Technique to test antibiotic resistance in a bacteria in presence of another compound

It sounds like you might employ a "Disk diffusion test" described in this Wikipedia article.  It could be done with and without the secondary adjuvant compound and be quantified by measurement of the varying diameters of the resulting zones of bacterial inhibition.

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


What causes bacteria to change their proteins to become resistant to antibiotics?

The bacteria doesn't know.

When an organism copies its DNA, it sometimes makes mistakes. Different organisms have different rates of making mistakes; the rate of mistakes can be really high in some organisms like bacteria.

DNA copying mistakes (or unintended changes without copying, like due to UV damage) can sometimes be a big problem for multicellular organisms. If some of your cells have different DNA than others, they might function poorly, or they might grow too fast, stealing the space and nutrients from other cells in the organism, causing cancer. Multicellular organisms like humans have a lot of DNA repair mechanisms and methods to detect DNA damage and have cells sometimes suicide when they have been damaged.

For bacteria, DNA copying mistakes aren't as much of a problem, and there are lots and lots of bacteria out in the world. That means a lot of different mistakes. When a mistake is bad for a bacterium, it is more likely to die. Those types of mistakes therefore don't get recopied over and over again.

Sometimes a mistake is accidentally helpful.

Occasionally, a mistake actually makes a positive difference for an organism. If there are trillions of bacteria, just a few of them might have mistakes that make them resistant to a particular antibiotic. Let's say it's 1 out of 1,000,000,000.

In normal conditions, that doesn't matter much. If it doesn't hurt them at all, they will just keep on replicating the mistake, and other bacteria keep on replicating no mistake, and the proportion stays 1 out of 1,000,000,000.

Accidentally helpful mistakes become more common in a population

Now, let's say you expose that population to antibiotics that kill 99% of the bacteria with no mistake, but kills none of the bacteria with the mistake. Now, your 1,000,000,000 bacteria is 10,000,000 bacteria, but you still have 1 with a mistake. Now when those bacteria replicate, 1/10,000,000 will have the mistake. If they grow evenly back to 1,000,000,000 now you have 100/1,000,000,000 bacteria with the mistake. As you repeat this process, eventually you will have lots of bacteria that have the mistake, and that proportion of individuals will be insensitive to the antibiotic.

Biologists call these mistakes "mutations" and they call the increased survival and reproduction of organisms with helpful mutations "natural selection" - over time, natural selection is an important contributing factor to evolution of species.

At no point in this process is any awareness of what's happening necessary! All you need is variation, caused by replication mistakes, and some selection pressure that gives an advantage to individuals with certain mistakes. Making some mistakes in replication is a constant source of variation in biology, and the key process that, along with selection, has led to the vast variety of life around you.


Are there any multi-cellular organisms out there that do not sleep?

Well, you may want to re-state your question. There are numerous multi-cellular organisms without a nervous system. So you could say that they never sleep: sponges, plants, mushrooms.

This paper on the evolution of sleep concludes:

  A phylogenetic evaluation of sleep demonstrates that all
  mammals, birds, and reptiles engage in sleep, and evidence
  for sleep in amphibians, ﬁshes, and invertebrates is strong if
  not certain.

So it seems that once you have a nervous system, you also have some rest periods. However, it may not be clear if the rest periods are dictated by the lifestyle (e.g. nocturnal foraging) or by a requirement to "recharge" the nervous system.


Difference In Telomeres Between A Thale Cress Plant And A Methuselah Tree

Telomeres do not "cause" ageing as such - although you are right that they limit the number of times a somatic cell can divide.

Each time a cell divides the chromosomes are replicated in an imperfect way, and as such a small amount of DNA is lost from the end of the chromosome during each round of cell division. Telomeres are just extensions to the chromosomes, so that the DNA that is lost is not important. When a cell runs out of telomeres it ceases to divide.

However it is a big generalization to say that telomere length is therefore correlated with lifespan. For instance a recent study has shown that mice have telomeres 5-10x the length of humans, but live 30x shorter (1).

Inter-species differences in lifespan

Whilst I am no expert on these 2 plants, it is quite an obvious thing to say that organisms age at different rates. Mice, for instance, live 3 years in a protective environment, whereas humans can live 30x that. The difference is down to the life strategies acquired by natural selection: it is more advantageous for a mouse to develop very fast to reproductive maturity and have as many offspring as possible, because there is a very high mortality rate for mice. Conversely for humans, in takes more than a decade for us to reach reproductive maturity! Our "rate" of development/ageing is lower, which is completely related to our reproductive strategies.

I imagine that a very similar story is true for plants - for some it will be advantageous for them to "live fast, die young", whereas for others the best strategy might be to take a long time creating less, but more robust, offspring.

At the molecular level

I have answered a related question previously (Do trees age on a microscopic level?) which might be of interest to you.

In short, the phenotype of ageing is associated with irreparable damage at the molecular level - be it to DNA, organelles, protein aggregations... you name it! Organisms that have a higher metabolic rate, such as mice, accumulate this damage faster. This gives them the benefit of being able to reproduce much earlier, at the cost of reduced overall lifespan.

Plants age slightly differently, but at the genetic level much the same repair pathways are conserved throughout the kingdoms of life, with some alterations of course - for instance plants seem almost completely immune to cancer (2)!

As I argue in the linked to question above, plants have a potentially indefinite replicative potential, as every cell has the capability of regenerating its telomeres, because plants do not have a conserved germ line as animals do - any cutting from a plant has the potential to create an entirely new plant. This varies from plant to plant of course, and plants are still susceptible to damage, they just have modified/adapted repair pathways to cope with their specific lifestyle.

You ask whether it is the telomeres or the "rate" that differs between the plants - the answer is almost certainly a combination of both, amongst the other myriad of factors that influence lifespan!

Refs

Colado, et al, 2013. Telomere dynamics in mice and humans. Seminars in hematology [PubMed]
Doonan & Sablowski, 2010. Walls around tumours - why plants do not develop cancer. Nature reviews cancer [DOI]


Why the smell of sweat greatly varies across the body?

Sweat is actually odorless regardless of what type of sweat gland it comes from, of which there are two types - apocrine and eccrine.

As suggested by canadianer, the odor comes from the mixture of bacteria and the resulting sweat. With regards to why your bacterial flora is so diverse is likely due to the different micro-environments found around your body.

In your armpits and feet (arguably where the strongest odor subsides), you'll find more anaerobic bacteria - bacteria that prefers low oxygen environments and sometimes, higher temperature, humid environments. Because they don't use oxygen to metabolize, their by-products in making energy are often organic acids, commonly lactic acid. Some anaerobic bacterias even have by-products containing sulfur.

Meanwhile, in less warm and damp environments on your body (i.e. face, hands), aerobic bacteria dominate. Oxygen is abundant and the temperature is just right for those strains of bacteria. Their by-products are much less putrid

EDIT: In addition, apocrine sweat is also high in the nutrients, such as lipids and proteins that bacteria can feed on. Once they metabolize the stuff in apocrine sweat, they start releasing the aforementioned by-products.


Can I train my non-dominant hand and make it dominant?

Of course you can train yourself and make your non-dominant hand to be equal or even greater than your actual dominant handedness. Handedness is directly wired to the right/left hemisphere of your brain, so by training, you will actually re-wire your brain and acquire new pathways. It's a hard process in terms of breaking habits, otherwise, it's non-invasive and non-painfull, where most humans tend to give up before acquiring this skill justifying it as an unnecessary/low priority goal.

Handedness is not decided upon birth. It's gained in the earlier process (while a child is still in mother's womb) based on personal/individual preference (expressed by sucking a finger btw) toward right-handedness (90%) or left-handedness (9%), cross-dominance/ambidexterity (1%).

https://youtu.be/DU3OdTLuHf0
https://en.wikipedia.org/wiki/Handedness
https://ghr.nlm.nih.gov/primer/traits/handedness


Floats of Algae, a house-made conjecture

One consideration is the energetic costs to the organism. It's going to be energetically more favorable for an organism to be in osmotic balanced (isotonic) with its environment than to constantly work to maintain lower internal osmolarity through active transport of water or solutes. Second thing to consider is cell size and density differentials. Air at sealevel is several hundred times less dense than water, so even tiny gas bubbles would create significant buoyancy for a cell. On the other hand, pure water is only about 2.5% less dense than sea water, which means a much (much) larger volume would be needed to generate equivalent buoyancy.

All that said, there seems to be some plausibility to your conjecture, as there are some large marine phytoplankton that use active water transport to maintain vacuoules at lower density than that of seawater (Source).

This paper discusses some other competing mechanisms as well, but as the author of the article states:

  "... most of the cases of positive buoyancy in phytoplankton not
  generated by gas vesicles concern diatoms..."

That's not an incontrovertable refutation of your conjecture, but it seems to me that gas vesicles are a much more efficient means of generating buoyancy, and would probably be energetically favored over other biological means of generating buoyancy.


The effect of 3D structure and solubility of the binding site of enzyme on its affinity Km and maximum activity Vmax?

Probably the big reason you were unsuccessful in your previous searches is that nobody quite knows exactly how enzymes' 3D structures lead to particular kinetic parameters.

It's wrapped up in the concept of "how the heck do enzymes work, anyway?" -- surprisingly, it's a question we don't really have a good answer to. The leading concept currently - influenced in large part by catalytic antibodies - is the transition state stabilization theory. That is, enzymes work by preferentially stabilizing the transition state, reducing the activation energy of the reaction. (A good overview of the theory can be found in Structure and Mechanism in Protein Science by Alan Fersht, one of the must-reads for anyone interested in enzymes.)

But that's probably not all of how enzymes work, or at the very least "bind the transition state well" is a rather coarse overview of the process. There's thoughts that the precise arrangement of active site sidechains are involved in a quantum mechanical interaction with the transition state. This is the "theozyme" concept put forth by Kendall Houk and colleagues.

The role of enzyme flexibility in catalysis is a highly disputed topic currently. The dynamics of proteins are an important concept for the understanding of the full reaction pathway, but there are some people who think that an important contribution of the protein is funneling vibrational energy into the appropriate bond motions for catalyssi. Nobel prize winner Arieh Warshel is (vocally) against it, though, favoring an electrostatic view of catalysis. (That is, enzymes work by stabilizing the charge distributions found in the catalytic pathways.)

So the long and the short of it is that we really don't understand how enzymes work, so we're rather far from being able to predict how the 3D structure changes the catalytic parameters. There are a number of efforts (particular from David Baker's lab) trying to use computational modeling of 3D enzyme structures to design enzymes, but the results have been rather modest. While such enzymes have been designed, their activities have been modest, and nowhere near the activity of native enzymes.

Doing the reverse - trying to predict the catalytic activity from 3D structures - is difficult, given the lack of knowledge. That's not to say people haven't tried. For example, there's been some efforts to use machine learning to predict catalytic constants from different mutants in a series. The problem with machine learning-type approaches is that the results tend to be only applicable for the particular system they've been trained on, and there's only limited interpretability of the results.


As a fisheries biologist these are what I would recommend to read.These are all science entertainment books(i.e., factual, but fun to read).The first 2 are more fish biology. The second  2 is more fisheries ecology.

Your Inner Fish: A Journey Into the 3.5-Billion-Year History of the human body.
Neil shubin
Demon Fish
Juliet Eilperin
Four Fish: The Future of the Last Wild Food
Paul Greenberg
Cod: A Biography Of The Fish That Changed The World
Mark kurlansky


Cannot see images beyond a certain magnification with a microscope

This is probably the problem: "We did not prepare the leaf; we just put a small piece of it between two slides.".

I suppose you mean you put a leaf fragment between two regular microscope slides, those measuring 26mm * 76mm (1in. * 3in.)?

That won't work. Long story short: microscope optics/objectives are designed with a specific working distance in mind, which is not an entiraly free choice, but dictated by the laws of physics/optics. An average achromat 40/0.65 has a working distance of about 0.6 mm. An average achromat 100/1.25 has a working distance of about 0.2 mm. An average microscope slide has a thickness of about 1 - 1.2 mm...

In the... well... regular microtechnique, a specimen is put on a slide and covered with a very thin coverslip, having a thickness of around 0.15 - 0.17 mm.

Also, as others mentioned, using a 25x eyepiece in combination with a 40/0.65 or a 100/1.25 is kind of overkill. With that combination, you enter the realm of "empty magnification". In short: structures appear larger, but no new structures are revealed and the image becomes more and more fuzzy.

And yes: you need to use immersion oil with the 100x objective, but keep in mind this is a very demanding objective to be used, on the part of the microscopist as well as on the part of the slide preparer.

Using a microscope is not all that simple for novices, but there's an easy way to find out -if no image can be produced-, if it's a microscope problem or an inexperienced user problem: take as a specimen an as thin as possible large object, such as a leaf of cigarette paper, and try to focus on it, using low power and gradually use stronger objectives up to 40/0.65. If an image can be produced, even if it's rather blurred at 40/0.65, the microscope is okay.


What happens in a nerve cell when a thought is generated?

This is a recurring question that many people are bothered with. I read an interesting answer on Quora. Basically, the author says that there is always on-going activity in the brain. Each thought is triggered by something, let it be conscious or unconscious. The brain is never silent, even in your deepest sleep with only slow-wave synchronized activity, there is still activity. Even when it seems that a certain thought pops up totally randomly, it is still triggered by certain inputs, let they be sensory or internal. Note that action potentials can be triggered either by signals from the outside world (sensory receptor neurons), or by signals from other cells in the brain and body.

Also note that most, if not all neurons show background activity ('neuronal noise'); they never stop firing even without inputs. When one or more of those background potentials impinge on a postsynaptic neuron, that neuron may be activated an fire an action potential. This may also explain some random events in the nervous system.


Species Identification: Waterborne larvae, Texas USA

The larvae are moth flies (Psychoda sp.)

The black head, black pointed tail, clear body with grayish intestines visible and also their small size 2-3 mm can be seen on both pictures.

Where they can be found in nature:

  In nature, moth fly larvae, Psychoda sp. (Diptera: Psychodidae) normally occur in aquatic habitats that experience intermittent submersion or flooding. The larvae develop in polluted, shallow water or highly moist organic solids where they feed on decaying organic material in mud, moss or water.

Where they can be found in households:

  In homes, the adult flies, which resemble tiny moths, are most likely found on the walls of bathrooms, kitchens, basements and other locations where sewer drains and plumbing fixtures are located. The flies are poor fliers and usually are found close to the drain or area from which they came. Moth fly larvae are known to live in drain traps, garbage disposals, toilet tanks, sides of drain pipes and overflow pipes in homes, wet areas around leaky pipes, sewer lines, and septic tanks where they feed on stuff that might accumulate in such areas. The moth flies that live in Michigan do not bite and are not known to transmit disease of any sort.

What to do against them:

  The best way to control moth flies is to eliminate or reduce the larval food sources by thoroughly cleaning drain lines and plumbing fixtures. Pouring boiling water down the drain where larvae are suspected to be may help to reduce their numbers. Adults can be controlled with the application of a household aerosol insecticide (like Raid) or a good flyswatter. Be sure to read and follow all instructions and safety precautions found on the label before.

There are various other methods which are far more precise, listing how to eliminate moth flies from drains.


Why is the number of cells virtually a constant?

You have to understand this is a very, very, very, very broad question. Decades of research in multiple disciplines allow us to answer this question in a million directions. However, I would start by looking up information about the cell cycle and its checkpoints. Here of course I would point you - for starters - to this page:
Khan Academy's page on cell cycle checkpoints
For further reading, you can consult the college-level chapter on Cell communication and cell cycle regulation. Here the most relevant section would be Regulation of cell cycle, it's a great introductory read, well researched and well presented didactically.
A short tl;dr
In short, cells have checkpoints at different stages of their life cycle - both before and after they divide. You can imagine that, for instance, a nutrient starved cell incapable of copying its DNA prior to division, will arrest its progress through the cell cycle at the checkpoint before S (DNA synthesis) phase. And under the right conditions, it will resume its progress and get ready for division. This example is only one of many checkpoints that exist, and varying types of cells may have varying checkpoint requirements.


Why do we spend so much time on creating taxonomies?

Biology is about observation and learning from nature. If you categorize the species, it helps you in quickly understand what the species is about, what are some of its common characteristics, phylogenetics, etc. It has applications not just in understanding evolution, but in population studies, ecology. Why do we give humans names? So we can find them quickly and easily and associate them with certain characteristics. It is the basic human nature of using patterns to quickly identify objects.


See this paper on link between inflammation and anxiety.

Also, quoting one of the paragraphs of this paper

  Clinical
  studies have shown increased serum inﬂammatory markers in patients with depression as well as a correlation
  between plasma cytokine levels and the severity of depression, and have described improvement in depression
  after anti-inﬂammatory treatment.

Even if you do a simple google search, you will get thousands of results on this.


What is the effect of TSH on the calcitonin?

I found a paper, where it is postulated that TSH secretion is inhibited by calcitonin. However, the paper is quite old (1984) and I'm not sure if there are any more actual paper.


Rank-specific rules for taxonomic classification

In short, no. Species are unique, in that they are thought to be biologically real categories that would exist whether there were humans trying to classify them or not. There are a variety of definitions for species, involving fixed characters that imply a lack of gene-flow. However, all higher categories, from genera on up are designed by humans to be able to talk about these groups. Each category is defined by phylogenetic relationships, but taxonomists have wide leeway to decide how broadly or narrowly to subdivide groups. (Lumpers vs. Splitters). For example, all ants are in the same family. Yet all it would take to change this would be for some ant taxonomist to submit a paper that divided ants into however many families s/he wanted to. The peer reviewers would then decide if such a division was reasonable, and once published, it would be the new taxonomy. There are no broad rules, other than peer review. Not age: one family could be 1 million years old, and another, 100 million. Not the magnitude of phenotypic or genotypic variation: some groups are radically different from one-another, and still in the same category, while other groups are heavily subdivided and barely distinguishable.


How to do whole genome sequence alignment in R or Ruby/C++, any good language?

I think you incorrectly identified what type of analysis you want.  You mention that you have numerous sequences in a fasta file (you mention at least 60,000) that need to be aligned to a single genome.  So your not doing a pairwise alignment, your aligning DNA sequences to a reference genome.  The fastest known algorithm for this is burrow-wheeler transformation mappings which can be accomplished with tools such as bowtie, bowtie2, BWA, etc...

I'm assuming your experimental design is something like this: You have sequencing data from a number of tissue samples with half or some number of samples being a disease state, the other being normal.  So you want to create alignment files for each sample, and than determine where these alignments differ.

After alignment, you will need to create a variant file (VCF) which can be accomplished using samtools or GATK.  The VCF file will give you all bp locations with alternative alleles from your reference genome.  Which seems to be what your looking for.

Citations that could be useful:

Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.

Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509

Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]

Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]

https://www.broadinstitute.org/gatk/about/cited-by

The last url contains 145 publications that used GATK to look at population-scale variant differences.  These publications could be very useful to see how other papers have accomplished variant discovery for the use for scientific inference.

For User137 - since I can't comment on this board yet; you want to use a program called muscle.  There is an MS-DOS version and it can align short sequences extremely fast.


Is the complement system a part of innate or adaptive immunity

Yes, the complement system is part of the innate immune system. It can be activated by the:

classical pathway (activated through bound IgM and IgG molecules but
also by DNA, collagen (both are usually not available freely outside
of cells) and c-reactive protein)
lectin pathway (activation by binding of mannose through the mannose
binding lectin on the cell surface)
alternative pathway (activation by the constant hydrolysis of the
complement component 3 (or C3) in an antibody independent way)

My guess here would be, that the classical activation via antibodies is evolutionary younger than the other two possibilities which act more directly on bacteria and do not depend on the availability of specific (at least to some degree) antibodies. The Wikipedia article on the complement system is pretty extensive.


Action potential changes in low sodium concentrations but constant osmotic pressure

High sodium extracellularly means an increased sodium concentration gradient across the membrane. This means there is a larger driving force for sodium to enter the cell once the sodium channels open at the start of the action potential, and hence a larger depolarization takes place increasing the action potential amplitude. The enhanced depolarization leads to an increased proportion of activated voltage-operated potassium channels that open upon depolarization. When more potassium channels open, more potassium will exit the cell, thereby repolarizing the cell to a larger extent, in turn stopping the depolarization step of the action potential faster. In all, the action potential develops quicker, as the depolarization is increased as well as the repolarization step, and hence the time it takes to execute an action potential is diminished.

Your subquestion as to the small sodium conductance is not valid, as during an action potential it is actually very high.

To increase the action potential duration you can increase the re-polarization step by increasing the extracellular potassium concentration, thereby diminishing the potassium concentration gradient and prolonging the repolarization step.


Hybridization in Darwin's finches is rare or frequent?

I actually just had to read a Grant & Grant paper, so hopefully, I can get this right. My understanding is that hybridization events have repeatedly seen to occur, but the events themselves usually do not repeat within a lineage, i.e. once a lineage becomes partially hybridized, it is unlikley to continue to breed with adjacent populations.

Due to the reproductive barriers that come from song patters of hybridized individuals (Grant & Grant, 2009), Repeated hybridations are unlikely to occur within a lineage, even when in the presence of a species with which hybridization can occur.

Grant, P.R. and B.R. Grant. 2009. The secondary contact phase of allopatric speciation in Darwin's finches. PNAS 106 20141-20148


First, when asking about a specific small term, it's best to check your spelling.  If you actually look at the sentience, you will note that you left out a very important hyphen:

  Pellequer compared several propensity scale methods using a dataset of
  14 epitope-annotated proteins. [emphasis added]

The phrase means that the protein sequences (amino acid sequence) has the epitopes marked on them.  If you look at the cited paper, you will see the various tables and break downs of determined epitopes.  Pellequer's group did a lot of the early work when people were still working on techniques to "map" out the locations of epitopes (which are often not in linear segments of the protein sequence due to the protein structure).


(my comment reiterating the answer seemed useful, so I've reproduced it here)

There are "NMDA receptors" in our body. There is not NMDA naturally in our body*. "NMDA receptor" is just a name people gave to one of the receptors that normally binds glutamate. They could have called it something else, like the "slow glu receptor", or "Glutamate Receptor A", but they called it the NMDA receptor because they discovered it was different from other glutamate receptors in that it was activated by a chemical called NMDA in their experiments.

(original answer)

NMDA receptors are in fact glutamate receptors natively: there is no endogenous NMDA*. They are named NMDA receptors because experimentally they were differentiated from other glutamate receptors using the compound NMDA. At first glutamate receptors were known as "NMDA" and "non-NMDA" glutamate receptors, and later the non-NMDA sort were found to be sensitive to AMPA or kainate and named thusly.

Many other receptors are named this way: the nicotinic acetylcholine receptor is the receptor that nicotine is an agonist at, but the endogenous ligand is acetylcholine; muscarine is an agonist to the muscarinic acetylcholine receptor but the endogenous ligand is acetylcholine.

Watkins, J. C., & Jane, D. E. (2006). The glutamate story. British journal of pharmacology, 147(S1), S100-S108.

*In the comments, @gilleain pointed out some research suggesting that NMDA does exist endogenously, although in fairly specific areas and not disputing that glutamate is the primary endogenous agonist for NMDA receptors. This work was long after the NMDA-sensitive glutamate receptor was discovered and named, but is some interesting trivia nonetheless.


Could potatoes that have been refrigerated for 142 days still sprout?

Yes, it is very common to do this on farms. I have grown potatoes that I stored loosely in my basement (~5 degree temperature during the winter when they would be stored) for about 6 months at a time every year for the past 20 years.


The cross you're studying is Mendel's monohybrid cross. Which looks something like this.

Now here, the genotype of F1 gen plants is Tt.

To draw this cross, proceed exactly like you decided. Draw the 2/2 grid and cross the alleles Tt x Tt

Your cross should look like this (ignore the plant drawings):

(Source: classes.midlandstech.com)


Are mosquitoes attracted to blue lights in particular?

It is not an urban myth. UV and blue lamps are good insect attractants. They have been used for many decades in insect traps, and these too work for mosquitoes. These lamps are routinely used in ecology at insect sampling sites. In some cases, such as with diurnal moths, yellow lamps can also be good attractants. The reason why UV is applicable is because insects are equipped with three photoreceptors, namely the UV-, blue-, and green-sensitive photoreceptors. Below you can see the spectral sensitivity curves of the genus Apis, which is typical for many insects.

As to why they are good attractants is probably variable across species, because it would depend on the neurological encoding of this information. For instance, some species may use this information to determine night and day, or may be superstimuli for nectar as used by plants to advertise themselves for pollination. Or it may simply be for some other reason.


Flower identification (Singapore, April)

This is called "Red Powder Puff" or botanically Calliandra haematocephala. See the images (from the Wikipedia article):

What you identified as the fruit appears to be the buds:

Some more information can be found here.


The Creature is "Debris-carrying Lacewing.".

(Source)


How to determine the probability that a mutation is lost / fixed?

The probability that a neutral mutation gets fixed after an infinite amount of time is equal to its frequency $p$ as you said. Therefore the probability of being lost is $1-p$. This post offers an explanation but there many ways to make the demonstration. You might want to have a look at any good book in population genetics for this demo. Here are book recommendations.

  how do you calculate the probability that it exists in 2 copies?

A probability always depends on a priori. What are your a priori? Let's assume that we know that the allele frequency was $\frac{4}{10}$ in the previous time step.

Under the Wright-Fisher model the probability of having 2 copies in the next generation is given by the binomial distribution. Let $N=5$ and therefore $2N=10$ and let the frequency of the allele of interest be $\frac{4}{10}$, the probability of having two alleles in the next generation is ${10 \choose 2} \left(\frac{4}{10}\right)^2 \left(\frac{6}{10}\right)^8 ≈ 0.12$.

Under the Moran model this probability is zero. Moran's model is a birth-death  model (Markov model) and therefore transition between time steps can only add or subtract (or make no change) a single allele. You will note that the time step does not mean the same thing for the two models. Loss of heterozygosity is twice as fast under the Wright-Fisher model but this discussion is definitely not what you were asking for!


This is probably a fly killed by the fungi Entomophthora muscae (or closely related) or maybe a Cordyceps fungus. These kinds of fungi mainly attacks insects, and you sometimes see attacks as white, swollen abdomens in flies.

(Picture of common infection, from bugguide.net)

These fungi are also known to change the behaviour of infected individuals, so that they e.g. climb up tall plants to die (sometimes called "zombie-insects"), to allow for better dispersal and transmission of the fungal spores. Lots of information about the behavioural modifications of hosts by fungi can be found in Roy et al. (2006), but they can involve both climbing to exposed locations and special mechanisms for host attachement at death:

  In many cases the final interactions, or endgames, between a host and pathogen involve complex behavioral modifications such as the infected insect seeking an elevated position where wind currents can effectively disseminate conidia. Elevation seeking by insects at late stages of infection is a common phenomenon that was recognized by early insect pathologists who noted that diseased lepidopteran larvae, such as Lymantria monacha (the nun moth), infected with baculoviruses migrated to the tops of trees where they died (94). This host-altered behavior was named “Wipfelkrankheit” or “Wipfelsucht” (meaning tree top disease in German) for viral diseases (41) and “summit disease” for fungal diseases (24, 57, 106).

and

  Some fungi do not produce rhizoids, but the host is held in situ by host structures alone, namely the legs or mouthparts (mandibles or stylets). The pose of the dead insect is generally characteristic of the pathogen species involved. For instance, E. grylli-infected grasshoppers (Figure 3a) and E. scatophagae–infected yellow dung flies (Figure 3b) seek elevated positions on grasses or other vegetation and cling tightly (death grip) with their legs (96). Tipulids infected with fungal species from the genera Eryniopsis and Entomophaga also attach to grasses with their long legs, often overhanging water (Figures 5b,c).

If you do google image searches on "Entomophthora fly abdomen" or "fly Cordyceps" you can see some examples of infections. I don't know about the fly species, but Musca domestica is probably likely.

For some more examples and information on Entomophthora muscae and related fungi see:

Roy et al. 2006. Bizzare Interactions and Endgames: Entomopathogenic Fungi and Their Arthropod Hosts. Annual Review of Entomology 51(1) (pdf)
Biological Control: Entomophthora muscae, webpage from Cornell Uni.
Harmon. 2012. Fungus that controls zombie-ants has own fungal stalker. Nature
Mind-controlling fungus turns insects into zombies (blog post)


Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs

The two most common families of scoring matrices are BLOSUM and PAM. Each of them has a score for every possible alignment combination between the 20 standard amino acids1. They both do more or less the same job but have been derived using different approaches.
BLOSUM matrices

(image taken from Wikipedia)
The BLOSUM matrices are built from actual alignments between very conserved regions of protein families. The score for a given pair of amino acids aligning with each other is the log-odds score measuring how often this particular alignment is found and how often it would be expected to be found by chance:
$$ S_{ij} = \left ( \frac{1}{\lambda} \right ) \left ( \frac{p_{ij}}{q_i * q_j} \right )$$
Where $p_{ij}$ is the probability of finding the two amino acids $i$ and $j$ aligned to each other in a homologous sequence and $q_i$ and $q_j$ the background probability of finding the amino acids $i$ and $j$ in any protein sequence. The $\lambda$ is a scaling factor set to ensure that the matrix contains easily computable integer values.
In simple words, the BLOSUM matrices give you a score based on how often the alignment you observe in your sequences is found in alignments of similar sequences.
There are several BLOSUM matrices which have been computed using proteins of more or less sequence similarity. The most commonly used one is BLOSUM62 which was built using alignments between proteins of $\ge 62\%$ sequence identity. This is a nice middle ground and will do for most cases. If you are comparing proteins that are very closely related, you might want to use a matrix based on more similar sequences such as BLOSUM90 (built from sequences with $\ge 90\%$ sequence sequence identity) and for less conserved proteins, you might use something like BLOSUM45 ($\ge45\%$ sequence identity).
PAM matrices
The PAM matrices are built using a different approach. First, a global alignment (as opposed to the local ones used in BLOSUM) of of a set of sequences sharing 85% sequence identity is computed. Next, a score for the alignment of all possible pairs of amino acids is calculated based on its observed frequency in the aligned proteins. Then, the scores are extrapolated to alignments of different sequence similarity using mathematical tools. The PAM matrices assume a model of protein evolution and score the alignments based on that model.
The PAM-I matrix is the only one that was actually built from real alignments. The rest were obtained by  multiplying PAM-I by itself N times. In PAM, unlike in BLOSUM, the higher numbers correspond to greater evolutionary distances between proteins.

With all that in mind, the scoring matrices are used by BLAST to calculate the score of the alignment. You can think of this score as the sum of the scores of each individual pair of aligned amino acids in your BLAST result.
Useful references:

http://statgen.ncsu.edu/st590a/notes/76_ST590A_100509.pdf
https://en.wikipedia.org/wiki/Point_accepted_mutation
https://en.wikipedia.org/wiki/BLOSUM
http://www.ncbi.nlm.nih.gov/pubmed/21356840

1The non-standard amino acids Selenocysteine and Pyrrolysine are not included in any matrix I know of, probably because they are too rare for any reasonable conclusion to be drawn from statistic analyses.


Do Alicyclobacilli produce carbon dioxide?

Alicyclobacilli are strictly aerobic and thus take up oxygen and secrete carbon dioxide, as opposed to the (facultative) anaerobic yeasts and bacilli that usually cause spoilage. So yes, alicyclobacilli produce CO2. But why doesn't the packaging swell? Compare the number of gas molecules in the simplest reactions for aerobic and anaerobic metabolism:

Aerobic metabolism: $C_6H_{12}O_6 + \underline{6 O_2} \Rightarrow \underline{6 CO_2} + 6 H_2O + 38 ATP$

Anaerobic metabolism: $C_6H_{12}O_6 \Rightarrow 2 Ethanol + \underline{2 CO_2} + 2 ATP$

Aerobes take in as much gas molecules as they excrete, while anaerobes (the ones producing ethanol at least) only make gas.


How does ubiquitin recognize misfolded proteins?

Ubiquitin and the UPS

The ubiquitin proteasomal system (UPS) is a common method of regulation for many proteins in the cell. The modification is actually generated by E3 ubiquitin ligase, of which there are ~400-800 in the mammalian cell and the main source of specificity in the UPS (E2 ~40 and only 1 or 2 E1).

Ubiquitin gets its name from ubiquitous, meaning found everywhere. It's a 76 amino acid molecule that modifies proteins at lysine residues. Monoubiquitination can act as a signalling molecule whereas polyubiquitination leads to degradation. Ubiquitin is first activated via an ATP-dependent pathway to create a high energy thioester with E1. This is transthiolated to E2 and finally E3 allows the addition to the target protein. So really, your question is how E3 ubiquitin ligase recognises its target. 1

E3 ligases

There are 3 classes of E3 ligases, according to whether they contain a RING, U-box or HECT domain. These domains are responsible for either directly catalysing the addition of ubiquitin or simply facilitating another E3 ligase to do so. RING and RING-like domains are by far the most common (<600). Exactly how these domains mediate the transmission of ubiquitin is not clear, but it can be via an E3-Ub intermediate or directly from E2 to the target. The domains are relatively standardised, due to the fact they bind to E2 proteins, which contain less diversity than target proteins. However, it's the combination of the E2 and substrate binding domains that generates the selection. 2

Target recognition

So how does the target come into all of this? Each E3 ligase recognises a specific sequence on the target protein due to it's own conformation and signal sequence creating a unique interface full of intermolecular interactions- just like any protein recognises any other protein. However, although individual cases vary, the tight control primarily comes from post translational modifications on the target. Phosphorylation in particular is common in signalling and may allow E3 to bind, inducing degradation of the target. I'll use some examples to demonstrate this point, but note that every case will be different.

c-Cbl (E3) recognises activated receptor tyrosine kinases and ZAP 70/Syk kinases (target) by binding a phosphotyrosine sequence through its tyrosine kinase binding domain (containing SH2 domain). The phosphorylation is controlled by other cellular signals
Glycosylation
Proline hydroxylation
Sumoylation

Other regulations of the process that are linked but perhaps outside the scope of your question include E3 post translational modifications (eg. autoubiquitination), sequestration of E3 via binding partners (Cand1 and Roc1), pseudosubstrates and substrate competition. 7

Misfolded protein degradation

Making protein is a large investment for the cell and so there are several protective measures to prevent misfolding/aggregation. Whilst there are many different types, chaperones generally work by isolating the misfolded protein and undergoing a series of binding release steps, triggered by hydrolysis of ATP. The protein can still be released unfolded, and the cell will continually try to isolate it for refolding. However, certain chaperones form a complex with the proteasome, and can recruit other UPS components. The choice to give up on refolding appears to be a stochastic process, and will depend on the concentration of the appropriate chaperones. Misfolded proteins tend to have significant regions of exposed hydrophobic residues, and E3 ligases are therefore likely to recognise this less specifically than the degradation pathway described above.

Relevant sources include endoplasmic reticulum associated degradation and chaperones.

Summary

The answer to your question is that there is no standard recognition sequence in E3 to know which protein to target, the binding needs to be diverse in order to give the control the cell needs. That means it could be anything, but each E3 is likely to be relatively specific for its target, and is often controlled by other post translation modifications on the substrate. Misfolded proteins can be recognised and degraded due to the association of the UPS with chaperones.

If you're really interested, you can download this file and open it in something like PyMol to actually see the ligase ready to transfer ubiquitin.


Geographic regions as subpopulations/demes

It is impossible to answer your question in the general sense. Yes, detailed population structure may matter. It very much depends upon what your question is and what parameter space you are willing to answer but it is possible that assuming panmixis would be unrealistic.

Note that accurate data on $F_{ST}$ won't suffice to estimate migration rate $m$.

Note also that many simulation platform already exist and you might not have to reinvent the wheel (see Sequence evolution simulation tool).


Why do people use anti-inflammatory drugs?

You are correct in that inflammation is a physiological process. It is vital for the correct development and localisation of a strong immune response, and contributes to tissue healing.

However, the beneficial effects are replaced by dangerous processes when they are prolonged or too intense. This includes both effects of leukocyte attraction and invasion, but also deleterious consequences of the accumulated cytokines. For example, TNF-alpha originally contributes to immune cell activation but in prolonged inflammation prevents tissue healing.

Note that "prolonged inflammation" does not necessarily mean that inflammation has been apparent or noticeable for the affected person for a long time. Often by the time symptoms present, the inflammation process has been persistent and become pathological. At this point, anti-inflammatory drugs need to be used as soon as possible to minimise irreversible damage.

Aside from this, quite often inflammatory and immune processes are triggered without a need for them. Our immune system is quite prone to errors, and cases of misguided immune reactions are actually increasing. Consider for example allergies, which often manifest with skin-symptoms such as eczema that can be treated with anti-inflammatory creams.


How greater magnitude implies greater frequency of action potential?

There are several important points to answering your question, each somewhat independent of the others. First, lets think about this problem from the perspective of the axon hillock, where action potentials are thought to be generated.

Conduction of action potentials requires voltage-gated sodium channels

When you talk about antidromic action potentials, you mean when they start at the "end" of an axon and return towards the cell body. You can also get backpropagating action potentials into the cell body and dendrites, but these are impaired by two things: 1) fewer voltage-gated sodium channels, so the action potential is weaker or not really an action potential at all, and 2) impedance mismatch. The axon is very narrow; the soma is very big in comparison (this is less of a factor in the context of peripheral sensory receptors where the soma is located far from the site of action potential initiation, but it is still true for the neurites there). A few sodium ions coming in around the axon hillock is enough to depolarize that membrane enough to start an action potential, but when those ions diffuse passively into the rest of the soma, they have a lot more membrane area to cover, and they don't cause as much depolarization.

What all of this means is that the "strength" of a backpropagating action potential isn't less than that of an action potential in the axon.

Frequency is relative

When people talk about frequency coding of intensity, they are talking about a gradual increase in frequency, not going immediately to refractory period. For example, a cell may fire at 1 Hz, then fire at 4 Hz, then fire at 16 Hz, then fire at 64 Hz. If the cell has a refractory period of 5 ms, even at 64 Hz it is nowhere near it's theoretical maximum firing rate.

Related to that point...moving ions takes time and cells are not isopotential

Threshold isn't reached immediately in the axon hillock when a "refractory period" ends: that's the difference between an absolute and a relative refractory period. Ion concentrations and ion permeabilities set an equilibrium potential, but, it takes time for the potential to actually reach that equilibrium, and both the present voltage and equilibrium potential can be different in different parts of the cell: this leads to current flow, which takes time.

After an action potential, the axon hillock typically hyperpolarizes for a bit, sometimes followed by a brief depolarization. During that time, if there are other parts of the cell (such as dendrites) that are still relatively depolarized from a receptor potential, ions will be flowing from those areas into the axon hillock. This depolarizes the axon hillock, but again, this takes time (I'm purposely repeating that to convey a feeling of this all being a dynamic, moving process, with ions moving through each step). The amount of time it takes will depend on the voltage difference, so a bigger depolarization in the dendrites will bring the axon hillock back to threshold sooner.

Not that many ions flow during an action potential

This has been a recurring theme here, see this answer: Why is it possible to calculate the equilibrium potential of an ion using the Nernst equation from empirical measurements in the cell at rest?

The change in membrane potential isn't just because ions flow: it's because permeabilities change, briefly creating a new equilibrium potential. If you have in your mind massive quantities of sodium and potassium ions flowing, completely upsetting the ionic balance in the cell and drowning out all other electrical activity, you have it wrong.

Stimuli are often long-lasting

Especially if you are talking about a mechanical stimulus, most will last a lot longer than an individual spike, which is only ~1ms long. So although one transient stimulus can cause several action potentials, often what actually happens is that those receptor potentials are quite long lasting. Effectively, they set a new "resting potential" for the cell which is above the cells' firing threshold.

In summary:

Receptor potentials depolarize the cell, bringing them to or beyond firing threshold. An action potential starts in the axon hillock and propagates down the axon, but only has a minor impact on the rest of the cell. Importantly, the action potential is really brief, not many ions move, and there is current flow in both directions, so the depolarized parts of the cell are still depolarized somewhat even after a spike. As the initial axon segment recovers from post-action potential hyperpolarization and sodium channels leave their inactivated state, current from the receptor potential is flowing in, depolarizing the cell to threshold and causing another spike. Repeat.


flavivirus virus genome, methylated guanine

Why do you think the methylated G is present in these sequences?

I have two reasons for thinking your question isn't answerable.

As I said in my comment, based on BLAST results I don't think your sequence is complete — it appears to be missing the 5' end.
If the 5' end is missing then the end that gets capped is missing.

The 5' cap gets added post-transcriptionally and has a linkage (5′–5′ triphosphate) that prevents it from being sequenced.
That means that sequencing reaction don't see the G that gets methylated in the 5' cap.
This is why I suggest that you make sure you understand the capping process.


How do non-dimorphic birds distinguish sex of possible partners/rivals?

As very well explained also in Wikipedia https://en.wikipedia.org/wiki/Sexual_selection_in_birds , visual signaling is only one of the way birds uses to pick a partner, olfactory and acoustic signals also play a major role.


Pyruvate dehydrogenase: Apparently anomalous NAD/FAD redox reaction

Summary
The redox potential widely quoted in text books for the half-reaction reduction of FAD to FADH2 is indeed inconsistent with the observed direction of several reactions involving this coenzyme, including its reduction of NAD+ in the dihydrolipoamide dehydrogenase reaction. The reason for this is that the value quoted is determined for free FAD in aqueous solution, which does not equate to the situation within the enzyme. In its tightly bound state in flavoproteins, the immediate environment (and, in some cases, covalent linkage) alters the affinity of the flavin ring for electrons, hence causing the redox potential to deviate from that in solution. The extent and direcction of this deviation differs in different flavoproteins.
Restating the problem
The basic idea of chemical theromodynamics is that reactions are energetic favourable if the (Gibbs) free energy change is negative (see e.g. Section 14.1.1 of Berg et al.). Although the actual free energy change, ΔG, is influenced by the relative concentration of the reactants, the usual starting point for assessing this in biochemistry is the ‘standard’ free energy change at pH7 and 25˚C — ΔG0′. In the case of oxidation/reduction reactions the standard oxidation–reduction potentials E0′ of each of the two half reactions are usually known (as they can be measured in solution), and one calculates the ΔG0′ from the oxidation–reduction potentials of the two half reactions, using the formula:

ΔG0′ = –nFΔE0′

What is important for this discussion is not so much calculation of actual values, but determining their sign, as for a negative ΔG (reaction energetically favourable) a positive ΔE is required.
Let us consider an example using the much abbreviated version of Table 18.1 of Berg et al. Biochemistry, below:
Oxidant     Reductant       n     E´o (V)
Succinate   α-Ketoglutarate 2   – 0.67
NAD+        NADH            2   – 0.32
FAD         FADH2           2   – 0.22
Fumarate    Succinate       2   – 0.03

Consider one of the energy-generating oxidation reactions of the Krebs tricarboxylic acid cycle:
α-ketoglutarate + NAD+ → succinate + CO2 + NADH
This is made up of two half reactions:
(+ 0.67 V) α-ketoglutarate  → succinate
(– 0.32 V) NAD+ → NADH
which gives an overall ΔE0′ of  + 0.35 V, i.e. a negative ΔG0′, which is consistent with the actual direction of the reaction and the production of energy. (Actual worked numeric examples can be found in Berg et al.)
Now if we consider the dihydrolipoamide dehydrogenase reaction
NAD+ + FADH2 → NADH + FAD
The two half reactions are:
(+ 0.22 V) FADH2 → FAD
(– 0.32 V) NAD+ → NADH
This gives an overall ΔE0′ of – 0.1V, i.e. a positive ΔG0′, which, as the poster astutely points out, is not consistent with the direction of the reaction.
Resolving the apparent anomaly
Berg et al. do, actually, remark on this in section 17.1.1 on the pyruvate dehydrogenase complex:

This electron transfer to FAD is unusual, because the common role for
FAD is to receive electrons from NADH. The electron transfer potential
of FAD is altered by its association with the enzyme and enables it to
transfer electrons to NAD+.

So, how is “the electron transfer potential of FAD altered by its association with the enzyme”? The quotation from Ghia and Massey1 provides a general summary:

The pyrimidine nucleus of the three-membered ring system is electron-deficient and can be viewed as an ‘electron sink’. In thermodynamic terms, any interaction which tends to lower its electron or negative charge density will increase the redox potential. The reduced flavin consists roughly of an electron-rich phenylenediamine moiety fused with a (4,5-diamino)-uracil. The latter is the moiety in which the negative charge (i.e. two electrons taken up by the oxidized flavin) is localized and, most importantly, stabilized. The degree to which this negative charge is stabilized or destabilized is an important factor governing the redox potential. Thus while a positive charge in the protein around the pyrimidine ring will contribute to increase the redox potential, the presence of negative charge or of a hydrophobic environment will lower it.

In the specific case under consideration — dihydrolipoamide dehydrogenase — it has been established2 that a positively charged lysine-57 sidechain (numbering for the A. Vinelandi enzyme) that increases the redox potential (with, perhaps, a small contribution from the backbone N of alanine-326):

[FAD environment in dihydrolipoamide dehydrogenase from A. Vinelandi. NAD is shown in light blue, except for the O and N atoms at the end of the flavin ring interacting with the protein. A section of the latter is shown as a wireframe in salmon pink without sidechains, except for lys57 and ala326. (Own diagram from 3LAD.pdb)]
A second apparent anomaly and its resolution
In drawing attention to the apparent anomaly in the reduction of NAD+ by FADH2, the poster suggested that this would imply one should by able to obtain enough energy to produce 3ATPs from reducing FADH2. The problem with this is that one actually needs FAD to have a lower redox potential to perform the reduction of fumarate that occurs in the Krebs cycle:

This can be seen by considering the redox potentials in the table above:
succinate + FAD + → fumarate + FADH2
The two half reactions are
(–0.22 V) FAD → FADH2
(+0.03 V) succinate → fumarate
Thus, there is an overall ΔE0′ of – 0.19V, i.e. a positive ΔG0′ — another anomaly!
Berg et al. are rather coy on this one. They do not comment, but in their Table 17.2 of free energy changes in the steps of the TCA cycle — where all the other values are given as exact figures — they quote  “~0” for this step.
This implies a higher (more positive) redox potential for FAD than the –0.22 quoted in the table — certainly not the lower one of dihydrolipoamide dehydrogenase.
I turns out that this is, in fact, the case. In succinate dehydrogenase (aka as fumarate reductase) FAD is covalently attached to a histidine residue (his44 in E. coli) at the other side (position 8) of the flavin ring3.

[FAD environment in succinate dehydrogenase from E. coli. NAD is represented as previously. A section of the latter is shown as a wireframe in salmon pink without sidechains, except for his44 and a backbone N. (Own diagram from 1L0V.pdb)]
An extensive review4 of the redox potentials of covalently and non-covalently bound flavoproteins shows that covalent attachment increases the redox potential.
Final observations

Chemistry is a powerful tool for understanding biology at the
molecular level. Biology is subject to the laws of chemistry, but the
chemistry of the special environments encountered (protein interiors,
spaces compartmented by membranes) need taking into consideration,
something that the classically trained chemist, new to the subject,
may not fully realized.
Elementary textbooks often have to walk a fine line between
comprehensibility and truth. The student of biological chemistry
should realize that the initial simplifications that enabled him to
get an overall grasp may mask greater complexities. One of the
intellectual satisfactions in science can be found by resolving these
complexities in a rationale manner.

References
1Ghisla and Massey (1989) Mechanisms of flavoprotein-catalysed reactions
2Maeda-Yorita et al. Biochemistry (1994) 33, 6213–6220
3Kim and Winge (2013) BBA 1827, 627–636
4Heuts et al. (2009) FEBS Journal 276, 3405–3427


Why do people with type O blood have anti-A and anti-B antibodies?

To understand what's happening here, let's have a look at the actual ABH (or ABO) antigens:

As you can see, they are not very big molecules: quite the opposite, they are relatively small globosides.
That being said, how it's possible a type O individual producing anti-A and anti-B antibodies without having any contact with the antigens? And that is the same as asking "how it's possible a type A individual producing anti-B antibodies without having any contact with the antigen?"
The answer is: there was contact with the antigens, even without a blood transfusion.
According to Laura Dean (Blood Groups and Red Cell Antigens, chapter 5):

ABO antibodies in the serum are formed naturally. Their production is stimulated when the immune system encounters the "missing" ABO blood group antigens in foods or in micro-organisms. This happens at an early age because sugars that are identical to, or very similar to, the ABO blood group antigens are found throughout nature.

Thus, from an early age, we have contact with the antigens, coming from food or bacteria in our digestive system. As we get in contacts with antigens A and B, this is what happens:

People with type A blood: they will produce anti-B antibodies.
People with type B blood: they will produce anti-A antibodies.
People with type O blood: they will produce anti-B and anti-B antibodies.
People with type AB blood: they won't produce antibodies (regarding A and B antigens).

Source: Dean, L. (2005). Blood groups and red cell antigens. 1st ed. Bethesda, Md.: NCBI.


You might want to take a look at Bacillus subtilis. Most of the lab strains don't contain plasmids, though they have been found in some environmental isolates.

https://academic.oup.com/femsre/article/21/4/337/490925

All this depends on exactly what you're looking for: a species with no known plasmids in any isolates, or some commonly used lab strains with no plasmids?

M. tb is a pretty unique case. Most of the other species in the Mycobacterium genus do contain plasmids.


Which cryogenic vials and caps are ideal for storing glycerol stocks?

For any kind of frozen cell stock (for cell culture or bacteria) we routinely use freezing vials similar to these: http://www.sigmaaldrich.com/catalog/ProductDetail.do?D7=0&N5=SEARCH_CONCAT_PNO%7CBRAND_KEY&N4=V9255%7CSIGMA&N25=0&QS=ON&F=SPEC

These tubes are internally threaded with a rubber grommet to seal the lid and make the tube air and water tight. I suspect the air tight seal prevents condensation from entering the tube and freezing within the tube, but I've never had a problem with either choice of tube.

The tubes don't really matter at -80 C for a glycerol stab. Freezing cells in liquid nitrogen on the other hand has a huge impact when storing in liquid nitrogen. Some tubes are meant to be stored in the liquid versus the vapour phase of nitrogen and not matching the tube to it's intended storage condition can result in explosion of the tube.


Yes. The dbDEPC 2.0 database for example.
If you want to extend your search to pathways the best database I know of is the KEGG.

There are multiple databases out there. You might want to look at this wikipedia page.

By the way what you are looking for is called a cancer proteomic signature.


As well as messenger RNA (mRNA) that encodes protein, there are a variety of RNAs that have structural or regulatory roles and do not code for protein. Ribosomal RNAs (rRNA) are one such structural RNA. Like mRNA, rRNA (and other stable RNAs) are  specified by genes in the chromosomal DNA, although the details of their transcription (the RNA polymerase employed and the nature of the promotors) may vary.

The mature eukaryotic ribosome contains three species of rRNA that are analogous to those in prokaryotes — 18S (cf. 16S), 28S (cf. 23S) and 5S (sizes for mammals). However there is an additional 5.8S species in eukaryotes. The questions addressed in the article are: 1. What genes and what transcripts give rise to these mature RNA species? and 2. Is there a single gene for each species or multiple repeated genes? A third, implicit, question is whether the situation in eukaryotes is similar to that in eukaryotes.

The answer to question 2 is given in the phrase “forms a tandem repetitive cluster” — there are multiple copies of the genes for 18S, 28S and 5.8S rRNA, clustered together one after another. These genes are separated (‘spaced apart’) by regions of the genome that are not transcribed, and are termed non-transcribed spacers (NTS).

(There are also multiple copies of the 5S rRNA gene, although these are only clustered in some species.)

The answer to the first question is that the 18S, 28S and 5.8S rRNA are transcribed from a single gene and are initially present in a single transcript. This is processed by ribonucleases to generate the three mature species. If one compares the sequences of the mature species with that of the gene/transcript one can identify portions of the initial rRNA transcript that are not present in any of the three mature species. These are termed transcribed spacers. The one at the 5′ end of the transcript is termed the external transcribed spacer (ETS), and those that are between the three mature species are termed  internal transcribed spacer (ITS).

The situation in prokaryotes differs from eukaryotes in so far as the 5S rRNA gene is part of the gene/transcript containing the 16S and 23S rRNAs, lying at the 3′ end of this. This is mentioned in the Wikipedia entry for Ribosomal RNA, rather than that for ribosomal DNA, quoted in the question, and illustrated in the figure below taken from the teaching web pages of Ross Hardison at Penn State University. Notice the transfer RNA gene in the transcript between the portions resulting in the mature 16S and 23S rRNAs.


It is a long time since I set in a Computer Sci (AI) talk about this….  This explains it a bit.

Once ants have eaten they return to the nest.
On the way back to the nest they put down a scent.
This scent fades with time.
Most ants follow the scent.
(A few ants walk randomly to find new food, or a new faster way to the current food.)

So if the agents eating your poison bait do not make it back to the nest, there is no scent trail leading to the poison for more ants to follow.     But the ants that went round the bait to find other food, did make it back to the next, so setup a new sent trail.

If a poison kills the ants quickly, the customer is likely to see dead ants and therefore buys more of the poison.   However a poison that kills the ants slowly, so the ants don’t die until they get back to the next, is likely to get more of them, as there is now a strong sent tail to the poison.


Maybe it's a Mabee's Salamander, Ambystoma mabeei.  Unfortunately, I can't really see the underside in your video, but I have the sense that it is a lighter color.  The clubbed tail, with an apparent break, seems like it may have been autotomized or otherwise injured, making it harder to compare.  I had the impression your example had dark spots dorsally and lightening ventrally, as can be seen in the image above.  Some other images are a bit different.  However, Mabee's Salamander is only found in "six localities in the coastal plain in extreme southeastern Virginia: the cities of Hampton and Suffolk and the counties of York, Southampton, Gloucester, and Isle of Wight. It is also found in Newport News." and is considered threatened, so unless your location matches what you read there it is still not likely to be the answer.


Is there evidence that children should play in dirt to get healthy?

This answer focuses primarily on allergies, for which there is more reliable research, but touches on general immunity towards the end.

It is certainly true that the prevalence of allergies is increasing worldwide, and seems to be related to a rise in the so-called 'modern lifestyle' which avoids exposure to potentially harmful environmental factors.

  The prevalence of allergic diseases and asthma are increasing worldwide, particularly in low and middle income countries. Moreover, the complexity and severity of allergic diseases, including asthma, continue to increase especially in children and young adults, who are bearing the greatest burden of these trends. - World Allergy Organisation Journal

The idea that playing in the dirt builds an individual's immune system and reduces the chances of allergies etc. is known as the "hygiene hypothesis" (or, more accurately, the hygiene hypothesis states that

  due to reduced exposure to microbial components, the proposed allergy-preventing potential of these factors is no more present in sufficient qualities and/or quantities, which leads to an imbalance of the immune system with a predisposition to the development of allergic disorders." - Epidemiological and immunological evidence for the hygiene hypothesis.

)

Aside from potential mechanisms, there is certainly evidence for the hygeine hypothesis

  The researchers studied the immune system of mice lacking bacteria or any other microbes ("germ-free mice") and compared them to mice living in a normal environment with microbes.
  They found that germ-free mice had exaggerated inflammation of the lungs and colon resembling asthma and colitis, respectively. This was caused by the hyperactivity of a unique class of T cells (immune cells) that had been previously linked to these disorders in both mice and humans.
  most importantly, the researchers discovered that exposing the germ-free mice to microbes during their first weeks of life, but not when exposed later in adult life, led to a normalized immune system and prevention of diseases.
  Moreover, the protection provided by early-life exposure to microbes was long-lasting, as predicted by the hygiene hypothesis. - Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

As far as I know there is no consensus on this issue, however a number of scientific studies have proposed potential mechanisms to explain the rise in allergies and other such conditions; one of the most widely accepted ideas is that an avoidance of germs and microbes early on in life leads to

  changes in the fine balancing of T helper cell 1 (Th1), Th2 and regulatory T cell (Treg) responses which are triggered by altered or missing innate immune cell activation. In fact, proper activation of cells of the innate immune system via their so-called pattern recognition receptors has been demonstrated to play a crucial role in early shaping of the immune system and suppression of the development of Th2-driven allergic immune responses. - Epidemiological and immunological evidence for the hygiene hypothesis.

this would seem to explain the observed phenomena.

It is definitely true though that there has been and will continue to be an element of natural selection involved here, as you have pointed out, because it is a force that is found pretty reliably in these sorts of situations. It is certainly logical that exposure to microbes during infancy will help weed out those with a weaker immune system (assuming they died because of infection/disease etc.), which over time would create a population and species that was more resilient. However, I can't find any studies to back up this idea. It is also a somewhat separate issue to the idea of the hygeine hypothesis, which describes changes to a specific individual within their lifetime rather than necessarily across a population due to natural selection and evolution, which is the explanation you have provided (unless I misunderstand your point?).

I only have a general understanding of immunity, however it is generally accepted that exposure to a pathogen (if this episode is survived) will result in an immune system which is better able to counter that pathogen in the future - this is the whole concept of vaccinations. therefore it makes sense that, again, low levels of contact with 'germs' will build a child's immunity.

Overall I think that it is a complex issue without a generally accepted answer as yet, however it seems to me based on this research that "playing in dirt" (in other words, being exposed to low levels of pathogens, microbes and toxins) does in fact build immunity and reduce the likelihood of developing allergies in later life, even if we don't know the exact mechanism for this yet.

aside from any potential immunity benefits, most children find playing in dirt fun (I know i did), so for the most part i'd say let them do it anyway!

My sources:

https://www.sciencedaily.com/releases/2012/03/120322142157.htm
https://www.ncbi.nlm.nih.gov/pubmed/17544829
https://waojournal.biomedcentral.com/articles/10.1186/1939-4551-7-12


Can the human body enter "Power Save" mode?

If you are performing the fast for ritualistic or spiritual purposes, then that mental state likely overcomes the feeling of thirst or hunger, especially if you are an otherwise healthy person.

As for the physiological aspects. The Human Body is made up of 2/3 water, and as your kidneys are still functional, they are constantly filtering, and creating urine. The body can last a few days without water.

As for food, the body has about a one day supply of sugar, assuming limited exertion, that it can consume before it begins to break down other substances. Then there are the fat reserves. The average person will likely have on the order of 7 to 15 kilograms of fat in reserve. There are 9 calories per gram of fat, so roughly 63 to 135 thousand calories worth of energy. Since the average adult will use about 2000 calories a day, then you can see that burning body fat alone would allow about a months worth of energy.

I am not saying that these are optimal conditions, but the body of a healthy human adult can easily withstand a 24 hour fast with no adverse effects. You would likely encounter more problems if you tried to go without sleep for the same period of time than if you refrained from food or water.


Does neuroeconomics study the brain or study economics?

As @Kyle beautifully summed-up,

  Neuroeconomics is the study of the neural basis of economic behavior.

The terms applies to studies concerning the appeal of new logos for marketing purposes to the understanding of the neural correlate of subjective value. The term neuroeconomics has been subject to some debate which made it sometimes unclear. In particular, the term is ambiguous with regards to its applications.

Are the theories that are built upon these studies used for marketing purposes (some would say "to optimize brain washing you in the necessity of buying a 7 blade razor") or for the sake of knowing how the brain may be better understood and to the therapeutical applications of these new theories.

My answer would therefore be this:

the brain is a complex system for which science often used analogies to make progress. It has been compared as steam machines in the 1800s, electricity in the 1900s, or to computers in the this century.
The complex interactions present in an economic system -as studied by game theory for instance- present a powerful analogy to understand the brain.
Of course, it thus impacts our knowledge on economics as these are often based on our knowledge of decision making. Thus, your two options are (1) and (2) are interconnected.


Binucleate cells of transitional epithelium (bladder)?

In other stratified epithelium, it is the basal cells that replicate to replace the cells lost in the top layers.  In transitional epithelium, which is also a stratified epithelium, the most superficial layer of cells are replaced or  turnover occurs because of mitosis of the superficial facet cells themselves.  In this case it is not unusual to see dividing cells in its last stage of division as a large cell containing two nuclei, which soon that cell will be 2 cells.


Hormones have antigens.  Usually they are antigens our immune systems recognize as self.

Pretty much any big biological molecule will have antigens.  FSH is no exception.  The binding of FSH to anti-FSH antibodies (in a laboratory system) is one way to measure FSH levels in a human.

 Definition and Measurement of Follicle Stimulating Hormone

  B. High-affinity binding assays
  1. Immunoassays. Immunoassays are widely used for clinical determination of FSH for diagnosis and in physiological studies
  because they are rapid, readily available, relatively cheap, and
  sensitive... Most commercially available assays are now based on
  sandwiches of monoclonal or monoclonal-polyclonal antibodies with a
  variety of detection modes and are generally more sensitive and
  precise than one-site assays. The latter assays are highly specific
  and may exclude some forms of the hormone of interest (e.g., Ref.
  176).

The antibodies used to measure FSH are from other species of mammals - usually mice but sometimes other animals. People (and other animals) normally do not form antibodies to molecules that have been present in their bodies since development.  The immune system is educated early on about what is self and so exempt from attack.  Mouse FSH is antigenically different enough from human FSH that mice can be induced to form antibodies against human FSH and then those mouse antibodies are used to make the lab test.   You can find out how those tests work with a little googling because they are for sale and their owners will brag about them.

It is possible to form antibodies against your own FSH or any other biomolecule in your body.  That is autoimmunity and usually that is not good.  The woman in the linked article was infertile because of antibodies against FSH.  Her FSH level was very high because her pituitary was cranking it out.  Her immune system bound it up as fast as it came out and so the FSH did not work.

Abnormally Elevated Follicle-Stimulating Hormone (FSH) Level in an Infertile Woman

  We describe here a case of anti-FSH autoantibodies leading to
  persisting very high FSH serum levels in an infertile woman.

Bullet points

Any biological macromolecule has antigens.
The immune system may tolerate antigens it has been educated to recognize as self.
Sometimes the immune system becomes intolerant of an antigen it should recognize as self and attacks that antigen.  This is autoimmune disease.


This is a common misconception about evolution, many skeptics ask something along the lines of "If humans evolved from monkeys, why are there still monkeys?" The answer is that evolution is not a linear process of one species becoming the next species becoming the next. Species branch off much more like a tree. At some point in the past the last common ancestor of humans and monkeys split into two directions, one that became the apes including humans, and one that became modern monkeys. Evolution did not stop for either branch, but only our branch became humans, after several more branchings. Sometimes species adapt and evolve without major changes in morphology, for example modern turtles look a lot like turtles from 100 million years ago, but this doesn't mean they haven't evolved.

The intermediate species are often lost with time as environmental conditions and competition changes. For example, if one early human group found itself competing with a slightly more advanced human group with better tools, the more primitive group would have trouble getting enough food and eventually die off, leaving the more advanced group to pass its genes on.

Now, if those more primitive humans were more suited to a particular niche, they could survive there. Lets say they could climb trees better ( assume REALLY primitive ancestors, barely out of the forest ), they might survive in the forested areas while the more advanced groups become dominant in the grasslands. Something like this is why our ancestors didn't totally displace monkeys, the monkeys were better suited for their forested ecosystem. If those same monkeys had to live on dry savannas we would have eaten them all long ago.


meaning of binding capacity and binding affinity

Without any context... is hard to give a detailed answer.

I understand for bindind capacity the ability of a molecule to bind or attach to another molecule.
Binding affinity is the strength of the binding interaction between a single molecule and the other one.


Why is sedimentation rate significant for a ribsome

Summary

Ultracentrifugation was necessary to identify and ribosomes, and characterize them on the basis of their size. The method does not allow an absolute measurement of molecular mass, but uses a relative quantitation as sedimentation coefficient, expressed in Svedberg Units (S).
Nuclei and mitochondria were characterized by light microscopy and, being much larger than ribosomes, sediment at speeds which do not require an ultracentrifuge and would not be resolved in an ultracentrifuge.
Nuclei and mitochondria vary in size, so their size is not a defining property for them. Ribosomes from one source all have the same size, which may differ from that of ribosomes from other sources in a definitive manner.
Ribosomes are composed of smaller subunits, which are assembled from precursor particles of a different size. They occur in larger complexes on mRNA (polysomes). These forms of different but specific size can be separated and characterized by on the basis of size in the ultracentrifuge — i.e. by their sedimentation coefficient.

Amplification and examples

Prokaryotic monoribosomes (e.g. E. coli) have a sedimentation value
of 70S, the cytoplasmic monoribosomes of eukaryotes (e.g. rat) 80S,
and those of mammalian mitochondria between 50 and 60S. The values may differ for different eukaryotes and prokaryotes, but are constant for one species, reflecting the constant ribonucleoprotein composition of the particles.
All ribosomes have two subunits — a large subunit (50S and 60S for the prokaryotes and eukaryotes mentioned, respectively) and a small subunit (30S and 40S). The subunits are identified by ultracentrifugation, which is also used to separate them preparatively. Hence it is natural that their S values should be used to name them.
The formation of ribosomal subunits from RNA and protein involves sequential addition of proteins. The different sized intermediates at different stages can be differentiated by their sedimentation, and it is natural to refer to them by their S values.
Ultracentrifugation is also used to separate and characterize the ribosomal RNAs in a similar manner.

Bibliography

The Wikipedia entry on ribosomes corroborates some of the factual data I have presented.


The principal function of spermaceti and the associated structures in a sperm whale head, is echolocation. The composition of spermaceti suggests that it functions as an acoustical transducer, helping to focus the powerful sound waves used for echolocation. These sound waves likely do not actually stun squids, but they do help sperm whales to find and pursue squids in deep, dark waters.

An echolocation click is formed at the tip of sperm whale's nose, where it is directed backwards, through the spermaceti, toward the sperm whales brain. It then is reflected off an air sac on the sperm whale skull, and redirected forward through a series of lenses before it moves into the water. Check out an illustration of this in the Møhl et al 2003 paper: https://pdfs.semanticscholar.org/88d4/271e9f7490c1173234a2445cf8ddf92fd51f.pdf

The complicated anatomy in a sperm whale's head seems to be directly evolved for echolocation.

Sources:
Karol, R., Litchfield, C., Caldwell, D.K. et al. Mar. Biol. (1978) 47: 115. https://doi.org/10.1007/BF00395632

Møhl, B., Wahlberg, M., Madsen, P. T., Heerfordt, A., & Lund, A. (2003). The monopulsed nature of sperm whale clicks. The Journal of the Acoustical Society of America, 114(2), 1143-1154.


What is considered incorrect for a cladogram's time axis?

In your first example, each species becomes "frozen in time" once it evolves implying there is no further change. A slightly more complex cladogram will help.

Imagine the species A ancestor, after branching off the remote ancestor, serves as the ancestor to species E. You need to draw that line in some direction other than along A. Most popularily, that line would extend upward to the right. With the temporal axis as you first show, how did species E even evolve since A is frozen in time? Furthermore, the advantage of a vertical time axis allows us to see that species E appeared after species B and a bit before species C (horizontal dashed line).


How semi-synthetic cell with artificial DNA works

The altered E Coli still only made use of the regular 20 amino acids (presumably).

Looking at the original citation, Malyshev et al didn't characterize the RNA in their altered E Coli at all. All they did was add free X and Y to the E Coli's growth medium and add a gene to the E Coli that expressed an algal nucleotide triphosphate transporter. Malyshev et al then demonstrated that replication (copying of the DNA) proceeds normally and in such a way as to preserve the X and Y content.

So no information as to whether any of the products downstream from the DNA (ie mRNA, proteins, etc) were affected by their modifications.


Is there a way tell apart dinosaurs from similar extinct reptiles?

There are several defining morphological characteristics of dinosaurs. Including their ankle structure and perforated acetabulum, Aka the hole in their hip goes all the way through, as well as a few other minor features. These combined makes it literally impossibly for a dinosaur to take on a sprawling pose without breaking hind leg in many places, this is why you will often see an erect posture given as the reason, but that is a product of these feature not the defining feature itself, there are many ways to achieve upright posture.

Now of course we are moving away from purely morphological definitions, cladistically dinosaurs are defined as The last (most recent) common ancestor of Triceratops horridus and Passer domesticus (common pigeon), and sometimes Diplodocus carnegii as a third, and all of its(the ancestor's) descendants.

A more superficial quick and dirty method is if it is a pterosaur or lives in the ocean it is not a dinosaur, If its limbs sprawl it is also not a dinosaur. I should also include this guys work, since he attempted to create a complete cladogram of every dinosaur, so you can visualize the group.


How do animals avoid the problem of inbreeding?

The question is interesting. However, it will be impossible to answer accurately for all birds as the mechanisms actually used vary from species to species. So I will give you some information in the general sense.
Recurrent inbreeding reduces inbreeding depression
Inbreeding depression is caused by both

Recessive deleterious alleles that are brought to homozygosity
Some epistatic interaction

In any case, in a population where inbreeding is common, those recessive deleterious alleles and alleles involves in these deleterious epistatic combinations will be washed out (or at least brought to lower frequency) of the population via selection and the population will end up suffering less from inbreeding than a typical outbreeding population. In the extreme, a population of exclusively selfer individuals, such deleterious recessive alleles are brought to extremely low frequency within lineages.
How to avoid inbreeding?
Now, sure animals and plants typically don't have a big book that allow them to tell how related they are to another individual. However, there are other mechanisms of kin detection
Self-incompatibility
For example, in plants self-incompatibility is thought to be relatively uncommon. There exist many mechanism, so I-ll just consider a simple example. Consider a self-incompatibility locus as a specific loci for which if the same allele is shared by both the pollen and the ovule, then no fertilization occurs. This prevents selfing and prevents mating with many of the closely related mechanisms.
Body odour and sexual attraction
Also, there are mechanism that can mediate sexual attraction toward individuals that differ. The classical example is Major histocompatibility complex (MHC) and sexual attraction (vertebrates), where individuals tend to be attracted to individuals that have a different MHC.


Is molecular oxygen (O₂) consumed in any process (in humans) other than acting as an electron acceptor for the ETC?

Molecular oxygen also has roles in antimicrobial defense1,2. Specifically macrophages use O2 to create cascades of reactive nitrogen intermediates (RNI) and reactive oxygen intermediates (ROI; aka ROS) — these compounds have antimicrobial effects.

The RNI cascade starts with nitric oxide (NO) and is catalyzed by a nitric oxide synthase, which converts arginine and O2 into citrulline and NO.
The ROI cascade starts with superoxide (O2•-) and is catalyzed by a NADPH oxidase, which transfers an electron from NADPH to O2 creating superoxide.

Figure 1 from2 gives an overview of these reactions:

Legend for figure 1:

  ROI and RNI production in mammalian cells via phox and NOS: parallel but connecting paths. Nitroxyl anion (NO−), a one-electron reduction product of nitric oxide (•NO), is unlikely to arise from •NO under physiologic conditions, but is considered by some investigators to be a primary and more toxic product of NOS. Reaction of RNI with cysteine sulfhydryls can lead either to S-nitrosylation or to oxidation to the sulfenic acid, as well as to disulfide bond formation (not shown), all of which are potentially reversible. Peroxynitrite anion (OONO−) and peroxynitrous acid (OONOH) have distinct patterns of reactivity, but for simplicity, the text refers to both as peroxynitrite. OONOH spontaneously decomposes via species resembling the reactive radicals, hydroxyl (OH•) and/or nitrogen dioxide (•NO2). When L-arginine is limiting, NOS can produce superoxide (O2⨪) along with •NO, favoring the formation of peroxynitrite.

References:

1: Weiss, G., & Schaible, U. E. (2015). Macrophage defense mechanisms against intracellular bacteria. Immunological reviews, 264(1), 182-203.

2: Nathan, C., & Shiloh, M. U. (2000). Reactive oxygen and nitrogen intermediates in the relationship between mammalian hosts and microbial pathogens. Proceedings of the National Academy of Sciences, 97(16), 8841-8848.


The reason why cells (and tissues) die during freezing is that ice crystals rupture the cell membranes1,2, so to me it seems the question is actually why early embryos can survive this process.

The answer depends on the technique used, but it comes down to size.  Small tissues (or cells) have a large surface area to volume ratio.

In techniques that use cryoprotectants (compounds that suppress ice crystal formation), the small size allows efficient replacement of water by cryoprotectant prior to freezing (and the reverse after thawing) so that the cells don't have time to die1,2.

In flash freezing (vitrification), the small size allows the entire tissue to be frozen instantaneously, which also suppresses ice crystal formation1,2.

This Scientific American article is very relevant as well.

References:
 1: Konc, J., Kanyó, K., Kriston, R., Somoskői, B., & Cseh, S. (2014). Cryopreservation of embryos and oocytes in human assisted reproduction. BioMed research international, 2014.

2: Loutradi, K. E., Kolibianakis, E. M., Venetis, C. A., Papanikolaou, E. G., Pados, G., Bontis, I., & Tarlatzis, B. C. (2008). Cryopreservation of human embryos by vitrification or slow freezing: a systematic review and meta-analysis. Fertility and sterility, 90(1), 186-193.


How bad is ethidium bromide in your plasmid for downstream applications?

Purification and isolation of DNA bands by cutting them from agarose gel is commonplace (Lee et al., 2012). The purification step after excision of the band gets rid of most of the EtBr and other impurities. E.g., see the websites from Isogen and Sigma-Aldrich.

Reference
- Lee et al. J Vis Exp (2012); 62: e3923


What is the difference between how motor function is controlled in cerebrum vs frontal lobe?

The motor cortex, basal ganglia, and cerebellum all contribute to motor control.

Cortex stores movement memory, basal ganglia is responsible for "chunking", or segmenting the memory, and cerebellum compares cortex memory and current movement to correct for errors and to update perception of movement. So to answer your question they all control different components/processes of learned movements at the same time and in conjunction.


Possible for bacteria to burst container?

Yes. Bacteria (and fungi) can digest sugar to produce CO2 gas. The latter occupies more space, and can burst contains such as closely sealed bottles (e.g.: for a bacteria / yeast co-culture: http://kombuchahome.com/how-to-prevent-your-kombucha-bottles-from-exploding/ )


Properly changing the time scale of a parameter in a growth model

These values are not absurd: it's just a different unit, it does not change the reality of th phenomenon.

The fact that your population can grow by a $48$ or $36~\mathrm{log}$ factor in one day, while the carrying capacity is $10^7$ bacteria, only means that the growth happens in less than one day (once the latency phase is over). Many bacterial population can grow in less than one day, it is not shocking.

In my opinion, it is not absurd to use the growth rates in $\mathrm{log}~ \textrm{bacteria} \cdot \textrm{day}^{-1}$. There is not need to rescale values if you just want to convert hours into days.


Can you make sperm and eggs from the same person using in vitro gametogenesis?

At present (early 2017) the answer is No.

The trick to make spermatid like cells (ie they are not real sperm cells and need to be injected into an oocyte to accomplish fertilization) from ES and iPS in a dish was just achieved last year http://www.sciencemag.org/news/2016/02/new-method-grows-sperm-dish

The trick to make oocyctes from stem cells is not as complete and still requires an lab grown ovary to complete the process. http://www.sciencemag.org/news/2016/10/mouse-egg-cells-made-entirely-lab-give-rise-healthy-offspring.

The methods above still use ES cell of the appropriate gender. Female ES cells to make oocytes. Male ES cells to make sperm.  No info on female ES cells being driven to make sperm or even spermatid like cells.

That said... we have this paper http://news.nationalgeographic.com/news/2004/04/0421_040421_whoneedsmales_2.html, where a mouse is genetically engineered to produce oocytes that have imprinting patterns similar to a sperm. This genetically modified oocyte is then forced to fuse with a normal oocyte. Success rate was very low. 371 fused oocytes, 10 live births, 1 surviving to adulthood.


Short answer
Based on shape and approximate position, I think it is the corpus callosum.

Background
I think it is the corpus callosum (Fig. 1). The corpus callosum is approximately 10 cm in length and is C-shaped. It becomes thicker posteriorly, as is also evident in your image. The corpus callosum is a structure consisting of white-matter, containing about 200 million axons.

Fig. 1. Mid-saggital section of the brain showing the corpus callosum. source: University of Central Florida

I think it is not the caudate nucleus, alhough it has also the curved shape. The caudate is positioned more laterally than the corpus callosum and by the looks of it your picture shows a mid-sagittal section of the brain. The caudate seems to be positioned too far laterally in the brain as far as I can see (Fig. 2).

Fig.2. Nucleus caudatus. source: Brain Notes


Would the human body react faster to touch or sight

A "touch" or "haptic" sensation will be much faster due to several reasons:

Haptic feedback can be processed without the presence of any higher-order cognitive processing, therefore meaning that the signals are being processed via a monosynaptic route.
There are short reflex arcs between the spinal cord and the limb (meaning that you can react before you are consciously aware of it)

A visual sensation will be much slower:

The processing of the signal will require higher-order cognitive processing, and this takes time. I read that it takes between 50ms-200ms. (polysynaptic route)

Interesting article about this topic


Why aren't mitochondria and plastids considered symbiotes of eukaryotic cells?

I would say it has to do with the amount of mitochondrial or sequence that has been transferred to the host genome. As a consequence of all this information stored in the host genome, mitochondria cannot reproduce without the host. In this way, they are not their own organisms, but rather organelles.

Over evolutionary time, the line between organelle and intracellular endosymbiont gets blurry, but in their current state, mitochondria are organelles.

The same goes for for plastids, in general.


Why is a mosquito feeding on human blood not a parasite?

A mosquito is a biological parasite, it is not a medical parasite.

There are two definitions of parasite. A biological/ecological definition and a medical/physiological interaction definition.

A parasite in biological terms is an organism that benefits from a parasitic relationship; a parasitic relationship being a non-mutual relationship between species, in which one species benefits at the expense of the other. Generally the host is not killed by a small number of parasites. When the host is killed the organism is usually called predator or parasitoid.
A parasite in medical terms is an organism that lives on or in a host and gets food from or at the expense of its host.

The difference is small but important; only the medical definition requires the parasite to live in or on the host for prolonged periods. It is a much narrower definition.

Biologically, a female mosquito is an indirect ectoparasite, it can be facultative or obligate depending on the species. It harms its host to benefit itself, that is all that is needed to be a parasite by the biological/ecological definition. And just like a leech or vampire bat it is hemophagic and leaves the host as soon as it is done feeding. Brood parasites are another great example of a biological parasite that does not live on or in the host. So a cuckoo would be a biological parasite but not a medical parasite. When you consider the function and practice of medical science the more narrow definition makes sense, they are not concerned with parasites that are not going to stick around or not affect the host organism's physiology directly. By the narrower medical definition, none of these organisms are parasites even though by the biological/ecological definition they are.

Consider the wiki or a paper on parasite evolution vs say the CDC to see the difference.