/4) + (2/3)(2/3)(1/4) ] / [ (1/3)(1/3) + (1/3)(2/3) + (2/3)(1/3) + (2/3)(2/3) ]
 = 1/9 or about 0.11
It's left as an exercise to the student to derive the remaining probabilites.
Nr 4/9
NN 4/9
rr 1/9

question A asks for the probability that the male in the couple is a carrier. the male's grandparents must have been Rr (R=red ear dominant, r=recessive red ears).  Therefore the male's father has a  1/2 chance of being a carrier.  since the male's mother can't be a carrier, her genotype is RR.  Therefore the male's parents are Rr and RR.  so 1/2 * 1/2.  why isn't this right?

You are correct that each grandparent is Rr. The male's father then can either be RR (1/4 chance) or Rr (2/4 chance) but not rr (0/4 chance). We only know the male's father has a normal phenotype. We normalize this to the possible genotypes, and then the male's father has 1/3 chance of being RR and 2/3 chance of being Rr.
The male's mother, being RR, makes the male a carrier only if the male's father is himself a carrier. To put it mathematically, he has a 1/2 chance of being a carrier with 2/3 probability that he was a carrier to begin with. (2/3)*(1/2) = 1/3.

Made the question more clear, and corrected the solution to question A since misread it.

thank you.  my error was not normalizing the probabilities as rr is impossible if the person is a carrier.


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What causes light to be brighter in the corner of the eyes?
I have noticed when in a dark room light and color seem to be brighter and more intense in the corner of my eyes. For example the light that comes from my digital clock seems like a dark pink when I look straight at it. But when I see it in the corner of my eyes it looks red.
What causes this?
Is this normal, does everyone perceive it that way?

Your retina has two kinds of light-sensing nerves: cones and rods. Cones are responsible for color vision, i.e. hue, while your rods handle differences in the value, as in how bright it is.
Humans have adapted to have cones mostly in the center of the eye (which corresponds to what you're looking directly at), where the most distinguishing color information is needed. It's not often that you'd use your peripheral vision to identify the actual color of something, and this explains why you're seeing a difference between pink and red. The intensity of the color is correct, but you aren't able to identify the hue because of a lack of cone nerves.
So yes, this is normal. A fun trick (and also totally helpful if you have a messy room) is to look a foot or so above the floor when you're walking in the dark. It allows you to see what you're walking on better, since you need intensity receptors more than color receptors.
References:
http://regentsprep.org/Regents/physics/phys09/ceyes/sensing.htm
http://hyperphysics.phy-astr.gsu.edu/hbase/vision/rodcone.html


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Which came first: The Chicken or the Egg?
Has there been any serious scientific inquiries into answering this age old question?

-1 as the attempts at answers show this question needs to be much more constrained to be answerable.

Perhaps the question can be better worded as: "Are there any scientific inquiries to the Chicken or the Egg question?"

This question is invalid but it's such a known question that it's worth putting forth, if only to give an opportunity to point out why it's invalid.

This question is more a philosophical question. The chicken or egg dilemma is not really framed in the proper way according to our understanding of biology today, it's more than 2000 years old.

Since the egg carries new mutations and recombination in each generation, and grow (usually) with the same DNA to the adult chicken/cock, we may assume the egg always comes first. In other words, the theropod lays an egg a little more avian than itself. It IS a philosophical question that, as many others, has perfectly viable biological approaches. I vote to reopen it. We should stop being so closed to "strange" questions.

Most theories about origin of life say that unicellular organisms were first and multicellularity (like chicken) evolved much later, so in that meaning egg (single cell)* was first. Also, almost all chicken ancestors lay eggs (primitive birds, non-avian reptiles, amphibians, fishes and so on...) so eggs existed much earlier than chickens.
*in the meaning of zygote. The development of chicken embryo starts in hen's oviducts, so it's not a single cell at the moment when hen lays it (Gilbert, 2000).

@Hermann_Ingjaldsson Thanks, I've fixed it. Is it better now?

This is a classic case of "it depends on the context."

The Egg: As Marta Cz-C points out, the amniotic eggs that chickens lay were inherited virtually unmodified from their theropod dinosaur ancestors. So when considering the type of eggs, the egg came first.
The Chicken: From a systematic perspective, you must first have an animal that you would call a chicken before it can lay a "chicken" egg. So considering the animal, the chicken.

The question makes the false assumption that chicken and eggs are different life forms.
A life form at stage x is not a different life form than that very life form at stage y.
You might as well ask of which came first, a 7 year old kid or an 8 year old kid.
But they are the same thing and therefore this question is invalid.

Dunno about any serious scientific inquiries into the answer but I always thought the answer is egg. At some point the modern chicken has come into being as the progeny of two pre-modern chickens, however it had to be an egg before it could be a chicken and its parents couldn't have been modern chickens.
However, all that presupposes that you can draw a line in the evolutionary history of the modern (extant) chicken and say this is modern and what goes before is not. I dunno if that really can be done.
Edit: came across this guardian article: http://www.guardian.co.uk/science/2006/may/26/uknews

"Whether chicken eggs preceded chickens hinges on the nature of chicken eggs," said panel member and philosopher of science David Papineau at King's College London.
"I would argue it's a chicken egg if it has a chicken in it. If a kangaroo laid an egg from which an ostrich hatched, that would surely be an ostrich egg, not a kangaroo egg. By this reasoning, the first chicken did indeed come from a chicken egg, even though that egg didn't come from chickens."

And from Prof. Brookfield of the University of Nottingham:

The first chicken must have differed from its parents by some genetic change, perhaps a very subtle one, but one which caused this bird to be the first ever to fulfil our criteria for truly being a chicken; Thus the living organism inside the eggshell would have had the same DNA as the chicken that it would develop into, and thus would itself be a member of the species of chicken

Evolution does not happen over the course of a generation. You are confounding evolution of a species with mutations of a single individual.

That's why I wrote I don't think its possible to draw a line in the evolutionary history and say this is an extant version of a chicken and the previous generation is not.


text:
Is there a biological basis for different accents?
How did accents first develop? Was it climate dependent? or was it a social behavioural issue?
Is there any biological reason for the development of accents?

Your question is (badly) based on the assumption that there is something out there with no accent. EVERYONE has an accent, just like everyone has a fingerprint.

It has to do partly with brain wiring and partly with the mouth musculature, as nicely examplified by this: http://en.wikipedia.org/wiki/Foreign_accent_syndrome

A better question: "Is there a genetic basis for different accents?" Almost everything in biology has a biological reason.

Surely the evidence indicates that it is unlikely and that this is strictly nurture rather than nature? Take a kid from anywhere and raise them while they learn to speak and they will have the accent of those around them with exceptions being rare.

No. Accent is purely environmental. The ability to pick up the unique sounds of a language or variation of a language ceases around puberty: http://en.wikipedia.org/wiki/Language_acquisition
This is why adults learning a second language have trouble distinguishing the unique sounds of the second language. For learners of English, the "th" sounds and the difference between "l" and "r" can be difficult. For languages based on Sanskrit, there are a variety of aspirated/unaspirated consonants somewhere between "b" and "v" that English-speakers have a hard time distinguishing, much less imitating.


text:
What are the various types of protein-protein interactions
I understand there are a number of protein-protein interactions, but what types of interactions exist? and what are the characteristics of them?

Characteristics? They happen between proteins.

characteristics of the interaction type, i.e, what makes a hydrophobic interaction?

I would suggest asking "what are the various types of protein-protein interactions"

There are so many types of protein-protein interactions via various domains, such as SH2 binding (in RTK signaling), Pleckstrin Homology domain (involved in signaling) among others. This site gives a nice list: http://pawsonlab.mshri.on.ca/index.php?option=com_content&task=view&id=30&Itemid=63
Of course, protein-protein interactions rely on the premises of basic biochemistry:

van-der waals interactions (at the most basic level)
Electrostatic interactions
"Lock and Key" model: Some proteins have specific binding pockets for domains of other proteins
Induced fit

There are many ways to study protein-protein interactions, including, but not limited to

Pull-down assays
2D SDS-PAGE / MS
Yeast two-hybrid
Immunoprecipitation

jp has a good point - technically there is no 'hydrophobic force' but when computations are done, a hydrophobic term is often made in the calculations.

Although hydrophobicity isn't a "force", shouldn't it still be included in the answer (creates an entropic advantage)?


text:
Is there an enzyme for the transformation of the hydroxyl group?
I would like to know, is there any enzyme which does the transformation of hydroxyl group to any other functional group using the enzyme.
The substrate is aromatic hydroxyl group. Product should not have hydroxyl group.
How should these types of queries be searched for?

This question is not answerable without a lot more detail. Enzymes are often very specific about which substrates they accept, so you need to provide more detail about the substrates.

I will start querying for some dehydratase or dehydroxylase and look if some of them work on aromatic groups.

@MadScientist, I wish to have the enzymes which are non-specific, i mean which works on hydroxyl group rather than looking at the complete molecule.

if possible can i have some other functional group apart from replacing "OH" group with "H"

Does it have to be an enzyme?  There are plenty of organic reactions you can carry out on that group.

Sounds like any redox chemistry on the hydroxyl group would satisfy  the desired constraints. I would start there.

Can you give us some background? What is your aromatic compound? Why do you want to avoid having OH group on it? What do you want to use it for?

@Jonsca and Gergana Vandova, I am an organic chemist / synthetic chemist and would like to try with enzyme reactions. I had done the reactions using chemical route. The aromatic part is coumarin.

I'm beginning to like this question more and more. Try looking up "retro-biosynthetic design". Kristala Prather has done a lot of work in the type of question that you're specifically looking at.

What's wrong with using standard chemical reactions to accomplish the substitution?

@leonardo, as i have already mentioned, i would like to diversify my research towards biochemical reactions. Being an organic chemist, i have manipulated the functional groups and now i wish to manipulate using biochemical reactions.

It is possible to search for enzymes or a series of enzymes that will take similar reactants to similar products.
ReBIT allows you to query enzymes by your molecular structures of interest using their SMILES code. Unfortunately, a quick search using coumarin didn't produce any results but searches for phenol and phenolate gave some hits.
If you're seeking to do a more extensive search, I would suggest BRENDA. There you can search for reaction substrates and reaction products and even both. Both strategies may provide you with an enzyme that does the transformation chemistry that you're looking for.
Lastly there is always ENZYME, The Enzyme Data Bank. There you can search for chemical compounds. I did a search of coumarin and there are a few hits but they are for methyl-transferases and hydrolases. A more extensive search may give you a few leads.
Most of the concepts that I just suggested are explained in the following review: De novo biosynthetic pathways: rational design of microbial chemical factories.


text:
How do white Caladiums perform enough photosynthesis to support their mass?
In some white caladiums, there is less than a square inch of green space spread over the whole leaf. How do these plants perform the photosynthesis necessary to support the large leaves, the roots, the flowers, and build a corm?

There are many different kinds of plants that have independently evolved this sort of variegation (non-green areas) in the leaves. However, the mechanisms by which they effect this vary between species.
Some have little or no chlorophyll in the non-green areas, but many others have changed the architecture of their leaf cell layers in the non-green areas, creating refraction effects that make the leaves appear white, but don't significantly change their photosynthetic efficiency (Sheue et al.) In fact, Arum italicum white areas actually have higher efficiency in certain light conditions! (La Rocca et al.)
I can't find any information on which type of variegation Caladium shows. The genus Caladium is related to the Arum I mentioned above which uses the "architecture" method, but it's also related to Epipremnum, which seems to use the "no-cholorophyl" method.
Sheue et al. mention that with some species that use the architecture method, using transmitted light instead of reflected light reveals that the white spots are actually green; while in no-chlorophyll plants the spots remain white. If you have a Caladium around, you could try holding its leaf up to a bright light, and see!
So, to answer your question: if Caladium is an 'architecture-variegation' plant, its white areas perform photosynthesis at or near the efficiency of the green areas of the leaf. If it's a 'no-chlorophyll-variegation' plant, it would have reduced efficiency, but might make up for this with strategies including:

Having a larger total leaf area (La Rocca et al. and also see this question)
Only developing large white areas if there's plenty of light as they grow (Garland et al.)
Increasing the mitochondrial activity in its white areas, which could lead to other energy efficiencies (Toshoji et al.)
Using Homo sapiens to help it reproduce and provide plenty of light for it. Many of these extreme variegation patterns are found in horticulturally bred varieties!
Just using its green areas for photosynthesis, and "accepting" the fact that the white areas are not producing energy. In natural populations, you often don't find varieties as completely white as in that picture: they usually show white spots and plenty of green. This is true of Caladium species in the wild, which may use the variegation to mimic and to prevent herbivory: potential pests think the leaves are already infested, and avoid them (Soltau et al.). In other words, even if the white patches represent decreased photosynthesis efficiency, it could be a trade-off in order to achieve less herbivory.

Garland KF, Burnett SE, Stack LB, Zhang D. 2010. Minimum Daily Light Integral for Growing High-quality Coleus. HortTechnology 20: 929–933.
 La Rocca NN, Rascio NN, Pupillo PP. 2011. Variegation in Arum italicum leaves. A structural-functional study. Plant Physiol Biochem 49: 1392–1398.
 Sheue C-RC, Pao S-HS, Chien L-FL, Chesson PP, Peng C-IC. 2012. Natural foliar variegation without costs? The case of Begonia. Ann Bot 109: 1065–1074.
 Soltau U, Dötterl S, Liede-Schumann S. 2009. Leaf variegation in Caladium steudneriifolium (Araceae): a case of mimicry? Evolutionary Ecology 23: 503–512.
 Toshoji HH, Katsumata TT, Takusagawa MM, Yusa YY, Sakai AA. 2012. Effects of chloroplast dysfunction on mitochondria: white sectors in variegated leaves have higher mitochondrial DNA levels and lower dark respiration rates than green sectors. Protoplasma 249: 805–817.

Any free growing (non parasitic) plant will rely on photosynthesis.
Plants do not have to be green though. It says in this article that the white caladium has chlorophyll, but relatively little, or the white color may come from other pigments that reflect other kinds of light.

“As with other white caladiums, there’s a little bit of mystery surrounding Florida Moonlight,” Miranda said. “Where’s the chlorophyll? Chlorophyll is a pigment that caladiums and other plants use to produce food by photosynthesis, and it gives the leaves their green color. White caladiums either get along with very little chlorophyll, or they somehow conceal its presence

And my question is, how does it maintain itself with so little chlorophyll. I know that it does already.


text:
What's the distinction between a tetrad and a synaptonemal complex in meiosis?
What's the distinction between a tetrad and a synaptonemal complex in meiosis?  Are they synonyms?
I ask because the concepts seem very closely related, but it seems like there may be a subtle distinction.  Unfortunately, none of the sources I've been consulting use both terms.

As far as I can tell there is a distinction.
A tetrad refers to the entire group of four chromatids after they have come together for crossing over in Prophase I (synapses).
A synaptonemal complex as you would expect is formed in synapses.  This is a protein-RNA complex that connects the intervening regions of matched chromosomes in some circumstances - it is not required. Mutated yeast that can not form this complex has still been shown to be able to exchange genetic information.
In other words, you can have a tetrad without a synaptonemal complex, but not vice versa.


text:
What would cause bands to appear lower on a nonreduced SDS-PAGE gel?
I have a protein gel and I'm comparing the reduced with the non-reduced gel. On the reduced gel, I have a few shorter bands but these bands appear with low intensity. In the non-reduced gel, I'm seeing more of the shorter product? What would case the protein to run "smaller" in the non-reduced conditions?

By reduced and non-reduced gel, do you mean native PAGE under reducing and non-reducing conditions? Does your protein have any cysteins and is it known to form disulfide bridges?

SDS-Page and yes.

So you're trying to run a denaturing gel? Strange, I've only seen protocols under reducing conditions for them, a denaturing gel under oxidizing conditions where disulfide bridges can form doesn't really make much sense.

You just remove the reducing agent. Its a pretty standard procedure and a quick search for non-reducing SDS-PAGE seems to show it.

The major effect of changing the redox environment of a protein is the formation or breakage of disulfide bonds. Under sufficiently reducing conditions no disulfide bridges will be present, while under oxidizing conditions your protein will form disulfide bridges if it has the ability to do so.
Disulfide bridges can significantly change the tertiary structure of a protein and change the behaviour of the protein on a gel that way. Generally, disulfide bridges should make the protein more compact and make it run faster on a gel.
It is therefore plausible that your faster band is the protein with disulfide bridges, which will appear to run like a smaller protein as it is more compact. The slower band then is the protein without disulfide bridges which can adopt a more extended conformation.
I'm assuming you're talking about native gels here, as denaturing gels usually contain DTT or beta-mercaptoethanol in the sample buffer to reduce any disulfide bonds and avoid this effect altogether.

Just to add on to this answer, the reason we are able to measure protein size against a ladder with SDS-PAGE gels, reducing conditions and denatured proteins is because this treatment effectively linearizes all protein species in your samples. This make them well sorted by mass, rather than 3D conformation.