How are bioremediation microbes removed from the environment once they perform their function? In the case of bioaugmentation, microbes are introduced into the environment to clean up and absorb a certain pollutant. My question is how is that microbe then removed from the environment once it performs its function?

Usually you have to introduce conditions which hinder multiplication of the microbe such as altering the pH and emperature. This is hard to achieve in a large environment, alternatively, you can introduce a recombinant of that microbe which posses a survivability threat to the initial microbe.


Why don't we have vaccination against all diseases caused by microbes? People can be vaccinated against certain diseases. Principle of vaccination is to use live attenuated load or inactivated. My question is - why we dont have vaccination against all diseases which are caused by microbes?

Mainly cost/benefit analysis. Using vaccines has a cost, both in dollars and in risk. That cost may be very low (cheap safe vaccines, like measles vaccine), or may be relatively high (smallpox vaccine is relatively risky, with around a 1 in 300,000 chance of moderate to severe side effects); but there is always some cost.

Vaccines may not have any significant benefit. I live in the urban USA; it's unlikely that an Ebola vaccine would offer me any benefit (as of the current situation in 2019). Very few people in 2019 have a significant chance of being exposed to smallpox, since it's extinct in the wild; the benefit of universal smallpox vaccine would be small.

So if the risk of a vaccine is greater than the benefit, delivering the vaccine would be more harmful than good. This calculation is done as a routine, and the vaccines people receive are known to be ones that confer more benefit than risk.

In fact, with vaccines, the benefit needs to be much higher than the risk, because with vaccines the benefit is invisible (nothing happens - you don't die of measles) while the risk is something that happens. Typically, vaccine benefit/cost ratios are very high, for that reason.

Monetary cost is also a factor. It may seem harsh to think that saving a child's life with a vaccine is given a price, but at some point the finite supply of money can be used more effectively elsewhere. If it costs a billion dollars to give a particular vaccine, and it ends up saving one life, is that the best use of money? Could it be better spent on nutrition, sanitation, etc?

This applies to quite a few diseases. There are, in academic labs and in the freezers of pharmaceutical companies, vaccines against a lot of pathogens that are not being used, because the cost is too great for the benefit. That's an equation that changes all the time; it applied to the Ebola vaccines at one point, but in the face of an Ebola outbreak those vaccines -- in those areas -- are now cost-effective.

Finally, there are a handful of pathogens for which a reasonably-priced good vaccine would certainly be cost-effective (HIV, malaria, tuberculosis, for example) but for which reasonably-priced good vaccines don't exist, because vaccines are sometimes really hard to make.


Where do the antibodies that trigger the specific immune response come from? In A level Biology, we are taught that in order to trigger the specific immune response of the body, antibodies must first attach to the pathogen. The macrophages contain antibody receptors, and this allows them to attach to the antibody carrying pathogen and subsequently engulf them by phagocytosis. This then triggers a certain pathway that involves T helper cells activation, which release cytokines to cause differentiation of B helper cells into plasma cells, and THESE release the antibodies.

The question is: where do the antibodies that start off the whole process even come from?

First: What your teacher says about the free floating antibodies is not correct. The first contact with a new antigen to generate specific immunity is done by naive B cells which have a membrane bound B cell receptor and their effector T cells. This contact can either happen directly or by the presentation of the antigen to the cell by antigen presenting cells (APC).

Short answer:
These naive B cells are present in our body without antigen contact, but are not highly specific.

Long answer:
Our body has the possibility to express a vast variety of different antibodies - estimations go up to 10 billion different antibodies which the human body can produce, each of them capable of binding a different antigen (see reference 1).

To begin with, naive B cells express antibodies as a membrane-bound version, the so called B cell receptor. The antigen specificity of these receptors is random and occurs before the individual had contact with the antigen. These receptors bind a wide variety of different antigens, more or less good. This is the so-called affinity of the receptor (or the antibody) against an antigen.

Upon binding of an antigen, the B cells get activated (if the receive a co-stimulatory signal from a T cell). When activated, the cells starts to proliferate and to differentiate, as shown in the figure below (from here).

Basically, the cells start to re-arrange the genes which are responsible for generation of the variable region of the antibody (the part which does the actual binding of the antigen) to generate highly specific high affinity antibodies to the antigen and then mature into relatively short lived plasma cells, which produce big amounts of antibodies and long lived memory cells. The later are dormant in the body and get reactivated, when the body is challenged by the same antigen, against which it already produced highly specific antibodies.

When re-exposed to an antigen, the antibodies in the blood stream bind to the antigen and mark it for phagocytosis. The phagocytes will then take up the antibody bound antigen, process it and present parts of it on their surface to B/T cells. This either starts the process of selection and clonal expansion as described above or if there are specific memory cells, these cells will proliferate and differentiate into antibody producing plasma cells.

The initial process of adaptive immunity takes about two weeks until highly specific antibodies are available, if you only have to "wake up" the cells from the memory pool, this will take a few days. This is also how vaccinations work.
See also the Wikipedia page on Antibodies for much more details.

References:

Development of the immunoglobulin repertoire.


Is the ratio Brain Mass/Total Mass still considered a valid indicator of intelligence? I was reading this(1) and it led me back to ask a very basic question (I'm not a neuroscientist).  All the way back to undergrad anthropology and neuroscience courses I remember being taught the general rule of relative intelligence was that one looked at the ratio of the brain mass over the total mass of the animal (or the estimations therein from let's say fossils).

I know a lot of the interesting neuroscience research going on these days does looks into bird brains, particularly within Corvidae.  It would seem that birds are often much more efficient in the abilities they seem to show with considerably less brain mass.  I do realize that birds often weigh very little as well, so perhaps the ratio is preserved?

I also realize that within birds, they see better ratios in more intelligent birds.  But what about the comparison from mammals to birds?

Dinosaurs are often predicted to not be intelligent because of the enormous body size and small cavities for a brain.  Now I realize that some dinosaurs were actually quite tiny, but this is just an example.

Given birds' close genetic link to dinosaurs, could it simply be that they were just doing more with less?  The mammalian brain is a huge caloric burden, so perhaps this would show an efficiency that could be selected for?

Thus as the title suggests, my main question:

Is the ratio of brain mass to body mass still considered to be a valid indication of intelligence of a species in modern (current) neuroscience?  Certainly there are exceptions, but is it still considered the rule of thumb?

EDIT: I also wanted to point out the first article(2) I started to read after formulating the question.  It made me question the usefulness of encephalization in addressing this issue at all, but I don't/didn't feel adequately trained to evaluate the conclusions of the meta study.

Again, this still leaves us comparing within primates, which still leaves me feeling that Corvidae have some really impressive efficiency going on with their overall brain mass.  Which then leads to hope that some dinosaurs could be at least equally intelligent, if not more so (noted that this is complete conjecture).

(1) Front Hum Neurosci. 2013 Jun 6;7:245. doi:10.3389/fnhum.2013.00245. Print 2013.

(2) Brain Behav Evol. 2007;70(2):115-24. Epub 2007 May 18.

I don't know about brain mass to body size, but ratio of neocortex to brain volume is correlated with primate evolution (Figure 3, here). If you subscribe to the view that humans and more closely related primates are more intelligent than more distantly related primates, then that is an important correlate.
I think the issue with this question is that we're still having trouble defining intelligence.


How many teeth can "African wild dogs" have? The New York Times article In Mozambique, a Living Laboratory for Nature’s Renewal discusses reintroduction of what the article calls only "African wild dogs" into Gorongosa National Park in Mozambique.

I was taken aback by the "smile" of one of the dogs shown below. Though I'm not particularly familiar with canine dental situations, this looks like an awfully large number of teeth. Is there a known limit to the number of teeth wild African dogs (or any canine) can have?

above: "A wild dog in Gorongosa. One pack has been reintroduced, and a second will be brought in next year.CreditBrett Kuxhausen/Gorongosa Media, via Associated Press" Cropped, from NYTimes.

above: "Wild dogs, apex predators missing from Gorongosa National Park for decades, have been reintroduced and are slowly making a comeback, part of an ongoing experiment in reviving the park ecosystem after years of devastating war.CreditBrett Kuxhausen/Gorongosa Media, via Associated Press" From NYTimes.

I found conflicting information on different websites with a humanima article stating that they have 4 toes and 40 teeth (reference). However, multiple sources state that they have 42 teeth (reference 1, reference 2 and reference 3) with the different teeth being (i= 3/3; c=1/1; p=4/4; m=2/3) x2. I did search for official journal publications but could not find any.

However, since more sources state that there are 42 teeth, I am led to believe that 42 is the right number rather than 40.


Would we know about a virus that causes no symptoms? I've heard that there are a number of viral illnesses that humans can get from animals, which cause no symptoms in the animals. If there was such a virus in humans, which was very widespread but caused no symptoms, would we know about it?

As far as I know most pathogens have only been discovered when people were specifically looking for the cause of some disease. With bacteria, I think we know / can discover any that can be found in a human body, though we don't necessarily know what each type does. But viruses are much smaller.

With the modern rise of meta-genomics, symptom-less viruses can be identified by the presence of their genomes. Certainly, there is more interest in pathogenic viruses than in harmless passengers, but today it's not necessary to have symptoms to identify viruses.  For example:

  Investigators can now go beyond pathogenic viruses and have access to the thousands of viruses that inhabit our bodies without causing clinical symptoms. By studying their interactions with each other, with other microbes, and with host genetics and immune systems, we can learn how they affect health and disease. This article reviews current knowledge of the composition and diversity of the human virome in physiologically healthy individuals. It focuses on recent results from metagenomics studies and discusses the contribution of bacteriophages and eukaryotic viruses to human health.

--Metagenomics and the Human Virome in Asymptomatic Individuals.

Even prior to metagenomics, some "silent viruses" were identified:

  Viruses are the most abundant obligate intracellular entities in our body. Until recently, they were only considered to be pathogens that caused a broad array of pathologies, ranging from mild disease to deaths in the most severe cases. However, recent advances in unbiased mass sequencing techniques as well as increasing epidemiological evidence have indicated that the human body is home to diverse viral species under non-pathological conditions.

--Describing the Silent Human Virome with an Emphasis on Giant Viruses


What is the maximum amount of different bacteria in the drinking water in Europe? I am looking for a statistical amounts which are allowed.
Some students say it is 0 for all bacteria, which I think is false.
I found this USA source.

I found there

Total Coliforms (including fecal coliform and E. Coli) mg/l. No more than 5.0% samples total coliform-positive (TC-positive) in a month.
Giardia lamblia: 99.9% removal/inactivation.

What is the right place to look for such information?

No, your colleages are right: There should be no coliforms in drinking water in Europe following the Council Directive 80/777/EEC.
This PDF from the Northern Ireland Environment Agency (which follows the directice mentioned above) shows this a bit nicer.
It makes sense, since coliforms are a sign of mixing sewage and fresh water. Nothing you want to have happening.

This is the relevant table from the linked PDF:


What inactivates pepsin in infants? In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach.

Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk proteins in infants? Does the production quantity of rennin play a role in inhibiting the action of pepsin?

EDIT: Thanks a lot to @abukaj for pointing out the mistake in my answer (and to @paracetamol for asking such a beautiful question). I am rewriting my answer to incorporate the (hopefully) correct background knowledge this time.

NEW ANSWER: As @paracetamol and @AlanBoyd (in their answer) pointed out the lack of credible support for the claim that infants produce rennin/chymosin, the previous answer attributing the digestion of casein in infants to chymosin had to be corrected. So, lets now look at the other possible candidates for casein (or, more specifically, $\kappa$-casein) digestion in infants.

As Martin et. al. (2016) claim, milk casein has some bioactive roles, such as forming masses with calcium and phosphorus1. Also, infant milk formulas mostly have higher casein content than human breast milk, making the former harder to digest than the latter. Back to the digestion point, human breast milk is known to contain many proteases in itself, including anionic trypsin, elastase, plasmin, cathepsin and kallikrein, while prothrombin has also been identified in human colostrums2. In fact, Ferranti et. al. (2004) also identified fragments of casein created by plasmin cleavage3. However, Chatterton et. al. (2004) were able to detect $\beta$-casein after 1 hour of in vivo gastric digestion in 8 day old infants, but not in 28 day old infants, suggesting the increase of digestive capacity of the infants4. This increase can be attributed to the development of gastric acid production system in the infants. For the case of newborns, Nakai and Li-Chan (1987) suggested that Pepsin C, also called gastricsin, can hydrolyze casein at the pH range of 4-5 (the lowest pH newborns can reach)5. However, the buffering effect of human and bovine milk proteins does not allow the gastric pH to reach the optimum pH required for activity of pepsin A and pepsin C.

How, then, is casein digested by infants at all? This is summarized (to some extent) by Chatterton et. al. (2013), according to which, although gastric pH is unable to reach the optimum pH for pepsin activity, it is sufficient for minor initial digestion of human milk proteins. This causes the release of glycomacropeptide, the C-terminal portion of casein. The combination of this initial digestion and the gastric pH, close to the pI of caseins (~ pH 4.6) causes precipitation of caseins and slowing down of their digestion. The casein peptides, on the other hand, are absorbed into plasma where they show a number of biological activities, including inflammation modulation and blood pressure regulation6.

Thus, even though infants lack chymosin and a fully mature digestive system, this is compensated by a combination of proteases in breast milk and the slower digestion process until the digestive system of the infants develops completely.

source

References:

Martin CR, Ling PR, Blackburn GL. Review of Infant Feeding: Key Features of Breast Milk and Infant Formula. Nutrients. 2016;8(5):279. Published 2016 May 11. doi:10.3390/nu8050279
Dallas DC, Underwood MA, Zivkovic AM, German JB. Digestion of Protein in Premature and Term Infants. J Nutr Disord Ther. 2012;2(3):112. doi:10.4172/2161-0509.1000112
Ferranti, Pasquale & Vittoria Traisci, Maria & Picariello, Gianluca & Nasi, Antonella & Boschi, Velia & Siervo, Mario & Falconi, Claudio & Chianese, Lina & Addeo, Francesco. (2004). Casein proteolysis in human milk: Tracing the pattern of casein breakdown and the formation of potential bioactive peptides. The Journal of dairy research. 71. 74-87.
Chatterton DEW, Rasmussen JT, Heegaard CW, Sørensen ES, Petersen TE. In vitro digestion of novel milk protein ingredients for use in infant formulas: research on biological functions. Trends in Food Science & Technology. 2004;15:373–383
Nakai, S. and Li-Chan, E. (1987) "Effect of Clotting in Stomachs of Infants on Protein Digestibility of Milk," Food Structure: Vol. 6: No.
2, Article 8.
Chatterton, D. E. W., Nguyen, D. N., Bering, S. B., & Sangild, P. T. (2013). Anti-inflammatory mechanisms of bioactive milk proteins in the intestine of newborns. The International Journal of Biochemistry & Cell Biology, 45(8), 1730–1747


Difference between Genus, Genus sp. and Genus spp What is the difference between the three following sentences?

There is significant increase in Bifidobacterium
There is significant increase in Bifidobacterium sp.
There is significant increase in Bifidobacterium spp.

Of course, this could be applied to any genus.

Wikipedia:

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


Mechanism of Muscle Growth According to this video (sorry for the poor reference but it represents my level of understanding in physiology), muscle grow as a consequence of repairing micro-lesions.

How are these micro-lesions sensed in order to activate protein synthesis? What are the key molecules that trigger myosin synthesis and muscle growth?

During exercise muscles are put under stress which eventually causes micro tears in the muscle fibres.

These micro tears put pressure on the nerve endings which causes the pain.
The body will then repair the tears during rest and recovery using proteins and sufficient fuel. The muscle will then become slightly bigger and stronger.

Energy systems used to repair these lesions are the following

There are three different types of energy systems:

Phosphocreatine
Lactic Acid
-Aerobic

1.Phosphocreatine Energy System

The ATP-PC system lasts for 8-10 seconds.
During the ATP-PC system a phosphate breaks off of the ATP to form ADP and a lot of energy.
ADP will then bind with another free phosphate to form ATP.
The ATP-PC system is an anaerobic energy system as it dose not use oxygen.

Lactic Acid Energy System

Glucose is broken down sustain performance for a longer amount of time than the ATP-PC system.However this system does not use oxygen so is not suited for events over 90 seconds.
When the ATP-PC system starts to fade the process of anaerobic glycolysis begins.
Glycogen is stored in the liver and is broken down without the presence of oxygen.
This produces lactic acid which limits energy production.

Aerobic Energy system

The aerobic energy system is constantly being used in your body to supply the muscles with energy.
In sport the aerobic energy system is used for events that last anything over 90 seconds.
The aerobic system can be used constantly but only if there is a constant supply of glycogen and fatty acids.
The aerobic system uses oxygen, glucose and fatty acids to yield large amounts of ATP.
The system takes place within the mitochondria and produces two bi-products, carbon dioxide and water.


What constitutes the determination of a normal blood glucose level? Several on-line resources (e.g. MedlinePlus) suggest:

Normal range for non-diabetic people who are fasting should range between: 70 and 100 milligrams per deciliter (mg/dL)

Non-diabetic people who are not fasting should have a blood glucose level below 125 mg/dL

What I am interested in however, is the coverage interval of the population that was used to determine these 'normal' values.

Also are there differences based on age, sex or any other factors.

Determining what is considered to be "normal" is quite challenging indeed. Both the ADA and the WHO look at upgrading diagnosis limits and both have a conservative approach, primarily due to the difficulties in conducting large scale studies and the anomalies between assumptions of plasma glucose distribution and what is probably actually present in populations. Digging through, I found a very good WHO document here:

http://www.who.int/diabetes/publications/Definition%20and%20diagnosis%20of%20diabetes_new.pdf

I am not going to regurgitate from this document, but I believe Issue 2 provides a detailed answer to your question detailing several determination methodologies.

As to your second question on age/sex variations, are you asking if the criteria are different? At least with reference to FPG, they don't appear to be so.


Can a bacterium express a virulence gene and not produce toxins and what may be the cause of this? I am preparing a seminar on viable but non-culturable (VBNC) state in bacteria, mainly foodborne pathogens and I just saw this line in a journal article by Lothigius et al that "the expression of the virulence gene in VBNC cells does not necessarily indicate the cells will produce toxins". Any explanation on what this statement means?

Lothigius, Å., Sjöling, Å., Svennerholm, A.-M., & Bölin, I. (2010). Survival and gene expression of enterotoxigenicEscherichia coliduring long-term incubation in sea water and freshwater. Journal of Applied Microbiology, 108(4), 1441–1449.

To expand a bit on @Mohamed's answer, there are several mechanisms by which virulence gene products can be up- or down-regulated without changes to mRNA expression.
Post-translational modifications
Adenylate cyclase-hemolysin (AC-Hly) is a toxin produced by the Bordetella pertussis, the causal agent of whooping cough.  There are very few amino acid differences between the AC-Hly of B. pertussis and closely related Bordetella species.  Palmitoylations of lysine residues on the C-terminus of the B. pertussis AC-Hly are necessary for its specific cytotoxic activity.  [Bouchez 2017]
RNA secondary structures
After transcription, mRNAs can form secondary structures by base pairing, preventing ribosome binding and translation.  For some pathogens, virulence gene mRNAs forms these structures, which melt at human body temperature, allowing for fast production of toxins without the need to increase virulence gene transcription. [Narberhaus 2010]


Physiological indicators of happiness and well being If I understand it correctly, levels of serotonin in the brain can indicate if a person is happy. What other physiological measures indicate happiness or well being for a humans?

I am looking for indicators which can be measured quantitatively but don't be very strictly correlated with 'happiness'. And on the flip-side is there physiological  indicators that a person is/not depressed?

There are beahvioral, physiological, and psychological indicators of happiness, and on the flipside of depression, all of which are quantitative.

Levels of the neurotransmitters serotonin and dopamine in the brain are a physiological indicator of depression. Higher levels of serotonin are correlated with increased happiness and decreased anxiety. Dopamine also contributes to good mood, and in addition causes an increase in activity and willpower. Both serotonin and dopamine show decreased levels in depression. However, it is important not just to look at general levels of the neurotransmitter, but to also consider which parts of the brain show decreased neurotransmitter levels. Depression correlates with decreased serotonin and dopamine levels in the amygdala, thalamus, and hyppocampus. (http://www.health.harvard.edu/newsweek/what-causes-depression.htm)

Behavioral tests of depression are used on laboratory animals. The most common tests are the forced swim test (in which scientists measure how long a mouse persists swimming in a water container before it gives up) and the tail suspension test (in which scientists measure how long a mouse struggles to free itself when suspended by its tail). (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270071/)

In addition, self report questionnaires are designed to quantify depression in people. Some popular ones are the Beck Depression Inventory (BDI-II) (http://en.wikipedia.org/wiki/Beck_Depression_Inventory) and the Beck Hopelessness scale (BHS) (http://en.wikipedia.org/wiki/Beck_Hopelessness_Scale).


Highly spherical Radiolaria; does this image accurately depict the organism? If I understand correctly, Cenosphaera spp. is a type of Radiolaria, which is a type of zooplankton.  The following is an image of Cenosphaera spp. is from the supplementary material (Figure S2) of the following paper:

  F. Lejzerowicz et al., Ancient DNA complements microfossil record in deep-sea subsurface sediments, Biol. Lett. (9) 2013.

  Question: Does this image accurately depict the organism?

More specifically, in other images of this organism, there are numerous thorns pointing outwards.  Is this thorn-less version a natural variation (or e.g. the result of the process of imaging the organism)?  Also, is it largely a sphere with a hollow inside?

The authors give the following description of the process involved in obtaining these images.

  Eighteen sediment samples were wet washed over 63 μm and 20 μm sieves. The >63 μm residua were dried and picked for radiolaria and foraminifera. From most samples all specimens were picked. Rich samples were divided with a dry microsplitter into fractions, from which at least 100 specimens were picked for each group. Specimens were arranged by taxa on micropaleontological slides. Radiolaria are classified on the generic level, according to the classification utilized by [8]. Foraminifera above the species level are classified according to [9]. In addition, for radiolaria, the 20-63 μm fractions were soaked in peroxide, then washed with tap water and propanol. For each sample, a few drops of suspended material was left on a glass to dry, covered with Durcupan ACM resin and a cover glass. The micropaleontological slides were analyzed under Olympus BX50 light microscope (electronic supplementary material, figures S2 and S3).

According to the Marine Species Identification portal, the presence of these thorns is variable.  They also vary in size, shape, and the presence of polygonal frames.  I don't think there is anything about the imaging process described that would result in the uniform loss of spines (unless the sieve/microsplitter broke them all, but I think that would be a non-uniform loss).

Re: whether it's hollow or not, that appears to be variable too.  One species is filled with oil, while another appears to be hollow.


Do any animals prepare food? I was just wondering if any animals (are smart enough to) enhance the flavor of their food by, for example, mixing ingredients or seasoning or letting it cure in some ways. In the first episode of Life (on Netflix), they show a monkey who dries some oily nuts for a week but that's just to make it easier to break the shell. But do any animals prepare their food in any way similar to human cooking?

Some animals do like;
Ants prepare their meat not by heating but by marinating it with digestive enzymes to create a glistening protein slurry. With their hourglass figures, adult ants have such tiny waists that solid food can't pass through to their abdomens. Biologists already knew that the blob-shaped larvae predigest meat. Some scientists had suggested that the adults feed meat to the larvae and return later for some regurgitated protein slurry.
some animal chew and regurgitate for their young, monkeys have been observed washing potatoes, and other animals bury and allow food to rot before consumption.
But cooking is certainly unique to humans. There’s no other species that does it. There’s obvious reasons for that because we’re the only ones that can make fire which is a pre-requisite. In a away fire comes first and cooking becomes a process after it. It’s becoming clear that really cooking provides quite a number of advantages. Richard Wrangham from Harvard has been doing a lot of experiments looking at how cooking can change the nutritional value of food. What it seems is that the process of warming food up: in a sense denaturing it has a number of effects. One is that food is much more tender. That we know. If you eat a cooked carrot instead of a raw carrot it’s much easier. We can spend less time chewing, we can swallow it faster and we can digest it faster. It seems that it’s an extension of things we see in other animals. Animals who use techniques often in their stomachs to tenderise food seem to try and make it more easily absorbable. If we turn to the other question of when all this happened the real question is when do we first find evidence of fire? That seems to be about half a million years ago or so. We don’t find direct evidence of cooking then but we do see over the next 100,000 years or so the beginnings of things like burnt stone which suggests that meat is cooked. It’s probably goes quite a long way back in our evolutionary history and some people would argue it’s really a very major change in the way we are able to live and survive.

The second possible advantage for cooking is that it improves digestion. We’ve done a model study here particularly with Zhongquan Sui when she was here – she’s now at the University of Perdue. She found that yes, cooking does to a certain extent improve digestion. You only need cook something for a fraction of the time that you actually do in order for it to be digested properly. The cooking times that people adopt when they normally say this is cooked seem to reflect strong mechanical changes in the food. In other words, these are things that affect you perception of food texture and allow you actually to eat it very much easier, very much shorter eating times than you would do if they’re raw. That I think I would give as the essential answer at the moment.

References:

http://www.sciencenews.org/view/generic/id/6910/title/Ant_Iron_Chefs_Larvae_fix_dinner_but_dont_sneak_snacks
http://www.thenakedscientists.com/


Is the human lifespan still expanding? Description

200 years ago, the human lifespan was roughly 35 to 40 years long. And it has doubled in length since then.

Question

Will the human lifespan continue to expand in length?

You will find here on the UN World Population Prospects plenty of data and visualization about change in life expectancy over time (among other things). The data also include predictions until year 2100.

For example, here is the life expectancy data and predictions over time for men in Morocco.

and here it is for women in Norway (note that x-axis range differs between the two graphs)

I picked two random countries but the general trend is very consistent among countries.

  Is the human lifespan still expanding?

Yes, life expectancy is still increasing in pretty much all countries and is expected to keep increasing.


Viruses and Transformation Would the lysogenic cycle for the reproduction of viruses be considered a form of naturally occurring transformation since DNA from the virus is being incorporated into the DNA of the host cell?

The answer lies in the definition itself of transformation. See from here:

  In molecular biology, transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s). For transformation to take place, the recipient bacteria must be in a state of competence, which might occur in nature as a time-limited response to environmental conditions such as starvation and cell density, and may also be induced in a laboratory.

What is clear from this definition is that host cell needs to be competent for taking up extracellular DNA to call the process transformation. Also, the term direct uptake does not seem to fit here as, you know why, bacteria do not just go on collecting viral DNA from their surroundings.

Obviously, bacteria are not competent to take up viral DNA, nor the virus makes them so. The virus simply injects and joins its own DNA into baterial genome. Now, it would be some common sense to know that the host does not like it, so whether it is competent or not, is just a matter of debate (did anyone ask them?). In short, No, the process of lysogenic cycle would not be considered transformation as the bacteria are not made competent for this process.


How is genetic speciation defined? What determines speciation at a molecular level?

At what point does a scientist determine two lineages are different enough to be considered separate species?

Does it have a margin of error?

Speciation in sexually-reproducing organisms can be identified as the inability to produce viable offspring. In other words, when two suspected sub-species are not able to produce viable offspring, they can be considered to be two species. In this case it is not so much determined at the molecular level, but at the organismal level.

This mating procedure does not work in asexually reproducing species. In this case molecular techniques are needed. Navarro & Barton (2003) investigated what the molecular differences were induced by evolution by comparing the genomes of humans and chimpansees. These two species diverged relatively late in evolution and their DNA differs by about 2.1%. It turned out that the main differences between the two genomes were clustered around regions where chromosomes were rearranged. Although indicative of the cause of speciation, it can nonetheless also be the result of it. We can never be sure.

Reference
- Navarro & Barton, Science (2003); 300: 321-4


To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!) I have to answer a question about a sub-task of my thesis: Can the bacteria X produce the protein Y?

I searched of course Google and BLAST. There is no data supporting that this specific bacteria ever produced this protein sequence.

However, my thesis supervisor wants me to go deeper[1], but I don't know how to do it in silico in a way to offer a proper answer.

What I'm thinking of doing with the data at hand is to create a DB on localhost with all the versions of the protein listed in BLAST (I'm using ruby, not sure how can I fetch all this data in FASTA format yet, but I'll figure it out), and all the strains of the bacteria listed in BLAST and perform a fuzzy string matching.

That's like brute-forcing. After I have a possible score I can get the closest score of them all, study it a bit and then submit my answer.

Is there any other way to attack this problem in order to submit a proper, at least partially polished answer?

NOTE: I don't have access to any lab, any experiment must be performed in silico.

[1] My supervisor believes that IF this bacteria needed this protein it WOULD be able to to produce it at will without undergoing mutations. And since his level of dedication and knowledge revolving molecular biology is scary, it's kind of hard to believe that he is wrong.

Your problem will finally boil down to searching your sequence in the Blast databases. Performing Blast seems to be probably the best way to find out if your bacteria has that specific protein expressed or not. If you could not find it in the nearest species using Blast, then try running PSI-BLAST, which would return you distant homologs, by which you can see if your protein is expressed in the other bacterial species.


cerebral edema and blood pressure, pulse What happens to blood pressure in cerebral edema; does systolic and diastolic rise equally? So the pulse actually slows down? Can't find anything about that, please help

In cerebral oedema the observations (blood pressure, pulse, respiratory rate etc.) can be all over the place. They can depend on the cause e.g. infectious more likely to have raised pulse (tachycardia) with lower blood pressure (shock) but with the anxiety there might be raised blood pressure. Then with the vomiting, a symptom of cerebral oedema, this could lead to dehydration which leads to lower blood pressure or movement of fluid from the blood to the brain because it is oedematous could also drop the blood pressure. With the cerebral oedema affecting different structures, particularly the brain stem in coning (brain swells, pushes brain out through the big hole at the bottom where all the nerves come out particularly affecting respiratory rate) the respiratory rate could be low. It could also be high due to structures getting less oxygen causing the body to push the sympathetic nervous system to increase heart rate and respiratory rate.

In conclusion, things can be completely over the place but usually blood pressure is low and there's reflex tachycardia for the reasons explained above. For these reasons, to diagnose cerebral oedema we usually use the characteristic symptoms of nausea, vomiting, faintness and other features in a patient we know is at risk because of the signs and symptoms of the original disease or cause of the cerebral oedema e.g. the cancer, trauma or infection.


Cloning problem. Digestion test at the end of the cloning is always negative I have a problem with my cloning, I'm trying to clone a 483 pb in a pSecTag vector with restriction sites HindIII and BamHI. Here are the procedures I'm doing:

•   I introduce the restriction sites BamHI and HindIII into my insert by PCR with Pfu (blunt end polymerase) and gel purified it.
•   I clone my insert in a pJET1.2/blunt vector. I get enough colonies and I tested few of them with an internal insert primer and a vector prime via PCR. The results are positive.

The problem came when I digest my insert from pJET and try to clone it in a pSecTag vector.

•   I digest my insert and the vector with HindIII and BamHI in Buffer Red during 1.5h at 37ºC (fermentas). I purify the insert and the vector from the gel and checked that all fragments run at the correct size on a gel. All correct.

•   I do the ligation (T4 DNA ligase) using a 5:1 Insert:vector and less tham 100ng of total DNA. The ligation (20ul) is performance at 22ºC for 30 minutes.
I get few or not transformant colonies. When I get colonies, I tested them by PCR:

**
•   With internal primers, the result are positive

With a primer for the vector the result is negative.
The strangest thing is that when I use pJET primers that do not anneal in the pSecTag I get positive results.**

For transformation i'm using chemocompetent DH5-alpha, with a heat-shock of 42°C at 45 seconds. I tested the bacteria with a plasmid before using them.

I change condition several times but always obtain the same result. I follow all the protocols but I don’t get my construction.

Anybody knows where the problem is? Thank you.

Even minute amounts of undigested vector will contaminate your transformation. You could PCR amplify your insert from the pJet cloning plasmid and then digest the PCR product with BamHI and HindIII. In order to get rid of the pJet template either gel purify the digested insert, digest pJet with some times which cuts it multiple times (less preferable) or put everything on a column and hope that pJet is diluted enough (less time consuming but a bit risky).

The other thing you could exploit is that pJet is ampicillin resistant while your target vector is also Zeocin resistant. If you add Zeocin to your E. Coli it will kill a pJet positive clones while sparing the pSecTag positive clones.

Your insert is fairly small so using a bit more DNA than usual won't hurt.

If you can post some pictures of your gels this might be helpful as well.


species ID: garden bush from Bangalore, India Please help to identify this plant. It is a garden bush growing in soil. The pictures were taken in Bangalore, India.

Could be anything, if it's ornamental. However, it would appear to be some kind of Pinaceae or other evergreen conifer. Possibly a juvenile hemlock or araucaria. I know that in Northern India there is Tsuga dumosa

Maybe an Araucaria?


How do we sweat immediately after drinking water on a hot day? On hot summer days, when I drink water to quench my thirst, my body immediately responds by sweating in 5 to 10 seconds or maybe less. How does our body detect the presence of water in the stomach so fast. Does our body detect the sudden decrease in temperature of the stomach or is it by some other mechanism. Why do we sweat after drinking water in the first place. Is it to remove the excess water or to cool the body down on a hot day?

Not everyone sweats in seconds after drinking water in summer.

Also, sweating in seconds after drinking water is not likely due to water being absorbed (Nutrition Reviews, 2015):

  Ingested fluids are not immediately available for assimilation into
  the body. They are initially stored in the stomach, and there is
  little net absorption of water or solute across the gastric mucosa.

There are a lot of receptors, including stretch receptors and various chemoreceptors, in the stomach, so your stomach will likely recognize water as water and signal the brain via the nervous system, probably via the visceral afferent fibers.

One of two things may then happen:

Your brain can perceive a sudden appearance of water in your stomach as stress and react with sweating, like when you are embarrassed or excited.
When dehydrated, you sweat less to prevent further dehydration; when your brain recognizes there is new water in your stomach, it can now allow the signals coming from warm skin to trigger sympathetic nerves to release some sweat to cool you down.


What controls leaf senescence in deciduous tree species, and how can I predict it? If I want to predict litterfall, what data do I need to collect, and what statistical model might I use?

For example, I might use the following coding to record phenological stage every other day, or perhaps once per week:

|value| description
|-----|--------------
| 0   | all leaves fallen
| 0.5 | most leaves fallen
| 1   | no more green in canopy half of leaves have fallen
| 2   | most leaves yellow or red few leaves have fallen
| 3   | noticeable reddening or yellowing, green still present
| 4   | summer condition

Once I have these data, I can also collect weather data. Now, say I want to predict the day on which each of the transitions ($4\rightarrow 3$, $3\rightarrow 2$, etc) occur.

Many studies use a temperature metric of growing degree days $GDD = (T_{max}+T_{min})/2-T_{base}$, but I have also seen chiling days and photoperiod used to predict changes in phenological stage. I would like to develop a function (statistical model) $f$ that would allow me to predict a date of state change from environemental variables, such as $$D_{4\rightarrow 3} = f(GDD)$$

My questions:

what controls litterfall? Is it photoperiod, temperature, other?
do the controls vary by species?
is there a "standard" approach to modelling senescence?

One can sometimes notice street lights delaying the annual shedding of leaves in some species (a well-lit branch will be mostly green while the rest of the tree is turning). So at least part of it would be day/night length in at least some species.

I would expect, however, that the answer varies based on species, genus, and/or family, and that there are probably multiple causes at work (one obvious alternate cause being temperature). Just going from memory of my personal observations, years when autumn weather patterns start earlier do tend to have trees turn and lose leaves earlier, so it's not all day/night length.

Drought is also a factor. I live in a seasonal-rainfall part of the world (US Pacific Northwest), and if summer is drier than normal (and normal is pretty dry), by mid-August many of the native deciduous trees will be starting to drop leaves. (Not all of them, but some of them, definitely more than just a few, will be turning and dropping.)


How does paracetamol work? Hinz et al. 2008 found that COX-2 may be inhibited by paracetamol, and this is attributed to it's analgesic and antipyretic properties. However, there are other more recent claims from Andersson et al., 2011 that a toxic intermediate metabolite, NAPQI, may be acting on TRPA1-receptors in the spinal cord. Whilst I'm vaguely aware that the end goal is to affect prostaglandins, to me at least it remains unclear how that translates to painkilling.

There are also other theories I would imagine.

This exceedingly common drug seems shrouded in mystery. I know very little about pharmacology (evidently!), so some expert insight into the popular theories, and why they're popular, would be greatly appreciated.

What are the most popular theories in a nutshell?

Why are they a popular theory?
Which protein is targeted?
How does that inhibition introduce the analgesic and antipyretic properties?

Is it possible multiple theories are correct?
Why is so little known about paracetamol? Is it exceptionally difficult, or the norm in pharmaceutical research of relatively old effective drugs? If it ain't broken, why fix it!

What are the most popular theories in a nutshell?

To date, the mechanism of action of paracetamol is not fully understood. There are some experimental evidences, but it is difficult to put things togheter. It is now clear that  paracetamol acts contemporaneously via at least three pathways:

The inhibition of cyclo-oxigenase (COX)

The main mechanism proposed is the inhibition of COX, it's highly selective for COX-2.
COX are molecules involved in the metabolism of arachidonic acid (aa). It catalyzes the reaction to form prostaglandin H2, a pro-inflammatory compound, from aa.
Paracetamol, as other NSAIDs,  block this step , thus reduce the amount of prostaglandin H2. The reduced amount of prostaglandin H2 in the CNS, lowers the hypothalamic set-point in the thermoregulatory centre.

The exact mechanisms by which COX is inhibited in various circumstances are still a subject of discussion.

Some authors state that paracetamol works by inhibiting the COX-3 isoform—a COX-1 splice variant—of the COX family of enzymes.
This variant is expressed mostly in brain, so it is the one supposed to be involved in the antalgic effect of this compound.

There is another physiopathologic possibility to explain its action, that is: paracetamol would block COX, but in an inflammatory environment where the concentration of peroxides is high, paracetamol itself is oxydated and thus inactive. When it founds a non inflammatory environment, such as CNS, it become reduced and thus active (it reduces temperature, it has anti-dolorific action, etc).

The modulation of the endogenous cannabinoid system, through its metabolite AM404, a compound that inhibits the reuptake of the endogenous cannabinoid/vanilloid anandamide by neurons.

The COX model can explain quite well the action of paracetamol, altought it has been demonstrated an important role of the endocannabinoid system aside of COX. When cannabinoid receptors are blocked with synthetic antagonists, paracetamol's analgesic effects are prevented.  This is tought to be due by an active metabolite of paracetamol, that is called AM404 and inhibits the reuptake of anandamide.

Anandamide reuptake lowers synaptic levels of anandamide. This results in a more activated pain receptor (at least the main one, called TRPV1, or according to an old nomenclature: vanilloid receptor). The high levels of anandamine, due to inhibition of its reuptake, desensitise this receptor in a way similar to the capsaicine.
Furthermore, this active metabolite (AM404) inhibits sodium channels, this chemical behaviour is shared with lidocaine and procaine, two common anesthetic drugs.

These two actions by themselves have been shown to reduce pain, and are a possible explanation of paracetamol's mechanism of action; but one other specific activity of this compound remains unexplained by these two models.

Serotonin receptor agonism.

It has been observed that this compound can reduce the social rejection in humans. This can't be explained with COX or type I endocannabinoid system modulation.
Increase of social behavior in mice dosed with paracetamol, wich models a reduction of social rejection response in humansdoes not appear to be due to cannabinoid receptor type 1 activity. .
In the animal model, it seems a result from  serotonin receptor agonism.

Aside of this main features, some other evidences are in bibliography.

In 2011 a debate started on scientific journals. Some has found  a hint to the analgesic mechanism of paracetamol, being that the metabolites of paracetamol e.g. NAPQI, act on TRPA1-receptors in the spinal cord to suppress the signal transduction from the superficial layers of the dorsal horn, to alleviate pain.
This findings has been contested in a  new hypothesis paper  on how paracetamol might act.
This second study concedes that NAPQI is the active metabolite but that this reactive compound should react not only with the thiol in TRPA1 but also with any other suitably available nucleophile that it happens to encounter. This broad interaction with thiol groups in cysteine proteases, like the ones that process  procytokines, might be the targets giving rise to overall analgesic effects, changing the global cytokyne environment.
Even if there are evidences of drug-body interaction with formation of active metabolites and there are some models of drug action, many things are not fully cleared and the debate is still open.

  Why are they a popular theory?

Are popular because are based on experimental and clinical evidence. Also, this theories can model lot of the biological effects of this compound.

  Which protein is targeted?

Not any time it can be possible to reduce a pharmacological interaction at this level. For instance, in one theory it inhibits an enzyme, the cyclooxygenase (COX); in one other model entire classes of molecules, the sodium channels, are modulated...
Unfortunately many times, dealing with living organisms, it is not possible  to offer an hard, mechanicistic explanation of things.

  How does that inhibition introduce the analgesic and antipyretic properties?

In the COX inhibition model, the analgesic properties can be explained trough an affinity for COX3; and the antipyretic activity can be due to the reduced amount of prostaglandin E2 in the CNS, in the thermoregulatory centre it lowers the hypothalamic set-point. The endocannabinoid model can explain preety well the anti dolorific actions, as well as the serotonin receptor interaction the behavioral one.

  Is it possible multiple theories are correct?

Yes, there is a substantial overlap between different regulatory systems, so that is straight to think that the same chemical (or some of its different active metabolites) can modulate different systems.

  Why is so little known about paracetamol? Is it exceptionally difficult, or the norm in pharmaceutical research of relatively old effective drugs? If it ain't broken, why fix it!

Is it not that difficult topic! One can say that is as tricky as any clinical pharmacology topic. The problem is that many compound are clinically used as drugs even if their molecular functionig is unknown if they are safe and of proved usefullness. This is true for paracetamol as well as many other drugs, like a lot of anaesthetic agents as Propofol.


How to clone and sequence a gene transcript of unknown sequence? How might I go about amplifying a gene transcript (mRNA) from animal tissue of which little is known about the genome? In some applications, I have used reverse transcriptase PCR to amplify all mRNA transcripts from cultured cells, but this required that I knew the sequence to PCR amplify.

How do I go about this without knowledge of the gene or transcipt?

Perhaps you can draw inspiration from classic paper on lambda cloning:  Maniatis T, Hardison RC, Lacy E, Lauer J, O’Connell C, Quon D, Sim GK, Efstratiadis A. 1978. The isolation of structural genes from libraries of eucaryotic DNA. Cell 15: 687–701.

Try selecting tissues from the animal which you think is "enriched" (i.e. highly expressed) for the specific gene you're looking for. This might take a little bit of guessing. For example, if gene A is very highly expressed in tissue B, then you can "assume" most of the mRNA transcripts will be for that of gene A. Do a RNA purification, RT-PCR, and clone the cDNA into lambda vectors and pick plaques. With a little bit of luck, you'll be able to identify the gene by cloning, hybridisation, and subsequent chromosome "walking" to determine it's structural origin.

This was done back in the day to identify novel genes way before genomics, sequencing, or even PCR!


Spatially Encoded GPCRs? I'm reading this paper, and I'm already lost in terms of what they mean by GPCR signaling is spatially encoded.

  The trafficking of G protein coupled‐receptors (GPCRs) is one of the
  most exciting areas in cell biology because of recent advances
  demonstrating that GPCR signaling is spatially encoded.
   …
  …
  Some GPCRs appear to regulate their own endocytic rate through
  modulation of clathrin‐coated pit (CCP) maturation.12-14 This
  regulation, which can differ between ligands acting at the same GPCR,
  is an additional method by which GPCR signaling can be spatially
  encoded.

How can signaling be spatially encoded?

How can (GPCR) signaling be spatially encoded?

Terse explanation: During endocytosis the G protein-coupled receptor can be spatially constrained.
Your paper refers to: "Fulfilling the promise of “biased” G protein-coupled receptor agonism", by Luttrell LM, Maudsley S, and Bohn LM, in Mol Pharmacol. 2015;88(3): 579-588. https://doi.org/10.1124/mol.115.099630.

Abstract: The fact that over 30% of current pharmaceuticals target heptahelical G protein–coupled receptors (GPCRs) attests to their tractability as drug targets. Although GPCR drug development has traditionally focused on conventional agonists and antagonists, the growing appreciation that GPCRs mediate physiologically relevant effects via both G protein and non–G protein effectors has prompted the search for ligands that can "bias" downstream signaling in favor of one or the other process. Biased ligands are novel entities with distinct signaling profiles dictated by ligand structure, and the potential prospect of biased ligands as better drugs has been pleonastically proclaimed. Indeed, preclinical proof-of-concept studies have demonstrated that both G protein and arrestin pathway-selective ligands can promote beneficial effects in vivo while simultaneously antagonizing deleterious ones. But along with opportunity comes added complexity and new challenges for drug discovery. If ligands can be biased, then ligand classification becomes assay dependent, and more nuanced screening approaches are needed to capture ligand efficacy across several dimensions of signaling. Moreover, because the signaling repertoire of biased ligands differs from that of the native agonist, unpredicted responses may arise in vivo as these unbalanced signals propagate.".

A relatively simple explanation is offered in another paper: "Temporal Bias: Time-Encoded Dynamic GPCR Signaling", by Manuel Grundmann and Evi Kostenis DOI: https://doi.org/10.1016/j.tips.2017.09.004:

"The notion that information is not only encoded by the chemistry of the signaling components but also by their spatial and temporal occurrence, brought about the term of ‘spatiotemporal signaling’ $^{[3]}$. Signal transduction can thus be categorized into at least three dimensions, (i) quality (which substances take part), (ii) space (where the event takes place) and (iii) time (when the event takes place). The interplay between these dimensions will hereinafter be designated as ‘dynamic signaling’ or ‘signaling dynamics’. Dynamic signaling is deeply entrenched in GPCR signal transduction as an increasing number of reports provide us with a glimpse into spatiotemporal aspects of receptor function $^{[4, 5, 6, 7, 8, 9, 10]}$.".
[3] Kholodenko B.N. et al. Signalling ballet in space and time. Nat. Rev. Mol. Cell Biol. 2010; 11: 414-426
[4] Irannejad R. Functional selectivity of GPCR-directed drug action through location bias. FASEB J. 2017; 31 (664.2)
[5] Mullershausen F. et al. Persistent signaling induced by FTY720-phosphate is mediated by internalized S1P1 receptors. Nat. Chem. Biol. 2009; 5: 428-434
[6] Irannejad R. et al. Conformational biosensors reveal GPCR signalling from endosomes. Nature. 2013; 495: 534-538
[7] Eichel K. et al. β-Arrestin drives MAP kinase signalling from clathrin-coated structures after GPCR dissociation. Nat. Cell Biol. 2016; 18: 303-310.
[8] Thomsen A.R. et al. GPCR-G protein-β-arrestin super-complex mediates sustained G protein signaling. Cell. 2016; 166: 907-919
[9]  Jean-Alphonse F.G. et al. β2-Adrenergic receptor control of endosomal PTH receptor signaling via Gβγ. Nat. Chem. Biol. 2016; 13: 259-261
[10] Plasma membrane localization of the μ-opioid receptor controls spatiotemporal signaling. Sci. Signal. 2016; 9: ra16

See: "Spatial encoding of GPCR signaling in the nervous system", by Zara Y Weinberg, Stephanie E Crilly and Manojkumar A Puthenveedu, DOI: https://doi.org/10.1016/j.ceb.2018.12.006:

"Several GPCRs, including receptors previously thought to signal primarily from the cell surface, have been recently shown to signal from many intracellular compartments. This raises the idea that signaling by any given receptor is spatially encoded in the cell, with distinct sites of signal origin dictating distinct downstream consequences.".

During endocytosis the G protein-coupled receptor can be spatially constrained.
See: "Spatial resolution of cAMP signaling by soluble adenylyl cyclase", by Giusi Caldieri and Sara Sigismund
DOI: https://doi.org/10.1083/jcb.201606123 which offers a easy to understand image:

Figure 1. Spatial and temporal control of GPCR signaling by ACs. In hippocampal neurons, CRHR1, upon binding to agonist CRH, activates the trimeric G protein complex, composed of α, β, and γ subunits. Stimulatory Gα subunit is released and activates tmAC and cAMP production (Irannejad and von Zastrow, 2014). In parallel, activated GPCR can also induce local Ca$^{2+}$ release that activates sAC, followed by an increase in cAMP levels (Inda et al., 2016). (1) These two sources of cAMP at the PM contribute to the early phase of ERK activation via the effectors protein kinase A (PKA) and EPACs (Inda et al., 2016). Activated GPCRs once released from the G proteins are phosphorylated and recruit β-arrestin (β-ARR) to be internalized via clathrin-coated pits (CCPs; Irannejad and von Zastrow, 2014). (2) At the endosomal station, GPCRs activate sAC to trigger a second wave of cAMP production and to sustain Erk signaling in an EPAC-dependent fashion. sAC activation at the PM and at endosomes requires Ca$^{2+}$ and bicarbonate (not depicted for simplicity; Inda et al., 2016). The signaling cascade leading to Ca$^{2+}$ and bicarbonate release (particularly at the endosomal station) and the exact mechanism of action of sAC are not completely characterized. The different forms of ACs, and the corresponding cAMP gradients generated by them, are depicted in different colors to highlight their different roles. Whether this specificity reflects different isoforms and/or regulation remains to be clarified.

"The work reported by Inda et al. in this issue integrates and expands our emerging knowledge of localized GPCR signaling at the endosomal level. In a previous work, these authors showed that Erk activation by corticotropin-releasing hormone receptor 1 (CRHR1) signaling is biphasic, with an early response originating from the PM and a late response that is endocytosis dependent (Bonfiglio et al., 2013). In their new work, Inda et al. (2016) reinforce these findings, showing that distinct cAMP sources are differentially involved in the two phases of Erk signaling. Whereas tmAC and sAC both contribute to the acute Erk signaling response, sAC is specifically involved in the sustained “endocytic” phase of Erk signaling in hippocampal neuronal cells (Fig. 1).".

Note phase 1 and 2, targeting one phase or another, rather than continuous action, is spatially encoded.


Do all animals exhibit comparable reflex velocity? First, my exposure to biology is high-school. Should the answer to the question be obvious - please take a moment to laugh, and then point me in the right direction.
A quick google search (or perhaps my search parameters were wrong) didn't give me what I seek.

Animals usually exhibit some form of reflex. What I'm curious about is this -
Do all animals exhibit comparable reflex velocity? Here I use 'reflex velocity' to mean the amount of time elapsed between stimulus, and initiation of the reflex action.

Simply stated, the reflex speeds of diverse animal species should not be the same. First, even within an individual, signal conduction speeds actually vary between nerves, on a fairly significant range of about two orders of magnitude. Conduction speeds between species, and likely even between individuals, will differ. Second, not all species possess the same reflexes, which can be, in fact, quite elaborate neural events. To qualify speeds for similar reflexes, one must use closely related species. I did find one article that found the pupillary light reflex in monkeys is essentially similar to that of humans, but this information is not sufficient to speak of the similarities between reflexes in general between the species.


Can a certain part of human dna can be replaced with other animals dna? Human DNA consists of adenine, thymine, guanine and cytosine. Can thymine of other animal can be placed with humans thymine?

Yes. They're identical. When we eat animals or plants we digest their DNA to use to make our own DNA.


How do people measure how many calories or proteins/fats/сarbohydrates are in some food? How is the composition (in fats, proteins or carbohydrates) of a certain food estimated and how is the amount of calories provided by the food calculated?

Messured by the amount of energy it will take to raise 1 degree celsius in 1 kg of water. You really can never go by what the packaging says either. All depending on how food is prepared, even your digestion differs the count person to person.


Have there been any successful studies showing that it is possible to increase IQ? I am curious if there have been any leading studies that show improvement in general IQ. For example, an adult with an IQ of 130 reaching an IQ of 140, over many different IQ tests and then averaged, after some sort of practice (perhaps playing video games, reading books, taking lots of IQ tests, or doing memory exercises).

It would be interesting to know. If you can, please reference sources with your answer, so that I may look at the studies myself.

When talking about increasing intelligence there are a few things you have to keep in mind. Can you increase your IQ score? Probably, yes. Just take the same test twice, or more realistically practice a lot of IQ-type problems. You will probably raise a few points.

But this is just a score. When experts are talking about raising intelligence, they are talking about raising the underlying ability that tests can only estimate. Raising your test score does not necessarily mean that you raised your intelligence. What you want is something that transfers over to some general ability.

Richard Haier, the editor-in-chief of the journal Intelligence, has written extensively on this topic. In his 2014 article Increased Intelligence Is A Myth (So Far) he writes about this very subject of increasing intelligence (Haier, 2014). You can probably guess what the conclusion is from the title of the paper. This topic is also a substantial portion of his book The Neuroscience of Intelligence (Haier, 2016).

Technically, when you ask whether there are any studies that purport to have found a way to increase intelligence, then the answer is definitely yes. There are many (hundreds, probably thousands). The correct question to ask is whether any of these ways consistently replicate. At the moment, the answer to this question appears to be no. One of the most infamous "ways of increasing intelligence" was the supposed Mozart Effect. The hypothesis was that listening to Mozart music would increase intelligence, and there were studies providing evidence for this. Fairly silly, yes. It was not until a meta-analysis came out of Mozart Effect studies that this hypothesis was finally laid to rest (Pietschnig et al, 2010). There is a history of many supposed ways of increasing intelligence being suggested, but typically the more scientific scrutiny they are put under they tend appear less and less impressive. Therefore, whenever a new way of increasing intelligence is suggested, it may be good to have some scepticism.

Given the current body of evidence, the most plausible way of raising intelligence is probably education (Ritchie & Tucker-Drob, 2017). However, it is unclear whether education really increases general intelligence or just specific skills (Ritchie, Bates & Deary, 2015).

The best  non-genetic way to get high intelligence is probably not to increase your intelligence per se, but just to avoid decreasing it. This means avoiding things like lead exposure, don't suffer from iodine deficiency (Qian et al, 2005), get decent nutrition and so on. Anything that realistically could interfere with the development of the brain may be implicated in intelligence.

See also my answer to a similar question on the Psychology & Neuroscience Stack Exchange, which is slightly more comprehensive.


What happens to potassium after an action potential? If I understand right, after repolarization, much of the potassium is outside the membrane and much of the sodium / calcium is inside. How does it get back to the original concentrations (i.e. potassium inside and sodium/calcium outside)?

During the repolarization, relatively few ions need to cross the membrane for the membrane voltage to change and therefore the change in ions concentration outside and inside the cell is neglible. After repolarization, the concentrations are restored by the continuous action of Na⁺/K⁺-ATPase. The same happens for calcium, but I don't know exactly what kind of pump is used.


What is open complex in E.coli DNA replication? The E.coli DnaB helicase is essential for replication initiation from the chromosomal origin of replication ( oriC ) and is present in vivo as a protein complex with six monomers of the DnaC ATPase protein and six ATP molecules (Wickner and Hurwitz, 1975; Lanka and Schuster, 1983). DNA replication initiation at oriC begins with binding of multiple molecules of the bacterial DnaA initiator protein to a 9 bp repeats (DnaA boxes). This binding promotes destabilization of nearby AT-rich sequences, resulting in unwinding of the DNA double helix and the formation of an open complex.

I looked up in DNA Replication by Arthur Kornberg, Tania A. Baker (the authors who probably coined this term), Google and Google.Scholar but didn't stumble upon any definition.

What is it actually?

The sentence itself is actually the definition of open complex: It is the structure that is created once the DNA double helix is unwinded due to the DnaA proteins.

  This binding promotes destabilization of nearby AT-rich sequences,
  resulting in unwinding of the DNA double helix and the formation of an
  open complex.

I have also found a papera co-authored by Arthur Kornberg himself where the authors self-define "open complex" as well:

  Three tandem repeats of a 13-mer in the AT-rich region are essential
  to the unique replication origin of E. coli and of remotely related
  Enterobacteriaceae. These iterated sequences are identified by
  deletion analysis and sensitivities to endonucleases as the site for
  initial duplex opening by the initiator dnaA protein. This “open
  complex” requires ATP and 38% for optimum formation and stability.

There are several papersb,c that use "open complex" in the same way.

References:

a David Bramhill, Arthur Kornberg, Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome, Cell, Volume 52, Issue 5, 1988, Pages 743-755, ISSN 0092-8674, http://dx.doi.org/10.1016/0092-8674(88)90412-6.
(http://www.sciencedirect.com/science/article/pii/0092867488904126)

b Ozaki, Shogo, et al. "A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin." Journal of Biological Chemistry 283.13 (2008): 8351-8362. (http://www.jbc.org/content/283/13/8351.full)

c Mukhopadhyay, Gauranga, et al. "Open-complex formation by the host initiator, DnaA, at the origin of P1 plasmid replication." The EMBO journal 12.12 (1993): 4547. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413885/)


Why would pedophilia exist? From an evolutionary perspective, why would anyone ever be sexually exited by small children who could not possibly have started puberty?

Is it a confusion between some combination of sexual and non-sexual systems?

Is it a evolutionary imperfection?

Or is Darwinian thinking not necessarily applicable to human behaviour?

I am guessing on this one, and there may be some good research on it, but I do know that there can be combinations of genes acting on different behaviors, such that if you have a certain combination of 5 genes, you are a nurturing parent (which would be selected for), but when you accumulate more of these tangentially related genes past some threshold, you end up with non-selected behavior. For example, for homosexuality, which has been shown to be genetically heritable, it may be that 5 genes in a suite make you super attractive to women (thus these genes stick around), while 10 genes combine to make you gay. (Note, I am NOT equating homosexuality with pedophilia in ANY sense. Homosexuality if a healthy normal trait for humans. I am just saying that this is a theory about how suites of genes can be individually selected for while some combination of them is non-selective. Similarly, heterozygous sickle-cell genotype produces resistance to malaria, which is adaptive enough to keep the gene around, which is non-adaptive in the homozygous condition.)
In answer to the other parts of your question, humans are absolutely subject to natural selection. Darwin was dead-on correct about virtually everything he said, to the point where it is frustrating for evolutionary biologists today to work in his shadow, because he pretty much got it all right in 1859. "Theory" is the strongest conclusion that science can ever come to, and people have been trying to tear down Darwin's theory for 160 years without being able to put a single dent in it.


Why aren't there any transitional animals today? You have probably heard this question before and in different formats. Usually, it is used as a "proof" to disprove the theory of evolution.

I understand that the apes we descended from are not the same apes we see today. However, I can't understand why there aren't any human-ape creatures anymore.
In the world of today, wouldn't an intermediate species (between apes and humans) "win" over both because it has the "feature" of the two.
A creature that can both climb trees and walk on two legs would be more suitable to live in forests than the current forest inhabitants. (apes and humans)

Every species on the planet is "transitional" - this is because there is no ultimate or final species. Species branch out from one another, sometimes species go extinct, leaving gaps between the extant branches. But it also comes down to how you look at it; if you were comparing blue whales and humans, then chimpanzees (and many other species) would be "transitional", so some "transitional" species are extant, others are extinct. In fact, it is estimated that 1% of species that have ever existed are extant, the remaining 99% are extinct.

It's very hard to say why the "transitional" species of chimpanzees and humans went extinct. There's a lot of (sub-)species that would fall in that bracket, thus to answer that specifically would be too broad and speculative for this site.

Some concepts and key points

Speciation is a gradual process with species forming over time out of one in to two (or more).
Species is a hard concept to pin down because it applies binary/categorical classification to a very much continuous distribution
Evolution is a process of change, and in all likelihood it will be an unceasing process because at least one of the mechanisms will likely be affecting every species in some way. This means that every species is "transitional" because no species represents an end point.


Is this a large bee? (species identification) While hiking in some low hills near Taipei in the late afternoon in July an hour after it rained, I saw this large flying insect visiting flowers the way bees do.

I'm curious, is it a bee (if so, what kind), does it come from a hive or live on its own, and does it sting?

I'm estimating its body to be about 5 cm long. While not captured in photos, I'm pretty sure I remember it sticking its head into flowerers. It was moving flying from place to place fairly quickly and difficult to get any photos at all, this is the best I could do.

edit: Since further clarification of the size was asked for in comments, I'll add here also that the length of "about 5cm" that I mentioned wold be for nose to tail when stretched straight, (rather than in it's current somewhat curled position) and it could certainly be 4.5 cm. But I'm fairly sure it's closer to 5 cm (2 inches) than to 4 cm. I've added a few more images of the flower sans insect. I've cropped my friend on the left out of the images.

Note: My mistake. I did not notice the OP info that he is in china. There are giant honey bees in China, such as Apis dorsata Fabricius, however their size is only 17-20mm.

========

I suggest  Bombus dahlbomii. It can grow up to 40 mm long, 1.6 inch

Picture

Wiki


How does an animal having toes create more friction than not? I was looking at the morphology of different animals when I found that apparently part of the reason vertebrate mammals have toes is that they grip the ground. But, why is that better than having a solid foot with no toes if friction increases with the surface area in contact with the ground?

I would say that the premise that "the surface area of contact with the ground increases in case of solid foot" is incorrect.

In practice, the ground is very far from being even and flat, and the animals need to navigate themselves throughout different terrains that include very uneven ground, stones, growing & lying plants, etc. In that case, having toes, in general, offer an advantage of gripping to the ground (and increasing contact area in multiple directions) in a large set of terrains. Then, different animals will develop their toes in different shape/form tailored to the dominating usage (including, but not limited to gripping the ground).


What insect is this? Found this at home, India Found this insect in Kolkata India. Has a sting at its rear end. The wings are shiny.

That is a parasitic wasp in the family, Ichneumonidae. You can tell by looking for a cell in the forewing that looks like a horse head. The "stinger" is an ovipositor. These wasps lay their eggs in the larvae of other insects


How do alcohols and aldehydes destroy the plasma membranes of bacteria? I am interested in knowing why a 60-80% solution of alcohol (usually ethanol or 2-propanol) can effectively kill vegetative bacteria and fungi. I know that it can coagulate essential proteins like enzymes but the process has never been explained to me.

I'm also interested in knowing how aldehydes like the polymerized form of glutaraldehyde inactivates proteins and nucleic acids. Could someone with any insight / knowledge share what they know?

Alcohols are dehydrating - they remove water from the cell. And since cells need water to survive, this is lethal to bacteria. However, in order to work effectively, an alcohol needs the proper amount of time to penetrate the cell membrane of the bacterium. If the percentage of alcohol is too high, it will evaporate before entering the cell. Too low, and it will enter the cell but not be lethal. 70% alcohol turns out to be the most effective concentration for use as a surface disinfectant with many different types bacteria.


How can cats' claw grow sharper without replacing the claw? I cut my cat's claws once a month. The claws always have pointed and sharp tip even though I had cut them last month. I assumed cats cannot change the shape of the claw by growing new keratin at the tip. Also it does not looks like the cat grow a new claw and abandon the old one every once a month or so. How is it possible that the claw grow sharper?

The horn has a specific structure which is different from the round edge that we see on our fingers. It splinters and cracks into flakes, so it is more similar to a flint than a chalk.
The outside of the cone dries out and flakes and is scratched off by the cat, while the inside of the cone is the newer horn that grows towards the apex as a new blade edge.

The image is from this research. If you search "sharp" you will find astonishing vetinary descriptions quoted. Also see page 641 for the conclusion of the research. He sais that it seems to have evolved in the aim of keeping the feline claws sharp.

If someone has the technical ability to rewrite the researcher's descriptions into everyday words, you would be a first.

Vetinary research quote:

The horn-generating living blade epidermis that is
located most centrally on the slanted face of the curved
ledge is continuous with the parietal epidermis (Fig. 9b),
so that the blade epidermal cells generated here lie next
to the parietal epidermal cells. Therefore, the cornifying
parietal epidermal cells are deflected and entrained apically
as the blade horn is pushed apically by the proliferating living
blade epidermis. The direction in which the blade horn is
pushed forward can also be inferred from the arrangement
of the ridges visible on the dermo–epidermal interface of
the parietal horn (Fig. 7). The living blade epidermis that
is located at the outer edge of the face of the curved ledge
is continuous with the living epidermis of the proximal
cone horn (Fig. 9b). These lateralmost blade epidermal
cells, therefore, form a layer that lies directly underneath
the deepest layer of proximal cone horn, so that the
boundary between the blade horn and proximal cone horn
is indistinct. Hence, the layers of horn that are generated
in the dorso-proximal bend of the curved ledge underneath the combined horn layer of the external coronary
and proximal cone horn cover the sides of the apical cone
horn and are designated as part of the blade horn. As
the superficial coronary horn on the dorsal side of the
cornified claw sheath is worn off through normal use, the
superficial layers of the blade horn are exposed and are
shown to hug the sides of the apical cone horn (Fig. 13a).
Remnants of these blade horn layers are discernible near
the very tip of the cornified claw sheath, which consists
mostly of apical cone horn, because the rest of the coronary
horn, including most of the blade horn, has been worn off
(Fig. 13b,c).
The remaining soft-cornified horn segments of the
cornified claw sheath are found in places where the
hard-cornified horn divisions need to be supported and
cushioned.
The soft-cornified terminal horn is a segment of the
third major horn division (i.e. the Hyponychium; see Table 2).
It is generated by the living terminal epidermis, which is
continuous caudally with the parietal living epidermis and
is supported by the dermis that covers the medial, lateral
and palmar sides of the tip of the bony unguicular process
(Figs 3a, 4a,c, 7, 9b, 11a, 12a–j). It supports the apical cone
and crest horn on its dorso-distal side (Figs 3a, 4a,c, 7, 9b,
13b) and the blade horn on its lateral and medial sides
(Figs 4b, 8, 9b–d, 13a,b). By filling the space created by
these converging segments of hard-cornified internal
coronary horn, it is shaped into an elongated, pointed
cone and extends proximally between the blade and
sole horn (Figs 12c,d,f,h,j, 13a,b). Because the terminal
horn is soft-cornified, it can adjust its shape to the
changing conformation of the space it fills in the course of
the deformations of the cornified claw sheath during its
normal use.
The friable soft-cornified sole horn is generated by the
living sole epidermis, which is supported by the dermis
that covers the proximo-palmar side of the bony unguicular
process (Figs 3a, 4, 7, 8, 9b–e, 12c,d, 13a,b). Along its medial
and lateral sides, it is embraced by the terminal and parietal
horn (Figs 1b, 4b, 8, 9c,d, 13a,b). The sole horn, therefore, fills
the space between the paired cutting edges of the cornified
claw sheath. It is worn off through natural wear and tear,
as well as through repeated compression and release, as
the cornified claw sheaths are deformed when they are
subjected to tensile forces during climbing and prey capture.


Why are minor introns bounded by nucleotides AT-AC, where T is not normally in RNA? Major intron boundary nucleotides are GU-AG. Minor intron boundary nucleotides are AT-AC. Why does the former use RNA Uracil and the latter use DNA thymine? Since introns are in the primary RNA transcript, shouldn't both be RNA and use U rather than T?

It is not unusual for RNA sequences to be reported with T instead of U; the writer is reporting the cDNA sequence instead of the RNA sequence.  In RNA at the boundary of the minor intron, there is a uracil.  In the following page, the writers follow the oft-used convention of describing RNA with T instead of U (writing the cDNA sequence).  https://en.wikipedia.org/wiki/Minor_spliceosome


Why are insects unafraid when you tap at them from the other side of glass? In the summer months we frequently try and kill mosquitos in our home. They are tremendously skittish and get airborne pretty quickly as you approach them. However, if they land on a piece of glass (a window for example) they don't seem at all bothered at you approaching from the other side and tapping the glass where they have landed.

Is this some strange physiology of insects (or at least mosquitos) that they cannot look down? Is it that their eyes function differently to our eyes and cannot see through the glass? For sure, their brains cannot be  developed enough to understand the safety afforded by the glass.

Since insect brains do not contain enough neurons for higher level emotions such as fear, much of their behavior is programmed and reflexive. When you approach them, they have evolved to fly away. Glass, on the other hand is not something they evolved to "understand". They likely are not programmed to see something approaching them from below their legs as they are sitting securely on a hard substrate as a threat. They can look down. They just don't "get" glass.


Example of well understood/modeled biological mechanism I am working on modeling psychiatric disorders, where multivariate time series data - which I think is necessary to do any interesting modeling - is only broadly available recently, due to the availability of surveys via mobile devices.

To get into the dynamic systems modeling literature, I would like to look into a biological mechanism, which is well-modeled, by which I mean that the error/misfit is negligible for many applications. Basically, I am looking for a (historical) example, where I can follow the steps that were taken to get from the observed (maybe experimental) data to a good model, with the hope that I can learn some lessons for my own work. Ideally, it would be an example with about 5 < p < 20 variables.

Any hints and suggestions are greatly appreciated and my apologies if this is a too trivial question.

I would point out that, assuming (as the other commenter noted) you are interested in analytic rather than statistical modelling (which seems a little unlikely to me given your area), most mathematical models are derived from first principles (often from physics) or other assumptions.
This suggests (to me) that looking at models of totally unrelated systems is not so useful; the whole idea of such models is to formalize your domain knowledge!

But I'll give some examples anyway.

For example, consider
 biophysical models of neurons or continuum mechanical models of cardiac tissue, both of which have rich histories of mathematical models developed over decades of work, based on both theoretical and empirical considerations (albeit largely from physics).
Perhaps slightly more related (or at least empirically driven) are the advances in systems biology, which tend to derive from some underlying laws of chemical kinetics, but utilize enormous amounts of (multivariate, temporal) data in fitting (often non-linear stochastic) systems of differential equations. Methods for computational protein structure prediction tend to use a mix of ad hoc rules (for computational time-cost reasons) and physics-based considerations in their models.
Evolutionary biology and population dynamics also have wonderful models (see the book from the commenter above).

My guess, given that your question does not have much detail, is that you would prefer statistical, i.e. probabilistic graphical or stochastic process, models instead.

Let's suppose you have a bunch of variables over time (e.g. the actions or status of a person) but you want to estimate an unobservable quantity (e.g. say, the degree to which they are insane [not my field, sorry]).
One simple probabilistic model is the hidden Markov model.
It has many examples of applications in sequence biology.
It also lets you figure out, in a way, which variables are important, and let's you tune certain parameters (e.g. it's order, which here describes how much the person's state at time $t$ affects their state at time $t+\Delta t$).
In terms of predictive modelling power, though, the state of the art is in deep learning models for time series.

Anyway, I'd consider what your goal is more carefully. If you indeed have a strong idea of an analytic model (motivated by some theory you know), then by all means formalize it. However, if you want the data itself to suggest a model for you, then use a statistical approach.

Note: apologies if this answer was too trivial, I was not sure what you did and did not know.


Shigella's O antigen (PAI synthesised) and passage through host defences The O antigen is synthesised by Pathology islands (PAI).
O antigen may be a factor why Shigella survives the passage through host defences.
I am interested in which step of pathogenesis.

There are Bacterial ATPase (actin tail, intracellular movement), M-cell (enter) ...-> extracellular movement.

Where can the O antigen affect in Shigella?

The outer layer of the cell envelope of Gram negative bacteria is the outer membrane, and the outer leaflet of that membrane is composed largely of lipopolysaccharide (LPS). The O antigen is the name given to the outer glycan portion of the LPS - there is a nice diagram at the Wikipedia article I have linked to which makes this clear.

Because this structure is exposed at the bacterial surface it is a target for the immune response, and the serotyping of many bacterial species incorporates this O serotype information.

Table 1 of the review that you link to indicates that PAI SHI-O carries genes gtrA,B,V (originally derived from a bacteriophage - not unusual for a pathogenicity island). These genes encode enzymes which modify the O-antigen via a glucosylation reaction. Presumably this helps the bacteria adapt to an immune response via a shift in serotype. It may be, for example, that an invading population of Shigella includes variants which do or do not express these genes so that a subpopulation can arise which is not recognised by an existing immune response. This is what is meant in Table 1 of the article by "evasion of host immune response". It is a common strategy - examples in Salmonella (flagellar phase variation) and Helicobacter (induced transformation) spring to mind.


Can a bacterium infect another bacterium? I researched about it by searching on Google and reading some bacteriological articles, but I did not get any answer. I also asked some of my teachers, and they were also a bit confused. Some said that it is possible and others said not. So the question remains:
Can a bacterium infect another bacterium? If so, how?

Bdellovibrio bacteriovorus (BV) “infects” other bacteria:

Similar to a virus, BV attacks bacteria such as Escherichia coli (E. coli) by attaching to and entering its prey, growing and replicating within the cell, and then suddenly bursting out, releasing its progeny into the surrounding environment. — How bacteria hunt other bacteria


Why do fully grown organisms need protein intake? If proteins are building blocks of an organism then it makes sense why a growing organism would need an intake of them, but why would a fully grown organism need proteins (aside from those lost by shedding skin, growing hair etc.) and not recycle other proteins back into amino acids.

I understand that protein can be broken down to generate energy when needed or when there's too much of it in the body, but given enough energy from other sources (like glucose), it seems that proteins wouldn't need to be used for these processes.
Is there perhaps a net loss of amino acids during protein biosynthesis?

My question was inspired after reading this study of a man who was fasting for 382 days and was given only water and mineral supplements:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2495396/pdf/postmedj00315-0056.pdf

Protein is polymerized amino acids.

Humans do not require protein intake, but certain essential amino acids are required.  These essential amino acids are usually obtained through protein intake, but intake of the free amino acids themselves would suffice.

Amino acids, in free or protein form, are lost from the body due to urination (see Diverse characteristics of the urinary excretion of amino acids in humans and the use of amino acid supplementation to reduce fatigue and sub-health in adults), perspiration, menstruation, ejaculation, tear drops (see Amino Acid profiles in human tear fluids ), skin exfoliation, hair and nail growth, nasal mucus (see Identification of human nasal mucous proteins using proteomics), and vaginal mucus (see Proteins of Cervical Mucus).  Additional loses can occur due to additional bleeding, lactation, child birth, spitting (and other activities causing loss of saliva), and coughing up mucus.

Synthesis of new proteins from amino acids is constantly required by the body (see NUTRITION AND PROTEIN TURNOVER IN MAN). Though there are chemical pathways to reuse amino acids, it is necessary for the concentration of each amino acid to be non-zero, and therefore some fraction is necessarily lost through excretion.

Beyond just direct excretion of amino acids and proteins, there is excretion of nitrogen-containing metabolites such as urea, uric acid, creatinine, ammonium salts and bilirubin.


Did the Great Oxygenation Event also cause a mass extinction? It's usually assumed that the Great Oxidation Event around 2.3 billion years ago caused a great extinction of anaerobic life on earth. However, I was reading Nick Lane's book, The Vital Question, and he writes the following:

The 'oxygen holocaust', which supposedly wiped out most anaerobic
cells, can't be traced at all; there is no evidence from either
phylogenetics or geochemistry that such an extinction ever took place.
On the contrary, anaerobes prospered.

Is there really no evidence of such a mass extinction?

The proposed mass extinction due to Great Oxidation Event is actually an elucidation by scientists.

After reading many articles online, although there are evidences of GOE, every article states the extinction of most anaerobes as something that should have happened as a fact (Because $O_2$ is considered poisonous for obligate anaerobes). To better understand this, imagine if there was a spike in Carbon Monoxide in the atmosphere, for Oxygen dependent organisms like us, inhaling $CO$ is harmful and therefore a spike in $CO$ would be toxic and lead to death.

Here are some excerpts, which state the extinction of anaerobes being factual more than anything else:

From Arizona State University, Origins Project >>

  In a relatively short amount of time, Earth went from having very
  little oxygen to what may be the highest levels of atmospheric oxygen
  it has ever had. This event had wiped out most of life on the planet
  to which the oxygen was poisonous. Some of these anaerobic organisms
  were though to have survived by burrowing into the earth where oxygen
  levels were survivable.

From Slate.com - Bad Astronomy Blog >>

  At some point, though, as cyanobacteria flourished, the minerals and
  other sinks became saturated. They could no longer absorb the oxygen
  being produced. It built up in the water, in the air. To the other
  bacteria living in the ocean—anaerobic bacteria, remember—oxygen was
  toxic. The cyanobacteria were literally respiring poison.

  A die-off began, a mass extinction killing countless species of
  bacteria. It was the Great Oxygenation Event.

From Imperial College London >>

  The permanent introduction of oxygen into the atmosphere fundamentally
  changed the ecology of the planet. The first impact was on anaerobic
  organisms, which didn’t need oxygen to survive. The rise in oxygen
  levels was poisonous to them and led to most them becoming extinct.
  Some managed to survive, but they retreated deep into the subsurface
  where there is no oxygen.  This was one of the first mass extinctions
  in the history of our planet, and it was also the catalyst for the
  evolution of oxygen-based life – us!

As a result, based on what I have read so far, we really dont have any stone cold proof that rise in oxygen lead to mass extinction of anaerobes. The mass extinction is what scientists consider should have happened as we know $O_2$ is poisonous for strict anaerobes.


Are flowers / flowering plants vital to all life on Earth? Not a biology student so forgive me if this is a very basic question. Are flowering plants (angiosperms) vital to all (or most) life on Earth?

In other words, if flowering plants disappeared, would all (or most) life on this planet be gone as a result?

To give a bit more context, I'm arguing with a friend who claims (from a biblical perspective) that without flowering plants life couldn't exist.

Angiosperms -- that is, flowering plants -- only evolved relatively recently on an evolutionary timescale, about 125 millions years ago. So for most of the history of life on earth there have been no flowering plants. Thus it seems highly likely that if angiosperms were to suddenly disappear, life on earth would continue. There might be a massive disruption of current terrestrial communities, but it's hard to imagine this resulting in total global extinction. In particular it seems unlikely that ocean communities would be undermined by the loss of flowering plants.