Is it possible to merge the genomes of photosynthesizing and electron-transporting bacteria to make an electric cell? I had an idea of making electric current from bacteria. There are some bacteria that can photosynthesize, and some others are capable of transmitting electrons through each other. Is it possible that through genetic engineering, we could insert the genome that allows bacteria to perform photosynthesis, with other capable of transmitting electricity, and therefor making a bacterial culture, big enough to make a free energy source?

What you're describing is a phototrophic biofilm microbial fuel cell! They're pretty neat.

Essentially the sun powers the bacteria and the bacteria in the anaerobic side passes electrons through the graphite electrode to use oxygen at the cathode. There's another explanation here. You could also "unfold" cyanobacteria and layer them and you'd probably get an efficiency increase but the system would be pretty fragile. Compared to other MFCs, though, everything is fragile. Dirt even works(not very well, but it's dirt).


Do trees have genes for stopping growth? Do trees have genetically encoded to stop growing at some height, to keep dividing the cells only to a certain amount, or to pump nutritions only till it's advantageous because they've already overgrown their companions? Or do they just keep growing till they can?

I was inspired by this article, according to which the height limit is about 130 m. Since if the second one was true, it would be possible to grow a 130 m tall tree with enough nutritions.

Also, the evolution of trees wouldn't mean to getting more genes of height, but to use nutrients more efficiently.

The answer I got from Jan Kolář of Charles University:

  Traits of trees like height and mass are a result of the genes and
  environment. The determinative factor for the studied plants and
  animals is a big amount of various genes. When we get to know all the
  functions of all the genes, we should be able to determine the most
  important ones but for now we know just that gibberelin and auxin are
  very important for the growth of the tree, so we'll be looking for those
  genes which control the level of those hormones.

  In case of trees, a big part of the height they can grow are utterly
  mechanical factors. The stem and the main branches have to be enough
  strong not to break with their own weight and the roots have to be
  enough firmly rooted in the soil. This limit is determined mainly by
  genes that control the grow of the cell walls, their mechanical
  resistance etc.


Why do heterozygous individuals have increased resistance to malaria? I am aware that there is such a thing called heterozygous advantage, which is due to the presence of a certain single allele, and that an example of this could be with "sickle-cell anemia".  I am quite curious as to how exactly this heterozygous advantage is created.

Could the increased resistance against malaria be due to natural resistance or natural selection?

Very interesting explanation has been proposed by Ferreira A. et al. 2011. Briefly, red blood cells of individuals carrying homozygous point mutation in haemoglobin beta-chain tend to be more prone to disruption.

Red blood cells are full of haemoglobin, so once their membrane is damaged, they release free haemoglobin and heme to the plasma. This is called intravascular haemolysis. Too high level of free heme is toxic and you can read about its consequences, for example here.

In the plasma of individuals with heterozygous mutation also there is an increased concentration of free heme, but definitely below harmful level.

However, it is enough to trigger mechanism that protects us from toxic effects of free heme. Heme oxygenase-1 (HO-1)catalyses heme to biliverdin, iron and carbon monoxide (CO). CO makes the vascular environment very unfavourable for Plasmodium.sp and probably protects from infection.

The study was performed in the mouse model.


Is there any other function of DNA? We all know that DNA acts as a genetic molecule. Does DNA have any other function in the cell other than being a genetic material and carrier of information?

In eukaryotes DNA has a structural as well coding function. Parts of chromosomes called centromeres bind to proteins and form a scaffold which helps chromosomes attach to each other and correctly segregate during division. Technically this is still related to the transmission of genetic information though.

Since RNA can act as an enzyme (the so-called ribozymes), scientists have hypothesized that DNA can also have an enzymatic function, but no such function has been found in nature. Artificial DNA enzymes (deoxiribozymes) have been designed to cleave DNA, covalently modify proteins, ligate RNA molecules, and even catalyze reactions between small molecules. See this lab's website.


Is it possible to have different genes in different parts of our body? I want to understand genetic mutation specially in the context of multicellular organisms like humans.
I studied biology only till high school and I can’t fully understand wikipedia pages on this subject.

I know that genetic material is in chromosomes inside the nucleus of a cell. When that cell multiplies, the chromosomes too generates a copy of themselves and both child cells get one set of the chromosomes.

I would like to know:

Does genetic mutation mean an error in chromosome generation at fission stage or will it occur later in the life of the cell?
Multicellular organisms begin their life from a single cell (zygote). Under normal circumstances, every cell that grows from this single cell should have the same genetic material. Can genetic mutation eventually result in us having different genetic material in cells of different parts of our body? For example, when only a part of our body gets exposed to radiation.
If answer to question 2 is yes, which genetic material will control the behaviour of the cells? Let’s say, for example, that the genetic material of cells in our stomach favour high growth rate of hair but the cells in the scalp themselves do not have that particular gene. What will be the result?

The general answer is that no, it's not possible to have different genes in different parts of the body.  There are two interesting classes of exceptions, but they are exceptions.

The first is that mutations can and do occur in cells during their growth.  Most of these are probably neutral - they occur in the vast wasteland of genetic junk in the chromosome, and nothing happens.  But some of them are harmful, and this is what puts cells on the pathway toward cancer.  Outright cancers, that we can detect, are the result of at least a half-dozen mutations occurring in the same cell lineage, that cumulatively allow the cells in that lineage to grow in uncontrolled manner, to avoid immune clearance, to encourage their own blood vessel growth, and so on.  (In fact, cancer cells generally have far more than a half-dozen mutations, because a route toward getting the mutations they need is to turn down DNA repair, allowing mutations to accumulate with minimal control.  For example, Genomic landscape of DNA repair genes in cancer, Genomic profiling of pediatric acute myeloid leukemia reveals a changing mutational landscape from disease diagnosis to relapse.)

The second set of exceptions is in the immune system.  Both B cells and T cells specifically modify their chromosomes during their development, making huge numbers (trillions) or new genes.  The catch is that these are all in the same region, the antibody or T cell receptor genes.  It's part of the mechanism by which the adaptive immune system "remembers" which pathogens it's interacted with in the past.  The wikipedia article on V(D)J recombination is a starting point.


About excessive cellular growth When there is 'excessive' cell growth 'ordered' by the human body in some specific part of the body that is not part of the usual repairing mechanisms, does this cause extra telomere 'shortening' or damage even though a lot of cell growth and repair is 'required'. If a lot of cell growth is 'activated' with problematic telomeres does this cause telomerase to be formed which then might shut down the apoptosis mechanisms and keep the cell 'going' indefinately. Note; I read some acid reflux problem causes parts of the throat to scar or be damaged causing excessive cellular repairs on those parts of the throat where tumors have later developed. When someone gets sunburned on the shoulders say, and this damages the skin there, then does every future time the persons shoulders get in the sun ,do those same areas get further damage causing excessive growth and repair of skin cells on the shoulder. With a lot of excessive repair tumors might develop. SO could excessive cell growth (that might be caused by many different factors ) help to cause cancer??

Long story short: Absolutely.

Short story long:

While your intuition that growing a lot of cells can increase the risk of damage that might cause cancer is spot on, your specifics are a little off. It's not the telomeres themselves that are the problem, but broad spectrum DNA damage and transcriptional changes. The condition of the telomeres doesn't directly affect the likelihood of a cell growth becoming more cancer-like. A cell with perfect telomeres fresh from a telomerase-expressing stem cell and cell with shortened telomeres have an equal chance of becoming cancerous. Cell populations with longer telomeres have 'more time' or more chances to develop mutations and cell expression damage, however. You're more likely to get in a car crash if you go to the store across town  than the neighborhood convenience store, even though it's not intrinsically more dangerous per mile driven.

The sunburn example can be a little misleading. It's not cell regrowth that's the key carcinogenic factor, but instead the direct DNA damage UV radiation can cause. In a particularly bad sunburn your skin cells may be killed or commit suicide(apoptosis) because of the DNA damage they've sustained. If the cells are damaged but do not die, they're likely to recover. Over time and repeated sun exposure, the skin cells that are most resistant to orders from the body to stop growing or die stick around and may grow and divide. Freckles are when this happens to a population of skin cells that ignore orders about how much brown pigment to be, but still listen to the orders that instruct them on how to be skin. When they stop listening to the skin orders, they officially become precancerous.

The acid reflux example is excellent. There are populations of stem cells throughout the adult body that produce skin cells and hair follicles and blood cells and all the other kinds of cells that are more or less expendable. Generally speaking these stem cells don't have do very much work replenishing esophagus cells, so when they are taxed by something killing off the esophagus lining regularly, they can 'break down' and lose control of their own replication.

It seems like you're both pretty interested in cellular mechanisms of cancer and a little shaky on current theories of cancer formation(there are a few), so if there's a section of this answer that needs to be more detailed or followup questions please let me know.


How does gas equilibration occur in the alveolus, numerically? I am attempting to model gas exchange across the alveolar membrane.  My main question is there a direct exchange of O2 molecules for CO2 molecules?  If so, then my model predicts (assuming alveolar PO2 107mmHg and CO2 40mmHg; and venous PO2 40, PCO2 46) an arterial PO2 107mmHg, but PCO2 of only 37mmHg (taking into account pH change and equilibration with bicarb and haemoglobin carbamates).  If I remove the plasma bicarb equilibration process (as this takes ~15 seconds, but alveolar transit time is ~0.75 seconds), then the arterial PCO2 is even lower, ~33mmHg.  The expected results should be somewhere in the range of an arterial PO2 of 107 and PCO2 of 40.
The only alternative I can think of is that there isn't a molecule for molecule exchange, with the O2 absorption and CO2 removal being separate processes.  If this is the case then overall there will either be a reduction in alveolar air pressure and/or volume during gas exchange.  However, I can find no references to inhaled tidal volume being different to exhaled tidal volume.  Nor does there seem to be any evidence for N2 or H2O molecules to participate in this process (at standard atmospheric pressure).
Any ideas??
Ultimately I want to then extrapolate model to deal with pathology (eg high alveolar CO2, high venous CO2 etc).
EDIT to include references...
Mechanistic physicochemical model of CO2 transport in the blood
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5341128/
Modeling of the oxygen transfer in the respiratory process
https://hal.archives-ouvertes.fr/hal-00714239/document
Modeling pulmonary gas exchange and single-exhalation profiles of CO
https://www.frontiersin.org/articles/10.3389/fphys.2018.00927/full
Respiratory Physiology
https://derangedphysiology.com/main/cicm-primary-exam/required-reading/respiratory-system
Other materials I have read include:

Pilbeams Mechanical Ventilation
Nunn's Applied Respiratory Physiology
Guyton and Hall Medical Physiology

There is no known mechanism for exchange of $\ce{O2}$ and $\ce{CO2}$ in a one-for-one fashion. Their transport across the alveolar membrane takes place by diffusion alone: both of them attain their equilibria with blood independently.
Note that it is not necessary for inhaled and exhaled tidal volumes to be the same. In fact, under physiologic conditions, the exhaled tidal volume is slightly less than inhaled tidal volume. This is because humans normally produce slightly less $\ce{CO2}$ than they consume $\ce{O2}$. In other words, the respiratory quotient is less than $1$.
Thus, we see that the assumption of preservation of alveolar volume and pressure is not valid. Apart from inspiration and expiration, the diffusion of gases to and from blood also affects alveolar volume.

Reference and further reading:
Boron WF, Boulpaep EL, editors. Medical physiology. 3rd ed (international edition). Philadelphia: Elsevier; c2017. 1297 p. (I found this textbook an excellent resource for learning physiology in general and respiratory physiology in particular.)


Why are babies rarely born with cancer? Childhood cancer is fundamentally a disease of dysregulated development. Why does it rarely occur during the fetal period, a time of enormous growth and development?

Nature tends to turn against cancer not towards it. Cancer exists when cells begin to multiply with abnormal features, without correction. Cancer is the consequence of many many harmful mutations, which inhibit the correct reading of DNA.

Cancer takes time to develop, not months, but years. Also, babies don't have old tissues, so there haven't been as many divisions, or as many opportunities for mutations, as a 5 yr old or a 10 yr old has gone through.

Although rare, Neuroblastoma is a cancer that babies CAN be born with. Nerve cells develop early, week 5 of fetal development.

Perhaps someone else could talk more about the biological mechanisms which really make cancer more a reality for older organisms, but probablistically, it doesn't make sense that a newborn baby would have cancer.

I looked up these links, to try and address your question.

cancer in general
https://www.cancer.gov/about-cancer/understanding/what-is-cancer

why cancer takes time to develop
https://sites.duke.edu/missiontomars/the-mission/cancer/why-do-most-cancers-take-so-long-to-develop/

cancer in babies
https://blog.dana-farber.org/insight/2015/02/can-babies-be-born-with-cancer/


What species of butterfly is this? This big fellow came to visit my kitchen (in Hong Kong) a bit earlier.
It is brown with some longitudinal white stripes, banana/boomerang-shaped patterns towards the middle, and an eye-like marking on each forewing tip. Picture below.
What kind of butterfly is it?

I helped it find the exit in the meantime, not before taking a lot more pictures.

It isn't a butterfly, it's a saturnid moth -  Samia canningi, also known as the wild eri silkworm moth.

There is a good image on Flickr here, and some more information here.


What is the consensus in the scientific community over COVID-19's mode of transmission? I've read from many news and scientific sources that COVID spreads primarily through respiratory droplets, but I've also read multiple sources that have said we don't entirely know yet. Is it fomites, droplets, or aerosols? Is it some combination? Do we have a complete understanding of it?
With how infectious the B117 variant appears to be, it seems like it would spread through aerosols, since most other infectious diseases that are very contagious tend to spread through aerosols, like measles, tuberculosis and varicella. If that's the case, why do so many sources keep claiming that it's through droplets? I've also read an article on the Johns Hopkins website that suggested the scientific community was initially wrong about the mode of transmission for tuberculosis, so is that possible for COVID?
Thank you!

The terminology really depends on the scientific field. You also have to be aware that sometimes terminology is simplified for the purposes of presenting information to the general public.
A droplet can really mean anything from a few micrometers up to several millimeters and it does not necessarily have to be spherical. The key point is that the virus may spread through droplets.
Aerosols typically refer to small solid particles or liquid droplets, maybe less than 20 micrometer in size, but again, it depends on the field.
In quiescent air, any heavy (more dense than air) particulates (solid or liquid) which are about 1 micrometer  or less will remain suspended in the air for several hours due to Brownian motion and also the fact that their gravitational settling velocity is small.


Making positive charged polyacrylamide I am interested in positive charged polyacrylamide to electrophorese molecules I am interested in.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643323/
http://onlinelibrary.wiley.com/doi/10.1002/bip.360300309/pdf

The articles shown above use allyltriethylammonium bromide (ATAB), but I am not sure which chemical they mention.

Or is there any other chemical to add to acrylamide to get positive charged polyacrylamide copolymer?

ATAB contains a quaternary amine and a terminal carbon-carbon double bond. The polyacrylamide reaction links acrylamide by their double bonds forming the polymer. The double bond on ATAB can be incorporated into the growing polymer chain, and the quaternary amine holds a positive charge, making a positively charged polymer.

The immobilines mentioned are probably just a weak acid or weak base group with a terminal double bond like ATAB or acrlyamide. They get trapped into the polymer and if you pour the gel with a pH gradient, they pick up charges according to the pH. I haven't found a good concrete immobiline example, I can't access that second article you linked.

I am away from my good computer and cannot make chemical structures right now.


What is this spider found in day time? .

South India
Arm to arm about 3 inch in length. Day time. was hiding inside a cardboard storage box.

It's definitely a species of Huntsman spider maybe of the genus "heteropoda" or "olios". Sorry I couldn't be more help.


What Animal is This Skin From? A Wooly Mammoth? I was at the American Museum of Natural History in New York City today, and I saw the skin pictured below. Because it was next to stuff about wooly mammoths, I thought it might be a mammoth skin. However, there was no sign accompanying the skin. What is it from?

Yes, this is the remains of a wooly mammoth. Many mammoths have been found frozen and well preserved in Siberia.


How to correlate the pattern by which CAP activator from E.coli binds to DNA and its mechanism of action? The catabolite activator protein (CAP) activates the expression of more than 100 genes involved in secondary sugar metabolism in E.coli.
Apparently, it always binds in sites that are away from -10 and -35 elements of the promoter by multiples of 10 base pairs (-70 or -60, for example). How could this be related to its mechanism of action?

I've searched about this particular activator and I found that it acts mainly by recruiting RNAP to weak promoters, although it does alter the architecture of the DNA, introducing an abrupt bend (for some CAP-dependent genes, this favours conformational changes in RNAP involved in the initialization of transcription): here's the crystallographic data.

However, I did not find anything conclusive about the pattern of binding to distances which are usually multiple of 10 base pairs (which is close to the number of base pair in a complete turn of the double helix).

I found a great article that might help. To summarize the contents of the article, there are two classes of CAP dependent promoters/genes, and the distance of the CAP bindings site in these classes are different. Also the actions in which CAP is involved are different in the two classes of promoters. In the first class it does not overlap with the promoter region and is only involved in RNAP recruitment. In the second class it overlaps with -35 element of the core promoter and is involved in multiple interactions.
So the binding distance of the CAP is determines what interactions is it involved.

You can see the difference between the two classes on the picture below (taken from the article i linked). And I think this answers your question on why the patterns are multiples of ten - because this is the space needed for alpha-CTD to make a bridge between the protein complexes, or the CAP to interact with the RANP complex.

I only took a glance at the paper I linked and quickly extracted the info, but I hope it still helps


How can we move our lips even though they don't have any bones? How can we move our lips even though they don't have any bones?

We can move everything if it is attached to the bones. Example: Legs & Arms.

otherwise we can't move it.

Because of the Orbicularis oris muscle, it's a complex of muscles in the lips that encircles the mouth, It forms the greater part of the substance of the lips, lying between the skin and the mucus membrane, and extending from the edge of each lip to its root.


What is this white stuff inside apples? I live at Vancouver, BC, Canada and I often find this kind of white stuff inside the apples I buy

I used to live in Europe (Switzerland) and never saw that before. It very much look like a fungus. Is it? What species is it? What is the geographical range of this species?

When I cut my apples open, I just remove it and assume it did not lay too many mycotoxins in the rest of the apple but when I directly bite into the apple, it has happened to me to eat some of this white stuff. What are the health consequences of it?

I am pretty sure that it is a moldy core rot which would be caused by a fungus that infects the apple during the flowering stage. The fungi is also referred to as "apple fuzz".

From SF Gate

  fungus sometimes does enter apples at the blossom end and damage the core, especially if weather is wet, a condition called "moldy core,"

From PennStateExtension

  Moldy core is caused by several different fungal pathogens. Many cultivars of apples are affected, including Delicious, which is very susceptible. Moldy core may develop into dry core rot if the pathogen penetrates into the core flesh, but the fungus is generally restricted to the core or carpel region.

The Disease cycle

  The moldy core fungi colonize the flower parts as soon as the blossoms open. The fungi then enter the developing fruit through an opening in the calyx. Moldy core is primarily a problem during years with light fruit set or when dry weather in early summer is followed by heavy rains in late summer. In addition, wet weather during bloom may cause conditions favorable for the fungi to produce spores.

What kind of fungi is it?

Mycelium

Geographical range

The fungi is mostly found in the apple sorts “Delicious” and “Idared”. Idared's origin is from Idaho, and delicious is originally from Iowa, USA.

Is it dangerous to my health?

Not more dangerous than usual mold would be to your health. You can find more information here. On some forums online I read about people consuming the white fuzz, and did mostly not complain about any problems. However, I read about one case where the fungi evoked an allergic reaction.

Picture

Further reading

Principles of Forest Pathology page 558


Concentration of DNA by isopropanol I have read that DNA can be concentrated by addition of isopropanol.

What does "concentrated" mean? What does isopropanol do on a molecular level to concentrate DNA?

What you are asking about is the precipitation of DNA (or any other nucleic acid) by isopropanol (or ethanol, which is more common). To do so, you add salt (usually slightly acidic sodium acetate) which makes sure that the phosphate backbone of the DNA is saturated with sodium ions to make it less soluble. Then you add the organic solvent, which precipitates the DNA from the solution by changing the polarity of the solution. This makes the ions form salts and the DNA precipites. The principle is explained in the Wikipedia article on ethanol precipitation. Finally the solution is centrifuged to collect the DNA at the bottom of your reaction tube and to be able to take off the supernatant.


How can I estimate the CO₂ uptake of a plant? I would like to make an estimation of the CO2 uptake of plants I cultivate, including, lettuce and aromatic herbs, such as thyme, basil, rosemary. What I want is to end up with a rough indicator for business purpose, not some super-accurate measurement.

Is there already average CO2 uptake data per plant type available?
Will this uptake vary drastically per plant type?
Can I calculate the estimate through a simple measurement (e.g. of plant weight) or does it require tight lab experiments? In the former case, how is that measurement made?

Please bear in mind I'm not a scientist, but and end-user of science. Thank you for helping me this question if needed.

Can I calculate the estimate through a simple measurement (e.g. of plant weight) or does it require tight lab experiments? In the former case, how is that measurement made?

In the textbook Plant Physiological Ecology*, they state that about 40% of the dry weight of plants is carbon, and I believe the vast majority of that is from CO2 from the atmosphere. You can take a fresh weight of an entire plant, and then dry it at the lowest temperature in your kitchen oven for a couple of days to get a reasonably accurate dry weight. That dry weight times 0.4 will give you an estimated total carbon, though I have seen other factors used. Plants can also be analyzed for Total Organic Carbon in some agricultural laboratories. Fast growing plants are going to absorb more carbon than slow growing ones.

* Lambers, H, Thijs L. Pons, and F S. Chapin. Plant physiological ecology. New York: Springer Verlag, 2008. Print. ISBN:978-0-387-78341-3


What are the applications of predicting the structure of proteins? Protein molecules are very important as they are used for catalyzing almost all the chemical reactions in the cell, regulation of gene activity and provide cellular structure.

However, in predicting the structure of protein I haven't been able to find many use cases. In the omicsonline I was able to find a paper on Computational Methods for Protein Structure Prediction and Its Application in Drug Design:

  Most modern drug discovery projects start with protein target identification and verification to obtain a verified drug target. For structure-based drug design the three-dimensional structure of the protein needs to be determined experimentally by using either x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy.

Therefore, since proteins are vital for maintaining the body are there any other use causes for predicting the structure?

Just off the top of my head, protein structure is very important for determining how proteins interact, for example determining molecular pathways or viral capsid structures. Knowing the structure of a protein can help scientists better understand what it does and how it does it. By looking at protein structures, scientists can determine exactly how a different allele for a gene causes changes in an organism's phenotype at a biochemical level. Predicting sites within a protein's structure that have an enzymatic function allows scientists to predict how various factors effect it's function. Differences in temperature or pH can have an effect on protein structure as well, and understanding how a proteins changes based on pH or temperature changes can help scientists determine how a protein functions in its specific environment.


Why Didn't Evolution Cause the Human Body to become Streamlined? If streamlining makes movement/locomotion quicker and easier, why didn't the apes evolve into life-forms that had streamlined bodies (much like fish)?

If streamlining makes movement/locomotion quicker and easier, why didn't the apes evolve into life-forms that had streamlined bodies (much like fish)?

As with everything in Evolutionary Biology, you must ask yourself: Gain vs. Cost?

In your specific case, the Gain is very little.  Air isn't nearly as dense as water, so a streamlined form won't show a major benefit unless the organism is traveling very, very quickly. This is why you see it in birds; raptors can travel over 100mph while diving, and at those speeds small changes in drag can mean the difference between dinner and starving. Smaller birds often make very quick turnabouts and changes in direction mid-flight where, again, small changes in efficiency can mean the difference between life and death. The cost was is worth it.

For apes and monkeys, moving very quickly isn't a case of living or dying. That's what we evolved opposable thumbs and prehensile feet(/tails) for. You don't need to run fast when you can climb a tree and simply get away from any predators on the ground. After we came down from the trees permanently, our larger brains allowed us to use tools to fend off predators - which, again, is much simpler than evolving an aerodynamic form that won't make a difference until you're running at the speed of a car.

So, in lieu of becoming a land-shark, we have hands that can use keyboards and minds that can invent the keyboard. Unfortunately, while the gains are many, the costs do include both a very long period of time where humans are helpless without parents, and an absolutely terrible form of locomotion with our upright stance on forward-pointing knees. Though you won't catch Cheetahs digging sewers anytime soon.


The meaning of the $\alpha$ helix and $\beta$ sheets in proteins I asked this question to my Biology teacher and he, in collaboration with a Chemistry teacher, couldn't find the answer. My question is the following: "What does the $\alpha$ and $\beta$ represent in the secondary structure of a protein? I do reference to the $\alpha$ helix and $\beta$ sheets in proteins." I had a similar question with the glucose and we concluded that it was related to the Chemistry, the $\alpha$ or $\beta$, was related with the functional groups bonded to the carbon.

The answer is very simple. As described in the accepted answer to the related question about alpha-subunits vs alpha-helices the alpha- and beta- are arbitrary names. It could easily have been 1 and 2 or A and B based on ordering of letters or numbers; indeed, there are "type I" and "type II" turns.
The history, from the wikipedia page on alpha-helices says:

In the early 1930s, ... William Astbury initially proposed a kinked-chain structure for the fibers. He later joined other researchers (notably the American chemist Maurice Huggins) in proposing that:

The unstretched protein molecules formed a helix (which he called the α-form)
The stretching caused the helix to uncoil, forming an extended state (which he called the β-form).

(Emphasis added). In other words, he named the "α-form" first, and considered the "β-form" to be an uncoiled form of the first one. These names later became "α-helix" and "β-sheet". It could easily have been the other way around.
Indeed there are other types of helix; the 310 helix and the π-helix. If either of these had been discovered first, perhaps they would be the alpha-helix. Of them all, the 310 helix has the most 'logical' name as:

the helix has three residues per turn, and ... has 10 atoms in the ring formed by making the hydrogen bond

so if we followed a similar naming scheme, the alpha helix would be a 3.613 helix. Admittedly this is a bit of a cumbersome name.
As well there are the alpha sheet - a sheet made of helical strands - and the beta helix - a helix made of strands. For both of these, the "alpha" and "beta" part of the name has been chosen because of the naming of the original structures they are related to.


What biological functions does crying serve? Tears suddenly start flowing out of our eyes when we find our long lost friend or when someone unexpectedly decides to break up with us. Do tears really save us from harm? Or are they just the reflex shown?

What biological purpose do tears serve for the body?

As I understand it, crying causes endorphin release, specifically leucine-enkephalin. This serves as a painkiller for us. Are tears the only way to accomplish this? It seems I am missing something because oozing out of our eyes is an inferior pain distribution system to say; the circulatory system.

Lets break this question into parts and answer them one by one.

  Do tears really save us from harm?

Well, yes. Tears, mucus and saliva contain an enzyme lysozyme that breaks down the cell wall of many bacteria. Those that are not killed immediately are trapped in mucus and swallowed.1

You can, obviously, search on google for another reference if you do not believe this one.

  Or are they just the reflex shown?

It depends on what type of tears you are talking about. Tears are divided into 3 categories:

Basal tears
Reflex tears
Psychic tears

In "reflex action" part, the cause is reflex tears. Reflex tears result from irritation of the eye by foreign particles, or from the presence of irritant substances in the eye's environment, which trigger TRP (Transient Receptor Potential) channels in the ophthalmic nerve. It can also occur with bright light and hot or peppery stimuli to the tongue and mouth... These reflex tears attempt to wash out irritants that may have come into contact with the eye.

These are, of course, different from those tears which "suddenly start flowing out of our eyes when we find our long lost friend or when someone unexpectedly decides to break up with us". These are psychic tears i.e. increased tearing due to strong emotional stress, pleasure, anger, suffering, mourning, or physical pain. This practice is not restricted to negative emotions; many people cry when extremely happy such as during times of intense humour and laughter.2

But the actual relation of tears with emotions can be summarized as:

There is an area of your brain specifically to deal with your emotions, called the limbic system (specifically the part of it called the hypothalamus), which is hard-wired into your autonomic nervous system (that’s the part you don’t have any control over).
This system, via a neurotransmitter called acetylcholine, has a degree of control over the lacrimal ‘tear’ system; and it is this tiny molecule which then stimulates tear production.
So in short, your emotional reaction to the break-up triggers your nervous system, which in turn, orders your tear-producing system to activate.3

Moving on to next part:

  crying causes endorphin release...Are tears the only way to accomplish this?

Certainly not. Even when you exercise, your body releases endorphins. These endorphins interact with the receptors in your brain that reduce your perception of pain. So, tears are not the only way to accomplish this.4

At last, I would answer this part

  What biological purpose do tears serve for the body?

as tears are necessary for the continued health of the ocular surface. Normal constituents include water, mucin, and lipids, electrolytes, non-electrolytes, and proteins. Retinoids are also important for ocular health and prealbumin may be a carrier for vitamin A in the tears to supply corneal epithelium with its requirements. Changes in tear constituents may cause certain ocular disorders.5

It is important to know here that by the above part, I meant basal tears and not psychic ones. Basal tears lubricate the eye, and help to keep it clear of dust. Tear fluid contains water, mucin, lipids, lysozyme, lactoferrin, lipocalin, lacritin, immunoglobulins, glucose, urea, sodium, and potassium. Some of the substances in lacrimal fluid (such as lysozyme) fight against bacterial infection as a part of the immune system. Lysozyme does this by dissolving a layer in the outer coating, called peptidoglycan, of certain bacteria. It is a typical body fluid with a salt content similar to blood plasma.

EDIT 1: Now, as you asked in the comments

  what if we don't maintain our ocular surface?

I can tell you a very common example of dry eye syndrome. Dry eye syndrome is a common tears and ocular surface multifactorial disease, described by changes in the ocular surface epithelia related to reduced tears quantity and ocular surface sensitivity, leading to inflammatory reaction. It is believed that decrease in the tear volume on the corneal and conjunctival surface caused by either a decreased tear secretion or accelerated evaporation plays the main role. The clinical features of dry eyes include ocular discomfort, feeling of dryness, feeling of eye fatigue, hyperemia, kerato-conjunctival epithelial disorders and abnormalities of vision.6

EDIT 2: When it comes to function of psychic tears, then how could one leave talking about why we feel better after crying (except headache). It is now proven that psychic tears contain a higher amount of hormones than basal or reflex tears. See this article7:

  Emotional tears are composed of more protein-based hormones, such as prolactin, adrenocorticotropic, and leucine enkephalin (a natural pain killer), which is suggested to be the mechanism behind the experience of crying from emotion making an individual feel better.

Though these hormones do not have any direct relation with emotions (excluding prolactin which counteracts the effects of dopamine), they can be related to emotions as long as another biological reason for their secretion through tears is discovered.

Bonus: From the same article 7, here is a very unusual function of tears i.e. controlling arousal! See this paragraph:

  On a study conducted by the Weizmann Institute of Science in Rehovot, Israel, emotional tears from women have been found to reduce sexual arousal in men. Also, emotional tears are made up of a different chemical component than those evoked by eye irritants and can relay chemical messages to others. The change in sex drive could be attributed to a drop in testosterone provoked by the tear chemicals, reducing aggression. In the animal world, it has been found that some blind mole rats rub tears all over their bodies as a strategy to keep aggressive mole rats away.

This way, we can soon have a long list of functions. I hope these many functions are enough to answer your question.

References:

1: The body’s first line of defence

2: Tears - Wikipedia

3: Why do we cry? The science of tears

4: Exercise and Depression

5: Eyelid secretions and the prevention and production of disease

6: Recent developments on dry eye disease treatment compounds

7: Chemicals in tears - Wikipedia


What's the meaning of this notation? In Wang et al., the authors state on page 663 at the top that

  Furthermore, Bax-/- Bak-/- cells were completely
  resistant to paclitaxel-induced apoptosis.

What's the meaning of the -/- notation? Bax and Bak are proteins involved in apoptosis.

-/- means both copies of the gene (both alleles) are knocked out


Minimal viable EEG equipment for dissertation research on BCI / BMI I am planning out a dissertation study of Brain-computer Interface (a.k.a. Brain-machine Interface, BCI, BMI, etc) applications.

One of the 3 papers in that dissertation will involve collecting original data, analyzing it, and writing a biofeedback application based upon this data.

I'm in a Computer Science department at a university which does not have a med school, so as far as I know I'll have to purchase the equipment myself out of a very modest research budget.

Thus, my question is "what's the lowest-end (i.e. cheapest) kind of EEG machine which would still be considered modern and sophisticated enough to be publication worthy in journals?".

Of course, I've done a good bit of research on this by reading recently publications on Google Scholar and will continue to do more research, but there's a lot of information overload and I have no prior background with EEG equipment, so any insight would be greatly appreciated.

From what I can tell the main thing driving price is the number of leads or sensors. They seem to range from 1 lead in consumer EEG toys to 100 leads, with a lot of products being advertised that have 16 or 24 leads. There are of course a lot of other features, so feel free to answer using either specific products or in terms of whatever features you've found important.

I have been working with BCI since some time and would recommend you to try these ones. They all have been widely used in MS/PhD research and their results are more or less accepted everywhere:

Emotiv
NeuroSky  (Starts from 99$)
g.tec (Most accurate/Expensive one - not recommended for startups)

P.S: Last, but not least, feel free to have a look at BCI Competition datasets. I remember I used them in my semester project. Plus, if you are interested in getting the dataset of invasive BCI, I can provide you the email of respective research as well. Best of luck in your Research!!


Has anyone modelled calcium oscillations using Matlab software? I have been trying to model calcium oscillations using MatLab, but I cannot obtain the oscillation.

I created a function where I put all the equations and used ode15s to call the function.  I have listed the equations and the code.

Can anyone tell me why I am not obtaining the oscillations?

These are the equations along with the codes:

r(:,3) = ( (((.029*0.13*1.049 + .21.*.5.*.144).*initi(:,1)) ./  (.144.*1.049.*(.5+ .13)) ) .*( 1- initi(:,3)) ) - (( (.21 *.5 + .029 *.9434) ./ (.5 +.9434) ).*initi(:,3));

  The values of the upper case Ks are obtained as follows:

  and the value of p is 0.5

a(:,1) = power (( (.5 .* initi(:,1) .*(1 - initi(:,3))) ./ ((.5 + .13 ).*(initi(:,1) + .0823)) ),3); % p_o

  Jserca is directly substituted in the equation shown below

r(:,1) = (( 1.11.*  a(:,1) + .02 ) .* (  initi(:,2) - initi(:,1) ) ) -( .9 .*  power(initi(:,1),2)) ./ ( power(.1,2) + power(initi(:,1),2) );

 r(:,2) = - r(:,1) .*5.5; % Ce

  The constants are shown here:

  And this is the desired result:

  But I obtain this!

  And this is my code:

function[t, initi, r,a]= deyoung()
clear all;
clc;
close all;

%--------------------------------------------------------------------------
% Initial conditions
%--------------------------------------------------------------------------
initi(:,1) = 0;  %  C
initi(:,2) = .9; %  y
initi(:,3) = .5; %  Ce

%--------------------------------------------------------------------------
% ODEs
%--------------------------------------------------------------------------
icon=initi;

tspan=[0 100];

options = odeset('RelTol', 1e-08, 'AbsTol', 1e-08);

[t,initi] = ode15s(@(t,initi) oper(t,initi),tspan,icon, options );

[r,a] = oper(t,initi);

figure();
plot(t,initi(:,1),t,initi(:,3));

end

function [r,a]=oper(t,initi)

    initiSize = size(initi);

    initiColumnCount = initiSize(2);

    if ( initiColumnCount == 1)
        initi = initi';
        a = zeros(1,1);
    else
        initiRowCount = initiSize(1);
        a = zeros(initiRowCount, 1);
        r = zeros(initiRowCount, initiColumnCount);
    end

    % y
    r(:,3) = ( (((.029*0.13*1.049 + .21.*.5.*.144).*initi(:,1)) ./  (.144.*1.049.*(.5+ .13)) ) .*( 1- initi(:,3)) ) - (( (.21 *.5 + .029 *.9434) ./ (.5 +.9434) ).*initi(:,3));

    %Po
    a(:,1) = power (( (.5 .* initi(:,1) .*(1 - initi(:,3))) ./ ((.5 + .13 ).*(initi(:,1) + .0823)) ),3); % p_o

    %C
    r(:,1) = (( 1.11.*  a(:,1) + .02 ) .* (  initi(:,2) - initi(:,1) ) ) - ( .9 .*  power(initi(:,1),2)) ./ ( power(.1,2) + power(initi(:,1),2) );

    %Ce
    r(:,2) = - r(:,1) .*5.5; % Ce

    r = r';

end

I wish to share an open-source modelling study on Ca2+ oscillations in astrocytes which contains a detailed description of the underlying math and even better, it has supplementary Matlab code published alongside (Zeng et al., 2009). This may be of help to check your formulae and script.

Unfortunately I do not feel inclined to start troubleshooting and bug-fixing your formulae and Matlab code, because, as mentioned in the comments, the issue can be anywhere in the chain of events.

Reference
Zeng et al., Biophys J (2009); 97(9): 2429–37


Explanation of protocol in DNA extraction experiment In the Materials and Methods section of this paper on DNA extraction and analysis from hair I do not understand some parts of their protocol methods. In particular:

  "The digested hair solution was then extracted twice with two volumes of phenol saturated by Tris-EDTA (TE) buffer (Sigma), and once with two volumes of chloroform. "

How do the volumes of phenol and chloroform come into play? I know they are used for an organic-solvent extraction, but what was the actual procedure used, i.e., the steps for adding each chemical?

Another question I had was on the buffer they used:

  "0.01 M Tris-HCL(ph8), 0.005 M EDTA, 0.1 M NaC1, 0.039 M DTT, 2% SDS"

That whole combination would be the "Tris buffer" then yes? And the proteinase K would then be added to some of this buffer to digest the hair?

The DNA solution has a fixed volume (e.g., 0.1 mL). To a suitable test tube is added 0.2 mL of buffer-saturated phenol. After closing the test tube the mixture is mixed well, typically using a vortex mixer, but possibly by careful, repeated inversion. The aqueous phase and the organic phase are barely miscible. The tube is centrifuged to speed up the equilibration, and concentrate the denatured protein at the interface. After centrifugation the aqueous layer is carefully removed to a fresh test tube.

That is one organic extraction. This is repeated with a fresh aliquot of buffer-saturated phenol (another 0.2 mL). Then the aqueous phase is decanted again and extracted with 0.2 mL of CHCl3.

According to the recipe you provided, the buffer-saturated phenol was purchased from a vendor (Sigma-Aldrich Chemicals, of St. Louis, Missouri, USA), so you can look up the ingredients and composition on their online catalogue (no doubt).

The buffer recipe you provided is the proteinase K digestion buffer. It is typically performed at an elevated temperature.

This protocol is designed to isolate DNA from the nuclei of hair cells. Fully half of the contents of a eukaryotic nucleus are chromosomal proteins, by mass, so the proteinase K digestion step not only breaks open the hair cells, but also helps to remove all of the unwanted, contaminating cellular and nuclear proteins.


Parasite - host equations The Lotka–Volterra equations describe how predator–prey interactions affect population growth. Do these equations describe parasite-host interactions? If not, how would they change by adding these interactions as well?

Parasite vs predators

In terms of ecological interaction, a parasite is essentially a predator. As such, of course the Lotka-Volterra equations apply to host-parasites interactions.

Lotka-Volterra equations

However, Lotka-Volterra equations are very simple and very general. So much so, that in order to make good prediction about the real world, one most often have to build more advanced models.

Host-parasite interaction models

There exist a whole set of models specific to host-parasite interactions. You should have a look at the wikipedia entry for epidemic model which is a pretty good overview and introduction.

Most models of host-parasite interactions fall into the category of the SIR (or SIRS and other derivatives) model. The term SIR comes from Susceptible-Infected-Recovered. The whole point of the SIR models is to categorize host individuals on whether they are Susceptible, Infected of Recovered (hence the abbreviation SIR).

The SIR models are very much used by national and international centers for epidemiology and underly many of the decisions of vaccination and other methods of disease control.

Host-parasite co-evolution

Of course, the Lotka-Volterra model and the SIR models assume absence of evolution and only track changes in population size (within each category for the SIR models). There are models that also take into account that populations also evolve in response to the interaction and demographic events that the interactions are causing. Such models are much more complicated to keep track of and we often (I think) make use of technics such as separation of time scales. These models are essential though typically for to control viral epidemic but not only. But these models are outside the scope of your question.


Proteins: Post translational modification I am a physicist and trying to understand some protein chemistry for a small project. Basically, amino acids combine to form proteins and after forming the primary structure, some chemical modification may occur, such as phosphorylation or glycosylation (post translational modification). In case of the enzyme carbonic anhydrase a zinc ion is added post-translationally as a cofactor. (The amino acid sequence can be seen here (scroll down to 'sequence' title).

Is the attachment of zinc regarded as a type of post-translational modification?
When carbonic anhydrase is denatured, is the zinc ion released in the medium?
Will the amino acid sequence (primary structure) be changed after denaturation? If yes, are amino acids removed after denaturation, if yes, which?
I guess Zinc will be removed after denaturation. Is the remaining structure the primary protein structure?

1) Is the attachment of zinc regarded as a type of post-translational
  modification?

It is not really considered a post-translational modification because the zinc atom is not covalently bound to the protein. Binding to zinc is adsorption.

  2) When carbonic anhydrase is denatured, is the zinc ion released in
  the medium?

Yes, but it depends on the extent of denaturation too. Metal ions can be removed using chelating ligands like EDTA, without actually denaturing the protein.

  3) Will the amino acid sequence (primary structure) be changed after
  denaturation? If yes, are amino acids removed after denaturation, if
  yes, which?

Denaturation does not include cleavage of covalent bonds. There won't be change in the amino acid sequence.

  4) I guess Zinc will be removed after denaturation. Is the remaining
  structure the primary protein structure?

Yes; just the polypeptide.


Values of the blood tests pancreatic amylase and lipase Anyone know what is considered slightly elevated, moderately elevated and strongly elevated values of pancreatic amylase and lipase?

Many different laboratories in my country divide between these categories for interpretation, but they don't specify which values qualify for each category.

Hope this is the right place for this kind of question.

Thanks in advance.

It is not necessary a fixed value. I think it depends on the doctor that interprets it. For e.g if amylase's normal value is 70, and laboratoy value is 80, i would say it is slightly elevated. A value of 300 is strongly elevated.


Size of DNA in phage I have read that DNA(after recombination) is packaged in bacteriophages lambda only if it's between 40000 and 53000 bp long. This constraint can be used to ensure packaging of recombinant DNA.

I don't understand why shorter DNA can not be packaged.

Source : Lehninger Principles of Biochemistry

For lambda:

  If the distance between the two cos sites is less than ~37 kb, the resulting phage particle will be unstable. When the DNA is inside the capsid, it exerts pressure on the capsid. Likewise the capsid exerts an inward force on the DNA. If there is not enough DNA inside the capsid, it will implode from the inward force of the capsid. If the distance between the two cos sites is too far (~52 kb), then the capsid will be filled before the second cos is reached. The tail cannot be added because the DNA hanging out of the capsid is in the way and no infectious phage particle is produced.

http://www.microinmuno.qb.fcen.uba.ar/03-Bacteriophage.pdf

In contrast filamentous phage like M13 have no upper size limit, but since they get longer with more DNA they become physically fragile.


How to differentiate male and female mosquitoes at pupal stage? There are many differences between male and female mosquitoes in their adult stage. But for my experiment, I need mosquitoes before they mate. So I need to sort them before they develop in to an adult. The best option is to sort them in their pupal or larval stage. I tried to search the differences, but most of them were very general. So, if someone knows about it, please share your answers.

Male and female pupae are consistently slightly different sizes. This isn't particularly obvious to look at them, but allows them to be sorted mechanically by using two sheets of rigid, waterproof material (aluminium, glass or acrylic) fixed at a slight angle to each other, and washing the pupae down between them until they get stuck. The pupal sorter in most common use is described in this paper and you can buy one commercially here:

http://johnwhock.com/products/laboratory-equipment/larval-pupal-separator/

I think I've seen a video of one in use at Virginia Tech somewhere online but I can't find it right now; I'll edit it in later.


Length of sleep time Why do we wake up after 6-8 hours of sleep ? Why don't we sleep for lets say 20-30 hours ? What mechanism is it that controls when to wake us up and how does it determine the moment that we should wake up ?

Think this review from Nature can answer your question. A brief summary  ( with slight simplification):

The ascending activating system (that is responsible for wakefulness) has two branches:

The first one ascends to the thalamus and activates the thalamic relay neurons - these transmit information to the cortex. They get their main input form two acetylcholine producing group of cells:  the pedunculo-
pontine and laterodorsal tegmental nuclei (PPT/LDT). These two group of cells are also the source of main input for reticular nucleus of the thalamus.

  The neurons in the PPT/LDT fire most rapidly during wakefulness and rapid eye movement (REM) sleep, which is the stage accompanied by cortical
  activation, loss of muscle tone in the body and active dreams

The second branch, directly activates neurons in the hypothalamus, basal forebrain (BF) and cortex, bypassing the thalamus. This pathway has origins in monoaminergic neurons in the upper brainstem, caudal hypothalamus, as well as the noradrenergic locus coeruleus (LC), serotoninergic dorsal (DR) and median raphe nuclei, dopaminergic ventral periaqueductal grey matter and histaminergic tuberomammillary neurons. Input from this pathway to the cortex is extended /augmented by the lateral hypothalamic peptidergic neurons (that contain melanin-concentrating hormone (MCH) or orexin/hypocretin), and BF neurons(that produce acetylcholine or GABA).

Sleep is promoted by the so called VLPO (ventrolateral preoptic nucleus).
The VLPO send outputs to major group of cells of the arousal system in the hypothalamus and brainstem.

  The VLPO neurons are primarily active during sleep, and contain the inhibitory neurotransmitters, galanin and GABA.
  The VLPO also receives afferents from each of the major
  monoaminergic systems. Both noradrenaline and serotonin inhibit
  VLPO neurons. The latter do not have histamine receptors, but the
  tuberomammillary neurons also contain GABA, which is inhibitory
  to VLPO neurons, as well as several other potentially inhibitory pep
  tides, such as galanin and endomorphin. Therefore, the VLPO can
  be inhibited by the very arousal systems that it inhibits during sleep.

As you can see in the quote from the paper these two systems can mutually inhibit each other and basically work as a seesaw or 'flip-flop switch'. In this system activity in one  subsystem shuts down the inhibition from the other subsystem and disinhibits its own action (selfreinforcing loop). The transition from one state to the other is relatively fast. Orexin plays important role in stabilizing the switch in one position or the other.

Regulation pf sleep:

Homeostatic:
It is unclear how homeaostatic regulation of sleep work, yet it has been proposed, that adenosine accumulation in the brain may signal for 'need for sleep'. The extended wakefulness causes the exhaustion of brain glycogen reserves and depletion of ATP levels. As ATP is degraded to ADP, AMP and eventually adenosine, extracellular adenosine levels rise in some parts of the brain including the BF.

  In addition, adenosine might disinhibit the  VLPO via presynaptic A1 receptors by reducing inhibitory GABAergic inputs.

This implies that during sleep ATP and energy sources are regenerated and free adenosine levels drop, thus inhibition of VLPO might take place again.
Also it is important to note that the amount of sleep we need is proportional to the time we spend awake.

Circadian regulation:

It is known that humans have quite precise :circadian rhythm:

  The suprachiasmatic nucleus (SCN) serves as the brain’s ‘master
  clock’. Neurons in the SCN fire in a 24-hour cycle that is driven by a
  transcriptional–translational loop, which persists even when the neurons are dissociated in cell culture.

The SCN has moderate output to the VLPO or orexin neurons, but it has more important projections to the adjacent subparaventricular zone (SPZ) and the dorsomedial nucleus of the hypothalamus (DMH).

  The SPZ also has relatively limited projections to the VLPO, orexin
  neurons and other components of the wake-sleep-regulatory system. However, a major target is the DMH. This region receives inputs from many more neurons in the SPZ than the SCN, so the SPZ is in a position to amplify the output of the SCN. (...) The DMH is one of the largest sources of input to the VLPO and orexin neurons and is crucial for conveying SCN influence to the wake–sleep-regulatory system. The DMH projection to the VLPO comes largely from GABA-containing neurons (that is, those that promote wakefulness by inhibiting sleep), and the projection to the LHA originates from neurons containing glutamate and thyrotropin-releasing hormone (which should presumably be excitatory and promote wakefulness).

So as you can see our circadian rhythm as direct control over our sleep-wake cycle, and that the SCN can heavily promote awakening through SPZ and DMH.

Thorough review and details can be found in the article I linked at the beginning, I only tried to select key information to provide a (not so ) brief summary. We only sleep about 7-8 hours normally because this is enough for homeostatic regeneration and our circadian rhythm promotes wakefulness in the morning (this is quite simplified).

Based on their abstract these limited access papers might also be useful (unfortunately I do not have full access to them right now):

http://www.eurekaselect.com/87813/article
http://www.sciencedirect.com/science/article/pii/S0074774210930018
http://www.sciencedirect.com/science/article/pii/S0896627315001312


Non-coding DNA correlation with rate of evolution Non-coding DNA can be helpful in generating useful mutations that can go on to become new features/functionality of an organism.
Non-coding DNA also indirectly reduces chances of mutation of useful/functional genes.

So if an organism has a larger proportion of non coding DNA it'll be safer from mutation. Humans have 80%-90% non-coding DNA. But this number is far lesser in many other species especially plants. Some plants have as few as only 3% non-coding DNA.

My question is, do these species with less non-coding DNA undergo evolution faster? Because their functional genes are more susceptible to mutations (which would be disadvantageous on average I guess). Would it be fair to say that evolution tries to keep expanding this proportion of buffer DNA? Lastly, is my question related to C-value paradox?

My assumption that non-coding DNA indirectly offers adaptive advantage (evolutionarily speaking) seems to be questioned. Let's consider the following case:

Let A and B be two genomes of equal size. Let A have 80 % non-coding DNA and 20% coding DNA. And let B have the opposite i.e., 20% non-coding DNA and 80% coding DNA. Let both A and B be exposed to the same amount of UV radiation for the same amount of time. All conditions being the same, let's assume that this causes the same amount of mutation in both A and B, say 10%. Now what is the probability that this mutation happened in non-coding DNA (which means it doesn't harm the organism) in each of A and B? Evidently, the probability is higher in A meaning it's safer from mutation caused due to UV radiation. So A has an advantage of surviving over B.

Whether or not species with less non-coding DNA evolve faster, the assumption that this could be explained by their genomes being more susceptible to mutation would seem to me to be based on a false premise.

Let us examine the logic of the assumption by making an analogy to drawing of tickets from an urn in a lottery. If you buy one ticket (coding region), and only one ticket is drawn (there is a single mutation) from the urn (the whole genome), the probability of winning (your gene suffering a mutation) decreases as the number of tickets (the size of the genome) increases.

So the question is “does mutation follow this model?”, i.e. are the number of mutations in a genome independent of its size? To answer this, let us look at two examples of known mechanism of mutation.

Misreading during DNA replication: Here (and in other types of misreading) the error frequency is, quite logically, related to the number of bases replicated i.e. it has a specific (if very low) value of n per 1,000,000 bases — not n per genome.
UV radiation: Here the source of the radiation is external and its flux will be proportional to the area it strikes — hence the larger the target area the more interactions with thymine causing dimerization. Although our linear-centric view of DNA tends to ignore its area, the larger the genome, the larger the target. The only way I can see the non-coding DNA buffering the coding DNA from radiation is if it somehow formed a protective shell around the latter. I know of no evidence that this is so.


The Hawk-Dove game: why is the average payoff half of the difference between reward and cost? My question is about the well known Hawk-Dove model used in game theory. It concerns two strategies: the Hawk, which always fights the opponent, and the Dove, which does not fight and will either retreat or share. The payoffs for each of the possible encounters are presented in a matrix. Now, say that the reward (R) is 10 units and the cost of fighting (C) is 5 units. When a Dove meets a Hawk, it will retreat: Dove gets 0 and Hawk gets R=10. Vice versa, when a Hawk meets a Dove, Hawk gets R=10 and Dove gets 0 because it retreats. When two Doves meet, they will share the benefits; both Doves get R/2, in this case 5. These three, I have no problem understanding.

My issue is with the payoff when two Hawks meet. I understand that, under the assumptions of the model, both Hawks have a 50% probability of winning. I also understand that the winner gets R and loser pays C. But I'm completely stuck at why the average payoff is given as (R-C)/2. When you input the numbers above, it gives you a value of 2.5. How is the average payoff in an encounter between two Hawks 2.5 if one receives 10 and the other loses 5?

One hawks gains 10, the other loses 5. So together, they gain only 5 (=10-5). On average, they gain 5 / 2 hawks = 2,5


Are any biology research journals free to publish in? The research journals Ive published in require significant financial cost to publish. On top of that many require a membership to the society the journal is associated with, in addition to publication fees. I was wondering if anyone is familiar with any journals (reputable hopefully) that do not require fees like this to publish a research article?

Many biology journals are free to publish in. As a rule of thumb:

Most journals from for-profit publishers such as Elsevier, Wiley, etc. charge nothing to the author (but of course bill the libraries handsomely).
Many but by no means all society journals charge page charges even if they are not open access.
Most but not all open access journals charge substantial publication fees. You could try this website to search for open access journals that do not charge publication fees.


Meiosis pairing of chromosomes How do the X and Y chromosomes synapse during the zygotene stage of when they have almost no homology between them?

There is 'homology' at the pseudo-autosomal region, a recombining region of the X and Y chromosomes.


What is the difference between SNP and STR? I thought that these were just different format of the same data.

But it seems there isn't a way to convert SNP (single nucleotide polymorphism) data to STR (short tandem repeat) data. Am I right?

As I understand SNPs is basically a "diff" between some base human dna (parts that never change) and given dna. While STRs are strands of dna that differs between individuls.

But if there are enough SNPs (i.e. all of them), it would be trivial to deduce STRs, right?

For example, currently 23andMe tests the whole mitochondrial genome. Does it mean that one can easily deduce STRs?

The solution is in the name!

SNP: single nucleotide polymorphism

The name tells us that it is a change that affect one single nucleotide and that there can be multiple of these (polymorphism could be rewritten as multiple forms)

From the SNP Wikipedia page:

  [A SNP] is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in a human.

So, for instance, if you take 8 individuals and sequence their gene XYZ, you may find, at a certain locus (=position) on the gene:

Individual 1: AAGGTG C AGCAGTC
Individual 2: AAGGTG T AGCAGTC
Individual 3: AAGGTG T AGCAGTC
Individual 4: AAGGTG T AGCAGTC
Individual 5: AAGGTG C AGCAGTC
Individual 6: AAGGTG C AGCAGTC
Individual 7: AAGGTG T AGCAGTC
Individual 8: AAGGTG T AGCAGTC

The position highlighted in bold is a SNP. In this case we only have either C or T (and this produces 2 different alleles for gene XYZ).

This page from University of Utah has a very clear animation on SNPs.

STR: short tandem repeat

These are short repeated sequences. They're in tandem, that is, one after the other.

STR consist of a few (2-6) nucleotides that are repeated several (5-100) times.
For instance this page from the University of Arizona gives the example of D7S280, one STR with sequence (GATA)n (that is, GATA repeated n times)

  1 aatttttgta ttttttttag agacggggtt tcaccatgtt ggtcaggctg actatggagt
 61 tattttaagg ttaatatata taaagggtat gatagaacac ttgtcatagt ttagaacgaa
121 ctaacgatag atagatagat agatagatag atagatagat agatagatag atagacagat
181 tgatagtttt tttttatctc actaaatagt ctatagtaaa catttaatta ccaatatttg
241 gtgcaattct gtcaatgagg ataaatgtgg aatcgttata attcttaaga atatatattc
301 cctctgagtt tttgatacct cagattttaa ggcc

In this case, variations between individuals reside in the number of times the sequence is repeated.


How can the Ames test detect a human carcinogen? Using the Ames test, we add a mutagen to auxotrophic salmonella with mutations in the histidine pathway and rat liver extract to simulate metabolism.  How would we know if the carcinogen is a human carcinogen or not?

I'm guessing that if a mutagen showed no growth without the rat liver extract, but then growth with the rat liver extract this would mean that it is a human carcinogen. Is this true?

The Ames test aims to find out if a chemical (not yet known to be mutagen) is indeed a mutagen, either directly, or following treatment with liver enzymes (which may metabolise a chemical to mutagenic derivatives during "detoxification"). As you explain, the test involves looking for reversion of various histidine auxotrophic strains of Salmonella.

If the chemical is found to mutagenic in the Ames test then there is a good chance that it will be a carcinogen because of the link between mutagenesis and cancer. In practice further unrelated tests are needed to eliminate false positives.

In this review of the method

  Mortelmans & Zeiger (2000) The Ames Salmonella/microsome mutagenicity assay. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 455: 29-60

the authors state that:

  ...there is a high predictivity of a positive mutagenic response in the Ames test for rodent carcinogenicity...ranging from 90% to 77%...


Nutrient agar as the medium for antibiotic susceptibility testing I couldn't get Mueller Hinton agar to conduct antibiotic susceptibility testing. I'm thinking of just choosing nutrient agar as the growth medium for the bacteria Staphylococcus epidermidis. Will there be any major issue in choosing nutrient agar as the growth medium?
Thanks in advance

The standard breakpoints used in clinical susceptibility testing (Kirby-Bauer/disc diffusion assay) are considered reliable when every part of the testing method is standardized. If you change any part of that standardized method without properly validating those changes, it may or may not affect the outcomes and there would be no way of knowing without some sort of comparison study for validation.
Difficulty obtaining the proper media would seem common enough that this exact problem has been studied. This study did a head-to-head comparison of nutrient agar (NA) and Mueller-Hinton agar (MHA) for susceptibility testing on 149 clinical isolates along with a few QC reference strains. They found that NA agar did not produce acceptable results for the QC strains according to the relevant Clinical & Laboratory Standards Institute (CLSI) guidelines. Use of NA also resulted in many errant determinations among their clinical isolates (including many isolates of Staphylococcus aureus).
Given the error rates in this study, I would say that you should not rely on susceptibility testing results using nutrient agar in any sort of clinical context.
Reference:
Nassar, M.S.M., Hazzah, W.A. & Bakr, W.M.K. Evaluation of antibiotic susceptibility test results: how guilty a laboratory could be?. J. Egypt. Public. Health. Assoc. 94, 4 (2019). https://doi.org/10.1186/s42506-018-0006-1


Why does Anti-A antibodies make type-A blood type clump? A-type blood has B-antibodies; it also clumps anti-A antibodies are inserted. Why is that? The blood has no antibodies against the A-antibodies to make clump in this way.

When an antibody meets its antigen it will bind it. So if you add anti-A antibodies to A blood, these antibodies will bind the red blood cells. Because of its Y-shaped form, each antibody can bind two epitopes. These can be located on the same red blood cell, or on two different. If they are located on two different, this leads to cross-linking of two blood cells. Since this happens many times, the blood cells will clump. The whole process is called hemagglutination.

See the image (from here) for illustration:


Ribosomal RNA amount in a Drosophila cell I am isolation RNA from Drosophila larvae brain with TRIzol method. What percentage of extracted RNA will be ribosomal RNA? I am only interested in mRNA, so I am trying to figure out whether I need to get rid of rRNA. Thanks

The protocol you are using will not only leave the sample with rRNA but also non coding RNA.

Many RNA protocols will separate mRNA by affinity of a carrier to the polyA tail.  This protocol references an older paper that estimates that only 5% of RNA is mRNA.  I'd be surprised if this ratio changed by more than 2-3 fold in drosophila.

I assume that %age is by weight but it could be a densitometry measurement which is similarly interpreted.


Terminology regarding cross-immunoreactivity After reading an article, I saw expressions like "cross-immunoreactivity among epitopes", "cross-immunoreactivity among variants of virus", "immunological reactions among pairs of peptides" and so on.

I wish to verify my following understandings:

An epitope is also called antigenic determinant, and it is part of the antigen that is recognized by the antibody. An epitope, then, is a part of a virus variant. Peptides are short chains of amino acids. Thus, we can talk about the immunological reactions among peptide-pairs, because the virus variant itself is a protein, which is composed of peptides? Did I understand it correctly?

Moreover, I saw a sentence like "this antibody is against a few variants while reacting with all tested peptides", so I guess reacting here includes against? Reacting may include other situations, right?

Everything you state is correct, except that I disagree with your statement that a "[...] virus variant itself is a protein, which is composed of peptides.

A virus is typically composed of a protein capsule with genetic material on the inside. So technically, a virus is not a protein, but its outer shell is composed of proteins. Further, a protein does not necessarily have to be composed of (multiple) peptides - it can be a single amino acid chain.


What would classify those findings of the University of Sheffield experiment as aliens? It's in the news that some experiment was able to capture some alien specimens during a meteor shower:

http://www.ibtimes.com/aliens-are-here-scientists-say-they-have-proof-alien-life-there-should-be-plenty-skepticism-1408322

Despite all the skepticism that has already been said about this finding, what would be a proof that such specimem came from outer space? Is there any established protocol to assure that some form of life didn't come from Earth?

I wouldn't say that there is an established protocol - claims of alien life are not commonly testable or even legitimate - but if something were discovered and deemed "alive," a fairly good sign it was alien would be if its genetic makeup were based on something other than DNA or RNA.  That would be a dead giveaway the organism had side-stepped every known organism on Earth and while that doesn't prove alien-ness, it would certainly hint strongly of a non-Terran genesis.  There are arguments for and against carbon/CHNOPS-based life but that is nowhere near as definitive.

Also, there's another really good technique.  I don't like to resort to ad hominem attacks, but ideally the discovery should be by someone who has not already made verifiable false claims on the same topic.


Do neurons that *don't* fire together unwire? We all know the classic Hebbian theory, often phrased as "neurons that fire together wire together."  I'm curious about how other connections get pruned when two neurons start to fire together.
If two neurons start to make a strong connection and fire together often, will they prune connections to other neurons faster than if they were merely "dormant," becoming more and more selective towards that channel.  Or is the result simply a more connected structure and the pruning of connections continues to occur at the usual pace?

"Specific" unwiring via timing
A more modern understanding of the classic Hebbian aphorism is spike-timing-dependent plasticity. It is observed that connections are strengthened or weakened according to the relative timing of spiking and inputs. Specifically, synapses that are active shortly before a cell fires an action potential tend to be potentiated ("wire"); synapses that are active shortly after a cell fires an action potential tend to be depressed.
So it isn't just that cells that fire together wire together, it's that cells that fire together in a certain way wire together, and cells that fire together in another way "unwire". I think it's important to recognize that a reduction in synaptic strength doesn't necessarily mean immediate loss of a synapse. Weak synapses are common, and only the very weakest are pruned entirely.
Non-specific unwiring via homeostasis
Another general principle, which may be closer to what you are thinking about, is homeostatic plasticity including synaptic scaling. Just like other physiological processes are under homeostatic control, neurons tend to adjust their responses to maintain an overall activity (firing rate) homeostasis. This process occurs on many different time scales and systems, but stated generally, high levels of activity in neurons tend to activate cellular processes that will reduce future activity, and low levels of activity tend to activate processes that will increase future activity.
Current thinking is that synaptic scaling occurs generally rather than specifically. By increasing the strength of specific synapses via Hebbian plasticity and at the same time slightly decreasing the strength of all synapses, the overall balance of input stays about the same (homeostasis).
Of course, things are a bit more complicated when you look over the whole nervous system and the whole time course of development through adulthood, but I think that's outside the scope of this answer.


If we can make magic bullets that are basically artificial antibodies, why has a cure for cancer not yet been developed? So protonsil and salvarsan 606 where both used as the first magic bullets in the modern period of medicine in the 1900s. However, if we can create artificial antibodies that target specific diseases how have we not come up with a cure for cancer? It seems it shouldn't be that difficult. But if we COULD create artificial antibodies that target cancerous cells would we be able to do it effectively without the drug having any bad or quite noticeable side effects on the body?

By the looks of it chemotherapy is the closest we have gotten so far in chemical drugs, but it does have some nasty side effects.

I was aware of 5 of the approved treatments.
However each type of cancer is similar but different, would it be ever possible to create a generic treatment?

Edit: I have found something interesting, scientist have come across a way to change the antigen on a cell however it is not fully understood.

This is a good question.
The first answer is that there are antibody therapeutics for cancer.
These fall into two categories which I will call therapeutic and immunotherapy (this is not typical naming but, keeping it simple they will do).
Therapeutic antibodies are designed to bind to an enzyme or signalling protein that will weaken the tumor specifically.  An example is an antibody to nutrient intake receptors (cancers eat a lot more than other cells). HER2 is a receptor that is heavily populated on breast cancer tissue.  Antibodies that inhibit HER2 activity can slow the growth of breast cancer specifically with minimal toxic effects.
There are also antibodies to proteins found only on cancer cells.  These can be specific antibodies (monoclonal antibodies) to proteins from a mutation that only the cancer cell has.


Why do plants fruit? This is a two-part question:

What is the point of fruit if not to be eaten? It’s my understanding that organisms will adapt to survive and thrive. I understand that being eaten can spread seeds, but this just seems like too much of a risky tactic to rely on.
Following on from part one: If being eaten is the best way to spread seed, why do some plants avoid this (such as by being poisonous or thorny)?

Seeds are spread by many mechanisms

Wind dispersal: When air currents used to spread seeds. Often these plants have evolved features to facilitate wind catching, for example dandelions. Aka, anemochory.

Propulsion & bursting: When seeds are propelled from the plant in an such as in these videos. This is called Ballochory.

Water: Similarly to wind dispersal plants can spread seeds by water movement/currents, aka Hydrochory. This is used by many algae and water living plants.

Sticky Seeds: There are many ways a seed can attach to the outside of an animal - by using hooks, barbs, sticky excretions, hairs. Seeds then get carried by an animal and fall off later. This is epizoochory.

Fruiting: Plants can use seed-bearing fruit to encourage animals to eat the seeds. They will then be spread when the waste is excreted after digestion. This is a process of endozoochory.

More than one way to spread a seed

From above you can see there are many ways to spread a seed. This means that many plants (those that do not use fruit) will want (from an evolutionary perspective) to avoid being eaten at all costs, and therefore evolve poison/taste cues that reduce the frequency of this. However, if investing in producing fruit bears a net benefit, ie many seeds are spread and successfully propagate, then the cost of fruit production is not a risk. A fruiting plant can minimize the risk by limiting reward (making fruit taste good and be nutritious) to only the right spatiotemporal moment when the seeds are primed for dispersal, if the fruit is eaten before the seeds are ready/present in the fruit then there will be no benefit of producing the fruit. (I expect this is why unripe fruit doesn't tend to taste so nice - it doesn't taste nice unless it's ripe because those where mutations made fruit taste good before the seeds were ready had no offspring, and those that time the ripening well were much more successful).

Producing an edible fruit is not necessarily the best way but is the way many plant species have evolved to spread their seeds. Evolution works by random mutation and selection, which can only work with the variation it has available - only if a mutation to produce fruit arises in a species and it improves fitness is it then likely to spread. It appears that endozoochory could be a very good methods of long distance dispersal.

Some interesting stuff

Interestingly, according to this blog post, unripe fruits taste bitter because they are full of tanins. Cranberries are an odd fruit because they taste bitter which means they are unattractive to animals, but they do float - which is a good dispersal method - because of an air-pocket inside the fruit that evolved. It could be the case then that once a mutation arrived for the air-pocket the fruit could just float away on water to a new location, and then using resources to make the fruit sweet and tasty became an unnecessary cost so was lost (to some degree).

This article contains this text:

  Like many species of plants native to North America, the cranberry is specially adapted to wetlands -- water-soaked areas that create transition points between dry land and open water. But cranberries do not grow directly in the water. Instead, they typically lay their roots at its edge, taking advantage of the rich soils created by alternating layers of peat, sand, clay and rock.
  Other fruits are dependent on hungry creatures to spread their seed,
  so sweetness can help their chance of being eaten and transported
  elsewhere. Not cranberries. Because of their little air pockets, the
  fruit falls from the plant's long vines when ripe and lets the water
  transport it to distant beds.

  This advantage dictated the fruit we eat today.

  Blueberries and cranberries are close cousins and are in fact not
  berries at all; they belong instead to a class of fruits known as
  epigynous or false berries. Unlike a true berry, the fruit grows from
  beneath the rest of the flower parts and as the fruit ripens the
  flower stays attached and ripens as well.

  Vorsa believes that at some point during the last ice age there were
  fewer animals to eat the fruits, and this might have driven the two
  species to diverge. The cranberries developed an acidity level five
  times higher than blueberries because it came to rely on water for
  seed dispersal. Cranberries did not need to produce large amounts of
  sugar that their blue-colored relatives required to entice consumption
  by animals in order to spread their seeds.


What fraction of bacterial proteins are membrane bound? Almen et al. showed that around 27% of the human coding proteins are membrane bound.
How does this compare with bacteria such as E.coli or B.subtilis (or any other bacteria)? Is there a paper out there demonstrating this?
I assume that there would be massive variation among bacteria, so although one specific example would be enough as a ballpark, I expect that this may not represent all bacteria well.

As a proxy for asking which bacterial proteins are membrane-bound, we can ask which proteins harbor transmembrane domains. A popular tool for detecting transmembrane domains is TMHMM, which looks for transmembrane helices in protein sequences using a hidden Markov model.1
For E. coli strain K12, UniProt reports 4,391 protein sequences corresponding to unique genes. Of these, TMHMM predicts 1,072 proteins have at least 1 transmembrane helix (24.4%), and 775 proteins have 2 or more transmembrane helices (17.6%).  Expanding this analysis to the E. coli pan proteome, which contains 165,127 non-redundant protein sequences, TMHMM predicts 28,369 proteins have at least 1 transmembrane helix (17.2%), and 16,105 proteins have 2 or more transmembrane helices (9.8%).
For B. subtilis strain 168, UniProt reports 4,260 protein sequences corresponding to unique genes. Of these, TMHMM predicts 1,175 proteins have at least 1 transmembrane helix (27.6%), and 845 proteins have 2 or more transmembrane helices (19.8%). Looking at the pan proteome for this species, which contains 18,046 non-redundant protein sequences, TMHMM predicts 3,967 proteins have at least 1 transmembrane helix (22.0%), and 2,463 proteins have 2 or more transmembrane helices (13.6%).
The relative depletion of transmembrane domain-containing proteins in the pan genomes of both species relative to their reference genomes could point to a functional skew of accessory genomes towards proteins that are less likely to be membrane-associated, such as strain-specific virulence factors, antibiotic resistance genes, integrated phage proteins, and proteins involved in niche-specific metabolism.2,3 Additionally, the relative enrichment of transmembrane domain-containing proteins in B. subtilis compared to E. coli could reflect the different membrane compositions of Gram positive and Gram negative bacteria, though it's hard to say without sampling more species.
One important caveat to TMHMM -- predicted transmembrane segments in the N-terminal region are sometimes just signal peptides. Signal peptides are likely to appear as single transmembrane domains, which is why I've also reported the fraction of proteins with 2 or more transmembrane helices, above.  A more complete analysis may run the same protein sets through SignalP 4 and cross-reference the TMHMM hits to identify transmembrane domain-containing proteins that also contain signal peptides.
Note that the cited publication by Almen et al. uses TMHMM and directly references the results of the original TMHMM paper,1 which reports transmembrane protein abundance in the proteomes of several species.

One of the most referenced papers regarding the percentage of membrane proteins in proteomes is from 2001 where the membrane topology prediction method TMHMM was applied on a number of proteomes from different species to estimate the membrane protein content, for example, Caenorhabditis elegans (31%), Escherichia coli (21%) and Drosophila melanogaster (20%).

Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001 Jan 19;305(3):567-80.
Kung VL, Ozer EA, Hauser AR. The accessory genome of Pseudomonas aeruginosa. Microbiol Mol Biol Rev. 2010 Dec;74(4):621-41.
Álvarez VE, Quiroga MP, Galán AV, Vilacoba E, Quiroga C, Ramírez MS, Centrón D. Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1. Front Microbiol. 2020 Mar 18;11:342.
Nielsen H, Brunak S, von Heijne G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng. 1999 Jan;12(1):3-9.


Can animals use the nitrogen in chitin to build proteins? Fungi and insects contain chitin, which is about 6% nitrogen.
Can an animal - like me - make use of this as a nitrogen source to build proteins?

Are there any animals that can do this?

Are there other uses an animal can put Nitrogen from this specific source to?

This article suggests a certain amount of chitin digestion is possible.

http://www.bio.unipd.it/agroecology/download/pdf/papers/2009/Chitin-Chitinases-Paoletti-From-Binomium-Chitnchitinase-Recent-Issues-Fp-Version.pdf

I can't quantitatively say how much of any of the myriad potential chitin sources (fungal, crustacean or other arthropods) would be digested within a 'normal' time frame in the human digestive system. That work should probably be undertaken, though.


Why do cockroaches burst from soapy water? (careful, disturbing!)

I was experimenting with some stray cockroaches that ended up falling in my bath tub overnight (there is currently an infestation undergoing in my apartment building) and I found out that they are very easily killed by simply soaking them in soapy water.

I read that soap blocks some pores in insects' bodies which leads to suffocation, which appears to be the cause of death for my test cockroaches. But what I don't get is why about a half of them died with their innards bursting from their tail end. The water wasn't too hot to make them boil. Is it that they suffocate so hard that attempting to breathe they blow out their insides? Or is it the soap's reaction with the cockroach's bodily materials? Or is something else causing this?

I remember watching a documentary on injecting various insects with hydrogen peroxide which caused much more dramatic explosions, but it's not like I was injecting cockroaches, I just sprinkled them with soap water.

As far as I am aware, cockroaches don't burst from being sprayed with soapy water (water + some liquid dish detergent). We previously had many cockroaches in our apartment (some came back after a year of nothing!), and we regularly sprayed the cockroaches with soapy water plus some vineger (more as a disinfectant/cleaner) and they never burst. We've killed at least 30 using this method.

Having said that, what you likely witnessed was the egg sacs dislodging from the back of the female cockroach. As you didn't mention what species of cockroach you were dealing with, I am assuming you had German cockroaches as they seem to be the most common type in non-tropical/hot areas.

According to a number of biology sites, German cockroaches are particularly difficult to control and eradicate is because they carry their egg sacs with them until they are ready to hatch. At which point they drop the sac.

If you are able to catch a few that seem especially big, you will notice that they have a sac at their back.

If you don't have German cockroaches, I have not idea why they would burst...


Gradual slowing breath, its effect on health I've written a computer program which beeps, then beeps after 10 sec, then beeps after 11 sec, then beeps after 12 sec, etc.

I tried the following "experiment" on myself: do only one breath between the beeps, so slowing breath until I can't do it.

After finishing this "training" and starting to breath normally again, I felt enormous "freshness".

Is this experiment safe for health? How does it influence health?

You can try as much to slow down your breathing but the body will speed it up if it requires. What you've probably done is relaxed and just basically meditated. It's not the breathing but the relaxing yourself to slow your breathing and the focus which has refreshed you. I say conduct some experiments, like listen to calming music and relax and don't monitor your breathing and see if you feel the same.

//updating answer

Slowing your breathing builds up the carbon dioxide in your body. This is bad for the body so it forces you to breathe. In fact our breathing is seriously tightly controlled so that our body tightly controls the carbon dioxide (or more correctly the pH) in our blood. There are some groups of patients in which permanent slow breathing exists. In these people their carbon dioxide climbs and the kidneys have to compensate.


difference in genetic instuctions between male and female I'm a computer science graduate so please bear with me the following computer program :
mov  ecx, -1
INC  ecx
consist of 2 instructions (mov,inc) each working on specific data , can genetics instuctions be expressed in the same way ? if so what is the difference between male and female(humans) when it comes to the number of instructions and the difference if any (eg , n-instuctions being exclusive to female ... etc) ?

Edit#1
:what I mean by instructions is something like a computer program and a programming language commands.

The typical Male has a Y-chromosome, which consists of about 100 genes.

Genes are the instruction sets to make proteins, and proteins do the work of the cell.

Those 100 genes out of about 21,000 in the human genome are what differentiate Males from Females.

That being said, because of how signaling works, Males and Females can exhibit different expression patterns, like function calls, even though they have the same instruction sets, for the most part.

Expression patterns are how genes are activated and deactivated, it is basically a regulatory process that controls the functions of the cell, tissues, organs, and organism.


What are these Insects? I live in my hostel in NIT Tiruchchirapalli, in India. My hostel is infested with these beetle-like insects.

These insects posses a hard shell, if you flick them off the wall, they make a "tap" sound when they hit the ground. They're capable of flying but mostly stay on walls, sometimes even motionless. They also seem to be rather stupid, even for an insect. They don't attempt to escape even in life-or-death situations
tl;dr
What are these insects?

I'm trying to answer my own question. I did a bit of searching, and I found out that my insect resembles the Mupli beetle the most. From Wikipedia:

  The Mupli beetle, Luprops tristis (ഓട്ടുറുമ in Malayalam), is a plant detritus eating Darkling beetle found in parts of India. The adult beetle is black and around 8 millimeters (0.31 in) long.

I hope someone can verify if my findings are correct or not.


What is the difference between multiple allelism and polymorphism? From the Scott Freeman textbook Biological Science 4th Edition:
https://www.amazon.com/Biological-Science-4th-Scott-Freeman/dp/0321598202,

Multiple allelism is defined as "the existence of more than two alleles of the same gene within a population."

Polymorphism is defined as "the occurrence of more than two distinct phenotypes of a trait in a population."

I don't really understand the difference - unless it means that two alleles may not result in two different phenotypes?

Additionally, another definition of polymorphism also in the textbook was "the existence of more than one allele at a certain genetic locus."

What does this mean? I was under the impression that all genes had at least two alleles.

The term polymorphism is broad and can have different meanings. Here are your definitions

Multiple Allelism: The existence of more than two alleles of the same gene within a population.
Polymorphism: the occurrence of more than two distinct phenotypes of a trait in a population.

Considering your definitions only, then multiple allelism has to do with genetics while polymorphism has to do with the phenotype.
Most loci (=position in the genome) that contain more than one allele (=genetic variant) have no effect on the phenotype. So multiple allelism does not necessarily yield to phenotypic polymorphism.
On the other hand, plenty of phenotypic variation in a population is due to environmental variation (including what an individual eats) and not to genetic variation. So phenotypic polymorphism is not necessarily caused by a case of multiple allelism.


Black bumps on the cut surface of an avocado I cut an underripe avocado in half and put half of it, without the pit but with the peel, in the refrigerator. A day later, I see very small black bumps along the cut surface. What are they? What causes them?

It looks to me (although I'd want to use a microscope to check) like the black dots are xylem. When you cut the fruit, you've severed the xylem and also exposed the flat surface. Three main things have then happened:

The increased surface area has led to the 'fleshy' part of the fruit contracting as the cells dehydrate.
The stiffer, lignified xylem tubes have retained their structure and have not contracted with the rest of the fruit, so they've become exposed.
The exposed xylem have blackened due to oxidation - this eventually happens to all the flesh but, again speculating here, the oil in the fleshy tissue might protect it from oxidation longer than the exposed xylem which don't have the oil coating.