How is the carrying capacity of a logistic growth model calculated? I am reading a book in epidemiology where the carrying capacity for a standard logistic growth rate is given by

K = (b - delta) / gamma

where:

K is the carrying capacity
b is the birth rate
delta is the death rate

but what is gamma?

Thank you

@Remi.b is correct that you haven't given us very much information, but I think we can reconstruct what's going on. Suppose the population growth rate is written out as

$$
\frac{dN}{dt} = N ( b - \delta - \gamma N)
$$

then the equilibrium (carrying capacity) occurs when $N>0$ and $dN/dt=0$, i.e. $b - \delta - \gamma K = 0$.  Solving this for $K$ gives $(b-\delta)/\gamma$ (as you stated).

So what is $\gamma$?  It is the decrease in the per capita growth rate per unit of increase in population density, or more biologically speaking it's the decrease in the birth rate or the increase in the death rate per unit of increase in population density. This could be due to increased competition for resources, or decreased environmental quality, or attraction of predators, or ...

Another, vaguer way to say this would be to call it the "effect of density-dependence".

Given the equations you list in the comments, with a $-\gamma N$ term included in the per capita growth rate for each compartment ($S$, $E$, $I$), we can say more specifically that $\gamma$ determines the rate of density-dependent increase in the ("natural" or disease-independent) death rate per unit population density. This parameter would not typically be broken down into lower-level processes.


How would the human body adjust to sleep times if we were to live in a place with different day lengths? You sleep at night and are active during the day that's how things work for humans, but theoretically if a human whose parents lived on earth were to be born in another planet resembling earth but the difference was that this planet has an 8.5 hour day, what kind of changes will this person undergo?if a human who grew up on earth suddenly had to move to this planet how would his body adapt? what would be the difference between a person who moves to this 8.5 hour day planet with the person that was born there? and would the person who was born on this planet be active for 4.25 hours and then sleep for the other 4.25?

Humans have evolved for 24 hour days and our bodies would not adapt well to this short of sleep/wake cycles (whether or not they were born there, unless they have been there for many generations and have been able to evolve for the new time). Our bodies would still want to spend about the same amount of time sleeping and being awake.

If we tried to adjust our sleep cycles to this planet with 8.5 hour days, we would experience many of the stresses that occur during jet lag (Google Scholar search), which can cause depression. Jet lag is identical to experiencing one day which is shorter or longer than the typical 24 hours.

The sunlight helps set our circadian rhythm, but 8.5 hours would be too fast. I thought I heard for an experiment that used mice that supports this, but I still haven't found the reference yet.

Nbogard referenced the article Plasticity of the Intrinsic Period of the Human Circadian Timing System, which showed that the circadian rhythm in humans can be altered by up to 0.65 hours by the use of lights. This is consistent with what I mentioned that the sunlight helps to set our circadian rhythm.

The best way to adapt would be to use artificial lighting to keep your days about 24 hour days (artificial light during waking hours, heavy curtains during sleeping hours), as mentioned in ThePopMachine's answer.


What is the mechanism of action of lithium-induced polyuria? I was reading in my pharmacology textbook on lithium in treating bipolar disorder, and I was curious to know if there was any specific action lithium takes to produce symptoms such as polyuria and polydipsia. Any help would be great. Also, what is the most common way to monitor lithium levels in the body?

Lithium changes the effect of at least three substances that play a role in diuresis:

aldosterone:  lithium partially inhibits its ability to increase the expression of ENaC receptors on apical membrane thus increasing sodium losses [1].
arginine vasopressin (AVP): because lithium can induce hyperparathyroidism, parathyroid hormone can act as partial agonist to AVP, inhibiting its hydroosmotic action [2].
antidiuretic hormone (ADH): lithium blocks its stimulatory effect on adenilate cyclase. The result is a decrease of cAMP levels in the cells from collecting tubules. cAMP promotes formation of water channels, thus improving absorption from collecting tubules. Because lithium decreases cAMP levels, diuresis is stimulated [1].

All these result in polyuria.

Lithium levels can be determined from the blood. Usually the test should be performed 12 hours after last dose of Lithium [3].

References:

Eleanor Lederer, MD; Lithium Nephropathy on http://emedicine.medscape.com/article/242772-overview#a0104
Carney SL, Ray C, Gillies AH. Mechanism of lithium-induced polyuria in the rat. Kidney Int. 1996 Aug;50(2):377-83.
http://labtestsonline.org/understanding/analytes/lithium/tab/sample/


why can a queen wasp sting many times but a worker bee can only sting once? wasp queen and workers can each sting you several times but a bee can only sting you once. As all of the stings have barbs on them, how can this happen?

It's not true that all stingers have barbs. Wasps, and many other species, don't have barbed stingers, and therefore they can afford to sting you repeatedly without being killed. Worker bees, on the contrary, have a barbed stinger that gets stuck in your skin.

Although wasps have a more powerful venom than bees, with bees usually the venom sack remains attached to the stinger and will keep pumping venom even after the bee itself has run away and died, causing the sting to be more painful. However, because bees died after stinging, they are less likely to sting you compared to wasps, hornets, yellow jackets and bumblebees.


Do females retain oogonia after puberty? Oogonia are the precursors of oocytes in females present during embryonic development. I was wondering whether these stem cells are still present in the ovaria at puberty?

From Developmental Biology, 6th edition I learned the following:

In humans, the oogonia divide to form a limited number of egg precursor cells. In the human embryo, the thousand or so oogonia divide rapidly from the second to the seventh month of gestation to form roughly 7 million germ cells. After the seventh month of embryonic development the number of germ cells drops and most oogonia die during this period, while the remaining oogonia enter the first meiotic division. These latter cells, called the primary oocytes, progress through the first meiotic prophase until the diplotene stage, at which point they are maintained until puberty.

Hence, at puberty the cells from the lineage of oogonia are called primary oocytes. So from a terminological perspective, you are correct that no oogonia are thought to be left at puberty.


What purpose do the opening(s) serve in diapsid and synapsid skulls? Did synapsid skulls evolve from diapsid skulls or vice versa?

Aditionally, do birds have diapsid skulls? The research I have done has yielded some mixed results.

It is believed that originally the holes evolved to give the jaw muscles a place to expand into as they contract. They evolved as the the  otherwise larger jaw muscles are trapped between the bones and cannot contract properly. I say "believe" because the original function is still debated, and it is not something that can be easily tested.

Diapsids likely evolved from early synapsids, however the evidence is tentative at best and it is just as likely that they both evolved independently from anapsids.

Birds are diapsids. However many modern birds have lost the bony partition between the two holes, separating them by cartilage and soft tissue only. Just as some mammals have lost the bony partition between the jaw muscles and the orbit. Additionally in many mammals and birds the expansion of the braincase makes it harder to identify the holes for the laymen as they are pushed down and to the side.


TCGA gene expression data are missing matched normal I'm trying to use the TCGA data portal to get gene expression data for cancer tissues, but I'm not sure what "Tumor matched normal" means.

It is unclear to me if the values are already compared to a control (non cancerous) tissue or there is another sample which gives the healthy tissue values. Assuming it is the latter, I don't see these samples anywhere.

This is a screenshot of my filter

http://www.clipular.com/c/5452873408184320.png?k=rlA9jy3Kb2U47JT7GrXBTzdsln4

And here is a picture of the result (only TNs appear).

The TCGA Project has been collecting primary tumors and matched normals per patient per cancer indication and has been exome (WXS) profiling those samples, and genome (WGS) profiling a subset of them. In those cases, the primary tumor is tissue collected from the primary tumor and the matched normal is usually a blood samples, but could be derived from a buccal swab or some other source. As you can imagine, it would make less sense in terms of expression to assay matched control that derives from another tissue type such as blood.

For the expression data, the majority of the data comes from RNA-Seq and array-based profiling of the primary tumor data, and in some cases where adjacent normal tissue was collected and submitted, the TCGA has also profiled those samples. These are probably what you are seeing with your TN filter, and generally why you are having trouble finding equivalent amounts of matched normals as compared to primary tumor samples for the expression projects.

Incidentally, the company I work for has recently launched a free genomics data portal for the research community called GeenPool Reference. As part of it, we have deposited all of the publicly available TCGA RNA-Seq. The data along with all the associated clinical metadata is readily available for navigating and data mining. You'll easily be able to figure out the quantity of samples, and their matched pairs. If you're interested, you can take a look at the data projects available in GenePool Reference here: http://www.stationxinc.com/reference-library

~Sandeep


Why does uncompetitive inhibition decrease the Michaelis constant? I can't seem to find a good resource online that clearly outlines the difference between an uncompetitive, noncompetitive, and mixed inhibitor (I understand competitive inhibitor though).

More specifically, why does uncompetitive inhibition decrease the Michaelis constant?

From wikipedia:

  This reduction in the effective concentration of the E-S complex increases the enzyme's apparent affinity for the substrate through Le Chatelier's principle (Km is lowered) and decreases the maximum enzyme activity (Vmax), as it takes longer for the substrate or product to leave the active site. Uncompetitive inhibition works best when substrate concentration is high. An uncompetitive inhibitor need not resemble the substrate of the reaction it is inhibiting.

The Lineweaver-Burk Plot:

  By TimVickers - Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=4549560

The uncompetetive inhibitor essentially "locks" the substrate in the enzyme thereby preventing the enzyme from catalyzing the substrate which would then decrease the amount of free enzyme. That should not, however, alter the value of $K_m$ because any copies of the enzyme that are still active ("not locked") maintain the same affinity for the substrate. I applied that same logic to noncompetitive inhibition (no change in $K_m$), hence the confusion.

First off, the difference between the types of inhibition:

competitive inhibition: The inhibitor only binds to the substrate-free form of the enzyme. (Not necessarily at the active site!)
uncompetitive inhibition: The inhibitor only binds to the substrate-bound form of the enzyme.
noncompetitive inhibition: The inhibitor binds equally well to both the substrate-bound and substrate-free forms of the enzyme. (Some people feel this is just a non-special special case of mixed inhibition.)
mixed inhibition: The inhibitor binds to both the substrate-free and substrate bound forms of the enzyme. (But not necessarily with the same affinity.)

Secondly, you need to separate out the concept of binding affinity of the substrate from the concept of $K_m$. The binding affinity of the enzyme towards the substrate is just what you think it is: the equilibrium constant between the bound and unbound forms of the enzyme, in the absence of catalysis and inhibitor.

The $K_m$, on the other hand, is an overall parameter of the rate equation, and doesn't necessarily have a direct relation to substrate binding. The confusion between the two arises from the fact that in simple enzymatic systems, under the simplified conditions we normally study them in, $K_m$ is a pretty decent approximation of the substrate binding affinity. Thus you'll have introductory textbooks saying that "$K_m$ is a measure of substrate affinity". -- a gross oversimplification. They're certainly related, but they're not exactly identical - especially when you get to more complex reaction schemes. Confusing the two leads to problems.

The enzyme inhibition cases are an example of this. Enzyme inhibitors (even competitive ones ones) don't change the intrinsic binding affinity of the free enzyme to substrate. Instead, they draw off some of the enzyme from the productive pathway. Because they change the concentration of particular enzyme species, they change the observed rate equation. How they change the rate equation depends on which enzyme species they change the concentration of.

For a full accounting, you really should look at the derivations of the rate equations, and how the extra equilibria of the inhibitor binding changes things. (e.g. here or here) But for something of an intuitive explanation:

pure noncompetitive inhibition reduces the concentrations of substrate-bound and substrate-free forms equally. (The concentration of product-bound forms being negligible in the standard initial rate equations.) This is basically the same as reducing the total amount of enzyme, i.e. reducing $V_{max}$ or apparent $k_{cat}$.

competitive At saturating substrate concentration, the amount of free enzyme (and thus the effect of inhibition) is negligible. The rate at saturating substrate (i.e. $k_{cat}$) is thus the same. Therefore, it's the apparent $K_m$ that changes. (NOTE! The actual affinity to the substrate isn't changed by the inhibitor. Instead, the inhibitor specifically reduces the amount of free enzyme available, in a way that can be compensated for by higher substrate concentrations. This just so happens to change the rate equation in the same way changing the $K_m$ does.)

uncompetitive At negligible substrate concentrations, the amount of substrate bound enzyme (and the effect of inhibition) is negligible. Thus the rate should be the same with and without the inhibitor. If you recall, the enzymatic reaction rate at negligible substrate is parameterized by $k_{cat}/K_m$. For uncompetitive inhibition, this needs to stay the same. Thus both $k_{cat}$ and $K_m$ need to change in the rate equation, to the same proportion.

mixed - A mixture of the above effects, depending on the relative affinities to the substrate bound/unbound forms of the enzyme.


Are these Gram stain substitutions acceptable? In the context of a Gram stain on a blood smear:

Are the following acceptable substitutions and/or what differences could arise by substituting them?

Using methylene blue instead of crystal violet
Using carbol fuchsin instead of safranine

I've seen text implying they are OK substitutes, but didn't find anything saying the if, why, or problems associated with replacement.

I'm not a biologist.

From a chemist's point of view, these molecules should have similar polarity. Their structure is very similar, actually.

Considering your replacement rule is correct, I would say there wouldn't be much effect other than observing different colors. What is also plausible is that you'd have to reverse the interpretation of your results, e.g. methylene blue stains X, but crystal violet stains Y whereas carbol fuchsin stains Y and safranine stains X.

Was that clear?


Why is full cell/high antigen dose pertussis vaccine dangerous for adults? I do remember that I have read (or heard) somewhere that as a human is older, the whole cell vaccine (and high antigen dose one) has more and more adverse effects.

As it is consistent with the target age group mentioned in the leaflets attached to the vaccines:

whole-cell DTP vaccine (Instytut Biotechnologii Surowic i Szczepionek BIOMED S.A.) is suitable "for children not older then 3 years",
high antigen doseInfanrix-DTPa (GlaxoSmithKline Biologicals S.A.) "shall not be used for children older than 7 years",
low antigen dose Boostrix (GlaxoSmithKline Biologicals S.A.) is "suitable for a person older than 4 years",

I suspect it is true. Unfortunately I lack a reliable source to both confirm that and read more about the effects. Can anyone provide a reference.

As there is a strain of pertussis "resistant" to acellular vaccine, IMHO it would make much more sense to use whole-cell vaccine for adults too.

It seems it is not about pertussis.

I have found information in the Infanrix-DTPa characteristic that it is not recommended for adults due to high dose of diphteria toxoid.

Both Infanrix-DTPa and whole-cell DTP vaccines contain over 30 international units (whatever it is) of diphteria toxoid while Boostrix contains "not less than 2 i.u.".


qrt-pcr and short fragments I plan to measure the effects of Tenofovir a Nucleotide analog reverse-transcriptase inhibitors useing qrt-pcr with HIV-RT as the rt enzyme. Tenofovir causes early termination of the reverse transcriptase by binding to reads preventing the continuation of the chain process rather than stopping the action all together. How will qrt-pcr quantify the low molecular weight short incomplete fragments? I think since the areas complementary to the forward and reverse primers will rarely be on the same continuous double stranded dna expression will be decreased uniformly. Is this correct? Will I need to use absolute qrt-pcr since the changes will be the same for all genes?

You have to design your primers properly. Usually, in real-time PCR, you don't choose a very long product. Ideal product size is 150-300.
Next, see what your NRTI is analogous to. For e.g. if I am using AZT (Azathymidie), I would place my reverse primer at or after the last T.

There are alternate techniques as well. You can use primer extension (radiolabeled) and then quantify different products by scanning the photograph. However, this technique won't be as  quantitative as real-time PCR.


Influence of temperature on protein binding and decay rates For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on the dynamic of biochemical reactions.

Question

In particular, my question is:

How does temperature influences rate of protein binding to a DNA-binding motif?

I am NOT looking for..

I am not looking for a theoretical explanation of how temperature influences this process (I have basic understanding of the importance of the activation energy as displayed on a Maxwell-Boltzman distribution and of the michaelis-menten equation).

I am looking for..

I am looking for a function (eventually expressing the michaelis-menten constant as a function of the temperature) that I can plug in my algorithms to incorporate the influence of various temperatures on the process I want to simulate. I want to simulate the average gene network from an average standard eukaryote. For other purpose, I chose parameter values coming from the yeast. A index such as the $Q_{10}$ would be very useful as well.

Similar already-answered question

A similar question (influence of temperature on transcription rate) has been asked and answered (by @rhill45) here.

Let's do your second one first, you want to find the rate of binding:

Yes you are right you need to calculate for km

I think I found the paper that ties temp into the reaction rate:

statistical approach called response surface methodology (RSM) is used for the prediction of the kinetic constants of glucose oxidase (GOx) as a function of reaction temperature and pH. Lineweaver–Burk transformation of the Michaelis–Menten equation was utilized as the integral part of the RSM algorithm. The effects of variables, namely reciprocal of substrate concentration (0.033–0.5 mM−1), reaction temperature (14.9–40.1 °C) and reaction pH (pH 4.4–8.5) on the reciprocal of initial reaction rate were evaluated and a second order polynomial model was fitted by a central composite circumscribed design (CCCD).

Biochemical Engineering Journal
August 2005, Vol.25(1):55–62, doi:10.1016/j.bej.2005.04.001
A new approach for determination of enzyme kinetic constants using response surface methodology
İsmail Hakkı Boyacı

For the decay

I'm still working on the first I'm suggesting to check this out but need sleep I can read it tomorrow

http://www.eastcoastbio.com/productcart/pc/stability_testing.asp


Is the appendix a vestigial structure in all vertebrates? In humans the Appendix is a vestigial organ. Does it serve no apparent purpose in all the vertebrates that have one?

Smith et al. (2009) provide a survey of the morphology of the cecal appendix. One current hypothesis is that the appendix provides "safe harbor" for symbiotic gut bacteria. Among mammals, there is a vast array of cecal appendices:

In summary:

  A comparative anatomical approach reveals three apparent morphotypes
  of the cecal appendix, as well as appendix-like structures in some
  species that lack a true cecal appendix. Cladistic analyses indicate
  that the appendix has evolved independently at least twice (at least
  once in diprotodont marsupials and at least once in Euarchontoglires),
  shows a highly significant (P < 0.0001) phylogenetic signal in its
  distribution, and has been maintained in mammalian evolution for 80
  million years or longer.


Is there any way bicondylar/bigonial, bizygomatic or bitemporal breadth can change in adults? Without cosmetic surgery or etc., are there any cases/example wherein a human adult has had a change in significance regarding these regions of the face? I have seen many anecdotes where people have asserted that certain things (not surgery) like diets, drugs, or etc. has affected these regions.

Is this possible and what are any such means in which these regions of the face can change?

This isn't a personal medical question as this is widely applicable and generic to any human adult.

Acromegaly (pituitary gigantism) is a disease that causes enlargement of the bones of the face.  There is interest in computerizing facial measurements to catch subtle enlargements and prompt testing for the disease.

https://www.researchgate.net/publication/261409008_Three-dimensional_facial_analysis_in_acromegaly_a_novel_tool_to_quantify_craniofacial_characteristics_after_long-term_remission

  Sixteen patients in remission of acromegaly for over 24 months (50 %
  male, mean age 56.0 ± 10.7 years, mean body mass index 29.3 ± 5.5
  kg/m(2)) were compared to 16 matched control subjects. A 3D cone beam
  computed tomography scan and 3D stereophotograph of each individual
  were acquired and analyzed using 3D cephalometry. In addition to an
  accurate quantification of the classical craniofacial characteristics,
  3D cephalometry, shows that many typical soft tissue deformities
  persist, even after long-term remission. Furthermore, we found that,
  compared to controls, the patients in remission of acromegaly have a
  wider face at the level of the zygoma and longer maxilla (p < 0.05)

Apocryphally, enlarging hat size goes along with acromegaly.

Pagets disease of bone causes enlargement of the skull and also an increase in hat size (so bitemporal dimension); the hat size increase was one of the chara eristics first described in the disease.

Thalassemia is a group of blood diseases characterized by ineffective red blood cell production.  The body compensates by making more marrow anywhere it can.  Some people wind up with expanded bones in the skull or maxilla as a result.

https://www.slideshare.net/ismahharon/thalassemia-is

These are all systemic diseases that affect the bone.  Of course one can have a tumor of bone (primary or metastatic) that expands it and changes the shape of the face or the head.


Do all polygenic traits involve epistasis? Consider the following statement

  All polygenic traits involve epistasis.

I think its true because polygenic traits involve several genes interacting together to result in a certain phenotype and if one of these genes is altered, the resulting phenotype is different.

A polygenic trait is a phenotypic trait for which the variance in the population is explained by two or more loci. Epistasis is a case there is a statistical interaction between several loci on the value of a phenotypic trait.

The several loci underlying a polygenic trait might be purely additive (no interaction) and therefore a polygenic trait does not necessarily involve epistasis.


Structure of adenoids I am not sure this question belongs in biology, but I can't find a more suitable stack exchange site, feel free to delete it if this doesn't fit here.
Also, this question is going to be slightly gross, just a warning, but I promise it comes to a point.
I have read that the adenoids have a texture to them but, unlike say the palatine tonsils, they don't have crypts.
Last year my palatine tonsils became fairly badly infected and had to be removed over the summer. Before the surgery, I discovered I could reach back to the tonsils with my tongue, enabling me to remove the tonsil stones that built up. Gross, I know, but I believe it actually did make the infection noticeably better. After the surgery, and after the area had healed, I resumed discovering the back of my throat and, eventually, up the nasal cavity, all the way to the back of the nasal septum, which means I can reach the Eustachian tubes, adenoids, and posterior nares. If that sounds impossible, I assure you, it is perfectly achievable, and only mildly uncomfortable. With my tongue I can feel the texture of the adenoids but, more toward the posterior nares, this texture changes and resembles folds or crypts like I remember the texture of the palatine tonsils. Three times, always in the morning after waking up, I have discovered debris in this region strongly resembling tonsil stones but green instead of off white. The mucus, however, is always clear.

My question has several parts:

What are these crypts? Are they even crypts at all? Are they part of the adenoids?
Why can I not find mention to these structures in any diagrams or medical articles?
Why can I not find mention to tonsil stone like debris except in the palatine tonsils? I am quite convinced that, if these are not tonsil stones of a sort, they are closely related.

The proportions of diagrams and cross sections of the nasal cavity all seem wildly different. Some of them are just blatantly wrong, depicting, for example, the Eustachian tubes coming from the roof of the nasal cavity instead of the sides. It has been very difficult to find good information on any of this. I am not even sure if I am referring to the region correctly. By nasal cavity, I mean everything between the back of the throat and the posterior nares, although I am aware the nasal cavity includes the region all the way up to the anterior nares as well.
This is the only picture I can find that shows the nasal septum.

This is a better diagram of the rest of the structures. The pharyngeal tonsils are the adenoids.

I'm impressed to stumble upon someone who can do that with his tongue. And mainly because I can do that myself!

Looking at the images and feeling with my tongue, this rugged area you mention is definitely too close to the nose to be the adenoids.

So I googled a bit (well, more like a lot) and I found this cool webpage which details that area.
http://www.theodora.com/anatomy/the_pharynx.html
and I found this snippet of text:

  Above the pharyngeal tonsil, in the middle line, an irregular
  flask-shaped depression of the mucous membrane sometimes extends up as
  far as the basilar process of the occipital bone; it is known as the
  pharyngeal bursa.

I've found stones in my tonsils but never in my adenoids. What I've sometimes found was dried mucus adhered to it when waking up in the morning.
I believe those stones might be rests of food (which can't really get up there).
Maybe this green mucus you found was just dried mucus? Maybe a little infection on a particular day?
I hope you get the answer, since it's passed a quite long time since you asked :)


Do findings on promoter methylation of the serotonin transporter gene and amygdala activity contradict the established view of serotonergic function? In this article http://www.nature.com/neuro/journal/v17/n9/full/nn.3778.html it states that

  Increased promoter methylation of the serotonin transporter gene predicted increased threat related amygdala activity.

I'm finding this somewhat difficult to understand. Increased promoter methylation would imply that the serotonin transporter gene is less expressed, so less serotonin is taken up by the presynaptic neuron, leading to increased serotonin levels in the synaptic cleft. Surely the increased serotonin levels would lead to decreased amygdala response to threat? After all, selective serotonin reputable inhibitors (SSRIs) are used to treat anxiety disorders and depression by reducing uptake of serotonin and increasing serotonin levels as well. It seems like these two are suggesting two contrasting effects for the same cause?

I would be grateful if someone could point out where I have misunderstood. Thank you in advance :)

I don't think there is an obvious contradiction here.

(1) Mapping neuronal function to the perception of threat (or emotions in general) is often advertised as well-understood, but in fact it is not. Serotonin-concentration-based models (such as the monoaminergic theory of depression) are unavoidably imprecise because ”the brain is not soup”. Additionally, it is also impossible with current technology to measure actual serotonergic signalling in vivo with whole-brain comparability (though progress is being made, e.g. via: fMRI contrast-agents and stimulus-evoked opto-fMRI for monoaminergic systems).

(2) Numerous pharmacological interventions which increase signalling at the serotonergic synapse have been documented to cause widely varying effects (compare e.g. monoamine reuptake inhibitors, monoamine release agents, and monoamine receptor agonists). While selective serotonin reuptake inhibitors (SSRIs), such as fluoxetine and citalopram, are commonly reported to decrease anxiety, serotonin receptor agonists, such as LSD, are reported to induce acute anxiety (though interestingly small numbers of LSD administrations, in conjunction with psychotherapy, have also been reported to reduce anxiety in the long term).

The conclusions thus far would be: (1) we can't be entirely sure about how serotonin mediates or counterbalances anxiety (2) but the specific kinetics of activity at the serotonergic synapse seem to be just as relevant as the actual amount of signalling. You may think, however, that the effects of SSRIs are kinetically similar to reduced expression of the serotonin transporter, SERT. This is however not the case, as under SSRI treatment it is generally believed that chronic downregulation of 5-HT1A inhibitory autoreceptors is responsible for the therapeutic effect, rather than the acute increase of serotonin concentration in the synaptic cleft (this being in line with the fact that therapeutic SSRI effects are observed chronically rather than acutely). Further evidence corroborating the notion that constitutively reduced expression of the serotonin transporter increases anxiety can be found from studies on the 5-HTTLPR polymorphism. In these studies the short version of the allele, which leads to reduced expression of SERT, has also been reported (though afaik this effect is not very robust) to correlate with increased activity in the amygdala.


When endothelial cells in blood vessels (arteries or veins) are damaged, does atheroma form first or blood clot? I have learnt from Khan Academy's video on atheresclerosis that when the endothelial cells of an artery are damaged, atheroma forms at the site, and if the atheroma’s fibrous cap is ruptured, thrombogenic material is released from the atheroma, causing a blood clot. Having read other articles on this issue, this phenomenon is known as the atherothrombosis. And I believe that the fact that atheroma is formed before thrombosis is because thrombogenic material isn’t released when endothelial cells are damaged; thus cholesterol deposits in the area to form atheroma first.

However, in another video, when endothelial cells in blood vessels are damaged, platelet activation occurs due to the exposed collagen, and thrombosis occurs. Why is it that blood clotting occurs first instead of atheroma?

I have also learnt from my other question on Biology StackExchange that hypoxemia in the valve pocket of the large veins can cause endothelial damage that triggers the clotting cascade.

Therefore, I am confused as to which of atheroma or blood clot is formed first when endothelial cells are damaged; and if either one is formed first, why is that so? I’m certain that after a blood clot is formed, atheroma won’t be formed as I’ve not found any article that supports this sequence.

References:

https://www.khanacademy.org/science/health-and-medicine/circulatory-system-diseases/coronary-artery-disease/v/atherosclerosis
https://www.youtube.com/watch?v=R8JMfbYW2p4
https://academic.oup.com/eurheartj/article/25/14/1197/509341
How do veins's valve pocket sinus tend to become hypoxic?

It is unlikely that atheroma would develop as a complication of a thrombus.

Atherosclerosis and thrombosis are two independent disorders and not two stages of the same disorder. Atherosclerosis is a disorder of the arterial wall and atheroma develops in the arterial wall. Thrombosis is a disorder of the blood and thrombus is merely attached to the atheroma or arterial or vein wall.

In veins, only thrombosis, but not atherosclerosis can occur, as mentioned here.

In arteries, thrombosis usually occurs only as a complication of an atheroma or calcification (PubMed, 2017):

  The majority of coronary thrombi are caused by plaque rupture
  (55–65%), followed by [plaque] erosions (30–35%), and least frequently
  from calcified nodules (2–7%).

It is very rare that thrombus develops in arteries that have previously not been damaged by atherosclerosis (PubMed, 2015).

Further evidence that thrombus formation is an unlikely initial event in the development of an atherosclerotic plaque:

Thrombosis is not mentioned as an initial stage or risk factor in development of atherosclerosis in various texts: Textbookofcardiology.org, Pathophys.org
Genetic coagulation disorders are not likely risk factors for atherosclerosis (Atherosclerosis, Table 2 (PubMed, 2010):


Why are humans only so tall/large? In biology I've learned that cells rapidly divide and can grow and split undefintely, and that certain parts of the body have to grow and evolve before growing, but I am tied up on the fact that the body produces hormones to have only grow up to a few feet tall and stops growing at a certain age.

Why does it stop in terms of height or physical mass when it can still keep on growing? Why do the hormones tell the body to stop growing when it can continue?

The question is a bit vague but I will take it to mean the following

  Why does it (the body) stop in terms of height or physical mass when it can still keep on growing?

The answer is physics, specifically the ability for a body of a specific shape and structure to support itself and move itself, followed by the energy requirement to feed all those cells.

Strength of a bone scales with its cross sectional area, similar to muscle. Mean while mass scales with its volume. As a result, mass increases faster than bone strength. So the bigger your are, the weaker your bones become if all proportions are maintained. As a result for a certain design of animal there is an upper limit of how big it can become before it unable to support its own weight or able to move.

Next comes energy requirement. In general the more living bio mass you have, the more energy you require to keep it alive. The scaling isn't proportional but there is a general trend. And the more energy required the more food is needed, and given the habitat an animal lives in, there is only so much food around. And this places a limit on how big an animal can grow. An animal living in its niche has an energy budget.

Associated with energy budget, we meet biology and natural selection. Energy placed into growing, isn't energy placed into reproducing. All animals eventually die, either by predator or bad climate (winter, drought, even bad luck) . So it becomes a balance, given the amount of energy available, how much energy should be put into growth to give a more robust structure to survive vs how much energy should be put into reproduction so that the organism can multiply.

Put too much energy into growing bigger, your probability of dying before reproducing increases as you take too much time growing before becoming sexually mature. Put too much energy into reproducing, upon sexual maturity your body is small and weak and your die before you spend much time reproducing.

The ultimate right answer is dependent on the animal's niche, the physical environment around it, its biology, and the predators around it.


How does the human body metabolize gasoline? A Chinese man has been drinking gasoline to relieve his pain for 25 years. How does the human body metabolize gasoline? Also, what are the side-affects to gasoline?

Gasoline toxicity through ingestions seems to be a topic where there's not a great deal of in-depth information available. I don't know how this works for chronic use, as most literature refers to acute scenarios. Either way, orally ingested, 30-50g is said to be toxic to humans while 350g can be fatal.[3].

So...

Gasoline's Constituents

A lot of components that make up gasoline are toxic to humans. This includes for example, benzene, toluene, xylene and butadiene. It's a mixture of more than 500 hydrocarbons and additives made up of:

60–70% alkanes (paraffins)
25–30% aromatics
6–9% alkenes (olefins).[2].

If you really want to know specifics about metabolism of gasoline, you can probably check out how some of the constituents are metabolised (processed) and their effects. This is because different components have varying metabolic pathways.

If you want to check this out, see Reese, et al at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1520023/pdf/envhper00383-0118.pdf.[3].

Ingestion and Toxicity

Apparently, most reported cases of toxicity from gasoline occur from inhalation or absorption through the skin (intravenous use has also been reported). Even though ingestion is a frequent occurrence, there's not much data on outcomes after oral ingestion.[1],[2]. Gasoline can however be well absorbed through the gastrointestinal tract[2].

The main target organ of gasoline toxicity is the nervous system and at high doses, this effect can cause death within minutes.[3]. However, generally, the primary cause of mortality seems to be related to gasoline's toxicity to the lungs. There are severe effects on the pulmonary system. Other effects of ingestion hasn't been as well documented.[1],[2].

It's suggested that these compounds have a direct effect on lung tissue and  disrupts gas exchange and causes fluid buildup in the lungs (pulmonary edema). This in turn causes the oxygen levels in the body to drop (hypoxemia).[2]. There are many other toxic effects on the lungs as well.

Additionally, liver damage, kidney damage, damage to blood cells, gastric ulcers and toxicity in the heart can occur.[2],[3]. Again, this is discussed in Reese, et al.

Hope that helps!

Rahman I. Gasoline ingestion: a rare cause of pancytopenia. Am J Med Sci. 2009. 338(5):433-4.
Domej W. Successful outcome after intravenous gasoline injection. J Med Toxicol. 2007. 3(4):173-7.
Reese, et al. Acute Toxicity of Gasoline and Some Additives. Environmental Health Perspectives. 1993. 115-131.


Could deutrium oxide be used to make organic compounds with Deutrium instead of hydrogen? I am wondering for prokaryotes if Deutrium Oxide could be made into Deutrium Glucose or other biological compounds with Deutrium.

Yes, this is possible and inter alia used to clarify biosynthetic pathways.

For example in this study. Rats were given deuterated water and the average number of D atoms incorporated in cholesterol and fatty acids was determined. Also deuterium was found in plasma glucose and liver lactate and pyruvate.


How do insects survive the winter? I had an interesting discussion today in which the question arose how insects survive in the winter. Since they need a high enough external temperature to be active, this seems a bit difficult in the winter. With frost they should completely freeze and I don't think they will survive this. Do they rely on eggs laid in the fall (which have to survive freezing temperatures as well) or do they employ other techniques for that?

As there are many insects, there are also a number of different strategies. As you already said, insects depend on the temperature of the environment and cannot produce enough heat with their metabolism. The major strategies are:

Migration,
Communal living
Cold tolerance (by means of antifreeze proteins)

Only some of the insects can opt for " Migration" , those which are big enough to travel long distances. A good examples for this migration of insects is the monarch butterfly which migrates from summer habitat in the north-eastern US and southern Canada to Mexico in the fall. Using this strategy the insects avoid live threatening temperatures.

"Communal living" helps insects to get over the winter, as the colony produces enough heat to survive. A prominent example are bees, which maintain relatively high temperatures in their hives, another would be ants.

"Antifreeze proteins" are also employed by a few. Some insects contain special proteins or glycerol in their hemolymph (the equivalent to blood) which either prevents it from freezing and/or prevents the formation of ice crystals which destroy the cells. An example for such an animal would be the New Zealand Mountain Stone Weta which can stay frozen for month until the temperature gets high enough for living again. Some insects go into some kind of winter sleep, in which they survive the cold temperatures. Their living cycle is synchronized with the seasons of the year.

The answer is based on this and this article, have a look for further information and references.


What are the differences between white and brown adipose tissue? What are the differences between white and brown adipose tissue? Here are some that I have come across:

Brown Adipose Tissue                        White Adipose Tissue

Thermogenic                                 Non-thermogenic
Multilocular                                Unilocular
Relatively many mitochondria                Relatively few mitochondria
Vascularised                                Relatively few capillaries
characterized by the presence of leptin     characterized by the presence of UCP-1

Not sure what you are asking, except to add to the list?

Its worth mentioning that brown adipose tissue is the only organ in the human body whose primary purpose is to generate heat.  We are warm blooded, but the body temperature is regulated by other organs generating heat while they do work (like muscles or I suppose the stomach, kidney, etc).

Brown Tissue is supposed to not a juvenile attribute - doesn't show up in adults to the same extent (usually being limited to neck and upper chest.

Brown Tissue is thought to be present in only critical areas of the body - even in infants.  Its found in the inner body cavity around vital organs.

The color comes from the large number of mitochondria in the cells, which is where the heat is generated via uncoupling protein 1 (UCP1).

White adipose tissue is what we more commonly call fat tissue - its primary function is to store energy in the chemical form of long chain fats.  Fat tissue as it grows can inhibit the function of insulin in the body, increasing insulin resistance.

You could almost call them 'good fat' and 'bad fat'


Why is the brain dependent on glucose? The strict dependence of the (human) brain on glucose has always been puzzling to me. While ketones can substitute for a portion of the brain's energy needs, it cannot substitute completely: blood glucose levels below 2--3mM somewhere causes serious neurological problems and can lead to unconsciousness.

Other body tissues are not strictly dependent on glucose, but can oxidize amino acids as well, which is a good backup solution since there is always lots of protein around. But not the brain.

In terms of evolution, this strict glucose dependence must be a major drawback --- falling unconscious just because you don't get enough sugar is probably a bad thing out in the wilderness, when the lions are after you ... So there must be a very important reason.

So why is the brain so dependent on glucose?

I want to present another (possibly more practical) approach towards this phenomenon. Lets begin with amino acids as alternatives.

Amino acids, apart from being a source of toxic ammonia, are also harmful to the brain in another way. The two (concerned) types of amino acids, aromatic and acidic ones, are a lot more than just energy sources for the brain. Aromatic amino acids: tyrosine, phenylalanine and tryptophan, are precursors for the biosynthesis of neurotransmitters like serotonin, melatonin, norepinephrine, dopamine, etc. The greater the amount of precursors, more the product formed. Talking about acidic amino acids, glutamate and aspartate are themselves neurotransmitters. So, same case could apply to them too. So, it might have been that neurons, in evolution, decided to just get rid of such sensitive and powerful energy sources which can disrupt their basic function. You can see Fernstrom, 1994 for a study on this.
Fatty acids are definitely a nice candidate. But they have some side effects too. For a long time, it was thought that since fatty acids (or lipids in general) are attached to albumin while in blood, they cannot cross the blood-brain barrier (see Stryer for example). But, this is not the case, as now proven. Then why are fatty acids not a preferred energy source for brain? There might be quite a few reasons for this.

First, $\beta$-oxidation of fatty acids demands more oxygen as compared to glucose, making neurons more vulnerable to hypoxia. For example, the reaction for complete oxidation of glucose is (from Molecular Cell Biology):

$\ce{C_6H_{12}O_6 + 6 O_2 + 36 ADP^{3-} + 36 P_i^{2-} + 36 H^+ \rightarrow 6 CO_2 + 36 ATP^{4-} + 42 H_2O}$

On the other hand, the reaction for $\beta$-oxidation of palmitic acid is (from pharmaxchange):

$\ce{C_{37}H_{66}N_7O_{17}P_3S (Palmitoyl-coA) + 23 O_2 + 108 P_i^{2-} + 108 ADP^{3-} \rightarrow C_{21}H_{36}N_7O_{16}P_3S (coenzyme-A) + 108 ATP^{4-} + 16 CO_2 + 23 H_2O}$

where palmitic acid is $\ce{C_{16}H_{32}O_2}$. This clearly shows that glucose oxidation requires less oxygen (1 molecule per carbon) as compared to fatty acids (almost 3 molecules per 2 carbon).

Second, nonesterified fatty acids (NEFA) decrease membrane potential at inner mitochondrial membrane, causing collapse of electrochemical proton gradient.
NEFA also interfere with electron transport chain, stimulating generation of reactive oxygen species like superoxide ions (see Zhang et al, 2006 for example).
Apart from this, the rate of ATP generation from fatty acids is slower as compared to glucose, which makes glucose a better option for neurons (see Stryer).

All these factors might have a played a role in making neurons choosy for glucose. This is also supported by the fact that one of the enzymes of $\beta$-oxidation, 3-ketoacyl coenzyme-A thiolase, has significantly lower activity in neurons as compared to other tissues (Yang et al, 1987). You can see Reiser et al, 2013 for a study on this.

PS: It has been shown that the brain can also use lactate along with ketone bodies as an energy source. See Wyss et al, 2011 to know more about this.


Flow Cytometry to learn about Cell cycle I am posting my Flow Cytometry data here again because I realize that there are many people who are willing to help me, and I can learn a lot from you guys.

In this cell culture Lab, we use Cell U-937 Lymphoblast. And we want to learn how can we analyze cell cycle by using flow cytometry.

Could anyone help me to explain how to read the flow cytometry result related with cell cycle? I will be very glad to learn from you guys.

Thanks in advance!

The basis of analysing flow cytometry data in regard to the cell cycle is the fact that DNA synthesis occurs in S-phase and therefore cells before S-Phase (G0/G1) have half the amount of DNA compared to cells after S-phase (G2). [M-phase lasts to short to be of any relevance for this kind of analysis]. Signals that have less DNA than the cells from G0/G1 phase are either artefacts or apoptotic cells with fractured DNA (these are labelled as sub G1).

In order to measure the amount of DNA per cell the dye PI (propidium iodide) is used, since its quantitatively binds to DNA. Therefore the distribution of the PI signal can taken as a distribution of the different stages of the cell cycle.

This wikipedia article also explains the analysis in more detail and provides further references.


Which primates can swim underwater? I saw a documentary awhile back and they were profiling a certain species of monkey which regularly swims underwater. I can't recall which species it was but they said it was rare for primates to do this - diving under the surface, holding ones breath, and swimming completely submerged.

I'm wondering which type of monkey this was and what other primates, besides humans, are known to engage in underwater swimming? Is there a reason this behavior evolved? My guess is that it has to do with foraging for food in mangrove type environments and possibly for avoidance of predators.

The Allen's swamp monkey (Allenopithecus nigroviridis) is also know to live near water-rich areas and they sometimes dive to avoid danger.

Also, it was recently shown that the chimpanzee (Pan troglodytes) and the orangutan (Pongo) can swim, dive and even retrieve items form the bottom of a swimming pool. (source)


What is the specific role of the cerebellum when it comes to 'coordinating movement'? In elementary biology (high school level in the UK - A levels), we are told that the cerebellum is the part of the brain that 'coordinates movement'. Literally nobody takes the time to explain what the word 'coordinates' encompasses. Hence, I do not know the specific role of the cerebellum in coordinating movement.

For example, one very daunting thing that we are told is that the frontal lobe contains the 'primary motor cortex', which supposedly contains motor neurons that connect to the spinal cord and brain stem and can send nerve impulses that enable movement in the body. Where is the distinction between such a role and the role of the cerebellum in 'coordinating movement'?

The principal function of the cerebellum, which was detected years ago, is to calibrate detailed movements rather than initiating movements or deciding which movements to execute (Ghez et al, 1985). This was concluded by observing the changes which occurred after damaging cerebellum. Animals and humans with cerebellar dysfunction show, above all, problems with motor control, on the same side of the body as the damaged part of the cerebellum. They continue to be able to generate motor activity, but it loses precision, producing erratic, uncoordinated, or incorrectly timed movements. Thus, cerebellum helps in coordinating fine-tuned movements and inhibits involuntary movements. Apart from this, fMRI studies have indicated that more than half of the cerebellum is intertwined with association areas (Buckner et al, 2011). But since it is out-of-scope here, I'll leave it at that much.
See it like this:

For a more detailed mechanism and circuitry of the cerebellum, you can have a look at this interactive page from the University of Texas. @FilipeRocha have also come up with some fine details in their answer.

References:

Ghez C, Fahn S (1985). "The cerebellum". In Kandel ER, Schwartz JH. Principles of Neural Science, 2nd edition. New York: Elsevier. pp. 502–522.

Buckner RL, Krienen FM, Castellanos A, Diaz JC, Yeo BT (2011). "The organization of the human cerebellum estimated by intrinsic functional connectivity". J. Neurophysiol. 106 (5): 2322–2345. doi:10.1152/jn.00339.2011.


Why do people feel shame when exposed nakedly? Why do people feel shame? Meaning the kind of shame specifically related to exposing 'private parts'.

Where does it come from (i.e. social factors due to upbringing, inherent in our genes etc.)?
What is its evolutionary purpose?

Probably a cultural effect

In many tribes, people are naked. Also, the naturist movement is very popular in the western culture and they don't feel shame. In northern Europe, it is common to be naked in spas.

I would guess it is mainly a cultural effect and there is little heritability for this trait. I doubt you'll find a study on this particular question, so the best one can do is just to formulate a guess here.

If you don't quite understand why I talk about heritability here, then you should have a look at Why is a heritability coefficient not an index of how “genetic” something is?. In layman terms and in vague terms, I meant that there is probably little role of genes to explain why we feel naked.

Yes, but let's assume it was selected for...

If we were to assume that feeling of shameful in front of nakedness had been selected for, one may hypothesize that it could be due to sexual selection, where rich and wealthy wear clothes. It could also be due the social presssure of showing off what you are worth as sexual body parts are likely under strong sexual selection as well.


Who was the first to coin the terms of soft and hard selection? Soft and hard selection are sometimes used with different definitions. I have been told that at first place hard and soft selection has been defined in the following way:

soft selection: Each deme makes the same contribution to the next generation
hard selection: Different demes make different contribution to the next generation

Who first described these concepts? What was the first paper?

I believe it's Wallace, B. 1968 "Polymorphism, population size,and genetic load" In R. C. Lewontin Population Biology and Evolution. Wallace also discusses his distinction between soft and hard selection in his 1975 paper "Hard and Soft Selection Revisited" (JSTOR link).


probability of having normal daughter If  father has hemophilia, mother is a carrier of the disease, then
  what is the probability of having a normal daughter ?

My question: Should the probability of having a daughter be also multiplied ? Should the answer be 0.5 or should it be 0.25 ?

I can't understand what you mean by "Should the probability of having a daughter be multiplied?" But yes, the probability of having a normal daughter is 0.25, but she will be a carrier like her mother.

Let H represent normal allele for blood clotting (dominant); h represent allele for hemophilia, XY represent the male chromosomes and XX represent the female chromosomes.

Parental Phenotypes :

   Normal female(carrier) x Hemophiliac male

Parental Genotypes (2n) :

   X(H)X(h)         x     X(h)Y

Gametes (n) :

   X(H)     X(h)    x   X(h)     Y

Possible Outcomes :

X(H)X(h) - A normal female, carrier.

X(H)Y    - A normal male.

X(h)X(h) - A hemophiliac female.

X(h)Y    - A hemophiliac male.

So probability of having a normal daughter, that is X(H)X(h) is 0.25.


What is sequential passaging? I have read a journal that describes sequential passaging with the purpose of measuring resistance development in bacteria. I would like to know more about how the method works ie. what does "passage" mean?

https://www.nature.com/nature/journal/v517/n7535/pdf/nature14098.pdf, Methods part, under resistance studies

I am normally reluctant to cite Wikipedia articles, however, the one for Sequential or Serial Passaging explains it quite nicely.

In short:

  In microbiology, sequential or serial passaging refers to the process
  of growing bacteria or viruses in iterations. In essence this means
  that a virus or a strain of bacteria will be isolated and allowed to
  grow for a period of time. After the sample has grown for some time,
  part of it will be transferred to a new environment and allowed to
  grow for the same period of time.This process will be repeated as many
  times as desired. The final product is studied, often in comparison with the original virus or bacterial strain to see whether it has evolved or any other changes have occurred.


Are these statements about the effectiveness of condoms in preventing HIV transmission reconcilable? Can the following statements be reconciled:

Condoms form an essentially impermeable barrier to HIV
Sexual activities other than penetration carry a very low risk of transmission
The consistent use of condoms reduces the risk of HIV transmission to about a fifth of what it would otherwise have been (source: Am Fam Physician. 2004 Oct 1;70(7):1268-1269 as summarized at aafp.org/afp/2004/1001/p1268.html)

Obviously the effectiveness of condoms is going to depend on them being used correctly, but surely they are not used so incorrectly that the effectiveness drops as much as these statements imply - assuming all 3 statements are correct, is there a more plausible explanation?

Note that those three statements are also approximately equivalent to pregnancy risk in the context of vaginal intercourse:

Condoms form an essentially impermeable barrier to sperm
Sexual activities other than penetration carry a very low risk of pregnancy
The use of condoms has an annual failure rate around 15%, i.e. on average 15/100 couples using exclusively condoms will conceive in a year

There are dozens of sources that reconcile these issues, and it all comes down to the failure rate and misuse rate of condoms. Even the source you cite talks about this explicitly, so I'm not sure why you still have a question about it that isn't already answered there.


Can anyone identify this spider? I was hiking and saw this spider in the mouth of a cave in the Ozarks in Arkansas (USA). I believe it is some kind of wolf spider. I have never seen a spider in the wild this large, except for tarantulas in Texas (USA). The approximate size from the tip of back leg to front was 7-8 inches. It was bigger then my hand and I am 6'1" tall man. The spider did not have anything to reference size and did not want get too close, though I am sure it was harmless. I can go back to cave and take same picture holding a ruler to the rock if needed.

I believe my initial guess was off mark. I am thinking this may be a fishing spider. I only say this due to it being on a vertical surface and having banded/striped legs. I have never heard of one attaining this size before. Any info on this spider is greatly appreciated.

looks most like a Meta ovalis with a span of about 10 CM.


Why is graft-vs-host so selective against phylogenetically close cells? Is there a well established explanation for the phenomena that graft-vs-host is so much more selective against phylogenetically close cells? See historically significant references below,
"This type of aggression of the immune system is thus particularly directed against allo-antigens and is much less in evidence across two animals species. “ - Jerne, 1971
"Normal lymphoid cells obtained from animals that are phylogenetically unrelated or only distantly related to the chicken do not initiate graft versus host reactions when introduced into chicken embryos. " - Lafferty, 1968
References
Lafferty, K., & Jones, M. (1969). REACTIONS OF THE GRAFT VERSUS HOST (GVH) TYPE. Australian Journal of Experimental Biology and Medical Science, 47(1), 17–54. https://doi.org/10.1038/icb.1969.3
Jerne, N. K. (1971). The somatic generation of immune recognition. European Journal of Immunology, 1(1), 1–9. https://doi.org/10.1002/eji.1830010102

Since this has gone unanswered, I'll give my best guess. My guess is that closely related MHC* can still be recognized by CD4/CD8 (while not in distant relatives phylogenetically), but, the MHC + eventual bound peptide will not be recognized as self (with or without bound peptide), since its structure may differ even when binding self-antigen peptides that were exposed to T-cells during central tolerance "traning".
I am very intersted in what the established explanation is including references, and invite better answers if there is competence to produce that.
*in the context of the question, i.e., at species level, within species sufficiently close MHC genes are not attacked at all and compatible.
I'll attach potential reference to my guess that ability to recognize MHC as... MHC, decreases with phylogenetic distance,
Vignali, D. A., Moreno, J., Schiller, D., & Hämmerling, G. J. (1992). Species-specific binding of CD4 to the beta 2 domain of major histocompatibility complex class II molecules. Journal of Experimental Medicine, 175(4), 925–932. https://doi.org/10.1084/jem.175.4.925
that references this,
Lamarre, D., Ashkenazi, A., Fleury, S., Smith, D., Sekaly, R., & Capon, D. (1989). The MHC-binding and gp120-binding functions of CD4 are separable. Science, 245(4919), 743–746. https://doi.org/10.1126/science.2549633
that says this,

"although human and mouse CD4 share a high degree of amino acid sequence identity (19), the murine homolog does not bind gpl20 (11) and does not interact with the human class II MHC molecule HLA-DP as assessed by functional and adhesion assays (20). "


How do ants sense imminent rainfall? I have always been told to watch to see if ant-hole mounds are built up as a sign of imminent rainfall.  My questions are,

if what I have always been told is true, then by what mechanism do ants 'sense' the imminent rainfall?  Is it a case of sensing air pressure drop, increasing humidity or both?

This article claims that ants do sense approaching rain and modify their activities in preparation. The claim is not sourced. This weather site also speaks of ant mound-building before a rain but frankly places it in the "some folks say" category. The AntBlog is associated with AntWeb, a large multi-university-affiliated database. The author of the linked blog states that ants can sense humidity with their antennae, which strikes me as a plausible means of anticipating rain.

That ants might sense changes in barometric pressure is an intriguing idea but has not to my knowledge been demonstrated.

A 2010 article in Journal of Neurophysiology reports an almost unbelievable sensitivity to temperature in ant antennae, allowing them in principle to sense minute temperature changes ($0.005^o$C) over a wide range of temperatures and over 0.2 second time intervals (5Hz). This is said to assist them in orientation in their microenvironment but I think it goes a long way to accounting for an ability to detect looming weather fronts. Humans can sometimes 'smell' rain and we can detect gross temperature changes that almost always accompany rain, but to be able to detect humidity and micro-scale temperature changes would give the ants a real advantage in forecasting. After all, not all rainstorms are preceded by a dramatic drop in temperature but probably the majority are preceded by minute step-wise drops in temperature that evidently the ants can sense.

So while I think the building activity may be anecdotal (and probably true for some species) the ability to sense humidity changes and micro-scale temperature changes accounts for their ability to sense rain ahead of time.

Ants are very well-studied and it's hard to rule out that one has missed something. There are a few "ask the expert" questions on this topic online and no one seemed sure.


How does optogenetics work? I am aware of the post here 'Optogenetics - How do microbial opsins work?'
however it is a bit too technical for me. I am struggling to understand how the neurons can be genetically engineered to produce these light-sensitive molecules in optogenetics, and how genetically engineering the neurones is even a usable method considering it seems you would have to genetically engineer the neurons one by one. So I suppose my question is: in the trials run of optogenetics so far (with mice), how where the neurons made to respond to the light stimulus?

Also, I was wondering whether the principle behind optogenetics- controlling calls with light- could be used for other treatments e.g. to kill cancer cells?

My biology knowledge is limited to A-Level (final year of high school), however I really want to understand this topic thoroughly, so detailed but not too technical answers would be much appreciated! Thank you!

EDIT: I just wanted to add two more quick questions...

Are the light-sensitive molecules (which I now have read are channelrhodopsins) present all along the axolemma, or just the membrane of the soma of the neuron? (I hope I used those terms correctly!)
Wikipedia says that these channelrhodopsins are non-specific (with some exceptions: The L132C mutation (CatCh) increases the permeability for calcium and generates very large currents.[17] Mutating E90 to the positively charged amino acid arginine turns channelrhodopsin from an unspecific cation channel into an anion channel. This chloride-conducting channelrhodopsin (ChloC) inhibits neuronal spiking when illuminated with blue light.[18]). How then can these channels work, if any cation can diffuse any way through the channel?

Short answer

Optogenetics can be used to make cells responsive to light. One striking use of this technology is to restore vision in the blind by making the surviving neurons in the retina light-sensitive. This can be done by transfecting the retina with genetically engineered viruses that induce the expression of bacterial channelrhodopsin proteins in retinal neurons.

Background

I will explain optogenetics by focusing on one of the most striking applications: to make the blind see. In humans light is sensed by photoreceptors in the retina (see further reading #2). Rods infer grey-scale vision (i.e., night vision), while cones provide color vision when there is enough light available. Rods and cones contain light-sensitive proteins: the photopigments. The pigment in rod photoreceptors is called rhodopsin, in cones they are referred to as cone pigments, which are used for color vision. When light hits the rods and cones, the photopigments catch the light and activate a cascade of second messenger reactions, eventually causing hyperpolarization of the membrane. This hyperpolarization in turn activates secondary neurons in the retina, which eventually carry the receptor signal to the brain, where it is processed and used to generate a visual percept.

Light sensing across single-celled and multicellelar animals is mediated by two large families of proteins: the opsins. Opsin genes are divided into two distinct superfamilies: microbial opsins (type I) and animal opsins (type II). The rohodpsin and cone pigments found in humans belong to type II. Among other differences, type I opsins are bound to ion channels, while type II is not. Type II opsins therefore need a battery of intracellular second messenger molecules to operate. In contrast, the type I opsins, being channel proteins, directly cause intracellular changes by changing the membrane potential upon activation due to ion flow. Type I opsins, being channel proteins are referred to as channelrhodopsins.

In retinal degenerative diseases such as retinitis pigmentosa (RP) the photoreceptors degenerate and patients eventually loose their vision. The secondary neurons in the retina, however, partly survive. As explained above, these secondary neurons are responsible for processing the photoreceptor signal and sending it to the optic nerve. Hence, although RP patients miss the photoreceptors, the rest of the visual pathway is ready to rock! Hence, somehow these neurons should be activated. There are a battery of approaches to do just this. Retinal implants activate the neurons directly by electrical activation (see further reading #3).

Optogenetics (Fenno et al., 2013) is another approach where the secondary surviving neurons are made photosensitive, thereby bypassing the photoreceptors by turning the secondary neurons into photoreceptors. The neurons are made photosensitive by making them express channelrhodospins. This is done by injecting a viral vector into the eye such that the virus infects the retinal cells. Instead of a viable virus, however, it is tinkered aound with and the only thing the virus does is incorporate the channelrhodopsin into the genome of the neurons, which start to express it.

Channelrhodopsins are cation channels, and therefore, upon light activation, they allow positively charged ions (notably Na+, but also Ca+) into the cell. This depolarizes the neuron and can induce action potential firing (see further reading #1). Action potentials is the neuron way of transmitting signals to the brain. Hence, by activating the secondary neurons through channelrhodopsin transformation, they start sending light-induced neural activity to the brain. The brain will handle this input as if evoked by photoreceptors and hence will interpret it as light-evoked visual stimuli.

With regard to cancer: It has been shown that expression of channelrhodopsin and illumination of whole-mice resulted in diminished subcutaneous cancer cell counts (yang et al., 2013).

With regard to your first added question: dependent on the exact peptide regulatory sequences added to the protein, or by using viral vectors specifically targeting axons, expression of channelrhodopsins can occur wherever one likes.

Your second added question: Cation channels activate neurons, anion channels inhibit them. This means you can play around with different variants to control neurons at will.

References
Fenno et al. Annu Rev Neurosci 2011;34:389–412
Yang et al. Cell death and disease 2013;4:e893

Further reading
 1. Action potentials and neurons: how-do-the-brain-and-nerves-create-electrical-pulses
 2. Photoreceptors: parallels-between-pixelized-image-and-the-human-retina
 3. Retina and retinal implants: does-the-retina-encode-visual-information-like-a-bitmap-or-an-svg


Why is it so hard to find the amount of biotin in food? According to the WHO publications biotin is a thing we need. Although its non toxic, so you can't get too much.

However, excluding a few (small) lists that deal exclusively with biotin content there doesn't generally seem to be any information on how much of it given foods contain. For instance this page gives a very impressive summary of a kiwi, but there is no mention of biotin.

If this is something we need, why is it not normally listed?

Apparently, it's really hard to measure biotin levels in food accurately.

From "Determination of the biotin content of select foods using accurate
and sensitive HPLC/avidin binding" (2004, emphasis added):

  Total biotin content of 87 foods was determined using acid
  hydrolysis and the HPLC/avidin-binding assay. These values are consistent with published values
  in that meat, fish, poultry, egg, dairy, and some vegetables are relatively rich sources of biotin.
  However, these biotin values disagreed substantially with published values for many foods. Assay
  values varied between 247 times greater than published values for a given food to as much as 36%
  less than the published biotin value. Among 51 foods assayed for which published values were
  available, only seven agreed within analytical variability (720%). We conclude that published values
  for biotin content of foods are likely to be inaccurate.


Headshot = instant kill? While whatching a film, I've been thinking about how does a headshot kill someone, and how long does it take?

For example let's say you've beeing shot by a normal (police) handfired weapon - no shotgun or sniper weapon.

I know that the rhombencephalon regulate the most important vital functions like breathing and if the shoot goes throught it, that there will be no change.

Question:
But if the bullet passed the brain throught the telencephalon, which function is mainly thinking, and don't hurt any
brain regions who handles life keeping functions (like the rhombencephalon)  do you die instantly (like in movies) or have any change (fall into a coma)?

According to this article appearing on the website of the American Association of Neurological Surgeons, gunshot injuries to the head are fatal in 90 per cent of cases. Many victims die before reaching the ER, and the 50 per cent who survive the initial trauma die in the ER.


What is the speed of neurotransmitter release and receptor binding in a neuronal synapse? Obviously neural signals travel at extremely high speeds, but I'm wondering how much that speed is affected by the release and binding time of neurotransmitters.

If my sources are correct, a well myelinated axon generates an action potential with a speed of roughly 119.807 m/s. How much does the speed of neurotransmitter release by the presynaptic neuron and binding to the postsynaptic neuron's receptors impact that speed? In other words, I am wondering how much the total speed of a neural signal from one neuron to another is affected by the time it takes for the first neuron to release neurotransmitters and the second neuron to receive the neurotransmitters and propagate an action potential within its own cell.

I assume it takes at least some time, but exactly how much does it slow the signal down?

Thank you for your answers.

It seems to depend on the size of the neurotransmitter. The bigger the neurotransmitter is the longer the neuron has to be stimulated to actually release the neurotransmitter. But in the case of Acetylcholine it seems to need only about 2ms after a presynaptic stimulus to generate a postsynaptic membrane potential and after about 5ms all the Acetylcholine in the synaptic gap is cleaved allowing the postsynaptic cell to repolarize. The example get described here.


How fast do hummingbirds fly? Hhhmz! A hummingbirds flew past me while I was in the garden and yet, it still managed to halt perfectly in front of a blooming flower nearest to me. Just as soon I began to wonder, how fast do hummingbirds fly and in which way do they achieve their flight in addition to their distinctive hum.

Hummingbirds can give the impression by their small body size that they are very fast and of course they are. The Anna-Hummingbird, about ten centimeters in size, reach speeds of 385 body lengths per second (27. 3 m/s or 98 km/h).
So they can get acceleration values of about ten times the acceleration due to gravity.

To the comparison: Peregrine falcons come on speeds of up to 200 body lengths per second in the nosedive and fighter jets, like e. g. the MiG-25 (a Mach 3 fast interceptor), reach only the approximately by 40 times of its total length by one second.

They got this enormous achievement mostly by their biological construction.

For example: the heart of the hummingbird is very large in relation to the body and beats 400 to 500 times per minute, its respiratory rate is up to 250 strokes per minute, so  lots of oxygen gets into their wings and they can perform so strong. During sleep, many hummingbirds reduce their heart rate to save energy.


How to convince suspension cells to adhere more tightly? I'm developing a cell-based assay in 96-well plates that requires adherent cells, as they need to be washed at least twice during the protocol. I'm using in-house strains of HT1080 cells (some overexpressing a certain protein of interest) that unfortunately have been selected for suspension growth in chemically-defined media (50/50 CD-CHO/CD-293). I can convince them to adhere by culturing in DMEM with 10% FBS and growing them in CELLBind flasks, but they still tend to pull away if there is very much shearing force, such as during the wash steps, or when they're in PBS during the assay wash and incubation steps (maybe 2 hours total for now, I'm still optimizing that).

Unfortunately, the parameters of my experiments don't allow me to keep the cells in serum-containing media during the assay, as it would interfere with the uptake of my drug. Like I've said, when in PBS they start detaching, and I would assume the same in HBSS, which I don't really want to use anyway due to its low buffering capacity in CO2 incubators.

Might DMEM alone (without FBS) provide a little more impetus to stay attached during the assay? What would the effect be of increasing the amount of FBS to say 15 or 20% during culturing - would that promote stronger attachment? I'm a little hesitant to coat the wells with poly-D-lysine, as my readout is on a fluorescent imager, and I'm worried it would substantially increase background. I don't really have enough time to re-select the cells for adherent growth (although if I'd known about these issues from my predecessor 3 or 4 months ago I would have started right away...), so are there any other tricks I can try in the meantime? Are there any media supplements I could use to promote adherin expression or something like that? Any tips or advice at all would be appreciated.

My main concern here is why you are using suspension-culture selected cells for an adherent cell-based assay? Is it possible to obtain a clone of adherent HT1080? Depending on what you are assaying with your protein of interest, the cell biology may be altered changing from suspension/adherent culture systems.

Here are my experiences using PC12 cells in culture, which are weakly adherent cells, with a preference to grow in clumps, rather than monolayers. I have found that these cells have a preference for specific tissue plastic; (without mentioning names), these cells will adhere on some poly-D-lysine coated plates while they won't adhere on others. I routinely perform immunofluorescence microscopy with these cells, and grow them on glass cover slips which I have skim-coated with rat tail type I collagen. This coating provides minor background in the green range and only when imaging close to the glass. With a bright fluorophore (e.g., AlexaFluor or cyanin dyes for fixed cell; enhanced GFP for live cells), this backgorund is not a problem for quantitative microscopy.

Lastly, for secretion assays we use high-glucose DMEM supplemented with 1% dialyzed FBS. If memory serves, this retains all serum components less than ~15 kDa, which includes various growth factors. I have observed these cells continue to live for up to one day (and maybe longer?) in supplemented medium, while they die after a few hours without. This may also help with non-specific binding you may be worried about with drug addition.


Is the promoter region of a gene transcribed? If the RNA polymerase attaches to the promoter region of the gene, would it form the initial mRNA portion soon after attachment by reading the promoter region? Or should it slide across the DNA then form the initial mRNA portion?

Also, does the RNA polymerase read DNA base pairs one by one and add the RNA base pairs to the chain one by one? Or, does it read groups of base pairs just like tRNA which reads triplet of bases during translation?

Similarly, is the terminator region transcribed too and then the process of transcription ends, or does the process end immediately after the RNA polymerase reaches the terminator region? How does the process end just by reading the terminator region?

So, should the promoter and terminator region of a gene be considered parts  of the gene or separate entities?

would it form the initial mRNA portion soon after attachment by reading the promoter region?

The RNA Polymerase binds to the promoter, however since it is so large the front end of it hangs off the end of the promoter.  When Transcription begins the promoter is not included, as the transcription process occurs at the front of the polymerase.

  Also, does the RNA polymerase read DNA base pairs one by one and add the RNA base pairs to the chain one by one?

The RNA polymerase adds nucleoside triphosphate (NTP) one by one.  As the picture shows below, there is only room for one NTP in the active site and once the correct NTP is placed it is added to the RNA chain.

  How does the process end just by reading the terminator region?

The question of termination is dependent on the cell.  Prokaryotes terminate in either a Rho independent or dependent process.  Independently, a hairpin occurs in the RNA that breaks off the transcript, dependently, a Rho factor binds that causes termination.  Eukaryotes are less well known, but it is generally believed that after the poly-A site there are also factors that bind and induce termination.

  So, should the promoter and terminator region of a gene be considered parts of the gene or separate entities?

This question is slightly more about definitions that biology.  The Oxford Engligh dictionary defines a gene as "The basic unit of heredity in living organisms".  Since the promoter, non-coding, and non-translating regions are still paramount in getting the protein made, I would argue that they are still part of the gene and the larger hereditary unit.


Are there any benefits/disadvantages/traits from having a permanent lower core temperature? My body temperature as far as I remember has always been around 35.6 degrees Celsius, that's a degree less than what is the usually quoted as the average temperature for humans.
Are there any known correlations such as a shorter/longer average lifespan or pronounced traits such as being more sensitive to warmer temperatures or later/earlier onset of hypothermia symptoms?

Or is it not low at all or low enough to have any noticeable effects.

Yes absolutely. Body temperature is associated with basal metabolic rate which is linked to life-span/body mass. Keeping your body at temperature is responsible for the majority of your caloric burden majority of your caloric burden, and having a lower resting temperature would mean you require fewer calories to survive. Higher body temps are thought to have been a defense against parasite infection, so reductions in body temperature might leave you more susceptible to disease, however a paper came out recently discussing falling body temperature in the US and its implications, and I think it addresses many of your questions in detail in the discussion.
Edit: To elaborate on that elife paper, they've identified a small reduction in average body temperature overtime using military medical records going back to the civil war. They postulate that the reductions they observe are due to improvements in healthcare and a potential decrease in chronic inflammation in the population which increases your body temperature.


How do infectious bacteria determine when their numbers are high enough to attack a host? When you get sick, you generally don't contract enough bacteria at once for them to succeed in battling your immune system, right?  Their numbers must gradually increase in the host's body before they know that they can attack.  How does that work?

I think the current answer to this for bacterial infections is quorum sensing.  Quorum sensing is a signalling pathway in bacteria which senses a molecule that the bacteria themselves secrete.  When the concentration of the quorum signal reaches a certain level, the bacteria interpret this as their population density reaching some threshhold.

Bacteria are always around - even infectious Staph, as described in the other answer, the bacteria are always being cleared out by the immune system, but when they find the right place where they can get critical mass, they dig in, form a biofilm and secrete toxins, which can help them divide more successfully.

This is a description of the process from a paper on Staph infection, a common bacterial infection in humans.

  S. epidermidis is considered part of the of the normal human microbial flora, while S. aureus is usually regarded as a transient member. Colonization by either species usually does not lead to adverse events. However, when these organisms or their extracellular products are allowed to breach the epithelial layer, serious disease can result (1). S. aureus has many cell surface virulence factors (such as protein A and clumping factor) and secreted exotoxins and enzymes that allow strains to cause a myriad of infections. These diseases range from relatively benign furuncles and subcutaneous abscesses to scalded skin syndrome, sepsis, necrotizing pneumonia, and toxic shock syndrome (TSS). While no single cell surface virulence factor has been shown to be uniquely required for mucous membrane attachment, once colonization occurs, numerous secreted exotoxins, including the pyrogenic toxin superantigens and exfoliative toxins, definitively cause serious human disease. Other secreted exotoxins, such as the four hemolysins (α, β, δ, and γ) and Panton-Valentine leukocidin have also been suggested to contribute to significant illnesses. S. epidermidis does not possess the array of extracellular toxins that S. aureus does, and its primary virulence factor is considered to be its ability to form biofilms.

  To improve their ability to cause this variety of human disease and to occupy numerous niches within the host, staphylococci have developed quorum-sensing systems that enable cell-to-cell communication and regulation of numerous colonization and virulence factors.

Viruses are typically simpler - as @MattDMo describes. They seem to rely on finding an environment where they can infect more cells at such a rate greater than the immune system can clear them out.  For influenza, this is more of a 'shock and awe' offense where they infect and multiply quickly, trying to outpace the immune system.  Another virus like HIV will actually multiply so slowly that the immune system can't find the host cells, allowing HIV to slowly spread over the host cell population.

Here's a bonus topic... When they were looking a cholera in the 1990s they found that V cholerae bacteria actually take up phage with toxins in them that convert benign bacteria to virulent ones (that cause dysenteric cholera).  They do this by conveying both the pili that attach to human cells and the toxin that causes the violent G.I. reaction of dysentery.  I think this is not unusual for bacterial diseases.  (the reference is Science 272, 1910-14 BTW).

This has lead to a suspicion that bacteria might be even adapting to infectious phenotypes through genomic changes.  This study had sequenced the genome of C difficile from 486 patients and found that relatively few of them really were capable of patient to patient infection:

  The results of the study indicated that, although transmission between patients is likely to occur, it actually happens at relatively low frequency. In particular, concerns that healthcare teams were spreading infection between different hospitals seem to be misplaced. One exception to this general finding is that there were a large number of cases of infection from one particular strain that does appear to have been due to patient-to-patient transmission, emphasising the epidemic nature of this lineage. Notably, this strain has declined in UK hospitals in the last five years.


What triggers creative thought in humans? Creativity, innovation and ideation. Is there something in the brain that makes the brain think that way, as opposed to "normal baseline". What triggers creative thought in humans?

This is a part answer to your question.

The three-factor anatomical model of human idea generation and creative drive presented in "frontotemporal and dopaminergic control of idea generation and creative drive" (Flaherty, 2005) focus on interactions in and between the temporal lobes, frontal lobes, and the limbic system.

Increase in the quantity of idea generation, at times at the expense of quality is associated with changes in the temporal lobe.  Conversely, frontal lobe deficits may decrease the quantity of ideas generated, largely due to judgements of an idea's worth.  The authors assert that interaction between the two mainly affects verbal and some non-verbal creativity
.
Further,

  Mesolimbic dopamine influences novelty seeking and creative drive. Dopamine agonists and
  antagonists have opposite effects on goal-directed behavior and hallucinations.

The authors emphasise that creative drive is not the same as skill, and that the 3-factor model is an alternative to the left and right brain hemisphere skills based model.


How do colds and flu not infinitely recur? I'm in my third week of university, and a large number of people I know, including myself, still have "fresher's flu", which is probably just a cold and a cough. My lectures are constantly punctuated by the sound of violent coughing. What I don't understand is: how do colds ever go away, given these conditions? Surely by the time you've gotten rid of your cold you've passed it onto someone sitting near you in a lecture, who could then spread it back to you directly or indirectly later? Why don't we have an infinite recursion of colds, coughs and other minor infections throughout the year?

Short answer:
Because your immune system adapts to the virus causing the flu or the common cold and, thus, you become immune to it.

Longer answer:
When B cells first encounter an antigen (usually a protein on the surface of a pathogen), the antigen attaches to a receptor, stimulating the B cells. Some B cells change into memory cells, which remember that specific antigen, and others change into plasma cells. Plasma cells produce antibodies that are specific to the antigen that stimulated their production.
After the first encounter with an antigen, production of enough of the specific antibody takes several days. Thus, the primary immune response is slow and that's the reason you experience the symptoms of the disease.
But thereafter, whenever B cells encounter the antigen again, memory B cells very rapidly recognize the antigen, multiply, change into plasma cells, and produce antibodies. This response is quick and very effective.
This means that, theoretically, you shouldn't be able to become sick twice by the same virus.
However,
virus are very prone to mutations. If these mutations occur in the genes that code for antibody-binding sites, the antibodies produced by B Cells become less effective. This is called Antigenic drift and the reason you might catch the Flu every year (because, with enough time, the virus antigens become different enough to "fool" your immune system).

Also, there are a few explanations why the flu has a seasonal pattern, with a peak usually at winter. One of the theories postulates that in cold weather, people tend to stay indoor, favoring virus transmission.
Recently, an interesting article was published that found that:

transmission of influenza B viruses is enhanced at colder
temperatures, providing an explanation for the seasonality of
influenza epidemics in temperate climates

source


How do plant galls form? I am curious how Gall Wasps, bacteria and other organisms induce galls to form.

Specifically, what chemicals induce gall formation?

I'd like to add to Amy's excellent answer.

Generally, galls are induced by the forced accumulation of plant hormones at different levels to those naturally maintained by the plant, in a localised area. Usually the hormones targeted are auxins and cytokinins which are both involved in the regulation of normal growth patterns; disrupting these patterns leads to disorganised growth, or in some cases a differently organised growth. There are several methods that I know of:

The gall inducer directly synthesising the hormone.
The inducer chemically inducing the host to synthesise more hormone.
The inducer chemically inducing the host to transport more hormone to the site.
The inducer genetically modifying the host to cause synthesis of the hormone in the host cell.

Some examples of the different methods:

Direct production: The bacterium Pseudomonas savastanoi directly produces indole-3-acetic acid (IAA, a type of auxin). This direct accumulation has been shown to be responsible for gall formation in oleander knot disease. Some key papers: Palm et al. 1989, link 1; Glickman et al. 1998, link 2.

Chemical induction of transport: Root-knot nematode worms induce root gall formation in clover. They probably do so by producing flavonoids which up-regulate transportation of auxin into cells (see link 3).

Genetic induction: As already mentioned by Amy, Agrobacterium tumefaciens is a very well characterised example of induction by genetic modification, however, A. tumefaciens is also known to directly produce auxins in large quantities. Another interesting example of genetic modification is in viral gall-inducers. They are not so well studied as their bacterial counterparts, but in some cases (e.g. white clover mosaic potexvirus) it has been shown that virus infection initially leads to a complex change in the types of cytokinins produced by the plant (e.g. Clarke, 1999; see link 4). It has also been shown that if cytokinins are applied exogenously (i.e. injected into the plant) after viral infection, that the virus cannot replicate well. This suggests that the virus is manipulating the host's hormone production in a complex way.

There is also the interesting case of Rhodococcus fascians, which seems to produce a chemical which is not structurally similar to any known cytokinin, and yet has similar effects (Goethals et al., 2001; link 5).

You specifically asked about gall wasps, but unfortunately this mechanism is, as far as I can tell, not completely known. It is speculated (e.g. in Shorthouse & Rohrfritsch, 1992; link 6) that this involves direct injection of phytohormones. The evidence to support this is simply that other insects, particularly aphids, excrete phytohormones in their salivary sheaths when they inject them into a plant.

Finally, I'll just say that the fact that gall induction is carried out by bacteria, viruses, nematodes, fungi and wasps, and that some mechanisms are shared across all those associations,  demonstrates the ability of evolution to converge on the most elegant solution to a problem. It also shows that plants are so great, everyone wants a piece (but I would say that, because I'm a plant biologist).

References:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC209694/
http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI.1998.11.2.156
http://www.publish.csiro.au/?paper=PP98157
http://www.plantphysiol.org/content/120/2/547.full
http://www.annualreviews.org/doi/full/10.1146/annurev.phyto.39.1.27
http://www.nhbs.com/biology_of_insect_induced_galls_tefno_3838.html


How was the first ribosome theorized to have been made? Seeing as ribosomes are what help perform the act of translation itself, and the blueprints for they themselves are in nucleotide sequences, how was the first ribosome theorized to have been made? Also, before there were any ribosome, how was translation theorized to have taken place?

An interesting take on this question is addressed in Bokov and Steinberg's hypothesis.

They have proposed the ribosome has evolved from a short length (~110bp) of RNA that did not have the translational activity that we associate with ribosomes today.

Instead this short length of RNA carried out alternative functions on RNA in RNA based life. Then overtime the accumulation of mutations occurred, such as duplication events that allowed the RNA strands to fold around one another forming a larger unit. This larger unit may have been able to add building blocks together. Over time natural selection will have guided these strands to be more precise in their building actions.

The details of course aren't entirely filled in yet (it's difficult to do because how long ribosomes have been a staple of life), but it's important to take any seemingly complex structure in organisms, and break them down into potentially useful intermediate evolutionary steps.

Some more reading on this subject here -

An article giving a background of Bokov and Steinberg
Bokov and Steinberg's 2009 paper (believe it's paywalled)
Origin and Evolution of the Ribosome (paper)


What is the use of an antibody that is non-neutralizing? When we generally speak of the immune response to viral infections, we talk of neutralising antibodies. These are antibodies that can neutralise the effect of the virus and reduce its load.

My question is, what do the rest of the antibodies produced, which are not neutralising, even do?

Is it a failure of the immune response of the body to produce antibodies that are not neutralising? But isn't binding enough for opsonisation?

How is 'neutralising' even defined? Are such antibodies neutralising just based on binding (since I assume neutralisation assays are in-vitro) or do even these antibodies require downstream antibody effector mechanisms like complement, opsonisation, ADCC etc. for neutralisation?

The term "neutralizing" depends on context. In virology, it generally (not always) means it prevents the virus from binding to its receptor(s) and getting its genetic material inside the now-infected cell. Other antibodies can bind other epitopes besides the sites of binding between capsid and receptor (or enveloping membrane and receptor), yet still contribute to the immune response. Such antibodies are often opsonizing. Still more antibodies are just ineffective, a byproduct of the antibody maturation process.