The colour of human eyes is determined by the pigmentation present and the scattering of light. Variance in the colour and density of the pigments affects how light is absorbed and reflected causing the different iris colours we see. Wiki has a fairly comprehensive coverage on the topic so,I'll use a few of the wikipedia examples to explain how the pigmentation and scattering of light interact to give colours:

Blue eye colour is the result of pigment in low concentration and Rayleigh scattering (or Tyndall effect) of the short light wavelengths (blue is short, red is long).

  "There is no blue pigmentation either in the iris or in the ocular
  fluid. Dissection reveals that the iris pigment epithelium is brownish
  black due to the presence of melanin. Unlike brown eyes, blue eyes
  have low concentrations of melanin in the stroma of the iris, which
  lies in front of the dark epithelium. Longer wavelengths of light tend
  to be absorbed by the dark underlying epithelium, while shorter
  wavelengths are reflected and undergo Rayleigh scattering in the
  turbid medium of the stroma. This is the same frequency-dependence
  of scattering that accounts for the blue appearance of the sky.
  The result is a "Tyndall blue" structural color that varies with
  external lighting conditions.

Brown eyes are the result of higher melanin concentrations which absorbs more of the light, reducing the amount of light being reflected.

  "In humans, brown eyes result from a relatively high concentration of
  melanin in the stroma of the iris, which causes light of both shorter
  and longer wavelengths to be absorbed."

Green eyes appear to be mid-ground between blue and brown, they have more pigment than blue but less than brown.

  "As in the case of blue eyes, the color of green eyes does not result
  simply from the pigmentation of the iris. Rather, its appearance is
  caused by the combination of an amber or light brown pigmentation of
  the stroma, given by a low or moderate concentration of melanin, with
  the blue tone imparted by the Rayleigh scattering of the reflected
  light."

More can be read on this in these two studies: study 1 & study 2

What is Rayleigh scattering / the Tyndall effect and why do they turn eyes blue?

I shall refer to this as the Tyndall effect but in the literature both Rayleigh and Tyndall are used because they are apparently very similar though Tyndall occurs with much larger particles. The Tyndall effect is caused by the variable scattering of light by particles depending on the wavelength of the light and relative size of the particles. Shorter wavelength lights are scattered more than the longer ones (so more red light is absorb than blue) which means more blue light is reflected. When more melanin is present in the iris it will better absorb the short wavelength light than when there is little melanin, therefore, people with low melanin levels appear to have blue eyes.

  "An analogy to this wavelength dependency is that longwave electromagnetic waves such as radio waves are able to pass through the walls of buildings, while shortwave electromagnetic waves such as light waves are stopped and reflected by the walls."

Why do eye colours change?

Again, wikipedia has a fairly thorough section on this and I will just summarise and directly quote it. Eye colour can change because the melanocytes responsible for the pigments have to continually produce pigment and, just like those causing colour in hair, they can become less productive (which is why we have grey hair) and this happens more with age. Infants often have blue eyes that turn dark, just like yours did, because the melanin is gradually accumulated - it just takes time for enough pigment to build up and allow the eye colour to match it's genetic determinants:

  "Most babies who have European ancestry have light-colored eyes before the age of one. As the child develops, melanocytes (cells found within the iris of human eyes, as well as skin and hair follicles) slowly begin to produce melanin. Because melanocyte cells continually produce pigment, in theory eye color can be changed. Most eye changes happen when the infant is around one year old, although it can happen up to three years of age. Observing the iris of an infant from the side using only transmitted light with no reflection from the back of the iris, it is possible to detect the presence or absence of low levels of melanin. An iris that appears blue under this method of observation is more likely to remain blue as the infant ages. An iris that appears golden contains some melanin even at this early age and is likely to turn green or brown as the infant ages.
  Changes (lightening or darkening) of eye colors during puberty, early childhood, pregnancy, and sometimes after serious trauma (like heterochromia) do represent cause for plausible argument to state that some eyes can or do change, based on chemical reactions and hormonal changes within the body.
  ... eye color over time can be subject to change, and major demelanization of the iris may also be genetically determined."

In this study 10-15% of those studied had changes in eye colour beyond childhood so, al though colour is generally stable past childhood, it is not uncommon for eyes to change, and this is likely due to changes in melanin composition. This study is an example of clour change in birds too.

A side note: Animals with other colours

It is common for animals to have other eye colours, for example Blackbirds (Turdus merula) have an Orange eye, which is caused by Carotenoid pigments, rather than melanin as in humans. The reason they have this could be as an indicator of quality in courtship - carotenoids are hard to get, males with bright orange eyes therefore have access to good food resources, and female blackbirds find that attractive. (This section is all from my memory after a talk with a tutor on my undergrad field course in the Isles of Scilly).


What is the best current understanding of how yeast transformation works?

I have never worked much with yeast, but I can still give some answers:

Salmon sperm is used as a the so called "carrier DNA". It is thought to bind to the yeast cell wall and thus prevents that the DNA which shall be transformed does so. This raises the transformation efficiency. See here for more details: "Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method.".

Effect of the recovery time: In this time you typically give the cells the chance to recover from the relative rude treatment and to express the resistance gene (when used) before moving them to a selective medium. This raises the efficiency of the transformation.

Spheroblasts: As far as I remember they are terribly fragile and painful to handle. However, when you succeed making them, you have cells which take up high quantitaties of DNA which makes them pretty efficient.

I think these reviews are definitely worth looking at (they also contain a lot more references):

Genetic Transformation of Yeast
Transformation of Saccharomyces cerevisiae and other fungi - Methods
and possible underlying mechanism
Foreign gene expression in yeast: a review

If you have a chance to get hands on a copy of "Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual", I think this will be very helpful.


Do humans have any biological adaptations to eating cooked food?

Humans are incredibly good at processing maillard compounds, which include both beneficial and mildly toxic byproducts of cooking. Humans are better at breaking them down than other animals. This is presumed to be an adaptation to eating cooked food. Malliard reactions are also a good indicator of when most plant and animal products are safest to eat via cooking, (browning) which may explain why humans on average show a preference for them or even adaptations to detect them. we are also learning that one place animal testing may be problematic is in dietary tests becasue of this.
extra reading on hominid adaptations to diet


How realistic is to use DNA for long term storage?

I can at least answer the question about the stability of the stored information. With my colleagues, I worked for several years to estimate the rate of DNA degradation at room temperatures. Our results showed that the information could  be retrieved after 100,000 years storage.


I am afraid this question is too broad and I am voting to close. Evolution of inter-specific mutualism is a large subject. Here is not a complete answer but just a few comments on your two conditions

  1.If mutualism gives one specie a competitive edge over its competitors then it could arise.

This is mainly wrong. Mutualism is likely to increase if mutualistic behaviour offer increases the fitness of the individual performing it, you would expect mutualistic behaviour to increase. You would not really expect the same by comparing species ability to survive in relation to their level of mutualism.

  2.The benefits received from the partner species outweighs the costs involved in helping it out.

Again, you are talking about the benefit for a species. You should boil down your arguments to the individuals. It is true that mutualism can evolve only if the individual performing the mutualistic behaviour enjoy a higher fitness benefit than fitness cost (if any).


salamander is right about triclosan being the active ingredient in antibacterial soap, but the reason why it doesn't kill human cells doesn't have anything to do with the skin. From salamander's same source:

  Once they are in microbes cells, triclosan poisons a specific enzyme (enzymes are proteins that have particular functions, think of them as cellular machinery) that is used in making microbes cell membranes. Humans dont have this enzyme, so triclosan doesnt poison us.

The enzyme in question is called Enoyl-acyl carrier protein reductase (ENR), and is used by bacteria as part of their fatty acid synthesis. Eukaryotes use a different set of enzymes for fatty acid synthesis, so we aren't effected by this activity of triclosan.

For some more specifics about the interaction of triclosan and ENR, we can turn a study about the antibacterial mechanism of triclosan that was done soon after triclosan was first crystalized in situ with its target enzyme.

From Heath, et al (1999):

  Triclosan is a broad-spectrum antibacterial agent that inhibits bacterial fatty acid synthesis at the enoyl-acyl carrier protein reductase (FabI) step... The ubiquitous occurrence of type II fatty acid synthase systems in bacteria and the essential nature of the FabI reaction make this enzyme an attractive target for antibacterial drugs. Accordingly, triclosan is effective against a broad spectrum of bacteria, including multi-drug-resistant Staphylococcus aureus.


In there natural state no, tartigrade have absolutely no way to survive the acidic content of stomachs and are fragile.

In their cryptobiosed form (extremely resilient form) there has been no research to determine if they could survive extremely acid environnements. The things that we know they can survive is:

Temperature
Pressure
Dehydration
Radiation
The outer space environnement
Toxins

However, very few organisms possess mechanisms to tolerate highly acid environnement since acid affect cell membranes by "attacking" mainly the proteins and lipids. These organisms have evolved these traits because they live in acidic environnements, tartigrades on the other side don't.

Another point to add is, entering cryptobiosed form takes time, if the tartigrade would be eaten in it's natural form, it wouldn't have the time to cryptobiose and thus it would die.

Tartigrades

I hope this gives you some useful information


Is there a database providing information about optimum temperature and inactive temperature of enzymes?

UniProtKB has annotations for biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.
http://www.uniprot.org/help/biophysicochemical_properties

Such annotations are currently available for about 6800 reviewed entries: http://www.uniprot.org/uniprot/?query=annotation%3A%28type%3Abiophysicochemical_properties%29&sort=score

More specifically, temperature dependences is annotated in about 2000 entries: http://www.uniprot.org/uniprot/?query=annotation%3A%28type%3A%22temperature+dependence%22%29&sort=score


Why do people's hands get cold for the first half an hour and then suddenly they are warm when they are doing exercise outdoors in winter?

Cold extremeties are a reaction of endotherms where they reduce warm blood circulation to prevent losing core body temperature, otherwise the cold blood in your hands would lower your central blood pressure from 37'C, which makes the body less efficient and at risk of catching colds.

The reaction is called vasoconstriction.
quote:
Active cutaneous vasodilation occurs via cholinergic nerve cotransmission and has been shown to include potential roles for nitric oxide, vasoactive intestinal peptide, prostaglandins, and substance P (and/or neurokinin-1 receptors). It has proven both interesting and challenging that no one substance has been identified as the sole mediator of active cutaneous vasodilation. source
The above research can give you some clues about exercise and cold hands:

When you have exercised for 30 minutes, the above quote applies, and perhaps there is also a hormone contribution from natural opiates, endorphins, and other chemicals like nitric oxide.
quote:
The endomorphin peptides, endogenous ligands for the mu-opioid receptor, and nociceptin (orphanin FQ; OFQ), an endogenous ligand for the ORL1 receptor, have substantial vasodilator activity. source
For some very good reading on the subject, search for "thermoregulation vasodilation", the corresponding pages give advanced general knowledge of the biology.


If number of children born were spread more evenly among all parents, would our species' genetics have more variability?

Well the obvious answer is of course yes of course it would. That is the essence of natural selection. Variability leads to different phenotypes and selection for and the amplification of beneficial traits. Evolution. Except if there is no selection (everyone has the same amount of kids) no traits are amplified so everything in a large population is static. Until you introduce mutations and that increases variability. Eventually each individual would have such a large degree of variation from the next that I would assume speciation would be a very imminent result of any form of seperation or selection, which is against your original premise.


Note: In your PCR program you always set extension time.

Case:

Product length = 500bp
PCR extension time = 50sec
Assuming that polymerase adds 1000 nt/min

Cycle 1:

Strand that binds FP: extends ~800nt to the right (as per the polymerization rate): 300 bp ahead of RP complementary site. This product is lets say P1
Strand that binds RP: extends ~800nt to the left: 300bp ahead of FP complementary site. This is P2

Cycle 2:

The products of cycle-1 become templates for next round.
FP binds to P2 -300nt from its 3' end. Similarly RP binds to P1 -300nt from its 3' end.
The resultant products will be 500nt which give rise to a 500bp perfect dsDNA.

Some P1 and P2 will keep forming at a linear rate; since your template is low in amount compared to the amplified cycle1 and cycle-2 products, your expected PCR product will be much higher (which gets produced at an exponential rate).


Approximately how long do bacteria live for?

They're effectively immortal, albeit in a Phoenix-rising-from-the-ashes sort of way.

In general, a bacterial cell will divide as soon as it's biochemically able to do so, leaving behind two daughter cells. Neither daughter cell is actually the same as the mother cell, so in one sense the mother cell will have "died". On the other hand, the daughter cells are genetically identical to the mother cell and all of the physical material present in each of the daughter cells at the moment right after they split came from the mother cell.


How do viruses or bacteria survive outside the body long enough to spread?

It depends entirely on the environment the virus or bacterium is in and also the size of it.

Virus

With regards to viruses, the most important thing is typically whether or not the virus has an outer membrane or envelope.

Non-enveloped viruses such as rhinoviruses, noroviruses and adenoviruses can in fact survive for long periods outside the host (up to several days) whereas viruses with membranes such as HIV, influenza and the herpes viruses which do well in the host survive for shorter time periods.

Experiments with rhinoviruses and influenza viruses have shown potential survival times ranging from a few minutes to 48 hours or more.  They remain active longer on stainless steel, plastic and similar hard surfaces than on fabric and other soft surfaces.

This is because many enveloped viruses rely on the proteins on the surface of the membrane to attach to the host cell, this envelope is generally sensitive to degradation to sunlight and normal cleaning procedures.

Outbreaks associated with the non-enveloped viruses can continue for many months due to their relative stability in the environment, think of winter vomiting outbreaks, hand foot and mouth in animals as good examples of this phenomenon.

Bacteria

Because bacteria can undergo metabolism, synthesise proteins etc. for themselves, their life span is usually longer. If we split them into gram positive and gram negative its easier to discuss. Gram positive bacteria have a protein coat that prevents drying allowing them to survive longer. An example is the bacteria Staphylococcus aureus, which is responsible for toxic shock syndrome, food poisoning, and wound infections. With its protein coat it can withstand temperature and humidity extremes. The spore may survive for weeks on dry clothing using sloughed skin cells for food. The Bacillus anthracis, the anthrax bacteria, can also form spores and survive tens to hundreds of years. This is in comparison to gram negative which need humidity. An infamous example is Escherichia coli which survives typically only a few hours at best.


I have settled for two GAPDH primers with a short amplicon (~50bp):

>gapdh_rv3 <unknown description>
GAGACCTGAATGCTGCTTCC

>gapdh_fw3 <unknown description>
CTCCATTTCCCCTGTTCTCC

They provide consistent and good controls, as seen here (lower bands):


how did we breed after the fusion ? and why can't we bread with chimps?

There are plenty of people today with balanced Robertsonian translocations, they breed mostly fine, though Down's is more common than in the rest of the population, because meiosis is more likely to be messed up. If due to drift, people with those translocations became more common, eventually they could breed with each other, and make offspring with 22 pairs of chromosomes.  In theory, this drift could take over the whole human population.


What do we call these containers used in biotechnology?

That would be a Reagent Reservoir, or just a Reservoir. These tall and narrow ones are specifically designed for use with a robot, but there are also shorter and wider ones for manual pipettes:

120 mL Reagent Reservoirs


Why there is no neurovascular drug-eluting stent?

Despite some superficial similarities, the design of coronary stents and neurovascular stents are quite different. Coronary stents are hard metal, made out of stainless steel. They are quite solid, and if you crush one, it will remain crushed. They are deployed by expanding a balloon at potentially very high pressures (10-20 atm). Coronary stents are relatively short, and are deployed in vessels that are relatively straight given the length of the stent.

Drug-eluting variants of coronary stents are additionally coated in a polymer (i.e., plastic) matrix that contains the active ingredient and releases ('elutes') it over time. The common commercially available drug-eluting stents release anti-proliferative agents to prevent neointimal growth.

The purpose is also somewhat different: you mention flow diverters, so you are likely thinking about the context of aneurysms, where they may be used alongside coils to seal off the aneurysm from the normal flow. They are not providing structural scaffolding to prevent vessel occlusion from atherosclerosis.

Neurovascular stents, including flow diverters, are often made of self-expanding metals like nitinol. They are more flexible, but try to keep their nominal shape. These stents are deployed by retracting a sheath and then they themselves pop out to their nominal diameter. Because of this different deployment strategy, they can also sometimes be retracted and repositioned. The way these stents deploy is a lot more gentle, and they are also typically longer than the coronary varieties. They also may be placed in vessels that can be accessed superficially, such as in the neck. A stainless steel stent in the neck would be a disaster: if you laid pressure on that part of the neck you could permanently collapse the stent. A self-expanding stent will bounce right back open.

Back to your actual question...

The actual purpose of coronary vs flow-diverting stents are different; the purpose of drug-eluting coronary stents, preventing neointimal hyperplasia, is not as relevant in the neurovascular context. Additionally, there are lots of good reasons to use self-expanding metals in the neurovasculature because of tortuous anatomy and superficial vessels in the case of the carotids. The hard plastics that are coated onto steel stents can't be easily placed onto self-expanding stents, so other techniques would need to be developed.

The article you read talking about the complex shape of cerebral arteries is in large part correct.


Why do pandas have a high probability of giving birth to twins?

Charnov and Ernest (2006) present data on offspring number per year and neonatal mass for 532 species of mammals. The two are related by the linear regression equation:

ln(offspring/year) = 2.4 - ( 0.3 * ln(neonate mass) )

Giant panda neonates weigh 100-200 g and are weaned at 46 weeks.

So, according to the regression, pandas should have, on average, 2.8 to 2.2 offspring per year (for 100 and 200 g respectively). With a weaning time of 46 weeks, they could have 1.13 (52/46) litters per year. If every litter were exactly twins, that would be 1.13 * 2 = 2.26 offspring per year, which is within the predicted range.

Humans (neonatal mass of 3400 g) are predicted to have 0.96 offspring/year.

Charnov EL and SKM Ernest. 2006. The Offspring‐Size/Clutch‐Size Trade‐Off in Mammals. American Naturalist 167:578-582.


How does different sensory stimuli differ in nerve signal?

I think the short answer to your question is that the contents of different types of sensory stimulation are communicated to different populations of cells in the brain (note this transmission is mostly glutamatergic, not cholinergic). From there, the remaining associations and experiences derive from connectivity with other networks of brain neurons that result in different types of experience, based on the networks that those networks form and learned associations over development and a lifetime.

Computer analogies aren't always appropriate to understanding things about the brain, but maybe it could work out a bit here. How does a computer distinguish between input on your keyboard vs your mouse? On many modern computers, it is common for both to be connected with USB. The computer has some software that distinguishes between the different inputs - the brain has hardware that does the same.

Later on in the brain, or at a different stage in a computer program, those inputs can be mapped to functions that underlie experiences or functional outputs. Movement of the mouse can be converted to the movement of a screen cursor ("motor output"). Proprioception (the sensation of the relative position of the body from receptors in the muscles, tendons, and joints) can be combined with motor plans to create an error signal to move a particular muscle to match the intended movement.

Explaining any further than this probably requires entire textbooks of material, so I will leave it there.


What will happen if we expose the brain to intermittent light?

It is thought that there are no active optical receptors in the brain normally, its possible some effect might show up in the future, it would be minor at best.

Shining light into the brain is standard procedure in optogenetics experiments. A subpopulation of neurons is transformed to express an optical receptor to modulate genetic or signalling properties of the cell.

So the reason I say it would be small effect on a native brain is that these experiments do give good results and are run with controls which do not have the optical receptors added, which typically show no change in brain activity.

  Channelrhodopsin-2 (ChR2) induces temporally precise blue light-driven activity in rat prelimbic prefrontal cortical neurons. a) In vitro schematic (left) showing blue light delivery and whole-cell patch-clamp recording of light-evoked activity from a fluorescent CaMKllα::ChR2-EYFP expressing pyramidal neuron (right) in an acute brain slice. b) In vivo schematic (left) showing blue light (473 nm) delivery and single-unit recording. (bottom left) Coronal brain slice showing expression of CaMKllα::ChR2-EYFP in the prelimbic region. Light blue arrow shows tip of the optical fiber; black arrow shows tip of the recording electrode (left). White bar, 100 µm. (bottom right) In vivo light recording of prefrontal cortical neuron in a transduced CaMKllα::ChR2-EYFP rat showing light-evoked spiking to 20 Hz delivery of blue light pulses (right). Inset, representative light-evoked single-unit response.

Image taken from the linked Wikipedia page and originally from Baratta et al..


how many times can a spitting cobra spit its venom?

I presume it can only spit once or twice only An unwise presumption.

  These cobras exhibited distinct control of venom flow with spits averaging 1.7% of the volume of the venom gland, thus enabling the cobras to rapidly expel over 40 consecutive spits ... There was no significant difference in the amount of venom spat between the first few spits and the 20th spit, however there was a significant (Student's t-test with unequal variance, p=0.017) decrease in the amount of venom spat between the 20th and 40th spits.

--Protein variation in the venom spat by the red spitting cobra, Naja pallida (Reptilia: Serpentes)


What are these little creatures living inside a silk web?

From the comments above (in particular, "it's head and mouthpart vaguely resemble that of the termite") it is possible that what is here is a Webspinner colony (Order Embioptera); if so you either have one of the few species in which the male is wingless, or the colony was without adults of that sex when your question was asked.  Webspinners are distantly related to termites, but have little or no economic importance (some species have been accidentally spread by man).  The Wikipedia article (https://en.wikipedia.org/wiki/Embioptera) has some basic information on the group (including photographs of both sexes and of nymphs), and references for further information; identification of species from Bangladesh will be problematic, as Edward S. Ross (the expert on this group from the mid-1940s, and not fully replaced--he has retired) had reportedly collected enough undescribed species to more than double the known diversity.


Difference between Genus, Genus sp. and Genus spp

Wikipedia:

Books and articles sometimes intentionally do not identify species fully and use the abbreviation "sp." in the singular or "spp." (standing for species pluralis, the Latin for multiple species) in the plural in place of the specific name or epithet (e.g. Canis sp.) This commonly occurs when authors are confident that some individuals belong to a particular genus but are not sure to which exact species they belong, as is common in paleontology. Authors may also use "spp." as a short way of saying that something applies to many species within a genus, but not to all. If scientists mean that something applies to all species within a genus, they use the genus name without the specific name or epithet. The names of genera and species are usually printed in italics. Abbreviations such as "sp." should not be italicised. When a species identity is not clear a specialist may use "cf." before the epithet to indicate that confirmation is required. The abbreviations "nr." (near) or "aff." (affine) may be used when the identity is unclear but when the species appears to be similar to the species mentioned after.


Is it possible to grow brain tissue in vitro? Can we make a super-brain this way?

This is actually not an unheard of idea among neuroscientists and is an aspect of much research.  Brains in general have amazing computational powers and abilities that allow them to circumvent the limitations of computation which is usually based on a Turing Machine. Neurons pursue highly parallel architectures and exhibit cognition or even emotions or do highly sensitive signal processing, which has heretofore been unapproachable with computational methods such as Machine Learning.

As such many researchers are focused on understanding the brain or at least the brain's structure to augment or produce computation.  Here are a couple of examples of neuron arrays flying virtual or real drones....

The ethical issues aren't great concerns because neural cell networks can be encouraged to grow differentiating from easy to grow cell lines like fibroblasts.

Another approach to augmented computing is to interface directly into a living brain. Model brain organoids are a popular topic of interest and could one day be used to interface to other computational systems.  There are of course many devices that try to interface to the brain via electrical fields in the same way EEGs work.

there are connectome projects that are trying to understand the neural connections between cells that are so important to brain development, with the theory that the topology of these networks might enable even computers to perform like brains.


After the crosslink reversal step, you still have some DNA connected to protein fragments.

So at that step, instead of doing a normal DNA purification, we also need to use a phenol-chloroform extraction or special columns to seperate DNA from protein fragments.

Thermofisher usually gives really good explanations too.

Please let me know if I didn't understand the question correctly! :)


Why are human titin and mice titin considered the same protein?

Human and mouse titin are orthologs, and can be confirmed through an NCBI query for TTN.

Orthologous proteins are not the same, per se. They retain the same function, and basically result from speciation: the common ancestral gene got divided between two species. However, the sequence may potentially differ because obviously the species have diverged.

Homology between the two can be confirmed computationally, through phylogenetic and alignment analyses, but I believe the naming convention Titin for both mouse and Human stems largely from the function of the protein in either organism.

Naming convention and explanations of homology are nicely outlined in this Bio.SE post.


Biology and dna samples to determine parental lineage

Before DNA sequencing was widely available, some lineage information could be determined using restriction fragment length polymorphism, a kind of "DNA fingerprinting".
https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism

Analyzing nuclear DNA would give information about both parents, while mitochondrial DNA would give information specifically about maternal lineage, as we inherit our mitochondrial DNA only from our mothers.


Does evolution only give rise to traits that confer fitness?

I'll try to beat @Remi.b to the suggestion that you review Understanding Evolution as a general overview of evolutionary topics.

For a quick answer: no.

Sometimes people confuse the great importance of natural selection in evolution with an equivalency between natural selection and evolution. However, there are many many contributors to evolution, many of which do not involve fitness.

I'll list just a couple examples:

Genetic drift is random change in allele frequency because of random sampling of reproductive organisms.

Founder effect is a somewhat related concept, referring to the change in allele frequency in a population that becomes isolated from the rest of the individuals of a species: that population has a selection of traits that might differ from the species as a whole, and lead to future speciation.

There are many more.


Are there viruses that affect cells across different species?

Firstly, it's important to recognize that "plant viruses" do not exist. There are only "viruses that affect particular plant cells", or "viruses that affect a particular cell type". You'll see why in a moment.

One of the structural components of many virus is its protein coat. Different types of biological molecules protrude from the surface of this protein coat, deemed signalling molecules. The structure of these molecules are specific to a certain type of virus.

Analogously, specific cell types have specific biological molecules that protrude from their plasma membrane, deemed receptor molecules. For a virus to affect a particular type of cell, their signalling and receptor molecules must "fit within each other", like lock and key. Once they do so, a virus may interact with this molecule, in whichever way it does.

Although your hypothesis wasn't entirely correct, as viral contact with a cell must first be established, viruses do interact with DNA replication in different ways, as in the lytic or lysogenic cycle.


Pasteurisation of orange juice and Vitamin C

Hodgins AM, Mittal GS, Griffiths MW. 2002. Pasteurization of Fresh Orange Juice Using Low-Energy Pulsed Electrical Field. J Food Sci 67(6):2294-2299

This is a study of non-thermal food preservation, but it cites two studies that measured ascorbate loss from pasteurisation. I can't cite the studies directly because I can't find them online. According to these authors, they reported losses of 7.0-15.0% and 18.0% after 95°C for 15s. This is high compared to the pulsed electrical field method.

Yeom HW, Streaker CB, Zhang QW, Min DB. 2000. Effects of Pulsed Electric Fields on the Quality of Orange Juice and Comparison with Heat Pasteurization. J Agric Food Chem 48(10):4597-4605

This study compared ascorbate loss during storage after PEF or thermal treatment. While no difference was observed when stored at 22°C, PEF treated orange juice maintained significantly higher ascorbate concentration than thermally treated orange juice when stored at 4°C. The authors attribute this to the "higher processing temperature".

They also say (and reference other studies):

  Ascorbic acid is a typically heat sensitive nutrient. High temperatures during processing and storage cause loss of ascorbic acid.


How do processes of one osteocyte establish contact with processes of the adjacent cells within the mineralized matrix?

Osteocytes attach to each other by cytoplasmic extensions through gap junctions [1]. The connections between these cells are formed since they were osteoblasts and osteoid-osteocytes (type II preosteocyte) [1]. Osteoblasts have a greater volume than osteocytes and the lack of extracellular matrix favors their adhesion. As they begin to synthesize extracellular matrix, their volume is reduced and this matrix takes space between cells, but with respect to the existent intercellular junctions around which matrix forms canaliculi.

"Osteoblast Organization" by Physio Muse - I drew this figure in drawperfect, printed to .pdf, and converted to .jpg
Previously published: Not published in any form, including not used on any website. Via Wikipedia.

Osteoblasts are connected via gap junctions mediated by connexin43 protein [2]. Mature osteocytes attach to the bone matrix by integrins (alphavbeta3) [3].

References:

Wikipedia contributors, "Osteocyte," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Osteocyte&oldid=618657480 (accessed July 27, 2014).
Civitelli R. Cell-cell communication in the osteoblast/osteocyte lineage. Arch. Biochem. Biophys. 2008 May 15;473(2):188-92. doi: 10.1016/j.abb.2008.04.005. PubMed PMID: 18424255.
McNamara LM, Majeska RJ, Weinbaum S, Friedrich V, Schaffler MB. Attachment of osteocyte cell processes to the bone matrix. Anat Rec (Hoboken). 2009 Mar;292(3):355-63. doi: 10.1002/ar.20869. PubMed PMID: 19248169.


If fully colorblind people only see shades of white,gray, and black, does that mean that the colors black, white, gray are colors humans can’t see?

Based on your question: if fully color-blind people see whites, blacks, and greys, that means that humans can see them colors. After all, aren't color-blind people humans?

If you actually think about it, is color just created by evolved cells? If so, should we not see just black, grey, and white?


How much DNA of Albert Einstein is recoverable?

During the generation of gametes (sperm, eggs), chromosomes can cross-over - this swaps paternal and maternally-derived genetic material.  So none of the descendant's chromosomes would be a direct copy of Einstein's, and furthermore, each offspring receives half of its genetic complement from each parent.  This means that if you pool the DNA data from small number of offspring you may not obtain all the elements of one parent's DNA or be able to assign that data back to a specific 'original' chromosome. (On top of this you would have to determine which sequences in the offspring came from the other parent).

If I was cloning Einstein, I'd use his DNA.  Is his comb in a museum ? A tooth? A letter he licked?  A large chunk of Einstein still exists (formalin fixed brain) and lab protocols can recover DNA from formalin fixed tissues. It wouldn't be easy, but in theory, you could: i) derive its full sequence and ii) synthesize artificial chromosomes with suitable epigenetic modifications, and iii) inject those into enucleated eggs for human cloning or iv) transfect them into enucleated cells from a cell line, make iPSCs and then fuse those with ~8-cell fertilized embryos.

(Spoiler - not technically do-able today and almost certainly illegal in most states/countries).
For a related movie treatment, the Boys from Brazil  tells a good story - warning Nazi content.


Can rigor mortis change the anatomical position in which a person died?

Rigor mortis does not cause movement. It causes rigor (Latin for stiffness.)

This is only a comparison, but think of it this way. Superglue doesn't shrink or change the shape of the connection of the two things glued together; it just holds them there with powerful 'stiffness'. So imagine that at death, part of our muscle cells exuded superglue. You would get stiff (the muscle to bone/fascia connections would not change) but you would not move. Immediately after death, some muscles relax; most obviously the eyelids open partially, the mouth, hands, and sphincters relax (you won't have to pry a gold coin from someone's dead hands like in the movies.) But aside from general relaxation, you very closely stay in the position you were in when you die.

Physiologically, this is roughly how muscles work: muscle cells are filled with filaments, actin and myosin (I'm leaving out tropomyosin and  troponin for brevity.) Contraction occurs when the myosin can bind to the actin, break the bond and reform it on the next spot on actin, and repeat, like crawling along the actin. ATP and Calcium ions are necessary for this crawling movement. In death, ATP is quickly depleted (aerobically then anaerobically), whereas Calcium floods the cell, and the bonds within each muscle cell which were formed when death occurred become stable. The muscle does not contract any more; it just stiffens. But since stiffening requires contraction in life, it's called contraction in death.

As a parallel, touch your fist to your shoulder. Without resistance, there is some contraction there. Now keep it there while someone tries to move it; that requires much more forceful contraction, but the position of your arm doesn't change (remember, you're keeping your fist to your shoulder.) All this is thanks to the number and stability of those tiny bonds between actin and myosin. Those tiny bonds develop and stabilize in death. But they don't last forever, hence rigor reverses.

Rigor mortis has been studied extensively for an astonishing number of reasons including forensic studies and how it affects the meat we eat.

I have seen a lot of death; one of my duties was to "pronounce" people dead. Sometimes when someone died during the night in a nursing home, a nurse would wait until morning to call - what difference did it make, anyway? - and I saw bodies in rigor. They were not all drawn up as in a fetal position. The nurses would usually straighten the patients out before rigor set in to make it more dignified and easier to transport the patient. If rigor caused movement, they wouldn't be straightened yet stiff  (rigor is something one needs to document, as is lividity.)

Rigor Mortis


Why is the upper respiratory tract so vulnerable to infections?

Mostly because it is in almost constant contact with aerosols from the outside world (with regard, of course, to a thin layer of mucus), therefore any pathogens they might contain.

You also have to remember what separates an airborne pathogen from any other pathogens- infection location. A pathogen is airborne when it infects and irritates the throat or nasal passage enough to make the organism's normal deterrence functions kick in. In most cases this would be coughing or sneezing, which produce contaminated aerosols for other organisms to inhale through their own upper respiratory tract.

I hope this answers your question!


Is the activity of enzymes in the human body affected by the outer temperature?

Enzymes usualy have a relative narrow temperature optimum, for those of our body this is usually around 37°C. It is around 37,2°C in the morning and goes slightly up to 37,7°C in the evening (see reference 1 for details). The temparature optimum for most enzymes looks somewhat like displayed in the figure (from here, interesting to read):

Enzymes are relatively tolerant to lower temperatures (although their reaction rate is much lower), but generally they work. If you go too high with the temperature, the activity will soon be reduced to zero, as the enzymes are denaturated and are not able to catalyze any reaction.

The human body does quite a lot to control its temperature and to keep it within a pretty small limit. It does either excessive sweating (when it's hot) or shivering (when it's cold) to maintain its temperature within or at least near the optimum. For further details on the themorgulation have a look on the Wikipedia article on this topic or reference 2 and 3.

Although our enzymes work at slightly lower reaction rates when the body temperature is higher (think of fever), this is not a major issue. Slightly higher temperatures can thus be tolerated, although you don't feel very nice.

The effect of to hot temperatures is different, though. It is mostly due to not consuming enough water, so that the body has not the possibility to control its temperature via sweating. This condition will ultmatively lead to a heatstroke, see here for more details. Before you reach the temperature in which your enzymes reaction rate will go down drastically, you have long collapsed.

References:

A critical appraisal of 98.6 degrees F, the upper limit of the
normal body temperature, and other legacies of Carl Reinhold August
Wunderlich.
Skin blood flow in adult human thermoregulation: how it works, when
it does not, and why.
Thermoregulation: some concepts have changed. Functional
architecture of the thermoregulatory system


Is it possible to derive the Michaelis-Menten equation under conditions where the product formation is reversible

No it is not possible to derive the equation for the reversible case. This is because the Michaelis-Menten equation is derived on the explicit assumption that the substrate concentration is much greater than the product concentration so that the back reaction does not occur. This is true at the start of a reaction in the lab when you add enzyme to your substrate. At later times when product builds up these conditions no longer hold and the M-M equation breaks down.

It is possible to derive a different equation for the reversible case (as some other posters do) but this begs the question of the importance of the Michaelis-Menten equation for biology. The poster seems to think that it is some universal truth, important in its own right or because it models the reaction in the living cell. I think this misses the point, which I think is as follows.

It originally was a prediction from, and hence a test of, the hypothesis that enzymes have a single active site at which the substrate binds and is converted to products.
It allowed two fundamental aspects of this enzyme model to be quantified: (i) the binding affinity of the substrate for the active site, as the inverse Km, and (ii) the catalytic efficiency ('smartness') as the turnover number or kcat, which is derived from Vmax (and enzyme concentration).
These enzyme constants can be used to address biological questions, for example whether an enzyme capable of a particular reaction in the test tube is able to account for the observed reaction rates in a tissue. Or whether the substrate you find the enzyme can use is likely to be the physiological substrate in a tissue.
It turns up enzymes that do not exhibit M-M kinetics, implying that some aspect of the model does not apply to them. This can be of mainly chemical interest (ping-pong kinetics and the like) or of physiological importance, as in allosteric kinetics (S-shaped rather than hyperbolic curve) shown by multi-subunit enzymes where the individual subunits show co-operativity, allowing more finely tuned regulation.
And if you do want to model reactions within cells, the kinetic constants can be of use. However as one is normally dealing with a chain of reactions in an open system the mathematics are complex (and nothing to do with the equation for a single reversible reaction in the test tube).

Most biochemistry students (and many teachers) would be hard pressed to explain why they should learn the derivation of the Michaelis-Menten equation. The answer is partly so they see that it is based on a particular model of the enzyme, but also so that they are aware of the assumptions on which it is based. Hence they need to be aware that the Michaelis-Menten equation is only true for initial rates of reaction, otherwise their determination of the practically and biologically useful Km and Vmax will be incorrect.


Why is cognitive maturity related to organism lifespan in larger animals and mammals?

This answer might not completely answer your question, since this just explains the case in humans, but I think you can give this a read while waiting for a more accurate one. I would recommend you to read this amazing paper.

Generally, across animal species, the longer it takes an organism to reach maturity, the longer it lives. How the timing of onset of maturity relates to longevity in humans, is still a matter of debate. In this regard, it is of special interest whether the onset of intellectual maturity is associated with longevity, as the brain and associated parts of the central nervous system comprise an organ system that is widely thought to have played a vital role in humans’ evolutionary success.

First, they talk about defining cognitive maturity:

  It would seem intuitive to define intellectual development as that part of the lifespan in which ability increases and intellectual maturity as that part in which ability plateaus or decreases. In such a model, an inflection point or peak in ability would mark the onset of intellectual maturity. It is unlikely, however, that the multidimensional abilities of composing and writing reach their peaks when a composer's or writer's work is made public for the first time. Rather, we regard maturity as a state that is attained when a certain relevant threshold is crossed, regardless of whether ability increases after that point.

Looking into the case of humans, it may be either a genetic mechanism or plasticity that couples rate of development and maintenance and repair. In the former scenario, genes that alter the rate of development such that maturity is reached earlier, would have as a concomitant effect the downregulation of maintenance and repair, leading to a shorter lifespan. (This is a shortened version- please go through the paper for more detail)

They conclude stating that the onset of intellectual maturity is associated with longevity. So, you are right about cognitive maturity of an organism being related to its age, and it points out to a really interesting result- blooming composers and writers live longer than child prodigies- as pointed out in a paper in ResearchGate.

What could be the reason for it? American psychologist Jerome Bruner proposed the purpose of the period of immaturity as being a time for experimental play without serious consequences, where a young animal can spend a great deal of time observing the actions of skilled others in coordination with oversight by and activity with its mother. So, there is the obvious need for a period of immaturity and this varies amongst different mammals. (source)


How does electroporation mediated recombination work?

Electroporation is a fairly common way to introduce exogenous nucleic acids into cells. Its name essentially describes the process - an electric voltage potential is applied across a biological membrane, eventually leading to the production of conducting hydrophilic pores. The image below is from the Wikipedia page linked above, showing non-conducting (upper) hydrophobic and conducting (lower) hydrophilic pores. Depending on the voltage, membrane composition, and other factors, these pores can eventually "heal" and close back up, or join together and lead to the rupture of the cell.

Electroporation is used in the lab as a method of transfecting or transporting nucleic acids (usually DNA) into cells, to make them express genes they otherwise wouldn't, or to otherwise alter the genetic machinery. The transfected DNA can either remain in its own structure (such as a plasmid), or be incorporated (recombined) into the host genome, similar to what happens during a retrovirus infection. Whether or not this happens is dependent on the structure and sequence of the construct being introduced, not the method of introduction.

So, in reference to your question, electroporation doesn't do anything that directly allows more recombination to occur - all it is is a method of transportation. However, electroporation may allow for certain constructs to be introduced into the host more efficiently, or for a larger quantity of them to be introduced, leading to a greater transformation efficiency. Some cells, especially primary cells like neurons, for example, may only be transfected with any sort of efficiency with electroporation. However, electroporation can also have its down sides, as it can be rather stressful to the cells, and if the voltages and timing aren't properly adjusted can lead to high levels of cell death.


Inward rectifying potassium channels during undershoot of action potential

I hope I can maybe shed some light on this concept for you.  Rather than complicate anything more than necessary, let's start small and build. To directly answer your question, these channels can function as leak channels (so ions are always flowing through them at some rate) or can be open at select voltages (ions will only flow upon voltage-selective opening of the channel).

Here's a little more detail.  These channels are involved in a number of physiological processes (not only in neurons, but smooth muscle and cardiac cells as well).  One such process is, as your professor pointed out, to drive the membrane potential back to rest after you hyperpolarize the cell following an action potential.  I completely understand your confusion with this concept because in order to properly answer your question, I've gone through a number of resources to make sure I give the most complete answer possible.  Here goes:

Maybe the most important part!!!  These inward rectifiers were originally called “anomalous” rectifiers because, let's face it, they're goofy.  They don't do what you expect them to do (as you have pointed out).  Part of the reason is that there are molecular mechanisms that cause these channels to be blocked and preferentially permit an inward conductance, despite what you'd expect.  There's a decent review article on these channels that might help your understanding (the introduction is the most important part).  You can find it here http://physrev.physiology.org/content/90/1/291#ref-233.

Now I'll try to get into a different explanation that kind of oversimplifies things, but I believe might help.

Remember that the gradient is not solely electrical in nature, it is an electrochemical gradient.  Now you're probably thinking to yourself "I know that, dude, don't patronize me!"  I only bring this up because it appears your biggest concern is how the electrical properties of the gradient regulate K+ flow across the membrane (heavily considering the electrical driving force by focusing on membrane potential minus the Nernst potential for K+).  However, flip that thinking for a second.  Specifically, think about what happens during an action potential solely in terms of concentration.  Your rising phase is sodium influx to the cell (you go from lots of sodium outside the cell to lots of sodium inside the cell).  On your falling phase, sodium channels close and potassium channels open.  Thanks to the good ol' Na+/K+ pump, you have a gradient of little K+ outside the cell and a ton inside.  So what happens?  All that K+ rushes out of the cell (as you would also predict from the electrical component of your gradient now!).  That means you had a lot of K+ inside and a little outside, but you now have a lot outside and a little inside.  This goes on too long and you get an undershoot/hyperpolarization, but you have to get back to your resting membrane potential.  Enter the inward rectifiers.  These K+ channels open and (again, thinking solely about concentration) the K+ is going to flow down the gradient back into the cell.  If you throw in the electrical component, remember this:  Neurons exist in a multi-ion system which complicates things like reversal potential for a single ion.  This is a complicated subject that I won't get into, but it boils down to reversal potential being a different property from equilibrium potential, which becomes important in a multi-ion system.


Action potential: why called "depolarization" when polarity is reversed, not removed?

While the cell is polarized (in the positive direction) at the height of the action potential, it has been depolarized from its resting, negatively charged state, meaning the original polarity has been lost or reversed. In my mind, the slight (30mV max) positive polarization for that brief period of time is kind of an "overshoot" of neutral charge, just like during recovery the potential exceeds -70mV for a period of time before coming back to the resting state.


Any examples of life forms on Earth that could have survived on Mars or Moon?

Yes, research studies that were conducted have found that methanogens (microorganisms) are able to survive in conditions similar to Mars (reference). Another study conducted has also concluded that some lichen and cyanobacteria is also capable of survival.  Surprisingly, they were also found to be active (reference).

There is speculation now on whether organisms from earth have been accidentally transported to Mars on the Mars Curiosity Rover which would be funny or a cause of concern, depending on how you look at it (reference).


Your question is a little vague and as Christiaan mentioned, linking to the papers would be useful. If I understand, though, you want to know why cellular metabolic activity that takes places after someone dies?

If that's the case, the answer is essentially that whatever kills a complex organism in the sense of causing the heart to cease beating, doesn't immediately cause every cell in the body to stop functioning at the same moment.

Now for a slightly longer answer...Consider someone who suffers a heart attack and dies. Blood stops flowing through their veins and cessation of breathing means gas exchange stops. For cells with extremely sensitive oxygen and nutrient demands like cardiac cells, cell death begins to occur rapidly. Other cells farther down the blood and oxygen supply chain have a greater tolerance to disruptions in nutrient supply and would have at least some store of nutrients to work with after blood flow stops. Those cells will keep doing whatever they were doing for a little while; metabolizing nutrients, transporting metabolites, transcribing genes, etc.

After a while, though, even they will feel the lack of oxygen. At that point, most cells will switch over to anaerobic respiration. The eukaryotic fraction of cells in our body isn't particularly good at this, but can struggle on for a little bit until they simply run out of fuel and begin to die, largely through apoptosis.

Apoptosis of some cells will actually help prolong the lives of some of the cells neighboring the apoptotic ones, an effect that probably encouraged the evolution of apoptosis. After a while, though, too much apoptosis will have occurred and an uncontrolled sort death called necrosis will begin, leading to cascades of cell death and cessation of cellular metabolic activity. This process can take days to occur, depending on many variables surrounding the death of the organism.

So far, this has all been about eukaryotic cells; cardiocytes, adipocytes, myocytes, etc. These are the smallest fraction of cells in our body, by cell count. The rest of our bodies are composed of prokaryotic, or bacterial cells. This is our microbiome and this is where (for me) things get really interesting.

Although our microbiome exists in a symbiotic relationship with our eukaryotic cell fraction, many members of the microbiome are less dependent on the nutrients found in our blood system than those eukaryotic cells. The cells of our microbiome are also frequently much more capable of surviving in low-oxygen or even anaerobic environments. These parts of us will continue to thrive for some time after we "die".

Some of our microbial cells, if left to their own devices, could even find new environmental niches outside our bodies and continue to live long after "we" have died. The quotes around 'die' and 'we' become necessary at this point because from here, questions of identity and life branch into the philosophical.

This became a lengthy answer, but I find it a really interesting topic. Here's a nice article from the Guardian, that discusses post-mortem cellular metabolism and our microbiomes in particular: https://www.theguardian.com/science/neurophilosophy/2015/may/05/life-after-death


Radial Basis Function Network (RBF Network)

In RBF networks each neuron in the hidden layer applies a computation that is related to its "center vector".

First consider the set of input neurons as a vector $\mathbf{x}$, and that each hidden layer neuron receives the complete input vector as its own input.

Second, each hidden layer neuron $i$ is parametrised through a vector (center vector) $\mathbf{c_i}$ of equal dimension than $\mathbf{x}$.

The computation of each hidden layer neuron $i$ consists of:

Evaluate the distance (according to a metric, which may or may not be Euclidean) between the input $\mathbf{x}$ and the center vector $\mathbf{c_i}$. When the input is equal to the center vector, the output for that neuron will be maximal (see 2).
Evaluate a Gaussian function that decays with increasing distance between the vectors. That's the output of each hidden layer neuron. In the following equation, $\beta$ is a parameter that specifies the decay rate of the Gaussian (converse to the standard deviation in a regular Gaussian distribution).

\begin{equation}
\rho_i(\mathbf{x})=\exp{[-\beta\Vert\mathbf{x}-\mathbf{c_i}\Vert^2]}
\end{equation}

Now combine linearly the output of all hidden layer neurons to obtain the total neural network output. For that, you need an additional set of parameters or weights $a_i$ (one $a_i$ for each hidden layer neuron, but the $a_i$ values are scalars while each $\mathbf{c_i}$ is a vector).

The final equation, that yields the total network output (a scalar value), is:

\begin{equation}
\varphi(\mathbf{x}) = \sum_{i=1}^N a_i \rho(||\mathbf{x}-\mathbf{c}_i||)
\end{equation}

And that's it.


why don't antibiotics reduce our weight?

First, you present as fact that antibiotics therapy (say AT) does not reduce weight. To show this fact, a study must weigh persons before AT and after. Confounders to this measurement are 1. weight differences because of bladder content (up to around 1 liter urine = 1kg), 2. weight differences because of bowel content (100g-200g), 3. Food weight (up to 2kg and more). High salt foods can cause water retention that can easily reduce your urine output one day by 500-1000ml (=g), increasing it with the same amount the other day. So your confounders can add up to +/- 4kg easily. But what you want to measure is a change of 1kg.

This means that you need to account for all these. I don't know any study that did this. Please cite such a study before presenting as fact that there is no weight loss from AT.

Assuming there is no weight loss, there are several hypotheses that can be advanced: from the fact that no antibiotic (even broadband) can kill all bacteria, the remaining bacteria in the gut may simply feed off the highly nutritional content of those bacteria cells that were killed. Note that although we know which bacteria of those that we can cultivate in a lab are susceptible to AT, we don't know at all about those that we can't grow, and that is the majority of bacteria in the gut.


You misunderstood slightly what PAM1 means; it's actually (from Wikipedia) "1 [PAM] mutation to occur per 100 amino acids". So PAMn makes sense for any n, as in the 100 amino acids may mutate more than once each, on average.

Or if you put it in terms of PAM distance...

  Is possible for two sequences to be more than 100 PAM
  apart?
  Yes: One position can mutate multiple times.

An attempted analogy: what does 600% casualty rate (for soldiers) mean? Well it means not only the original guy died, but his 5 replacements got (successively) killed as well.


Interesting question! I searched briefly and came up with an answer from this short paper.

I won't repeat all the details of the paper, but to be not a completely link-only answer I will give a brief summary:

The technology used at the time was a lot different than modern ECG leads: it used a Lippman capillary electrometer that used moving mercury to detect brief current changes.

With this relatively primitive device, there were 4 apparent features in the trace, which were named A B C D (earlier, a different physiologist saw only two ventricular features that he logically named V1 and V2).

However, it was known that this primitive measurement was not showing the actual electrical signal, but rather a filtered version due to the physics of the mercury in the tube, which was subject to inertia and friction. When a physiologist used mathematics to essentially "deconvolve" the filtered signal to get the original signal back, he plotted both curves next to each other: one labeled A B C D, the other labeled P Q R S T (note that in this deconvolved version of the trace, there were 5 components rather than 4).

As for the choice of P Q R S T, the source I reference notes that these were the letters commonly used by Descartes, and since then have been commonly used to refer to series of variables when one needs to distinguish between ABCD, XYZ, etc.

Later measurements that directly displayed the 5-component PQRST wave continued to use that terminology.

Original: Einthoven W. Ueber die Form des menschlichen electrocardiogramms. Arch Gesamte Physiol.. 1895;60:101–123.
Reproduced in: Hurst, 1998

References:

Hurst, J. W. (1998). Naming of the waves in the ECG, with a brief account of their genesis. Circulation, 98(18), 1937-1942.


I keep somewhat up-to-date with pest control measures. I haven't heard of chemicals being used to alter rat behaviour but using parasites that alter rat and mouse behaviour (Toxoplasma spp.) has been studied. The infection increases predation rates and also appears to increase the rate at which they are trapped. Toxoplasmosis also affects humans with cats being the main source of infection. I am uncomfortable about approaches that increase the prevalence of toxoplasmosis.

If you're going to the trouble of administering a drug to a pest why not make the drug lethal? The extra step seems unnecessary but I personally would opt for traps given that many poisons (particularly warfarin) seem cruel.

For traps good bait (uncooked bacon, lard, peanut butter, dog biscuits) makes rats;

  less cautious/sensible and/or more hungry.

The right trap can make a big difference. This one can self-reload > 20 times and is instantaneous. The linked website contains advice for setting traps.


The main reason for the color of our stool (or feces) is the presence of bilirubin, a breakdown product of the hemoglobin. The amount of it causes different variations from yellow to dark brown. When the passage time of the food in the intestine and the amount of bilirubin is constant, the color changes very little. Illnesses like diarrhea, which cause a lower passage time have therefore a ligher color because a lower amount of bilirubin can accumulate.

The color of the stool can also indicate illnesses of the internal organs, white stool (or pale clay like colored) can for example indicate problems with the biliary system (drainage system of the gallbladder, liver and pancreas).

You can find some more information here and here.


Do the two catalytic cores of DNA polymerase III operate in the same direction?

The DNA polymerase-III holoenzyme moves in one direction (along the fork). One of the DNA polymerases works on the lagging strand but the enzyme is oriented in the same direction as the one that is working on the leading strand. For details see this review (it is old but this fact is also old enough).

The second diagram shown in your question is an accurate representation of what happens. This, statement is confusing (and misleading):

  The other core-polymerase molecule, which elongates the lagging
  strand, moves with its β-subunit clamp in the direction opposite to
  that of the fork movement.

Both polymerases move in the same direction but elongate DNA in opposite directions. The opposite elongation direction, as shown in the second figure, is facilitated by looping of the lagging strand.

You can simply google "DNA polymerase-III holoenzyme" and you'll get many sources that will corroborate this.


What is the recommended PPM when foliar feeding L-amino acids

I know that some of the amino acids you listed are commonly found in fish fertilizer. I haven't read any studies on the use of these amino acids individually and not sure where you would purchase them separately. If you're just experimenting in your own garden I would just use fish fertilizer according to the label directions. If you look for fish fertilizer studies you'll probably find more info.

Also, I've never heard of these opening up the stomata of the plants. The only references I've read indicate that foliar sprays are best applied in the early morning or late day when the stomata is already open. This is how the nutrients get absorbed from the leaves.

I don't know that I would want to intentionally manipulate stomata closure. The plant knows when it needs to breath.

Where did you read the above info? I'd be interested in seeing it.


Those bumps are aerial surface hairs, a type of trichome. They are epidermal outgrowths.
Therefore it's vines are of pubescent type.

In addition to facilitating better exchange of gases, it also facilitate the vining process, turning into roots wherever the plant is in contact with the ground and moisture, especially if the vine's connection to its original root has been damaged or severed.

Sources:

1:https://en.m.wikipedia.org/wiki/Trichome#/search

2:https://en.m.wikipedia.org/wiki/Tomato


There's a decent presentation here that basically goes over what you're asking.

As an inhibitor, azides are similar to cyanide in that they inhibit complex IV by binding cytochrome oxidase, resulting in a sort of chemical asphyxiation.

Uncouplers are a little harder to wrap your head around. They embed in the membrane space, and we know that ETC and proton pumping depends on the established proton gradient across a membrane. Uncouplers uncouple the proton gradient from the electron transport chain, allowing protons to diffuse across the membrane, effectively negating the proton gradient.


Cancer a method for early Earth Evolution?

There is a lot of terminology, semantic and biology to be discussed if one was to fully answer your question and it would take a whole book. Below I am just trying to push you to reading more on the subject.

Evolution of cancer prevalence

The probability of getting a cancer is under selective pressure for sure. Citing cancer.net, here is some information on the genetics of cancer:

Many of the genes that contribute to the development of cancer fall into broad categories:

Tumor suppressor genes are protective genes. Normally, they limit cell growth by monitoring how quickly cells divide into new cells, repairing mismatched DNA, and controlling when a cell dies. When a tumor suppressor gene is mutated, cells grow uncontrollably and may eventually form a mass called a tumor. BRCA1, BRCA2, and p53 are examples of tumor suppressor genes. Germline mutations in BRCA1 or BRCA2 genes increase a woman’s risk of developing hereditary breast or ovarian cancers. The most commonly mutated gene in people who have cancer is p53. In fact, more than 50% of all cancers involve a missing or damaged p53 gene. Most p53 gene mutations are acquired mutations. Germline p53 mutations are rare.
Oncogenes turn a healthy cell into a cancerous cell. Mutations in these genes are not inherited. Two common oncogenes are:

HER2, which is a specialized protein that controls cancer growth and spread, and it is found on some cancer cells, such as breast and ovarian cancer cells
The ras family of genes, which make proteins involved in cell communication pathways, cell growth, and cell death.

DNA repair genes fix mistakes made when DNA is copied. But if a person has an error in a DNA repair gene, these mistakes are not corrected. And then they become mutations, which may eventually lead to cancer. This is especially true if the mutation occurs in a tumor suppressor gene or oncogene. Mutations in DNA repair genes can be inherited, such as with Lynch syndrome, or acquired.

Somatic Evolution in cancer

A cancer is a group of cells that proliferate. In other words a cancer is a group of cells having a higher fitness than other cells.

See Wikipedia > Somatic Evolution in cancer

Can a cancer be beneficial?

I am here attempting to answer your specific question.

We define a cancer based on the fact that it is detrimental to the organism carrying it. If a group of cells divide a lot more than the others and this is beneficial to the organism, then it is not a cancer but an adaptive developmental process.

Let's generalize the definition of cancer

To generalize the definition of cancer, one can say that a cancer is a group of individuals that proliferate to the detriment of the group. In other words, we need a social group of individuals (such as a multicellular organism) to get a cancer. Depending on your definition of a social group, one could consider a criminal organization as a cancer to human society.

If you push the definition a little further by either leaving out the need of a close phylogenetic relatedness between individuals of the group, one could say that "humans are a cancer of the earth". If you google this sentence you will get many hits!


According to the Gilson Pipettman User Guide you can autoclave the following parts: Tip ejector, Tip holder and the connecting nut (have a look into the PDF linked above if you are not sure about the parts). All other parts can not be autoclaved. Gilson says the following conditions can be used (page 17 in the user guide): Autoclave for 20 minutes at 121°C, 0.1 MPa.

However, when you really have a DNAse contamination, you will not get rid of it with autoclaving, since RNAses are too stable. You can either try the various solutions on the market which made for killing RNAses or simply get a new set of pipettes used only for RNA work (on a different bench in a different lab with a completely different and fresh set of chemicals and plastic ware). And I would recommend filter tips for this work. They are more expensive but in the long run it will save money since you don't have to repeat experiments.

Regarding your leaking pipettes: The pipettes contain rubber rings and teflon seals in the inside which have to be replaced from time to time. The image below shows how (parts C and D), the ring can be purchased from Gilson. If you don't know how to do this work (and have no technician who does) you can also send in the pipettes for service. This costs a bit of money, but is ways better than to use unreliable, leaky pipettes.

And don't worry, Gilson pipettes are pretty good. I have used now more or less all brands on the market and I still prefer them. They only need some service from time to time.


How would you effect bulk DNA gene therapy for a human?

Let's imagine that we understood DNA programming and our genome very well and >realized that there were some significant flaws (we die, we need sleep, etc.) And >let's imagine that we understand how to make our genome do what we want, but it's a >major refactor. We're going to have adjust 10-15% of our DNA.

I think we both recognise that this is a very naive view of biology and the nature of how organismal properties emerge (through multiple levels of systems) ultimately from the genetic code, the information in the genome, and the developmental process.

It is more pertinent and promising to think about treating genetic diseases.

Some genetic diseases are caused by mutations to single basepairs (e.g. the HgbS variant of the haemoglobin beta chain, which causes sickle-cell anaemia).
Other genetic diseases are caused by rearrangements of large segments of chromosomes, and the gene dosage imbalances that arise from this (e.g. Charcot-Marie-Tooth syndrome 1A). Finally, some genetic diseases are caused by a major gene-dosage imbalance caused by having an unusual set of chromosomes, "aneuploidy" (e.g. down syndrome, where chromosome 21 is present in 3 copies).

'Large-scale' gene therapy could be something useful for aneuploidy. Recently, the mechanism for inactivating one X-chromosome in female somatic cells has been applied to silencing the surplus chromosome 21 of Down Syndrome.

In yeast, a 'designer chromosome' has been chemically synthesised, and has been used to replace the corresponding native chromosome in yeast cells.

So although I think the premise of your question is basically science-fiction and naive, it is becoming possible to silence or replace whole chromosomes. More realistically than making our species immortal and ever-awake, this technology could possibly translate to therapies for some genetic diseases. But of course, the problem of retrospectively getting your therapy in to many somatic cells is still there. Engineering zygotes is feasible but has ethical problems - also, where pre-implantation screening is permitted, IVF can simply include genetic selection rather than genetic engineering!


Might new bones evolve from soft tissue?

New bones do form occasionally so it is not impossible, Ornithischian dinosaurs are defined by a evolution of a new bone (predentary). There are many pieces of cartilage in the body that become ossified in some animals and not others, the kneecap is a great example since a bony kneecap has evolved and been lost many times independently, it is just a matter of ossifying existing tissue. The trunk however is more difficult since it does not have any suitable cartilage.

Cartilage however is not necessary to form bone, but it is the most common way to get it. Endochondral ossification forms bone from cartilage and is responsible for the majority of the bones in the body. Intramembranous ossification forms bones in other connective tissue, the bones of the skull and dermal bones are examples of this process. Dermal bone has evolved separately many times but tends to form in the skin.

Given enough time  and the right selective pressures it is certainly possible for bones to evolve in the trunk but it is not going to happen quickly.


Look up "phage purification." Basically, you add your phage solution on top of your host bacteria on a plate and incubate. As the bacteria grow, you should see plaques (clear areas in the bacterial lawn). Each plaque should be the progeny of one original phage, although sometimes two or more phages could be very close to each other on the plate and it will look like one plaque. So you have to take a sample of a plaque, re-plate on another lawn of host bacterium, and repeat this process for several rounds until the plaque morphology seems to indicate that there is only one type of phage present. Here is a good resource for phage protocols: http://phagesdb.org/workflow/


Is this what you mean?

It's pretty hard to tell from this photo, and I'm no entemologist, but to me, it looks like it may be a wireworm, a larvae of a click beetle. This is a diverse group, so I think it would be pretty difficult to give a specific identification. (More images)


What do lower case nucleotides mean in this gene sequence?

The case refers to the degree of conservation of a particular nucleotide in the consensus sequence. Highly conserved nucleotides are written in uppercase. At positions where the sequence varies, the most common nucleotide is given in lower case. That said, I'm not sure what the cut-off would be between "highly conserved" and "most common" and, in my opinion, is something that should be explained in the paper (though, in this case, it does not appear to be). This paper, for example, uses uppercase where a base is conserved in four of the five sequenced promoters. There may be some convention I am unaware of.


Function of an VEGF inhibitor in the treatment of macular degeneration

The Wikipedia page for vascular endothelial growth factor (VEGF) looks pretty useful - it explains that VEGF stimulates the growth of blood vessels. If this gets out of balance, for example in diabetic retinopathy and wet form age-related macular degeneration, one treatment is to attempt to reduce levels of VEGF in the circulation, using monoclonal antibodies directed against VEGF, or to antagonise the action of VEGF using drugs that target the VEGF receptors.
Two milestones in anti-VEGF therapy are described in these papers:

Ng et al. (2006) Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nature Reviews Drug Discovery 5: 123-132 (This paper describes the first approved aptamer drug: an RNA directed against VEGF.)
Ferrara et al. (2006) Development of ranibizumab, an anti-vascular endothelial growth factor antigen binding fragment, as therapy for neovascular age-related macular degeneration. Retina 26:859-870 (This paper describes a therapy based upon an antibody fragment directed at all isoforms of VEGF-A.)

A very recent review of anti-VEGF therapies is:

Freund et al. (2013) An update on the pharmacotherapy of neovascular age-related macular degeneration. Expert Opinion on Pharmacotherapy 14:1017-1028


Have bacteria evolved antibiotic resistance in a laboratory setting?

Yes, many times.

For just one example, see this paper; you could also see this review for numerous examples.

These are examples of spontaneous mutations that lead to antibiotic resistance, so this is sort of an extreme version of evolution of antibiotic resistance. You could also say that antibiotic resistance "evolves" in terms of selection any time an experiment is done that uses a resistance gene to mark a subset of cells, which occurs on a daily basis in labs all over; fortunately these experiments use antibiotics that aren't used to treat patients.


Enzymes extracted from diferent tissue, may have diferent $K_m$ values under the same conditions?

You would not expect the same enzyme from different tissues to have different Km values if the enzymes are truly identical.

In addition, you would not expect the Km value to change during purification: the Michaelis constant for the purified enzyme should be the same as that determined with a crude sample.  If this is not true, it might mean that the enzyme has become modified during purification, perhaps by proteolysis (not something you want your examiner to point out or suggest!).

One advantage of the Michaelis constant is that it is independent of enzyme concentration (and so does not depend on the degree of purity).

Having said that, I think it would not be considered too unusual for enzymes isolated from different tissues to have different Km values.

Possible reasons are:

The assay conditions are not really the same. pH, ionic strength, temperature and buffer composition may all affect  Km.  The Michaelis constant determined at pH 7 in 100mM phosphate at 37oC may be very different from that determined in 50mM Tris pH 7 and 25oC
Post-translation modification may be important.  The enzyme from one tissue may be phosphorylated, for example. One laboratory may have isolated the modified from, whereas another laboratory may routinely include phosphatase inhibitors.
Proteases present in the crude tissue preparation may have modified the enzyme.

In the case of succinate dehydrogenase, there are two other important considerations.

Succinate dehydrogenase is a membrane-bound enzyme (containing a covalently bound flavin) and the method of extraction will be all-important, and a key area to examine is whether extraction conditions may account for the difference in Km.
Finally, and this one is important I think.  SDH is a two-substrate enzyme and the Km for substrate A will depend on the concentration of substrate B ! To determine the 'true' Michaelis constant for a two-substrate enzyme (assuming no substrate inhibition), we must extrapolate to 'infinite' concentrations of the co-substrate. Otherwise we are dealing with apparent Km values.

I'll bet the last point is important. Is the problem that at least some of the reported Kms are apparent values, ie the concentration of co-substrate is different under the different experimental conditions?


All green plants do Photosynthesis as well as Respiration.

Plants respire during the day and night, but they only photosynthesis during the day when it is light:
there is equations for aerobic respiration and photosynthesis:

C6H12O6 + 6O2 → 6CO2 + 6H2O (aerobic respiration)

6CO2 + 6H2O → C6H12O6 + 6O2 (photosynthesis)

In terms of reactants and products, they are the reverse of each other. In terms of gas exchange:

Process        -------Carbon dioxide    -----------------Oxygen

Respiration     -----------Out  ----------------------------    In

Photosynthesis  -------In         ----------------------------    Out

Photosynthesis is only in the presence of Sunlight . So it occurs only during the day .

For photosynthesis they require Carbon Dioxide gas ( CO2 gas )

This gas enters the leaves through tiny pores on them called stomata .

The byproduct of photosynthesis is Oxygen gas ( O2 gas )

It is either passes out through the same stomata OR used for respiration

For respiration they require O2 gas .
It enters the leaves through the same pores or stomata .

The by product of respiration is CO2 gas .

During day time it is immediately used for photosynthesis .

During night time the CO2 gas is released in the atmosphere

Net gas exchange

The net (overall) effect depends on the time of day and the light intensity. Photosynthesis doesn’t occur at night. When there is no photosynthesis, there is a net release of carbon dioxide and a net uptake of oxygen.

If there is enough light during the day, then:

the rate of photosynthesis is higher than the rate of respiration
there is a net release of oxygen and a net uptake of carbon dioxide

(consider CAM plants)

in a plant using full CAM, the stomata in the leaves remain shut during the day to reduce evapotranspiration, but open at night to collect carbon dioxide (CO2)

https://en.wikipedia.org/wiki/Crassulacean_acid_metabolism#During_the_night

this link help you understand the process better by simple language :

http://www.bbc.co.uk/education/guides/zxtcwmn/revision/1


What is the reason for fear induced defecation?

If your mice are stressed or scared during those manipulations, as we can expect them to be, defecation can be a consequence of the "Fight-or-Flight response": in this situation, the organism try to focus its energy to act quickly, and a wave of specific neurotransmitters (noradrenaline in particular) is released. In consequence, mice's bladders relaxe, which cause them to urinate, the digestion stops, but the transit of the faeces in the colon is accelerated: they defecate.

This is all controlled by the activity of the sympathetic nervous system, which secrets acethylcholine and noradrenaline.


Is there a formula for determining the % of ligand bound to a given receptor in a mixture with multiple ligands and receptors?

The answer is here, but depending on your level of comfort with the math I'm not sure how enlightening it will be. I think that the reason people tend to stick to one ligand/one receptor models is that they capture all the intuition without the tedious algebra.

It's interesting that you are asking for the fraction of ligand bound to receptors ($[RL]/[L]_{tot}$). Typically one is interested in the fraction of receptors that have ligand bound ($[RL]/[R]_{tot}$). This is for two reasons:

Typically the fraction of bound receptor is the physiologically relevant variable for a cell, determining the response of the cells to the ligand stimulus. Since the cell can only sense the concentration of ligand when it binds to the receptor, the fraction of bound receptor is the natural variable to study.
In most contexts, the number of receptors is much smaller than the number of ligands. This motivates the approximation found in pretty much all treatments of receptor-ligand equilibrium that the concentration of receptor-ligand complex is negligible compared to the total concentration of ligand. For cells, this is a fairly reasonable assumption. In this limit, the fraction of ligands bound to receptors ($[RL]/[L]_{tot}$) is always negligible. It's the fraction $[RL]/[R]_{tot}$ that is  interesting. Another reason this assumption might be adopted is that in practice, ligands tend to be soluble while receptors are insoluble. In this case, it is easier to control the concentration of ligand, adding it in excess to a pellet of receptors, and then measure the amount of bound receptors (maybe by radioactivity): in this experiment the total concentration of receptors is measured, not controlled, so you want your equation to be a function of your controlled variable, the concentration of ligand. This requires adopting the approximation above.

The situation in which there are two ligands binding to one receptor has been solved (in the limit that $[RL]\ll[L]_{tot}$): this case is known as competitive inhibition. In your notation, the fraction of receptor 1 bound to ligand 1 (ligand 2 is the "competitive inhibitor," i.e. rival ligand):

$$\frac{[RL]}{[R]_{tot}} = \frac{[L_1]}{[L_1]+K_{11}(1+\frac{[L_2]}{K_{12}})}$$

So I'm going to generalize to the case that there are $N$ ligands and I am interested in the fraction of a given receptor $R_i$ bound to ligand $L_j$. The equilibrium constant for this reaction is $K_{ij}\equiv [R_i][L_j]/[R_iL_j]$.

The receptor is also binding to all the other ligands, so that the free concentration of receptor $[R_i]$ is equal to the difference between the total receptor concentration $[R_i]_{tot}$ and the concentration of each bound complex $[R_iL_k]$ for $k$ from 1 to $N$. And the ligand is also binding to all the other receptors. In order to get a reasonable equation, we have to invoke an approximation very similar in spirit to the one mentioned above, namely, that the concentration of all ligand-receptor complexes is small compared to the total concentration of each ligand individually. Thus I can ignore the difference between $[L_j]_{free}$ and $[L_j]_{tot}$.

In this approximation, I expand out the expression for the equilibrium constant (using $[L_j]$ as shorthand to stand for $[L_j]_{tot}$).

$$K_{ij} = \frac{([R_i]_{tot}-[R_iL_j]-\sum_{k\neq j}^{N}[R_iL_k])[L_j]}{[R_iL_j]}=\frac{[R_i]_{tot}[L_j]}{[R_iL_j]}-[L_j]-\sum_{k\neq j}^N\frac{L_kK_{ij}}{K_{ik}}$$

Note that the sum is over $k$ from 1 to $N$ except $k=j$, which I pulled out of the sum early. I also used the definition of each dissociation constant to write the sum in terms of dissociation constants instead of $[R_iL_k]$, which makes the algebra a lot simpler.

This can then be simplified to solve for the fraction of bound receptors:

$$\frac{[R_iL_j]}{[R_i]_{tot}} = \frac{[L_j]}{[L_j]+K_{ij}(1+\sum_{k\neq j}^N\frac{[L_k]}{K_{ik}})}$$

Suppose instead of being interested in the fraction of receptor $i$ bound to a particular ligand $j$, one is interested in the fraction of receptor $i$ bound to any ligand. I'll call this quantity $[R_i\mathbf{L}]/[R_i]_{tot}$. We can figure this out by noting that

$$[R_i\mathbf{L}]\equiv \sum_{k=1}^N[R_iL_k] = [R_i]_{tot} - [R_i]_{free}$$

We obtain $[R_i]_{free}$ from the formula for each $K_d$:

$$[R_i]_{free}\equiv[R_i] = \frac{K_{ij}[R_iL_j]}{[L]_j}$$

And so using our equation for $[R_iL_j]$, we obtain (I'll spare you some of the gory algebra details)

$$\frac{[R_i\mathbf{L}]}{[R_i]_{tot}} = \frac{\sum_{k=1}^N\frac{[L]_k}{K_{ik}}}{1+\sum_{k=1}^N\frac{[L]_k}{K_{ik}}}$$

(these sums are again unrestricted, from $k=1$ to $N$ including $k=j$).

Happily, if there is only one ligand, these formula reduce to the regular result, namely $[L_1]/([L_1]+K_{i1})$. As another check, if all the $K_d$s are equal, then the fraction of receptors bound to any type of ligand is the same as the bound fraction for the same amount of a single type of ligand with the same concentration as the whole pool of different ligands ($\sum_{k=1}^N[L_k]$), and the fraction of receptor bound to a particular ligand $L_j$ is smaller by the fraction of the total ligand pool that is species $j$, $[L_j]/\sum_{k=1}^N[L_k]$.

If you are really interested in the fraction of ligands bound to receptors---that is, you are working in the limit in which there are tons of receptors compared to ligands, so that the number of receptor-ligand complexes is tiny compared to the number of receptors---then you can use the above equations just by switching $L$'s and $R$'s. In this case you would obtain

$$\frac{[R_iL_j]}{[L_j]_{tot}} = \frac{[R_i]}{[R_i]+K_{ij}(1+\sum_{k\neq i}^{N}\frac{[R_k]}{K_{kj}})}\qquad [R_i]\equiv[R_i]_{free}\approx[R_i]_{tot}$$

A caveat

To derive these equations, I made a pretty strong assumption that the total concentration of all receptor-ligand complexes (for different receptors as well as different ligands) is small compared to the total concentration of each ligand individually. In this limit, we can assume that the pools of free ligands of each species are so large that each receptor equilibrates with this pool independently of each other receptor (there's plenty of ligands to go around). You might be interested in the limit in which ligand binding and unbinding to one receptor affects the binding and unbinding to another receptors, so that receptors are not independent. I am not sure how to approach this problem. I'm skeptical that there will be any sort of closed form solution; in my preliminary thinking about this limit, I think I can imagine situations in which stationary equilibria are not possible: depending on rates, receptor A might partially equilibrate, depleting the pool of ligands, affecting the equilibration of receptor B, which would cause receptor B to "pull" more ligands away from A, in some sort of oscillation. However, that is just speculation, and I'd be very curious if someone could provide more insight to this case, in which receptors are able to "interact" through the pool of free ligand.

One of the take-aways of this whole analysis is that it is very helpful to be aware of the assumptions made in standard derivations that lead to the nice results we learn in biochemistry class, and how those assumptions might have to change if we generalize the system somewhat.


Are we more/less resistant to infectious diseases during an allergic reaction?

There are a number of issues with your question, and the short answer is no.

Immunity to pathogens is conferred by antibodies, but not usually of the IgE group. Pathogens usually stimulate IgM -> IgG; IgAs are present in mucosal surfaces.

There are multiple kinds of "allergic responses", and each carries its own risks.

  Type I reactions (ie, immediate hypersensitivity reactions) involve immunoglobulin E (IgE)–mediated release of histamine and other mediators from mast cells and basophils.
  Type II reactions (ie, cytotoxic hypersensitivity reactions) involve immunoglobulin G or immunoglobulin M antibodies bound to cell surface antigens, with subsequent complement fixation.
  Type III reactions (ie, immune-complex reactions) involve circulating antigen-antibody immune complexes that deposit in postcapillary venules, with subsequent complement fixation.
  Type IV reactions (ie, delayed hypersensitivity reactions, cell-mediated immunity) are mediated by T cells rather than by antibodies.

Limiting ourselves to allergic responses mediated by IgE, we have anaphylaxis, allergic asthma, urticaria, angioedema, allergic rhinitis, some types of drug reactions, and atopic dermatitis. These reactions can result in something as mild as urticaria or as life-threatening as anaphylaxis. None of these conditions carries an increased or decreased general immunological response to pathogens.

If allergy affected immunocompetency, one would expect to see, for example, an increased incidence of fungal infections in allergic individuals, but this is not the case. Allergy does not result in an immunocompromised condition, nor does it result in a primed response (an idea popular in the 90's). They are mediated by different pathways.

Effector mechanisms in allergic reactions
The production of IgE
Allergy, Parasites, and the Hygiene Hypothesis
Immunocompetence and allergy


It might be pretty straightforward. Common window/mirror glass is opaque to UV, so as far as the fly is concerned mirrors are just translucent surfaces.

This of course leads to the question of why flies can't see window glass. Maybe the large amount of light passing through at visible frequencies makes it look like a tinted fog to the housefly? Maybe they're trying to fly through mirrors too, but land on their feet and just roll with it?


A large number of prokaryotes do indeed have nucleosome-like structures.  The most well studied is H-NS in E. coli, Salmonella and some other deltaproteobacteria.  H-NS like molecules have also been found in mycoplasma (Lsr2).  One of its roles is to bind AT-rich DNA and silence transcription.  The binding is usually to suppress the expression of foreign DNA which tends to have a lower GC content than the host organism.  There is a great paper that did ChIP on ChIP with H-NS in Salmonella by Navarre et al in Science (Pubmed ID: 1676311).

As a side note H-NS does compact DNA and there is a paper by Dame et al. that demonstrates it with atomic force microscopy.


Contig or scaffold N50 is a weighted median statistic such that 50% of the entire assembly is contained in contigs or scaffolds equal to or larger than this value.

Mathematically:

  Given a set of sequences of varying lengths, the N50 length is defined
  as the length N for which 50% of all bases in the sequences are in a
  sequence of length L < N. This can be found mathematically as follows:
  Take a list L of positive integers. Create another list L' , which is
  identical to L, except that every element n in L has been replaced
  with n copies of itself. Then the median of L' is the N50 of L. For
  example: If L = {2, 2, 2, 3, 3, 4, 8, 8}, then L' consists of six 2's,
  six 3's, four 4's, and sixteen 8's; the N50 of L is the median of L' ,
  which is 6.

In simple words:

  scaffold N50 is the median contig size of your genomic assembly. It's
  a metric that you can use to evaluate the quality of your assembly,
  since an overly small N50 suggests that you were unable to generate
  many contigs of biologically meaningful size (i.e. you probably have a
  lot of bogus little contigs in your assembly). You can increase your
  N50 by eliminating sequences which are bound to cause you problems,
  e.g. short repetitive stretches.

  note that this metric only applies when doing de novo assembly. If you
  are aligning to a reference (i.e. for variant discovery applications)
  this metric doesn't apply

For a sample workout on an arbitrary small dataset:
http://www.r-bloggers.com/calculating-an-n50-from-velvet-output/

This answer was compiled from multiple sources:

http://www.researchgate.net/post/What_is_N50_Scaffold_in_Genome_sequencing_Technique
http://seqanswers.com/forums/showthread.php?t=2332
https://www.broad.harvard.edu/crd/wiki/index.php/N50