transcription - determining genome-wide exogenous binding of pathogens to host genome?

I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice genome to the advantage of the pathogen.

It's an interesting concept but left me wondering how one would determine de novo the binding of these pathogen effectors into the host if one didn't know them. What would be the steps to determine where are the pathogen's TFs binding the host genome?

Edit: there is the possibility of not knowing which proteins bind to the host genome, so what would be the way of developing the antibodies in this case?

Reference:

What factors are known to affect evolution?

What is evolution?

The first step is to remind ourself of the definition of the term "evolution". Evolution is most often defined as "any change in allele frequency in a population".

Forces that drive evolution

Categorizing the processes that affect allele frequencies might be subject to issues of semantics. Without going into the details, we generally recognize 4 forces that drives evolution

1. Natural selection
   
   
   • Natural selection refers to the deterministic change in allele frequency due to a differential in fitness among different genotypes.
   
   


2. Genetic Drift
   
   
   • Genetic Drift refers to the stochastic sampling process of individuals
   
   


3. Mutations
   
   
   • A mutation refers to any spontaneous change (substitution, indel, chromosome duplication, etc...) in an individual's genotype.
   
   


4. Gene flow (aka. migration)
   
   
   • Gene flow refers to the transfer (migration) of DNA sequences among populations.
   
   

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KennyPeanuts's answer, random mating and hardy-weinberg equilibrium

In his answer, @KennyPeanuts also talk about random mating. Random mating refers to the condition where the probability of two individuals to mate depends only on their respective fitness. Many people phrase random mating as absence of mate choice but it actually refers to the absence of variation for mate choice in the population.

Hardy-Weinberg states that under the above four conditions and random mating, then the frequency of the genotype that has the allele $i$ derived from the mother and the allele $j$ derived from the father, where $x_i$ and $x_j$ are the frequency of these alleles is $cdot x_i cdot x_j$. This means that for a bi-allelic locus, the allele frequency of the genotypes AA, AB, BA and BB are $x^2$, $x(1-x)$, $x(1-x)$ and $(1-x)^2$, respectively where $x$ is the frequency of the allele A. For the heterozygotes (AB and BA), we often care little which of the two allele is inherited by the mother and which is inherited by the father (assuming there are genders) and we therefore call AB both AB and BA genotypes (which can eventually be confusing). As such, the frequency of the AB genotype is $2 x(1-x)$.

The condition of random mating ensure that there is no deviation of genotype frequencies from the Hardy-Weinberg's expectations and it ensure that there is no change in genotype frequencies from the first to the second generation considered (after one generation, the equilibrium genotype frequency is immediately reached). Random mating is therefore not a condition for evolution to not occur.

microbiology - Vigorous shaking for HFR interrupted mating

I remember doing this experiment many years ago in an undergraduate practical where we used vigorous vortexing of culture samples in glass tubes to achieve interruption and separation.

According to Griffiths AJF, Gelbart WM, Miller JH, et al. Modern Genetic Analysis. Bacterial Conjugation:

... sampling is accomplished by using a kitchen blender to separate
the joined cells, resulting in interrupted conjugation.

homework - Genetic carrier Pedigree of Recessive Traits

Let's take Question A:

Both fathers have siblings with red ears, and red ears are an autosomal recessive trait. The grandparents did not have red ears, we know then that they were carriers of the recessive allele. Each grandparent was Nr (for Normal and red alleles respectively).

The fathers have normal ears, so they could be NN (probability 0.33) or Nr (probability 0.67).

The answer then is that each father independently has a 2/3 chance (0.67 probability) of carrying the red ears gene.

The male's mother, being RR, makes the male a carrier only if the male's father is himself a carrier. To put it mathematically, he has a 1/2 chance of being a carrier with 2/3 probability that he was a carrier to begin with. (2/3)*(1/2) = 1/3.

Therefore the male can be carrier with 1/3 chance.

Now Question B:

Short answer:

Since the male and female have symmetrical pedigrees, and we just solved the chance of the male being a carrier with 1/3 chance, then the chance of them having a child with red ears is (1/3)*(1/3) = 1/9.

Long answer:

The male's and female's fathers may each be heterozygous or homozygous normal, given the information, with both mothers being homozygous normal (NN).

If Father A is NN (crossed with Mother A, also NN), there is a 0 probability of passing on the red ears allele.

If Father A is Nr, then Person A has a 0.5 probability of carrying the red ear allele.

Person A can now be NN (with 0.25 probability) or Nr (with 0.5 probability).

Likewise with Person B.

Now lets consider all 4 combinations of genotypes that Person A and B can have when they have a child. I will write a table with one Person on each side of the table, with the probability of their genotype written in brackets beside. Each intersection will represent the frequency of carrying the red ears allele.

                Person B
             (1/3)     (2/3)
Person A      NN        Nr
(1/3) NN      0/4       2/4
(2/3) Nr      2/4       2/4

Carrying the red ear gene: (A more interesting example)
There are a total of 6 outcomes in which the child carries the red ears allele, but these must be weighted by the probability that each parent has the associated genotype.

Probability of carrying 'r' = [ (1/3)(1/3)(0/4) + (1/3)(2/3)(2/4) + (2/3)(1/3)(2/4) + (2/3)(2/3)(2/4) ] / [ (1/3)(1/3) + (1/3)(2/3) + (2/3)(1/3) + (2/3)(2/3) ]
= 0.25

Having a child with red ears:
Probability of having red ears = [ (1/3)(1/3)(0/4) + (1/3)(2/3)(0/4) + (2/3)(1/3)(0/4) + (2/3)(2/3)(1/4) ] / [ (1/3)(1/3) + (1/3)(2/3) + (2/3)(1/3) + (2/3)(2/3) ]
= 1/9 or about 0.11

It's left as an exercise to the student to derive the remaining probabilites.
Nr 4/9
NN 4/9
rr 1/9

genetics - Bicoid regulation of hunchback

I'm learning about development via the example of Drosophila embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? In other words, does the level of bicoid directly govern the expression of hunchback, or are there steps in between?

What temperature should mammalian B-Cells be stored at outside of the incubator?

I'm working with murine B-cells. The general protocol is to keep cells on ice to keep them from dying but I've noticed that it makes these cells aggregate and precipitate out. I've heard suggestions that these cells should just be kept at room temperature. How would I be able to determine which conditions at which I should be keeping my cells?

I was trying to collect cells to prepare them for cell binding studies to antibodies and then assess the cells on a filterplate. Typically, you keep them on ice to pause the metabolic state as well as to prevent endocytosis of the bound molecules. However, that shift seems to cause settling. How do you troubleshoot the appropriate temperature to process cells and what are the usual scientific justification for making such decisions.

gel electrophoresis - How many agarose gel bands are typical for circularised DNA

I don't have hands on it, but I will not be surprised if supercoiled DNA migrates at different distances according to some inner topological conformation (i.e., more or less coiled AND/OR more or less nicked). Similarly, this picture highlights >8 conformations. What is run in the gel is circularized phage DNA with some degree of knotting due to the circularization (phage DNA is otherwise linear).

Figure from: Arsuaga et al. 2005, PNAS 102 (26) 9165-9169 (free on PubMed Central)

Another theoretical possibility is that two or more plasmids of different sizes were grown in the same maxiprep because of some contamination. But in this case, you will spot the problem also in the digestion, so it does not seem to be your case.

evolution - How did the huge dinosaurs cope with gravity and loads on bones, etc.?

Assuming that gravity was essentially the same (other answers to this question notwithstanding), very large dinosaurs were dealing with the same forces that they would today. There are two clades of dinosaurs in which gigantism evolved, Sauropoda (quadrupdeal sauropods) and Theropoda (including T. rex). Each "solved" the problem of large size in different (but also somewhat similar) ways.

The main reason why large size was not a problem was that, if posture changed to align the forces between the animal and the ground, the bones are compressed. Bone is very strong in compression.

Theropoda

Theropod essential operate as a see-saw, with a large muscular tail balancing a large head. As such, they did not likely use much active muscular force to balance. The analogy is a human standing. Just standing, you don't need much muscle force to balance.

Hutchinson and Garcia (2002) showed that, because of a lack of plausibly large leg musculature, T. rex could not run. For a range of postures, they estimated how much muscle would be required to balance the animal and found that running behavior was unlikely.

Hutchinson, J.R. and M. Garcia. 2002. Tyrannosaurus was not a fast runner. Nature 415:1018-1021.

Sauropoda

Sauropods show many similar adaptations as elephants, the largest extant land mammals. Their limbs were held upright (erect), which requires less energy for balance. Some sauropods had air-filled bones, which would also lighten the skeleton. Wilson and Carrano (1999) document the evolution of posture through sauropod evolution from a biomechanical perspective.

Wilson, J.A. and M.T. Carrano. 1999. Titanosaurs and the origin of “wide-gauge” trackways: a biomechanical and systematic perspective on sauropod locomotion. Paleobiology 25:252–267.

metabolism - What are the differences between white and brown adipose tissue?

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

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

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

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

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

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

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