evolution - What evolutionary mechanism caused felines to develop purring?

It makes sense that the ability to express your emotions improves the quality of the interaction you have with those around you. If a cat purrs those around it know it's feeling good, which can be useful information for future interaction.

I'm sure there have been cats who had a worse life because they didn't bond as well because they didn't purr, and consequently had a slightly lesser tendency to have their DNA end up in the next generation.

This argument goes for every ability to express emotions.

entomology - Herbal vs Chemical Insecticides

I think you probably mean insect and pest control from plant extracts.

I have seen posters where extracts from herbs were pretty effective in killing insects. Really common herbs - rosemary, basi. It makes sense that plants (and animals) would evolve chemical defenses against insects.

For instance, a quick search under google scholar talks gives you an idea of the research going on (mostly not in the US) here. Pestoban, an Indian herbal preparation is quite effective against some pests while less effective (~50% effective) in removing fleas from treated livestock.

It also stands to reason that the compounds found in edible herbs and plants would tend to be selectively effective against insects found in the environment local to the plants.

Another related topic is the search for antibiotics in herbs and spices. Tumeric is a common topic of research, which explains one of the possible reasons its used in cooking. Garlic components show interesting medical properties too.

While this may seem suspect to some, the research is done in the West too, but it is usually spun a different way. In general if you are looking for bioactive compounds that are not completely toxic (like heavy metals or cyanide for instance), you would want to look at compounds which are made by living things. Nearly all pharmaceutical designs come from or are derived from plant or microbial / fungal extracts. This is in fact the field of Natural Products Chemistry which is still a big thing in chemistry and biochemistry. Few if any of the hot targets of organic synthesis are not some fancy compound found in a plant, fungus or sponge extract. E.g. the surreally complex Palytoxin, the miracle breast cancer drug Taxol, and the venerable cholesterol control drugs, the Statins.

Transmission of epigenetic regulation through surrogate mother

Epigenetic information is information that can be inherited through cell division that is not encoded in the DNA sequence. This includes, but is not limited to, DNA methylation and histone modifications (there is also non-chromatin based epigenetic information). A nice example is the centromere, the chromosomal region that binds the kinetochore and is important to attach chromosomes to the mitotic spindle during cell division. The location of the centromere on the chromosome is encoded by a specific nucleosome composition and does not seem to rely on the DNA that wraps around those nucleosomes: The DNA sequence at centromeres is not even conserved from chromosome to chromosome (with the exception of budding yeast), and there are several known examples of people and families where the centromere is in a different place. However, all the mechanisms for maintaining this epigenetic mark are encoded genetically.

As epigenetic information is transmitted through cell division, it is directly inherited from the biological mother (with the exception of e.g. the centromere, most epigenetic marks from the father's chromosomes are removed when sperm is created).

However, (some) epigenetic information can be modified. This is obviously important during development where gene expression patterns of a liver cell need to be stable but different from gene expression patterns of a neuron, even though both descend from the same cell.

There is evidence that the metabolism of the mother will influence the epigenetic program of the child; diet being one of the determinants. It has also been suggested that epigenetic changes may influence behavior. Thus, it is indeed possible for the surrogate mother's epigenetic state to influence the epigenetic information of the children.

biochemistry - How can I avoid digesting protein-bound DNA?

Are you interested in transcription factor binding (and similar), or in histone modifications?

If you are looking at investigating something with a short binding motif that occurs redundantly across the genome, ChIP-exo works: http://www.cell.com/abstract/S0092-8674(11)01351-1

This technique involves digesting one strand of the DNA up until the bound protein-DNA complex via exonuclease, while leaving enough of a tag on the other end to uniquely identify it's location within the genome. I have no first-hand experience with it, and it's yet to be independently replicated, but it looks fantastic. I don't recall whether they investigated the extent to which off-target DNA was digested by the exonuclease, but theoretically I expect a significant portion would have been eaten up.

If you are interested in ChIP of histone modifications, you can use micrococcal nuclease (MNase) for your sample prep instead of sonication. Again, I have no first-hand experience, but I understand that this enzyme can be used to digest DNA until it reaches the nucleosomal core particle, and there are published ChIP-seq experiments employing this strategy. The MNase would be expected to digest unbound DNA fragments.

evolution - Why hasn't mother nature made us aware of our lizard brain?

Just to echo what others have said here, the term lizard brain is a remnant of "recapitulation theory" which rigorously proposed that the embryo develops through more primitive animals. This is an intriguing idea when looking at embryos - early stage embryos of flies, birds, fish and primates really do resemble each other. So the idea was that our lower brain, near the spinal chord was the brain of a lizard, whereas the prefrontal cortex, which is highly developed in humans compared to lizards, birds etc was 'added later' and represents a 'human brain'. This idea is flawed because it basically assumed that the lizard part of us never evolved and was based on a linear idea of phylogeny, as opposed to Darwin's idea of evolutionary trees where lizards and insect continue to evolve. In evolution there are no 'lower animals'.

In practice, the parts of the brain we have in common with lizards do handle more physiologically autonomous functions (heart rate, etc). While cortex and prefrontal cortex do show greater activity in emotional and rational decision making. This is now more of a rule of thumb, not a rigorous statement or a theory of development, merely the result that structures that were developed later tend to have newer functions. A good discussion of this can be found in Gould's "Ontogeny and Philogeny".

Your question also asks why we can't rationally understand our lower brain functions...

Awareness itself is not an intrinsic property of the brain. Some aspects of the rational mind and articulate self consciousness are so far fairly unique amongst brains.

I should mention at this point that I do not mean that conscious thought is unique to humans - its clear that primates are aware that they exist and have empathy for feelings of others. Its likely that other animals have similar amazing abilities we think of as human.

Just the same, the level of development in humans is distinctly unique. Insofar as it is a unique development, not a typical brain function, we should understand that it is far from all encompassing. Given all this, its not surprising that the physiological functions of the brain such as regulation of breathing, many hormonal levels, stress are not conscious. I usually only know I've run too far and too hard because I can feel my chest heave - its actually only something I'm aware of because my brain is receiving signals from my chest that its heaving and my heart is beating rapidly.

The limits of our consciousness are the subject of much study now. From cognitive psychology and behavioral economics we've been surprised over and over in the past 20 years how there are limits to the amount of information we can process at a time and, how limited we are in being rational to the point that we can make foolish decisions, and lastly how much of those decisions are made subconciously, only to be rationalized later by our thoughts.

I will give three examples.

1) Experiments in cognitive psych show that as subjects turn over cards in a deck, our pulse and respiration indicate they know that the deck is stacked before they consciously know.

2) Psychologist/Philosopher Joshua Greene is famous for observing that moral decisions are made in parallel in more than one region of the brain before the decision is rationally made. This is a great radiolab podcast on this story.

3) Behavioral economists have shown that we don't even know a good deal when we see it. We are often convinced by cues in the environment about the profitability of our decisions which comes from pre-set processes embodied in our minds. Studies showing what happens when we pay CEOs too much money, manipulate decision making by offering too many choices and how poor people are more generous than wealthy ones.

This discussion goes back to Descartes, who felt we could be fooling ourselves to the point that we might even be deluding ourselves to believe in mathematics.

If there are ever times when people do things that don't make sense, we have often found that the faults go back to the limitations of our brains. If you have never had that experience ... "Ill have what @Sylvain's having"!

Looking at references for cognitive dissonance, optical illusions will tell you a dozen more fascinating stories. Highly recommend it :)

mitochondria - Pancretic Acinar Cell - ATP, calcium concentration data

In this study, even though they have used fluorescence based method, they have reported concentrations.

When we studied basal intracellular calcium concentrations in acini from control rats they were in the low nanomolar range (140 ± 5 nmol).

For ATP concentrations you can see here.

Is it possible to find this information in a specific book or website, to avoid trawling though vast amounts of literature?

There is the human metabolome database. However, it doesn't have data for all cell types. Either more studies are required or the database needs updation.

Similarly there is the yeast metabolome database (you may not require it for your query but just another piece of information that I thought is worth adding).

genetics - phylogenetic analysis of gene enrichment?

Phylogenetically analyzing genes that are not present in every species may present you with some problems, but it is completely feasible to simultaneously analyze the relatedness of the species (based on your enrichment score), and the relatedness of the scores themselves.

Forgive me if this is too 'simple' an analysis, but you have not said what you have tried.

My choice of approach would be to use R (open source stats package) to generate a heatmap of your matrix of data. There are plenty of options for the method of clustering, but the defaults tend to produce quite a nice heatplot, with hierarchical cluster analysis performed on both dimensions of the data (you can specify only 1, or even none, if you prefer). I have used the following code to simulate some data to generate the below heatmap;

# generate 10x10 matrix using random data
x <- as.matrix(data.frame(rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10)))
# use heatmap function on the data. "labRow" and "labCol" simply remove the labels.
heatmap(x, xlab="Genes", ylab="Species", labRow="", labCol="")

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Because it is randomly generated data there are no patterns really, but if you were to stick you real data in there it would look better no doubt. (In an actual analysis you will want to leave the labels on, I was just simplifying the plot). The function can handle missing values, so you could put all the genes you want to analyze in there, even if not all species have them.

Using this method you could see the most closely related species by gene enrichment, and also which are the most closely related genes (in terms of enrichment for your TF).

bioinformatics - Can two protein secondary structures "overlap" in the PDB?

TLDR; Answer: You could consider this particular residue to belong to both structural elements, but it's a tricky call and depends on the method of secondary structure assignment.

Ambiguous secondary structure allocation comes up fairly often. Whilst obviously, not many people will be able to use this protein specifically, the below approach could be useful for other proteins.

In PyMol I used fetch 1ae9 and highlighted M at position 255 on the A chain in red. I can see why this isn't a satisfying representation: the beta sheet allocation is very short, and the residue in question is clearly the beginning of a helix.

To run a more conservative secondary structure allocation run dss in pymol (watered down dssp). This reveals that the beta sheets were actually quite putative.

We can see why when we look at the stick model (below). There are only a few (2-4) residue pairs in proximity that would be available for hydrogen bonding, even assuming all 4 form H-bonds, calling this a bona fide beta sheet could be seen as a bit generous.

Looking at this example (1ae9), we see the potential for H-bonding with another putative beta sheet, as well as a backbone angle that starts to form a helix. It's a classic case of ambiguous dual assignment. @AlexanderDScouras draws a reasonable conclusion that both is okay and to directly answer the question: dual assignment is possible, and allowed. I would prefer to rule out beta sheets in this particular case, but on the condition that one highlights that there is plenty of hydrogen bonding in the hairpin loop.

So long as you can reasonably justify the assignment it's probably okay. You can manually assign any residue and secondary structure.

# set residue 155 to be alpha-helical
alter 155/, ss='H'

# update the scene in PyMOL to reflect the changes.
rebuild

Evidence is always a good idea to support manual assignments. A quick and thorough way would be to run the sequence through a few secondary structure predictors, or use the genesilico metaserver to save yourself some hassle (you'll need an account) (this does feel like going back a step since you now have a structure, so exercise caution - if the sequence prediction doesn't look correct according to the structure, it's probably not). Another method as suggested by shigeta is running this through a Ramachandran plot (RAMPAGE is a favourite).

If it's very very unclear then discuss it thoroughly and clearly whenever this part of the protein is relevant. These secondary structure assignments have somewhat arbitrary cut-offs after-all, and when things get near the thresholds, it's important to approach the situation with clarity and specificity.

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Ramachandran plot image source: By Dcrjsr - Own work, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=9105708

molecular genetics - Measuring reverse transcriptase activity in E. coli

I like that you are considering a simple and standardized approach. However, there are a number of potential pitfalls to consider with this proposal. First of all, what specific RT activity are you trying to quantify? Is the the transcription speed or accuracy, or are you trying to characterize something else entirely? If you are measuring speed, how and what will you measure, reliably and will be reproducible, for speed? If you are going for accuracy, you will need a whole lot of sequencing to check the bases are correct. Both of these can quickly become expensive.

Also, is it necessary to use HIV-1 RT? Since you mention E. coli, would you want to consider using msr, a prokaryotic RT?

Though I've never heard or tried it myself, is it possible to transform mRNA into bacteria? I would imagine that it would be degraded as a natural defense mechanism. You may need to consider some alternative form of gene delivery, such as a standard expression plasmid. Genomic integration may not be necessary to achieve your goal.

As mentioned, you cannot just have naked cDNA to translate a protein. You need at least the promoter, RNA pol binding site and polyA signal. You could take advantage of viral infection systems (a replication defective HIV) to deliver your GFP and RT genes into a mammalian system (like HEK-293 cells), but this adds a lot of complexity and expense that may not be worthwhile.

The last thing off the top, you would benefit greatest from taking advantage of a directed evolution experiment to generate some potential leads. For example, you may PCR amplify the RT cDNA with an error-prone Taq to purpose create RT mutants for use in your assay.

Keep thinking about this, and maybe check the websites of the some of the RT commercial vendors. It is possible one of these companies have already done something similar.

senescence - Does AMP/ATP ratio affect lifespan in vertebrates?

The reference below says that a higher AMP/ATP ratio is associated with lower lifespan in C. elegans.

Is this finding also generalizable to vertebrates as well?

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Reference:
Apfeld, J., O’Connor, G., McDonagh, T., DiStefano, P. S. & Curtis, R. The AMP-activated
protein kinase AAK-2 links energy levels and insulin-like signals to lifespan in C. elegans.
Genes Dev. 18, 3004–3009 (2004). PMCID: PMC535911.

zoology - Does cockroach lay eggs in human flesh when they "bite"?

Recently, i have "bite" by cockroach, not only the "bitten" area red and swallowing, and more specificly, it have a big hole in that area, when i clean it with hydrogen peroxide solution, something is happening, that is, the yellowish/greenish thing came out from the holes from each infecting area, so does hydroxide solution kill the eggs and parasite insde those holes, much importantly, Does cockroach lay eggs in human flesh when they "bite"?