Hamilton's inclusive fitness approach The underlying intuition of Hamilton's model of inclusive fitness is that we should study social behaviors from the point of view of actors -- rather than the recipients. To build his model, Hamilton expresses the genotype of the actor $j$ in terms of the genotype of the recipient of
the behavior, $i$. The genotype of $j$ is decomposed in two parts,
``genes which are copies by direct replication of genes in $i$; the
other part consists of non-replica genes'' (Hamilton 1970, p. 1219).
Hamilton (1970) further defines $q_{i}$ as the gene frequency of the
replica part, $b_{ij}$ represents the replica fraction, and $q$ is the average gene frequency in the population. From these definitions Hamilton (1970) jumps to the equality:
\begin{equation}
      E (q_{j}) = \frac{1}{1-b_{i}}\left\{ (b_{ij} - b_{i})q_{i} + (1-b_{ij})q\right\}
\end{equation}
where
\begin{align*}
  b_{i} = \frac{1}{n}\sum_{j}b_{ij}
\end{align*}

How did Hamilton derive the above equation?

Here is what I think Hamilton is doing. My impression is that the above equation expresses $E(q_j | q_i)$ as a linear regression on $q_i$. In other words, I think the above equation is equivalent to:

$E(q_j | q_i) = E(q_j) + \beta (q_i - E(q_i))$

$E(q_j | q_i) = q + \beta (q_i - q)$

In fact, this equation is equivalent to Hamilton's equation if the regression coefficient is:

$\beta = (b_{ij} - b_i) / (1 - b_i)$

However, I haven't been able to derive this regression coefficient. Given that $\beta = Cov (q_j, q_i)/Var (q_i)$, I suspect that the way to go is to rewrite $q_j$ and $q_i$ in terms of $b_{ij}$ and $b_i$ and calculate the regression coefficient.

Reference:

Hamilton 1970 "Selfish and Spiteful Behaviour in an Evolutionary Model"
http://www.nature.com/nature/journal/v228/n5277/abs/2281218a0.html

From the limited information, I can provide the following but I am not sure if this is what you are looking for. Also, I still don't see the statement where the author concludes we get the Linear regression model $E(q_i) = Aq_i + C$ which is odd notation since it says the expected value is a linear regression. In fact, if it is a linear regression, it should say $q_j = Aq_i + C$.
$$
A = \frac{\text{cov}(q_i,q_j)}{\text{var}(q_i)}\quad\text{and}\quad C = E[q_j] - \frac{\text{cov}(q_i,q_j)}{\text{var}(q_i)}E[q_i].
$$
Now, we can write the variance and covariance as
\begin{align}
\text{var}(q_i) &= E[q_i^2]-E^2[q_i]\\
\text{cov}(q_i,q_j) &= E[q_iq_j]-E[q_i]E[q_j]
\end{align}
where the expected value of a discrete random variable $X$ is calculated as
$$
E[X] = \sum_{i=1}^Nx_ip_X[x_i]
$$
where $p_X[x_i]$ is probability of $x_i$ and $N$ can be countable infinite.

The mean of conditional PDFs comes up in optimal prediction where the minimum mean square error is $E_{Y\mid X}[Y\mid x]$. This optimal prediction covers linear and nonlinear. For the standard Gaussian PDF, the optimal prediction will be linear since $E_{Y\mid X}[Y\mid x]=\rho x$ where $\rho$ is the correlation coefficient. I am going to short hand $E_{Y\mid X}[Y\mid x]$ to $E[Y\mid x]$
$$
E[Y\mid x] = \mu_Y + \frac{\rho\sigma_Y}{\sigma_X}(x-\mu_X)
$$
where $\mu_i$ $i=X,Y$ is the mean and $\sigma_i$ is the standard deviation. If $X$ and $Y$ are not Gaussian, then the model can be nonlinear. Are there examples of non Gaussian be linear probably.


How does natural selection favour large body mass and size (or so it seems) I was walking through a park this afternoon and observed a few birds having fun flying around and it got me thinking why would natural selection favour birds with flesh at all if it hinders their flight.

We started first with single-cell and micro-organisms flourishing the ponds and then they evolved into massive dinosaurs. It therefore seems, there are some unique reasons for growing to such a large size.

However, I thought it's counter intuitive because the large body slows down locomotion, requires lots of food and energy upkeep, is a big flesh target for predators, makes hiding ineffective.

Although it is obvious that the flesh protects the internal organs, but it seems like a chicken and egg problem because without a massive body, perhaps then there is no need for the internal organs.

On a different perspective, perhaps those animals that evolved without flesh are called plants.

That sums up my naive train of thoughts.

So, any expert can shed some light?

Well first of all I don't know if natural selection favors larger animals - most of the living things in the world are single celled.

Still there are advantages to being larger.  I don't know if I can list them all!  In no particular order:

1) Living things that are large are more metabolically efficient. The amount of food required goes as a 3/4 power of the size of the animal.  Thus a cat 100 times the mass of a mouse requires only 31 times more food.  I don't believe that it is not known how this works.

2) r vs K selection: larger animals have greater individual "value".  Smaller animals tend to live by r-selection - they are cheap and reproduce in large amounts, then lead short and highly competitive lives where most offspring die without reproducing.  Larger animal tend to live longer and reproduce offspring with a greater chance of life. In the extreme case you can compare a cockaroach to an elephant here.  This is not a hard and fas rule, but cheap offspring do tend to be small.

I seem to remember that there are lots of other surveys done and body size correlates to life span and any number of other attributes, which I will try to add after I get some sleep unless someone slips in and lists them all.

3) Cope's rule - an observation as much as a rule that size must convey some advantge because most animals become larger the longer they are around.  Not always true, but there is a trend that the longer evolution works, the more likely a large animal will show up.  This might be because as niches for smaller animals are filled, niches for larger animals become more accessible?


Why doesn't HDL cause diseases like LDL? LDL particles pose a risk for cardiovascular disease when they invade the endothelium and become oxidized, since the oxidized forms are more easily retained by the proteoglycans. A complex set of biochemical reactions regulates the oxidation of LDL particles, chiefly stimulated by presence of necrotic cell debries and free radicals in the endothelium.

Why doesn't HDL cause diseases like LDL ? What's the reason?

Thank you for the fascinating question! It was tough to research but very worthwhile.

LDL is actually not such a bad molecule. It is formed from VLDL/IDL after VLDL/IDL distribute triglycerides, phospholipids, cholesterol and cholesterol esters to peripheral cells. With less to give, LDL subsequently tries to be helpful by providing any needy peripheral cell with leftover cholesterol necessary for plasma membrane synthesis and other cellular functions. In fact, even endothelial cells, which line the vasculature, have LDL receptors to welcome any cholesterol packages from LDL. Another function of LDL is to make HDL even ‘healthier’ by removing cholesteryl ester from HDL molecules in the periphery and returning it to the liver.

Remember that LDL does not contain exactly the same components as its precursors. LDL does not have the ApoE & C proteins that VLDL and IDL have. LDL has only ApoB-100 and a concentrated level of cholesterol. LDL-family receptors generally recognize ApoE and ApoB, which are located on VLDL and IDL, thus easily pulling them into the liver out of the bloodstream, via endocytosis. Because LDL contains only the ApoB protein, it is less easily recognized. Thus, more LDL lingers in the blood. This is supported by the lengths of their half-lives--- with VLDL and IDL half-lives being about 6 hours and LDL half-life being about 3 days.

Where disease comes in is with an imbalance of fat in our diet. This is explained in detail by this extensive article on Managing Dyslipidemia: The Triglyceride/High-Density Lipoprotein Axis. The article explains that disease cannot solely be blamed on LDL alone. A high fat diet leads to elevated triglycerides in the blood stream, which increases blood viscosity, interference with endothelial function, stimulation of arterial inflammation, and interference with normal blood coagulation. These conditions can predispose to atherosclerotic lesions. In addition, there is an up-regulation of protein ApoC-III, which subsequently increases the half-lives of VLDL and IDL particles. It even increases the activity of an enzyme called cholesteryl ester transfer protein (CETP), which can exchange cholesteryl ester in HDL and LDL for triglycerides in VLDL and IDL, and vice versa. This leads to change in composition of HDL and LDL, making them more triglyceride-rich, physically smaller, and less interactive with their respective membrane receptors. With HDL even smaller, it is also easily filtered through the kidneys, leading to lower levels. All this means there is more circulating LDL in the blood.

LDL enters the endothelium via breaks in the endothelial wall created naturally (by dying or dividing cells) or through injury (by inflammatory processes including infections, chemical exposures) or it leaks in through junctions between endothelial cells when there is high intraluminal pressure (such as in hypertension). From there, LDL can become oxidized and ingested by macrophages, forming foam cells, which can rupture spewing its contents into the surrounding arterial wall, leading to the beginning of atherosclerotic lesion.

Why can’t HDL cross through endothelial wall, too? Actually, it can! According to the above-mentioned article, “HDL particles [in its native form] appear to have the potential to delipidate cholesterol from foam cells” at the site of a lesion. With HDL being smaller, it can enter the endothelium to interact with foam cells. Its interaction, however, is the opposite of LDL. Cholesterol is transferred back from the foam cell to HDL, reversing the oxidized LDL-induced process. In addition, “HDL protects LDL from oxidation by [using] metal ions” before oxidized LDL can lead to further damage. This mechanism is still unknown.

Why can’t HDL become oxidized, too? Indeed, this can also happen! However, it appears again than oxidized HDL behaves oppositely to oxidized LDL. “Oxidative tyrosylation of high density lipoprotein by peroxidase enhances cholesterol removal from cultured fibroblasts and macrophage foam cells [5].” There is a caveat though. This function seems to depend on how HDL is oxidized. If oxidized by copper or hypochlorous acid, HDL “loses its ability to remove cholesterol from cultured cells [6].”

In short, given the very same conditions including oxidative environment and entry into the endothelial cell, HDL inherently behaves oppositely to LDL. This likely is related to their inherently different composition, but we have yet to understand how this occurs at a molecular level. However, HDL could technically be 'bad' under the right oxidative conditions. In the end, LDL is given a bad reputation because its relatives IDL/VLDL easily escape into other cells via receptors and HDL concentration is lowered partially by renal filtration.

References:

Mera, Steven L. Understanding Disease: Pathology and Prevention.
http://www.ncbi.nlm.nih.gov/pubmed/19592615
http://www.nature.com/nrmicro/journal/v8/n2/fig_tab/nrmicro2269_F1.html
Libby, P (2006). "Inflammation and cardiovascular disease mechanisms". American Journal of Clinical Nutrition. 83(suppl) (2): 456S–460S. 994471841.
http://www.medscape.org/viewarticle/582014
http://atvb.ahajournals.org/content/23/9/1488.full#ref-16


Could murder be modeled as an infectious disease? Background

  "When swine flu hit the population it spiked in certain areas and
  tapered off in neighboring regions, it hits hardest where people have least protection and this pattern is more pronounced (here)"

Apparently incidences of murder spreads in a similar pattern to infectious diseases such as swine flu according to a 26-year study of the city of Newark, New Jersey (summary).

Questions

It would be interesting to hear your opinions, but some interesting questions I would like to ask are:

To what extent could murder and the epidemiology infectious disease
patterns resemble each other?
What factors could you suggest may lead to their apparent
similarities?
Given that murder could be modeled as an infectious disease could we
apply epidemiological interventions to murder?

Disclaimer: I'm an infectious disease modeler, and generally pretty skeptical of "We modeled X like an outbreak!" claims, because many are just an exercise in curve fitting.

Given that, the answer is both "Yes" and "No".

"No": Murder as an act really isn't transmissible, and if its not transmissible, it can't be modeled as an infectious disease.

"Yes": It is probably possible to model some things in the same way we model infectious diseases, because the underlying causes of murder may be somewhat 'transmissible'. Certain behaviors, cascading effects (if one family member is incarcerated it increases the likelihood that other members of that family will be incarcerated) etc. might give crime "disease-like" properties.

That's probably largely driven by underlying social networks and the like, which are also important to infectious diseases. But then you have a problem in reasoning. For example, did murder "spread" along a social network, or did we merely sample a group of people with a shared underlying cause (for example, poverty, membership in gangs, etc.)

It's probably useful to model some of these things, but it's more useful, in my mind, to model them as their own process, rather than trying to shoehorn them into being like a disease.


Why do most organisms depend on water? Most organisms depend on water for metabolisms. Even the higher organisms need to maintain their daily water intake.
Why water and not something else (for example like H2S)?
I know H2S is poisonous for our body but isn't that just because our body is not compatible with it?
Is there a possibility that we could have been compatible with H2S and not H2O?
What are the factors that prevent this?

One source says,

  Reactions cannot happen without water molecules.

It's not the most impressive source, but here's another source that has the same theme, with more details:

Cosmo Quest Forums

  The water molecule forms non-covalent bondings. It is bipolar and
  easily 'gets inbetween' other molecules which want to marry by charing
  their electrons more permanently. This makes water a great dating site
  where for example aminoacids quickly can try out their fit to many
  different parts of an RNA molecule. If they don't make good enough
  covalent bondings, water will immediately be there to separate them
  until the next one comes along for a try.

  Methane (on Titan) is as liquid as water and does transport stuff
  around. But it lacks the ability to interfer with how other molecules
  bond. Biochemical processes would be much slower in methane liquid
  than in liquid water.

Water is also a fabulous solvent; so many things can be dissolved in it. As others have mentioned, the simple abundance of water in the universe may be a factor.

However, I don't know anything about H2S' bonding ability or its power as a solvent.


Can I estimate leaf temperature from air temperature? What other information would be required? Physiological measurements such as respiration rate and assimilation rate depend on temperature.

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

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

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

My model is:

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

And I currently assume X = 0 in my calculations

Is there a better way to estimate X?

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

One way to do this is to use the "humid operative temperature" equation, or something similar. A variant of this equation, specifically for estimating leaf temperature, is derived using a leaf energy balance equation in chapter 14.1 of the Environmental Biophysics book (cited below).

I'll let you look up the actual equation since I'm not sure how to do math symbols here. But, in addition to air temperature, you will need to know a few pieces of information:

Vapor pressure deficit - calculated from humidity and temperature.
Incoming radiation - Measured, or you could model this using time of day, latitude, etc.
Emissivity of your leaves - you can probably look this up for your species or a similar one.
Windspeed
Characteristic dimension of leaves - measure, or look up a value for your species (Use this with windspeed to calculate boundary layer heat conductance).
Leaf vapor conductance - a combination of stomatal and boundary layer conductance to water vapor. You must know something about where the stomata are on your leaf (both sides or one side), but you can often look this value up for a given species.
A few other constants that are easy to look up.

That's about it - its a somewhat hairy calculation, but if you have standard weather data and a little knowledge of the plants you are estimating the leaf temperature of, it should be manageable.

This equation and other relevant info are in this book:

Campbell, G.S. and Norman, J.M. An Introduction to Environmental Biophysics. Springer Science, 1998


Killing enveloped viruses with soap Unlike non-enveloped viruses, enveloped viruses can be killed with soap, alcohol, etc. Why?

Why does just having an envelope make it susceptible to soap and alcohol?

Soap molecules are amphiphilic. This means they have parts which are hydrophilic (water-loving, or "polar") and parts which are hydrophobic (water-avoiding, or "non-polar").
Fat molecules are non-polar. They avoid water. This is why a mixture of oil and water will separate into layers. In this mix, oil molecules prefer to hang around other oil molecules, and water molecules prefer to hang around other water molecules. Soap "likes" both oil and water, so it can be used for cleaning, by helping dissolve this mixture. (For a similar reason, this is why vinegar is used to dissolve or emulsify oil in salad dressings.)
The coat of an enveloped virus is made up of layer of phospholipid molecules and proteins. Phospholipid molecules are similar to detergents, made up of polar and non-polar ends. These lipids arrange themselves into a two-layered sandwich called a "bilayer". The polar ends of this sandwich are the "bread", while the fatty non-polar ends are the "filling".
Detergents can help disturb this by pulling or dissolving out phospholipids from the virus coat to form micelles, tiny bubbles of fat and soap that can be washed away. This puts holes in the virus coat and helps dissolve it.
The insides of the enveloped virus particle cannot infect directly and must rely on its envelope to get into and infect a cell, so breaking down the coat inactivates (or "kills") the virus.
Alcohols are also amphiphilic. There are many different alcohols, but they all have a hydroxy group at one end, which is polar, and a saturated or partially-saturated carbon chain on the other end, which is non-polar. Like detergents, this property allows an alcohol — at a sufficient concentration — to disturb and break down the virus envelope phospholipid bilayer, inactivating it.
Non-enveloped viruses lack this phospholipid bilayer coating and are instead protected by a protein capsid. The proteins in a capsid will not dissolve with detergents, but they can be attacked with other disinfectants that chemically denature the proteins. Examples of such disinfectants are chlorine (bleach), iodine, peroxides, etc.
Just as soap can put holes into the phospholipid coating around enveloped viruses, destabilizing them, denaturing agents change the structure of proteins that protect non-enveloped viruses, also destabilizing the capsid. If the capsid proteins are damaged sufficiently, the virus particle is not able to infect a cell and so is deactivated.


Did the eclipse make the leaves fall? I live in Pittsburgh PA, the eclipse on Monday August 21 was only about 80% coverage here.  It was notably darker, but less dark then an overcast day. The night of August 21, had a low temp of about 70F.  On my daily walk the following day (Aug 22) there was notable amount of fallen leaves from the trees along my daily walk (mostly maple), by this morning (Wednesday Aug 23) the leaf fall has increased such that the grounds crews are out cleaning the leaves.

Did the eclipse make the leaves fall?

What said by ebrohman is correct. In fact there are two factor that led to leaves falling when fall approaching: photoperiod and the circadian rhythm (24 hours) of the plant.
In the circadian rhythm is possible observe oscillation in proteins expression. Some of the proteins that regulate leaves abscission (aka falling) have an oscillations in their expression and present a pic of the expression in the late afternoon. Moreover to be active this protein need to be on "a dark" condition because the light will lead to proteins degradation.

For exemple

Imagine that in summer there is a long day condition with sunlight present from 7am until 20am (photoperiod) and that the proteins that lead to leaves abscission is expressed by the plant around 6pm (circadian rhythm). Due the presence of the sunlight the proteins will be degrade.
When the hour of sunlight decrease (with fall approaching) the proteins is day by day less degraded and this could led to the plant to prepare itself for the winter, also with the leaves abscission.

If you are interested to know more about the argument I can suggest you an interesting review write by Pin and Nilsson (2012)

Cold
Is possible that a decrease in the temperature lead to a leaves falling. However I think that temperature has to decrease significantly over more day to allow any changes in plants structure.

I hope that my answer could help, if you do not understand something let me know. I will try to explain it in a different way.


Is there a short-term, very strong anesthetic, which can be blocked/delayed by other substances? Question migrated from World Building SE.

(For fictional use only, of course :) )

I am looking for an anasthetic which fulfills the following criteria:

very strong effect, induces a comatose state in a very short period of time
quickly wears off (30 minutes~) with only minor impediments to the recipent upon awakening.
Can be 'partially blocked' or delayed by the intake of some medicine or other substance (which needs to be not too uncommon). Maybe some receptors for the anasthetic are blocked by the substance or something similar. Ideally this would result in the recipent falling into a dream-like state for some minutes before the real effect kicks in.

Does the anasthetic have to be made up, or does something like this actually exist?

Xenon. It is like an ideal anaesthetic. See here.

  Xenon is an interesting anesthetic as it appears to lack negative
  inotropicy and vasodilatation, giving great advantages to both
  patients with limited cardiovascular reserve or those who require
  hemodynamic stability. It has low toxicity and is not teratogenic.
  Xenon gives rapid induction and recovery, due to its low blood/gas
  partition coefficient (0.15), and has a MAC of 63%. Several vitro
  studies showed that Xenon may protect neural cells against ischaemic
  injury. Its low blood solubility can take to diffusion hypoxia if
  Xenon is not substituted by 100% oxygen at the end of anesthesia. It
  has been shown that, compared to other anesthetic regimens, Xenon
  anesthesia produces the highest regional blood flow in the brain,
  liver, kidney and intestine. In conclusion, the most important
  positive effects of Xenon are cardiovascular stability, cerebral
  protection and favourable pharmacokinetics. Negative points are high
  cost and the limited number of ventilators supplying Xenon.


Sodium hydroxide grade in library denaturation for NGS If the NaOH, 1N which I bought does not have the label of molecular biology grade can it be used safely for library denaturation in NGS? Thank you!

The "molecular biology grade" is just a gimmick in many situations. The reagent grade NaOH is quite pure (≥98%). The usual impurities (major being Na2CO3; ~1%) are also chemically insignificant (See the Sigma-Aldrich products 1 and 2). For the product that you have, read the label for details. It should be more or less the same.

Just prepare your solution in MilliQ water and pass it through a 0.2µm filter.


What kind of spider is this and is it dangerous? Found this spider on my couch the other day in Steubenville, Ohio. The spider is about 1 - 1.5'' (2.5 - 4 cm) long. The spider looks brownish in the image, but tends to a pale yellow color in reality.

That's a nice female Nursery Web Spider, related to the Fishing Spiders.  They're rather pretty animals, and like almost all spiders, quite harmless to anything that's too big to eat.  The very rectangular cephalothorax ('head' end) pattern and the simple wavy line down the abdomen are the key clues for this one.  They also like to sit with the front legs arranged in pairs.
https://bugguide.net/node/view/2919/bgimage


Identifying a thin, black, worm-like creature with a hammer-shaped head I came across the creature shown in the photo below yesterday evening while walking the dogs. At first, I thought it was an earthworm, but a flashlight revealed it to be something I had never seen before.

It is approximately 12 inches (300 mm) in length and about 1/3 of an inch (10 mm) in diameter at its maximum. It is pitch black and very shiny—like piano black. It moves very slowly, using a snake-like motion. It had a very strange head, like a hammerhead shark.

I live in Durban, South Africa, if that helps to narrow down the possibilities.

Can anyone help in identifying this creature?

Hmm, I don't believe I have ever seen that before, but it looks  like a Hammerhead Worm (Bipalium kewense).


What happens if nerve impulses go the wrong way? So in nerve impulses, I get that the refractory period is important because it stops the action potentials going the wrong way along the axon. I have two questions:

What would the impact be of the action potential going the wrong way along the axon?
Are there any diseases that maybe cause the refractory period to be shortened so that the action potential goes the wrong way?

Thanks for any help!

The propagation of the action potential is MUCH slower than the refractory period. The propagation speed is determined by the cable equation http://www.cnbc.cmu.edu/~bard/passive2/node9.html which is a formalism developed by Hodgkin & Huxley in the 1930s to measure signal transmission through a biological cable (e.g. an axon). The speed of the propagation is measured by a constant. The voltage does decay and thus spread in all directions, but the propagation only matters towards the direction of signal transmission. Ionic action in the soma would destroy the usefulness of transmission not down the axon. With that being said, neurites in arthropod nervous systems for instance http://stg.rutgers.edu/ can receive input and deliver output leading to very complicated patterns of waves inwards and outwards. Despite this, the stomatogastric ganglion can produce very robust and stable rhythmic neural patterns.


poor RNA quality from zebrafish embryos Does anyone routinely do RNA isolation from zebrafish embryos?

I have embryos from different stages but all below 24hpf. This is the protocol I follow:

Take 10-20 embryos
Wash once with milliQ water
Treat with 1mg/ml Proteinase-K (5min with gentle shaking) to dechorionate
Wash again with milliQ water
Remove water and add 250 µl Trizol
Homogenize by pippeting
add 750µl more of trizol
Do the standard trizol extraction step (with chlorofom)
Take the aqueous phase and wash again with 200µl chloroform
Precipitate RNA with isopropanol
Wash thrice with 70% ethanol
dissolve in nuclease free water

Despite all this I get a poor A260/A230 : ~0.4

Moreover, this happens consistently in all samples. The RNA bands look fine on the gel.

I have done RNA isolation many times from cell lines and tissues and never faced this problem. Is this common with zebrafish embryos? Is there a way to fix this other than by using kits?

Usually I had no problems with RNA extractions - from various cultured cells as well as a number of different tissues from mouse. If I look at your protocol this is pretty much the same as the one we used or the one recommended here for zebrafish embryo. This protocol "Purification of RNA Using TRIzol (TRI Reagent)" seems also interesting.

What can happen is a contamination by phenol or carbohydrates, then we usually used the protocol below to clean up the sample. You can also use column based methods, but they are more expensive.

add 1/10 vol of NH4OAc (5M), 2.5 volume 100% cold EtOH (100%) and 10µg
glycogen (for total RNA we usually didn't use any co-precipitation
agents) and mix well
incubate 30 min at -80°C
centrifuge 20 min at 12000g at 4°C and remove the supernatant
wash with 75% ice cold EtOH
centrifuge 5 min at 12000 g at 4°C and remove supernatant
Re-suspend the pellet in RNAse free water (can take some time)


Evolution- Variations, adaptations and selective advantages I am trying to understand Variations, adaptations and selective advantages  and how they are all related.
Feel free to add or correct me if I'm wrong- Variations are structural, functional, or physiological differences between individual's within a species that result from mutations.  If the variation provides a selective advantage (genetic advantage) the organism's chances of survival in terms of both survival in a changing environment and reproduction increases. The variation is then considered an adaptation. So basically adaptations are variations which provide a genetic advantage and give some organisms within a species a better chance of survival than those without the adaptations. This survival advantage allows those organisms to reproduce and pass on their adaptation more frequently than those who do not possess these adaptations.

I would define variation as something a little less specific. When talking about evolution I would consider it to mean any phenotypic variation that exists. I say phenotype because that is what selection "sees" but there can be genetic variation without phenotypic variation (see synonymous mutations). The trait could be physiological, morphological, behavioral or a life history trait (a trait which, all else remaining constant, affects fitness e.g. Lifespan or development time). This is also not necessarily just within species too, comparing homologous trait between two species could reveal between-species variation. For example, in one species every individual might day at exactly 100 days old, in another it may be 102 days, there is no variance within species but there is variance between. The phenotypic variation can be a result of genotype, environment, or a genotype-environment interaction.
If a trait positively affects fitness it is an adaptation, it is a trait that offers some kind of benefit over other current or previous incarnations of the trait. The variance for that trait can be zero - a highly adaptive trait is likely to spread rapidly and variation for that trait would zero if it was entirely genetically defined and fixed in the population but that trait would still be considered an adaptation. I would define fitness as the lifetime reproductive success of your evolutionary unit, commonly thought to be the gene. If a variant of a trait increases relative fitness it provides a selective advantage, and any genes (alleles) causing that trait should spread through the population at the expense of other alleles.
It is important to remember that not every biologist will define these in the same way, there is some debate about definitions in biology.


How does the brain train its neural network? One question that came up learning how artificial neural networks are working was how the brain can train its neural network?

When we say we have an artificial neural network, the problem behind it is a typical, but uncommon minimizing problem. The math behind it is logical and pretty easy. But it's math, so an computer can calculate it by doing millions of iterations. But the brain can't do that (I would be surprised)

So, how does the brain solve this task. Trial & Error, we don't know or is there an even more complex system behind it?

Thanks in advance.
GA

The answer to this question is probably Hebbian Learning.

Hebbian learning can be nicely summarised with "Cells that fire together, wire together". So basically the synapses of neurons are strengthened if they fire in sync, and weakened otherwise.

One can easily see that a) this kind of local learning mechanism makes a lot more sense for the brain then some global method like gradient descent and b) this mechanism leads to stable representations of patterns.

In artificial neural networks this kind of learning is modelled in Hopfield networks and Restricted Boltzmann Machines.

Of course this simple rule barely scratches at the surface of what goes on in the human brain, when we are learning something. A complete picture would probably involve complex feedback mechanisms of inhibitory and excitatory connections between neurons, functional modules of neurons, and different parts of the brain.

But I fear these details are not yet well understood …


importance of cDNA sequencing of a specific gene in different plants i want to know what if i made a sequence of cDNA of a specific gene in different plants - what is the important from the sequence and can if found difference between plants , and can i use this sequence to determine cis regulating element

No, cDNAs are copies of spliced mRNAs, and typically contain a 5'-UTR (untranslated region), an open reading frame, or ORF, and a 3'-UTR.
The cis-regulatory information might be revealed by sequencing the genomic DNA upstream of the gene(s).  That is where one usually finds the promoter (although there are some rare exceptions, particularly for genes transcribed by RNA polymerase III).


B Cell Differentiation During the differentiation of B cells in bone marrow, recombination occurs in light chain and heavy chain genes to produce a single type of functional gene which determines the type of light chain and the heavy chain produced by that B cell.
Therefore, a single B cell and its generation displays a single type of antigen receptor on its cell surface.

My question is-
Recombination will occur in both the copies of the light chain gene present on the homologous chromosomes (same with the heavy chain gene).

So, the combination produced on the homologous chromosomes should be different.
Is it really so?  And if not, then how come they are identical?

There is a mechanism in T and B cells called allelic exclusion. This means that most of the times only a single allele is used by building the light chain and the other is excluded. Incomplete allelic exclusion may contribute to auto-immune diseases, because cells using two different light chains can potentially recognize both pathogens and healthy human cells1,2,3,4,5,6,7,8.


In Darwinian evolutionary theory, does the environment has any role? In Darwinian evolutionary theory, does the environment has any role?

To state it clearly:

Suppose I have an isolated system. First, I place several types of entities (organisms) in an environment. According to Darwin, eventually, the fittest will survive.

Next time, I place Only one organism. Will it survive this time as there's no one else in the system?
If not, did Darwin also consider the whole environment as another entity, so that in the above case, there are two entities, the organism and the environment. The environment is more evolved and it survives, other dies?

Moreover, if the climate is favourable and the organism reproduces sexually results in the same fate as the case if climate is unfavourable, organism reproduces asexually, what conclusion does it leads to?

"According to Darwin, eventually, the fittest will survive"

Darwin never said this. Fitness and survival are two separate concepts.

In a simplistic version, fitness is measured by reproductive output. Survival is, well, survival. You can have higher output than your brother, but have a lower chance survival. In fact, the very act of producing offspring can negatively affect your ability to survive.

No, the environment is not an other organism, in any context. It is the place (stage, arena, etc) in which the measure of fitness (reproductive output) can be measured. The environment can directly influence and affect fitness, and other organisms (inter and intraspecific) ARE part of that environment.

A single isolated organism does not evolve, but can have offspring. However, you need a more than one organism for fitness to have any meaning in a Darwinian model.


What are these Cocoons/Seeds? I have found these thingies in my institute at Tiruchchirapalli in India. I have no idea what they are:

Can someone tell me what they are, exactly?

They look like seeds from palm trees. It reminds me of seeds from Phoenix canariensis which I once planted. However, since this particular species is not native to India, they could be seeds from another Phoenix palm species. Do you have Phoenix palm species in your area in India?


Are vacuum centrifuges the same as normal centrifuges? I came across a method that used a vacuum centrifuge:

Carvalho et al. 2012. The diversity, antimicrobial and anticancer activity of endophytic fungi associated with the medicinal plant Stryphnodendron adstringens (Mart.) Coville (Fabaceae) from the Brazilian savannah. Symbiosis 57(2):95-107

  Five-millimetre-diameter plugs of each filamentous endophytic fungus were inoculated into the centres of Petri dishes (60 mm diameter, 20 ml PDA). The plates were incubated at 25±2 °C for 15 days. The culture materials from each Petri dish were cut and transferred to 50-ml vial tubes containing 35 ml of ethanol (PA, ≥99.8 %, Vetec, Brazil). After 48 h at 10°C, the organic phase was decanted and the solvent was removed under a vacuum centrifuge at 35°C

I couldn't find information online as to whether a vacuum centrifuge is the same as a normal centrifuge. Is there a difference?

A "normal" centrifuge = piece of laboratory equipment, driven by a motor, which spins liquid samples at high speed to allow centripetal acceleration to separate substances of greater and lesser density.

Without further information regarding the method you read, a "vacuum" centrifuge might be a reference to one of the following:

Ultracentrifuge

a centrifuge optimized for spinning a rotor at very high speeds.

  The vacuum ultracentrifuge was invented by Edward Greydon Pickels in the Physics Department at the University of Virginia. It was his contribution of the vacuum which allowed a reduction in friction generated at high speeds. Vacuum systems also enabled the maintenance of constant temperature across the sample, eliminating convection currents that interfered with the interpretation of sedimentation results

Centrifugal evaporator

device used in chemical and biochemical laboratories for the efficient and gentle evaporation of solvents from many samples at the same time.

  The system works by lowering the pressure in the centrifuge system [via a vacuum pump] - as the pressure drops so does the boiling point of the solvent(s) in the system.

  The centrifugal force generated by spinning the centrifuge rotor creates a pressure gradient within the solvent contained in the tubes or vials, this means that the samples boil from the top down, helping to prevent "bumping".

"Vacuum Concentrators"

  Use a combination of centrifugal force, vacuum and heat to speed evaporation of multiple small samples. They offer maximum throughput required by biology, microbiology, biochemistry, pharmaceutical research and analytical chemistry laboratories

UPDATE: Based on updated info from the OP quoting the method of the paper, it sounds like they're most likely talking about using a centrifugal evaporator to remove solvent.


What causes the pain when a bone fracture is healing? Why does a fracture still hurts when it is healing? I understand the pain at the beginning - the bone is not in its place, there is a pressure against the nerves, also the swelling pushes the nerves etc. But why does it still hurt after several weeks, when the swelling is gone, the bone is more or less fixed? Is the cause of the pain mechanical, or chemical?

At the initial phases of the healing the broken ends are mobile (and this is time when it can be set and put into a cast).

At later stages soft callus than hard callus forms and now any movement will pull on the broken ends and stimulate the nerve endings: it hurts.

This also has the effect that the nearby muscles will spasm in an attempt to immobilize the bone. Another source of the pain can be that these muscles become tired and start to hurt as well.

The pain will continue until the two broken ends are completely welded together so there is no longer any movement that would stimulate those nerves.


Is anaerobic activity during ketosis possible? When a person's glucose and glycogen stores are depleted, which can occur due to fasting or due to a diet consisting largely of fat (like eskimo diets), the body produces its energy by breaking down triglycerides into fatty acids.  Fatty acids can be then converted to Acetyl-CoA, which can consequently enter the citric acid cycle, generating ATP.*

Now normally when a cell does not receive sufficient oxygen to undergo its natural processes, it usually breaks down glucose anaerobically to generate ATP and lactic acid.  However, in the case where the body is running off fatty acids (e.g. fast, or fat/protein only diet), how does the body respond to such anaerobic situations?

*(Note:  In this situation many fatty acids are first taken up into the liver and converted to ketone bodies, which are subsequently converted to Acetyl-CoA after being taken up in the required tissues, hence causing "ketosis" as in the title)

You are correct in thinking that fatty acids cannot be metabolised anaerobically. However, in the type of metabolic state that you are describing, blood glucose will be maintained by the liver to support tissues or cells which are more or less dependent upon anaerobic metabolism. The classic example of such a cell type is the red blood cell which as no mitochondria and so cannot use the TCA cycle. The brain is also heavily dependent upon glucose.

The liver exports glucose that it has produced via gluconeogenesis from amino acid skeletons, as well as from glycerol produced as a result of fat metabolism.


What is this stick-like creature? My wife noticed this on her trousers immediately after coming home - probably acquired after brushing past a bush. It's about one inch long, and does not move much - but when poked it will flex and appear to try to roll.

It looks for all the world like a stick - but I've googled "stick insect", and this doesn't seem to have enough (or the right kind of) legs.

We live in England, in a suburban setting. We both work in offices and don't have a lot of contact with nature.

Could it be a thorn moth larva?

Apologies for the quality of the photo; I can try to take a better one if it would help to get another angle.

This appears to be an inch-worm, the larval caterpillar stage of a moth (order Lepidoptera) in the  Geometridae family. According to Bugguide (my emphasis):

  Larva - generally have only two pairs of prolegs (at the hind end) rather than the usual five pairs in most lepidoptera; the lack of prolegs in the middle of the body necessitates the peculiar method of locomotion, drawing the hind end up to the thoracic legs to form a loop, and then extending the body forward.

The systematics/taxonomy of this group is unclear, debated, and in flux. However, the majority of stick-like larval forms I could find seemed to be associated with the current Ennominae subfamily, which is also the largest of subfamilies in this family of moths.

Müller et al. (2019) just published the 6th volume of "The Geometrid Moths of Europe", which might be a good starting point for IDing this specimen more precisely. A book description from NHBS:

  More than half of the European Ennominae, a total of 181 species, plus 21 new species for the European fauna are covered in two hardback parts (with text and plates in separate volumes), including difficult genera...

You could also keep an eye on or alternatively submit an ID request over at Wildlife Insight's Illustrated Guide to British Caterpillars.


Molecular Evolution: Mrbayes never stops? When I use my own data to build Bayesian phylogenetic trees using the software Mrbayes, after many generations, it never reaches stopping status (namely, the average standard deviation of split frequencies below 0.01).

What should I do to get to this point?

The dtype is protein, 37 taxa were included, the model I used was as follows:

prset aamodel=fixed(wag);
lset rates=Invgamma;
mcmc ngen=100000 samplefreq=100

There are a few things you can try to get better convergence. I'd try the following in increasing order of difficulty/effort/processing time.

Be satisfied with a higher standard deviation of split frequencies. The MrBayes manual says "A rough guide is that an average standard deviation below 0.01 is very good indication of convergence, while values between 0.01 and 0.05 may be adequate depending on the purpose of your analysis." Especially if you are interested only in the best supported parts of the tree, this is a viable option. 0.01 is only a guideline.
Run the model for more generations. Maybe it is on the way to converging, but it hasn't gotten there yet. 100000 is not really that many. Try 200000 or 500000 and see if the model space is still being explored. You can examine the .p files using Tracer. You may already be doing this, and this is why you know it is not converging. If you look at the plots of the log-likelihoods, they will become relatively stable when the run has reached the optimal location.
Try running with a different amino acid model or without the inverse gamma rate prior. If you can get a simpler model to converge, then
Increase the number of chains to 4 or 8. If you have the ability to run in parallel, this will greatly speed up your analyses.
Try iteratively changing the heating parameter by setting Temp to a lower value, which will increase the likelihood of a swap. By default, Temp = 0.1. You can watch the progress of the analysis in the command line and see which are the heated chains and which is the cold chain.


Marker validation using transcriptome and genomic sequences derived from a single cell I conducted a SSR marker analysis using bioinformatic tool on some RNA-seq data of human tissues. Now, my supervisor believed that we have to validate these SSR on a transcriptomic and genomic sequences derived from single cell.

My question is: why I should do validation on sequences from single cell? Thanks for sharing your idea and experience here.

I think your supervisor wants to see if there is inter-cellular variation in the repeat length and if so, calculate the variation. This may be compared with inter-tissue or inter-individual variation.

Usually when you take a pool of cells for any assay, you would average out the properties of individual cells.

Using sequencing you may actually be able to find the variability in the repeat length if your reads are long enough. According to wikipedia, the SSRs are 2-5bp long motifs that are repeated 5-50 times. So the max length would be 250bp, sequencing which, is an easy task. So you would be able to know the fraction of the SSRs with a certain length from a pooled sample and obtain a length distribution. This is quite easy if you know the locus of the repeats and use specific primers for sequencing.

However, if you do not know the exact locus of your SSRs and you are doing random RNA/DNA fragmentation and total RNA/DNAseq, then you may not be able to do that so easily.

In any case I think that it is easier to determine the locus and do targeted sequencing in pooled sample, than doing single-cell RNAseq (At least if the objective is to obtain repeat length distribution).


What is the relationship between independent assortment and cross over? During meiosis, the independent assortment will be made first and then cross over will be made. I am so confused, what is the difference between this two process? I looked at the diagram on internet.It is said that law of independent assortment is alleles of genes on non homologous chromosomes assort independently during gametes formation, but I don't quite understand that.
So, another way for understanding this topic, independent assortment is tetrads can line up four different ways between homologous separate. Is that right.
Appreciate your help.

During meiosis, the independent assortment will be made first and then cross over will be made.

No, independent assortment occurs after crossing over. Crossing over occurs in prophase I while independent assortment occurs in metaphase I and anaphase I.

  I am so confused, what is the difference between this two process?

During prophase I, a process called synapsis occurs. That is, homologous chromosomes (one from your mother and one from your father) come together and bind together, forming a tetrad. This binding is due to crossing over, which is when the genetic material on the maternal chromosome and the paternal chromosome exchange places. The maternal chromosome gives some of its genes to the paternal chromosome, and the paternal chromosome gives some of its genes to the maternal chromosome. Crossing over increases genetic variety by creating a new chromosome with a new combination of genes.

During metaphase I, the tetrads line up at the equator of the cell. During anaphase one, the tetrads are broken apart and each homologous chromosome that made each tetrad up is pulled toward one end of the cell. Look at the image below, where the blue represents paternal chromosomes and the red represents maternal chromosomes.

Independent assortment describes the phenomenon where the paternal and maternal chromosomes can be lined up randomly at the equator. There are many combinations. For example,

Both red chromosomes could face the top pole and both blue
chromosomes could face the bottom pole.
Both blue chromosomes could face the top pole and both red could face the bottom.
One red on the left and one blue on the right could face the top, as shown in the picture.
One blue on the left and one red on the right could face the top.

This random alignment at the equator makes it so that during anaphase, random proportions of maternal and paternal chromosomes get assorted into each of the resulting daughter cells. Some cells could get more maternal chromosomes and the other would get more paternal chromosomes, and vice versa. On the other hand, they could get similar amounts. Independent assortment increases genetic variation by allowing daughter cells to each randomly receive a different proportion of paternal and maternal chromosomes.

In conclusion, crossing over and independent assortment (sometimes called random assortment) are different independent processes that both lead to an increase in genetic diversity.

References

Reece, Jane A., Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, and Robert B. Jackson. “Meiosis and Sexual Life Cycles." Campbell Biology. 10th ed. Glenview: Pearson, 2014. 252-266. Print.
https://www.quia.com/files/quia/users/dschnepp/Meiosis/Metaphase-I


Are there diseases for which a placebo treatment is state of the art? I was reading about the placebo effect, and I wondered if there exists or ever existed a disease with the following properties:

There are no known treatments for the disease that perform better than a placebo.
The placebo has a positive effect on patient outcomes.

If there is a disease like this, what do doctors do? Do they give out prescriptions for sugar pills because the pills will do better than nothing?

Doctors sometimes use "open-label placebos" - substances that have no known physiological effect on the treated disease, but have been associated with symptoms improvement in some studies. Open-label means doctors openly tell people it's placebo. The example is treatment of irritable bowel syndrome.

Doctors use not only fake drugs, but also real drugs as placebos. There are some doctors who don't have a courage to say they don't know how to help, so they just prescribe "something" (a real but ineffective drug) in the hope they will convince someone that they provided some help.

Prescribing "placebo treatments": results of national survey of US internists and rheumatologists (BMJ, 2008)

  Prescribing placebo treatments seems to be common and is viewed as
  ethically permissible among the surveyed US internists and
  rheumatologists. Vitamins and over the counter analgesics are the most
  commonly used treatments. Physicians might not be fully transparent
  with their patients about the use of placebos and might have mixed
  motivations for recommending such treatments.

There is a common practice to prescribe:

Vitamins or antibiotics for common cold, flu and other viral infections (Montana DPHHS ; JRSM Open)
Antipsychotics, antidepressants and sedatives for personal problems that can't really help to solve those problems
Various drugs for fibromyalgia

The seeming effect of placebo can discourage a person to seek for the real treatment.


Why does ice reduce swelling? It is common practice to use ice packs on injuries that cause bruising and swelling. It seems to be  an effective method to assist in reducing swelling.

Why does ice reduce welling?

Swelling is one of the signs of inflammation. Inflammation involves release of histamine by mast cells present in the tissues. Histamine causes vasodilation and leads to leakage of fluid from the blood, along with which neutrophils and other WBCs also enter the area. They phagocytose microbes that might have entered with the injury.

Applying ice would cause vasoconstriction* (i.e. narrowing of blood vessels.) which would reduce the leakage of tissue fluid and hence swelling.

*If you wonder why ice(or any cool thing) causes vasoconstriction think why you turn pale in winter ? Vasoconstriction reduces blood flow to the particular area and hence the exchange of heat is reduced which conserves body heat in cold environments.


Could random male-only-offspring mutation wipe out a species? If we can engineer the extinction of a whole species of mosquitos with male-only-offspring genetic mutation, how come such scenario never happened naturally in the past to other species? Or has it?

It has happened the R2D2 mutation in mice is famous for it, the mutation prevents or drastically reduces female offspring.  It can wipe out entire populations when it shows up, it doesn't wipe out the species becasue there are frankly too many mice, separated by too much distance, while breeding too fast for the gene to spread fast enough before the population crashes. If mice happened to live on only one island however they would be gone. These events are called selfish sweeps or selective sweeps that result from a transmission bias in a gene.

the opposite can also occur (female only) however this is slighly less likely to lead to instant extinction since a possible out exists. Lepidodactylus lugubris(a gecko) being a famous example and is a female only species that reproduced through parthenogenesis. These types of species are exceedingly rare and have problems however as they are very vulnerable to disease since they have low diversity. Species like this are driven extinct indirectly by the mutation that led to a female only species as their diversity sufferers drastically so disease or environmental change can wipe them out more easily.


Identification of an insect from Florida Any entomologists or there that can identify this bug? I live in north Florida, found this guy in my bedroom and thought it was a bedbug but I think it was too big, about half an inch long.

It's a cockroach nymph. Unfortunately it's barely visible given the angle of the photo, but it looks like the pronotum (head shield) has a pale margin - which, coupled with the pale markings at the sides of the tergites, makes me think this is a late-instar nymph of the Australian cockroach (Periplaneta australasiae). This looks very similar to the American cockroach apart from the pale markings, and is found in the southern US as well as many greenhouses. Within the US, it is most abundant in Florida and the coastal southern states. It is found primarily outdoors, where it prefers to live under tree bark, in piles of firewood and other locations that are moist and sheltered, but it can also be found indoors (source). It is the most prevalent cockroach outdoors in south Florida.

It mostly eats vegetable matter but when it enters homes it may eat holes in clothing and feed upon book covers (source).

(image copyright J L Castner; source: University of Minnesota).


Excretion of various wastes and water requirement A common fact is that Ammonia, Urea and Uric acid are the most common excreted metabolites and their removal needs varying amount of water, highest for ammonia (hence suited only for aquatic animals) and lowest for uric acid (suited for desert animals). Why is this so? Is it because of different solubility of these compounds in water or their toxicity? If it is the latter, how would excess water reduce the toxicity of a compound? This is a bit over-simplistic question, but I want to understand the tradeoffs involved in selecting the mode of excretion, ammonotelic, ureotelic, uricotelic.

Ammonia is more water soluble and also more toxic than either urea or uric acid but it is energetically less expensive. So, in regions where deficiency of water is not a problem, ammonia is an excretory product. Where water is scarce urea or uric acid is the excretory product but it is energetically more expensive to manufacture them. So, you can see an obvious trade off between energy expenditure and water conservation.

You can refer to any introductory biology book like campbell for further reading.

UPDATE :

Ammonia    : Most toxic , Easily Soluble , Less Energy Requirement

Urea       :Moderately toxic , Moderately soluble , More energy requirement(As needed to be processed from ammonia

Uric Acid:Least toxic , Least soluble , Highest energy requirement ( As needed to be processed from ammonia )

It is obvious now what tradeoffs are involved.

The only tradeoff not deducible from above is that of the eggs/youngs. In birds, eggs are not permeable for water so the best option is to excrete waste in form of uric acid so that high concentration of waste does not build up. Uric acid is excreted in form of solid palette which can stay in the egg without any harm.

We can also think of tadpoles which live exclusively in water and so they excrete ammonia but the frogs live both in land and water and so while on land they excrete urea as dessication is the main problem there.


how do we prevent restriction enzyme of bacteria to cut and destroy our new recombinant? Based on cloning principle, the new DNA recombinant will be introduced to host cells, commonly bacteria, how do we prevent restriction enzyme of bacteria to cut and destroy our new recombinant ?

You're essentially looking for a restriction modification system. You modify the restriction sites with methyl groups in a way that blocks restriction enzymes from accessing them. The DNA methylation should also be maintained through replication. So if you have an EcoRI site, you can use an EcoRI methylase to block the action of EcoRI.


Role of calcium chloride during competent cell preparation I am aware of the fact that $CaCl_2$ settles down on the cell wall making it less negative may be by forming bond with Teichoic acid. Also due to the positive charge it attracts DNA (DNA is negatively charged due to phosphate group). But is there anything else the $CaCl_2$ does? Also if its the work of $CaCl_2$ why we are adding $MgCl_2$ first in the standard protocol of the making competent cell preparation chemically?

Although we do not have any conclusive proof about how $CaCl_2$ works, the suggested mechanism is much similar to what you have suggested. When $CaCl_2$ dissociates in aqeous solution, $Ca^{2+}$ ions bind to the phosphate groups in DNA as well as the inner core of lipopolysaccharides in cell membrane (Dagert et al, 1979), neutralizing them. After this, heat shock allows uptake of this DNA into the host (how heat shock works is also not known; it is suggested that increased temperature creates pores in cell membrane, see this answer). For visual representation, see this diagram (from here):

Regarding $MgCl_2$, the role of $Mg^{2+}$ is not completely understood either. However, $Mg^{2+}$ is known to promote cell growth (Hanahan et al, 1983). It might be because $Mg^{2+}$ is an important factor required for functioning of ribosomes (Nierhaus et al, 2014). Anyhow, its role in increasing competence seems to be lesser than that of $Ca^{2+}$.

P.S.: during the experiment, $Mn^{2+}$, $Rb^+$ and $K^+$ also work effectively along with $Ca^{2+}$ (Hanahan et al, 1983).

References:

Dagert, M.; Ehrlich, S. (1979). "Prolonged incubation in calcium chloride improves the competence of Escherichia coli cells". Gene. 6 (1): 23–28. doi:10.1016/0378-1119(79)90082-9. PMID 383576
Douglas Hanahan, Studies on transformation of Escherichia coli with plasmids, Journal of Molecular Biology, Volume 166, Issue 4, 1983, Pages 557-580, ISSN 0022-2836, http://dx.doi.org/10.1016/S0022-2836(83)80284-8.
Nierhaus K.H. $Mg^{2+}$, $K^+$, and the ribosome J. Bacteriol.  2014 196 3817-3819


Why do some proteins "use" a beta barrel structure instead of alpha helices in transmembrane space? Most proteins are fixed in the membrane by alpha helices. But some use beta barrels.

Wikipedia describes beta barrels as used for porins, preprotein translocases, and lipocalins. To me, a coiled coil alpha helix structure could surely perform the same functions and given the vast number of proteins using alpha helices there might be some out there.

So my question is twofold:

Are these functions exclusive to beta barrels?
If so, what about alpha helices makes them unsuitable for those functions?

As you can see on the wikipedia page you linked yourself that beta barrels have far larger diameters (in some cases up to 40 angstroms as stated in this paper) depending on the numbers of beta sheets that make up the barrel, compared to the diameter of an alpha helix (that is fixed) of 6 angstroms. (source http://www.chem.uwec.edu/Modeling/GGProteinStructures/Pages/alpha_helix/helix.html). Alpha helices are good to anchor proteins into the membrane, or forming small holes that is suitable for compounds like ions, while with beta barrels larger compounds such as sugars, or various drugs can be transported.

There's a good list of proteins with different functions for both types on wikipedia


How stable is in vivo whole cell patch clamping? For a head fixed animal, how stable is the current state-of-the-art whole cell recording from a cortical neuron? The animal's breathing, and heart beat must move the neuron relative to the recording device quite a bit, and I was wondering how stable the seal would be. How long can one hold a cell, and what is the typical quality of such recording?

After talking to a few electrophysiologists, I found out that they have very diverse opinions.

It seems that a common way of stabilizing the movement of the brain with respect to heart beat is to press the brain with some softish-rigid material like agar. Also, draining the CSF could help but then this cannot be done without sacrificing the animal.

The quality of the patch degrades over time, and it could be held for an hour or more (anecdotal).


Do residue sequence numbers in PDB files correspond to the positions in the backbone? In other words if two residues have sequence numbers, say, 20 and 21 then are they next to each other in the backbone? If no (or not necessarily) then is there any way to find consecutive residues from a PDB file?

The residue numbering convention in the PDB is more-or-less entirely up to the depositor of the structure. While generally speaking sequential numbers are next to each other, there is no guarantee of that fact.

For example, the PDB allows for what are called "insertion codes", which are extra residues which interrupt the regular sequence progression. For example in the PDB entry 1IGY in between residues 52 and 53 on chain B is residue "52A". Normally, these insertion codes are used because the depositors want the numbering scheme to correspond with some external numbering standard, and there are extra residues (e.g. from affinity maturation) which would throw off this numbering.

Alternatively, the depositor might choose to mix up the numbering significantly. An example of this is the PDB entry 4OO9, which is the transmembrane domain of human mGlu5 with a lysozyme insertion to help crystallization. The mGlu5 is numbered from chain A from 568 to 832, but between residues 678 and 680 are residues 1002 to 1162, representing the inserted lysozyme. (So it goes 677, 678, 1002, ...)

Ultimately, the only reliable way to tell if two residues in the PDB which are sequential in numbering are actually sequential polymerically is to actually look at the coordinates and see if they're in a bonding configuration. There may be some information about "out-of-order" residue numbering in the header lines, but that's not always clear. Usually you have to deal with such situations on a case-by-case basis.


Ambiguity about the relation between membrane potential and concentration gradient in neuron cells I am stuck in an ambiguity about the equilibrium potentials of neuron cells. The following text is picked up from khanacademy website:

In one part it is said that:

We'll start out with K at a higher concentration inside the cell than in the surrounding fluid, just as for a regular neuron. (Other ions are also present, including anions that counterbalance the positive charge on K but they will not be able to cross the membrane in our example.)

If potassium channels in the membrane open, K will begin to move down its concentration gradient and out of the cell. Every time a K ion leaves the cell, the cell's interior loses a positive charge. Because of this, a slight excess of positive charge builds up on the outside of the cell membrane, and a slight excess of negative charge builds up on the inside. That is, the inside of the cell becomes negative relative to the outside, setting up a difference in electrical potential across the membrane.

As potassium continues to leave the cell, separating more charges, the membrane potential will continue to grow. Thus, the building membrane voltage is an increasing force that acts counter to the tendency for net movement of potassium ions down the potassium concentration gradient.

Eventually, the electrical potential difference across the cell membrane builds up to a high enough level that the electrical force driving K back into the cell is equal to the chemical force driving K out of the cell. When the potential difference across the cell membrane reaches this point, there is no net movement of K in either direction, and the system is considered to be in equilibrium. Every time one K leaves the cell, another K will enter it.

In another part it is said that:

The electrical potential difference across the cell membrane that exactly balances the concentration gradient for an ion is known as the equilibrium potential. Because the system is in equilibrium, the membrane potential will tend to stay at the equilibrium potential. For a cell where there is only one permeant ionic species (only one type of ion that can cross the membrane), the resting membrane potential will equal the equilibrium potential for that ion.

The steeper the concentration gradient is, the larger the electrical potential that balances it has to be. You can get an intuitive feeling for this by imagining the ion concentrations on either side of the membrane as hills of different sizes and thinking of the equilibrium potential as the force you'd need to exert to keep a boulder from rolling down the slopes between them.

I concluded the two following information from the above text:

The closer we get to the equilibrium state, the membrane potential
decreases because the concentration gradient decreases. (The steeper
the concentration gradient is, the larger the electrical potential
that balances it has to be)
The closer we get to the equilibrium state, the membrane potential
increases, because positive ions leave the cell.

How to solve this paradox?

I interpret your question to be roughly: "the equilibrium potential is based on a concentration difference, but as ions move to create the electric potential, the concentration difference is changing. Why doesn't this in turn change the equilibrium potential such that the concentrations become equal and the potential becomes zero?"

If I'm correct...

The answer to your paradox is that very few ions have to move.

The number of potassium ions that would have to move across the membrane to establish the resting membrane potential is tiny. Electrical forces are very very strong. The imbalance in ions doesn't affect the concentrations inside and out appreciably.

  For a typical cell, 1 microcoulomb of charge (6 × 10^12 monovalent ions) per square centimeter of membrane, transferred from one side of the membrane to the other, changes the membrane potential by roughly 1 V. This means, for example, that in a spherical cell of diameter 10 μm, the number of K+ ions that have to flow out to alter the membrane potential by 100 mV is only about 1/100,000 of the total number of K+ ions in the cytosol.

from Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2002). Ion channels and the electrical properties of membranes.

However, because membranes are also a little permeant to sodium, and because action potentials and synaptic transmission allow some additional ions to flow across the membrane, if you gave infinite time, eventually the ion concentrations inside and out would equalize, and the membrane potential would eventually be zero. The sodium-potassium pump solves this problem by continuing to keep potassium high and sodium low inside the cell.


Stardust or the elements in our bodies How do we know we are made of stardust? As our cells divide, are our atoms repurposed from existing materials or spontaneously generated? Do we consume materials after we are born that contain elements that were in stars? This I would understand. Or, as our cells are initially dividing after conception, but before birth, are we already repurposing existing materials to grow?

The saying that you are referring to is from Carl Sagan, when he stated that:

  "We are a way for the universe to know itself. Some part of our being knows this is where we came from. We long to return. And we can, because the cosmos is also within us. We're made of star stuff,"

Quote source

In answer to your question, yes, we are 'repurposing' the elements that make us up, as are all living and non-living matter.

Chris Impey, professor of astronomy at the University of Arizona is quoted in the article Are We Really All Made of Stars? (Melina, 2010) as stating:

  the fact that the carbon, nitrogen and oxygen atoms in our bodies, as well as atoms of all other heavy elements, were created in previous generations of stars over 4.5 billion years ago. Because humans and every other animal as well as most of the matter on Earth contain these elements, we are literally made of star stuff

The elements that make up the cells etc in humans and any life forms, as with the materials that make up the Earth itself were ultimately formed by nucleosynthesis processes (mostly fusion and neutron capture) in stars, explained in the webpage Origin of the Chemical Elements as being:

  the early Universe consisted almost entirely of the element hydrogen, with a small amount of helium present too. Hydrogen, therefore, is thought to be the starting material from which all other elements have been built. This is consistent with the very high abundance of hydrogen in the solar abundance profile. The process may be thought of as a series of fusion reactions which weld together simple atomic nuclei to build increasing complex atomic nuclei.


How fast is the patellar reflex? I have found a lot of content on the patellar reflex, but I cannot find any studies on how fast the reflex is, from onset of stimulus to innervation of muscles.  Does anyone know of either a study or at least a ballpark number for how fast that reflex is?

Mamizuka et al. (2007) calculated acceleration data of the patellar reflex.

Their study measured the reflex generated in response to the tapping force applied to the patellar tendon with a customized tendon hammer. They measured using a tri-axial accelerometer placed at the ankle joint.

They found:

  the time delay (29.6+/-6.0 ms) and the acceleration time (150.8+/-19.5 ms) of the speed response were quite constant for all participants.

Mamizuka, N., Sakane, M., Kaneoka, K., Hori, N. and Ochiai, N., 2007. Kinematic quantitation of the patellar tendon reflex using a tri-axial accelerometer. Journal of Biomechanics, 40(9): 2107-2111


What is the efficacy of Pertussis booster vaccine among different age groups? The Murray Microbiology book says that it is prefentially 10 years, similarly Estonian and Finnish health associations.

However, my professor says that it can be 5-7 years.

I started to think if the age is affecting here to the result.

When should you take booster vaccination of Pertussis if you are
a) 25 years old,
b) 50 years old,
c) 70 years old, and
d) 90 years old?

My professor says that there is no significant studies about the efficacy of Pertussis booster vaccination among different age groups.
Is this true?

No, it is not true, see references 1 and 2 for this purpose. From these articles which followed up booster vaccinations for pertussis it seems that there is at least some protection 5 and 8 years after the boost.

There is another study, which says that 10 years are relatively safe to assume, as the reduction in antibody levels over time estimated from the 5 year study would still allow protective levels of antibodies. See reference 3 for details.

One of the problems to make statements about the duration of the protection is the lack of data. Additionally there was a change in the vaccine from whole cell (which is pretty immungenic, but has higher number unwanted side effects) against a acellular vaccine. This change happened in the 90s, so there are no longterm data available. See reference four for more details.

The common recommendation at the moment for adults is to repeat the booster vaccination every 10 years (together with tetanus and diphteria) and for people which have close contact to unvaccinated persons every 5 years to prevent infections (see reference 4).

References:

Immunity to pertussis 5 years after booster immunization during
adolescence.
Immune responses to pertussis antigens eight years after booster
immunization with acellular vaccines in adults.
How long can we expect pertussis protection to last after the
adolescent booster dose of tetanus-diphtheria-pertussis (Tdap)
vaccines?
Acellular pertussis vaccine use in risk groups (adolescents,
pregnant women, newborns and health care workers): A review of
evidences and recommendations


Can specific B-cells be created in a lab? Instead of creating protein sequences, could that stepped be skipped and just have B-cells created to manufacture a particular type of immunity?

We aren't there yet.

There is a complex interplay between antigen recognition, presentation, and activation that would have to be worked out. You would also need to engineer the corresponding T-Cell which could recognize the antigen, become activated, which means you also need to develop a dendritic cell that can present to the T-cells, so that they could then go on to activate the B-Cells. Doing this in vitro would be a challenge.

You are actually asking to design highly specific receptors, and protein engineering then sequencing back to a genome would be difficult to do.

If you tried taking a known antibody, you would need to track down the actual B-Cell that produces it, due to somatic hypermutation creating a unique DNA sequence, which leads to the specificity that increases the affinity of antibodies for their ligands. I guess if you did it with germ free mice, you might have a shot at isolating their B-Cells and then finding out the gene sequence. Not impossible, in my opinion, but very difficult at this point.

The closest thing I have heard of so far is the work that is being done in Dr. Carl June's lab. They are working on taking cytotoxic T-Cells, and recombining their receptor DNA so that they can then recognize a patient's tumor and kill the cancer cells, but that is a bit different than what you are asking.


Making Cupriavidus metallidurans in laboratory? This is probably a stupid question but would it be possible to 'make' Cupriavidus metallidurans? And if so how? I'am guessing it wouldn't be possible without the use of expensive equipment for genome sequencing.

You can buy Cupriavidus metallidurans from various culture collections.

See these links below:

Cupriavidus metallidurans (Goris et al. 2001) Vandamme and Coenye 2004 - DSMZ
Cupriavidus metallidurans (Goris et al.) Vandamme and Coenye (ATCC® 43123™) - ATCC

As canadianer has already explained, it will be next to impossible to "find" a pure, viable culture out there in the environment.


Is it correct to regard archeaic humans (i.e.n Neanderthals and Denisovans) as distinct species to Homo sapiens? There is increasing evidence (e.g. here) that Homo sapiens interbred with contemporary homonins such as Homo neanderthalensis and the "Denisovans". Although these homonins do show differences in their mtDNA, since a species is generally defined as a group of organisms capable of interbreeding and producing viable offspring, should we not regard humans, neanderthals and denisovans as the same species and name them as such?

This question highlights the different species concepts.

If you go by the reproductive species concept (a population of actually or potentially interbreeding organisms), then yes. Apparently, the populations were interbreeding.

If you go by the typological species concept (morphologically distinct), then no. Homo neandertalensis and the "Denosovian" are morphologically distinct enough to be recognized as such.


Is the chemical composition of urine detrimental or beneficial for a tree? Seeing as a lot of people around the world urinate against trees it came to mind that I never thought about how the tree responds to this.
Is it detrimental for a tree if people urinate against them?

When looking on the internet, I found this explanation about urine:

  Human urine consists primarily of water (91% to 96%), with organic
  solutes including urea, creatinine, uric acid, and trace amounts of
  enzymes, carbohydrates, hormones, fatty acids, pigments, and mucins,
  and inorganic ions such as sodium (Na+), potassium (K+), chloride
  (Cl-), magnesium (Mg2+), calcium (Ca2+), ammonium (NH4+), sulfates
  (SO42-), and phosphates (e.g., PO43-). What Is the Chemical Composition of Urine?

Of course, it is possible that the small amounts present in urine are negligible in contrast to the amounts a tree absorbs on a daily basis.
What I am wondering: is the chemical composition of urine detrimental or beneficial for a tree?

Here is a book about dry-matter production of urine treated plants. If we consider that trees are large plants, it's fair to apply the study to trees too:

The findings of the study suggested that urine and urine products are equally as effective as mineral fertilizer especially in sandy soil and that splitting the application is a useful strategy to manage urine and urine products for optimum dry matter production.

Some plants do live in harsh environments with chalky pH and other specifics, and they may weakened by it. It's safe to say most trees are unaffected or improved by some urine, although the biggest trees are because of rain and steady underground streams (groundwater).


Sequencing inaccurate at the primer site The times I have sent a sample to sequence, both the forward and the reverse primer sites, show high inaccuracy while the rest of the gene is correctly sequenced. Because of this, the sequences of my in silico construct and the sequenced sample do not align in this section; but they do align at the rest of the gene almost 100%.

Is there a reason for this? Is this simply a sequencing artifact or is should I trust the sequenced sample and assume that the primer sites have mutated?

The very extremities of sequencing reads obtained by most if not all sequencing technologies are usually of lower quality, though more often so in the 5' region. You should disregard this data, or better yet design additional primers further away to encapsulate that region too if you desperately need it.

Below is a fairly typical output from FASTQC analysis of Illumina sequencing data. You can see how the quality is at its peak in the middle of the read (base index on the x axis. You'd likely see a similar thing for Sanger sequencing which is presumably what you're using.


Cellulose - why is it fibrous and not granular? I was reading a book where it said that the 1 - 4 Glycosidic bond of the Beta Glucose meant that cellulose is fibrous and not granular.

First, what does it mean to be granular and why is not granular unlike Amylose?

Thanks, Dave.

Cool I got something right :D

Cellulose is a linear polymer and therefore makes a fiber. I guess the linear in this case implies fiber. Amylose has a helical structure to it i think. Here is an image I found that shows the difference.


Nose breathing and swimming If you're standing and holding your nose closed, it becomes quickly uncomfortable; although you can breath fully through your mouth, it still feels like your lacking air since you're naturally trying to breath through your nose and you can feel the restriction.

On the other side, when swimming with a nose plug, you can have your nose totally shut down, breath only through the mouth and somehow you do not have the feeling of nose obstruction blocking your air intake.

Why is this?

One possible answer for your question could have to do with the level of exercise the subject is doing.

While the nasal passage is the main route for breathing, it provides cleaner air and allows for more even and slow respiration rates, a greater volume of air can pass through the mouth LaComb.

There is no discomfort in mouth breathing during exercise because mouth breathing can deliver greater amounts of oxygen and release greater amounts of CO2; it is the preferred method of breathing for increased activity.

Secondly, discomfort in oral breathing stems from a perception of breathlessness due to stimulation of receptors in the oral mucosa. When patients were required to breath orally with humidified air, no instances of breathlessness were reported (Source).

Based on these two studies, when exercising oral-breathing is required to deliver adequate amounts of O2. Therefore, nasal-breathing is not required and an obstruction of the nasal passage is not percieved. When exercising in a pool, discomfort of oral-breathing is diminished due to the humidity of the surrounding air. When not exercising, and breathing orally in low humidity air, discomfort is felt due to the stimulation of receptors in the oral mucosa.


Agglutination test using antibodies Agglutination test

  Latex agglutination using bound antigens : by coating soluble (non - particulate ) antigens on to microscopic latex spheres, their reaction with a particular antibody can be visualized.

  Haemagglutination : red blood cells can be used as agglutinating particles.

What are non-particulate antigens ? Why are they used instead of particulate ones ?

How are red blood cells used as agglutinating particles ?

If you have an antibody that is directed against, for example, a bacterial surface protein, then by mixing the bacterial cells with the antibody at a suitable stoichiometry you could observe clumping of the cells as the antibody molecules essentially cross link the cells together. This would be an example of using an agglutination (clumping) assay with a particulate antigen. You can also probably see why it is important that each cell (particle) carries many copies of the antigen for cross linking to take place effectively.

If, however, the antibody of interest is directed against a soluble protein, then mixtures of antigen and antibody are less likely to form cross-linked complexes, although it can happen and can be used for example in the Ouchterlony technique. If you want to use an agglutination test (i.e clumping of particles) with a soluble antigen then you can achieve this by attaching multiple copies of the antigen to macroscopic particles. This is what is being described in the definition of Latex agglutination in your question.

I imagine that there are ways of attaching a soluble antigen to red blood cells (e.g. by chemical cross-linking to the red blood cell surface) in which case you could observe clumping of the red blood cells when you added your antibody.


Identify a lone bone (jaw including teeth) found on a beach at Trouville-sur-Mer (France) in 2018 Found this on the beach at Trouville-sur-Mer in France, on 11 May 2018. It was laying in the sand, close to a trash can. Considering the strong smell of sand within the skeleton, it must have been near the sea for a very long time.

What species is this from?

Also posted on other identification websites and fora:

https://www.inaturalist.org/observations/14323892
https://observation.org/waarneming/view/160056539
https://forum.waarneming.nl/smf/index.php?topic=431852.0
http://www.nhm.ac.uk/natureplus/message/115302/

The length of the bone (the piece remaining) is under 12 centimeter.

The height of the only easily removable tooth (the smallest remaining one) is under 25 milimeter.

Old pictures in sunlight (all in low resolution & without measure bar):

Click the images for enlargement.

Update of 22 July 2018 (most in higher resolution & with measure bar):

This new set of pictures is archived at Wikimedia Commons.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, side A, photographed on 22 July 2018 - Image 1 of 3

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, side A, photographed on 22 July 2018 - Image 2 of 3

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, side A, photographed on 22 July 2018 - Image 3 of 3

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, side B, photographed on 22 July 2018 - Image 1 of 2

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, side B, photographed on 22 July 2018 - Image 2 of 2

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, top side, photographed on 22 July 2018 - Image 1 of 3

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, top side, photographed on 22 July 2018 - Image 2 of 3

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, top side, photographed on 22 July 2018 - Image 3 of 3

See Wikimedia Commons for a higher resolution.

Smallest remaining tooth from jaw (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, height smaller than 25mm, side B, photographed on 22 July 2018 - Image 1 of 2

See Wikimedia Commons for a higher resolution.

Smallest remaining tooth from jaw (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, height smaller than 25mm, side B, photographed on 22 July 2018 - Image 2 of 2

See Wikimedia Commons for a higher resolution.

It would be great to have a scale bar in the photo, so that the size would be easier to determine. However, by the shape of the teeth, I will propose that it is the back half of the jaw of a pig. Here is an image from the National Maritime Museum:

This one is from Vanuatu and has a rather elaborate mesial portion of the jaw, but the teeth look very similar. It's virtually impossible to know the bone's age or species, however.


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

I think it would affect some proteins, but ammonium sulfate precipitation usually requires such large amounts of salt, that you would have to add a lot of base to adjust the pH.

When I have done ammonium sulfate precipitation, its to take a rough cut of proteins out of a whole cell/whole organ lysate - its more like a hammer than a pair of tweezers as far as protein purification is concerned.  I would rather use a charged plastic resin or a sizing column if I were to care about the isoelectric purification.


How do eukaryotes terminate transcription? (clarification on Campbell Biology) I'm having trouble understanding how eukaryotes terminate transcription. Studying Campbell Biology (pg. 342, 10th ed.), I read:

  In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence on DNA, which specifies a polyadenylation signal (AAUAAA) in the pre-mRNA. This is is called a "signal" because once this stretch of six RNA nucleotides appears, it is immediately bound by certain proteins in the nucleus.

The text continues with:

  Then, at a point about 10-35 nucleotides downstream from the AAUAA, these proteins cut it free from the polymerase, releasing the pre-mRNA.

Does this mean pre-mRNA continues to be synthesized for 10-35 nucleotides after AAUAA is transcribed before finally being cut off?

Thanks so much.

According to Lewin's Genes XI - Krebs et. al on Eukaryotic Transcription, RNA Splicing, and Processing

  It is not clear whether RNA polymerase II actually engages in a termination event at a specific site. It is possible that its termination is only loosely specified. In some transcription units, termination occurs more than 1000 bp downstream of the site, corresponding to the mature 3' end of the mRNA (which is generated by cleavage at a specific sequence) Instead of using specific terminator sequences, the enzyme ceases RNA synthesis within multiple sites located in rather long "terminator regions." The nature of the individual termination sites is largely unknown.

It does go on to say,

  The site of cleavage/polyadenylation in most pre-mRNAs is flanked by two cis-acting signals: an upstream AAUAAA motif, which is located 11 to 30 nucleotides from the site, and a downstream U-rich or GU-rich element. The AAUAAA is needed for cleavage and polyadenylation because deletion or mutation of the AAUAAA hexamer prevents generation of the polyadenylated 3' end (though in plants and fungi there can be considerable variation from the AAUAAA motif).

I should add that the significance of 11 to 30, or as you said 10 to 35 nucleotides is that it is telling you the approximate size of the protein complex that is sitting on the RNA and where the active site of the protein is. The domain that recognizes the termination sequence is about 10 to 35 bases wide. It is likely that the variation is due to the RNA sequence following the termination sequence ability to form a stem loop structure.

Campbell takes a necessarily basic and less nuanced approach to the information that they provide on molecular biology. The approach is to provide some details and show the evolutionary commonalities between a diverse range of biological systems. The approach is okay as it gets you into the frame of mind of thinking about the interconnectedness of biological systems.

As you progress in your studies you will see that the reality and specifics are far more complex and exception based than was presented in introductory courses. But the more advanced courses spend an entire semester focused on what Campbell covers in one chapter. Campbell is accurate but incomplete out of necessity.


Is urine dirty as soon as it leaves the human body? Human urine is sterile as long as it is in the human body. But is it dirty after leaving the human body? Could you get sick from it, if you drink it or don't wash your hands, for example?

It was believed for a long time that urine stored in the urinary bladder is sterile. However, Wolfe et al(1). recently found evidence of bacterial presence in the urine extracted from bladders of healthy women. In an article just published, Hilt et al. found that at least some bacteria found in the bladder of healthy women are viable and can be grown in a laboratory after extraction from the bladder).2 (Paywall). They expect that the same is the case for men.

From the Hilt et al. paper:

  Thirty-five different genera and 85 different species were identified
  by EQUC. The most prevalent genera isolated were Lactobacillus (15%),
  followed by Corynebacterium (14.2%), Streptococcus (11.9%),
  Actinomyces (6.9%), and Staphylococcus (6.9%). Other genera commonly
  isolated include Aerococcus, Gardnerella, Bifidobacterium, and
  Actinobaculum.

Note that these species for the most part (Actinobaculum being one exception, as a possible uropathogen) appear to be part of the normal microbiome (collection of microorganisms) in healthy people in the same way as bacteria inhabit other parts of healthy persons. Additionally, the recovered organisms required special care to achieve growth:

  Most of the bacteria isolated required either increased CO2 or
  anaerobic conditions for growth, along with prolonged incubation, and
  they often were present in numbers below the threshold of detection
  used in routine diagnostic urine culture protocols.

Thus, fresh urine is non-sterile but probably unlikely to cause infection in healthy persons.

In the process of leaving the body, there is a chance of contamination from organisms living in the urinary tract or on the surface of the body. However, if organisms picked up from the urinary tract made you sick, I except that you would already be having symptoms of an urinary tract infection, as the stomach is hardly a more forgiving environment. The risk of contamination from the surface of the body would depend on personal hygiene.

See also this question on https://outdoors.stackexchange.com/questions/264/is-drinking-urine-safe

Edit: This might go without saying, but apart from possible pathogens, there are of course other aspects of urine which makes it unfit for general consumption.


Alternatives to fittest-win and Moran processes as simple mathematical models of selection When modeling selective sweeps as a micro-building block in models of macroevolution (not to be confused with misuses of this in creationist arguments), I use the fittest-win model of selection as a first approximation, or Moran process model when I want a more reasonable approximation.

In the fittest win model the probability for a mutant of fitness r to invade a host population of fitness 1 is 100% if r > 1 and 0 otherwise. In the Moran process model, the mutant of fitness r invades with probability $\frac{1 - r^{-1}}{1 - r^{-n}}$ for a finite population. Alternative in the limit as n goes to infinite, a mutant with r > 1 invades with probability $1 - \frac{1}{r}$ and 0 otherwise.

In general I am interested in simple models of selection of a single (or small concentration of) mutant invading an asexual host population of fitness 1 (with fitness constant and independent of frequency). Are there other common mathematical models for selection of this type?

I may suggest to give a look to game theory based model and their generalization from homogenous spatial diatribution to network like model. An easy review can be found in Martin A. Nowak's Evolutionary Dynamics (Harvard press 2006).

In particular you can see the classical Moran process as an evolutionary graph game going on a complete graph with identical weights. Changing the topology of the graph can give different results, though it is not necessary (and there're results showing in which case a graph behave just as a Moran process).

Graph related behaviour are, i.e., suppressing or amplifier of selection...


Is there any evolutionary/physiological advantage to multi-lateral symmetry? Just wondering ; I get the impression a large number of multicellular organisms are multi-lateral in their physical structure. Why would evolution/mutation have retained multi-lateral symmetry in an organism? What advantage/s does symmetry provide an organism?

EDIT:
By multi-lateral symmetry I mean at-least bi-lateral symmetry (as in the case of many beings such as elephants, crabs and fishes), but perhaps more than bi-lateral too (starfish come to mind)

END EDIT:

Signs of symmetry are determined by the environment. Completely isotropic ecological niche corresponds to the maximum degree of symmetry of organisms (spherical symmetry). Asymmetrization on the axis "up-down" took place under the influence of gravity field and lead to radial symmetry. Bilateral symmetry of the multicellular animals arose with movement.