Mechanism of syndesmophyte growth in AS Ankylosing Spondylitis (AS) causes inflammation around joints and the growth of syndesmophytes that may eventually fuse vertebrae. I'm familiar with the genetics (HLA-B27, IL1A) related to the condition, but I can't find any information about the mechanism that causes the actual growths to occur.

My current assumption is that AS causes the over-production or under-production of a particular compound or enzyme at the growth site, but I can't find any studies or papers that explain this. Is the mechanism known? Is it directly related to abnormal levels of a particular substance?

As far as I remember the pathology course from medical school, chronic long-lasting inflammation often leads to proliferation of connective tussie and ultimately to fibrosis.

The actual mechanism here is the lack of oxygen which is used-up by different immune system cells to produce peroxydes and superoxydes.


What color does the other cone in Tetrachromacy correspond to? Human with normal vision possesses 3 cones, which correspond to blue (S), green (M) and red (L). What about tetrachromacy, where people have 4 cones in their retinae? What is the fourth cone exactly, and what color does that other cone correspond to?

According to Deeb (2005), there are two relatively common types of causes for tetrachromacy in humans:

The common Ser180Ala polymorphism, which results in two spectrally different red pigments in the retina. This mutation also plays an important role in variation in normal color vision. This polymorphism most likely resulted from gene conversion by the green‐pigment gene.
Another common variation are several red/green pigment chimeras with different spectral properties. The red and green‐pigment genes are arranged in a head‐to‐tail tandem array on the X‐chromosome with one red‐pigment gene followed by one or more green‐pigment genes. The high homology between these genes has predisposed the locus to relatively common recombination events that give rise to red/green hybrids and deletions of green‐pigment genes. Such events constitute the most common cause of red‐green color vision defects. Only the first two pigment genes of the red/green array are expressed in the retina and therefore contribute to the color vision phenotype. The severity of red‐green color vision defects is inversely proportional to the difference between the wavelengths of maximal absorption of the photopigments encoded by the first two genes of the array. Women who are heterozygous for red and green pigment genes that encode three spectrally distinct photopigments have the potential for enhanced color vision.

Reference
Smeeb, Clin Gen (2005); 67:(5): 369-3

Further reading
- Color vision across species


Is a variable domain in immunoglobulin's heavy chain different from the one in light chain? I guess yes, there is difference in amino acid sequences of $V_L$ and $V_H$. And so we have 6 different complementarity determining regions (CDRs) per monomeric immunoglobulin as two heavy chains are identical, and two light chains are the same. Is that correct?

You are correct. In an IgG antibody, there are a total of four protein chains — two identical heavy chains, and two identical light chains, each heavy pairing with a light to form one of the two "arms" of the molecule. Each heavy chain has three CDR regions — H1, H2, and H3 — as do each light chain (L1, L2, and L3). When the full molecule is assembled, three "full" CDRs are formed — 1, 2, and 3 — from the "partial" CDRs in the respective heavy and light chains.

from novimmune

You can see on the left the six individual heavy and light CDR loops separately, and on the right they are combined into the full CDR1, CDR2, and CDR3.

Here is a slightly more molecular view:


Minimum and maximum exposure to virus Is it possible to say that there is a maximum exposure time for the virus so that even an exposure time beyond that - will leave us with the same chances of infection?
If so, is there a way to estimate the interval between the minimum exposure time for infection and the maximum exposure time for infection and what happens inside?

No, on cannot say it this way, since further expose always carries a risk of getting infected.
However, one could argue that after certain time of exposure one is nearly certainly infected, so being exposed longer doesn't really change the result. This statement could be formulated more rigorously in terms of compartamental epidemiological models. If we take the figure for the SIR model in the linked article, we see that the number of the susceptible individuals (S) quickly drops about time 0.2-0.4, after which it is almost zero, i.e., there are almost no uninfected individuals in the population.

The numbers of susceptible (S), infected (I), and recovered (R) individuals can be normalized by the total number of the individuals in the population ($N=S+I+R$), and then interpreted as the probabilities of a person being uninfected ($p_S=S/N$), infected ($p_I=I/N$) or recovered ($p_R=R/N$). These probabilities will behave in time in teh same way as shon in the figure (but with different y scale), i.e., the probability of being ininfected would first be nearly constant, and then quickly decrease to nearly zero.


In which of the following diseases structure of haemoglobin produced is normal but their amount reduced? The options provided are-

Chronic blood loss
Sickle cell anaemia
Haemolytic anaemia
Thallasaemia
Transfusion reactions
               -

*Q-15: pg-785; **Review of Medical Physiology - William F. Ganong;    International 22nd Edition***

Here, the answer provided is (4), i.e Thallasaemia...
My point is that, Thallasaemia is essentially a genetic defect resulting in mutation of either alpha or beta or both the chains, thus rendering the structure of haemoglobin fragile....the disease as far as I know don't cause any reduction in blood volume...

According to me option (1) i.e chronic blood loss is more feasible as in case of diseases resulting from nematodes like Hookworm (Ancylostoma duodenale)....

So, where am I wrong???

You are correct, Thalassemia is the wrong answer.

In Thalassemia and Sickle Cell Anemia, the structure of Hemoglobin is altered.

Chronic Blood Loss: Here the hemoglobin and packed cell values will be low, however there is no alteration in structure of either RBC or Hemoglobin
Hemolytic Anemia: This is a host of conditions which can cause hemolytic anemia. Some mechanisms where Hemoglobin structure remain normal would be:

The structure of RBC membrane is altered, this will make RBCs less maleable and cause early destruction - Example: Spherocytosis
G6PD Deficieny - In this the deficiency of G6PD will decrease the ability of Red Blood Cells to handle oxidative stress and when subjected to sudden oxidative stress, hemolysis will occur. Here the structure of both RBC membrane and Hemoglobin are normal.

Transfusion reaction (I am talking about only hemolytic transfusion reaction, there are other transfusion reactions too): Here the problem is the host reaction to transfused Red Cells. The host was initially severly anemic (Therefore low Hb) for which transfusion was done, now the host immunity is reacting against transfused RBCs which have normal Hemoglobin, resulting in reduced RBC counts and Hemoglobin. So this too can be taken as a correct answer as the end-result will be severe normochromic normocytic anemia.


Why is cognitive maturity related to organism lifespan in larger animals and mammals? I am not a student of biology, so I should provide some context to me asking this rudimentary question. While doing a graduate-level course on Reinforcement Learning, the instructors focused on how we as mammals have such amazing intellectual potential and how we tend to learn by examples of outcome based on our actions. This set me thinking about the high disparity between different species of multicellular organisms in how we mature.
I would state a couple of examples to back my point, I am unsure if this list is conclusive or not.

Elephants(Average Lifespan: 60-70 years): Elephant babies tend to stick to their families until they generally mature.

Humans(Average Lifespan: 70-80 years): Human babies are generally dependent on their parents for at least 8-12 years before they start demonstrating some intellectual maturity, which is a good 10-15 percent of their average lifespan)

Birds(Average lifespan is species-dependent, but assuming a 10-year span): Bird offsprings are extremely fast learners and tend to veer off independently within months of their birth.

Fishes (Medium to short lifespan): Not an extremely well-publicized parenting method for their offspring. Fishes learn to swim and hunt for food at extremely young ages, which is a sign of cognitive maturity.

Insects (Short Lifespan): Generally parenting is related to feeding offsprings for a short while before they become entirely independent.

As can be observed, the general span for the attainment of cognitive maturity in such organisms seems to be an inverse function of the average lifespan of the parent, and I wonder, what could be the reason for it?

I absolutely apologize for any inaccuracies I might have cited because what I state is purely from a layman's observational perspective. I would be delighted to know what the bright folks here have to say on this matter.

This answer might not completely answer your question, since this just explains the case in humans, but I think you can give this a read while waiting for a more accurate one. I would recommend you to read this amazing paper.

Generally, across animal species, the longer it takes an organism to reach maturity, the longer it lives. How the timing of onset of maturity relates to longevity in humans, is still a matter of debate. In this regard, it is of special interest whether the onset of intellectual maturity is associated with longevity, as the brain and associated parts of the central nervous system comprise an organ system that is widely thought to have played a vital role in humans’ evolutionary success.

First, they talk about defining cognitive maturity:

  It would seem intuitive to define intellectual development as that part of the lifespan in which ability increases and intellectual maturity as that part in which ability plateaus or decreases. In such a model, an inflection point or peak in ability would mark the onset of intellectual maturity. It is unlikely, however, that the multidimensional abilities of composing and writing reach their peaks when a composer's or writer's work is made public for the first time. Rather, we regard maturity as a state that is attained when a certain relevant threshold is crossed, regardless of whether ability increases after that point.

Looking into the case of humans, it may be either a genetic mechanism or plasticity that couples rate of development and maintenance and repair. In the former scenario, genes that alter the rate of development such that maturity is reached earlier, would have as a concomitant effect the downregulation of maintenance and repair, leading to a shorter lifespan. (This is a shortened version- please go through the paper for more detail)

They conclude stating that the onset of intellectual maturity is associated with longevity. So, you are right about cognitive maturity of an organism being related to its age, and it points out to a really interesting result- blooming composers and writers live longer than child prodigies- as pointed out in a paper in ResearchGate.

What could be the reason for it? American psychologist Jerome Bruner proposed the purpose of the period of immaturity as being a time for experimental play without serious consequences, where a young animal can spend a great deal of time observing the actions of skilled others in coordination with oversight by and activity with its mother. So, there is the obvious need for a period of immaturity and this varies amongst different mammals. (source)


Ligation without purifying insert I am planning to insert a 45 bp sequence in a vector. After restricting my insert to create compatible sticky ends, I am finding no way to clean it up. Is there any way for cleaning this fragment after restriction or should I proceed without clean-up?

Thanks all for your comments guys. I tried purifying using PCR purification kit. I could recover 120 ng of purified fragment from 500 ng. It is ok for my further work.


Why aren't plants and animals capable of assimilating $\ce{N2}$ directly from the atmosphere? From a E-book  written by Hungary scientists, the reason is $\ce{N2}$ is inert.

Is this correct?
How does the chemical properties of gas species ($\ce{SO2}$, $\ce{O2}$, $\ce{NH3}$, etc) influence the assimilation process by organisms?

As @Wolfgang Bangerth commented, inertness just means that nitrogen gas doesn't undergo reactions because the NN triple-bond has a very high bond energy and the activation energy for reactions that break the bond (even though thermodynamically favourable) is therefore high. So I suppose that you could say that a major chemical factor in the reactivity of gases is their bond energies.

The key reaction of biological interest for nitrogen is reduction to ammonia, as referenced by the comment of @aretxabaleta. Stryer makes a couple of points that seem chemically relevant (http://www.ncbi.nlm.nih.gov/books/NBK22522/). He says that the reaction pathway for the reduction of nitrogen involves unstable intermediates, and he also mentions that the nitrogenase enzyme in Rhizomium is extremely sensitive to inhibition by oxygen. I am no expert, but I presume that the instability of the intermediates is related to their ease of oxidation. Leguminous plants maintain a very low concentration of free oxygen in their root nodules by synthesising the protein, leghaemoglobin, which mops oxygen up.

So the answer to the question in the title — why animals (at least) don't fix nitrogen — could well be because as aerobic organisms they would find it very difficult to provide an oxygen-free environment to do this. And the fact that animals can get their metabolizable nitrogen second- or third-hand means that there is no evolutionary pressure to develop such a mechanism. (Most bacteria and plants manage without too.)


Where do the Ca ions that causes neurotransmitter release from synaptic bouton, come from? I hope the information you share will help clarify the following doubts and gaps in my knowledge:

Where do the Calcium ions in the influx (which then triggers the neurotransmitter vesicles) come from?
Are they traveling all the way from the ER of the neuron in the soma?
Are they stored locally within the neuron somewhere around the synaptic bouton?
Are they coming from outside the neuron cell?

And if you have some extra knowledge to dish out then:

Is it channels or pumps that cause this influx of calcium ions?
If these are channels then are they ligand-gated, voltage-gated or made more permeable via some other mechanism?

Thank you for reading :)

Short answer

Neurotransmitter release is triggered by an influx of calcium ions from the extracellular space into the cytosol through voltage-gated calcium channels in the plasma membrane.

Long answer

Typical synaptic vesicle release is triggered by calcium influx through T-type calcium channels. These are voltage-sensitive channels in the plasma membrane; calcium flows through these channels from the extracellular space and is bound by synaptotagmin, a type/family of proteins associated with the vesicle fusion machinery (the SNAP/SNARE complex) to trigger (or, more precisely, to increase probability of) vesicle release.

Like just about every important class of proteins, these channels can be regulated by various mechanisms: gene expression, trafficking/colocalization, subunit composition, phosphorylation, etc. See the Iftinca & Zamponi review.

Calcium from internal stores, released by various mechanisms (calcium-induced, IP3-induced, can also be important to neuron plasticity and homeostasis but does not need to travel from the soma (ER extends throughout the cell). In some special cases, these internal calcium stores can be involved in release (see for example Babai et al 2010), but this example is from in photoreceptors in the retina which use a different release mechanism than typical neurons (they don't fire spikes, they have graded potentials and graded release probability, etc). Internal stores can also influence spontaneous release probability and may modulate release probability (see for example the review by Collin et al) but are not the primary "trigger" for release.

For more on the basic synaptic machinery, I'd recommend any edition (though of course recent is always best) of the textbook "Neuroscience" by Purves and coauthors.

Babai, N., Morgans, C. W., & Thoreson, W. B. (2010). Calcium-induced calcium release contributes to synaptic release from mouse rod photoreceptors. Neuroscience, 165(4), 1447-1456.

Collin, T., Marty, A., & Llano, I. (2005). Presynaptic calcium stores and synaptic transmission. Current opinion in neurobiology, 15(3), 275-281.

Iftinca, M. C., & Zamponi, G. W. (2009). Regulation of neuronal T-type calcium channels. Trends in pharmacological sciences, 30(1), 32-40.

Dale Purves, George J. Augustine, David Fitzpatrick, William C. Hall, Anthony-Samuel LaMantia, Richard D. Mooney, Michael L. Platt, Leonard E. White. (eds) (2018). Neuroscience. New York: Oxford University Press.


Can nitrate be an electron acceptor for NADH generated in the citric acid cycle? Is the citric acid cycle aerobic or anaerobic? I know that the oxygen is required to accept the NADH electrons so that NAD+ could be regenerated. Nevertheless, if other electron acceptors, as nitrate (NO3–), are present, could they also be used to regenerate the NAD+? I am asking this because I read a thesis claiming that “acetly-CoA enters the citric acid cycle and through anaerobic nitrate-respiration a multiple amount of ATP is generated.” If you have some literature that you can share with me I would be really grateful. Thanks.

Yes, many microbes can use electron acceptors other than oxygen.

https://en.wikipedia.org/wiki/Anaerobic_respiration

https://www.sciencedirect.com/science/article/pii/S0168165611000289


How much does the distance between a transcription factor binding site and a promoter influence transcription? Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an activator binding site and a promoter - would placing the binding site closer to the promoter lead to significantly stronger activation, or more robust system behavior?

In some genomics-related models I saw authors assigned weights to binding sites based on position (orientation and distance from the promoter); the general idea was that binding sites farther away could have a weaker influence on transcription. This can be modeled e.g. by decreasing the binding affinity. But that was genomics, and I'm unsure how much of that has any relevance in smaller scale plasmid constructs.

For example, suppose we have a highly specific binding site (e.g. a TALE binding site) upstream of the promoter:

In Fig.1, the binding site A is only e.g. 40 bp away from the promoter. In Fig.2, it is e.g. 5000-7000 bp away. Should I expect this to make a noticeable difference? Would the same apply if it would be a constitutive promoter, with a repressor instead of an activator? What about more complex networks, could the answer change?

That really depends on your system. At least for yeast the difference influences the strength of the activation ("Analysis of Transcriptional Activation at a Distance in Saccharomyces cerevisiae").

For bacteria such long distance regulations have recently been identified. Before that it was thought that this does happen only in eukaryotes. See the paper: "Long distance relationships: enhancer-promoter communication and dynamic gene transcription."

I eukariotic cells the regulatory sequences (transcription factor binding sites and enhancers as well as silencers) can be really far away. An example for this would be the rs12913832 in intron 86 of HERC2, which influences the expression of the OCA2 gene, which is about 21 kB away. Both genes are not related in their functions. Normally three transcription factors interact here in the regulation of OCA2, HLTF, LEF1 and MITF, which leads to the formation of a DNA loop between the enhancer in HERC2 and the promoter in OCA2. The polymorphism reduces the binding of HLTF to the enhancer and hinders the formation of the loop which results in reduced expression of OCA2 (the whole story can be found here: "HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter.")

This paper ("Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma.")analyzed (among other things) the binding sites for the microphthalmia-associated transcription factor (MITF) and their distance from the transcription start site. Figure 1 a/b of the paper is shown below. Interestingly a lot of the binding sites where pretty distant.

To go deeper into the topic, the following reviews are interesting to read:

Long distance relationships: enhancer-promoter communication and
dynamic gene transcription.
Enhancer and promoter interactions-long distance calls.


What causes people to feel sleepy due to recycled air? I notice this the most in cars, when I set the air con to recycling air (instead of pulling in fresh air). After a while, I start to feel sleepy, and the sleepiness passes almost as soon as I open a window or change the air con setting to bring in fresh air.

I notice it also in shopping centers, or long bus rides, where there is inadequate fresh air. I know a lot of people who get sleepy from this, but also some people who just notice the air smelling 'stuffy' - but there's no particular smell, just 'stuffy'.

What causes recycled 'stuffy' air to smell stuffy? Is the sleepiness to do with increased Co2 / decreased O2 due to people breathing? Then is the 'stuffy' smell just the smell of CO2?

Any ideas how big of a change in concentrations we're talking about? Wikipedia says concentration of O2 in air is 20.95%. So are we talking about a drop by less than 1%, or a drop by a few %, etc.?

Is this 'stuffy air' bad for you? e.g. hypothetically if I have trouble sleeping, could I seal my bedroom (as sealed as an ordinary passenger car is), install an air con, and have it start recycling air when it's bedtime. Would this be bad for me long term?

Carbon dioxide is not the only waste product which is exhaled. NASA scientist Wolverton goes into detail in his book, "How to Grow Fresh Air".  We exhale 70% of the body's waste products in gaseous forms.  Breathing these in repeatedly and at ever-higher concentrations causes a whole host of health problems, starting with, you guessed it, an inability to stay alert and sustain full brain function.


Do voltage-gated channels in a neuron use ATP I have a question about action potentials in a neuron.
Do voltage-gated sodium and potassium channels use ATP? I mean when they are closed or when they want to open the gate, do they use ATP?

No, they change conformation in response to voltage. Wikipedia has some general discussion of the gating process, as would any basic neuroscience textbook.
The primary energy (ATP) cost of neurotransmission is in establishing ion concentration gradients, via the sodium/potassium ATPase. You can think of this as a special case of secondary active transport, where the energy costs are in establishing a gradient that is then used for a later process which does not cost any direct energy.


Are there any animals that maintain white fur year round? Besides examples of rare albino animals, it seems animals only have white fur during the winter.  Additionally, and not coincidentally, the examples I've found live in the northern latitudes with predicable snow cover and have different colored coats in the summer months.  Are there any examples of animals that maintain a white coat of fur year round, or are there simply no environments that such a trait would be beneficial in?

Polar bears (Ursus maritimus) have white fur all year long.

There are probably several other examples. @L.Diago gave sheep as example. There are also all white troglodyte species.


What determines the amount of data you would get from a sequencing experiment? When someone performs a sequencing experiment, what determines how much sequencing data you get from the machine (Illumina, PacBio, Nanopore, etc). Or maybe, put differently, how does the machine know that it is done?

On an Illumina machine, the instrument runs as many cycles as you tell it to.  If you tell it to run 150 cycles, you will get 150-mers as output.


What is the lowest intensity threshold of light for photosynthesis in any species? Recently, I was reading the question "Photosynthesis - light intensity, particularly the answer, that states that different species require different intensity of light.  My question is what is the lowest threshold of light intensity for photosynthesis of any species?

Specifically, how have that species adapted to take full advantage of the low intensity?

Disclaimer: photosynthesis is not my field of expertise.

I assume you are asking about the amount of light needed for photosynthesis to take place, not the light intensity needed to sustain the plant? Since photosynthesis is an interaction between chlorophyll and single photons I would assume that photosynthetic reactions could take place with just single photons of suitable wavelength (i.e. at the limit of defining light intensity), but to measure this might be extremely hard in practice. The article Photosynthesis in the Abyss indicates that this might be the case, saying that in deep sea environments "A single molecule of bacteriochlorophyll receives a single photon only about once every 8 hours" (see also this popular science article). The conditions for deep sea photosynthesis is described in Beatty et al. (2005), which report photosynthesis by green sulfur bacteria at hydrothermal vents, where the only source of light is geothermal radiation.

However, as stated earlier, photosynthesis is not my subject field so I do not know how credible this information is.


Which pair of primers should be used to amplify the ORF in PCR? So I want to choose the correct set of pair of primers to amplify the ORF of the gene that corresponds to amino acids in a protein. The start and stop codons are underlined. (I know that these need to be synthesised by the primer also for correct PCR technique)

The boxed sets of nucleotides are the primer options I have at hand. I know that the DNA synthesis can only carry out from 5' to 3' and there is a forward and reverse primer. The forward primer should be easy enough but non of the options seem acceptable? Could someone please explain to me how to go about this problem?

First of all, if this is a homework question, add that tag to it. And show what work you have done so far.

Secondly, primers for amplifications should lie on opposite strands. Primers are typed in 5'-to-3' direction (aka left-to-right on leading strand).

Appropriate primers will be: primer 4=GTG... and primer 5=GAA.... Note how those primers are always in 5'-3' orientation. That is how you order those.

Again, if this is homework (looks like it) it is very bad taste to just ask question without any work shown. It displays laziness and usually not respected behavior when asking for help.


Bacterial Conjugation/Horizontal Gene Transfer -- how does the plasmid exchange work? So according to a PPT I'm reading, bacterial conjugation works by the two bacteria joining pili and exchanging plasmids. So how exactly do the plasmids get across the gap? If I understand this correctly, the pili are little hair-like things on the outside of the bacteria -- so unless the plasmids were actually able to somehow be pushed through the pili, there would be gap. Right?

The only other possibility I can think of would be that the membranes fused or something like that. But that comes with it's own whole set of problems.

How does this work?

Thanks!

evamvid

The donor cell retracts it pilus upon contact with another cell and both cells form a pore between the two cells, which allows the transfer of DNA.
Take a look at the image, I think this makes it clearer (from the Wikipedia article on Pili):

This has even be seen in an electron microscope:


Number of elongating RNA polymerases on a gene I'm interested in knowing how many Pol II molecules are simultaneously transcribing any given gene. There are RNA pol II ChIP-seq (phospho-S5) data for different cells but these come from pooled cell samples. So the different peaks on any given gene would be the average of the cell population. Single cell ChIP-seq data would help but I can't find any.

The other way to check this is to calculate transcription rates of different genes, normalize with copy number and divide by the elongation rate of the polymerase on that gene. However, elongation rate is not unique for all genes.

Is there any resource – paper or raw data, which would help me find the answer to the question?

Regulation of RNA polymerase II activation by histone acetylation in single living cells by Stasevich et al. provides detail on how they were able to determine the number of elongating RNA polymerase II for a given gene array. The issue I had with the paper is that they used a ~1.8Mbp tandem repeat as their target, so they really upped the probability of seeing activity. You may be able to do similar for your gene of interest, but there may not be enough signal to tease out your data.


A grey water bird with brown head A greyish bird, with brown head and relatively long, pointy beak.
Size comparable to mallard.
Spotted in central Poland, on small, artificial pond, populated by mallards and Eurasian coots.
Photo has been taken today (late September).

I'd be grateful for any information that could be used to identify this bird.

Based on the location and picture I believe this a Goosander (Mergus merganser) which is the European name, the North American name is the Common Merganser.

You can find more information about them here.

They undergo two main molts, breeding plumage in December and eclipse plumage in May. Here is a description of the eclipse molt by Bent, 1923:

  In May the adult male goosander begins to assume its eclipse plumage.
  The adult male in August has the crown reddish brown, with a gray
  tinge; chin white, and the rest of the head and upper neck rich red
  brown.

By the looks of your photo, you either have 2 females during the breeding plumage phase (January - May) or either sex during the eclipse phase (June - December). It will depend on when the photo was taken.

Here is an image with a breeding plumage male (left) alongside some females:

References:

Bent, Arthur Cleveland. 1923. Smithsonian Institution United States National Museum Bulletin 126 (Part 1): 1-13. United States Government Printing Office


What is an on-line measurement? What is an off-line measurement? See it used here: http://en.wikipedia.org/wiki/Fed-batch. In the table giving the different strategies to control growth in a fed-batch culture, one finds, for example: "on-line measurement of glucose". What does it mean? Is there an off-line meassurement? What does it mean?

On-line means that's it's generally continuous, or constantly taking the measure, through a tube connecting the batch.

Offline is used for things that are taken out of the reactor, or removed from the process.

Thus it's "on" or "off" the system depending on whether it's contained within the normal piping/fludics of the system: "On" is in the system, "Off" is out of the system.


What does the placenta consist of? It includes the basal plate, the pool of blood between the chorionic plate and the basal plate and the chorionic plate, what else?

You could’ve easily googled this, but anyway...

Placenta is a composite structure made of embryonic and maternal tissues.
The placenta is composed of: The chorion, which is the embryonic-derived portion of the placenta. Chorion contains the trophoblast cells (cells that make up the outer cell layer of the blastocyst). finger-like structures called chorionic villi are also present in the placenta. Lastly, the space in the placenta that surrounds the villi and the maternal blood is called the intervillous space.

Source: https://study.com/academy/lesson/the-placenta-and-the-fetus-structure-and-function.html


Why use creatine phosphate? We use creatine phosphate as an energy storage to resupply ADP with a phosphate group as our muscle cells only contain about 2-5 mM ATP. But why doesn't the muscle cells just keep 20-30 mM ATP instead of 20-30 mM creatine phosphate?

Because all available ATP will likely be quickly spent by various cellular machinery.
If there was 20-30mM of ATP, what would stop muscle from contraction and how could you keep ATP level constant at rest, be ready for rapid movement? By blocking all myosin? This creates enormous regulatory problems for the cell.

Phosphocreatine buffers energy for a period of time when it will be actually needed. Having buffer allows for more robust control of energy spending, for example via regulation creatine kinases and other enzymes. Just by activating single enzyme you then start rapid conversion of ADT into ATP via phosphocreatine.


Is Ellman's reagent specific for low molecular weight proteins and thiols? Is it still possible to quantify cystein rich low molecular weight proteins such as Metallothionein in a given sample using Ellman's reagent if the sample is contaminated with some high molecular weight proteins?

It's specific for thiols in general. If the contaminating proteins contain solvent accessible thiols, DTNB will react with them.


What is "integrated spindle activity" in plain English? From a research article:

  To determine if a combination of spindle parameters allowed for a better group discrimination, integrated spindle activity (ISA) was calculated by integrating over time the amplitude of each detected spindle (and by dividing by non-REM sleep duration). We found that integrated spindle activity was markedly reduced in amplitude and number of detections during the first sleep episode in the schizophrenia group in relation to the comparison and depression groups (Figure 3A).

Is this ISA parameter calculated using integrals? I vaguely recall integrating functions in the university, but by now I've forgotten all - that was too long ago. And I don't know how one would "integrate" not functions (like we did in the university) but spindles. And what is the meaning of "over time"?

In short, I'm curious what this ISA parameter stands for. Is there a way to describe it in plain English?

Integrated spindle activity is just this paper's measure of the intensity of spindles. It isn't really a term of art, there is no defined thing "integrated spindle activity," it is just a description for their method of quantifying spindles, or in other words operationalizing their definition of spindle activity.

Spindles are brief bouts of (relatively) high-frequency oscillatory activity that occur occasionally during sleep - often they are called "sleep spindles."

Figure 1 of the paper you link shows their method for detecting and measuring these spindles.

Ferrarelli, F., Huber, R., Peterson, M. J., Massimini, M., Murphy, M., Riedner, B. A., ... & Tononi, G. (2007). Reduced sleep spindle activity in schizophrenia patients. American Journal of Psychiatry, 164(3), 483-492.

In summary, the top trace is a raw EEG trace. Spindles are present in this trace, but the authors want to quantify spindle activity in some way. By filtering between 12-15Hz, the spindles become more obvious (middle): they are the high-amplitude things bracketed by vertical lines.

On the bottom, they have rectified and smoothed the signal to approximate the amplitude of the spindles (that is, they aren't interested in the area under the curve in the middle plot, which has negative and positive going components, they just want a measure of the whole event).

They are defining the integrated spindle activity as the integral (i.e., the area under the curve, just like in calculus) of bouts of activity that exceed some threshold, indicated by the area shaded blue.

In summary, to answer your question, there isn't really a better or simpler English way to say "integrated spindle activity" without losing information for the reader - they are indeed referring to mathematical integration. You could say something like "total spindle activity" but then it is much less clear how exactly you are quantifying spindle activity. Probably the best plain English description of integration is the 'area under the curve' of a function or measurement, though this isn't a perfect mathematical description.

As someone who is familiar with general methods for analyzing electrophysiological data, it was pretty clear to me what they meant by "integrated spindle activity" before opening the paper - this is a fairly common way to report the amplitude of oscillatory activity, because it captures both average amplitude and duration in a sensible way.


How does water move throughout plants? I haven't yet found a decent explanation for how water moves throughout plants. It does seem to travel more efficiently upward than out or down. Why is that?  How does it travel through the plant?

Most water moves up through the xylem by capillary action. Imagine dipping a pipette into a small pool of water; the water would rush up into the pipette. Or, imagine dipping the edge of a paper towel in water. The water "runs" up the paper towel. This is capillary action.

As water evaporates out of the leaves and such in higher regions of the plant, a capillary force pulls up more water. If for instance, you were to dry the top of your saturated paper towel, more water would be pulled up from the pool below to wet that top section.

As for a molecular explanation, Wikipedia has a good explanation of Cohesion-tension theory.


Why isn't the ovum reabsorbed into the body (like sperms) if it is not fertilised? I have read that when sperms are not ejaculated out of the body, they are broken down and reabsorbed. Why can't the ovum be reabsorbed into the body instead of shedding it out during menstruation.

Apparently they are
Technically speaking, the ovum is not shed because it does not exist unless and until fertilization occurs.  Development leading up to the ovum otherwise stops before the final division of meiosis.
Now, you can ask why the body doesn't reabsorb oocytes, but then the answer is that it does, in a process called follicular atresia, with one or a few exceptions per  month.
Now what about that secondary oocyte that isn't fertilized?  Well, it's time to pull out a lovely article from 1917 (Harry Carleton).  Why are we so unable to match such prose today?  The paper describes a mouse study, giving quite recognizable descriptions of membrane blebbing and nuclear fragmentation characteristic of apoptosis in a decade during which it is usually said to have been forgotten.  (A 2005 work reports this for unfertilized human oocytes) Carleton likens the apoptotic changes he observed to atresia in the ovary, and says that the oocytes are reabsorbed by phagocytic cells.


Plant growth in blue light For the past two weeks, I have been in a group of 3 studying how different lights affect plant growth. So we growth two chickpeas plants and put one in white light and the other in blue light.

These are the results:

Days    Blue light    White light
           (cm)          (cm)
__________________________________
 1          6.6           8.2
 2          8.5           9.9
 3         11.0          11.6
 6         15.8          16.0
 7         17.2          17.6
 8         18.0          18.2
 9         19.6          18.7

The blue-light plant didn't really branch out a lot whereas the white-light plant branched out a lot.

My question is:

What caused the white light plant to not grow as fast like blue;
Why did the white light plant branch out?

What I read about the second question:

Experiments with blue light resulted in plants that are wider than usual. This can be explained by reference to the fact that more flowering buds (more branches) could form by reason of diminished apical dominance at the growth point.
http://www.canna.com.au/influence_of_colours

I don't understand why the blue lights plant did not branch out a lot like the white light ones?

With all the research I did this is my understand of why the plant that was exposed to blue light grew taller than the plant that was exposed to white light.

The results of this experiment proves the hypothesis that the plant that was exposed to the blue light will grow taller than the  plant that was exposed to white light. Chlorophyll is a green photosynthetic pigment that is found in most plants. The chlorophylls are found around pigments in the photosystem, chlorophyll helps the plant to get the right wavelength of light. There are two types of chlorophyll a and b. Chlorophyll a absorbs red and violet wavelength best, but it absorbs very little blue light. Chlorophyll b absorbs a lot of blue light. Understanding chlorophyll  b will explain why the blue plant grew taller than the white plant. It grew taller because in both of the photosystems there were more chlorophyll b then a, therefore there was a lot of pigments that absorbed the blue light and the plant was able to use the energy to produce more ATP which in the end resulted in more growth.  There were many factors that we could not control  temperature, time exposed to light, moisture, earth/fertilizer used, size of potting. In order to get an accurate result of different light affecting the growth of plants some of these factors must be implemented.

Sources:
http://scienceline.ucsb.edu/getkey.php?key=3155

Can someone Confirm if this is right?


Why does RNA adopt an A-form helix? RNA is known to form an A-form helix, while DNA generally forms a B-form helix under physiological conditions.

From left to right: A-form DNA, B-form DNA, Z-form DNA. Image created by Richard Wheeler

The preference of RNA for the different conformation is supposed to be caused by the 2'-OH, my question is now how exactly this favors the A-helix? Which interactions are important and cause RNA to adopt an A-form helix?

The beta-form of DNA and the alpha-form of DNA are based on the pucker on the sugar ribose. As DNA doesn't have a 2'-OH, it can obtain both conformations.

RNA does not have this luxury. The steric clash of the 2-OH with the 3'-OH makes the B-form to be very unfavorable thus constraining the RNA to adopt the A-form. Incidentally this steric limitation is also why RNA structures are more stable (see https://biology.stackexchange.com/a/769/389)


What is the standard deviation of adult human heights for males and females? The wikipedia article on human height reports mean height for many different countries by sex but it does not report standard deviations.

What is the standard deviation of adult human heights within sexes?

Obviously the size of the standard deviation would vary across countries and by other factors.  That said, I think good data on a few representative countries would be sufficient to get a reasonable sense of what it typically is and the extent to which the standard deviation varies.

It's probably around 7 cm for men and 6 cm for women.

The Evolution of Adult Height in Europe, which is a source for some of the statistics reported on that Wikipedia page, gives averages, standard deviations, and sample sizes for both sexes across 10 european countries (and across a number of different age cohorts).

Taking their numbers for men and women born between 1966 and 1978, the average male standard deviation of height across all ten countries is 7 cm (range 6.7-7.3) and female 6.1 (range 5.6-6.4).

For a more global context, Subramanian et al. give heights with standard deviations for a much wider selection of countries, mostly "developing countries". Unfortunately for your question, they only report numbers for women. However, these  look pretty similar to the Europe numbers: the across-country average SD for women is 6.3. (with all these countries, the range is greater at 5.4-8.1, but 32 out of the 54 countries have SDs within the Europe range for women, i.e. 5.6-6.4)

Note: for this estimate I just ran averages across years/countries, I didn't weight the averages by sample size.

 Subramanian SVS, Özaltin EE, Finlay JEJ. 2010. Height of nations: a socioeconomic analysis of cohort differences and patterns among women in 54 low- to middle-income countries. PLoS ONE 6: e18962–e18962.


Coincidence that navel is near the womb? The attachment point of the umbilical cord in a baby girl is very close to where her own baby would develop. Is there something in the evolutionary history of mammals that explains this, or some anatomical constraint? Or is it just a coincidence?

I would say it is a coincidence because:

the navel is in the same place in males, so if it was there for some evolutionary advantage the charachter would be sexually dymorphic, which clearly is not the case.
I cannot think of any specific function of the navel that is related to pregnancy or delivery (or of a specific function of the navel at all for that matters)


Are there neuronal firing artifacts produced by head movement? I'm experimenting with a consumer-grade ElectroEncephaloGram (EEG) sensor and have created the image below using the device. Because the sensor on the device does not use a suction cup, there are a lot of motion artifacts when the headband contact is poor (during motion).

This got me thinking - neurons have mass and thus inertia, and they are not glued to each other.  When the person moves (actually rotates) the head around, forces of inertia are applied to neurons/axons. I'm interested if such motion produces any kind of firing artifacts within the brain or how the brain filters out such firing?

This reminded me of this article: (5-HT and motor control: a hypothesis). Could it be that some neurons stop firing in response to movement?

There are certainly head-orientation cells (e.g. in the hippocampus).  But neurons are reasonably immune to the kind of mild physical stresses that come from turning the head around; computing head orientation requires complex analysis of input from e.g. the visual system (optic flow) and vestibular system.

However, the electrical activity of muscles tends to swamp that of (nearby) neurons, so various muscle-related artifacts are often visible in an EEG if not carefully filtered out.  And, of course, if the contact is poor you'll get artifacts from that: you're just measuring the variability in resistance between the sensor and your skin, not anything interesting about what faint potential changes are visible at your skin as a result of neuronal activity.


Do all mammals have a Ventricular system? I am familiar with the human Ventricular system that circulates Cerebrospinal fluid. This is needed among other reasons, to suspend the heavy human brain, and for injury protection. Do all mammals have a need a Ventricular system?

Maybe some did not have as strong of an evolutionary need for cerebrospinal fluid?

The ventricular system is common to vertebrates. It's also necessary for brain nutrition, assists in preventing under/over perfusion by exerting/releasing pressure, and forms part of the brain's glymphatic clearance pathway.

See also:

Totally Tubular: The Mystery behind Function and Origin of the Brain Ventricular System


How do the High-Energy Electrons During Chemiosmosis Come from Water? On Pg. 199 of Campbell, this is stated.

Both* work by way of chemiosmosis, but in chloro- plasts, the high-energy electrons dropped down the transport chain come from water, while in mitochondria, they are extracted from organic molecules (which are thus oxidized).

*Both refers to the to chemiosmosis in mitochondria and in chloroplasts (during photosynthesis).
My question is, how do the high-energy electrons in the transport chain for chemiosmosis come from water? Aren’t these high-energy electrons derived from light harvesting done by the light-harvesting complexes?

The light harvesting complexes use light energy to "lift" electrons to a higher energy state from which they can be used to reduce organic molecules (by way of an electron transport chain and NADPH), leaving a "hole" or cation behind in the LHC and thereby oxidizing it. If these complexes were not re-reduced by something, they would become non-functional after absorption of a single photon. So, they are re-reduced by removing electrons from water to generate molecular oxygen, which happens in photosystem II. So the photosystems I and II act as a series of "pumps" that make otherwise thermodynamically "uphill" (unfavorable) electron transfer from water to NADPH spontaneous, but they do not act as a net source of electrons--water does.


Cesium-137 From Fukushima Meltdown I've been reading up on the Fukushima nuclear meltdown and its effects it had on the environment. The iodine-131 initially released from the incident decayed after 8 days, but other isotopes such as cesium-137 and strontium-90 have a half-life of 28.7 and 30.2 years (about 300 years to completely decay).

Apparently, large quanties of cesium-137 were found in neighbouring countries as well as in seafood near Japan.

Now, for something like nuclear isotopes, not having the required knowledge can lead someone to fear something that might be harmless (or confirm some doubts about the issue), hence why I am here.

From my research on scientific websites and different governmental regulations, I found out that food and water in Japan have a legal limit as to how much cesium-137 a food item can contain. Especially since cesium-137 ressembles potassium and therefore being easily taken up by the body, this is worrying.

To my understanding, the way a radioactive isotope creates havoc in the body of an individual is that:

It ressembles a normal element we usually consume, like iodine, potassium for cesium-137 and calcium for strontium-90.
The body digests it and it is stored in the body.
It emits radation for a certain period of time, anywhere from 8 days for Iodine-131 to years for cesium-137.
The prolonged radioactivity from these isotopes causes cancerous cells to occur.
A tumour or other form of cancer develops.

If this is what happens for isotopes like cesium-137, how can it be possible to eat food or drink water containing ANY cesium whatsoever? Sure, the radiation isn't so bad, but what is important to take into consideration is that this is internal and highly centralized radiation. This is a completely different thing to external radiation.

For my questions about the topic, I would like to know three things (which could really put many doubts to rest).

QUESTIONS

The first is, is my understanding described above correct?

The second is, how does this affect us healthwise? We are stuck with these debris of cesium-137 and strontium-90 for the next 30 or more years, but what effect do they have on us?

If someone ingests an atom (or a small amount) of cesium-137, what affect will this have on this person's body?

Finally, for someone living in North America, how much of these debris are there, either that got here from the wind, products, food, water, etc.?

EDIT: If someone knowledgeable on the subject could answer the questions directly (highlighted by means of italics), it would be very much appreciated.

Good question, but I'm not sure if anyone really knows the answers. The governments of Japan and the U.S. have both been very secretive at best, while an army of propagandists have made it very difficult to distinguish between truth and fiction.

Any health effects are likely to be too small and gradual to make headlines. For example, suppose there was a 1% increase in thyroid cancer in California due to Fukushima radiation. How could investigators prove there's a link with Fukushima radiation?

Adding to the confusion is the fact that the Pacific Ocean and neighboring land masses are being battered by more than nuclear radiation. Ongoing reports of mass dieoffs of various creatures are variously linked to radiation, global warming, pollution or unknown causes. One famous example is the "melting starfish" disease.

A lot has been written about increases in radiation in tuna. For example, see Is Tuna Safe to Eat Post Fukushima?. Some sources say we shouldn't eat any seafood from the Pacific Ocean, period. Others say "Don't worry." The propagandists particularly like to focus attention on radiation that originated from atomic bomb tests.

When investigating the amount of radiation in North America, keep in mind that the levels are presumably increasing, as contaminated water is still being dumped into the sea (hundreds of tons a day, according to some sources).

You can glean more specific information from the Internet, but it's just very hard to know how truthful or accurate it is. I wanted to write an article about this very topic but gave up in frustration. I decided it might be better to wait until there was more irrefutable evidence - like several new extinct species. ;)

You might get a better feel for the potential damage by doing some research on a similar event that has received even less publicity - the dumping of nuclear wastes off the coast of East Africa. For example, read the article You are being lied to about pirates.

Regarding the effects of cesium on human health, you can start with Public Health Statement for Cesium. But you should solicit similar information from several other sources before reaching any tentative conclusions.


Ion-exchange vs Gel Permeation Chromatography for proteins For extracting Lysozyme from egg white which method would you recommend and please help me understand why.

Lysozyme has a higher isoelectric
point (pH 10.5) and a lower molecular mass (14 307 Da) than most proteins so both these methods make quite a bit sense. Use Sephahdax G100 for gel permeation chromatography and CM-Sephadex G25 ion exchanger for ion exchange.

From what I can understand, Gel Permeation will separate the egg white based on Mr of the various proteins and compounds. There is quite a bit of variation in the Mr of egg white proteins but lysozyme, in fact, doesn't have the lowest Mr as Cystatin and Ovomucoid have lower Mr. Furthermore, GPC requires around at least a 10% difference in molecular weight for a reasonable resolution of peaks to occur. The range of Mr is also quite broad in this method. Will this be disadvantageous perhaps? So GPC does have the plus side of it having a well-defined separation time due to the fact that there is a final elution volume for all unretained analytes.

Now Ion exchange chromatography is very specific in the nature of how the exchanger interacts with the mixture being separated. Lysozyme has a PI of 10.7 which is much higher than the rest of the proteins in the egg white. As with GPC we use 0.05M Tris-EDTA, pH 8.2, containing 0.05M NaCl as the standard. Can this setup result in Gibbs Donan effect or chromato- focusing ?

I'm currently leaning towards GPC as the option to yield the purist product especially seeing as it can be desalted afterwards with G25.

Please help guide me in the right direction. I'm quite new to this but am ready and very willing and keen to learn and expand my abilites.

Since lysozyme is so well studied, your best bet is to search the literature and see what methods other people use. See this paper, for example. They report that lysozyme can be affinity purified on Sephadex, but they also reference other methods in the introduction that you could take a look at.

Both of the methods you described sound reasonable. The only way to know which is best is to try them and see. In fact, the best approach, depending on your application, would likely be to use both methods for optimal purity. Even when I affinity purity a protein, I will still often perform ion-exchange as a polishing step.


Maximum length for PCR amplification Is there a recommendation for how long a target sequence for PCR amplification should be?

If there is how do you amplify a target sequence that exceeds the recommended length?

The answer depends a lot on the polymerase you are using. Some are engineered for better processivity, by fusion of a processivity-enhancing domain (Wang et al, Nucleic Acids Res. 2004), but even the best one will struggle after a few tens of kilobases.

You can push the length of the amplicons a little by playing around with conditions but to produce something significantly larger than the average limit of your polymerase, you will usually need to amplify smaller fragments, and then assemble them together. This is the strategy that was used to synthesize the 1079kbp synthetic genome of M. mycoides JCVI-syn1.0, the first "artifical genome" (Hutchison et al, Science 2016); the authors first amplified many fragments of 1.4kbp, and assembled them in vitro. To easily assemble large fragments in vitro, common one-pot enzymatic techniques include the so-called Gibson assembly (Gibson et al, Nature Methods 2009) and Golden gate assembly (Engler et al, PLoS One, 2008) for example.


What is meant by Remote Diuretics & Remote Vomiting? I have encountered the terms Remote Diuretics & Remote Vomiting separately or sometimes in association in various articles related to medicine.

But I am unable to find any reference to what they actually mean.

Can you help me understand these terms please?

Update

Examples:

  Urine sodium less than 10 mmol/L indicates extrarenal loss of urine
  (remote diuretic use and remote vomiting).

link: https://www.ncbi.nlm.nih.gov/books/NBK470386/

Go to google and search for "remote diuretic" to get more references, some are:

"Remote" can mean distant/far away, often in space but also in time (as in, the "remote past"). In just the search results you included in your question it is fairly clear that these sources are using the word "remote" to mean (relatively)"far away in time" or simply "not recent."

For example:

  associated with remote diuretic use, therefore, diuretic effects were already washed off

Referring to diuretic use in the past, so there is not current diuretic effect but the secondary consequences are still present.

Note that these terms are quite uncommon in the literature, I get 21 results in Google Scholar for "remote diuretic" and 16 for "remote vomiting" and nearly all seem to be related to the specific context of hypokalemia.


How does an antisense RNA molecule restore protein function in CF patients? I am researching a treatment for cystic fibrosis (CF) called Eluforsen and I am trying to understand the mechanism by which an RNA molecule can restore proper protein function. In many research articles I come across the same sentence:

"Eluforsen, is an antisense RNA oligonucleotide designed to bind specifically to the mRNA region around the F508-encoding deletion and to restore CFTR protein function."

But I cant find any literature explaining how an antisense RNA molecule can restore function of a protein on its own. When I think of antisense RNA I think of  RNA interference not restoring protein function.

The root of the problem for a majority of cystic fibrosis patients is that they have two defective genes for a particular protein and at least one of these genes is defective because it is missing a 3-base codon for the amino acid at position 508 of the protein.

Eluforsen, also known as QR-010, is a somewhat modified 33-base RNA molecule.  The bases in it are complementary to an area centered on the codon for amino acid 508 of the normal mRNA (messenger RNA) for the protein. Since the defective mRNA is missing 3 bases in the middle of this sequence, eluforsen binds to only 30 bases of the mRNA and has an unbound loop of three bases in the middle, as suggested by the wiggle in this diagram:

[image from SEC]

Such a double-stranded stretch of mRNA is abnormal, of course, but the effect of its presence at least some of the time is to cause the mRNA to undergo repair in the duplex area in a manner which makes a break in the main strand opposite the loop and inserts RNA bases that are complementary to the three "excess" bases present in the eluforsen loop.  Since these three bases are complementary to the normal mRNA bases at that point, the effect is to transform the defective mRNA into a normal mRNA.  When the repaired mRNA is translated by a ribosome, a normal protein is produced, and some of the symptoms of the CF condition are reduced because of the presence of normal protein.

The mechanism which causes the mRNA to be repaired in this manner is not yet well understood(1).  The condition improvement from a complementary mRNA fragment was noted back in 2004.(2)  One hypothesis is that RNAse H is involved in the repair.(1)  Some further information about QR‐010 effects can be found towards the end of reference (3).

(1) Matos & Matos, 2018

(2) Zamecnik et al., 2004

(3) Alton et al., 2016


What kind of crow is this? Years ago, when I lived in Greece, I saw crows from a close distance, but never with this peculiar colouration. Today I saw two individuals, both with these gray parts.

Location: Austria, Vienna. Pretty much in the city centre. Specifically Altes AKH Hof 2 near the rear yard of the department for East Asian studies.

Time: I am not sure. Probably before my lecture (around 10am) or after it (12am). I'll see, whether I find the timestamp of the picture anywhere.

Size: Now, at this I am really bad. I would say roughly the length of my boot, which is a 47-48 European continental size.

Behaviour: nothing interesting. Two of them came, stalked around the benches, did not make sounds and as far as I remember were gone quickly. They were not afraid of people.

My guess is Corvus cornix , but I have always been bad at identifying birds.

EDIT:
Unfortunately, I didn't see the linked answer. But had I seen it, I would probably have assumed my bird wasn't Corvus cornix. The plumage  in the linked answer looks significantly more colourful. Whether you want to mark it as duplicate or not, I am fine with your decision, since I have little practice in identification. However, I find the answer here more detailed when it comes to differentiating C. cornix from other corvids. The linked answer only states the results. The answer here teaches us what to look for!

I'd say you guessed correctly. This does appear to be the hooded crow (Corvus cornix).

In German, it's called Nebelkrähe (meaning "mist crow").

 A Hooded Crow Corvus cornix in the garden of Belvedere (Vienna). [Source].

Description: ashy grey bird with black head, throat, wings, tail, and thigh feathers, as well as a black bill, eyes, and feet.

C cornix is a Eurasian species that would be present in Austria:

Similar but incorrect species:

The only other similarly grey crow species I know are the grey crow (Corvus tristis), which is only present in New Guinea, and the western jackdaw Corvus monedula. The jackdaw is present in europe, but it can be ruled out because of its grey eyes and because of the grey feathers that creep superiorly from the birds nape onto its head (unlike your specimen).

Note: I exhaustively checked all commonly recognized species of the Corvus genus


Regarding apoptosis and turning it 'back on' Is there some chemical or chemicals or even special molecules that can be 'injected' into cancer cells that will turn any Apoptosis mechanisms 'back on'?

Or maybe chemicals and/or molecules that might cause a certain gene or set of genes to switch to a configuration favorable to apoptosis?

Yes, tons of things induce apoptosis. Here is a good list that you can get for research grade

Sigma-Aldrich

Even your immune system can tell cells to "commit suicide." Now the trick is, getting drugs, proteins, pathways, and your immune system to selectively target cancer cells.


What are the major evolutionary pressures for Bioluminescence? What are the major evolutionary pressures for Bioluminescence?

In many cases, and in particular in marine invertebrates, the bioluminescence is in fact produced by symbiotic bacteria of the Vibrionaceae family. In most cases the bacteria can sense when they are being hosted by the animal through quorum sensing mechanisms, and start producing light.

The evolutionary pressure for the bacteria to produce light is to be in the protected environment of the animal which often feeds them. On the animal side, there can be several reasons to host the luminescent bacteria. In many cases, the evolutionary pressure is linked to reproduction. In order to successfully reproduce in the immensity of oceans, marine animals need to know that they are among their kind before they release their gametes.

Another example is the one of some deep see fish like the anglerfish which have developed a special "flash light" organ to host bio-luminescent bacteria. Fish can use the bacteria to emit a light to aid in camouflage, hunting, and attracting mates. See http://microbewiki.kenyon.edu/index.php/Deep_sea_fish


Is there any danger in putting a magnet in your ear (next to your brain) I recently bought some wireless earbuds that fit right in my ear, so they're very small.
But the method it uses for charging is magnetic, so it has magnets built into the earbud.

I was wondering if there's any danger in keeping a magnet in your ear for many hours every day? I'm not sure if it would affect things in your skull/brain.

Every pair of earbuds/headphones have magnets in them, as of now there's no solid evidence that proves that they are harmful or harmless to humans. Keep in mind that, what may be harmful to lab rats may not be harmful to humans as we are more resilient to radiation, etc. (In reference to a study done on truly wireless earbuds.)


What is the biggest facultative anaerobic metazoan known to science? Related: What's the biggest obligate anaerobic organism discovered till now?

I had always assumed that the Riftia tube worms were obligately anaerobic since they lived next to anoxic volcanic vents, but a quick literature search showed it to be a facultative anaerobe, being able to survive at least 60 hours without oxygen.

If "facultative anaerobe" is defined as being able to survive at least 24 hours in the absence of molecular oxygen in an otherwise normal environment, are there any metazoal organisms larger than Riftia (which are up to 1.5m long)?

I think a tapeworm is your best bet. For tapeworms specifically, I found this textbook, Animal Physiology: From Genes to Organisms, which claims:

  Active facultative anaerobes include some parasitic worms such as tapeworms that can survive without oxygen indefinitely...

I was not able to find any primary research on the subject either @WYSIWYG (other than a paper from 1951 that doesn't seem to be available anywhere), but if the textbook's claim holds, I can't think of anything larger than a tapeworm.


How tolerant are ants to cold? There was a trail of what are commonly known as sugar ants (small, brown, hyperactive) in my kitchen. Three of them walked onto an ice tray placed in their path.

They only walked a short distance on the ice before being immobilized by cold. I put the tray in the freezer beside a very shallow dish of water. When the water in the dish had frozen (about a half hour later) I removed the tray/ants and let them passively drop onto a warm dry surface. After 2-3 minutes they revived, walked in circles a few times, then headed off to forage (they were released outdoors).

There is anecdotal evidence of ants' tolerance of cold but I was a little surprised by this. Do we know the extent of their tolerance of cold?

I guess it would vary with size and conditions. But an obvious question is whether, having survived freezing at (let's say) 22F, they could survive lower temperatures and/or longer periods of cold if properly handled? There may be cell structures that are sensitive to freezing because they break or change shape but it's already amazing to me that ordinary freezing does not distort water-bound structures in a lethal way.

Thanks for any insight.

Acclimatization increases cold resistance of ants [1]. They have a strong adaptability to different environments [2].

When it comes to the red imported fire ant (Solenopsis invicta) here are some numbers (from [2]):

  When the exposure time was 0.5 h, the survival rate of workers was 15.3% at -14°C. At the exposure time of 1, 2 and 4 h, the entire lethal temperatures for S. invicta were -13°C, -9°C and -9°C, respectively. When the exposure temperature was -10°C, all workers died within 240 min; while at -11°C, it took only 120 min.

References:

Modlmeier AP, Pamminger T, Foitzik S, Scharf I. Cold resistance depends on acclimation and behavioral caste in a temperate ant. Naturwissenschaften. 2012 Oct;99(10):811-9. doi: 10.1007/s00114-012-0963-8. PubMed PMID: 22955370.
Xu YiJuan; Lu YongYue; Huang Jun; Zeng Ling; Liang GuangWen. Cold hardiness of natural populations of the red imported fire ant, Solenopsis invicta Buren (Hymenoptera: Formicidae) in Shenzhen, Guangdong. Acta Entomologica Sinica 2009 Vol. 52 No. 9 pp. 974-983.


The reproduction patterns of fungi: what’s the difference between them? I am going to take TOEFL, and am getting perplexed by the difference between cell division and budding and fragmentation of fungi.

Those three terms seem like all the same all to me, so could anyone teach me fundamentally how they differ from each other?

Cell division

Cell division is the process by which one cell becomes two. If we consider multicellular fungi, cell division happens whenever the fungi grows by one more cell. Cell division allows the growth of the organism. Cell division does not necessarily contribute into making a new multicellular organism.

Fragmentation

Fragmentation is a type of non-sexual reproduction. An organism gets split ("intentionally" or "unintentionally") and the different fragments develop into independent mature organisms. Sometimes, on fragment is small than the other one, so that one fragment can be seen as the "parent" and the other one as the "offspring".

Budding

Budding is a type of reproduction by fragmentation, where the splitting occurs due to a specific developmental pathway and not through some external environmental cause (such as getting cut in two by a researcher's knife, a falling tree or the bite of a predator). In other words, in budding, the splitting is "intentional".

More information

wikipedia > Cell Division
wikipedia > Fragmentation (reproduction)

P.S. You won't need to know this biology stuff to get a good score at your TOEFL. On an unrelated personal note, I found this exam particularly unpleasant when I had to take it. Especially when we have to converse with a microphone while somehow ignoring the accents and english mistakes your neighbours are making while talking into their respective microphones. Good luck for your exam by the way :)


Why are high levels of epinephrine and low levels of cortisol signs of stress? According to my psychology textbook (Psychological Science: Modeling Scientific Literacy), high levels of epinephrine and low levels of cortisol are signs of stress. However, earlier in the textbook it is shown that the autonomic response of the human body releases norepinephrine and epinephrine, while the hypothalamic pituitary adrenal (HPA) axis pathway releases cortisol. So it seems to me that signs of stress would be high levels of both of these things. Is my textbook wrong or am I just understanding what stage of stress it's describing?

So it seems to me that signs of stress would be high levels of both of these things.

Yes. Wikipedia claims [1] the same:

  Stressors [...] activate the HPA axis, though via different pathways. [...] Stressors that are uncontrollable, threaten physical integrity, or involve trauma tend to have a high, flat diurnal profile of cortisol release (with lower-than-normal levels of cortisol in the morning and higher-than-normal levels in the evening) resulting in a high overall level of daily cortisol release. On the other hand, controllable stressors tend to produce higher-than-normal morning cortisol.

The same on a webpage of Society for Endocrinology [2]:

  In addition, in response to stress, extra cortisol is released to help the body to respond appropriately.

Yet, there are conditions in which stress can lower cortisol levels. One of them is psoriazis [3]:

  [...] patients with persistently high levels of stressors seem to have a specific psychophysiological profile of lowered cortisol levels and may be particularly vulnerable to the influence of stressors on their psoriasis.

And some psychiatric disorders [4]:

  Several stress-associated neuropsychiatric disorders, notably posttraumatic stress disorder and chronic pain and fatigue syndromes, paradoxically exhibit somewhat low plasma levels of the stress hormone cortisol.

References:

Wikipedia contributors, "Hypothalamic–pituitary–adrenal axis," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Hypothalamic%E2%80%93pituitary%E2%80%93adrenal_axis&oldid=619115237 (accessed August 7, 2014).
Society for Endocrinology. Hormones. Cortisol (2013). Available from http://www.yourhormones.info/hormones/cortisol.aspx (accessed 07.08.2014)
Evers AW, Verhoeven EW, Kraaimaat FW, de Jong EM, de Brouwer SJ, Schalkwijk J, Sweep FC, van de Kerkhof PC. How stress gets under the skin: cortisol and stress reactivity in psoriasis. Br. J. Dermatol. 2010 Nov;163(5):986-91. doi: 10.1111/j.1365-2133.2010.09984.x. PubMed PMID: 20716227.
Yehuda R, Seckl J. Minireview: Stress-related psychiatric disorders with low cortisol levels: a metabolic hypothesis. Endocrinology. 2011 Dec;152(12):4496-503. doi: 10.1210/en.2011-1218. PubMed PMID: 21971152.


All somatic cells contain the same genome, then how does it knows that it should develop into a specific organ? All somatic cells contain the same genome, then how it knows that it should develop into a specific organ. In https://www.youtube.com/watch?v=aeAL6xThfL8, Joe Hanson says that each cell has the same book that each has 20,000 same instructions. And each cell has bookmarks, where it finds which instructions to read.

Can you tell me where these bookmarks are stored in the cells? Is it outside the chromosomes or outside nucleus?

The answer to your question is not really know yet and there is whole scientific field dedicated to it: developmental biology. I'll try to explain the basics however:

Like you described the identity of a cell (its cell type; which organ it belongs to) is dependent on which of (actually) ~30000 human genes are activated (or read) in that cell. There are two fundamentally different ways this is done in cells:

Transcription factors:

These are proteins that bind to specific (regulatory) DNA sequences and thereby lead to the activation (or repression) of certain - usually nearby - genes. Since they are proteins, their own genes have to be activated in the first place, so we already at a 'chicken or the egg' type of problem. In principle proteins can 'survive' outside the nucleus of the cell for some time, but they are usually degraded within a few hours, so I guess the remaining factors from the mother cell are not very important (I have no idea if anyone ever checked this).
Additionally many transcription factors are not constitutively active, but are waiting for some outside (from the perspective of the cell) signal. These could be certain developmental signals, growth factors, hormones or environmental factors like nutrient availability (the list goes on ...). During embryo (& therefore organ) development not only the presence of these signals (morphogens), but also their intensity are a very important factor in determining the 'fate' of a given cell.

Epigenetics

The term epigenetics describes genetic regulation that does not happen on the sequence level. Instead the accessibility of the DNA is regulated through modifications of histones (which are part of the chromosomes) and the DNA itself. Thereby the cell can almost permanently shut down certain genes. Since epigenetics are also inherited during cell division, this regulation affects whole cell lineages and is therefore very important in regulating which cells are active in certain organs or tissues.


Why can't I smell things that aren't there? I can close my eyes and imagine a red cube with a yellow star on it. Although I don't literally see it -- if there was a red cube with a yellow star on the inside of my eyelids, I'd know the difference -- I can experience it in much the same way as if I was seeing it.

I can do much the same thing with sound, imagining (say) the sound of a bird, or of a bell ringing.

But I can't imagine any tastes, or smells. I know what cinnamon smells like: if several spices were placed in front of me, I could readily identify the cinnamon. But I can't call a familiar smell or a taste to mind in the same way I can call a familiar sight or sound to mind.

I don't think it's merely a memory thing. Even if I've never seen the box, I can still imagine it. I can imagine the sound of a bird tweeting in a large echoing hall, even though I've never heard it. But I can't synthesize unknown smells or tastes in my imagination in the same way I could unknown sights or sounds. I don't think I'm unusual in this respect (correct me if I'm wrong).

Are there any theories as to why this is?

Couple of contributing theories:

The olfactory system does not project to the thalamus, which serves as a relay to other higher processing areas.
Lack of a specialized working memory subsystem; we have fairly robust subsystems for movement,visual and auditory buffers of information, what is normally called working memory, things we can hold on for a little while, but it seems they are not as developed or engage the same areas for smell. see for instance:Working Memory in Another Dimension
It is not as useful,used or adaptive ( beyond recognizing odors) as the other senses, there is a relationship in between how much we use something ( could also be the above working memory systems )and the cortical real state devoted to it's processing, this is a competitive part of the brain and in comparison to other senses like vision the portion of the cortex devoted to olfaction is small.
Another way of looking at it, is that we do have the capability to imagine smells and gustation, but they are not as developed as the others since we don't use them as much.
Anectodally, I would argue that people whose jobs revolve around combining nice smells or tasty things do develop certain abilities like those in vision as well as for those who have been exposed to the same odor repeteadly and can imagine it at will.


By what mechanism can hypoglycemia induce fainting? Hypoglycemia (Low blood sugar) is said to be among the potential causes of human-faintings. I was wondering by which mechanism this happens. Google search results are abundant; there are lists of various causes and solutions, but I couldn't find a direct answer to my question.

Is it a controlled reduction of heart function to save energy? Is it an uncontrolled shock reaction (malfunction)? I'm looking for an answer along those lines.

Thanks.

There are regulatory mechanisms that may prevent moderate hypoglycemia to progress to a more severe state, however these mechanisms act before lack of conciousness sets in. The progression of hypoglycemia may depend on overall health and medical status and vary between healthy and diabetic persons, for example.

Rosenthal et al. (1) write that

  The brain is normally dependent on glucose for oxidative metabolism
  and function. Acute iatrogenic hypoglycemia, occurring as a result of
  insulin excess during the treatment of type 1 diabetes, can cause
  clinically significant cognitive impairment. In health, such
  hypoglycemic cognitive dysfunction does not occur. Endogenous
  counterregulatory mechanisms are activated in response to a small
  reduction in circulating glucose, preventing more profound
  hypoglycemia. In diabetes, the inability to reduce circulating insulin
  levels (1), the failure of glucagon responses (2), sometimes
  accompanied by defective autonomic and adrenergic responses (3), can
  allow plasma glucose levels to fall low enough to result in detectable
  disturbance of cognitive function, ranging from a subtle slowing of
  reaction times (3) to coma (4).

In short, the brain malfunctions due to lack of glucose (the sole energy source for the brain). Note that cognitive impairment and unconciousness can also occur in otherwise healthy persons, for example in the case of prolonged exercise combined with lack of nutrition. The exact cause of cortical dysfunction is not known:

  Impairment of brain function is a recognized consequence of acute
  hypoglycemia. It is known that different brain functions have
  different susceptibilities to acute hypoglycemia; for example, the
  triggering of autonomic activation, a hypothalamic function, occurs in
  response to quite modest decrements in circulating glucose
  concentrations (5,6,7), whereas significant cortical dysfunction
  requires more profound glucose deprivation (3). Even within different
  cortical functions, there is variation in hypoglycemia susceptibility
  (26). The mechanisms of cortical dysfunction during hypoglycemia are
  not known.


Why insects are so energy-efficient while flying? Why are insects so energy-efficient while flying? Is it because of their light weight and aerodynamics or due to very efficient biochemical transformations (food->energy)?

Insect flight muscle is capable of achieving the highest metabolic rate of all animal tissues, and this tissue may be considered an exquisite example of biochemical adaptation.

Locusts, for example, may (almost instantaneously) increase their oxygen consumption up to 70-fold when starting to fly.  In humans, excercise can increase O2 consumption a maximum of 20-fold, and for birds in flight the figure is about 10-fold (Wegener, 1996; Sacktor, 1976).

As Wegener (1996) has put it (in his definitive paper):

  The aerobic scope (the ratio of maximal to basal rate of respiration) of insects is unrivalled in the animal kingdom

Flight is powered by ATP hydrolysis, and these impressive metabolic rates are achieved by very effective control of ATP hydrolysis and regeneration.

 Metabolism is aerobic, thus allowing for much more efficient ATP production from hexoses (as compared with, say, anaerobic metabolism).

 Flight muscle may account for up to 20% of body mass.

 In insects, haemoglobin and myoglobin are absent. Instead, gaseous O2 is transported to the tissues by a system of tubules and deposited so close to the site of consumption that (seemingly) it may reach mitochondria by diffusion.

Locusts fuel flight by burning sugars in the early stages, gradually changing to use lipids as fuel. (In bees, flight is totally fuelled by hexose consumption).

This is achieved by effective control of glycogen breakdown and glycolysis, by modifying the activity glycogen phosphorylase (glycogen breakdown) and phosphofructokinase (PFK), a key control enzyme of glycolysis.

There is an enormous literature on these topics, but suffice it to say, in the case of glycolysis, control is very efficiently achieved by allosteric regulation of PKF, where fructose 1,6-bisphosphate and fructose 2,6-bisphosphate play key roles (see Sacktor, 1976).

This allosteric control very effectively allows glycolysis to be (almost instantaneously) turned on and operate at a maximum value, and to be (almost instantaneously) turned off.

References

Wegener, G. (1996) Flying insects: model systems exercise physiology
Experientia May 15;52(5):404-12. (See here)

Sacktor B. (1976) Biochemical adaptations for flight in the insect.
Biochem Soc Symp. 1976;(41):111-31. (See here)


Are harmful gases abiotic or biotic factors in our environment? As we all know, harmful gases play a negative role in our society and our environment. Are these gases playing as abiotic or biotic factors in our lives?

Bez is correct, biotic and abiotic refer to the nature of the agent performing the stress.

biotic = living thing (lion that is actively engaging in catching you as food)
abiotic = non-animated (far from optimal temperature)

Now the example "shade" is trickier; because it depends on the perspective you choose.

There's always a context. Does the element creating the shade matter in your context?
If so, and this element happens to be animated/living:  stress = biotic (though you should reference at some point that the object at hand is animated).

If it doesn't matter what object generates the stress since you are only interested in the effect of the shade on a system: shade = abiotic

Pipeline: Analyze the context, choose and communicate your choice of perspective/angle and then remember what biotic and abiotic literally mean.

Coming back to "harmful gases": What is your context meaning harmful for whom? Specify that first. Carbon Dioxide is an example of something that may be deleterious at a specific concentration for one system and at the same time beneficial for another.

Does it matter how these gases were produced? CO2 may be a product of an animated system's metabolism and thus may be called abiotic. It may also be a product of oxidation of a multitude of carbohydrates.

I don't know of an example where Carbon Monoxide is produced by living things.

You could of course circumvent this discussion by analyzing what harmful effect the gases have on your system of interest. For example: they generate respiratory stress on humans, and then you use the effect of the gases on the system to characterize them.


The concept of backpropagation in neural networks actually occurs in the brain? I am aware the Human brain has many functionally distinct components, but let us specifically consider the Human visual cortex: could Artificial Neural Networks (ANNs) be "trained" (through, e.g. backpropagation) in an analogous way to how the visual cortex "learns"?

Is the concept of backpropagation in ANNs a phenomena actually observed in the Human brain?

Related

Books on machine learning applications in Biology

I recommend Yoshua Bengio's recent works. E.g.: https://arxiv.org/abs/1502.04156 and his slides from the NIPS 2016 Brains and Bits workshop.

Also, Timothy Lillicrap's work: http://www.nature.com/articles/ncomms13276

This is still a big open question. In short, we (the neuroscience community) have little idea on how the brain learns at a circuit/systems level in general. We know a thing or two about how individual synapse changes under specific experimental protocols, but those are phenomenological models (e.g. STDP; there has been many many normative models of learning that concludes their learning rule is STDP-like). (Some systems such as cerebellum, we know relatively more, but the learning seems to be more specific to motor timing.)

The main technique we use in machine learning and artificial neural network are mostly gradient descent (or some sort of stochastic optimization algorithm), and people have been trying to find if the biological neural network learns in a similar way. There are several issues:

There's no error gradient being propagating according to chain rule. Information gets mushed together within a neuron, so there's no plausible way to trace exactly the forward-path during an backpropagation.
There's a lot of recurrent connections but they are not symmetrical.
Temporally, it is implausible that there's a clocked signal to backpropagate after a each forward path. Neuronal network doesn't seem to operate with clocks (some thing there are precise clocks, but I think there's little evidence).

Recent efforts have made some progress with random backprojection, decoupled updates using synthetic gradients, target prop, autoencoder, weight/signal quantization, deep belief networks, etc. But there seems to be several more jumps needed to make it biologically plausible such that it agrees with the neural architecture and information flow. Even then, there's no guarantee that neocortex is learning with a similar principle.


What repairs faster when injured: white matter or grey matter? This was the exact wording of a test question given by my biology teacher and she said that white matter would repair faster, because there is a myelin sheath to protect the cells.

Do you agree with this answer? Could you give me a more detailed, real life (not school, but real neuroscience, real data) explanation?

Short answer
As @BryanKrause indicates, neither answer really makes sense.

Background
This is basically per the answer of @BryanKrause. Myelin is the stuff that forms the main characteristic component of white matter. White matter being

  [the tissue] found in the deeper [in] the brain (subcortical). It contains nerve fibers (axons), which are extensions of nerve cells (neurons). Many of these nerve fibers are surrounded by a type of sheath or covering called myelin. Myelin gives the white matter its color. It also protects the nerve fibers from injury. Also, it improves the speed and transmission of electrical nerve signals

I think what the question aimed to target was your understanding what a myelin sheath is for (and, hence, what it is not intended for). Quoting from (Morell & Quarles, 1999):

What

  [A] greatly extended and modified plasma membrane wrapped around the
  nerve axon in a spiral fashion. [It] originates from and are a part of
  the Schwann cells in the peripheral nervous system (PNS) and the
  oligodendroglial cells in the central nervous system (CNS)

What for

  Each myelin-generating cell furnishes myelin for only one segment of any given axon. The periodic interruptions where short portions of the axon are left uncovered by myelin are the nodes of Ranvier, and they are critical to the functioning of myelin.

How

  In myelinated axons, the excitable axonal membrane is exposed to the extracellular space only at the nodes of Ranvier; this is the location of sodium channels. When the membrane at the node is excited, the local circuit generated cannot flow through the high-resistance sheath and, therefore, flows out through and depolarizes the membrane at the next node, which might be 1 mm or farther away []. The low capacitance of the sheath means that little energy is required to depolarize the remaining membrane between the nodes, which results in local circuit spreading at an increased speed. Active excitation of the axonal membrane jumps from node to node; this form of impulse propagation is called saltatory conduction (Latin saltare, “to jump”). Such movement of the wave of depolarization is much more rapid than in unmyelinated fibers. Furthermore, because only the nodes of Ranvier are excited during conduction in myelinated fibers, Na+ flux into the nerve is much less than in unmyelinated fibers, where the entire membrane is involved.

What not
Although the myelin sheath is formed by a glial cell type, and although glial cells do structurally and metabollically support neurons, I would not say that this means myelinated tissue heals faster. Instead, myelin is more about the functional role of white matter, namely efficient, fast and reliable long-distance transfer of information across distant brain regions.

Reference
- Morell & Quarles. The Myelin Sheath. In: Siegel et al (eds); Basic Neurochemistry. 6th ed. Philadelphia: Lippincott-Raven (1999)


Does the palate truly house the sense of taste? Source: Your “palate” is the roof of your mouth, and by extension, your sense of taste.

I was reading Etymonline's entry for palatable {adj.}, which cites and derives from palate {noun}:

  ... Popularly considered the seat of taste, hence transferred meaning "sense of taste" (late 14c.), which also was in classical Latin. ...

Are the quotes above factually right about mouth anatomy (I ask NOT about language here)? Or was this an outdated wrong idea?

Footnote: Did the etymology become corrupt? I heed the Etymological Fallacy.

Anatomically speaking, the palate is the roof of the mouth, separating the oral cavity (mouth) from the nasal cavity (inner nose). While the palate may be sensitive to heat and spiciness (via the capsaicin receptor, for example), it does not contain any taste buds, which are located on the tongue, and are part of the taste-sensing system. The other part of this system, olfactory receptors, are responsible for sensing odors, and are mainly located in the nasal cavity, as well as partway down the back of the throat.

So, unfortunately, while your palate is figuratively the center of your sense of taste, in reality it has almost nothing to do with it.


Is there a way to prevent an HIV infection after exposure to HIV infected Blood? If a person is accidentally injected with blood from an HIV+ person, is there a treatment option that can keep the person from developing an HIV infection?

The standard protocol for treating a healthcare worker that accidentally comes in contact with HIV infected body fluid is to receive HAART treatment.

HAART is an acronym that stands for Highly Active AntiRetroviral Therapy, and is a multi-drug cocktail that acts on a number of pathways to block the HIV virus from replicating.

There are early inhibitors which seek to block the binding of gp120 to CD4/CCR5.
There are Nucleoside analogs that are able to block the activity of Reverse Transcriptase.
There are Reverse Transcriptase inhibitors that can bind to allosteric sites on the enzyme, thereby effecting its ability to catalyze the reaction which produces the viral cDNA.
There are protease inhibitors which inhibit the viruses ability to make the necessary post-translational modifications, thereby causing the viral proteins to be non-functional, as they are produced from a single, long mRNA transcript.

UPDATED

This is the link to the CDC guidelines from prophylactic treatment for occupational exposure to HIV. http://www.cdc.gov/mmwr/PDF/rr/rr5409.pdf with an update to the guidelines here http://stacks.cdc.gov/view/cdc/20711

After confirmed exposure to HIV infected bodily fluid, it is recommended that HAART begin as soon as possible after exposure, that toxicity be monitored, and that the treatment be continued for 4 weeks.

The recommendations weigh the toxicity of HAART with the HIV status of the person. Even in cases where the status is not known, but the risk factors of the source are low, HAART is often not recommended.

Note that post-infection prophylaxis is less effective than preventing exposure in the first place. That is why barrier protection during intercourse (in the general case), proper handling of sharps, screening of the blood supply, and barrier protection to mucous membrane for healthcare workers is vitally important in preventing an HIV infection from taking hold.

These are the CDC guidelines for Prophylactic treatment from non-occupational exposure. http://www.cdc.gov/mmwr/preview/mmwrhtml/rr5402a1.htm

UPDATE

In the original, unedited question by the OP, they asked

  Yes It is possible to save a person when snake bites him, by sucking the poison from the bite region. so sucking AIDS Virus like snake's poison, will he get cured?

I do not know the answer to this question, nor do I think that there would be any published information regarding the efficacy of trying to suck out HIV infected blood, but given the nature of the virus and how a subcutaneous injection works, I think it is safe to say that it is highly doubtful that attempting to prevent the infection in this way would be an effective treatment option.

Also note, as March Ho stated in the comments, attempting to suck the venom of a snake bite from a wound is an ineffective method of treatment as well.


Cross-species infections I’ve heard that HIV developed from SIV, etc.

I’ve also heard that most species (including most monkeys) can’t get a common cold like humans.

So then what causes infections to be able to travel across species, or vice-versa?

For the sake of the question, I’ll narrow the scope. Let’s say we have a virus that can infect humans but not infect close human relatives, like Chimpanzees. What about that virus biology or animal biology causes that difference?

I know with some animals it’s about body temperature or skin composition, etc. But humans and chimps are physically pretty similar. Is it all about the immune differences?

Viruses evolve alongside their hosts. If you swapped a human chromosome into a chimp cell for the matching chimp chromosome, there would be a lot of genetic similarities but you would also surface a bunch of incompatibilities because the genes on each chromosome have been evolving independently from the rest of the genome.

Viruses interact with their host genome at many stages. First, they need a way to identify their target hosts (cells) in the environment and gain access to the cells. They do this by recognizing markers on the cell surface. For something like HIV, this identification is far more specific than identifying just humans even: they are identifying particular immune cells.

Once inside, viruses interact with the host to express viral genes, produce and assemble new virions, and get transmitted to subsequent hosts. If an incompatibility occurs at any of these stages, the virus won't be able to replicate.

However, because there is a lot of homology across related species, it is feasible for a virus to infect more than one host. If a virus evolves in a context where it commonly infects multiple hosts, there can be selective pressures for it to maintain those abilities across all the hosts. Alternatively, selective pressures might cause the virus to evolve into separate lineages, one infecting ducks and another infecting sparrows, for example.

For a virus that is specific to a certain host (or range of hosts), it is likely that it will have difficulty in another host outside the context in which it evolved. However, there is also variability in viral genomes, and if many viral copies are exposed to a novel host, there is chance that some of them can survive in that host. This will select for those particular viral genes, and subsequent viral generations will be further selected for traits that help replicate in that host.

Immune reactions could also play a role, but in most cases it is the specialization of the viruses themselves that hold the key to host specificity.

Ahlquist, P., Noueiry, A. O., Lee, W. M., Kushner, D. B., & Dye, B. T. (2003). Host factors in positive-strand RNA virus genome replication. Journal of virology, 77(15), 8181-8186.

Hao, L., Sakurai, A., Watanabe, T., Sorensen, E., Nidom, C. A., Newton, M. A., ... & Kawaoka, Y. (2008). Drosophila RNAi screen identifies host genes important for influenza virus replication. Nature, 454(7206), 890.

Schild, G. C., Oxford, J. S., De Jong, J. C., & Webster, R. G. (1983). Evidence for host-cell selection of influenza virus antigenic variants. Nature, 303(5919), 706.