botany - Which plants live for more than one year and less than two years?

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physiology - Can I estimate leaf temperature from air temperature? What other information would be required?

Physiological measurements such as respiration rate and assimilation rate depend on temperature.

Most papers report tissue temperature (e.g. leaf temperature for leaf measurements), although some report air temperature.

My goal is to compare measurements in the literature. I use leaf temperature at time of measurement to adjust the rates to a common temperature. Currently, I assume that if leaf temperature is not available, it is the same as air temperature. (This is often assumed in papers where the leaf temperature was not measured).

Is there a way to estimate the difference between air temperature and leaf temperature? I can get fairly good estimates of other physiological traits (e.g. leaf thickness, albedo, stomatal conductance) as well as climate data (e.g. humidity, soil moisture content).

My model is:

$T_{leaf} = T_a + X + epsilon$

And I currently assume X = 0 in my calculations

Is there a better way to estimate X?

Under what conditions would X < 0? X > 0?

biochemistry - Are quaternary protein monomers unique to a particular protein complex?

If I understand the question correctly, you're thinking something along the lines of modular tertiary domains, but in a quaternary sense?

For a reversible interaction, heterotrimeric G proteins spring to mind. Once activated by a G protein coupled receptor (GPCR), the alpha subunit and the beta-gamma complex dissociate from the receptor and from each other. They can both go on to affect signaling by binding to various effector proteins, depending on the particular pathway in which they are involved, and their activities can be mediated by other proteins (e.g. the alpha subunit GTPase regulated by GAP proteins).

I spoke to my Protein Engineering professor, and she also directed me to a few examples, although I'm not sure they're quite what you're looking for in the strictest sense.

• Cyclin-dependent kinases, as @Armatus mentioned, bind to all sorts of different cyclins. (I get the sense that subunits found in multiple protein complexes will probably be more common in signal cascades. I don't have any real data on that, but it makes sense that a signal protein could interact with two or more protein complexes and even have slightly different functions in each.)


• Alcohol dehydrogenase (ADH) is an example of a protein with different quaternary structures between species. According to my professor, it occurs as a homodimer in mammals, but as a tetramer with some slightly different residues in budding yeast. I can't say whether the sequence changes are what affect the oligomerization, although my prof also mentioned "oligomerization domains" that could mediate protein-protein interactions.


• She also directed me toward a slightly more interesting example (in my opinion), though, again, it's also more along the lines of oligomerization. Small heat shock proteins (sHSPs) undergo something called "dynamic subunit exchange" and can take on a wide variety of oligomeric architectures. Binding is transient, but it's still kind of neat. There's a review here: http://www.sciencedirect.com/science/article/pii/S0968000411001903. Figure 3 shows different oligomeric architectures from the one monomer.

It seems that pretty much any protein that interacts with two or more separate protein complexes could be considered an answer. Neither I nor my professor have managed to come up with an example of an irreversible assembly of common subunits, but she is of the opinion that, in all the different possible protein structures, there is probably at least one example of everything, no matter how outlandish it seems.

molecular biology - How Do Adherent Cells In Culture Attach To A Plastic Dish?

I doubt that hemidesmosomes are much involved in 3T3 adhesion, just because they are characteristic of epithelial cells and fibroblasts are mesenchymal.

You're on the right track, though. It's going to be the same basic processes as adhesion to the extracellular matrix. The major factors will probably be integrins and focal adhesion assemblies.

You're also raising an important point for in vitro work, which is that adhesion to plastic is a very imperfect substitute for ECM, and this probably has implications for the behavior of the cells. If you're interested in ECM-dependent processes like migration, adhesion, and invasion, consider coating your plates with collagen or Matrigel.

dna - How do cockroaches resist the effects of ionizing radiation?

Off the top of head as a medical professional I can imagine the following mechanisms (everything is just speculative reasoning):

1. Insects don't have blood. Instead, they have hemolymph whose primary role is not oxygen transport (they have an additional tracheal system for this purpose), but rather that of nutrients. Thus they don't need (and don't have) an intense proliferation of blood cell precusors -- these (bone marrow, spleen) are the most susceptible to radiation in a human and animal body.




2. Insects have a rather primitive immune system that is mostly humoral^[a] and much less cellular^[b] compared to the immune system of animals and humans. This eliminates the next common weak place in the body: lymphatic nodes, thymus, again spleen and bone marrow etc.




3. Insects have generally a much primitive and in many cases also rather decentralized nervous system: the ganglia are organized in a sort of a cord and even though the capital ganglia are usually larger, these dominance is not as prominent as in case of CNS and PNS in animals and humans. Therefore this system is much more tolerant to losses.

1.-3. Therefore, the only sensitive part of insects is the intestinal epithelium which gets renewed on a regular basis (similar to that of humans, also a known target of radiation), but...

1. Insects (and generally the arthropodes) are known to have exoskeleton. This potentially serves as a good "armor" for vulnerable intestine cells, filtering out the most heavy particles (like alpha- and in some respect also the beta-particles).
   EDIT: This seems not to be real protection, see the discussion in comments.

Therefore it is not a surprise that insects generally show much higher resistance against radiation.

EDIT:
As it was correctly added in the comments, there are also gamets, that are most sensitive to radiation (because they bear only the half of the normal genetic information and cannot repair mutations). Even though the lesions in gamets do not lead to immediate death, the potential sterility can easily cause the extinction.

However, cockroaches (and insects generally) are known to be r-animals, meaning that they favor the quantity (r) over quality (K) of their off-spring. This strategy is optimal when dealing with radiation-induced changes in gametes: the high number of offsprings compensates for the genetic imperfections in gametes.

---

^[a] -- meaning that is has secreted peptides in their hemolymph that protect them
^[b] -- there are phagocytes, somewhat similar to tissue magrophages in humans, but the rest of the cell chains in immune response in vertrebrates, like T- and B-cells, are completely missing. Those are responsible for the mediation and amplification of the immune response in vertebrates and are the cells that are most susceptible to radiation damage.

biochemistry - Why are omega-3 fatty acids so easily oxidized when they're incorporated in cellular membranes?

I think the explanation for this description of fish oils as "easily oxidised" can be found in the Introduction to the actual paper (Nutrition 27 (2011) 334–337) that is cited in the article linked to in the question.

Fish oil contains high levels of eicosapentaenoic acid (EPA; 20:5 omega-3) and docosahexaenoic acid (DHA; 22:6 omega-3), which are omega-3 polyunsaturated fatty acids. EPA, DHA, and fish oil have been shown to have protective effects against coronary heart disease, thrombosis, inflammatory processes, carcinomatosis, and metabolic syndrome. Therefore, fish oils and components of the oils are marketed as health supplements. However, the effects of omega-3 polyunsaturated fatty acids on aging and lifespan are unclear compared with those of omega-6 polyunsaturated fatty acids contained in safflower oil and soybean oil. EPA and DHA are oxidized easily compared with linoleic acid (18:2 omega-6) and oleic acid (18:1 omega-9) in vitro .

In other words, the fish oil omega-3 fatty acids EPA and DHA have, respectively, 5 and 6 double bonds, whereas the omega-6 fatty acids in safflower oil, linoleic acid and oleic acid have, respectively, just 2 and 1 double bonds. So the fatty acids in fish oil are more prone to oxidation simply because they have so many more double bonds.

Incidentally, as you can see from the two structures below, both of the omega-3 fatty acids, EPA and DHA, also have an omega-6 double bond.

EPA:

DHA:

evolution - Short-term Lamarckism in asexual single cell organisms

This phenomenon is well known and can be observed in several species. In fact, if you look at the time it takes for E. coli to change its transcription program in order to react to the environment (signal->transcription->translation), you will find it can be longer than its ~20 minute doubling time. You can indeed think of it as a form of Lamarckism. However, it is part of a field that has been booming in the last ~10 years, known as epigenetics.

Epigenetics is a field of research that deals with hereditary information that is passed by non-genetic mechanisms, i.e. not in the DNA sequence. This includes several mechanisms including passing of proteins/RNA, chemical modifications of DNA (methylation) and chromatin (histone modification). It turns out that epigenetic effects can be observed in virtually all species (including human) and affected phenotypes can be significant (leading to disease, for example).

This is a very interesting field of research and is very wide, so I would recommend reading a bit. Specifically regarding protein/RNA passing, I believe this is somewhat less deeply studied, perhaps due to the fact that the effect decreases exponentially (due to dilution), can be limited by protein/RNA stability and some measurement difficulties. However, I think I recall mathematical treatment of this in Prof. Uri Alon's book. You can also catch his systems biology course online on youtube, which I think touches on some of this material.

biochemistry - NADH vs. NADPH: Where is each one used and why that instead of the other?

The phosphate group in NADPH doesn't affect the redox abilities of the molecule, it is too far away from the part of the molecule involved in the electron transfer. What the phosphate group does is to allow enzymes to discriminate between NADH and NADPH, which allows the cell to regulate both independently.

The ratio of NAD⁺ to NADH inside the cell is high, while the ratio of NADP⁺ to NADPH is kept low. The role of NADPH is mostly anabolic reactions, where NADPH is needed as a reducing agent, the role of NADH is mostly in catabolic reactions, where NAD⁺ is needed as a oxidizing agent.

You'll find some more information about this in chapter 2 of "Molecular Biology of the Cell by Alberts et al.

dna sequencing - Sequence of ribosomal RNA

As far as I know it'spossible to reverse transcribe a rRNA gene, you may not get the best yields though. The secondary / tertiary structures will be a problem, however, there are reverse transcriptase's commercially available that can handle secondary structure: Thermo-X™ Reverse Transcriptase from Invitrogen or Sensiscript™ from Qiagen.

neuroscience - How does this illusion work?

If you zoom in on the image, you can see that it is not just composed of black vertical lines, but also has pixels with different gray tones in the white areas. When you move your head sideways, you perceive the gray tones more.

If you were to remove the black lines, you could see the face clearly. Initially I thought that by blurring the gray shapes when your head moved, they became more visible as they seemed larger. On reflection though I think that actually what's happening is that the high contrast between the black lines and the mostly white background causes your perception to adjust so it doesn't easily see the mid tones. This is because we have a low dynamic range in our vision (relative to absolute brightness, but compared to camera CCDs we have a high dynamic range) - we have to adjust the light sensitivity to compensate for the overall brightness of the image. This is called brightness adaptation. There's a good free textbook for further reading about this at Utah U's Webvision.

When you move your head, the black and white lines blur together which makes the overall brightness appear to be the average brightness of the black and white. So against that background your light sensitivity increases and the areas where the pixel tone is different from the average - the gray pixels of the face - start to stand out.

By reducing the brightness you can see the faint image in the background much more clearly...

biochemistry - 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

neuroscience - SPINAL CORD: Do the axons from white matter synapse with the cell bodies in grey matter?

Here is a great diagram (from here) that outlines all of the different white matter tracts running up (blue) and down (red) the cord.

The portion in the center, as you have found in your research, is the gray matter. In there are the different interneurons (cells that exist in the network to integrate information from descending controls and do further processing on it) and all of the different motor neurons. The corticospinal tract descends to the appropriate level (for example, a neuron in charge of moving your arm, to keep it simple, will have a cell body in the brain, and descend to the thoracic level), enters into the gray matter and either synapse on an interneuron or directly onto a motor neuron).

The sensory neurons are a slightly different animal. Some (pseudo-unipolar cells) have what are basically two "legs", one that runs out into the periphery, which will take the signal from something like a Pacinian corpuscle in the skin, propagates a signal to the cell body, which is outside of the spinal cord in the dorsal root (see below), and the other "leg" runs all the way up the dorsal column into the medulla of the brainstem.

^{from here}

So that should give you some idea of the two major tracts. To see some of the finer detail, you can look into the different layers (laminae) that the gray matter is composed of, so that you can trace the connections all the way in.

biochemistry - For how long and how cold should I perform ethanol/isopropanol precipitations of RNA or DNA?

I always did mine at -80 C, but I never compared the results to other protocols (I don't fix what's not broken). But, I was curious about the same thing, so I looked around. I found one paper discussing this: Paithankar and Prasad, Nuc Acids Res 19(6):1346 (1991)

It shows that at low concentrations, EtOH at RT actually outperforms the precipitations at both 4 C and dry ice/ethanol bath. That difference is quite big at 100ng/ml DNA and lost when there is more than 10 ug/ml DNA. For typical extractions, based on this data, I'd do it at RT.

On the other hand, Hilario and Mackay say in their book that:

for genomic DNA isolation, different DNA precipitation temperatures
and incubation times have little effect on recovery rates. One can
directly centrifuge after adding ethanol without the -20 C incubation,
and, it -20 C ethanol is not available, room temperature ethanol can
be used.

They do not, however, provide any citation for that statement.

evolution - Why is glucose our primary source of energy?

I thought this was a great question. In particular because it hints at two questions. The first is 'why carbohydrates are used to store energy' in general. The second being 'why glucose rather than other carbohydrates?' in particular.

Glucose metabolism (and glycogen storage) is a core gene pathway - its found in bacteria archaea and eukaryotes. So probably the most that we can readily say about question one is that as @rwst points out this pathway has proven to be useful at a critical juncture of the formulation of living things on earth. If you look at glucose metabolism pathways, you can see that glycerate compounds and pyruvate are the actual intermediates that are used to create energy. The first thing about these molecule worth noting is that they have a good mix of carbon and oxygen, which would make it easier to extract energy - creating CO2 from these compounds may even predates the existence of atmospheric oxygen. So glucose and fructose (which is actually derived from glucose in the metabolic pathway) are actually storage molecules themselves, easily broken down to smaller molecules.

As to the second question: there are quite a few ways to arrange oxygen around the carbohydrate ring. why glucose? The advantages of glucose is probably a subtle one. The structural properties of glycogen might be a reason that the use of glucose monomer is so important for glycogen. There is no evidence that I can find for this, so its always possible that glucose was just the first hexose carbohydrate to be biologically used. Its sort of hard to imagine that the structure of glucose does not play some sort of role in cell structure though.

amino acids - How do you calculate or predict the charge of a protein at pH 7?

To calculate the charge at different pH:

At pH 3 K, R, H are + and D,E have no charge so add up all of the K,R,H in the sequence and that is your net charge at pH 3
At pH 6 K, R, H are + but now D,E are (-) so subtract one total from the other to figure if your net charge is + or -.
At pH 8 K and R are +, H has no charge and D,E are (-).
At pH 10 R is +, K, H have no charge and D,E are (-).

That can give you a general idea. You can estimate the charge at pHs in between.

Where can I find the common names for the zoology taxonomy?

The UK accepted system has five kingdoms, for some it's hard to describe a single word common name so I hope you don't mind that I have written brief summaries too:

1. Animalia are multi-cellular organisms that have adaptations to allow them to move within their environment. They have membrane bound organelle but not cell walls or chloroplasts. They must absorb nutrients by ingestion. Common name is animals ;-)


2. Plantae are multi-cellular organisms that use photosynthesis to harness energy from sunlight. Their cells contain cell walls & chloroplasts (where cells are exposed to the sun). Common name is plants


3. Fungi are multi-cellular organisms with no adaptations to move independently. They range in size from microscopic to the size of mushrooms (literally, of course). They absorb their nutrients from their surroundings. Common name could be mushrooms & molds


4. Protista are marine organisms that are eukaryotoic (have membrane bound organelles) and some can photosynthesise. Common name could be algae


5. Prokaryota (a.k.a. Moneara) are single celled, with a cell wall but with no membrane bound organelles (i.e. they have no smaller 'bits' within the cell separated by a membrane). They absorb nutrients directly across their membranes or can photosynthesise to make their own nutrients. Common name could be said to be Bacteria.

Sources: 1, 2, 3 (for Protista)

You may wish to try the following website:
ITIS Database - enter a scientific or common name of an organism to get it's full taxonomic tree. For example the tree for the Panthera leo (Lion). This site also gives common names of Phylum, Class, Order & Genus - for example the lion is a member of genus Panthera ("roaring cats"). It may be slightly cumbersome but it is a way to get the info you want and is actually quite interesting once you get going, particularly if its just for your curiosity!

Additions after comments by OP

Have been hard at work, however it seems that a centralised repository is certainly elusive! I've found some sites which go a little of the way to amalgamating scientific and common names on a single page but I'm doubtful that you will be able to get much further than Phylum without having to write a script to harvest data from sites such as ITIS

1. List of all Phyla for the Animalia Kingdom with common names.


2. As above for Kingdom Plantae


3. As above for Kingdom Fungi


4. As above for Kingdom Protista

human biology - How does laughing gas (N₂O) work?

This information is all strictly for Entonox - a brand of analgesic gas comprising 50% Oxygen (O₂) and 50% Nitrous Oxide (N₂O), Laughing Gas. This mixture is known as 'Gas and Air' and is in very common use.

The active ingredient in Entonox is of course the nitrous oxide, so the discussion of the mechanism below refers solely to the N₂O as you asked for.

Nitrous oxide enters the blood by diffusion from the alveoli whilst it is being inhaled, but does not bind with haemoglobin. It is fat soluble so quickly moves into cells, including synapse ends in the brain. Because of the stability of the compound, N₂O is not metabolised by the body so has its effect as that molecule, then is eliminated by diffusion out of the lungs once inhalation has ceased (taking roughly 2 minutes for on and offset).

According to the material that BOC pharmaceuticals provide, the exact mechanism of the analgesia is not fully understood. It is known, however, to induce "inconsistent changes in the basal levels of thalamic nuclei".

N₂O inhibits NMDA receptors in the brain whilst simultaneously encouraging the stimulation of the parasympathetic GABA receptors. This eventually produces an anaesthetic effect. It is also understood that N₂O promotes the release of endogenous opioid neurotransmitters ('natural painkillers' e.g. endorphins) that specifically activate descending pain pathways. This inhibits the transmission of pain. In this way the analgesia provided by nitrous oxide is antinociceptive (literally pain reducing) rather than a generalised limbic depressor.

However, nitrous oxide also positively effects potassium ion channels too ^[ref] - reducing the chance of an action potential being generated in affected neurons. Research into this area of the effects of N₂O is ongoing.

Euphoria is a common side effect of N₂O usage, hence the name laughing gas. This is as part of wider emotional changes that can occur when nitrous oxide is being administered. For example, some people instead of laughing become scared or in other cases extremely aggressive towards those nearby. The emotional excitement may result in depressive or manic behaviour even to the point of psychosis and hallucinations especially in those who have a preexisting vulnerability to mental illness. The precise mechanism for these disinhibiting is again not fully understood.

Whilst it seems a lot of the answers are missing, the course I'm taking this information from is available online at Discover Entonox - modules 8-10 have relevance to this question. It's free to register and view the materials, they're all nicely narrated with diagrams etc.

molecular biology - Primer design for introduction of restriction sites flanking a gene of interest

I think the best way is option #2:

Suppose that your gene of interest is AAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGG

and you want to insert EcoRI restriction site GAATCC

Then your Fwd primer will be GAATCC AAAAAAAAAAAAAAAA

and your Rev primer will be GGATTC CCCCCCCCCCCCCCCC

But in general, it shouldn't matter which option you choose, as long as you calculate the Tm of only the part of the primer that hybridizes to your template.

molecular biology - How are there alternative initiation codons?

Actually, the start codon, no matter whether it is AUG or GUG/UGG, always encodes for Met. So the translation is initiated by tRNA^fMet (prokaryotic translation). The 30s ribosome subunit binds to the Shine-Dalgarno sequence and then it scans the dowstream mRNA sequence for AUG and the tRNA loaded with Met, which has the CAU anticodon form the most stable interaction. But apparently, only two-bases-interaction between the start codon (GUG, UUG) and the fMet-tRNA anticodon are sufficient for the initiation of translation (1). I will look more into the literature.

1. Initiation of translation in prokaryotes and eukaryotes

staining - Is there a photobleaching-resistant, cell-permeant viability stain in the far red part of the spectrum?

I am looking for a live-cell–impermeable dye for viability. (The cells cannot be permeabilized and fixed in this experiment.) I would prefer with excitation and emission spectra similar to Cy5, but I can be flexible here as long as the spectra are far away from Hoechst.

I have tried TOPRO3, but it seems to lose its brightness after a few exposures, so I would like something more resistant to photobleaching.