Understanding presynaptic and postsynaptic inhibition

Post-synaptic vs pre-synaptic inhibition

Yes, inhibitory post-synaptic potentials (IPSPs) are always in the context of post-synaptic inhibition, because they are post-synaptic potentials. They occur because of inhibitory neurotransmitters (for example, GABA) are released and bind to post-synaptic receptors, particularly ligand-gated chloride channels. We often just call this "synaptic inhibition."

Pre-synaptic inhibition, on the other hand, would reduce the frequency/amplitude of excitatory post-synaptic potentials, by reducing neurotransmitter release at excitatory synapses (for example, glutamatergic synapses). You can also have pre-synaptic inhibition at an inhibitory synapse, where the pre-synaptic inhibition is actually disinhibitory from the perspective of the post-synaptic cell (inhibiting inhibition).

In summary: post-synaptic inhibition is reducing the rate or probability of action potentials; pre-synaptic inhibition is affecting the quantity or probability of vesicle release.

Interneurons vs inhibitory cells

Inhibitory interneurons are a major class of interneuron in the neocortex, but not all interneurons are inhibitory (layer 4 spiny stellate cells, for example, are excitatory interneurons). In addition, not all inhibitory cells are interneurons; some brain regions have inhibitory projection neurons, for example the cerebellum (Purkinje cells) or striatum (medium spiny neurons).

Inhibitory cells are those that release inhibitory neurotransmitters, so they are best thought of as involving post-synaptic inhibition. Chandalier cells in cortex are a bit of a special case, because they synapse onto axons and interfere with action potentials that way, but I would not lump them in with presynaptic inhibitory mechanisms.

Sources of pre-synaptic inhibition

In general (because there may be exceptions, and almost certainly are in invertebrates who have very "weird" nervous systems from my mammal-biased worldview), presynaptic inhibition arises from three places: autoreceptors (self receptors), retrograde signalling from post-synaptic cells, and neuromodulation. One could fill textbooks with information on all the mechanisms, but I'll give one example of each of the three types:

Autoreceptors

Glutamatergic synapses, for example, can have pre-synaptic inhibitory metabotropic glutamate receptors. These are G-protein coupled receptors, not ion channels, and they typically respond when a synapse is very active. They are effectively a brake on over-activity: if a cell is firing too much, the effect of its firing will be decreased by pre-synaptic inhibition mediated by these self-receptors. This principle is common for other neurotransmitters, too. (Wu & Saggau, 1997)

Presynaptic inhibition by post-synaptic cells

Although we think of neuronal signalling as one way, that's not entirely true. Post-synaptic cells have mechanisms to communicate with the pre-synaptic cell, and this can include inhibiting that cell.

Endocannabinoids are one mechanism: they are released by the post-synaptic cell and can reduce pre-synaptic release probability (Maejima et al 2001; Melis et al 2004). At an excitatory synapse, that makes them inhibitory; at an inhibitory synapse, they would be disinhibitory.

Pre-synaptic inhibition by neuromodulators

Pre-synaptic cells can also be affected by local concentrations of neuromodulators, like dopamine (Bamford et al 2004). Dopamine isn't necessarily released directly onto a cell but more into the surrounding area. Dopamine D2A receptors, for example, are found presynaptically at cortico-striatal synapses. Release of dopamine in the striatum reduces glutamate release at those synapses coming from cortex.

Bamford, N. S., Robinson, S., Palmiter, R. D., Joyce, J. A., Moore, C., & Meshul, C. K. (2004). Dopamine modulates release from corticostriatal terminals. Journal of Neuroscience, 24(43), 9541-9552.

Maejima, T., Hashimoto, K., Yoshida, T., Aiba, A., & Kano, M. (2001). Presynaptic inhibition caused by retrograde signal from metabotropic glutamate to cannabinoid receptors. Neuron, 31(3), 463-475.

Melis, M., Pistis, M., Perra, S., Muntoni, A. L., Pillolla, G., & Gessa, G. L. (2004). Endocannabinoids mediate presynaptic inhibition of glutamatergic transmission in rat ventral tegmental area dopamine neurons through activation of CB1 receptors. Journal of Neuroscience, 24(1), 53-62.

Nadim, F., & Bucher, D. (2014). Neuromodulation of neurons and synapses. Current opinion in neurobiology, 29, 48-56.

Wu, L. G., & Saggau, P. (1997). Presynaptic inhibition of elicited neurotransmitter release. Trends in neurosciences, 20(5), 204-212.


Why does T-cell Cancer Therapy require a large tumor mutanome?

Understanding the link between the size of the tumor mutanome and its immunogenicity requires a basic understanding of T-cell development and regulation.

When normal human cells degrade proteins via the proteasome, some fragments of these proteins, called peptides, are bound to specialized cell-surface proteins called MHC. T-cells express a specialized receptor, called the TCR, which recognizes peptides bound by MHC proteins on other cells. The specificity of the TCR, what peptide/MHC combinations a T-cell can recognize, is randomly generated by targeted mutations and VDJ recombination in the TCR genes during a T-cells development. Each clonal population of T-cells (T-cells derived from the same precursor) have a unique TCR that recognizing different peptide/MHC pairs. When a T-cell's TCRs recognize a peptide/MHC combo on another cell, the T-cell is activated.

Because the TCR is generated randomly, many TCRs in T-cell precursors can recognize peptides derived from normal human proteins. To prevent these precursors from becoming T-cells that can attack the body, they are regulated in several ways. Many self-peptide recognizing precursors are destroyed in development, others are converted into regulatory T-cells that instead produce anti-inflammatory cytokines that tune down immune responses. Those those that escape these regulatory processes are later inactivated by other means.

What does this have to do with cancer? Well, most of a tumor's proteins are normal human proteins, and the human body does its best to suppress immune responses against normal human proteins, making it hard to generate an attack against cancer cells with T-cells that recognize normal self-peptide/MHC. Worse, overcoming this protective response could lead to an auto-immune attack on normal, healthy cells. Therefore, we want to make or use T-cells that recognize mutant-peptide/MHC combos. Such cells would not attack or be effectively suppressed in normal tissues, but could attack tumors.

However, to get these ideal, tumor-targeted T-cells, we need the tumor to produce mutant proteins whose peptide fragments ARE DISTINCT from the peptide fragments of normal proteins. Some tumors have far more of these kinds of mutations than others, and not every mutation is immunogenic (not every mutation can be differentially recognized by T-cells). For example, point mutations (single amino acid changes) that activate proto-oncogenes like BRAF don't necessarily lead to the production of structurally different peptide fragments. A larger mutanome offers a greater chance of immunogenic mutations.


Technical reason that specialized embryonic cells form

There is indeed chemical signaling that triggers the differenciation. There are gradients of chemical species during the development. Look at https://en.wikipedia.org/wiki/Morphogen ! There are also other references there.

PS: there is a stack exchange question from today about something related Can gap genes delay their expression?


The sieve tubes of the phloem in angiosperms consist of sieve tube elements or members. These are cells which lose their nucleus, ribosomes, and vacuoles at maturity.  They of course have cytoplasm, and it is connected by channels to companion cells (which do have these organelles).  The sieve tube elements retain mitochondria and plastids. See the Wikipedia page and this page for more details.


II:6 has a $2/3$ probability of being a carrier Aa.
II:3 has a $1/2$ probability of being a carrier Aa.
Assuming, just like canadianer
suggested, that the recessive gene is rare, autosomal, and
non-x-linked, this means II:5 and II:4 are both homozygous (AA).

If parents of III:2 are therefore Aa and AA, this gives III:2 the probability of being a carrier of $1/2$. However, we must multiply this value by $1/2$, because III:2's father has a $1/2$ probability of being Aa. Therefore $\frac{1}{2}\frac{1}{2}= 1/4 =$ probability of III:2 being a carrier.

Similarly for III:3, if her parents are Aa and AA, this gives III:3 the probability of being a carrier of $1/2$. However, we must multiple this value by $2/3$, because III:3's mother has a $2/3$ probability of being Aa. Therefore $\frac{1}{2}\frac{2}{3}= 1/3 =$ probability of III:3 being a carrier.

The probability of both III:2 and III:3 being carriers is the product of both their probabilities: $\frac{1}{3}\frac{1}{4}= 1/12$.


Different Effects of Detection Probability Between Presence and Count Data at the Same Location

Disclaimed: Not really an answer, but too long for a comment

If I understand you correctly, this must depend entirely on the accumulated probablity of detection over the entire detection period (the time the cameras were out). If the accumulated probability of detection across all habitat types is high (approaching 1, given that the animal is present), then the detection probability shouldn't be a problem for the binary occurrence variable. An indication of this would be if you have sites (cameras) with either zero or a very high number of occurrences, which should indicate that the binary occurrence is rather robust. On the other hand, if sites have 0-4 occurrences in total it will be extremely difficult to separate non-occurrence from random factors or detectability. I assume that the detection probability across habitats is unknown though (as well as the accumulated probability of detection), but you might be able to make an educated guess. Also, by using a binary response, you will completely exclude the possibility to estimate e.g. an effect of habitat quality (for instance a difference in abundance between habitats), since counts of 1 or 13 will both be represented by 1 in the binary detection variable. In the Q, you talk about "modeling relative suitability" which indicates that you are indeed interested in something similar to this (relative habitat quality). In that case, I think that a binary response will be too coarse to provide useful information.

One possible toy scenario could be that you have two habitat types A and B (10 camera locations/sites of each) with a binary detection variable as:

A: 1 1 1 0 1 0 1 1 0 1  (species found in 7 sites)
B: 0 1 0 0 1 0 1 1 0 0  (species found in 4 sites)

In that case, the species can obviously exist in both habitat types (as you have categorized them), so the higher amount if zeros in B can represent (among other things) 1) lower occupancy of this habitat (in a metapop perspective), 2) that the quality of B is heterogeneous which is not captured by your habitat categorization (so parts of B is just as suitable as A), 3) lower population abundance in B compared to A (but the same detectability), or 4) lower detectability in B compared to A (but the same abundance). I don't really see how you can separate between these cases with only the binary variable, and I don't believe that using a binary detection variable will solve any specific problems compared to using the count data.

This is all very hand-wavy, but can hopefully give you some useful ideas/perspectives.


How long do fishes survive in a milk environment?

I can't support this answer with scholarly articles. But it's an interesting question if you think of milk as highly polluted water.

Water from a tap (which is what goldfish usually live in) is 'fairly pure', with the naturally occurring minerals sodium, calcium, magnesium and potassium respectively in highest concentrations (varies by location.)

Milk, on the other hand, has not only a much higher mineral content, but also has fat, protein, carbohydrates, and white blood cells as 'pollutants'. In fact, whole cow's milk is only ~87.8% water.

Looking at calcium alone, the concentration of Ca in water is about  3 mg per 100cc, or .003%. Milk has .13% Ca, or 130 mg per 100cc. Since Ca is a major player in nerve and muscle function (in humans, a very relatively mild increase in serum Ca causes tetanic contraction of muscle), my guess is that the poor little fish would not be able to maintain normal serum Ca levels for long. It would die of inability to move fluid over its gills, that is, it would suffocate even in the presence of dissolved oxygen. Not to mention that the gills would also be coated to some extent by fat (3.5%), protein (3.8%) and other 'gunk'.

How long would it last? Probably not more than a few minutes.


What is the evolutionary reason behind human preference for salty foods?

The body needs more than energy to survive.

Salt is vital to the body's function. Ions of sodium and calcium perform numerous vital functions, but are particularly related to the function of the nervous system and contraction of muscles. Accordingly, seeking out sources of salt makes sense in a natural environment in which salt is relatively unavailable.


Has anyone attempted to add extra senses to a creature through a BCI/Neural interface?

Short answer
Yes

Background
This subject touches upon a related technologie, namely sensory substitution, where a lost sense is replaced by a still functional sense, for instance:

The BrainPort developed by Wicab that lets blind people taste light (Fig. 1) (Stronks et al., 2016).
The, now discontinued, yet still highly popular Optacon device developed by Telesensory Systems that allows blind folks to scan a normal printed book page with a camera and read it back through braille input via this device (Stronks et al 2016).

However, you are specifically asking for devices that add novel sensory information, referred to as sensory augmentation, or sensory enhancement. The technique of sensory substitution can,quite obviously, be easily extended to add novel sensory perceptions, simply by using a sensor capable of sensing stimuli that the human sensory systems cannot, for example magnetism, infrared light and what not, for instance:

Mapping the magnetic North on the human body through auditory or tactile actuators (Schumann & O'Reagan, 2017).
Electrically stimulation of the brain in response to otherwise invisible infrared light (Thomson et al., 2013).

References
- Schumann & O'Reagan, Sci Rep (2017); 7: 42197
- Stronks et al., Brain Res (2015); 1624: 140–52
- Stronks et al.., Exp Rev Med Dev (2016); 13(10): 919–31
- Thomson et al., Nature Communications (2013); 4: 1482

Fig. 1. BrainPort V100 vision substitution device. source: Plaid Zebra


Where should I start looking for an online gene library?

Databases
There are too many databases to list here, but Wikipedia has a decent list of the genome databases. For example, there are databases dedicated to genes of individual species, like Wormbase, SGDB and countless others. Alternatively, as others mention a great place to kick off your search is the NCBI.
Finding your nucleotide sequence in databases
It sounds like you already have your sequence. If you want to see if your sequence has been found elsewhere or if there are any similar sequences, you can use BLAST from NCBI. Although it is not strictly a database in itself, it looks to align your sequence to similar sequences in external NCBI databases and quantifies the sequence similarity. It will reveal the species for you to go to a more appropriate database along with a lot of other information about the gene.
There are plenty of parameters to alter to suit your specific needs, but generally, the default settings are a great place to start analysing your gene. You'll need to run a nucleotide test since you want to find the DNA sequence. The results might be difficult to interpret.


Cross section of actin network in neurites

Actin is required for the neurite architecture and is present throughout the shaft (along the direction of the neurite process)

See these images.

                                        [Source]

                                             [Source]

These are not from research papers but the sources are trustworthy.


This is highly unlikely because the immune system would detect these cells and atack them as foreign. There is at least one case described in the literature in which a woman died of lung cancer after receiving a donor organ from a smoker. This is due to the fact that after transplantations people have to take drugs to suppress their immune system to avoid an immune reaction against the transplanted organ. This allows tumor cells to survive.

The same problem is true in research animals. For the transplantation of tumor cells you need mice with a severely deficient immune system (so called "SCID" (Severe Combined Immunodeficiency) mice) to allow tumor cells to grow. This is different when you work with viruses (like the human papilloma virus) which can cause cancer. Here you have to take appropriate safety measures.


I have never had  problem with tubes leaking. However, if you are worried about them getting somehow popped open in transit, you might consider wrapping the lid in parafilm. Alternately, there are lid locks that you could use like these.

@Chris has a good point about screw-cap tubes, they could also work, and are probably a lot sturdier, in case of actual damage.


Is there any conclusive study relating the food consumed and the occurrence of acne?

The short and unsatisfying answer is no-- it remains controversial due to lack of high quality randomized clinical trials. According to an article in UptoDate, a reliable resource for many physicians, last updated September 2014, there is an association between acne and intake of milk in which milk components could exacerbate acne. Unfortunately, there have been no randomized clinical trials on this subject. According to the same article, "there is no reliable evidence that ingestion of chocolate is associated with an increased prevalence or severity of acne." In a similar light, the article continues on to say that "data on favorable effects of dietary factors such as zinc, omega-3 fatty acids, antioxidants, vitamin A, and dietary fiber on acne vulgaris are limited. Further studies are necessary to determine the roles of these supplements in acne vulgaris."

Reference:

http://www.uptodate.com/contents/pathogenesis-clinical-manifestations-and-diagnosis-of-acne-vulgaris?source=search_result&search=acne+and+food&selectedTitle=1%7E150#H8


Why do some Brown Pelicans have orange or reddish parts on their bills?

After doing some reading at the Birds of North America webpage on Brown Pelicans.
It does mention orange on the bill outside of the breeding season.
Brown Pelicans have a greenish gray bill once they are older than 24 days which becomes gray-brown in their first year. At around 12 to 14 months of age, yellow will begin to appear at tip and on the sides. At 16 to 19 months of age, the bill becomes gray-green-yellow with some orange, the orange becomes more distinct at 29 to 37 months.
It is difficult to define the plumage of a Brown Pelican during their first 2 to 3 years; they acquire definitive plumage between the ages of 3 to 5 years old.
Here are the descriptions of their bill in Definitive Basic and Alternate plumages:

In Definitive Basic plumage, proximal end of upper mandible pinkish
orange, distal end buff yellow over pinkish orange, and nail at tip
buff yellow. Lower mandible pinkish orange, except middle section gray
or mottled gray. Proximal end of gular pouch reddish orange (P. o.
californicus) or green-gray (P. o. carolinensis); distal end dark
gray-green. As breeding season approaches, colors intensify; bill
becomes brightest 4–6 weeks before pouch.
In Definitive Alternate
plumage, upper mandible bluish pearl-gray and pinkish on proximal end,
buff-yellow-orange-red over bluish pearl-gray on distal end, and
bright buff-yellow on nail. Lower mandible pale yellow on proximal
third, bluish pearl-gray elsewhere; yellow at maximum intensity when
young being fed; may serve as target for begging nestlings.
Colors
fade with onset of incubation through prebasic molt; upper mandible
gray proximally, buff-yellow and orange over pearl-gray distally, and
buff-yellow on nail; distal two-thirds of lower mandible gray;
proximal end of gular pouch faded yellow-gray (P. o. californicus) or
gray-green (P. o. carolinensis); distal end dark green.

It appears their bill does retain the orange after breeding although it may begin to fade and it does mention how the colour intensifies during breeding.
Reference:
Shields, Mark.(2014).Brown Pelican (Pelecanus occidentalis), The Birds of North America (P. G. Rodewald, Ed.). Ithaca: Cornell Lab of Ornithology; Retrieved from the Birds of North America: https://birdsna.org/Species-Account/bna/species/brnpel


Why don't intelligent animals like primates use plastic bags?

Bags are not that useful if your are not human.

Most primates are too small to get any benefit from it, the bags are too large and would drag on the ground or get snagged on branches, even chimps and gorilla don't have enough ground clearance to not have this problem. Primates have been known to play with plastic bags, but they would not provide much benefit. A primate would need to carry the bag around for hours to fill it and wait before they could eat anything from it, all the while dragging it and hoping it did not tear. Upright humans are the only primate built to carry things long distance, a bag would not help other primates much.

Most primates are frugivores, carrying around extra fruit is not actually very helpful, most primates live near their food sources. Not to mention getting fruit in a tree into a bag is rather difficult task. Carrying around fruit is not very helpful because many primates have a different and much better way of storing ripe fruit in other primates AKA food sharing. Most primates will call other primates of the same species to ripe fruit since sharing in this way means they are more likely to have other primates share with them, thats far better food security than carrying around some extra fruit. It is also a lot easier to call many others to you than carry enough for everyone else.

The primates in your pictures are zoo primates which are both extremely bored and often very anti-social due to being raised in isolation. They might get some benefit, but they are not going to do well in the wild, and no zoo in its right mind is going to give its animals plastic bags.


Proteins will be digested through a number of proteases in the stomach and intestines (pepsin, trypsin, etc) into their constituent amino acids. The amino acids are then absorbed in the small intestine. So any specific proteins you try to put into a pill will be digested into amino acids before being absorbed. If you somehow manage to defeat the digestive enzymes, the protein will simply pass through the digestive tract without being absorbed--the intestines don't have the capability to allow larger polypeptides through.

If you think about it, this is probably a good thing. We don't want random proteins from our food running around in our bodies. It would likely kill us in short order.


Ribosomes producing proteins, but need proteins to be produced?

Ribosomes are the only means we know by which cells produce proteins. Consequently, all proteins are made by a ribosome, including the proteins that then become part of a new ribosome. It's never a question of "more proteins than required" because there are different types of proteins and to make a ribosome, you need those specific types of proteins known as ribosomal proteins. The process of making ribosomes is known as ribosome biogenesis.

This raises the obvious question of where a cell gets its ribosomes from when it is "born". The answer is simple: from its parent. When a cell divides, each daughter cell is made of the components of the parent. The cytoplasm also gets divided, and each daughter cell receives mitochondria, ER, etc. from the parent cell. By the time those ribosomes break down, they will have produced new ribosomal proteins for new ribosomes already.

According to this review from 2017, it appears the ribosomal proteins made in the cytoplasm (so, cytoplasmic ribosomes) get shuttled into the nucleolus, where they get assembled with rRNA to make new ribosomes, which then get exported out of the nucleus into the cytoplasm.


How can sex ratios remain Fisherian (1:1) in species where only the dominant male gets to mate

Fisher's principle applies to such cases as much as it does to species where only pairs mate.  Consider a species where a successful male has exclusive mating with a harem of 20 females, and for each such male, 19 other males are not able to mate.  A female has 100% chance of mating, and a male has a 5% (1 in 20) chance of mating. Assume a female has two offspring.

In this scenario, an equal sex ratio would mean having a female offspring would lead to an expected number of grand-offspring of 2 (100% chance of 2 offspring from that female).  Having a male offspring would also lead to an expected number of 2 grand-offspring (95% times 0 offspring plus 5% times 20 harem females each having 2 offspring).

What would happen if the ratio of births was off from 1 to 1, say 5 females were born for each male? Then expected number of grand offspring would be for a female is still 2, but for a male it is 25% (chance of taking a harem of 20 females against the 3 other males born alongside those 20 females) x 40 (20 harem matings x 2 offspring) = 10. Hence with a lopsided sex ratio in this situation, having a male is much more valuable genetically than having a female.  If a mutant arose which produced more male offspring in this imbalanced situation, it would have success until the population sex ratio became close to 1:1.


By a hint from a FB forum, it should be meripilus giganteus and I have to agree.


What is the difference between a circular and a cat's-eye (slit) pupil?

Circular pupils are always functionally superior to vertical pupils; a slit does not correctly focus light from all directions whereas a circular pupil does. If you observe cats when they're hunting at dawn and dusk*, they have big, circular pupils; it's only when they're in bright light that the pupil shrinks to a slit. So why have vertical pupils at all? Because, as you mention they're capable of letting a more controlled range of light into the eye.

Thus vertical slits let you be active in a wider range of light conditions at the cost of poorer vision in bright light; whilst circular pupils continue to function well in brighter light but at the cost of not allowing such a large range of control over the amount of light entering the eye.

It is then easy to see why you get both kinds of pupil: circular pupils are favoured by animals that are typically active in bright light and need good vision under these circumstances; vertical pupils are favoured by animals that are primarily active in low light but need some ability to see in bright light.

*- it's often stated that cats are nocturnal, this is untrue; cats are crepuscular - that is they are most active at dawn and dusk.


glossary of biotechnological engineering

I found this glossary of Biotechnology and Genetic Engineering off Wikipedia, what do you think?

Or The Facts On File
DICTIONARY of
BIOTECHNOLOGY
and
GENETIC
ENGINEERING

What concepts are you necessarily hoping to include? I'm hoping someone actually experienced in this field can advise.


Why is my peripheral vision better for seeing in the dark?

Its down to the structure of your eyes. The eyes are made of rods and cones, which have difefrences in detecting light.

Now, compare the images below.

As you can probably see, the peripherl vision is predominatlty due to your rods, and your central vision made of cones.

  Measured density curves for the rods and cones on the retina show an enormous density of cones in the fovea centralis. To them is attributed both color vision and the highest visual acuity. Visual examination of small detail involves focusing light from that detail onto the fovea centralis. On the other hand, the rods are absent from the fovea. At a few degrees away from it their density rises to a high value and spreads over a large area of the retina. These rods are responsible for night vision, our most sensitive motion detection, and our peripheral vision.

(Taken from: http://hyperphysics.phy-astr.gsu.edu/hbase/vision/rodcone.html)

You can read about the photorecptors of the eyes here:
http://webvision.med.utah.edu/book/part-ii-anatomy-and-physiology-of-the-retina/photoreceptors/


Do human somatic cells have 46 chromosomes all the time?

Humans have 46 chromosomes, 23 come from the mother and 23 come from the father. I think The easiest way to remember this is to think of the sex chromosomes--if you are male, you have one X chromosome from your mother and one Y chromosome from your father. During S-phase, the cell will make another copy of the X chromosome and the Y chromosome, so you will (technically) have 4 sex chromosomes in the cell before it divides, although you only have 2 UNIQUE sex chromosomes. After division, each daughter cell will have 2 sex chromosomes (one X and one Y). The same holds for all the other chromosomes.

So, to answer your question, yes, in G2 phase, you have double the amount of chromosomes in your cell (46*2 = 92), but you only have 46 UNIQUE chromosomes in your cell.

EDIT: As many people have pointed out, there are examples that do not conform to this rule. For example, both skeletal and liver cells can maintain a second copy of their chromosomes (making them 2n). This, however, is the exception. In my opinion, it's more valuable to know the basic rules that govern chromosomal number.

As an exercise I'd suggest to think about what it means that a cell has '2n' chromosomes? What happens if a germ cell obtains 2n chromosomes and passes that to a viable offspring? Is that offspring now '2n', or do they just have double the number of chromosomes as the parent? When does a duplicated chromosome become an it's own chromosome and not just a "duplicate copy"?


I haven't really found much on this topic (besides popular sites) but I can summarize it here:
There are quite some tapeworms (or cestoda), I found numbers of up to 3500 species. They attach to the intestinal wall of the humans and then start to take up predigested food through their skin. With that, they reduce food from their host and start to grow, some get as long as 15 meters!

Some of the worms seem to be relatively harmless (besides stealing food), but this is more true for the first world. In poor countries, where there is not enough food, tapeworms can cause severe malnutrition.

Some tapeworms can migrate into the blood stream and from there into other tissues or organs like muscles, eye and brain. There they can cause cysts which can lead to organ failure and death.

For more information see this CDC webpage and this article: "Biochemistry and physiology of tapeworms.". This popular article is probably also interesting.


What effect does vortexing have on a fluid sample that simple mechanical shaking does not?

In my experience, shaking and mixing have different "dead spaces". Supposed you had an eppendorf tube and you stirred it around with a pipet tip for thirty minutes. You would have great convective mixing in the radial direction but virtually no mixing in the Z-direction. Supposed you had a very viscous fluid like PEG. If you set the tube on a shaker for an hour it will virtually not mix. The vortexer provides a very different profile of mixing.

Instances where I wouldn't use the vortexer would be for sensitive objects like DNA and cells.

(update)
We had some interesting suggestions from the FDA (since the FDA pays attention to these type of discussions). To get proper mixing, it is often not considered enough to merely swirl a tube a bunch. Their actual recommendation is to train technicians to perform a 90 degree angle arc with their forearm to generate proper force in mixing.


Should I use genomics or/and exomics or/and epigenomics?

Depends on what you want to look at. Whole genome sequencing will give you all the mutations. If you are interested only in the coding part of the genome then you can go for exome sequencing. Though, exome sequencing will save your time and resources considerably, you may lose out a lot of relevant information from the non-coding and regulatory part of the genome.

Epigenomics is a very broad term. There are several aspects to it. You can go for the DNA methylome, Nucleosome positioning, or ChIP-Seq for Histone modification/variants.

I would suggest that if you can afford it then go for whole genome sequencing. Next choice would be exome sequencing. Once you have these data it might be relevant to add the third layer of DNA methylome.

  If I do one of the above and proteomics, why could I need the transcriptomics for?

Transcriptomics is easier and better standardized than proteomics. There are also many good analysis tools.
There are several ncRNA, which has been shown to play important role in cellular homeostasis and gene regulation. You will miss out those.
You will save money. The reagents used for the transcriptomics experiments are the same as the ones used for the genomics experiments. Proteomics is a different domain altogether. You might need to look for collaborators.

  Would the metabolomics, which are mainly punctual measures, add any valuable information?

Sure, they do add information. Whether of great value or not depends on the study that you are carrying out. For e.g if you are studying the role of stress in diabetes then doing a metabolomics study may be of great value.


How do messenger RNAs regulate each other's expression levels?

Typically, these experimenters aren't thinking that the mRNAs directly regulate each others' expression levels, but rather that the proteins they code for affect expression. They're just mRNA as a proxy for the corresponding protein.


Is it possible to synthesize chiral version of an organism (incompatible with our pathogens)?

First off, quick clarification: "chiral" simply means distinct from its mirror image. All current life is chiral, in that it is made up of molecules  which have a "handedness". What you're asking about is life which is made up of molecules of the opposite handedness (which I'll term "mirror chiral").

Such a lifeform is theoretically possible - chemical and biological reactions and reaction rates are entirely the same between the two handednesses - presuming that all participants (substrates, products, catalysts, etc.) are flipped to the opposite chirality. A mirror chiral Jarek would look and function exactly like the normal chirality Jarek, although he would need to eat mirror chiral food instead of normal chirality food.

So what difficulties would you have to synthesize a mirror chiral organism?  The biggest one is the bootstrapping issue. There's a large suite of molecules in the cell which are all needed in order to replicate the cell, or even just maintain it. All of these need to be present in order for the organism to work. The organism can make all these components from scratch, but to do so it already needs to have these components.

Synthetic organisms - that is, organisms with a genome assembled in a computer and synthesized abiologically - have been made. The trick, though, was that the synthetic DNA was then placed into already existing organisms to be replicated and to have its genes expressed. There's no limitation (besides perhaps cost) to synthesizing mirror-chirality DNA - the same machines which synthesize normal chirality DNA can do it if you swap out the reagent bottles. But what do you do with it once you have it? There's no existing mirror-chiral organisms you can place it in to replicate and express the genes.

If one was to make mirror-chiral organisms, you would need to synthesize all of the necessary cellular components in their mirror-image form. So you would need mirror RNA polymerase, mirror ribosomes, mirror t-RNA, mirror ...  If you do things right you can skip most of the cellular components, but you still need a large number of them.

This is not necessarily a pipe dream. Last I knew, the J. Craig Venter Institute, the people who made the first synthetic DNA organism, are actively looking into it. The trick is to trim things down to the bare minimal number of chiral components needed to bootstrap the system. That's (more-or-less) where their current efforts are focused, from what I understand: what's the minimal number of genes needed for a viable cell? Which of these are needed to "bootstrap" a cell from bare DNA?

Personally, I'm pretty confident that a mirror-chiral organism will be created one day. The time frame for this is a little unclear, but there's nothing theoretically limiting it. The biggest issue is our current technical limits in synthesizing sufficient quantities of (non-DNA) biomolecules in a chemical (abiological) fashion. But those are constantly improving, and with additional research into what's needed for bootstrapping a synthetic cell, we'll push down the requirements even further.

Of course, the first mirror-chiral organism will be pretty simple. It's going to be less complex than even E. coli. It will also need to be fed a diet of (expensive) mirror-chiral food (amino acids, sugars), so its use will be limited as well.


What is the point of toxins without remarkable coloring?

This is a really great question. To take a specific example, let's consider Amanita phalloides, the death cap mushroom. It doesn't advertise its poison; in fact, it resembles several edible species of mushrooms, including Caesar's mushroom and the straw mushroom. It contains alpha-amanitin, an extremely potent poison that inhibits RNA polymerase, shutting down protein synthesis. The estimated minimum lethal dose is 0.1 mg/kg or 7 mg of toxin in adult humans. The poison has a delayed effect, taking between 10-24 hours for significant effects to appear, so it's not like a poisoned animal can learn to avoid the mushroom in the future. None of the amatoxins appear to have any purpose except as a mammalian poison. They aren't specific to humans, and are capable of poisoning dogs. So what's the evolutionary advantage of this poison?
According to an essay written on the California Native Plant Society blog by John Chesnut, a horticulturist, the answer might lie in where the mushroom grows -- on tree roots as ectomycorrhiza (emphasis mine):

Death cap is an ectomycorrhizal symbiont. This means it forms connections on the root-tips of forest trees; in California, its typical (but not exclusive) partner is coast live oak. [...] Ectomycorrhizal (EC) fungi collect major nutrients, nitrogen and phosphorous, and exchange these with the host tree for sugars. Delicate hyphal strands extend outward from the root tip mass into the surrounding soil and mulch. EC also allows efficient active transfer of macronutrients, micronutrients, and soil water to the tree. The chronic phosphorous limitation in serpentine soils makes the EC symbiosis especially important for local forest types on this soil. Studies in Norway discovered up to 50% of a birch tree’s sugar is exchanged at the root tips with EC symbionts.

So the poison might not be intended as a way of preventing itself from being eaten, but as way of defending the tree it lives with from nematode pests (emphasis mine):

So why are Amanita so poisonous? It is an unlikely deterrence to vertebrate predation of the fruiting caps, as the effect is slow-acting (36-72 hours before the toxic crisis in humans) and the toxin is not concentrated in the cap. Evidence supports the hypothesis that the fitness obtained from synthesizing the toxin is secured within the hyphal network. Perhaps toxic Amanita obtain nitrogen from poisoned nematodes, or protect themselves (and their symbiont hosts) from plant parasitic nematode predation.
Perhaps the toxin suppresses the growth of competing fungal webs. It seems clear the toxic effect of death cap is intrinsic to its invasive success worldwide.

Interestingly, he points to some research suggesting that some mushroom flies might have co-opted this mechanism to keep themselves parasite-free (link and emphasis mine):

An evolutionary entomologist working in New York State, John Jaenike, has discovered four species of mushroom flies in the genus Drosophila that lay eggs in the gills of fruiting Amanita phalloides. The fruit fly taxa are related to ones that inhabit rotting skunk cabbage, but in New England have recently transferred to the recently introduced Amanita fruitings.
Jaenike discovered that Amanita phalloides is toxic to the damaging parasitic nematodes Howardula that reproduce in the stomach of fruit flies. The toxicity of the death cap to the parasitic nematodes results in much greater egglaying (fecundity) by the fruit flies. The fruit flies are affected by the toxic amanitin, especially the males, but the poison is more than offset by the increase in reproduction.
Janike also discovered that most other insects using mushrooms as egg laying sites (craneflies and forest gnats) shun use of the Amanita (due to its toxicity).


Which are mobile and immobile elements in plants?

What does it mean for an element to be mobile or immobile in plants?

Generally speaking, mobile elements are those that can be moved from older to newer tissue in the plant, while immobile ones cannot be.  For example, calcium is incorporated into the cell wall, so it is immobile; it cannot be relocated later.

Plants with a deficiency of mobile elements (e.g. nitrogen) will exhibit damage to older tissues as the nutrients are moved to new growth.  Conversely, plants lacking immobile elements (e.g. calcium) will exhibit stunted new growth while the older tissues stay healthy.  Some elements (e.g. sulphur) fall somewhere between these two extremes.

To illustrate this concept, here is a plant with nitrogen deficiency (source).  Notice how the older leaves are dying while the newer leaves are relatively normal.

Is there an official list of mobile and immobile elements?

No.  You will probably have to survey the literature yourself to come up with such a list.

Why are some elements not mentioned in the sources?

Elements like Pb or Sr do not appear in either list because plants generally do not use these elements at all.  Only a few elements are present in any appreciable quantity in plants.  The main elements used are C, H, O, P, K, N, S, Ca, Fe, and Mg. Additionally, some other elements such as Cu, Mo, Al, and Cl are used in trace amounts as enzymatic cofactors.  Si is used for structural purposes in some plants.

However, even for "useless" elements, it is possible to study how these elements are absorbed transported through a given plant.  For instance, Rediske and Selders (1953) studied the absorption of strontium by bean plants using radioactive labeling, and concluded that the element was not relocated once absorbed by the plant.  This would make it an immobile element.

References

Feldman, Lewis J. (23 February 2015). Water Relations, Mineral Nutrition, Fruit Development (YouTube). Biology 1B. UC Berkeley. At 32:20.
Lewis, Helen (9 January 2012). "Mobile vs Immobile Nutrients". Mastering Horticulture.
Rediske, J. H. and Selders, A. A. (October 1953). "The Absorption and Translocation of Strontium by Plants". Plant Physiology 28 (4): 594–605. PMC 540423.


This is a bit hard because the usual composition statements are a combination of different types of molecules.

Most of faeces are, by dry weight, bacteria (30%), undigested food and fiber (30%), fat (10%-20%), inorganic matter( 10-20%), other protein(2-3%). (reference)

As you can see the bacterial portion contains proteins (amino acids) and other types of molecules.  the inorganic matter includes bilins which are part of the used up hemoglobin from red blood cells which have been retired.

There's also a lot of variation from one sample to the next - 10% seems pretty common here as you can imagine).  What makes faeces so dangerous is the bacterial portion, which can pose quite a health risk.


What is the difference between an alpha subunit and a non-alpha subunit in ACh receptors?

Achetylcholine (ACh) receptor is a pentamer of two alpha chains, and one each of the beta, delta, and gamma (in immature muscle) or epsilon (in mature muscle) chains.


How do archaea relate to eukaryotes and bacteria?

The relationship between the three is so overly complicated because of horizontal gene transfer, i.e. cells sharing parts of their genome with others instead of the normal passing-down to the next generation. This works between eukaryotes, archaea and bacteria and causes the mixing of the three.

An overview (originally proposed by Woese et al):

Bacteria are simplest considering cellular organisation. They have no nucleus or other internal membranes and no cytoskeleton. Their DNA is generally "junk-free"* (i.e. no introns), not bound by histones ("organising" proteins) and the organisation of regulatory sequences is relatively straightforward, typically with one 'operator' sequence before a gene.
Eukaryotes are complex cells in comparison. They have a nucleus and are full of internal membranes (ER, golgi, vesicles,...). Their complex cytoskeleton allows them to grow very large in comparison. Their DNA is usually full of more or less "junk"*, organised into tight bundles by histones and they tend to have a ridiculous amount of regulatory sequences way before, just at the start and even inside genes. Very importantly, they possess endosymbionts as you mentioned - mitochondria or plasmids, derived probably from some protobacterium.
Archaea at first appear to be a mixture between the two. A nice way to sum it up (though not very accurate) is "eukaryote in a bacterium's clothing". Their cells look a lot like prokaryotes because they are similar size, have no nucleus, endomembranes or cytoskeleton. However, some archaeas' DNA is bound by histones and they use similar machinery as eukaryotes for DNA replication, transcription and translation.

One possible explanation for this (theory by Margulis & Schwartz as explained by my tutor) is: From the last universal common ancestor, first prokaryotes and archaea diverged. After this branching, the differences in genetic machinery evolved. Archaea then branched, producing a protoeukaryote line which went on to endosymbiosis with some protobacteria. That would explain the similarities I outlined above: similar cell structure between archaea and prokaryotes but similar genetic machinery between archaea and eukaryotes.

It gets a bit more complicated though, because archaea and bacteria can exchange genetic material, and eukaryotes incorporated a lot of their endosymbionts' DNA in their own genome, so you end up with all of them having a huge mix of genes from the others.

Edit: Genetic machinery refers to the enzymes used for DNA replication and transcription (DNA and RNA polymerase and the transcription initiation factors) and translation (ribosomes and several other translation factors involved). For example: Prokaryotes only have one type of RNA polymerase which uses sigma factor to bind the initiaion site. Eukaryotes and archaea both have three types of RNA polymerase which use TATA-binding protein for initiation. Or: In Prokaryotes, the translation start codon codes for formyl-methionine while in eukaryotes and archaea it codes for "normal" methionine. (Source)

*) Unrelated to your question, but in my own defence: I am aware that the usage of the word "junk" is somewhat unaccepted nowadays, because it supposes that there is "useful" and "unuseful" genetic material. Also, some of what was thought to be junk has been identified to have regulatory function etc. However, it's also a fact that a lot has been identified to have no function to the cell whatsoever, most of it parasitic DNA which is dead or still happily replicating away (LINEs and SINEs). That is, "junk" to the cell.


Can yeast in a primary fermentation of wine be used as a source of yeast for new fermentation?

Yes, it is possible to reuse yeast in both beer and wine fermentation - commercial brewers do it all the time for cost savings and batch reproducibility, and although I'm not as familiar with making wine, many sites including this one say it's perfectly fine, as long as the viability of the cells is high enough.

The yeast aren't necessarily in stress-induced survival mode during fermentation, they're just living (and metabolizing) anaerobically. They may no longer be reproducing, or doing it very infrequently, but they'll remain perfectly happy little buggers (that's a technical term) for quite a while. Give them more food (sugar), and they'll keep fermenting. What eventually stops the process with wine is the level of ethanol rising too high for their comfort. If you were to dilute the ethanol out with water, they'd keep going.

Now, I wouldn't recommend doing this indefinitely (some strains may exhibit genomic instability, etc.), but new batches can certainly be produced with existing pitches.


How likely will 2 normal bacteria "attack" each other if they infect the same parts of your body?

Mixed bacterial populations, where not engaged in some kind of mutual or commensalistic relationship, are constantly at each others throats over resources. Even then, sometimes it's just rate of growth isn't terribly bad for each commensal. Not just nutrients, for example, but also precious space to colonize or attach to. There's a good review here, and among some of the tactics direct killing by antimicrobial production is an option. You also have other factors, however, such as secretion of molecules that impair attachment or quorum sensing. Also, virulence factors that give a competitive edge such as evading immunosurveillance (encapsulated B. anthracis strains vs unencapsulated, for example).

So here's the hard part: you want to engineer an attenuated bacterium that goes in and attacks a pathogenic strain. While I'm sure possible, you would certainly need to ensure that what you take away to attenuate your strain doesn't gimp it in vivo. You also need to realize that your target pathogen is very capable of simply "changing" itself to avoid dying to the engineered strain. Once your mechanism of action has been defeated, your product has been defeated. I think that it's fundamentally different from commercial virus-based products like T-VEC, as well, due to the level of variability.

One of my thoughts is your strain needs to be able to compete with the pathogen in the first place to stand a chance, which may be difficult if you cut out too many virulence factors trying to make it "safe."


Origin of term ‘confluency’ in cell culture

Besides the etymologic explanation that @aandreev gave, in cell culture this term is commonly used to describe the density of adherent cells and it is used as a measure of their proliferation. It is usually combined with an estimated (or counted) percentage, so 10% confluency means that 10% of the surface the dish or flask used is covered with cells, 100% means that it is entirely covered. The cells grow twodimensional on the surface of the flask in this case. The picture below (from here) illustrates different levels of confluency:

The level of confluency is important as the cells change their growth with changing densities. Low density cells (10-20%) usually grow slower than 50% confluent cells. If the plate is complete grown by cells, they tend to grow much slower again. This influences their genetic program, behaviour in experiments and transfections.

As @Roland pointed out it is important to say that confluency is not a hard measure, but rather an estimate of the cell density. Different people will get different estimations, but the trend should be the same.


What is the big plant with white flowers on the photo?

They both look like poison hemlock (Conium maculatum).  It can grow up to 3m tall and grows in moist areas including along creekbeds. One of it's common names is European Hemlock.  It is toxic to some domestic animals and humans.

Source: United States Department of Agriculture

Source: http://natureid.blogspot.com/2011/11/poison-hemlock-111211-elkhorn-slough.html


Which three functional groups are found in the general structure of amino acids?

Amine, alkyl, and carboxylate.

I'd guess the part that you're having trouble on is that the alpha carbon in the center of the generic AA structure is part of an alkyl functional group
Edit
The original answer that I gave might have been too clever for its own good. Depending on how one looks at the question, the third functional group could instead be the functional group of the particular side chain, i.e. for Alanine it would be a methyl group, for Tryptophan it would be an indole group, etc.


Is it possible nowadays to artificially create an organism just by inserting organism's DNA into an artificial environment?

There may be technical issues that make certain genomes easier to transplant than others, but it can and has been done. Craig Venter's lab used such a transplantation technique to discover what minimum set of genes are required for viability in an engineered bacteria.


Where do the 31 spinal nerves start/meet?

They don’t meet.

Some framework:

Spinal nerves contain motor, sensory, and autonomic fibers. Each of these have different pathways.
Spinal nerves don’t go to the brain. Rather, they synapse in the spinal cord with other neurons which in turn go to the brain (sometimes requiring one more synapse).
In the case of motor neurons, we talk about upper and lower motor neurons. In the sensory system, we talk about first order and second order neurons. Explanation below.

Regarding sensory (afferent) neurons:

Touch and limb position sense are mediated by the dorsal column-medial lemniscus system. The first order (primary sensory) neurons from the spinal nerves, synapse on a second order neuron in the dorsal column in the medulla. There it decussates (i.e. courses to the contralateral side) and ascends via the medial lemniscus to the thalamus. There it synapses with a third neuron that courses via the internal capsule to the primary somatic sensory cortex.
Pain, itch, and temperature sense are mediated by the anterolateral system. These first order (primary sensory) neurons synapse at the spinal level they enter. The second order neuron decussates at that level and courses rostrally via the anterolateral column, ending up in the thalamus. There it synapses with a third neuron that courses via the internal capsule to the primary somatic sensory cortex.

Conclusion: It takes three neurons (inclusive) to get from the spinal nerve to the primary sensory cortex in the postcentral gyrus of the parietal lobe.

Regarding motor (efferent) neurons:

Limb muscles are innervated by circuits beginning in the primary motor cortex. These upper motor neurons descend to the medulla, decussate here, and continue caudally via the lateral corticospinal tract. At the level of the spinal nerve, they synapse with neurons in the lateral ventral horn. These are the lower motor neurons that become the spinal nerve.
Axial/girdle muscles are innervated by circuits that also begin in the primary motor cortex. These upper motor neurons synapse in the midbrain, descend, and decussate at the appropriate spinal level. They synapse there with the lower motor neurons that exit the spinal cord and end up in the muscles.

Conclusion: It takes two neurons (inclusive) to get from the primary motor cortex in the pre-central gyrus of the frontal lobe to a spinal nerve.

In the cortex, these circuits also don’t all come together. They are actually quite diffusely organized across the sensory and motor cortices. Here is a representation of the sensory cortex.* It is a schematic of the post-central gyrus with pictures to indicate where the signals from various body parts end up. The motor cortex is similar. (Google homunculus if interested.)

In addition the pathways described for cognitive perception and control, there are others that help with sub-conscious control of movement (e.g. those involving the cerebellum and basal ganglia), sub-cortical perception of pain signals (e.g. amygdala), and even spinal reflex arcs that never reach the brain. Not all circuits that begin or end in the spinal nerves are destined for or originate from the cortex

This is already considerably over-simplified, and the autonomic system is more complex yet and is not confined to spinal nerves, so I won’t detail it. These signals originate in and feed back to an entirely different area of the brain (mostly hypothalamus). Similar to the motor and sensory systems, at least one synapse is required to connect the brain to the peripheral nerve.

Conclusion: they don’t meet.

Reference:

Martin, John. Neuroanatomy: Text and Atlas. McGraw-Hill Medical; 3 edition (March 27, 2003)

*The source of this image is: http://www.mindtrippingshow.com/mind-trip-of-the-week-17-how-do-we-feel-the-world


How does the stomach handle continuous eating?

First of all, the stomach releases the digested food continuously. Simply put, during digestion the pylorus regularly opens a bit so that small food particles (< 1-2mm) are able to leave the stomach – it's not a batch process (see also this question).

However, because humans tend to ingest a lot of indigestible materials (e.g. bones), there is a need to pass the larger indigestible particles – and this process only happens after all digestible food has left the stomach and thus is "reset" every time you ingest new digestible food.

So if you would continuously ingest food that contains indigestible parts (e.g. mice or other small mammals), the larger bones of those mice would accumulate until you take a longer break and the stomach could complete it's digestion – but for normal food, this does not matter since it will be broken down enough to leave your stomach continuously.

Source: According to Estimation of gastric residence time of the Heidelberg capsule in humans: Effect of varying food composition, 1985 (PDF), the  interdigestive migrating myoelectric complex (IMMC) is responsible for the emptying of of large undigested particles:

  Recently, Hinder and Kelly (1), using radiolabeled techniques, demonstrated differences in the gastric emptying patterns of a liquid, a digestible solid, and an indigestible solid in dogs. Based on such experiments, it has been suggested that the emptying of large (>1 mm) indigestible objects from the stomach
  is dependent on the interdigestive migrating myoelectric complex (IMMC)

Furthermore the study shows that the IMMC gets triggered only after all digestible matter has leaved the stomach:

  The longer GRT of the Heidelberg capsule compared with the t1/2 of the 99mTC-DTPA is consistent with the finding that large nondigestible solids are emptied by the IMMC once all of the digestible materials have passed through the pylorus into the duodenum

and

  the interdigestive migrating myoelectric complex can be markedly delayed by frequent feedings with solids, and the interdigestive migrating myoelectric complex is delayed by both liquid and solid meals

and

  Feeding has been shown to interrupt the IMMC; resumption of myoelectric activity is necessary for the passage of large nondigestible particles such as the Heidelberg capsule


Blocking buffer for actin and fetuin-b in western blot

I have only used milk for blocking a couple of times but it was always beaten by bovine serum albumin (BSA), casein, or BSA/casein.

My standard blocking buffer is 1 - 5% BSA in tris-buffered saline with 0.1% tween20. I have also used the Western Breeze kits from Invitrogen and in my hands their blocks and alkaline phosphatase detection reagents were very reliable. The preservatives that they include in the stock reagents also allow the block to be reused for up to a week if handled and stored appropriately; keep everything clean, use up to 4 times, and store @ 4 degrees when not in use.

Some antibodies will require specific blocking buffers to perform well.

Background can come from many sources so if you have background with both primary antibodies you should check for other issues as well. Background is a very general term and can be caused by many things, a few I can think of are;

Overheating during transfer
Primary/secondary antibodies binding to the membrane.
Primary/secondary antibodies binding non-specifically to the proteins.
The interaction of detection reagents with buffer components (phosphate and alkaline phosphatase, tween)


Chorophyll and photosynthesis in plants with coloured leaves

Most of ornamental (often variegated ) plants do performs photosynthesis. They do have chlorophyll even if their color is not green. They have non-green color due to various different pigments. These extra color has their own functions like blocking harsh sunlight or protection from insects (Karageorgou and Manetas 2006).

In many non-green plants carotenoid content is way higher than chlorophyll. One of the main functions of these carotenoids is to expand the range of wavelength where photosynthesis can happen (Hashimoto et al 2016). This is especially important for such plants living in low light conditions or other stress factors are dominant.

Some comparison of content in different color leafs of Acer saccharum is enlisted in table below. Image is taken from (Junker and Ensminger 2016)

Photosynthetic activity of such plants can be measured by chlorophyll fluorescence techniques (Borek et al 2016). Photosynthesis performance of many of these plants (like Actinidia kolomikta) is actually properly maintained (Wang et al 2016) and does not have high Photosynthetic Cost.

Just to extend this answer for little general information, plants without any chlorophyll (like Cuscuta europaea) are often parasitic plants and they need host to survive and get nutrients.


Why is the central tendon of diaphragm called a tendon?

A tendon usually connects a muscle to a bone, but not always.

According to InnerBody, the diaphragm muscle originates at the lumbar vertebra, lower ribs and sternum and inserts to the central tendon.

  The central tendon — a flat aponeurosis made of dense collagen fibers
  — acts as the tough insertion point of the muscles.

So, the central tendon acts as the diaphragm's own insertion.

A similar example is aponeurosis of the external oblique muscle in the lower part of the abdominal wall (Brazosport.edu, Picture 10.11.a.).

A tendon is the connective tissue that is always a part of a muscle and it fixes the muscle during its contraction.

A ligament is the connective tissue that merely connects two bones or two internal organs and is not actively involved in their movements.


Does Remdesivir interfere with human transcription?

However, how does Remdesivir intefere with human transcription, or does it?
Via https://www.ncbi.nlm.nih.gov/books/NBK548938/:

Nucleoside analogues can cause liver injury by several mechanisms. Most characteristic is a mitochondrial type of hepatic injury that is probably caused by the nucleoside analogue becoming incorporated into or blocking mitochondrial DNA synthesis by the mitochondrial gamma polymerase, leading to a depletion of mitochondria or decrease in their function. Mitochondrial injury can affect multiple tissues thereby causing myopathy, neuropathy, pancreatitis, bone marrow suppression and/or hepatic injury.

Remdesivir trials for treatment of Ebola virus infections included in vitro studies of hepato- or liver toxicity. Via https://www.who.int/ebola/drc-2018/summaries-of-evidence-experimental-therapeutics.pdf?ua=1:

Remdesivir and the parent nucleoside analog GS-441524 were extensively profiled for in vitro cytotoxicity and mitochondrial toxicity in multiple relevant cell types. Both remdesivir and GS-441524 exhibited > 3.5-fold margins in most in vitro toxicity assays. Data from in vitro studies with liver cell culture systems demonstrated that human hepatocytes are susceptible to remdesivir mediated toxicity, likely due to high cellular permeability and effective intracellular metabolism of the drug. Systemic metabolites of remdesivir detected in vivo in plasma do not exhibit any in vitro hepatotoxicity at pharmacologically relevant levels.

However, treatments in vivo did not show much in the way of negative effects:

Single dose of remdesivir IV infusion from 3 to 225 mg was well tolerated with no dose limiting toxicity observed. No treatment emergent AEs were observed in more than 1 subject per arm. No evidence of renal or liver toxicity was observed. All AEs were Grade 1 or 2.
Multiple-dose IV administration of remdesivir 150 mg once-daily for 7 or 14 days was generally well tolerated. No subjects had a Grade 3 or 4 treatment- emergent laboratory abnormality during the study. Reversible Grade 1 or 2 ALT or AST elevations were observed in several subjects without abnormalities in total bilirubin, alkaline phosphatase (ALP), or albumin. There was no abnormality or clinically significant change in international normalized ratio (INR) in any subjects. Remdesivir did not show any effects on renal function in the multiple-dose study.

Stereochemistry of the active portion of remdesivir may help make it less toxic.
Human DNA polymerase selects for or preferentially incorporates right-handed or "D" nucleosides. Nucleosides that are of the left-handed ("L") enantiomeric form will still be incorporated by RNA polymerase and have clinical effect from blocking viral replication, but will less likely be used by the machinery in human cells.
Here is another paper that explores how DNA polymerase selects for the D-enantiomer: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121797/
Other nucleoside antiviral drugs appear to have L-stereochemistry (ibid.) for this reason, to reduce toxicity, so I'd assume the same about remdesivir, as well. I tried looking through a paper on the organic chemistry of remdesivir synthesis, but I don't know enough about that subject to see whether there was a specific step or steps along the drug's synthesis, which involve separation and purification of enantiomers. Perhaps someone with more expertise there can comment.


Are there any forms of heart failure where cell size decreases?

Literature covers only hypertrophy of the heart.
Atrophy not mentioned.

Theoretically atrophy of the heart would require some factors

mutations (which can destroy the gene to build up the organ),
poor nourishment,
poor circulation,
loss of hormonal support,
loss of nerve supply to the target organ,
excessive amount of apoptosis of cells, and
disuse or lack of exercise or disease intrinsic to the tissue itself.

Atrophy can happen locally in some part of the heart only, like in some parts of myocardial infarction.
However, the surrounding healthy tissue then undergoes hypertrophy so the total heart undergoes hypertrophy.
Some discussion about Cardiac atrophy here.


How does the cardiac cycle and electrical activity all relate to blood pressure in the heart?

Blood pressure is determined by cardiac output and the total peripheral resistance, where, from Ohm's Law (Q= P/R):

Mean Arterial Pressure (MAP)= Blood flow (Q) x Total Peripheral Resistance (R)

The cardiac cycle and heart activity will essentially control the cardiac output through the FORCE and the FREQUENCY of contraction.

Cardiac output is determined by the stroke volume, and the heart rate:

CO= Stroke volume x HR

Changes in HR is linked to changes to the SAN and is controlled by sympathetic and parasympathetic inputs. An increase in HR, will cause cardiac output to increase, causing an increasing in blood pressure (simply put, other physiological changes can also influence blood pressure, such as vasoconstriction and vasodilation).

With regards to the AVN, SAN and bundles of His, this allows electrical conductance which causes the contraction of the heart. The contraction of the heart leads to blood being ejected (i.e. blood flow, which is linked to cardia output). This, together with the peripheral resistance of blood vessels will be linked to blood pressure.


How did parasitoid wasps evolve their life cycle?

This is similar to the seahorse problem, in that it requires a distinctly non-mammalian perspective. Parasitoid Wasps, Natural Enemies of Insects provides a more in-depth explanation.

Existing wasp strategies may illustrate the possible transitional forms. It is not a linear transition: all of these have branched off and there are multiple parasitic strategies.

Solitary wasp, captures prey to feed to its larvae
Ectoparasitoid wasp, which lays its egg directly on prey that is paralyzed or otherwise unable to resist as the larvae eats it alive
Endoparasitoid wasp, which has formed a symbiotic relationship with a virus that disables the prey's immune system thus allowing eggs to be laid inside the prey
Hyperparasitoid wasp, which preys on other parasitoid wasps


How can you band wheat chromosomes using Giemsa dye?

The Wright or Giemsa-stains can be influenced by the pH of the rinsing solution after the incubation in the dye-solution. The lower the pH the more pink will be the result. The higher the pH the more blue will be the result. Usually Giemsa-stains are differentiated at an approximately neutral pH. (Weise buffer pH 7,2 or acidified water pH 6,5). To lower the pH you can add few drops of acetic acid. This will also enhance the speed of differentiation.

Giemsa-stains are also sensitive for too long rinsing in diluted ethanol. The color turns blue and more faint.

Also it might be the trypsin that can digest some region rich in C or G. It's not condensed so appears light but the other region is very condensed so the trypsin can't enter and digest this region, which appears dark or the opposite.


How does chromosome fusion get fixed in the population?

Looking at this 2001 review paper by Rieseberg: http://evolution.powernet.ru/library/Scienc9.pdf (especially Box 2), drift and inbreeding are suggested ways that chromosomal rearrangements can become fixed. These forces are strongest small, isolated populations, such as populations experiencing the founder effect.

Another model discussed in that paper is the suggestion that some centric fusions (Robertsonian translocations) lead to little or no loss of fertility in the heterozygotes.


What is the function of the Hyoepiglottic ligament?

It's an interesting question. This 2010 paper contains some discussion of the function of the hyoepiglottic ligament. The following is a quote from the introduction:

  The epiglottis is connected to the
  hyoid bone by the hyoepiglottic ligament (ligamentum
  hyoepiglotticum), which is a connective tissue structure that
  serves as the roof of the paraglottic space and the
  preepiglottic space. Anatomically, the hyoepiglottic ligament
  separates the supraglottic larynx from the base of the
  tongue. Some clinical studies have shown that this
  ligament inhibits the spread and invasion of carcinoma... The hyoepiglottic ligament is elongated by
  approximation of the thyroid to the hyoid during swallowing.
  Tension on the ligament results in a “snap” retroversion
  of the epiglottis. Thus, the folded epiglottis represents a
  state of higher energy than that represented by the unfolded
  epiglottis; relaxation of the tension on the hyoepiglottic
  ligament releases the cartilage to automatically return to its
  normal resting position [emphasis mine].

In the study, the authors demonstrate histologically that the hyoepiglottic ligament is bipartite, with a part they call the pars hyoideus connecting the anterior epiglottis to the hyoid, and a part they call the pars lingualis connecting the epiglottis to the root of the tongue (they claim that this attachment to the tongue was previously unreported). Another quote from the paper follows:

  It is suggested that the pars lingualis plays an
  important role in active mechanisms such as upward
  movement of the epiglottis during phonation associated
  with tension of the lingual muscle and supraglottic airway
  patency during respiration.

To get some idea of how tension in a ligament anterior to the epiglottis can cause posterior movement (i.e. closure of the epiglottic 'flap'), I found this 1979 paper useful. They used cinefluorography to investigate the biomechanics of the epiglottis. The following lengthy quote should help to clarify the proposed model:

  The radiographic observations indicate that
  at the peak of the deglutitional excursion of the
  hyoid bone and the larynx the following circumstances
  prevail:

  (1) Forward translation of the hyoid bone in
  conjunction with extreme thyroid-hyoid approximation
  causes extreme elongation and
  tension on the hyo-epiglottic ligament at its attachment
  to the margins of the epiglottic
  tubercle.

  (2) The compression of the median thyrohyoid
  fold, secondary to extreme thyroidhyoid
  approximation, tends to make the epiglottic
  tubercle bulge backward transversely
  as well as vertically.

  The principle of the mechanism of folding
  deduced from these observations is demonstrated
  in a working model that can be set up
  in a few seconds. All that is needed is a rectangular
  piece of fairly stiff paper. The piece
  of paper represents the complete epiglottic
  cartilage (epiglottis and tubercle). A $\Lambda$-shaped
  crease is applied at the center (Fig. 4) to simulate
  the groove on the back of the cartilage,
  between the epiglottic tubercle below and the
  epiglottis proper above. One next applies stress to the model from the opposite side, at
  the site of attachment of the hyo-epiglottic
  ligament. This is done by grasping the paper
  lightly at the edges, below the level of the
  crease, whereupon the part above the crease,
  representing the epiglottis, immediately begins
  to fold down.
  Each limb of the crease functions as the
  directrix of a cone; the apex of the crease is
  the vertex of the cone. When the paper is
  gripped the directrices rotate towards each
  other and pull the attached paper after them,
  giving it a conical shape.

I've attached the figure 4 from the paper to illustrate better (I'm not sure if that's allowed on SE; please delete it if that's appropriate):

$\hskip 2 in$

The authors of this paper and this paper argue that the model just given does not fully explain the motion of the epiglottis during swallowing. The latter paper describes the existence of distinct lateral hyoepiglottic ligaments attaching to the ends of the greater horns of the hyoid bone. These, they argue, transmit the biomechanical forces generated by the movements of the hyoid and thyroid cartilage to the epiglottis to cause downfolding, although their full argument is too long to reproduce here.

Hopefully all of that has shed a little light on the possible function of this ligament. It seems to be quite complex, but there appears to be a relative consensus that the transmission of tension via this ligament is important in causing the folding down of the epiglottis during swallowing.


Why we do not get hurt from HCl secreted in the stomach?

Goblet cells.

These are specialized epithelial cells whose job it is to produce mucins. Mucous role is not only important in protecting the epithelium of the digestive tract from HCl, it is also a very important substance in the innate immune system, acting as a barrier defense to trap pathogens and/or prevent them from breaching the epithelium and gaining access to sterile parts of the body.


Mechanisms of extracellular stimulation of neurons

Good question. Just to set some stuff straight: In contrast to a comment placed earlier, there is definitely a current flow between electrodes in neural tissue, as long as the impedance is not too high. The potential difference between the electrodes and impedance determines how much current flows, basically following Ohm's law: I = U/R.

As to your hypothesis (A) - I confirm  WYSIWYG's answer - electrodes indeed do not have to be coated, as long as they are conductive. For instance, Ag/AgCl coatings are used to electrically stabilize the electrode, mainly for sensitive reference electrodes used for recording purposes (see a commercial link here). For stimulation purposes chloride salts are a big no no, as AgCl or comparable chloride salts will be converted into metal (e.g. silver) + Cl2, obviously a toxic gas.

As to your hypothesis (B) - It is the electrical field that activates neurons (Basser & Roth 2000) by means of inducing current flow. For example, imagine a cathode (negative electrode) placed close to a neuron. Normally in rest, a neuron's membrane is hyperpolarized (more negative ions inside the cell, the extracellular fluid can be considered to be neutral). The negative electrode will now cause the extracellular fluid to be negatively charged. Subsequently, positive current will flow out from the cell close to the electrode and into the electrode. According to Ohm's law, the membrane voltage is thus positive (note Ohm's law: U = IxR, with I being positive and R being always positive, means U is positive). Hence, the membrane is depolarized, as the resting state is a negatively charged state (hyperpolarized). With an anodic electrode neurons can also be depolarized but due to a slightly different mechanism. Basically, the flanking regions of the now negative current flow to the positive electrode become subject to positive current, as it counterbalances the negative flow to the electrode.  The chapter of two veterans in electrical stimulation, Abbas and Miller, in (Cochlear implants) is particularly helpful, as is (Basser & Roth 2000). I can't link a pdf to Abbas and Miller, excuse me for that. I bet your university library will have access to it. Hope this helps.


Is there something that makes flies slower at high altitudes?

The atmospheric density may not be the only factor, but from a physics standpoint, flying animals should in general move more slowly at high altitude.

As an example, New Mexico's Wheeler Peak is at an altitude of ~4 km above sea level. For a back-of-the-envelope air density calculation, a good estimate of scale height is 10 km, i.e. $\rho(h) = \rho_{sea}*e^{-h/10km}$ , which means the air density at Wheeler Peak is about $2/3$ the density at sea level (other air conditions being equal).
For wing-flapping animals, the power required to maintain flight is inversely proportional to the air density. I'm not confident about how flies' wing movements would be affected (this is where an entomologist should step in), but in any case their air speed should be reduced at high altitude.


According to this paper (Yoav Soen et al. PLoS Biology 2003), peptide:MHC microarrays are a type of cellular microarray (a microarray designed to identify cell types; Wikipedia). These microarrays have attached a MHC molecule bound to a peptide, which allows them to work as artificial antigen presenting cells (APCs) that activate specific subpopulations of T cells.

Another recent paper is here where they specifically use the word recombinant peptide:MHC.

The expression MHC restricted refers to the positive selection (in the thymus) of T cells that recognize MHC molecules of the host but not other self-antigens (Wikipedia).


Why is there no toxic effect on the bulbuls feeding on Cascabella thevetia (oleander) nectar?

The toxicity of Cascabela thevetia is due to the presence of cardiac glycosides such as thevetins A and B. Although these compounds are highly toxic for humans and several domestic animals, other vertebrates are much less sensitive to them.

This review article discusses various aspects of oleander toxicity, and the authors draw attention to species-specific differences in toxicity.

  In addition to dogs and cats, Szabuniewicz et al., (1972) also examined oleander toxicity in monkeys, goats, mice, rats and chickens. Dogs, cats, goats and monkeys were found to be very sensitive to the cardioactive glycosides extracted from dried oleander leaves. In contrast, the rodent and avian species were observed to be insensitive to oleander cardioactive glycosides.

They go on to suggest that differences in the toxin target molecule, the cardiac Na⁺,K⁺ ATPase, is the most likely explanation for this:

  Akera et al., (1979) postulated that the low affinity between cardiac glycosides and rat cardiac Na⁺,K⁺ ATPases could be due to stearic constraints in substrate (glycoside) binding. In this scenario, quaternary conformation of the OL-subunit glycoside binding sites physically precludes the simultaneous binding of all three glycoside structural components. Species-specific quaternary conformation of Na⁺,K⁺ ATPases coupled with subtle differences in glycoside composition (e.g. various sugar moieties attached to the steroid backbone) could, thus, conceivably account for the observed species-specific responses to cardiac glycosides, including those found in oleander.

We have a tendency to assume that susceptibility to the toxic effects of plant materials is universal, but the toxicity of onions and chocolate for domestic animals are clear examples that this is wrong. The variation in sensitivity to the toxins in oleander is a good example coming from the other direction.

Shannon D. Langford & Paul J. Boor (1996). "Oleander toxicity: an examination of human and animal toxic exposures". Toxicology. 109 (1): 1–13. PMID 8619248. doi:10.1016/0300-483X(95)03296-R.


What is possibly wrong with my gel electrophoresis when i don't see bands of DNA ladder?

As one attempts their daily Sisyphean challenge of uncovering a new fact there is one truism, or platitude, that informs all of our efforts at troubleshooting an unanticipated experimental outcome.  This can be paraphrased as:

The number one cause is pilot error.

Accumulated experience of bench scientists everywhere shows that their own human errors are the simplest explanation whenever they try to deduce what could have gone wrong.  In the real world this translates into an operating axiom:

Don't waste time and energy coming up with new physical laws, or multi-step explanations that require you to remake and test all of your reagents, just repeat the experiment and see if this phenomenon is reproducible.

With that new information, that it is, or is not reproducible, you can decide if there is any hypothesis to test. But please, don't just take my word for it. Survey experimentalists, and the more experience they have the better.


Short answer: Changing something (instead of everything) yes.

There are several studies on the impact of environmental factors on life span.
Of course it depends from organism to organism. Diet restriction for example has been shown to extend life span of worms and mice. Temperature is also working well, at least with microorganisms, the metabolism of E.coli for example (that usually grows at 37 Celsius) can be greatly slowed down at lower temperatures. Also, there are enzymes involved in the "ageing pathway" some of these enzymes can be promoted or repressed by small molecules, like resveratrol does, and as result you get some increment in life span. The opposite is also true, you can accelerate ageing with external factors. For plants works as well, changing the environment you can definitely have an effect on the life span and the overall metabolism rate, indeed tricking the light cycle is a very well known method to induce flowering for example.

Here some interesting links if you wanna dig more into this topic.
http://web.mit.edu/biology/guarente/
http://genetics.med.harvard.edu/sinclair/
http://www.ted.com/talks/cynthia_kenyon_experiments_that_hint_of_longer_lives?language=en
http://jxb.oxfordjournals.org/content/58/12/3099.full


There are 100, 200 and 1000 mile races for huskies, we can check the speeds of the winners of the races: http://www.eaglecapextreme.com/index.php/the-race/race-times

97 miles run in 17.23 hours, gives 5.6 miles an hour, 10 km/h, on a cold day, 12-16 dogs towing the musher and the sledge. without a sledge, a husky can probably run 150km at 15km/h average, so that's 10 hours of running.

there have been studies about husky mitochondria and their biology.


First of all lets have a look, what these guys want to accomplish: They want to use bacteria to make certain products. To do so, they want to exploit the bacterial metabolism at steps where no alternative pathways are available. One of these steps is the first step of glycolysis, when Glucose gets phosphorylated to glucose-6-phosphate (G6P). In bacteria the phosphorylation is done during the import of glucose into the cell by the "phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system", which uses Phosphorenolpyruvate as a phosphate source. This has the disadvantage, that there is almost no free glucose inside the cell, but mostly G6P.

To overcome this problem, the group expressed alternative transporters (which transport glucose into the cell) and Glucokinase (Glk) to allow the cells to survive. This steps decoupled import and phosphorylation of the glucose and resulted in free glucose inside the cell. This free glucose can now be used by different proceses. It also allows glycolysis, since the Glk phosphorylates the glucose which then enters the glycolysis pathway. The Glk was put under different promoters to make different mutants in order to test how the different expression of Glk affects the cells viability.

To bring in another enzyme which also metabolizes glucose, they used glucose dehydrogenase (Gdh) which was expressed from a plasmid with a strong, IPTG inducible promoter. They then used different concentrations of IPTG to test the effect on the production of gluconate and cell viability (I am not going into this).

The figure above is figure 5 from the paper and shows the effect of the three different IPTG concentrations used to induce the expression of the Gdh. For 10 and 25uM IPTG the yield of gluconate is getting smaller, the higher the Glk activity gets. Only the smalled activity shows a lower yield. This is complete different for the highest concentration, but here the cells get probably messed up by the high expression of the Gdh (which also consumes a lot of energy).

In the paper they give no explanation or at least discuss the behaviour of the gluconate yield at the smallest Glk activity (I would like to read the reviewers comments on that). From the data I would expect a higher production. It is possible that the lower energy production (low amounts of G6P means little glycolysis) has negative side effects on the cells. It is also possible, that the Gdh is inhibited at lower Glk activities by some other substances in the cell. Gdh activity is for example inhibited by higher concentrations of nucleotidtriphosphates (ATP and so on), see here. Since Glk needs ATP as a cofactor it would be possible that the ATP concentration at lower Glk activities has a negative effect on the Gdh activity (my own speculation).

Or it is simply some artefact from the experiment. This has some points which can be critisized (I would like to see the reviewers comments here as well). First the error bars are pretty big, so this can also be somewhat different. In the text they mention that the data was acquired by

  at least 2 parallel cultures in a representative experiment

I would expect some more repetitions (at least three independent experiments), which would make the data more reliable. Then (and this point is much more important) they can not measure the activity of Glk and Gdh in the same culture due to restrictions in the detection system. Glk activity measurements use a coupled system which in the end measure the concentration change in NADH, while Gdh uses NADPH as a co-factor. Both versions can not be differentiated by measuring a spectrum, so activity measurements of Glk can only take place in untransfected cells. Since the expression changes conditions in the cell (and we don't know how), I would expect at least some discussion about it, but it is missing.


How common is it to be pregnant with periods?

But many women (and doctors) still call it a period.

It is not a period:

  Pregnant women can have some light irregular bleeding during pregnancy, but it should not be like a “normal” period. Some women can confuse this for their period because often it can come right around the time she was expecting her normal period. [...] It should not be enough bleeding to fill pads or tampons over a few days [1].

It is quite common in the first trimester:

  Vaginal bleeding during pregnancy can occur frequently in the first trimester of pregnancy and may not be a sign of problems. But bleeding that occurs in the second and third trimester of pregnancy can often be a sign of a possible complication [2].

It happens to about 25 % of pregnant women:

  Up to 1 in 4 women have vaginal bleeding at some time during their pregnancy. Bleeding is more commonin the first 3 months (first trimester), especially with twins [3].

Repetitive bleeding is associated with preterm birth:

  Bleeding of multiple episodes, on multiple days, and with more total blood loss was associated with an approximate twofold increased risk of earlier preterm birth, PPROM (preterm premature rupture of the membranes), and preterm labor. In contrast, bleeding in the second trimester only, of a single episode, on a single day, and with less total blood loss was not associated with any category of preterm birth [4].

References:

American Pregnancy Association. Am I Pregnant: FAQs On Early Pregnancy. Available from http://americanpregnancy.org/gettingpregnant/pregnancyfaq.htm (accessed 29.07.2014)
American Pregnancy Association. Bleeding During Pregnancy. Available from http://americanpregnancy.org/pregnancycomplications/bleedingduringpreg.html (accessed 29.07.2014)
U.S. National Library of Medicine. A.D.A.M. Medical Encyclopedia. Vaginal bleeding in pregnancy. Available from http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0003748/ (accessed 29.07.2014)
Yang J, Hartmann KE, Savitz DA, Herring AH, Dole N, Olshan AF, Thorp JM. Vaginal bleeding during pregnancy and preterm birth. Am. J. Epidemiol. 2004 Jul 15;160(2):118-25. doi: 10.1093/aje/kwh180. PubMed PMID: 15234932.


She was probably referring to ex-situ conservation as a way to complement in-situ conservation. Indeed, if a population is endangered and fragmentation it thought to be one of the main factors causing the decline, it can sometime be hard to restore the habitat in a way that would permit the population reestablishment (in-situ conservation). Ex-situ conservation can therefore permit to protect some individuals. Then, we could reintroduce individuals to their natural habitats later on, and this could give us more time to restore the habitat.

If you want a good example of how hard it can be to restore the habitat to permit population reestablishment, have a look a the Caribou situation in the north of Québec.

If your question is about how fragmentation is affecting species then it's a very very large subject... it can reduce gene flow, induce stress that could leads to lower reproductive success, etc.

Hope this helps.


Why do 6-8% of diphtheria patients do not develop natural immunity after being affected?

There are two other, but rather exotic possibilites which explain why people do not develop immunity after an diphtheria infection. These are unlikely to get to 6-8% of the cases which @Masi writes, but I am missing the reference here.

The first possibility are people with chronic renal failure. They have problems with their immune responses since their antigenpresenting cells do not get the necessary co-stimulatory signal by the T-cells. See this paper. People with other problems in their T-cells or the co-stimulatory signal would have this problem, too. See this article.

The other possibility would be the distribution of the antibodies. The diphteria toxin is made out of two subunits, A and B. B is important for making the way of A into the cell, A gets cleaved in this process and fully active. When the antibodies made in the process are mostly against A (and then against parts, which change their conformation after the cleavage), this antibodies are mostly useless to fight the toxin. See this paper.

One (but is complete speculative) possibility is on the toxin itself. It could be possible, that some people are more sensitive to the diphtheria toxin, so that the amounts necessary for the negative effects are too small to trigger an adequate immune response. This is known for the tetanus toxin, where even a survived infection doesn't provide immunity (except when people are vaccinated afterwards) as the toxin is so toxic, that it doesn't trigger the immune system. The caveat is, that the diphteria toxin is about 3 orders of magnitude less toxic than the tetanus toxin.


Why is duck fat less saturated than cow fat?

Because ducks need to float and cows don't. If there was a densely fat duck it wouldn't float or fly very well and it wouldn't survive to reproduce.

To answer your question, the composition of fat varies because of the different conditions in which the organism needs to thrive. Fur is different as well. Bear in mind nature is a cruel place and any tiny edge you can get is vital for your survival.

My answer is a bit general but I hope it addresses the question.


TL;DR: It originally referred to abnormality in "secretion" by the inflamed tissue and later became used to mean any abnormality at all.

This fifth cardinal symptom of inflammation seems to be rather mythological as laid out in detail by Rather (1971, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1749862/?page=3). This source explains that the term seems to have been invented at some point in the 19th century without proper definition. Later authors seem to have interpreted it as basically just meaning "not functioning properly" (although this is literally the definition of unhealthy as opposed to healthy, and not specific to inflammation).

According to Rather, the original source of the confusion may have been the phrase: "...heat, redness, tumour and pain; to which should be added an alteration or suspension of the natural secretions of the part." by Macartney in 1838 (page 8 of the same document). Various versions of mentioning a fifth cardinal symptom that involved altered function made their way through pieces of writing, until it received the Latin term "functio laesa" in the late 19th century (Rather cites a piece from 1882), lending it credibility as an established concept. The passage by Macartney was later cited by Marchand in 1924, who was trying to clear up the confusion around who established the four and potentialy fifth cardinal symptoms of inflammation. Marchand rephrased it into a "fifth cardinal symptom the alteration or disappearance of normal secretion (thus a functio laesa)", trying to explain what, according to Macartney, is the fifth symptom, and adding why it could be called a "loss of function".